Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_029998
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 676078
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Found at i:15860 original size:19 final size:19
Alignment explanation
Indices: 15824--15860 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15814 ATGCTATAGA
*
15824 CATGCTATAGAGTAGTCAG
1 CATGCTATAGAGCAGTCAG
*
15843 CATGCTATAGAGCGGTCA
1 CATGCTATAGAGCAGTCA
15861 AAATCCCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (19 bp):
CATGCTATAGAGCAGTCAG
Left flanking sequence: Indices 15324 -- 15823
CATACCTAGCGCCGGGGGTCTCTTTTTACCTTCGCCGAGGGTTTGGTTTGCTTTATGTGTAGTAA
AATCTCTCCCTCATTGTTAGGAGCGGAATAGCTTATTATATATATGAGAAGGGAGGTGTAAAATG
CGGTCTCTGAAAGAAGAAATTCCAGTTTAGGACACCTTGTAGGGAATCGGAGAAGTTGCATGAAG
AGGTCCTTAGACTCTATTGGAACAAAGCTAAGTTTCGACTACTTCTCTCTCGGGTTCAATGAAAG
CAGCCTCGAAAGAACCAAGGCATAATAGTGTGGTACCTCGATTAGTCGCTGGTCAAAGCCCAAAC
TCAAAGGGTAGAAAATGCGGTGGAATAAAAGAGAAAATAGGAGATTGAACTCCTCATTGGGCATT
CAGGGATGAATGCTTTATATCATTACAATAGGCAGTGGAAATACATCCTTTGAGGAGTAAGAGCA
GGTACCTCGAACTCAAGTGAAGCTGTCGGTGAAGCATGCTATAGA
Right flanking sequence: Indices 15861 -- 16360
AAATCCCCAATGCTTGGCTGGAAGCAAGGTGCGTAGCCTCTTCAGCAGTAGGAGTCGGAGTAATA
GGTTCTGAAAGAAGGGAACAAAGGCTTGATGCAATTAAGCAGTAGCAGTAGCTAAAAGAGTAGTA
GCTGTAGGTTCTGAAAGAAGGGAACAAGAGTGAGACTTTCTTCCCACTCCCATACTCCTCTAAGA
GTCTCTCTCCTTTAATCAATTACATCGAACCAAAGGCTATATACTCAAATGGAGTGAGTTCTGGC
GTTCAGGTAATCCTCTCGTGGAGCACTTTACCAATTGATCAACCAGATTTGGGCTTTATGTGTAA
AAAAGAGAAGTTCTCACCAACAGCAGAAAGATACCAAGCAGCAGATACGGGTTTAGCGGGAACAG
CTAGCTTTATCGGAAGGAGCTGAATCCACATCTGCTATAGCTAAAATACCTGTTTCTGACCCATG
TGGTTTTACTCAACTTGAGGCCAAAACGCCTAATTTGAGCATCTT
Found at i:79730 original size:17 final size:18
Alignment explanation
Indices: 79708--79742 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
79698 ACCTCAAATA
79708 TAGAAA-CATATAGGAAT
1 TAGAAAGCATATAGGAAT
*
79725 TAGAAAGCATATGGGAAT
1 TAGAAAGCATATAGGAAT
79743 GCCATAACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (18 bp):
TAGAAAGCATATAGGAAT
Left flanking sequence: Indices 79208 -- 79707
TGCAACCCATTTGAATTTGAAAACAGCTTATTCTGATTAACTTCCTTCAACACCAGCAACGGATA
GGACCAGATCTTCTATTTTCTCGACAGCTCTTACTGTAACAGAAAAGACTTGCACCGGTTATTCC
ACAGAAAGAGGAACTTGAATTAGCCCTCGGGCTGTGAACCATTGTCACTCGTTACGTAACGAAGT
TCAGTATCCGTATGTTAGCCAAGATCGGTAACTTTTAACAAAAGATTTTCGAGATACGAATTGAA
TACGAAGGAAGGAAGCAATCGGAATAAATATGCACTCGATTCGGTCTTATTCATCGGAATAGACC
AAGAACCAAGGAAGGGGCAAAAAGCTCTCCTACGGTCACTGGCTTCTCTCCTATGTTTTGAGAAG
TGAAACGAAGTACTTCCCAACAGCCAACAGAAGCACGAGTCTAACGGTCTACAGAGTATCCCTGG
GCTGATGGCTTTTCTTCCTTCTCTAGAAGAATACTACCTCAAATA
Right flanking sequence: Indices 79743 -- 80242
GCCATAACAGAGAGAAACTAGAGCTTATGTCAAGGAAAGGATGACTTTCCCAACACTAGAAGTCC
TACTCATGCTTGTAAAAAAGAGGAAGGTCGCTAATTACAGGCAGCTACCTATGAGAAGATCCATT
AAACTAAATTAACAAGCATATAAACAACATACTAAGCAAAAGTGCGTAGACTCAAAAGAAGGAAA
AAGGGCAGAAGCTTCCTCTTCTATTTATGTTATGGGTGGCAAAGTCCCAAGGAAAAAAATCCTAT
TCTTCCCGAGTCTGATTCCCGAGACTGGCCTTCATCTTAGCATTCGTCTCCCCTCGAGTTCTAAG
TCTTTAGCGGGTAAAGCTCCCCCTTTCAATGAATAGTTGAAAAAACCTCTTTGGTGATCAAACTC
TTCTAAAGAGGGTGCCCTTTCTTTTTCAACTGTCCAAACTCTCGGCTTGAAAGAATCTCTCCTTA
CTCCATCGTCTGCATCAATAAGAGCATACTCTCTTTCGAAGAGAG
Found at i:85136 original size:19 final size:19
Alignment explanation
Indices: 85109--85150 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
85099 TAGCAGCACC
85109 AAAAGAAAAGTAAAA-AAAT
1 AAAAGAAAA-TAAAAGAAAT
*
85128 AAAATAAAATAAAAGAAAT
1 AAAAGAAAATAAAAGAAAT
85147 AAAA
1 AAAA
85151 ATATCTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAGAAAATAAAAGAAAT
Left flanking sequence: Indices 84609 -- 85108
GAACATATTAAAGCACTCCTTGGAGTTCCTAAAAAATACACTCTTTCTGCCATATTGTTGGTTGT
GCTTTTTGATTGTGCGCAGCTTTTCCAGACCATATTCTTTCTTCTTCGAGCATTTCGACGATTTG
TTGAATCTTATTAGGTGAGGGTACTTCGGATTTTCGTAAATCGATAATAAGGTCAGCTACCTGAT
TTTCCAATGGGGTGAGCTTTCGCATATGTGAGGCCTTGTTAGCTTAGCTCCACCCGTTGGTGCCG
GTTGCTCCTGCTGCTCCAACTCCCTCCAGATGTCCTCTTGGTTGACTTCAGCAGCTTGGATTTCA
AACGAAGGAGAAACAGGCTCCTGAGCTAGTGGTAGTGGCTCAGAAGCTTCCGGCACCGGGGGGAG
GGCTTGCTGCACCTCCATCGAATCGACCTTATCTTCCTCAAACTCGCAAGCTGCGACGATGATGA
TAGGAATTCAAAAATGTTAGTATGGAGTTGAACAGTAGCAGCACC
Right flanking sequence: Indices 85151 -- 85650
ATATCTGAAGAAATTTTAGGGTTCGTGATAATAGATCTGGGCCGGTTGAAAAGGCTCTTTTTCTT
CTTCTTCATTCTCGACAGGAATACATCAACAAAACAGCCCTTCCATATAGGTGCATGAACTTTGT
CAATAGATTCCTAGCTAACTCCTCTTCCTATTGATTCTTGATTAGTTCCAGCTTGTTGAGAGTTC
TCTTTTTTTTTTTGAATCGGACCCATTTTTAGACCGTCTCCTGAAATACCTGCTTATCCCGCATG
TGCTTTCGGAGCCCCCCACTCATTCAATCACTTGCTTGTGATTGCAGCCATTCCCCGAAAAGGGA
ATTGTCCGCTCCCGTTCATGGGACGAACCGAACATCGTTAGGTCCCGAATTCTGCGAACCACCGG
ATCTAGACCAAGATCTCCATTACGTCGTACGAGATATCGATCCGAAGAACTTACTTTCAGTTGTA
AGTTATCCATTCTGCTTCTATCTAAAGTGATGCTAGGCTGCTTCA
Found at i:97977 original size:15 final size:15
Alignment explanation
Indices: 97957--97986 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
97947 GGAGGCAGGC
97957 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
97972 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
97987 AATATACTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAGTGAAATAAAAT
Left flanking sequence: Indices 97457 -- 97956
ACGGCTTTCAAAAGACGAGTAAGAGACGGGGAGGGGGAGGCTCTCGAAACCAAGCGAGACTAAAA
AGAACATGGGAATTCGCACCATTCCTATGAGTGCTTTTTTTCGAAAAGCCAACAAAGGGACAGCC
CTCTTTCTCTATCTCGGTCTCGGTTTAGCATCATCATATATCGATCCGGAGATAATTTGGATTGG
TTGTAGTGCGGATTAAGGAGCTGCTCCTCCATGCTGTGGCTGTGGAGGTGGGGGCTGCCGCCGCC
TGATAGAGGCAGAAGCCGGGGCCACCGGAGCTATCTGCGTCGAGTGTGTCGATTGAAAGAGGAGG
GGAGACAAAATGAATTCCAGCGAAAAAATAGAAAGAGTCGTGCCGTTCAAAGTGGAATTCTTCTA
AGATCCATCCATTGCTCGATCGATTTTGCATGCTCTGCTCCCAAAATGCAGAGAGACTTGCGAGG
GCAGATCTGGGTTGGTTGGTCCGGAAAGTCATGGGGGAGGCAGGC
Right flanking sequence: Indices 97987 -- 98486
AATATACTGGTGCTACTATAGAATCTTTTGAATCACGCACGGCACACTTTCTATATCTCCTCCGT
CTACAAGGTGAACAGCTTGGCTTACAGCACAGCGTGTTCGCCACCACACCGGCTGGCTGGTGCAT
TGGCCCTTTGAATGAATAAGAGAAGGGCTTTGTATAGACACCCTTGAGCCATATTCGTCGCCCTA
GGCTCACCATTATTTCATTCTATTTATGGGTTCTAGCTCCAAAGAACATATACATGGAGCTATGT
CGACTTACGTACGTCTCGTTGACCAAACGATTAGGTTATACCACGCCACGTAAATCATCCCCTCT
TTCCAATAAAAAAAAAAAAAGAAAAGATATAGTGATCGATCGTGCCGTAAGACCTTGTTCGTTTC
TACTTGACGTTATTTTCCTCGGTTTTTTTTACATTACATAAGGTAGCTTGCTTACTTAGCGCTTG
CGCTAAGGATCTAATCAGAGTCAAACTTCAATTTAAAATGAAAAA
Found at i:147860 original size:21 final size:21
Alignment explanation
Indices: 147834--147880 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
147824 TTAAGGGATG
147834 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
147855 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
147876 TAACA
1 TAACA
147881 ATCGATGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (21 bp):
TAACAGAAGTTTCAAGAGAAC
Left flanking sequence: Indices 147334 -- 147833
TTAAGACTGTTGCAATTGGTACAACTGCTTCAATGGGATAGAAGGAAACTGGCTAAAAAGGATTA
GAAATGGACTAGTAAGAGACTCCAATGTATACCTCAAACTTAAATTGGAACCCTAGGAGGGGCAA
CTTCCACTCTTTTTTCACTCTTTCCATTGTCGTTTACTTTACGAAGCGAAGGAAATCAAAAGGTA
TGCCCATTTTATCGAGGAGAGGAATTACTAGCTCGCAGGCTTAAAAATGATAACTTCCTTCCTTG
CCCTCGAACCGACTATCCAACGGCATGGAACACTTAGCATTGGCCTATAACTCAAATTCCATTTT
ATAGCACGCCAACAGGAGGGGCTTCTTACAAAAGCACTCCAACAACTCGCTTGAACTTGAAGAGA
GAAGCAACTACTACTTCTCCATCAAAGGAAAAACAAGCATCGACTAAATAGAAGGCCCTTGAATC
TTATCGTTAGAGCGCTATCTACCCTTAAGACTTACTTAAGGGATG
Right flanking sequence: Indices 147881 -- 148380
ATCGATGGACTGGAAGGGCGAGAGACAGAACAGCAAAGAGAACTCAATCTAGAATTTCCACTCCT
TCTAAAACCCCAACCCCAAGTACGGCATTAGCAATTGAAGAGCTTAGTTAGGATGGGTGGAACTA
CAACCCCTCGAACAGGCTCGATAAAGTCTGGGAGATTAGATAAGCTGGCTAGGTATTTTTATATT
CTTTTTACTGAAAATGCACCGAAGGCAACTGCCATTGAAACTATATAGCTTTATATATAAAAGGG
AGAATTCCGCTCGAAAACCAGCCCTCTTCACACCAGTACCTCTGTCCCGACATTTGGTGAGATAG
GGGTAATGCCTACCAAAGGTAAAGGGGAGCCTTCATGCAAATCTATTGAAGGGTCACCTACGTTA
GCTGGTGCCCACAGTGCCAAAGTTTCAACCAAGATCCTTTGGCTCCGTGCTGGTAGCCGGCTTGT
TACTCCAGATTTTAGTGACAAGAACGTCTGTCACGTGCGTCCCTA
Found at i:186081 original size:17 final size:17
Alignment explanation
Indices: 186059--186094 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
186049 GGGAAGATAG
186059 AGAAAGAGAGACAAGAA
1 AGAAAGAGAGACAAGAA
* *
186076 AGAAAGAGATACAGGAA
1 AGAAAGAGAGACAAGAA
186093 AG
1 AG
186095 CTAAGGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.31, T:0.03
Consensus pattern (17 bp):
AGAAAGAGAGACAAGAA
Left flanking sequence: Indices 185559 -- 186058
TTATCCAGAAACAACTCAATCAATCAATTACCTTATTTAAGATACGCCCAAATCCATTCAACCAG
CCACTCAAGGGTTTGGAGTTACCATTTCCGCTATTCCTGCCAAGGAATAAAGTAAAGGGACTACC
GATACCCCTTCGCGTTCGCTTTGGTTTAGAGTAATCGCTTGTTCCTTCAGTCTTCAGAGGTAAGC
TCTTTTGCCTTCTTCCTAATGGACTACGAGGACCCTAGGATTTAGGACTCTTATAAAGAAGGATT
ATTGGCCTACTGCTGCCTTACCACTAGCTTAACACTAGCAGCACAGGCTTACCTATTAATCACAG
ACCCCCTTCCTTACTTGCTTACTTCCTTGCTTGCCTGGAGAGAAAGAATATTAAAAAGAAAGAAA
GGATCCCCTACTTACTTAGTACAAGGAAGGGAAAGACTTACTAAAAGACCAAAGACTGGCTTACT
TACTGTCTTGGCTCCTAGGACTTCTTACAAGGAATGGGAAGATAG
Right flanking sequence: Indices 186095 -- 186594
CTAAGGATATAACGAAGGGCGAAAGGGAGCACAGAAAGGCGCAATACCAAAGCTTTTTTGAAAGA
GAAGAATGCGCCATAGGTTTCTTCCTGCTTTGCTTTGGGAAGGGGCATTGAAAGAACACAGACAT
AGTGGAAATGCTCCTAGACTAGAGAAGGTTCCCCCGTAAGTCTGATCCTCTCAACTCATACTACA
GCAGGGAAATCCACTTTTCTGGACAGGGTCTTCCTTCTCGGAGAATAGGTCTACTATGCTGAAGC
AGAAGGGAACAGGATGCTCATTTAAATGTCAATGAGACTAGTCAGGATGCTCCCTGTAGTACATT
CCCAGATCTGAGCTACCTGGATCAACCCACCAATTAGTACAGTTCGTCAGTGAGTACGTGGGAAT
AGCCCAGTAATGAATAGAAATTTAAGTCACCGGGTAAAGAAGCGAGGGGATCAGCTCAATTGAAA
GAGAGGGCGCGATCGGCATACAATTATTCGATTTCATTTCTTGCC
Found at i:235185 original size:36 final size:36
Alignment explanation
Indices: 235143--235215 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
235133 CCTATGTCTT
235143 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
235179 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
235215 T
1 T
235216 TTTCTTGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.15
Consensus pattern (36 bp):
TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
Left flanking sequence: Indices 234643 -- 235142
AAAACAGGTACTGATAACAAAGTACAAGCCCTAGCTTTTAAGCCGAAGAAAGAAGCAATCATACT
CCTTAAACAGAAAGATATTGCACTTCAAAATCGTTACTAGAAGCACTACAAGCGCACTTCCTATC
TAAACAAACCAAAGCAGAAAAAGCACCTCCCTCCCGGATAAAGAGCAAGTGTGCGAGAGAATAGA
ACTGAGCATCAAGGCTGCAAGACAGAAGGAAGGTTCCTGCGTGCAGGAAAGCTTTTTCACCGTCC
ATTGGGTATTTGTCTTTATCTCGCTCTCCCAACTAACTCAGACTTATGATAGGCGGGCTCAATTC
CAGATATTGACCTCTGGGGATCCTTCTCTTTGAATTCCCGGTCTTCCGTTTTCTTCCTTGGTTCC
ACCCTTCCATTCATGAAGCAGATCGCCGGGAAGGCTTTTTCTCAAGCATAAAACGAGAGACCCGA
TCACATTGATCGACAAACAAAACTCCCGATAGAAGCCTATGTCTT
Right flanking sequence: Indices 235216 -- 235715
TTTCTTGGTATTCACGCTCATCGGACTGAAGTTGGTCCTCATTTATCTCAGCAGAAGTCTTTCAT
GATCTTTTCATAAAGTTGAATCTAGCCAATGCAAACTCAACTCAGTTAGTACTCCTATATCAATC
GTTGTCGCTGCCTTCTCAAGATGACGGGTAACCCCTTTCTTTAGGAGGATCCATCTCTTTATCGC
AGCATGGTAGGAGCCTTGCATTATTTAAGCATGACAGGGCCGGACATTGCCTTTGCCGTAAGCAT
TTGAAGCCAATTCCTCAATTGCCGCCCAGTACATCGTAAAGTGGATCGATCGATATCTTAAGGGA
ACTTCTCATTATGTCTTTTACCTCTTCTTCTGAGCTAGAGTTACATGCTTATGCTGATTGGGGTC
CTTGTCTTGATAGTCGACGTTCTCTTTCTGGGTATGCTCTCCTTTTTCTTGCCTAATCTCCTTTC
CTAAAACTCTGCGCTTCTCTTTTGAATCTTCTCACCCCGCCTAGC
Found at i:262787 original size:2 final size:2
Alignment explanation
Indices: 262780--262818 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
262770 ATTAGAAAAG
*
262780 TA TA TA TA CTA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
262819 CTAAAAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 262280 -- 262779
TTTCCGAAAGCGCAGTGCCCCACGGATAGAAGACGACTCCCCTGATTTGGTGTCGCCCATTTTTT
ATATTTATGGGGTTTACACCGTCGTGCACTAATGCTGTTTCTATCTTTTTTTCTAGCAGCATCCG
CTTTTCCAGAACACTAAAAAATGCTGACACCTCGTGGTGTCTCCCGACAAAATGCACTGCTAAGC
GGTCGAACAGTTCCATCCTTCTCGTGTGATCCGGCATCAGGGGTTGCTCGAGAATCGGGACGAGA
ACAGCCTGTGCTATTTCAGGATCAGTCAGGGGCCTCGGGAGCGCGCGGTTGGACCGCTTGATGGA
AATCCGCTGCGCCAGACGGGGAACCACTTCTTACGTCGCACATGGCTATCTCCAGGAGGGGCCCC
TGACTGATTATTCCAACGATAGATAGAATAAGACCCAGAAGTTGGATGGGACTGCCATGAAAGAT
CTCCTCCGGGATTGGATCCCGGTGAAAAGAGATCCATTAGAAAAG
Right flanking sequence: Indices 262819 -- 263318
CTAAAAAGGTGGATTTCGCCCTGCATATCCTAAGGGCCAGGATTCAATCTCCACTGGAGCCATTG
TGAGGAATAACCATTCTAGAACAATCATTTGGTTTGTTTCATTCTTTTTTGTTCTGCTCCCCCCA
AAAAAAAGGGAGACTTCCTCAGGAAATCGCTGGTTTTTCCAACCCAACCGAGGATTTCCGACAAG
TCCTTCTTCATTTTTAGAGACAAGAAGGGGAACTATAGAGATTCAATGAACAGTGTTTCTTACGA
TTACGCCCAGCCCAAAAAAGCCCTTCGGAGTTGAACCGAAAAAAAGCCTATTACTTAGGGCCCTT
CAAGAAGTTTGTGTTAAGCATATAGCCGGGCCCTCTTTCTGAGCCAGGATCAAACTCTTCTTTTT
TTACTATGATTGGGCCCTGCAGACGTACTACTTTCAATCAAACCTTTTCTTTCCTTTCCTTAAGA
TATATATGTTACCCACCATATTAATAAGGCACCAAACGCGCACTG
Found at i:272076 original size:14 final size:14
Alignment explanation
Indices: 272057--272087 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
272047 TATCTAAACT
272057 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
272071 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
272085 ATT
1 ATT
272088 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (14 bp):
ATTGGATTAGCGGC
Left flanking sequence: Indices 271557 -- 272056
AAGAAAAGCTTTTTCAGATGTTAAAAAAAGCATTGTAGGATAATCGGCATCTGTCCCTCGAGAAA
GAGTAAGATAGGCAAAAAGGCATAGAGACAACAGCGGTAATGCCGCATCTCTCGATGAGAAGGAA
TCCTGGAAAGAAGAGCAAAGAAAAGCCCTTCTTCTTCTGCCTTTTGACTCTATCTTGCCCTTTCT
TTAGGGAATTGCGGAGTGAATGAGTGCAACAAAACAAGGAAAGAAGGCTATAAGCTGCCTACATG
GAATTACTCTTCATGCACATTTCCCAGAAAGAGTATATTGCGATAATCGGATGCTAAGTCTCCCT
GGCTTCCTTCCTCCAGCGGATCTGTGGGCATTAAAAGAAGAAAGACTTTCAGGTTCTTCGCCACA
TTCCTTCTTAGGAAAGAAAGGCTCCCGTTCGTGCCCTGTAAGAAGGAAAATTAGAAAGGAAGGCA
TAGTCGAAAAGACTAGCAGCTTCTCTGTGCATGGATATCTAAACT
Right flanking sequence: Indices 272088 -- 272587
ATAATTCAAAAAGACTTTCGCGAAGCAGGAAAACAATCAGGTAATCAGGAAAGGCAGAAAGGGTA
GAGCCTTAGTTACCCGCAGCTCAAATAGCCAAGGTCGGTGGAAAAGGAATAGTACAGCTTGTTTG
GATAAAGGAAGCATTCATACTCGACCCGCGTCTGGACGCCCCTCTCGGGCTCACTTCCTGACAAC
CCAGCCCACAACAGGAAATGGACAGGCATTGACAAAAGCCGAAGCCTCTAACGATTTTTAAGCTG
GGTAACGGGTACCCTATCGGAAAGGGGTTTTCGTCTACCTCCCAAGCATATGGCGGGCTTATAGG
GCGCTGGTCTCCGTTAGGCTTTGAGTCTAGGAGTATAGCGATGGCTTCATCCACCGGTCCTACCA
TGGAACGAGTTTCTTCGCGCTTGGCCTTGAAATTTCGAGGCATCTTTCCCAAGACAAGAAGCGGC
GTCGGATCCCGGTAGTGCGGTAGTACGCCCAGCAGAATGTCGTAG
Found at i:280624 original size:26 final size:26
Alignment explanation
Indices: 280595--280647 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
280585 GACACGCTAT
280595 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
280621 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
280647 G
1 G
280648 CCTTTGTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.32, T:0.15
Consensus pattern (26 bp):
GATCGCCGTCAAAGACAGGATTCGAG
Left flanking sequence: Indices 280095 -- 280594
GTGGTAGTGGCTCTATTGACTATAGCCGTCCCAATGTGAAATATAGTATTCAGTAGACGCAAATG
CAGATACTATCCCCTACGGAATAAAACTTTCTTTCATTCCGTAGGGGTAAGACTCTTCAAATAAA
ACTAAAAATTCACCTAGGACTTTTTTCTTTTATAGGGACTTCTGGCTCTGATCCTTCTATAGTAG
GAAGACAAGATCGCAAGGGAATCACTAGTTCGAGTTCCATGCCTTCCTTCTGGTCCCAAACACTG
GGTTATTAACCGATGAGTTCATTTTCCCCTTACCCATTTCTTGTCCATGTGTCCCTTGCTTCTTA
GTGCTCCGTTGGACGGGGACTCCTTCTTCATTTGAATGCTTTGATGCTGGCCAACTGGGAGTAGG
TTCTGGCTGCTCTTTCTGTGATGCTATTTCGACCTCGTAAAGATATTAGGACTTTCACACTGACA
TTGAGACAGAAAACATTCGATCAGTTTCCCAGCGTGACACGCTAT
Right flanking sequence: Indices 280648 -- 281147
CCTTTGTCCCCATTGCTTGTTAGTTAAGTAGGGAGAGAGAACGCCCCATCTCTTGATTACGAAGA
TCACTTTCACAGCAAGCACGAAGCTTAACTATTATGTAAATTGAAACGATCTCCCCAGGAAAGCA
TGATGCCTGACTTGCCCCTGCTTTCCAAAACGGTAGACCAAAAGCACTGAAATGAATATGAGAAA
TGTGGCCTATCTATGGAAGGAATCTTTCGTTACTAGAACCCCTTCCTAGTGACTGTAAGCGAAAT
GCATTTAGCGAACGCCTGGGGGTACTGAGTTCCATATTTTTGATTATAGAAATGTTATCTCTATC
TAAACGACTAAGTCTTCCAGTGATCTCTCCCCCACCCAAAACCATCCCTTCCAGCGTTAGCGCAC
AAGAAGGAGCTTTTGGCAGTGAGTCGAAAGTCTTAGTGAGAAGCCCTCTTAGGACTCTTTCCACT
CTTCTCTGAGTGCCTTCAACAGTGCTTAGGTAGCGCTCACTGCGA
Found at i:307332 original size:17 final size:18
Alignment explanation
Indices: 307297--307343 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
307287 GCAGTAAATG
* *
307297 GAATAAACTAAGC-AAGA
1 GAATCAACTAACCAAAGA
307314 G-ATCAACTAACCAAAGA
1 GAATCAACTAACCAAAGA
*
307331 GAATGAACTAACC
1 GAATCAACTAACC
307344 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 10 0.40
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.13
Consensus pattern (18 bp):
GAATCAACTAACCAAAGA
Left flanking sequence: Indices 306797 -- 307296
TAAGCAGCCAAGGCCAAGAGCAAGCAGGAGTAGTCCTATCTGCCTATAAGGATTCGATAAAGAAA
GAGAATGTGAGTGGGCAGGAGATCAATAAACACAGAAAGCGAAGAGCAAAAGGAGCAGAAGACAC
TCAGTTGTTTATGTGAAATCAAGGAGCAGCAGGTTACACTTTTACACTTTCCCAAAGCAAAGAGA
GCTCAAAGCAATAAGATGAAAGCTGGGATGAGATGCTAGCCTTAGCTAGGAAGATCCATCATTGA
GCCTTAGGCCACTACCGAGCAGAAATGGAGGATCATAACACTTGAGAGATGATCCCTACTTGAAA
AGGCGGAGACAATACCTCTTGTTGCGACAAATCGAGTTTCAAAAGCCCATTTATCAATCACATTT
TCAGGCACACCAGTCAAAGAGCCATCGGACCCATTAAAGTCCCCTTTTTTACTAATATACAAGGC
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 307344 -- 307843
CCAAGGGATGATCTCGGATTGAAATCCAAGGCATGGTCCCATTGAAAGCCCAGGGATAAATTCCT
AAAACAGAAAAAAAAGTAAAGTCCAAGGGGGTATGATCCCAATAAAGATAGGATGGATTTTAAGT
CATTTTGGACGAAGCAGCGGGCATACCAGAAATGGCTTGTCAGGAATGGTAGATGGAGCAAGAAT
GCATAGCAGGCTTAAAACACGACACAAGTAGGACGCACTGAGGCCGAGCTTTCCTCTACTACTCA
TTGGAGCTAGCATACGAAATTATCCGTTGAAGGGTTCAACTCTCAGGGCGGCCATTGCAGAGCGA
TATTCACTTTCAAGAATCATCGAGCCTACGCCTATTTCATTACTCTCGAAGAGCTCATCAAAGAG
CTAAGGCTAAGGGATGAGAAAAAAAAGGAGGAGGTGGAATTTCTTTCAACTATAACATTTATTAC
AACACTTAATATTACAGACAGAGAATTCGGTAAGGGGATAGAAGC
Found at i:378478 original size:15 final size:14
Alignment explanation
Indices: 378458--378512 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 14
378448 TCATTAGAAG
378458 AACCAGCGGTAGCTA
1 AACCAGCGGTAGC-A
*
378473 AACCAGCGATAGCAA
1 AACCAGCGGTAGC-A
378488 AACCAGCGGTAGCA
1 AACCAGCGGTAGCA
378502 GAACCAGCGGT
1 -AACCAGCGGT
378513 TTTTGGCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 1 0.03
15 35 0.97
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.09
Consensus pattern (14 bp):
AACCAGCGGTAGCA
Left flanking sequence: Indices 377958 -- 378457
TAAAAAGCTTAAAAAATGTATCCCATTTCTTTGAAATCCCACTATAGTAATGCCAATAAAAAGAG
AAAATGAGAGACCCAAAGTAATGAGAAAATGACTTGTAACTGTGAAGCTATAAGGTATCATACCC
TGGGGATTACGAAATAACGAAAAAGTAAAAGTGACCGAGATGCAAGGGAAATACTTTTGTTTCAC
ATTACTGGAAAGACCGCCTATTTGTTCGTTTACCGGGTTCAGCACGAAATCATAAATAAGCTCTA
CCAAGGATTGCCAAGCATTTGGTACTAACTTTCCTCCTCCCTTTTTAGTAACAAAATGAACCAGA
AGTAGGAACAAACTGAGAGTTAGCAGCATAAACAAAGATGGATTTGTGAATGAGAAATACAAGTT
TCCAATCTTCAAATCAATCAATGGCACAATCTCAAATTGCTCAAGGGGGCTGGGGACGATGGGTG
GTTGGGGTGGTTCCATTTGCCCCCCCACCCCCAGGTCATTAGAAG
Right flanking sequence: Indices 378513 -- 379012
TTTTGGCCAAGGCCAAGACAAACATTTTGAAAAAAAATCTTTTGAATTTTGAATAGCCGTGGAAA
ACAATTTCATTTTTCTTTCATTCTTTTCATTCTCCGCTCCCCCCAAAAAAAGGAGAGACTTCATT
TTCACTGTACGAGTAGTGAAAAACTATAGTTTACTTTTATTGGTTGTTGACCAACGGAAAGCATG
GGAGTCTTTGGGCATTTCTTCTTCTCTTACGATATTTCTAATTACCTAATAGAATAAATACTTTA
GTTCGAACTAGTTTTTAGCTTGAACGTGGCGAATGCTATCTCTTTCCCGCAACTCGACTGTTTAA
CAGGATGGTACGAATCCGCTCTTTGACTTAGTTAAGGAAGGAAGCAATTGTTCTCTTTGCGTTTA
GCTGGGCAAAGCAAAGTGAAGGGAAGGATGAATCGCTCCCGAAAAGGAATCTATTGATTCTCTCC
CAATTGGTTGGACCGTAGGTGCGATGATTTACTTCACGGGCGAGG
Found at i:468216 original size:24 final size:24
Alignment explanation
Indices: 468174--468222 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
468164 ATTCGGATTC
* *
468174 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
468198 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
468222 G
1 G
468223 GAATCCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.41, T:0.29
Consensus pattern (24 bp):
GTTACTTCGGGCTCATGAGGATGA
Left flanking sequence: Indices 467674 -- 468173
CAAAAAGTTTAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATAATCATATGGGTCAAC
AATTCTCATTTCTTAGTTACAGAAAGCCCTTCTCAAGGAAGTAAGCCAAAAGCCACTCATCTGAG
CCAGCGGATTCTCATTCTGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAAT
CTTTGATCTGCCTATCATATGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGG
ATTATTCAACTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACCGA
CCTGTTGAGAGGATAGCAACAGGAGAAAGAAAAAAAGAAGTAGAGTTAGGTTCTGTTCTAGTATG
TAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCGTATGATTCTTATCCTACTTCCGA
TAAGTCTTATGAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 468223 -- 468722
GAATCCGTTGTTTCGGGATAAACTTGATATGTTAGTTCGGCCTCGGCTTCTTAGGATGATGCCTG
TGCAATGTATGATCCATCGGATTCTTTTTATTCTATTCTCGGTGCGTTGTTCTTCAGCGAATGAA
AGAAACCGCTGATTCCAAAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGA
ATGACTCAACTGATACTACTCAAAAATTTCCCACATGGAAGGAAATGGGATTTTTGAGAAAAGGG
GTTGGGAACCATCGAAGGACTAGCAACCTGACAGTCCTAAGCAACCTTGAACCAACAACGTTACA
TATACCATACTGCTATAGAAGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTG
GTGAGCTACTTACTGCCCCTTAAGTCAAGAGAATAATAGTACTTTCAGCAAAGGATATCGTAACT
ATGGCGAATACGTTTTTCTTGCTTTCCACATACCCGGAATGCGAA
Found at i:485598 original size:26 final size:26
Alignment explanation
Indices: 485564--485621 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
485554 TTCCATACTT
* *
485564 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
485590 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
485616 A-AGAAA
1 AGAGAAA
485622 ACTGCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (26 bp):
AGAGAAAGATTTTAAGTCAAGAAAAG
Left flanking sequence: Indices 485064 -- 485563
CTATCCGTCCCTTTTGCTAGAGTAAGTAATTCCCTTCCCTTTTGTTTGCCAGCGTAGCGCATTGA
TCATTGAAGTGGGGGCTAGGCGAGGGCATGGTCTACTTTTTGTTCTGAAATGACTAAGTACGGCT
TGGCTTCAGCTCGTGGGACTGGTTCTCTAGAAAAAGTCCCAAACCCCACATCCTGCAGTCCGCCT
GGATTCGATTCGCTTTTAGTAATTATATTACATTATATATATAAGTAATTAGAAGCTAAAGAGAA
ATTCAATATTACCATATTCTACCGCTCAACTAACGCTATGTGATCCGGTCAAGATGAATCGATCG
AATTTCACAGCTGAGGAGGCAAAGGGAGGCAAAGCGAGAGGTTCTGAAAGAAAAGACTTTATAGA
ACCTTACTCACACGATACGGGGATGGGCCTACACAAGCAGAAGGAAGAGCTATTAGCTTGTCGGC
GTAACGAATGAACTATCGGATGGTAGGCTAACTGCTTCCATACTT
Right flanking sequence: Indices 485622 -- 486121
ACTGCCTTTTTTTTGAATTGAAGGAGGAGTCGCGCATTCGTCTGCAGCGTATAGTATAGTAGCTT
CAATGGAAATCCGTTTGAATTGATGATTTTTCACCTGATTCCCCCAAAACCGTAGAAGCTACAGA
TCGGGGTTTAGCGATAACCTGAGATCCTTTATTCTGTCTCCACTTCTGAGCCGACCGAGCCTGAA
GCCAATATGTATGAAAGAAACCAATCAACGCAGGAATGGAGTTCGTAGCGAGAAGATAAAGTTCC
TCGCCTGAGAAGCACTTCACTGGGTAATAAAAAAGCTACCTAAAAGATCTTATTACCTTTACTCT
AAGATGCTATAAGATAATTGGGAATCTTTTAGCCGCTATTCCCGCACTATTGTAAACCAGCTTGA
TAAAGGGTAGTGGTAGAGTCTCAGTACCACTGAAAGTGCGATAGTCGGGCAAACAATCTCCTCTT
TTTATCATATCATATAAGGTAGGGTATTGTATATATGGAAATTCA
Found at i:530970 original size:17 final size:18
Alignment explanation
Indices: 530948--530982 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
530938 ACCTCAAATA
530948 TAGAAA-CATATAGGAAT
1 TAGAAAGCATATAGGAAT
*
530965 TAGAAAGCATATGGGAAT
1 TAGAAAGCATATAGGAAT
530983 GCCATAACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (18 bp):
TAGAAAGCATATAGGAAT
Left flanking sequence: Indices 530448 -- 530947
TGCAACCCATTTGAATTTGAAAACAGCTTATTCTGATTAACTTCCTTCAACACCAGCAACGGATA
GGACCAGATCTTCTATTTTCTCGACAGCTCTTACTGTAACAGAAAAGACTTGCACCGGTTATTCC
ACAGAAAGAGGAACTTGAATTAGCCCTCGGGCTGTGAACCATTGTCACTCGTTACGTAACGAAGT
TCAGTATCCGTATGTTAGCCAAGATCGGTAACTTTTAACAAAAGATTTTCGAGATACGAATTGAA
TACGAAGGAAGGAAGCAATCGGAATAAATATGCACTCGATTCGGTCTTATTCATCGGAATAGACC
AAGAACCAAGGAAGGGGCAAAAAGCTCTCCTACGGTCACTGGCTTCTCTCCTATGTTTTGAGAAG
TGAAACGAAGTACTTCCCAACAGCCAACAGAAGCACGAGTCTAACGGTCTACAGAGTATCCCTGG
GCTGATGGCTTTTCTTCCTTCTCTAGAAGAATACTACCTCAAATA
Right flanking sequence: Indices 530983 -- 531482
GCCATAACAGAGAGAAACTAGAGCTTATGTCAAGGAAAGGATGACTTTCCCAACACTAGAAGTCC
TACTCATGCTTGTAAAAAAGAGGAAGGTCGCTAATTACAGGCAGCTACCTATGAGAAGATCCATT
AAACTAAATTAACAAGCATATAAACAACATACTAAGCAAAAGTGCGTAGACTCAAAAGAAGGAAA
AAGGGCAGAAGCTTCCTCTTCTATTTATGTTATGGGTGGCAAAGTCCCAAGGAAAAAAATCCTAT
TCTTCCCGAGTCTGATTCCCGAGACTGGCCTTCATCTTAGCATTCGTCTCCCCTCGAGTTCTAAG
TCTTTAGCGGGTAAAGCTCCCCCTTTCAATGAATAGTTGAAAAAACCTCTTTGGTGATCAAACTC
TTCTAAAGAGGGTGCCCTTTCTTTTTCAACTGTCCAAACTCTCGGCTTGAAAGAATCTCTCCTTA
CTCCATCGTCTGCATCAATAAGAGCATACTCTCTTTCGAAGAGAG
Found at i:536370 original size:19 final size:19
Alignment explanation
Indices: 536343--536384 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
536333 TAGCAGCACC
536343 AAAAGAAAAGTAAAA-AAAT
1 AAAAGAAAA-TAAAAGAAAT
*
536362 AAAATAAAATAAAAGAAAT
1 AAAAGAAAATAAAAGAAAT
536381 AAAA
1 AAAA
536385 ATATCTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAGAAAATAAAAGAAAT
Left flanking sequence: Indices 535843 -- 536342
GAACATATTAAAGCACTCCTTGGAGTTCCTAAAAAATACACTCTTTCTGCCATATTGTTGGTTGT
GCTTTTTGATTGTGCGCAGCTTTTCCAGACCATATTCTTTCTTCTTCGAGCATTTCGACGATTTG
TTGAATCTTATTAGGTGAGGGTACTTCGGATTTTCGTAAATCGATAATAAGGTCAGCTACCTGAT
TTTCCAATGGGGTGAGCTTTCGCATATGTGAGGCCTTGTTAGCTTAGCTCCACCCGTTGGTGCCG
GTTGCTCCTGCTGCTCCAACTCCCTCCAGATGTCCTCTTGGTTGACTTCAGCAGCTTGGATTTCA
AACGAAGGAGAAACAGGCTCCTGAGCTAGTGGTAGTGGCTCAGAAGCTTCCGGCACCGGGGGGAG
GGCTTGCTGCACCTCCATCGAATCGACCTTATCTTCCTCAAACTCGCAAGCTGCGACGATGATGA
TAGGAATTCAAAAATGTTAGTATGGAGTTGAACAGTAGCAGCACC
Right flanking sequence: Indices 536385 -- 536884
ATATCTGAAGAAATTTTAGGGTTCGTGATAATAGATCTGGGCCGGTTGAAAAGGCTCTTTTTCTT
CTTCTTCATTCTCGACAGGAATACATCAACAAAACAGCCCTTCCATATAGGTGCATGAACTTTGT
CAATAGATTCCTAGCTAACTCCTCTTCCTATTGATCTTGATTAGTTCCAGCTTGTTGAGAGTTCT
CTTTTTTTTTTTGAATCGGACCCATTTTTAGACCGTCTCCTGAAATACCTGCTTATCCCGCATGT
GCTTTCGGAGCCCCCCACTCATTCAATCACTTGCTTGTGATTGCAGCCATTCCCCGAAAAGGGAA
TTGTCCGCTCCCGTTCATGGGACGAACCGAACATCGTTAGGTCCCGAATTCTGCGAACCACCGGA
TCTAGACCAAGATCTCCATTACGTCGTACGAGATATCGATCCGAAGAACTTACTTTCAGTTGTAA
GTTATCCATTCTGCTTCTATCTAAAGTGATGCTAGGCTGCTTCAC
Found at i:549195 original size:15 final size:15
Alignment explanation
Indices: 549175--549204 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
549165 GGAGGCAGGC
549175 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
549190 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
549205 AATATACTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAGTGAAATAAAAT
Left flanking sequence: Indices 548675 -- 549174
ACGGCTTTCAAAAGACGAGTAAGAGACGGGGAGGGGGAGGCTCTCGAAACCAAGCGAGACTAAAA
AGAACATGGGAATTCGCACCATTCCTATGAGTGCTTTTTTTCGAAAAGCCAACAAAGGGACAGCC
CTCTTTCTCTATCTCGGTCTCGGTTTAGCATCATCATATATCGATCCGGAGATAATTTGGATTGG
TTGTAGTGCGGATTAAGGAGCTGCTCCTCCATGCTGTGGCTGTGGAGGTGGGGGCTGCCGCCGCC
TGATAGAGGCAGAAGCCGGGGCCACCGGAGCTATCTGCGTCGAGTGTGTCGATTGAAAGAGGAGG
GGAGACAAAATGAATTCCAGCGAAAAAATAGAAAGAGTCGTGCCGTTCAAAGTGGAATTCTTCTA
AGATCCATCCATTGCTCGATCGATTTTGCATGCTCTGCTCCCAAAATGCAGAGAGACTTGCGAGG
GCAGATCTGGGTTGGTTGGTCCGGAAAGTCATGGGGGAGGCAGGC
Right flanking sequence: Indices 549205 -- 549704
AATATACTGGTGCTACTATAGAATCTTTTGAATCACGCACGGCACACTTTCTATATCTCCTCCGT
CTACAAGGTGAACAGCTTGGCTTACAGCACAGCGTGTTCGCCACCACACCGGCTGGCTGGTGCAT
TGGCCCTTTGAATGAATAAGAGAAGGGCTTTGTATAGACACCCTTGAGCCATATTCGTCGCCCTA
GGCTCACCATTATTTCATTCTATTTATGGGTTCTAGCTCCAAAGAACATATACATGGAGCTATGT
CGACTTACGTACGTCTCGTTGACCAAACGATTAGGTATACCACGCCACGTATCATCCCCTCTTTC
CAATAAAAAAAAAAAAAGAAAAGATATAGTGATCGATCGTGCCGTAAGACCTTGTTCGTTTCTAC
TTGACGTTATTTTCCTCGGTTTTTTTTACATTACATAAGGTAGCTTGCTTACTTAGCGCTTGCGC
TAAGGATCTAATCAGAGTCAAACTTCAATTTAAAATGAAAAAATA
Found at i:653244 original size:24 final size:24
Alignment explanation
Indices: 653217--653289 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
653207 CTTTCCTTTT
653217 TGTCTTGACTCTATGCCTTCCAGC
1 TGTCTTGACTCTATGCCTTCCAGC
* **
653241 TGTCTTGGCT-T-T-CCTT---TT
1 TGTCTTGACTCTATGCCTTCCAGC
653259 TGTCTTGACTCTATGCCTTCCAGC
1 TGTCTTGACTCTATGCCTTCCAGC
653283 TGTCTTG
1 TGTCTTG
653290 GTGAAGACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 9 0.24
19 1 0.03
20 1 0.03
21 8 0.22
22 1 0.03
23 1 0.03
24 16 0.43
ACGTcount: A:0.08, C:0.29, G:0.18, T:0.45
Consensus pattern (24 bp):
TGTCTTGACTCTATGCCTTCCAGC
Left flanking sequence: Indices 652717 -- 653216
AAAACGTTCTTTCTTTTCTACGCTACGATCTTTCTTCTCTTATGATATTTCTAACCAAATGAAAC
TGATTCAATGGCAGCCCCTCTTCCTTGTTCACAGAAACCATTTTATAAAGAGCAAAGAGAACAAG
AGCAATCGCAGCTGAGTCAACTCTATCCATTCTTGTTCCAAGCTAAAAGCTTGAGGAAGAAGAGC
TTATTCAACTCGAGGGTCAAAGAAGACCAAGAAAAGATCGATTCAGCATAAGCAAGGGATGAGAG
AGGCCTTTGTCGGGTAAGAGATGAATGAGGCCTTACGAGTGAACTGCCTTACCTTAAGGAGACGT
CGGACTTACCTTTGGAAACTTCCCATGAAGTAGTGCTTTCTTCTTTGCTAAAGAGAATGTCAAAC
CTGCAAACAAGCCATTCAAGCAAAGAGTCTATTCTGAGCCCTTTTCATGTACAGGGTATTCTCTT
GATTAACGCCTTTTCCGCTCTCATTCCTGGCTTGGCTTTCCTTTT
Right flanking sequence: Indices 653290 -- 653789
GTGAAGACTGTGGTAGTGGTATCGGTTCTTTGCTGGGTTGATTGAATATCTCTTTCGCTTGCTTC
TTTGCGGCAGAAAGACCGAGGGCAAGATCTCTTTATATAAGGATATAAGGAAAACCTCACATCCG
ATTCGTAAACAGACAGGAGACAGGCAAGAAAGTCACTAGAAGCACCGGAATGACTACCATCGACT
GGCTTGCCCGGAATACCAGGACTTAGACCGACAGACTGCTTTCAACCGCTTTGCTACTGGTTCGC
TTTGAATGAACCCTTACTGCACTGCTAGCGTTGGAGAGCTTGAAAGCGGCTTGGCTGGCACTCAT
ACTCACACGGATTGGACTTCAACCGTGCTACTAGGCCTAAATTTCCCTCTTCCTTCGGGTGTACT
AAGACTATCTCTTTCATAGACTATTCCTTCTCCCCTCGAGTCAGGAGCTAGCTTTCAATCTCCCA
CTCCTATCTGCTACTTACTCCTGATACAATCTTGCTTGGAAAAAA
Found at i:653261 original size:42 final size:42
Alignment explanation
Indices: 653202--653290 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
653192 TCATTCCTGG
653202 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
1 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
653244 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
1 CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
653286 CTTGG
1 CTTGG
653291 TGAAGACTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.07, C:0.28, G:0.18, T:0.47
Consensus pattern (42 bp):
CTTGGCTTTCCTTTTTGTCTTGACTCTATGCCTTCCAGCTGT
Left flanking sequence: Indices 652702 -- 653201
TCGTAAAGGCGAATCAAAACGTTCTTTCTTTTCTACGCTACGATCTTTCTTCTCTTATGATATTT
CTAACCAAATGAAACTGATTCAATGGCAGCCCCTCTTCCTTGTTCACAGAAACCATTTTATAAAG
AGCAAAGAGAACAAGAGCAATCGCAGCTGAGTCAACTCTATCCATTCTTGTTCCAAGCTAAAAGC
TTGAGGAAGAAGAGCTTATTCAACTCGAGGGTCAAAGAAGACCAAGAAAAGATCGATTCAGCATA
AGCAAGGGATGAGAGAGGCCTTTGTCGGGTAAGAGATGAATGAGGCCTTACGAGTGAACTGCCTT
ACCTTAAGGAGACGTCGGACTTACCTTTGGAAACTTCCCATGAAGTAGTGCTTTCTTCTTTGCTA
AAGAGAATGTCAAACCTGCAAACAAGCCATTCAAGCAAAGAGTCTATTCTGAGCCCTTTTCATGT
ACAGGGTATTCTCTTGATTAACGCCTTTTCCGCTCTCATTCCTGG
Right flanking sequence: Indices 653291 -- 653790
TGAAGACTGTGGTAGTGGTATCGGTTCTTTGCTGGGTTGATTGAATATCTCTTTCGCTTGCTTCT
TTGCGGCAGAAAGACCGAGGGCAAGATCTCTTTATATAAGGATATAAGGAAAACCTCACATCCGA
TTCGTAAACAGACAGGAGACAGGCAAGAAAGTCACTAGAAGCACCGGAATGACTACCATCGACTG
GCTTGCCCGGAATACCAGGACTTAGACCGACAGACTGCTTTCAACCGCTTTGCTACTGGTTCGCT
TTGAATGAACCCTTACTGCACTGCTAGCGTTGGAGAGCTTGAAAGCGGCTTGGCTGGCACTCATA
CTCACACGGATTGGACTTCAACCGTGCTACTAGGCCTAAATTTCCCTCTTCCTTCGGGTGTACTA
AGACTATCTCTTTCATAGACTATTCCTTCTCCCCTCGAGTCAGGAGCTAGCTTTCAATCTCCCAC
TCCTATCTGCTACTTACTCCTGATACAATCTTGCTTGGAAAAAAC
Found at i:663490 original size:5 final size:5
Alignment explanation
Indices: 663480--663511 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
663470 GCGTGACCCC
663480 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
663512 GGCGGGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Left flanking sequence: Indices 662980 -- 663479
CTTCCGCACAGTTTGTCACTAAGGAAAAATTGGATGAAAAACTCCGTTTAAAAAACCCAAAGAAT
GCAGGAACAATCCAGCCTTATCGCAGTCCATATCCTCCATATCATGACACGGTTCCTTATCCACC
AGGGTACCAAATCCCACCATTTTCTATGTTTGATGGGAGAGGTGGCCCTAAAAGACACTTATCTT
ATTTCATTACCATAGTATGGCAGAATGGTATGATTATACGACTAGAGAACAGATAACCAGGAAAG
ACAGAAAGGGAGAACCGACCGGGGCCTTGCCCTTACTTTAGCTTTAGGAAGAAATCCAGACTTTG
GAGCTCAGCTTAGGGATCAGAGGCGAACCACCTAGTATGGAACACAATCAGTTCACTAAGACAAT
CGGAGTGAGCGGGCTATGAAGTCCACCCAGCTTTTAGGGTTTACCGAGCTTAACTCGTGGAATGG
TGATTCGGAGTTAAGTTAACGGGCTTGGCTTGAAGGCGTGACCCC
Right flanking sequence: Indices 663512 -- 664011
GGCGGGGTTACCGCGGTTCCTTCGACTTTATATTCGGGATAAACGGGACCCTTATTTACTCAGAC
TCAGATTGGTAGGCAATCAACAGTCATAACAAGGAGATTCCCCACTGACAGCCTCTATCAGATAG
TACGCAGGTTTTTCTCCCGGAAAGAACTCATTTTCTAATCGAACCGGTTGTGCAATAAGATGTGC
TGCTCCTCCTTCTCTTGAGAGGTCCCTCGGGAAAAGAGCAATCCATCCTTGTACCCATACAAAGA
CGATTGTAGAAGGATACCAGGATTATACTCAAACAATAGCAGCGGTACTCTCCGAAGTAAGCCCT
GAAAATAAAGGTGCTACACTAATTGTAGTAACCAGAACAGGGCCTCGGCCCCAGATGCTATGGAA
GACCTTTCCTTCCTTGCCAAGGGCAGCTGCTCGACCAAGCAACCAATTACCACCCTAAAACGTAG
CCTGGGAAAAATTCCTGCTCAGATCTCAATCCTAGACTTTTTCTC
Done.