Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_035074
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: 644395
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Found at i:22901 original size:42 final size:42
Alignment explanation
Indices: 22842--22930 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
22832 ACAGTCTTCA
22842 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
22884 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
22926 CCAAG
1 CCAAG
22931 CCAGGAATGA
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:0.47, C:0.18, G:0.28, T:0.07
Consensus pattern (42 bp):
CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
Left flanking sequence: Indices 22342 -- 22841
CGGTTTTTTCCAAGCAAGATTGTATCAGGAGTAGTAGCAGTAGGAGTGGGAGATTGAAAGCTAGC
TCCTGACTCGAGGGGAGAAGGAATAGTCTATGAAAGAGATAGTCTTAGTACACCCGAAGGAAGAG
GGAAATTTAGGCCTAGTAGCACGGTTGAAGTCCAATCCGTGTGAGTATGAGTGCCAGCCAAGCCG
CTTTCAAGCTCTCCAACGCTAGCAGTGCAGTAAGGGTTCATTCAAAGCGAACCAGTAGCAAAGCG
GTTGAAAGCAGTCTGTCGGTCTAAGTCCTGGTATTCCGGGCAAGCCAGTCGATGGTAGTCATTCC
GGTGCTTCTAGTGACTTTCTTGCCTGTCTCCTGTCTGTTTACGAATCGGATGTGAGGTTTTCCTT
ATATCCTTATATAAAGAGATCTTGCCCTCGGTCTTTCTGCCGCAAAGAAGCAAGCGAAAGAGATA
TTCAATCAACCCAGCAAAGAACCGATACCACTACCACAGTCTTCA
Right flanking sequence: Indices 22931 -- 23430
CCAGGAATGAGAGCGGAAAAGGCGTTAATCAAGAGAATACCCTGTACATGAAAAGGGCTCAGAAT
AGACTCTTTGCTTGAATGGCTTGTTTGCAGGTTTGACATTCTCTTTAGCAAAGAAGAAAGCACTA
CTTCATGGGAAGTTTCCAAAGGTAAGTCCGACGTCTCCTTAAGGTAAGGCAGTTCACTCGTAAGG
CCTCATTCATCTCTTACCCGACAAAGGCCTCTCTCATCCCTTGCTTATGCTGAATCGAGATTTTC
TTGGTCTTCTTTGACCCTCGAGTTGAATAAGCTCTTCTTCCTCAAGCTTTTAGCTTGGAACAAGA
ATGGATAGAGTTGACTCAGCTGCGATTGCTCTTGTTCTCTTTGCTCTTTATAAAATGGTTTCTGT
GAACAAGGAAGAGGGGCTGCCATTGAATCAGTTTCATTTGGTTAGAAATATCATAAGAGAAGAAA
GATCGTAGCGTAGAAAAGAAAGAACGTTTTGATTCGCCTTTACGA
Found at i:22912 original size:24 final size:24
Alignment explanation
Indices: 22843--22915 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
22833 CAGTCTTCAC
22843 CAAGACAGCTGGAAGGCATAGAGT
1 CAAGACAGCTGGAAGGCATAGAGT
** *
22867 CAAGACA---AAAAGG-A-A-AGC
1 CAAGACAGCTGGAAGGCATAGAGT
22885 CAAGACAGCTGGAAGGCATAGAGT
1 CAAGACAGCTGGAAGGCATAGAGT
22909 CAAGACA
1 CAAGACA
22916 AAAAGGAAAG
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:0.45, C:0.18, G:0.29, T:0.08
Consensus pattern (24 bp):
CAAGACAGCTGGAAGGCATAGAGT
Left flanking sequence: Indices 22343 -- 22842
GGTTTTTTCCAAGCAAGATTGTATCAGGAGTAGTAGCAGTAGGAGTGGGAGATTGAAAGCTAGCT
CCTGACTCGAGGGGAGAAGGAATAGTCTATGAAAGAGATAGTCTTAGTACACCCGAAGGAAGAGG
GAAATTTAGGCCTAGTAGCACGGTTGAAGTCCAATCCGTGTGAGTATGAGTGCCAGCCAAGCCGC
TTTCAAGCTCTCCAACGCTAGCAGTGCAGTAAGGGTTCATTCAAAGCGAACCAGTAGCAAAGCGG
TTGAAAGCAGTCTGTCGGTCTAAGTCCTGGTATTCCGGGCAAGCCAGTCGATGGTAGTCATTCCG
GTGCTTCTAGTGACTTTCTTGCCTGTCTCCTGTCTGTTTACGAATCGGATGTGAGGTTTTCCTTA
TATCCTTATATAAAGAGATCTTGCCCTCGGTCTTTCTGCCGCAAAGAAGCAAGCGAAAGAGATAT
TCAATCAACCCAGCAAAGAACCGATACCACTACCACAGTCTTCAC
Right flanking sequence: Indices 22916 -- 23415
AAAAGGAAAGCCAAGCCAGGAATGAGAGCGGAAAAGGCGTTAATCAAGAGAATACCCTGTACATG
AAAAGGGCTCAGAATAGACTCTTTGCTTGAATGGCTTGTTTGCAGGTTTGACATTCTCTTTAGCA
AAGAAGAAAGCACTACTTCATGGGAAGTTTCCAAAGGTAAGTCCGACGTCTCCTTAAGGTAAGGC
AGTTCACTCGTAAGGCCTCATTCATCTCTTACCCGACAAAGGCCTCTCTCATCCCTTGCTTATGC
TGAATCGAGATTTTCTTGGTCTTCTTTGACCCTCGAGTTGAATAAGCTCTTCTTCCTCAAGCTTT
TAGCTTGGAACAAGAATGGATAGAGTTGACTCAGCTGCGATTGCTCTTGTTCTCTTTGCTCTTTA
TAAAATGGTTTCTGTGAACAAGGAAGAGGGGCTGCCATTGAATCAGTTTCATTTGGTTAGAAATA
TCATAAGAGAAGAAAGATCGTAGCGTAGAAAAGAAAGAACGTTTT
Found at i:126972 original size:15 final size:15
Alignment explanation
Indices: 126952--126981 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
126942 CCAGTATATT
126952 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
126967 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
126982 GCCTGCCTCC
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:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATTTCACTTA
Left flanking sequence: Indices 126452 -- 126951
TTTTTTCATTTTAAATTGAAGTTTGACTCTGATTAGATCCTTAGCGCAAGCGCTAAGTAAGCAAG
CTACCTTATGTAATGTAAAAAAAACCGAGGAAAATAACGTCAAGTAGAAACGAACAAGGTCTTAC
GGCACGATCGATCACTATATCTTTTCTTTTTTTTTTTTTTTTATGGAAAGAGGGGATGATACGTG
GCGTGGTATACCTAATCGTTTGGTCAACGAGACGTACGTAAGTCGACATAGCTCCATGTATATGT
TCTTTGGAGCTAGAACCCATAAATAGAATGAAATAATGGTGAGCCTAGGGCGACGAATATGGCTC
AAGGGTGTCTATACAAAGCCCTTCTCTTATTCATTCAAAGGGCCAATGCACCAGCCAGCCGGTGT
GGTGGCGAACACGCTGTGCTGTAAGCCAAGCTGTTCACCTTGTAGACGGAGGAGATATAGAAAGT
GTGCCGTGCGTGATTCAAAAGATTCTATAGTAGCACCAGTATATT
Right flanking sequence: Indices 126982 -- 127481
GCCTGCCTCCCCCATGACTTTCCGGACCAACCAACCCAGATCTGCCCTCGCAAGTCTCTCTGCAT
TTTGGGAGCAGAGCATGCAAAATCGATCGAGCAATGGATGGATCTTAGAAGAATTCCACTTTGAA
CGGCACGACTCTTTCTATTTTTTCGCTGGAATTCATTTTGTCTCCCCTCCTCTTTCAATCGACAC
ACTCGACGCAGATAGCTCCGGTGGCCCCGGCTTCTGCCTCTATCAGGCGGCGGCAGCCCCCACCT
CCACAGCCACAGCATGGAGGAGCAGCTCCTTAATCCGCACTACAACCAATCCAAATTATCTCCGG
ATCGATATATGATGATGCTAAACCGAGACCGAGATAGAGAAAGAGGGCTGTCCCTTTGTTGGCTT
TTCGAAAAAAAGCACTCATAGGAATGGTGCGAATTCCCATGTTCTTTTTAGTCTCGCTTGGTTTC
GAGAGCCTCCCCCTCCCCGTCTCTTACTCGTCTTTTGAAAGCCGT
Found at i:139820 original size:19 final size:19
Alignment explanation
Indices: 139796--139837 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
139786 CTTCAGATAT
139796 TTTTATTTCTTTTA-TTTTA
1 TTTTATTT-TTTTACTTTTA
*
139815 TTTTATTTTTTTACTTTTC
1 TTTTATTTTTTTACTTTTA
139834 TTTT
1 TTTT
139838 GGTGCTGCTA
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:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTTTACTTTTA
Left flanking sequence: Indices 139296 -- 139795
TGAAGCAGCCTAGCATCACTTTAGATAGAAGCAGAATGGATAACTTACAACTGAAAGTAAGTTCT
TCGGATCGATATCTCGTACGACGTAATGGAGATCTTGGTCTAGATCCGGTGGTTCGCAGAATTCG
GGACCTAACGATGTTCGGTTCGTCCCATGAACGGGAGCGGACAATTCCCTTTTCGGGGAATGGCT
GCAATCACAAGCAAGTGATTGAATGAGTGGGGGGCTCCGAAAGCACATGCGGGATAAGCAGGTAT
TTCAGGAGACGGTCTAAAAATGGGTCCGATTCAAAAAAAAAAAAGAGAACTCTCAACAAGCTGGA
ACTAATCAAGATCAATAGGAAGAGGAGTTAGCTAGGAATCTATTGACAAAGTTCATGCACCTATA
TGGAAGGGCTGTTTTGTTGATGTATTCCTGTCGAGAATGAAGAAGAAGAAAAAGAGCCTTTTCAA
CCGGCCCAGATCTATTATCACGAACCCTAAAATTTCTTCAGATAT
Right flanking sequence: Indices 139838 -- 140337
GGTGCTGCTACTGTTCAACTCCATACTAACATTTTTTAATTCCTATCATCATCGTCGCAGCTTGC
GAGTTTGAGGAAGATAAGGTCGATTCGATGGAGGTGCAGCAAGCCCTCCCCCCGGTGCCGGAAGC
TTCTGAGCCACTACCACTAGCTCAGGAGCCTGTTTCTCCTTCGTTTGAAATCCAAGCTGCTGAAG
TCAACCAAGAGGACATCTGGAGGGAGTTGGAGCAGCAGGAGCAACCGGCACCAACGGGTGGAGCT
AAGCTAACAAGGCCTCACATATGCGAAAGCTCACCCCATTGGAAAATCAGGTAGCTGACCTTATT
ATCGATTTACGAAAATCCGAAGTACCCTCACCTAATAAGATTCAACAAATCGTCGAAATGCTCGA
AGAAGAAAGAATATGGTCTGGAAAAGCTGCGCACAATCAAAAAGCACAACCAACAATATGGCAGA
AAGAGTGTATTTTTTAGGAACTCCAAGGAGTGCTTTAATATGTTC
Found at i:204694 original size:17 final size:17
Alignment explanation
Indices: 204672--204707 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
204662 GGGAAGATAG
204672 AGAAAGAGAGACAAGAA
1 AGAAAGAGAGACAAGAA
* *
204689 AGAAAGAGATACAGGAA
1 AGAAAGAGAGACAAGAA
204706 AG
1 AG
204708 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 204172 -- 204671
TTATCCAGAAACAACTCAATCAATCAATTACCTTATTTAAGATACGCCCAAATCCATTCAACCAG
CCACTCAAGGGTTTGGAGTTACCATTTCCGCTATTCCTGCCAAGGAATAAAGTAAAGGGACTACC
GATACCCCTTCGCGTTCGCTTTGGTTTAGAGTAATCGCTTGTTCCTTCAGTCTTCAGAGGTAAGC
TCTTTTGCCTTCTTCCTAATGGACTACGAGGACCCTAGGATTTAGGACTCTTATAAAGAAGGATT
ATTGGCCTACTGCTGCCTTACCACTAGCTTAACACTAGCAGCACAGGCTTACCTATTAATCACAG
ACCCCCTTCCTTACTTGCTTACTTCCTTGCTTGCCTGGAGAGAAAGAATATTAAAAAGAAAGAAA
GGATCCCCTACTTACTTAGTACAAGGAAGGGAAAGACTTACTAAAAGACCAAAGACTGGCTTACT
TACTGTCTTGGCTCCTAGGACTTCTTACAAGGAATGGGAAGATAG
Right flanking sequence: Indices 204708 -- 205207
CTAAGGATATAACGAAGGGCGAAAGGGAGCACAGAAAGGCGCAATACCAAAGCTTTTTTGAAAGA
GAAGAATGCGCCATAGGTTTCTTCCTGCTTTGCTTTGGGAAGGGGCATTGAAAGAACACAGACAT
AGTGGAAATGCTCCTAGACTAGAGAAGGTTCCCCCGTAAGTCTGATCCTCTCAACTCATACTACA
GCAGGGAAATCCACTTTTCTGGACAGGGTCTTCCTTCTCGGAGAATAGGTCTACTATGCTGAAGC
AGAAGGGAACAGGATGCTCATTTAAATGTCAATGAGACTAGTCAGGATGCTCCCTGTAGTACATT
CCCAGATCTGAGCTACCTGGATCAACCCACCAATTAGTACAGTTCGTCAGTGAGTACGTGGGAAT
AGCCCAGTAATGAATAGAAATTTAAGTCACCGGGTAAAGAAGCGAGGGGATCAGCTCAATTGAAA
GAGAGGGCGCGATCGGCATACAATTATTCGATTTCATTTCTTGCC
Found at i:253799 original size:36 final size:36
Alignment explanation
Indices: 253757--253829 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
253747 CCTATGTCTT
253757 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
253793 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
253829 T
1 T
253830 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 253257 -- 253756
AAAACAGGTACTGATAACAAAGTACAAGCCCTAGCTTTTAAGCCGAAGAAAGAAGCAATCATACT
CCTTAAACAGAAAGATATTGCACTTCAAAATCGTTACTAGAAGCACTACAAGCGCACTTCCTATC
TAAACAAACCAAAGCAGAAAAAGCACCTCCCTCCCGGATAAAGAGCAAGTGTGCGAGAGAATAGA
ACTGAGCATCAAGGCTGCAAGACAGAAGGAAGGTTCCTGCGTGCAGGAAAGCTTTTTCACCGTCC
ATTGGGTATTTGTCTTTATCTCGCTCTCCCAACTAACTCAGACTTATGATAGGCGGGCTCAATTC
CAGATATTGACCTCTGGGGATCCTTCTCTTTGAATTCCCGGTCTTCCGTTTTCTTCCTTGGTTCC
ACCCTTCCATTCATGAAGCAGATCGCCGGGAAGGCTTTTTCTCAAGCATAAAACGAGAGACCCGA
TCACATTGATCGACAAACAAAACTCCCGATAGAAGCCTATGTCTT
Right flanking sequence: Indices 253830 -- 254329
TTTCTTGGTATTCACGCTCATCGGACTGAAGTTGGTCCTCATTTATCTCAGCAGAAGTCTTTCAT
GATCTTTTCATAAAGTTGAATCTAGCCAATGCAAACTCAACTCAGTTAGTACTCCTATATCAATC
GTTGTCGCTGCCTTCTCAAGATGACGGGTAACCCCTTTCTTTAGGAGGATCCATCTCTTTATCGC
AGCATGGTAGGAGCCTTGCATTATTTAAGCATGACAGGGCCGGACATTGCCTTTGCCGTAAGCAT
TTGAAGCCAATTCCTCAATTGCCGCCCAGTACATCGTAAAGTGGATCGATCGATATCTTAAGGGA
ACTTCTCATTATGTCTTTTACCTCTTCTTCTGAGCTAGAGTTACATGCTTATGCTGATTGGGGTC
CTTGTCTTGATAGTCGACGTTCTCTTTCTGGGTATGCTCTCCTTTTTCTTGCCTAATCTCCTTTC
CTAAAACTCTGCGCTTCTCTTTTGAATCTTCTCACCCCGCCTAGC
Found at i:281409 original size:2 final size:2
Alignment explanation
Indices: 281402--281440 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
281392 ATTAGAAAAG
*
281402 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
281441 AAAAAAAGGT
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 280902 -- 281401
TTTCCGAAAGCGCAGTGCCCCACGGATAGAAGACGACTCCCCTGATTTGGTGTCGCCCATTTTTT
ATATTTATGGGGTTTAAACCGTCGTGCACTAATGCTGTTTCTATCTTTTTTTCTAGCAGCATCCG
CTTTTCCAGAACACTAAAAAATGCTGACACCTCGTGGTGTCTCCCGACAAAATGCACTGCTAAGC
GGTCGAACAGTTCCATCCTTCTCGTGTGATCCGGCATCAGGGGTTGCTCGAGAATCGGGACGAGA
ACAGCCTGTGCTATTTCAGGATCAGTCAGGGGCCTCGGGAGCGCGCGGTTGGACCGCTTGATGGA
AATCCGCTGCGCCAGACGGGGAACCACTTCTTACGTCGCACATGGCTATCTCCAGGAGGGGCCCC
TGACTGATTATTCCAACGATAGATAGAATAAGACCCAGAAGTTGGATGGGACTGCCATGAAAGAT
CTCCTCCGGGATTGGATCCCGGTGAAAAGAGATCCATTAGAAAAG
Right flanking sequence: Indices 281441 -- 281940
AAAAAAAGGTGGATTTCGCCCTGCAATCCTAAGGGCCAGGATTCAATCTCCACTGGAGCCATTGT
GAGGAATAACCATTCTAGAACAATCATTTGGTTTGTTTCATTCTTTTTTTGTTCTGCTCCCCCCA
AAAAAAAGGGAGACTTCCTCAGGAAATCGCTGGTTTTTCCAACCCAACCGAGGATTTCCGACAAG
TCCTTCTTCATTTTTAGAGCAAGAAGGGGAACTATAGAGATTCAATGAACAGTGTTTCTTACGAT
TACGCCCAGCCCAAAAAAGCCCTTCGGAGTTGAACCGAAAAAAAAGCCTATTACTTAGGGCCCTT
CAAGAAGTTTGTGTTAAGCATATAGCCGGGCCCTCTTTCTGAGCCAGGATCAAACTCTTCTTTTT
TTACTATGATTGGGCCCTGCAGACGTACTACTTTCAATCAAACCTTTTCTTTCCTTTCCTTAAGA
TATATATGTTACCCACCATATTAATAAGGCACCAAACGCGCACTG
Found at i:290698 original size:14 final size:14
Alignment explanation
Indices: 290679--290709 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
290669 TATCTAAACT
290679 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
290693 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
290707 ATT
1 ATT
290710 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 290179 -- 290678
AAGAAAAGCTTTTTCAGATGTTAAAAAAAGCATTGTAGGATAATCGGCATCTGTCCCTCGAGAAA
GAGTAAGATAGGCAAAAAGGCATAGAGACAACAGCGGTAATGCCGCATCTCTCGATGAGAAGGAA
TCCTGGAAAGAAGAGCAAAGAAAAGCCCTTCTTCTTCTGCCTTTTGACTCTATCTTGCCCTTTCT
TTAGGGAATTGCGGAGTGAATGAGTGCAACAAAACAAGGAAAGAAGGCTATAAGCTGCCTACATG
GAATTACTCTTCATGCACATTTCCCAGAAAGAGTATATTGCGATAATCGGATGCTAAGTCTCCCT
GGCTTCCTTCCTCCAGCGGATCTGTGGGCATTAAAAGAAGAAAGACTTTCAGGTTCTTCGCCACA
TTCCTTCTTAGGAAAGAAAGGCTCCCGTTCGTGCCCTGTAAGAAGGAAAATTAGAAAGGAAGGCA
TAGTCGAAAAGACTAGCAGCTTCTCTGTGCATGGATATCTAAACT
Right flanking sequence: Indices 290710 -- 291209
ATAATTCAAAAAGACTTTCGCGAAGCAGGAAAACAATCAGGTAATCAGGAAAGGCAGAAAGGGTA
GAGCCTTAGTTACCCGCAGCTCAAATAGCCAAGGTCGGTGGAAAAGGAATAGTACAGCTTGTTTG
GATAAAGGAAGCATTCATACTCGACCCGCGTCTGGACGCCCCTCTCGGGCTCACTTCCTGACAAC
CCAGCCCACAACAGGAAATGGACAGGCATTGACAAAAGCCGAAGCCTCTAACGATTTTTAAGCTG
GGTAACGGGTACCCTATCGGAAAGGGGTTTTCGTCTACCTCCCAAGCATATGGCGGGCTTATAGG
GCGCTGGTCTCCGTTAGGCTTTGAGTCTAGGAGTATAGCGATGGCTTCATCCACCGGTCCTACCA
TGGAACGAGTTTCTTCGCGCTTGGCCTTGAAATTTCGAGGCATCTTTCCCAAGACAAGAAGCGGC
GTCGGATCCCGGTAGTGCGGTAGTACGCCCAGCAGAATGTCGTAG
Found at i:299254 original size:26 final size:26
Alignment explanation
Indices: 299225--299277 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
299215 GACACGCTAT
299225 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
299251 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
299277 G
1 G
299278 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 298725 -- 299224
GTGGTAGTGGCTCTATTGACTATAGCCGTCCCAATGTGAAATATAGTATTCAGTAGACGCAAATG
CAGATACTATCCCCTACGGAATAAAACTTTCTTTCATTCCGTAGGGGTAAGACTCTTCAAATAAA
ACTAAAAATTCACCTAGGACTTTTTTCTTTTATAGGGACTTCTGGCTCTGATCCTTCTATAGTAG
GAAGACAAGATCGCAAGGGAATCACTAGTTCGAGTTCCATGCCTTCCTTCTGGTCCCAAACACTG
GGTTATTAACCGATGAGTTAATTTTCCCCTTACCCATTTCTTGTCCATGTGTCCCTTGCTTCTTA
GTGCTCCGTTGGACGGGGACTCCTTCTTCATTTGAATGCTTTGATGCTGGCCAACTGGGAGTAGG
TTCTGGCTGCTCTTTCTGTGATGCTATTTCGACCTCGTAAAGATATTAGGACTTTCACACTGACA
TTGAGACAGAAAACATTCGATCAGTTTCCCAGCGTGACACGCTAT
Right flanking sequence: Indices 299278 -- 299777
CCTTTGTCCCCATTGCTTGTTAGTTAAGTAGGGAGAGAGAACGCCCCATCTCTTGATTACGAAGA
TCACTTTCACAGCAAGCACGAAGCTTAACTATTATGTAAATTGAAACGATCTCCCCAGGAAAGCA
TGATGCCTGACTTGCCCCTGCTTTCCAAAACGGTAGACCAAAAGCACTGAAATGAATATGAGAAA
TGTGGCCTATCTATGGAAGGAATCTTTCGTTACTAGAACCCCTTCCTAGTGACTGTAAGCGAAAT
GCATTTAGCGAACGCCTGGGGGTACTGAGTTCCATATTTTTTATTATAGAAATGTTATCTCTATC
TAAACGACTAAGTCTTCCAGTGATCTCTCCCCCACCCAAAACCATCCCTTCCAGCGTTAGCGCAC
AAGAAGGAGCTTTTGGCAGTGAGTCGAAAGTCTTAGTGAGAAGCCCTCTTAGGACTCTTTCCACT
CTTCTCTGAGTGCCTTCAACAGTGCTTAGGTAGCGCTCACTGCGA
Found at i:326342 original size:17 final size:17
Alignment explanation
Indices: 326299--326344 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
326289 GCAGTAAATG
*
326299 GAATAAACTAAGCAAGA
1 GAATAAACTAACCAAGA
*
326316 G-ATCAACTAACCAAGA
1 GAATAAACTAACCAAGA
*
326332 GAATGAACTAACC
1 GAATAAACTAACC
326345 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (17 bp):
GAATAAACTAACCAAGA
Left flanking sequence: Indices 325799 -- 326298
TAAGCAGCCAAGGCCAAGAGCAAGCAGGAGTAGTCCTATCTGCCTATAAGGATTCGATAAAGAAA
GAGAATGTGAGTGGGCAGGAGATCAATAAACACAGAAAGCGAAGAGCAAAAGGAGCAGAAGACAC
TCAGTTGTTTATGTGAAATCAAGGAGCAGCAGGTTACACTTTTACACTTTCCCAAAGCAAAGAGA
GCTCAAAGCAATAAGATGAAAGCTGGGATGAGATGCTAGCCTTAGCTAGGAAGATCCATCATTGA
GCCTTAGGCCACTACCGAGCAGAAATGGAGGATCATAACACTTGAGAGATGATCCCTACTTGAAA
AGGCGGAGACAATACCTCTTGTTGCGACAAATCGAGTTTCAAAAGCCCATTTATCAATCACATTT
TCAGGCACACCAGTCAAAGAGCCATCGGACCCATTAAAGTCCCCTTTTTTACTAATATACAAGGC
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 326345 -- 326844
CCAAGGGATGATCTCGGATTGAAATCCAAGGCATGGTCCCATTGAAAGCCCAGGGATAAATTCCT
AAAACAGAAAAAAAAAGTCAAGTCCAAGGGGGTATGATCCCAATAAAGATAGGATGGATTTTAAG
TCATTTTGGACGAAGCAGCGGGCATACCAGAAATGGCTTGTCAGGAATGGTAGATGGAGCAAGAA
TGCATAGCAGGCTTAAAACACGACACAAGTAGGACGCACTGAGGCCGAGCTTTCCTCTACTACTC
ATTGGAGCTAGCATACGAAATTATCCGTTGAAGGGTTCAACTCTCAGGGCGGCCATTGCGAGCGA
TATTCACTTTCAAGAATCATCGAGCCTACGCCTATTTCATTACTCTCGAAGAGCTCATCAAAGAG
CTAAGGCTAAGGGATGAGAAAAAAAAAGGAGGAGGTGGAATTTCTTTCAACTATAACATTTATTA
CAACACTTAATATTACAGACAGAGAATTCGGTAAGGGGATAGAAG
Found at i:397496 original size:15 final size:14
Alignment explanation
Indices: 397476--397530 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 14
397466 TCATTAGAAG
397476 AACCAGCGGTAGCTA
1 AACCAGCGGTAGC-A
*
397491 AACCAGCGATAGCAA
1 AACCAGCGGTAGC-A
397506 AACCAGCGGTAGCA
1 AACCAGCGGTAGCA
397520 GAACCAGCGGT
1 -AACCAGCGGT
397531 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 396976 -- 397475
TAAAAAGCTTAAAAAATGTATCCCATTTCTTTGAAATCCCACTATAGTAATGCCAATAAAAAGAG
AAAATGAGAGACCCAAAGTAATGAGAAAATGACTTGTAACTGTGAAGCTATAAGGTATCATACCC
TGGGGATTACGAAATAACGAAAAAGTAAAAGTGACCGAGATGCAAGGGAAATACTTTTGTTTCAC
ATTACTGGAAAGACCGCCTATTTGTTCGTTTACCGGGTTCAGCACGAAATCATAAATAAGCTCTA
CCAAGGATTGCCAAGCATTTGGTACTAACTTTCCTCCTCCCTTTTTAGTAACAAAATGAACCAGA
AGTAGGAACAAACTGAGAGTTAGCAGCATAAACAAAGATGGATTTGTGAATGAGAAATACAAGTT
TCCAATCTTCAAATCAATCAATGGCACAATCTCAAATTGCTCAAGGGGGCTGGGGACGATGGGTG
GTTGGGGTGGTTCCATTTGCCCCCCCACCCCCAGGTCATTAGAAG
Right flanking sequence: Indices 397531 -- 398030
TTTTGGCCAAGGCCAAGACAAACATTTTGAAAAAAAATCTTTTGAATTTTGAATAGCCGTGGAAA
ACAATTTCATTTTTCTTTCATTCTTTTCATTCTCCGCTCCCCCCAAAAAAAGGAGAGACTTCATT
TTCACTGTACGAGTAGTGAAAAACTATAGTTTACTTTTATTGGTTGTTGACCAACGGAAAGCATG
GGAGTCTTTGGGCATTTCTTCTTCTCTTACGATATTTCTAATTACCTAATAGAATAAATACTTTA
GTTCGAACTAGTTTTTAGCTTGAACGTGGCGAATGCTATCTCTTTCCCGCAACTCGACTGTTTAA
CAGGATGGTACGAATCCGCTCTTTGACTTAGTTAAGGAAGGAAGCAATTGTTCTCTTTGCGTTTA
GCTGGGCAAAGCAAAGTGAAGGGAAGGATGAATCGCTCCCGAAAAGGAATCTATTGATTCTCTCC
CAATTGGTTGGACCGTAGGTGCGATGATTTACTTCACGGGCGAGG
Found at i:487261 original size:24 final size:24
Alignment explanation
Indices: 487219--487267 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
487209 ATTCGGATTC
* *
487219 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
487243 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
487267 G
1 G
487268 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 486719 -- 487218
CAAAAAGTTTAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATAATCATATGGGTCAAC
AATTCTCATTTCTTAGTTACAGAAAGCCCTTCTCAAGGAAGTAAGCCAAAAGCCACTCATCTGAG
CCAGCGGATTCTCATTCTGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAAT
CTTTGGTCTGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGA
TTATTCAACTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACCGAC
CTGTTGAGAGGATAGCAACAGGAGAAAGAAAAAAAAGAAGTAGAGTTAGGTTCTGTTCTAGTATG
TAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCGTATGATTCTTATCCTACTTCCGA
TAAGTCTTATGAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 487268 -- 487767
GAATCCGTTGTTTCGGGATAAACTTGATATGTTAGTTCGGCCTCGGCTTCTTAGGATGATGCCTG
TGCAATGTATGATCCATCGGATTCTTTTTATTCTATTCTCGGTGCGTTGTTCTTCAGCGAATGAA
AGAAACCGCTGATTCCAAAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGA
ATGACTCAACTGATACTACTCAAAAATTTCCCACATGGAAGGAAATGGGATTTTTGAGAAAAGGG
GTTGGGAACCATCGAAGGACTAGCAACCTGACAGTCCTAAGCAACCTTGAACCAACAACGTTACA
TATACCATACTGCTATAGAAGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTG
GTGAGCTACTTACTGCCCCTTAAGTCAAGAGAATAATAGTACTTTCAGCAAAGGATATCGTAACT
ATGGCGAATACGTTTTTCTTGCTTTCCACATACCCGGAATGCGAA
Found at i:504644 original size:26 final size:26
Alignment explanation
Indices: 504610--504667 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
504600 TTCCATACTT
* *
504610 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
504636 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
504662 A-AGAAA
1 AGAGAAA
504668 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 504110 -- 504609
CTATCCGTCCCTTTTGCTAGAGTAAGTAATTCCCTTCCCTTTTGTTTGCCAGCGTAGCGCATTGA
TCATTGAAGTGGGGGCTAGGCGAGGGCATGGTCTACTTTTTGTTCTGAAATGACTAAGTACGGCT
TGGCTTCAGCTCGTGGGACTGGTTCTCTAGAAAAAGTCCCAAACCCCACATCCTGCAGTCCGCCT
GGATTCGATTCGCTTTTAGTAATTATATTACATTATATATATAAGTAATTAGAAGCTAAAGAGAA
ATTCAATATTACCATATTCTACCGCTCAACTAACGCTATGTGATCCGGTCAAGATGAATCGATCG
AATTTCACAGCTGAGGAGGCAAAGGGAGGCAAAGCGAGAGGTTCTGAAAGAAAAGACTTTATAGA
ACCTTACTCACACGATACGGGGATGGGCCTACACAAGCAGAAGGAAGAGCTATTAGCTTGTCGGC
GTAACGAATGAACTATCGGATGGTAGGCTAACTGCTTCCATACTT
Right flanking sequence: Indices 504668 -- 505167
ACTGCCTTTTTTTTGAATTGAAGGAGGAGTCGCGCATTCGTCTGCAGCGTATAGTATAGTAGCTT
CAATGGAAATCCGTTTGAATTGATGATTTTTCACCTGATTCCCCCAAAACCGTAGAAGCTCAGAT
CGGGGTTTAGCGATAACCTGAGATCCTTTATTCTGTCTCCACTTCTGAGCCGACCGAGCCTGAAG
CCAATATGTATGAAAGAAACCAATCAACGCAGGAATGGAGTTCGTAGCGAGAAGATAAAGTTCCT
CGCCTGAGAAGCACTTCACTGGGTAATAAAAAAAGCTACCTAAAAGATCTTATTACCTTTACTCT
AAGATGCTATAAGATAATTGGGAATCTTTTAGCCGCTATTCCCGCACTATTGTAAACCAGCTTGA
TAAAGGGTAGTGGTAGAGTCTCAGTACCACTGAAAGTGCGATAGTCGGGCAAACAATCTCCTCTT
TTTATCATATCATATAAGGTAGGGTATTGTATATATGGAAATTCA
Found at i:572979 original size:21 final size:21
Alignment explanation
Indices: 572953--572999 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
572943 TTAAGGGATG
572953 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
572974 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
572995 TAACA
1 TAACA
573000 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 572453 -- 572952
TTAAGACTGTTGCAATTGGTACAACTGCTTCAATGGGATAGAAGGAAACTGGCTAAAAAGGATTA
GAAATGGACTAGTAAGAGACTCCAATGTAACCTCAAACTAAAATGGGAACCCTAGGAGGGGCAAC
TTCCACTCTTTTTTTCACTCTTTCCATTGTCGTTTACTTTACGAAGCGAAGGAAATCAAAAGGTA
TGCCCATTTTATCGAGGAGAGGAATTACTAGCTCGCAGGCTTCAAAATGATAACTTCCTTCCTTG
CCCTCGAACCGACTATCCAACGGCATGGAACACTTAGCATTGGCCTATAACTCAAATTCCATTTT
ATAGCACGCCAACAGGAGGGGCTTCTTACAAAAGCACTCCAACAACTCGCTTGAACTTGAAGAGA
GAAGCAACTACTACTTCTCCATCAAAGGAAAAACAAGCATCGACTAAATAGAAGGCCCTTGAATC
TTATCGTTAGAGCGCTATCTACCCTTAAGACTTACTTAAGGGATG
Right flanking sequence: Indices 573000 -- 573499
ATCGATGGACTGGAAGGGCGAGAGACAGAACAGCAAAGAGAACTCAATCTAGAATTTCCACTCCT
TCTAAAACCCCAACCCCAAGTACGGCATTAGCAATTGAAGAGCTTAGTTAGGATGGGTGGAACTA
CAACCCCTCGAACAGGCTCGATAAAGTCTGGGAGATTAGATAAGCTGGCTAGGTATTTTTATATT
CTTTTTACTGAAAATGCACCGAAGGCAACTGCCATTGAAACTATATAGCTTTATATATAAAAGGG
AGAATTCCGCTCGAAAACCAGCCCTCTTCACACCAGTACCTCTGTCCCGACATTTGGTGAGATAG
GGGTAATGCCTACCAAAGGTAAAGGGGAGCCTTCATGCAAATCTATTGAAGGGTCACCTACGTTA
GCTGGTGCCCACAGTGCCAAAGTTTCAACCAAGATCCTTTGGCTCCGTGCTGGTAGCCGGCTTGT
TACTCCAGATTTTAGTGACAAGAACGTCTGTCACGTGCGTCCCTA
Found at i:584509 original size:5 final size:5
Alignment explanation
Indices: 584499--584526 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
584489 CCGGTATGGA
584499 GTTTT GTTTT GTTTT GTTTT GTTTT GTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTT
584527 GTTTCGACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
GTTTT
Left flanking sequence: Indices 583999 -- 584498
TTTATCAAAGATTATAGATGTAACTGGTACTATGTCTCTGCCTTTGACCTATCGATTGAGGGGTG
CTTCTTTTCGTATCTGTGGTACGCCCTTTTGCCCTAAATCTAAGCGATGGAAGCGTCACTATCTT
TGTATGCTTTCGCCGTCAGGCGTATTCCCGTTACCATTGAAACTGTGGTTAGCTTTTCCAGATTT
GGGAGTGTTAACGCCGGGTGTCGCGCGGGCTTTCATTCTTTATAGGGCTAAGTAGCGCCTTCGCT
TTGTTTGTAATAAAAAGGAAAGAGAAGGTCTTCGGACATTTTTTCCAGTTTTTGGGGGGACTTTC
TTGATCGCCTCATTCTTTAACCATGGGTTAAAATGTGGCTAAAGTCTCTCCGATGGTACGCTGAT
GAGGTTAGCGTAAATTACGATGTGTCGCTCGAGGTCTGTCTCTCGAGCCTCCTGTTGTACCAATG
TCTATATTCCGTTTTAGGAAGAAGGTAATGATCTTCCGGTATGGA
Right flanking sequence: Indices 584527 -- 585026
GTTTCGACAGGCTGAGAGCAGTGCCCGCTCCCTTGTGTTTGAGGGAGTTGATGCGGCATTCGAAG
TAGGTGCGGGTGAGGCATTCGAGTTCGAGTGGCTTTGGTACCGGACAGAAGAAAGAAAGAGAATA
ATAACATTGAAATAGCTTACTTTATAGGGGCTTGGAGGTTTTTCCTATTCTTATTTCTCAGTTTA
AGCTAGCGATGGAAATAAGAAAGGCTAGGTAGCTGGCTTTCTTGGGATTGCTCGCTGGCTGACTA
TGACGATTGCCCTCACTCGAAAGCCGCTTCCAATAAGATTGTTTTCAACATTCCCCCCCACCATT
AGAGTTGGGCTTATGGTTGAGCCTCTTATTGCGTAGTCCGCTTTTTTTTTTAGAAAGCAAAGAGG
CGAGCTTTAAGACGTTCTTTAATCCTTGTTGTACTTTCGGGTTGGACTCCAGTCCTCGTCCTCCC
TTGCCTGCCAGCACACCTGAAGGAAAGGATACCGGTATAACACAA
Done.