Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_035076
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: 644460
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Found at i:22897 original size:42 final size:42
Alignment explanation
Indices: 22838--22926 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
22828 ACAGTCTTCA
22838 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
22880 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
22922 CCAAG
1 CCAAG
22927 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 22338 -- 22837
CGGTTTTTTCCAAGCAAGATTGTATCAGGAGTAGTAGCAGTAGGAGTGGGAGATTGAAAGCTAGC
TCCTGACTCGAGGGGAGAAGGAATAGTCTATGAAAGAGATAGTCTTAGTACACCCGAAGGAAGAG
GGAAATTTAGGCCTAGTAGCACGGTTGAAGTCCAATCCGTGTGAGTATGAGTGCCAGCCAAGCCG
CTTTCAAGCTCTCCAACGCTAGCAGTGCAGTAAGGGTTCATTCAAAGCGAACCAGTAGCAAAGCG
GTTGAAAGCAGTCTGTCGGTCTAAGTCCTGGTATTCCGGGCAAGCCAGTCGATGGTAGTCATTCC
GGTGCTTCTAGTGACTTTCTTGCCTGTCTCCTGTCTGTTTACGAATCGGATGTGAGGTTTTCCTT
ATATCCTTATATAAAGAGATCTTGCCCTCGGTCTTTCTGCCGCAAAGAAGCAAGCGAAAGAGATA
TTCAATCAACCCAGCAAAGAACCGATACCACTACCACAGTCTTCA
Right flanking sequence: Indices 22927 -- 23426
CCAGGAATGAGAGCGGAAAAGGCGTTAATCAAGAGAATACCCTGTACATGAAAAGGGCTCAGAAT
AGACTCTTTGCTTGAATGGCTTGTTTGCAGGTTTGACATTCTCTTTAGCAAAGAAGAAAGCACTA
CTTCATGGGAAGTTTCCAAAGGTAAGTCCGACGTCTCCTTAAGGTAAGGCAGTTCACTCGTAAGG
CCTCATTCATCTCTTACCCGACAAAGGCCTCTCTCATCCCTTGCTTATGCTGAATCGATATTTTC
TTGGTCTTCTTTGACCCTCGAGTTGAATAAGCTCTTCTTCCTCAAGCTTTTAGCTTGGAACAAGA
ATGGATAGAGTTGACTCAGCTGCGATTGCTCTTGTTCTCTTTGCTCTTTATAAAATGGTTTCTGT
GAACAAGGAAGAGGGGCTGCCATTGAATCAGTTTCATTTGGTTAGAAATATCATAAGAGAAGAAA
GATCGTAGCGTAGAAAAGAAAGAACGTTTTGATTCGCCTTTACGA
Found at i:22908 original size:24 final size:24
Alignment explanation
Indices: 22839--22911 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
22829 CAGTCTTCAC
22839 CAAGACAGCTGGAAGGCATAGAGT
1 CAAGACAGCTGGAAGGCATAGAGT
** *
22863 CAAGACA---AAAAGG-A-A-AGC
1 CAAGACAGCTGGAAGGCATAGAGT
22881 CAAGACAGCTGGAAGGCATAGAGT
1 CAAGACAGCTGGAAGGCATAGAGT
22905 CAAGACA
1 CAAGACA
22912 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 22339 -- 22838
GGTTTTTTCCAAGCAAGATTGTATCAGGAGTAGTAGCAGTAGGAGTGGGAGATTGAAAGCTAGCT
CCTGACTCGAGGGGAGAAGGAATAGTCTATGAAAGAGATAGTCTTAGTACACCCGAAGGAAGAGG
GAAATTTAGGCCTAGTAGCACGGTTGAAGTCCAATCCGTGTGAGTATGAGTGCCAGCCAAGCCGC
TTTCAAGCTCTCCAACGCTAGCAGTGCAGTAAGGGTTCATTCAAAGCGAACCAGTAGCAAAGCGG
TTGAAAGCAGTCTGTCGGTCTAAGTCCTGGTATTCCGGGCAAGCCAGTCGATGGTAGTCATTCCG
GTGCTTCTAGTGACTTTCTTGCCTGTCTCCTGTCTGTTTACGAATCGGATGTGAGGTTTTCCTTA
TATCCTTATATAAAGAGATCTTGCCCTCGGTCTTTCTGCCGCAAAGAAGCAAGCGAAAGAGATAT
TCAATCAACCCAGCAAAGAACCGATACCACTACCACAGTCTTCAC
Right flanking sequence: Indices 22912 -- 23411
AAAAGGAAAGCCAAGCCAGGAATGAGAGCGGAAAAGGCGTTAATCAAGAGAATACCCTGTACATG
AAAAGGGCTCAGAATAGACTCTTTGCTTGAATGGCTTGTTTGCAGGTTTGACATTCTCTTTAGCA
AAGAAGAAAGCACTACTTCATGGGAAGTTTCCAAAGGTAAGTCCGACGTCTCCTTAAGGTAAGGC
AGTTCACTCGTAAGGCCTCATTCATCTCTTACCCGACAAAGGCCTCTCTCATCCCTTGCTTATGC
TGAATCGATATTTTCTTGGTCTTCTTTGACCCTCGAGTTGAATAAGCTCTTCTTCCTCAAGCTTT
TAGCTTGGAACAAGAATGGATAGAGTTGACTCAGCTGCGATTGCTCTTGTTCTCTTTGCTCTTTA
TAAAATGGTTTCTGTGAACAAGGAAGAGGGGCTGCCATTGAATCAGTTTCATTTGGTTAGAAATA
TCATAAGAGAAGAAAGATCGTAGCGTAGAAAAGAAAGAACGTTTT
Found at i:126973 original size:15 final size:15
Alignment explanation
Indices: 126953--126982 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
126943 CCAGTATATT
126953 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
126968 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
126983 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 126453 -- 126952
TTTTTTCATTTTAAATTGAAGTTTGACTCTGATTAGATCCTTAGCGCAAGCGCTAAGTAAGCAAG
CTACCTTATGTAATGTAAAAAAAACCGAGGAAAATAACGTCAAGTAGAAACGAACAAGGTCTTAC
GGCACGATCGATCACTATATCTTTTCTTTTTTTTTTTTTTTTATGGAAAGAGGGGATGATACGTG
GCGTGGTATACCTAATCGTTTGGTCAACGAGACGTACGTAAGTCGACATAGCTCCATGTATATGT
TCTTTGGAGCTAGAACCCATAAATAGAATGAAATAATGGTGAGCCTAGGGCGACGAATATGGCTC
AAGGGTGTCTATACAAAGCCCTTCTCTTATTCATTCAAAGGGCCAATGCACCAGCCAGCCGGTGT
GGTGGCGAACACGCTGTGCTGTAAGCCAAGCTGTTCACCTTGTAGACGGAGGAGATATAGAAAGT
GTGCCGTGCGTGATTCAAAAGATTCTATAGTAGCACCAGTATATT
Right flanking sequence: Indices 126983 -- 127482
GCCTGCCTCCCCCATGACTTTCCGGACCAACCAACCCAGATCTGCCCTCGCAAGTCTCTCTGCAT
TTTGGGAGCAGAGCATGCAAAATCGATCGAGCAATGGATGGATCTTAGAAGAATTCCACTTTGAA
CGGCACGACTCTTTCTATTTTTTCGCTGGAATTCATTTTGTCTCCCCTCCTCTTTCAATCGACAC
ACTCGACGCAGATAGCTCCGGTGGCCCCGGCTTCTGCCTCTATCAGGCGGCGGCAGCCCCCACCT
CCACAGCCACAGCATGGAGGAGCAGCTCCTTAATCCGCACTACAACCAATCCAAATTATCTCCGG
ATCGATATATGATGATGCTAAACCGAGACCGAGATAGAGAAAGAGGGCTGTCCCTTTGTTGGCTT
TTCGAAAAAAAGCACTCATAGGAATGGTGCGAATTCCCATGTTCTTTTTAGTCTCGCTTGGTTTC
GAGAGCCTCCCCCTCCCCGTCTCTTACTCGTCTTTTGAAAGCCGT
Found at i:139821 original size:19 final size:19
Alignment explanation
Indices: 139797--139838 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
139787 CTTCAGATAT
139797 TTTTATTTCTTTTA-TTTTA
1 TTTTATTT-TTTTACTTTTA
*
139816 TTTTATTTTTTTACTTTTC
1 TTTTATTTTTTTACTTTTA
139835 TTTT
1 TTTT
139839 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 139297 -- 139796
TGAAGCAGCCTAGCATCACTTTAGATAGAAGCAGAATGGATAACTTACAACTGAAAGTAAGTTCT
TCGGATCGATATCTCGTACGACGTAATGGAGATCTTGGTCTAGATCCGGTGGTTCGCAGAATTCG
GGACCTAACGATGTTCGGTTCGTCCCATGAACGGGAGCGGACAATTCCCTTTTCGGGGAATGGCT
GCAATCACAAGCAAGTGATTGAATGAGTGGGGGGCTCCGAAAGCACATGCGGGATAAGCAGGTAT
TTCAGGAGACGGTCTAAAAATGGGTCCGATTCAAAAAAAAAAAAGAGAACTCTCAACAAGCTGGA
ACTAATCAAGATCAATAGGAAGAGGAGTTAGCTAGGAATCTATTGACAAAGTTCATGCACCTATA
TGGAAGGGCTGTTTTGTTGATGTATTCCTGTCGAGAATGAAGAAGAAGAAAAAGAGCCTTTTCAA
CCGGCCCAGATCTATTATCACGAACCCTAAAATTTCTTCAGATAT
Right flanking sequence: Indices 139839 -- 140338
GGTGCTGCTACTGTTCAACTCCATACTAACATTTTTTAATTCCTATCATCATCGTCGCAGCTTGC
GAGTTTGAGGAAGATAAGGTCGATTCGATGGAGGTGCAGCAAGCCCTCCCCCCGGTGCCGGAAGC
TTCTGAGCCACTACCACTAGCTCAGGAGCCTGTTTCTCCTTCGTTTGAAATCCAAGCTGCTGAAG
TCAACCAAGAGGACATCTGGAGGGAGTTGGAGCAGCAGGAGCAACCGGCACCAACGGGTGGAGCT
AAGCTAACAAGGCCTCACATATGCGAAAGCTCACCCCATTGGAAAATCAGGTAGCTGACCTTATT
ATCGATTTACGAAAATCCGAAGTACCCTCACCTAATAAGATTCAACAAATCGTCGAAATGCTCGA
AGAAGAAAGAATATGGTCTGGAAAAGCTGCGCACAATCAAAAAGCACAACCAACAATATGGCAGA
AAGAGTGTATTTTTTAGGAACTCCAAGGAGTGCTTTAATATGTTC
Found at i:204695 original size:17 final size:17
Alignment explanation
Indices: 204673--204708 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
204663 GGGAAGATAG
204673 AGAAAGAGAGACAAGAA
1 AGAAAGAGAGACAAGAA
* *
204690 AGAAAGAGATACAGGAA
1 AGAAAGAGAGACAAGAA
204707 AG
1 AG
204709 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 204173 -- 204672
TTATCCAGAAACAACTCAATCAATCAATTACCTTATTTAAGATACGCCCAAATCCATTCAACCAG
CCACTCAAGGGTTTGGAGTTACCATTTCCGCTATTCCTGCCAAGGAATAAAGTAAAGGGACTACC
GATACCCCTTCGCGTTCGCTTTGGTTTAGAGTAATCGCTTGTTCCTTCAGTCTTCAGAGGTAAGC
TCTTTTGCCTTCTTCCTAATGGACTACGAGGACCCTAGGATTTAGGACTCTTATAAAGAAGGATT
ATTGGCCTACTGCTGCCTTACCACTAGCTTAACACTAGCAGCACAGGCTTACCTATTAATCACAG
ACCCCCTTCCTTACTTGCTTACTTCCTTGCTTGCCTGGAGAGAAAGAATATTAAAAAGAAAGAAA
GGATCCCCTACTTACTTAGTACAAGGAAGGGAAAGACTTACTAAAAGACCAAAGACTGGCTTACT
TACTGTCTTGGCTCCTAGGACTTCTTACAAGGAATGGGAAGATAG
Right flanking sequence: Indices 204709 -- 205208
CTAAGGATATAACGAAGGGCGAAAGGGAGCACAGAAAGGCGCAATACCAAAGCTTTTTTGAAAGA
GAAGAATGCGCCATAGGTTTCTTCCTGCTTTGCTTTGGGAAGGGGCATTGAAAGAACACAGACAT
AGTGGAAATGCTCCTAGACTAGAGAAGGTTCCCCCGTAAGTCTGATCCTCTCAACTCATACTACA
GCAGGGAAATCCACTTTTCTGGACAGGGTCTTCCTTCTCGGAGAATAGGTCTACTATGCTGAAGC
AGAAGGGAACAGGATGCTCATTTAAATGTCAATGAGACTAGTCAGGATGCTCCCTGTAGTACATT
CCCAGATCTGAGCTACCTGGATCAACCCACCAATTAGTACAGTTCGTCAGTGAGTACGTGGGAAT
AGCCCAGTAATGAATAGAAATTTAAGTCACCGGGTAAAGAAGCGAGGGGATCAGCTCAATTGAAA
GAGAGGGCGCGATCGGCATACAATTATTCGATTTCATTTCTTGCC
Found at i:253800 original size:36 final size:36
Alignment explanation
Indices: 253758--253830 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
253748 CCTATGTCTT
253758 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
253794 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
253830 T
1 T
253831 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 253258 -- 253757
AAAACAGGTACTGATAACAAAGTACAAGCCCTAGCTTTTAAGCCGAAGAAAGAAGCAATCATACT
CCTTAAACAGAAAGATATTGCACTTCAAAATCGTTACTAGAAGCACTACAAGCGCACTTCCTATC
TAAACAAACCAAAGCAGAAAAAGCACCTCCCTCCCGGATAAAGAGCAAGTGTGCGAGAGAATAGA
ACTGAGCATCAAGGCTGCAAGACAGAAGGAAGGTTCCTGCGTGCAGGAAAGCTTTTTCACCGTCC
ATTGGGTATTTGTCTTTATCTCGCTCTCCCAACTAACTCAGACTTATGATAGGCGGGCTCAATTC
CAGATATTGACCTCTGGGGATCCTTCTCTTTGAATTCCCGGTCTTCCGTTTTCTTCCTTGGTTCC
ACCCTTCCATTCATGAAGCAGATCGCCGGGAAGGCTTTTTCTCAAGCATAAAACGAGAGACCCGA
TCACATTGATCGACAAACAAAACTCCCGATAGAAGCCTATGTCTT
Right flanking sequence: Indices 253831 -- 254330
TTTCTTGGTATTCACGCTCATCGGACTGAAGTTGGTCCTCATTTATCTCAGCAGAAGTCTTTCAT
GATCTTTTCATAAAGTTGAATCTAGCCAATGCAAACTCAACTCAGTTAGTACTCCTATATCAATC
GTTGTCGCTGCCTTCTCAAGATGACGGGTAACCCCTTTCTTTAGGAGGATCCATCTCTTTATCGC
AGCATGGTAGGAGCCTTGCATTATTTAAGCATGACAGGGCCGGACATTGCCTTTGCCGTAAGCAT
TTGAAGCCAATTCCTCAATTGCCGCCCAGTACATCGTAAAGTGGATCGATCGATATCTTAAGGGA
ACTTCTCATTATGTCTTTTACCTCTTCTTCTGAGCTAGAGTTACATGCTTATGCTGATTGGGGTC
CTTGTCTTGATAGTCGACGTTCTCTTTCTGGGTATGCTCTCCTTTTTCTTGCCTAATCTCCTTTC
CTAAAACTCTGCGCTTCTCTTTTGAATCTTCTCACCCCGCCTAGC
Found at i:281330 original size:2 final size:2
Alignment explanation
Indices: 281323--281363 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
281313 ATTAGAAAAG
*
281323 TA TA TA TA CTA TA TA TA TA TA TA TA TA TT TA 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 TA
281364 AAAAAGGTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 280823 -- 281322
TTTCCGAAAGCGCAGTGCCCCACGGATAGAAGACGACTCCCCTGATTTGGTGTCGCCCATTTTTT
ATATTTATGGGGTTTAAACCGTCGTGCACTAATGCTGTTTCTATCTTTTTTTCTAGCAGCATCCG
CTTTTCCAGAACACTAAAAAATGCTGACACCTCGTGGTGTCTCCCGACAAAATGCACTGCTAAGC
GGTCGAACAGTTCCATCCTTCTCGTGTGATCCGGCATCAGGGGTTGCTCGAGAATCGGGACGAGA
ACAGCCTGTGCTATTTCAGGATCAGTCAGGGGCCTCGGGAGCGCGCGGTTGGACCGCTTGATGGA
AATCCGCTGCGCCAGACGGGGAACCACTTCTTACGTCGCACATGGCTATCTCCAGGAGGGGCCCC
TGACTGATTATTCCAACGATAGATAGAATAAGACCCAGAAGTTGGATGGGACTGCCATGAAAGAT
CTCCTCCGGGATTGGATCCCGGTGAAAAGAGATCCATTAGAAAAG
Right flanking sequence: Indices 281364 -- 281863
AAAAAGGTGGATTTCGCCCTGCAATCCTAAGGGCCAGGATTCAATCTCCACTGGAGCCATTGTGA
GGAATAACCATTCTAGAACAATCATTTGGTTTGTTTCATTCTTTTTTTGTTCTGCTCCCCCCAAA
AAAAAGGGAGACTTCCTCAGGAAATCGCTGGTTTTTCCAACCCAACCGAGGATTTCCGACAAGTC
CTTCTTCATTTTTAGAGCAAGAAGGGGAACTATAGAGATTCAATGAACAGTGTTTCTTACGATTA
CGCCCAGCCCAAAAAAGCCCTTCGGAGTTGAACCGAAAAAAAAGCCTATTACTTAGGGCCCTTCA
AGAAGTTTGTGTTAAGCATATAGCCGGGCCCTCTTTCTGAGCCAGGATCAAACTCTTCTTTTTTT
ACTATGATTGGGCCCTGCAGACGTACTACTTTCAATCAAACCTTTTCTTTCCTTTCCTTAAGATA
TATATGTTACCCACCATATTAATAAGGCACCAAACGCGCACTGAC
Found at i:290619 original size:14 final size:14
Alignment explanation
Indices: 290600--290630 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
290590 TATCTAAACT
290600 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
290614 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
290628 ATT
1 ATT
290631 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 290100 -- 290599
AAGAAAAGCTTTTTCAGATGTTAAAAAAAGCATTGTAGGATAATCGGCATCTGTCCCTCGAGAAA
GAGTAAGATAGGCAAAAAGGCATAGAGACAACAGCGGTAATGCCGCATCTCTCGATGAGAAGGAA
TCCTGGAAAGAAGAGCAAAGAAAAGCCCTTCTTCTTCTGCCTTTTGACTCTATCTTGCCCTTTCT
TTAGGGAATTGCGGAGTGAATGAGTGCAACAAAACAAGGAAAGAAGGCTATAAGCTGCCTACATG
GAATTACTCTTCATGCACATTTCCCAGAAAGAGTATATTGCGATAATCGGATGCTAAGTCTCCCT
GGCTTCCTTCCTCCAGCGGATCTGTGGGCATTAAAAGAAGAAAGACTTTCAGGTTCTTCGCCACA
TTCCTTCTTAGGAAAGAAAGGCTCCCGTTCGTGCCCTGTAAGAAGGAAAATTAGAAAGGAAGGCA
TAGTCGAAAAGACTAGCAGCTTCTCTGTGCATGGATATCTAAACT
Right flanking sequence: Indices 290631 -- 291130
ATAATTCAAAAAGACTTTCGCGAAGCAGGAAAACAATCAGGTAATCAGGAAAGGCAGAAAGGGTA
GAGCCTTAGTTACCCGCAGCTCAAATAGCCAAGGTCGGTGGAAAAGGAATAGTACAGCTTGTTTG
GATAAAGGAAGCATTCATACTCGACCCGCGTCTGGACGCCCCTCTCGGGCTCACTTCCTGACAAC
CCAGCCCACAACAGGAAATGGACAGGCATTGACAAAAGCCGAAGCCTCTAACGATTTTTAAGCTG
GGTAACGGGTACCCTATCGGAAAGGGGTTTTCGTCTACCTCCCAAGCATATGGCGGGCTTATAGG
GCGCTGGTCTCCGTTAGGCTTTGAGTCTAGGAGTATAGCGATGGCTTCATCCACCGGTCCTACCA
TGGAACGAGTTTCTTCGCGCTTGGCCTTGAAATTTCGAGGCATCTTTCCCAAGACAAGAAGCGGC
GTCGGATCCCGGTAGTGCGGTAGTACGCCCAGCAGAATGTCGTAG
Found at i:299175 original size:26 final size:26
Alignment explanation
Indices: 299146--299198 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
299136 GACACGCTAT
299146 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
299172 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
299198 G
1 G
299199 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 298646 -- 299145
GTGGTAGTGGCTCTATTGACTATAGCCGTCCCAATGTGAAATATAGTATTCAGTAGACGCAAATG
CAGATACTATCCCCTACGGAATAAAACTTTCTTTCATTCCGTAGGGGTAAGACTCTTCAAATAAA
ACTAAAAATTCACCTAGGACTTTTTTCTTTTATAGGGACTTCTGGCTCTGATCCTTCTATAGTAG
GAAGACAAGATCGCAAGGGAATCACTAGTTCGAGTTCCATGCCTTCCTTCTGGTCCCAAACACTG
GGTTATTAACCGATGAGTTAATTTTCCCCTTACCCATTTCTTGTCCATGTGTCCCTTGCTTCTTA
GTGCTCCGTTGGACGGGGACTCCTTCTTCATTTGAATGCTTTGATGCTGGCCAACTGGGAGTAGG
TTCTGGCTGCTCTTTCTGTGATGCTATTTCGACCTCGTAAAGATATTAGGACTTTCACACTGACA
TTGAGACAGAAAACATTCGATCAGTTTCCCAGCGTGACACGCTAT
Right flanking sequence: Indices 299199 -- 299698
CCTTTGTCCCCATTGCTTGTTAGTTAAGTAGGGAGAGAGAACGCCCCATCTCTTGATTACGAAGA
TCACTTTCACAGCAAGCACGAAGCTTAACTATTATGTAAATTGAAACGATCTCCCCAGGAAAGCA
TGATGCCTGACTTGCCCCTGCTTTCCAAAACGGTAGACCAAAAGCACTGAAATGAATATGAGAAA
TGTGGCCTATCTATGGAAGGAATCTTTCGTTACTAGAACCCCTTCCTAGTGACTGTAAGCGAAAT
GCATTTAGCGAACGCCTGGGGGTACTGAGTTCCATATTTTTTATTATAGAAATGTTATCTCTATC
TAAACGACTAAGTCTTCCAGTGATCTCTCCCCCACCCAAAACCATCCCTTCCAGCGTTAGCGCAC
AAGAAGGAGCTTTTGGCAGTGAGTCGAAAGTCTTAGTGAGAAGCCCTCTTAGGACTCTTTCCACT
CTTCTCTGAGTGCCTTCAACAGTGCTTAGGTAGCGCTCACTGCGA
Found at i:326263 original size:17 final size:17
Alignment explanation
Indices: 326220--326265 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
326210 GCAGTAAATG
*
326220 GAATAAACTAAGCAAGA
1 GAATAAACTAACCAAGA
*
326237 G-ATCAACTAACCAAGA
1 GAATAAACTAACCAAGA
*
326253 GAATGAACTAACC
1 GAATAAACTAACC
326266 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 325720 -- 326219
TAAGCAGCCAAGGCCAAGAGCAAGCAGGAGTAGTCCTATCTGCCTATAAGGATTCGATAAAGAAA
GAGAATGTGAGTGGGCAGGAGATCAATAAACACAGAAAGCGAAGAGCAAAAGGAGCAGAAGACAC
TCAGTTGTTTATGTGAAATCAAGGAGCAGCAGGTTACACTTTTACACTTTCCCAAAGCAAAGAGA
GCTCAAAGCAATAAGATGAAAGCTGGGATGAGATGCTAGCCTTAGCTAGGAAGATCCATCATTGA
GCCTTAGGCCACTACCGAGCAGAAATGGAGGATCATAACACTTGAGAGATGATCCCTACTTGAAA
AGGCGGAGACAATACCTCTTGTTGCGACAAATCGAGTTTCAAAAGCCCATTTATCAATCACATTT
TCAGGCACACCAGTCAAAGAGCCATCGGACCCATTAAAGTCCCCTTTTTTACTAATATACAAGGC
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 326266 -- 326765
CCAAGGGATGATCTCGGATTGAAATCCAAGGCATGGTCCCATTGAAAGCCCAGGGATAAATTCCT
AAAACAGAAAAAAAAAGTCAAGTCCAAGGGGGTATGATCCCAATAAAGATAGGATGGATTTTAAG
TCATTTTGGACGAAGCAGCGGGCATACCAGAAATGGCTTGTCAGGAATGGTAGATGGAGCAAGAA
TGCATAGCAGGCTTAAAACACGACACAAGTAGGACGCACTGAGGCCGAGCTTTCCTCTACTACTC
ATTGGAGCTAGCATACGAAATTATCCGTTGAAGGGTTCAACTCTCAGGGCGGCCATTGCGAGCGA
TATTCACTTTCAAGAATCATCGAGCCTACGCCTATTTCATTACTCTCGAAGAGCTCATCAAAGAG
CTAAGGCTAAGGGATGAGAAAAAAAAAGGAGGAGGTGGAATTTCTTTCAACTATAACATTTATTA
CAACACTTAATATTACAGACAGAGAATTCGGTAAGGGGATAGAAG
Found at i:397417 original size:15 final size:14
Alignment explanation
Indices: 397397--397451 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 14
397387 TCATTAGAAG
397397 AACCAGCGGTAGCTA
1 AACCAGCGGTAGC-A
*
397412 AACCAGCGATAGCAA
1 AACCAGCGGTAGC-A
397427 AACCAGCGGTAGCA
1 AACCAGCGGTAGCA
397441 GAACCAGCGGT
1 -AACCAGCGGT
397452 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 396897 -- 397396
TAAAAAGCTTAAAAAATGTATCCCATTTCTTTGAAATCCCACTATAGTAATGCCAATAAAAAGAG
AAAATGAGAGACCCAAAGTAATGAGAAAATGACTTGTAACTGTGAAGCTATAAGGTATCATACCC
TGGGGATTACGAAATAACGAAAAAGTAAAAGTGACCGAGATGCAAGGGAAATACTTTTGTTTCAC
ATTACTGGAAAGACCGCCTATTTGTTCGTTTACCGGGTTCAGCACGAAATCATAAATAAGCTCTA
CCAAGGATTGCCAAGCATTTGGTACTAACTTTCCTCCTCCCTTTTTAGTAACAAAATGAACCAGA
AGTAGGAACAAACTGAGAGTTAGCAGCATAAACAAAGATGGATTTGTGAATGAGAAATACAAGTT
TCCAATCTTCAAATCAATCAATGGCACAATCTCAAATTGCTCAAGGGGGCTGGGGACGATGGGTG
GTTGGGGTGGTTCCATTTGCCCCCCCACCCCCAGGTCATTAGAAG
Right flanking sequence: Indices 397452 -- 397951
TTTTGGCCAAGGCCAAGACAAACATTTTGAAAAAAAATCTTTTGAATTTTGAATAGCCGTGGAAA
ACAATTTCATTTTTCTTTCATTCTTTTCATTCTCCGCTCCCCCCAAAAAAAGGAGAGACTTCATT
TTCACTGTACGAGTAGTGAAAAACTATAGTTTACTTTTATTGGTTGTTGACCAACGGAAAGCATG
GGAGTCTTTGGGCATTTCTTCTTCTCTTACGATATTTCTAATTACCTAATAGAATAAATACTTTA
GTTCGAACTAGTTTTTAGCTTGAACGTGGCGAATGCTATCTCTTTCCCGCAACTCGACTGTTTAA
CAGGATGGTACGAATCCGCTCTTTGACTTAGTTAAGGAAGGAAGCAATTGTTCTCTTTGCGTTTA
GCTGGGCAAAGCAAAGTGAAGGGAAGGATGAATCGCTCCCGAAAAGGAATCTATTGATTCTCTCC
CAATTGGTTGGACCGTAGGTGCGATGATTTACTTCACGGGCGAGG
Found at i:487331 original size:24 final size:24
Alignment explanation
Indices: 487289--487337 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
487279 ATTCGGATTC
* *
487289 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
487313 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
487337 G
1 G
487338 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 486789 -- 487288
CAAAAAGTTTAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATAATCATATGGGTCAAC
AATTCTCATTTCTTAGTTACAGAAAGCCCTTCTCAAGGAAGTAAGCCAAAAGCCACTCATCTGAG
CCAGCGGATTCTCATTCTGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAAT
CTTTGGTCTGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGA
TTATTCAACTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACCGAC
CTGTTGAGAGGATAGCAACAGGAGAAAGAAAAAAAAGAAGTAGAGTTAGGTTCTGTTCTAGTATG
TAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCGTATGATTCTTATCCTACTTCCGA
TAAGTCTTATGAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 487338 -- 487837
GAATCCGTTGTTTCGGGATAAACTTGATATGTTAGTTCGGCCTCGGCTTCTTAGGATGATGCCTG
TGCAATGTATGATCCATCGGATTCTTTTTATTCTATTCTCGGTGCGTTGTTCTTCAGCGAATGAA
AGAAACCGCTGATTCCAAAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGA
ATGACTCAACTGATACTACTCAAAAATTTCCCACATGGAAGGAAATGGGATTTTTGAGAAAAGGG
GTTGGGAACCATCGAAGGACTAGCAACCTGACAGTCCTAAGCAACCTTGAACCAACAACGTTACA
TATACCATACTGCTATAGAAGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTG
GTGAGCTACTTACTGCCCCTTAAGTCAAGAGAATAATAGTACTTTCAGCAAAGGATATCGTAACT
ATGGCGAATACGTTTTTCTTGCTTTCCACATACCCGGAATGCGAA
Found at i:504714 original size:26 final size:26
Alignment explanation
Indices: 504680--504737 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
504670 TTCCATACTT
* *
504680 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
504706 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
504732 A-AGAAA
1 AGAGAAA
504738 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 504180 -- 504679
CTATCCGTCCCTTTTGCTAGAGTAAGTAATTCCCTTCCCTTTTGTTTGCCAGCGTAGCGCATTGA
TCATTGAAGTGGGGGCTAGGCGAGGGCATGGTCTACTTTTTGTTCTGAAATGACTAAGTACGGCT
TGGCTTCAGCTCGTGGGACTGGTTCTCTAGAAAAAGTCCCAAACCCCACATCCTGCAGTCCGCCT
GGATTCGATTCGCTTTTAGTAATTATATTACATTATATATATAAGTAATTAGAAGCTAAAGAGAA
ATTCAATATTACCATATTCTACCGCTCAACTAACGCTATGTGATCCGGTCAAGATGAATCGATCG
AATTTCACAGCTGAGGAGGCAAAGGGAGGCAAAGCGAGAGGTTCTGAAAGAAAAGACTTTATAGA
ACCTTACTCACACGATACGGGGATGGGCCTACACAAGCAGAAGGAAGAGCTATTAGCTTGTCGGC
GTAACGAATGAACTATCGGATGGTAGGCTAACTGCTTCCATACTT
Right flanking sequence: Indices 504738 -- 505237
ACTGCCTTTTTTTTGAATTGAAGGAGGAGTCGCGCATTCGTCTGCAGCGTATAGTATAGTAGCTT
CAATGGAAATCCGTTTGAATTGATGATTTTTCACCTGATTCCCCCAAAACCGTAGAAGCTCAGAT
CGGGGTTTAGCGATAACCTGAGATCCTTTATTCTGTCTCCACTTCTGAGCCGACCGAGCCTGAAG
CCAATATGTATGAAAGAAACCAATCAACGCAGGAATGGAGTTCGTAGCGAGAAGATAAAGTTCCT
CGCCTGAGAAGCACTTCACTGGGTAATAAAAAAAGCTACCTAAAAGATCTTATTACCTTTACTCT
AAGATGCTATAAGATAATTGGGAATCTTTTAGCCGCTATTCCCGCACTATTGTAAACCAGCTTGA
TAAAGGGTAGTGGTAGAGTCTCAGTACCACTGAAAGTGCGATAGTCGGGCAAACAATCTCCTCTT
TTTATCATATCATATAAGGTAGGGTATTGTATATATGGAAATTCA
Found at i:573049 original size:21 final size:21
Alignment explanation
Indices: 573023--573069 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
573013 TTAAGGGATG
573023 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
573044 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
573065 TAACA
1 TAACA
573070 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 572523 -- 573022
TTAAGACTGTTGCAATTGGTACAACTGCTTCAATGGGATAGAAGGAAACTGGCTAAAAAGGATTA
GAAATGGACTAGTAAGAGACTCCAATGTAACCTCAAACTAAAATTGGAACCCTAGGAGGGGCAAC
TTCCACTCTTTTTTTCACTCTTTCCATTGTCGTTTACTTTACGAAGCGAAGGAAATCAAAAGGTA
TGCCCATTTTATCGAGGAGAGGAATTACTAGCTCGCAGGCTTCAAAATGATAACTTCCTTCCTTG
CCCTCGAACCGACTATCCAACGGCATGGAACACTTAGCATTGGCCTATAACTCAAATTCCATTTT
ATAGCACGCCAACAGGAGGGGCTTCTTACAAAAGCACTCCAACAACTCGCTTGAACTTGAAGAGA
GAAGCAACTACTACTTCTCCATCAAAGGAAAAACAAGCATCGACTAAATAGAAGGCCCTTGAATC
TTATCGTTAGAGCGCTATCTACCCTTAAGACTTACTTAAGGGATG
Right flanking sequence: Indices 573070 -- 573569
ATCGATGGACTGGAAGGGCGAGAGACAGAACAGCAAAGAGAACTCAATCTAGAATTTCCACTCCT
TCTAAAACCCCAACCCCAAGTACGGCATTAGCAATTGAAGAGCTTAGTTAGGATGGGTGGAACTA
CAACCCCTCGAACAGGCTCGATAAAGTCTGGGAGATTAGATAAGCTGGCTAGGTATTTTTATATT
CTTTTTACTGAAAATGCACCGAAGGCAACTGCCATTGAAACTATATAGCTTTATATATAAAAGGG
AGAATTCCGCTCGAAAACCAGCCCTCTTCACACCAGTACCTCTGTCCCGACATTTGGTGAGATAG
GGGTAATGCCTACCAAAGGTAAAGGGGAGCCTTCATGCAAATCTATTGAAGGGTCACCTACGTTA
GCTGGTGCCCACAGTGCCAAAGTTTCAACCAAGATCCTTTGGCTCCGTGCTGGTAGCCGGCTTGT
TACTCCAGATTTTAGTGACAAGAACGTCTGTCACGTGCGTCCCTA
Done.