Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_068714
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: 257880
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:7517 original size:18 final size:18
Alignment explanation
Indices: 7494--7530 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7484 CCTAGGGTAA
*
7494 GGTCCACCCCATGGATCG
1 GGTCCACCCCACGGATCG
*
7512 GGTCCACCTCACGGATCG
1 GGTCCACCCCACGGATCG
7530 G
1 G
7531 AGTTGCTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.38, G:0.30, T:0.16
Consensus pattern (18 bp):
GGTCCACCCCACGGATCG
Left flanking sequence: Indices 6994 -- 7493
AAGGGAGCAATCCCATGGGTAAGGCAACGGGTGGGTCACTACTTCTGTTACTTGTTCGTTTTTCT
TGGAATCCGTGAAATTCTATGCGCCGGAACGGAATTTACTGCGGAGCTATATAGAAGGCACTAAT
TGGTATTAGGGCCAAGCAATTGAAAGGAAGCCCTCGGCGTGTGAGAGGACCCCTTTTCAGTTCCA
AACCGGTACCAAGGAAGCCACTAAAAGGTATAGGTGTTCCTACCTATCCACTGACTATAACAATA
TGTTCTATATGTGTCTGTAGCTTAGCGCAACAAAAAACAGAATCAAACTCTTTTAGTAGCCTATT
GCTACTAAGAACACCTTTCGGGGGGAATATAATAAACCTGTGTGAAACCCCAGCAAGCTTCAAGA
AAAAAGGGTTAATGAATACATATCAAAAGGTCCCTTTTAAGAAATGAAATAAAACATCATGAACA
ACTATACCTTAATAGTAGGTAGACTAGGAGTATATCCTAGGGTAA
Right flanking sequence: Indices 7531 -- 8030
AGTTGCTTACCTTATAAAGCAGTTATTACGAGAGTATACTACCCTAAAGGGGTATCATGCATTTA
AAGTTAGTGTAGGGTCCAGCCCTAATATAGGCTCTTCTGTTAGTAATTCGGCGAGTCGTAGGATT
CATTCTGAAAAAAGAAGTCCAAGGGAGGCCCTAATCAAGCCTTTTTTCCGACGCTATACTAGCCT
TAATAGAATGAATAAATAAGTATTTAAGAATCCATTTATTCTTAGAAATTGGAGTCGTTTAATGG
ATATGCAGGGTTCTGAGCTATTCTATAATCTATATACGGGGTCGCTCCTAGCGGAAAACGAATTT
GTGGAGCCATACGCTCGATCCTGTGATTATGTGATTATATCGTTAGAGGTCCTGCGTTTATTATA
CCGCTATGCTTACAATATGGATTCAGACTACATTAAGTTCACCATAGGTTTAGTGGTTGAAACCT
CCTCCGGTATATATAGATTAACCGTTGGAAAGGCTATTCCCTTGT
Found at i:25799 original size:15 final size:16
Alignment explanation
Indices: 25774--25808 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
25764 TTTGGATTCA
25774 TCATCATTCATTATTT
1 TCATCATTCATTATTT
25790 TCAT-ATTCATTATTT
1 TCATCATTCATTATTT
25805 TCAT
1 TCAT
25809 TAGTAGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (16 bp):
TCATCATTCATTATTT
Left flanking sequence: Indices 25274 -- 25773
CACTGGTTCTTTTATTAGAAGGTTGACATATAACTCTTTTTCCATAAAACTGAATTCGTTAATCA
TTTTACCTTTTCTTTGCTCGCGACCAGAAAGACGTAATAATAATTGGGATAATCCCAATAACAAG
AATGTATCCTCTTTAGTTGGAAGAACCGCAATCTTTATATCAGGATCTGAGGTATTCATTAAATC
GGGAATATCAATGAATGAATTATAGTATTCATTATAATTTAAATAAAACTGAAAGATCTCGCTTT
TTTTTATGAATATAACTTCAAGCGGAGATAGAACGTATCTACCAGATAGTAGTATTTCCCTATTA
AGGATTTGGTCAATATTATATAAATCATCCTCATATGAATATAAGATATTATCAAGAATAGTAGA
CAGCTGCTGCAGTAAAGGATCTTCTACTGTACTAAAATATCTAGTAAAAATGGTAGTGGAAGGAA
GAAAATAATAACAACTCTTATACTTATACATTAATTTTGGATTCA
Right flanking sequence: Indices 25809 -- 26308
TAGTAGCATGAGGTACTATACCTACCGCTAGAAAGAAAGCAACCATCACACCTAAACCAACACCC
TTAAGAGCATTTCCGCTAGCAGGGATCATTATCTCAGCAAAAGGCTGCTCATTCCCAATGGCATT
GGCCACCGATTCGGAAATATCGTTTCTTTCAAGAAAATGAATCTTACGAAAGTTTGGTGCATCAT
ACAGTGCATCAAAAAAAGAAGAATATGTGTTAAACGGTGTGAACACCCCACCCTCGGGAGCAGAA
TAGACAGAGCCAGGCGCATACCCGTACCAGACAGTACAACCAATACCCAAGCTGACCAGAACCAA
GAAACGCCCATAGCTTCCATCACAATAAGTGATTACCTCAACCAAGATCTTGTTTAAGTTCTCGT
TGACAAAACTACGCAATCCGGCCCCAGAACTGCAATAAGGTAACATAGAATCGGTAAAAGGAGAT
ATGCTACTATATGATAAACCTAGAGTATTTTTTATAAAAGACAAC
Found at i:34651 original size:17 final size:18
Alignment explanation
Indices: 34618--34651 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34608 GGATCACTAA
*
34618 CTAATACTAATATAATAT
1 CTAATACTAATAGAATAT
34636 CTAATA-TAATAGAATA
1 CTAATACTAATAGAATA
34652 GAAAATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (18 bp):
CTAATACTAATAGAATAT
Left flanking sequence: Indices 34118 -- 34617
ACAACAACAAAACAAGCAACGGCTTCTAACGCTACTTAGCTATATGTTAATAAGAAGCCGTTGTG
CGTGAGTAAAGTGACGCTACGCGTCTTCCTTGTTCGTTTAGCTAACGCGCATCCGTTTTCTTGCT
TGCGCATTACAAGATTCGGCACTACAAAAAGGATAATGGTAACCCCACCATTCACTACTTCATTT
ATGAATTTAATAGTAATAGAAATACATGTCCTGCCGAGACAGAATTTGTAACTTGCTATCCTCTT
GCCTAGCAGGCAAAGATTGACCTCCGTGGAAAGGATGATTCATTCGGATCGACATGAGAGGCCAA
CTACATTGCCAGAATCCATGTTGTATATTTGAAAGAGGTTGACCTCCTTGCTTCTCTCCTGGTAC
ACTTCTCTTCCCGCCGAGCCCCCTTTCTCCTCGGTCCACAGAGACAAAATGTAGGACTGGTGCCA
ACAGTTCATCACGGAAGAAAGGACTCACTAAGTCGGGATCACTAA
Right flanking sequence: Indices 34652 -- 35151
GAAAATAACTGTATTTTCTGTATACTTTCCCCGGTTCCGTTGCTACCGCGGGCTTTACGCAATCG
ATCGGATTAGATAGATATCCCTTCAACATAGGTCATCGAAAGGATCTCGGAGACCCACCAAAGTA
CGGCTGCGTTAGCGCAGGAGTTTTCTTGGTCGCTTTCAGTTTGAAAATGTGTACGTAGCTTCCTT
GTACAAGAGCTCTCTCTCTGAGAGCTTGATCGGGAAGCACTCTCTCTGTCCCTCCGCCTCCGTAT
CTGACCCACCACCCTTGCTTAGCTTGAAGCTTGCTCTGGCTTGGTCTAAACCTACCTACCTTGAA
TGGCTTGTTTGTGAGTCCCTACCCCACCGGCCGGAGCAGGAAGACCTGAACATGTCGTCTATGAA
GCCTCAAAGATGCTGCTTATGTTTACCTAAAATGCCGTTGACGTTGATGAAGGAGACTACTGTCG
ATTGACGATTGAAGGCACATCCTTCCCCTATTGTCCTTCTAGCGC
Found at i:80805 original size:12 final size:12
Alignment explanation
Indices: 80788--80840 Score: 97
Period size: 12 Copynumber: 4.4 Consensus size: 12
80778 CGAAGCGGCG
80788 CCGGTACCTCAA
1 CCGGTACCTCAA
80800 CCGGTACCTCAA
1 CCGGTACCTCAA
80812 CCGGTACCTCAA
1 CCGGTACCTCAA
*
80824 CCGGTACCGCAA
1 CCGGTACCTCAA
80836 CCGGT
1 CCGGT
80841 TGTTATTCCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.23, C:0.42, G:0.21, T:0.15
Consensus pattern (12 bp):
CCGGTACCTCAA
Left flanking sequence: Indices 80288 -- 80787
TACATTTCAGGAAATTCATACGCTCCGCGGACGGAGCAAAAAGGGGAGTCTTGGTCAGAGCAAAC
CGCCCTATTCTATTACTAGACAGAATTGGGAGAAGCTCATCCGAAACTAGAGCTAGAAACGCTTT
ATTAGGTTTCGTTTTCCTTATTCATTTCCTTCTTCTCAAATACAAGGGGGGCTTCTCATATTTAG
AATCTTTCTGCGGTGTGCTCCGTTTACTATTCTTTAGTACTTTATTTTTCTTTTTTTTACCAAGG
TCAGCGAAGCGTTTACCACGCGATAGGTCAGCGAAGCGTGAGCGGGCGCGGAGAAGGAAAGGCCA
AACACTTCGGCCTAACTGGAAAGAATGCTTTTCCCTTGTGATAAGGCACTCTCCTCTCGTTGGGC
TTGTGATAGGGTGCGTTGAAGCTGCCCATTGCGAGGGTTTAAACGCTTTCTCTCCCCCACAAAGT
CCAGCGCAATTGCCGGAAGAACCACTTACTCCACCCGAAGCGGCG
Right flanking sequence: Indices 80841 -- 81340
TGTTATTCCCCAATTGGCCCACCCTCTTATCCCCGATGATGTGCGAGGGGCCCTTCTTTTTCAAA
GGTATTCACTCCTGAATCTCGGGGGGGGTTGGGACCCACAACGACTGGTATCCATAATTGACACA
CAAGTCGTAGTAGAGCGCCATATAGAGGCGGCTTTGGTGGCCGATGGATTTCATCCGAATTCCAT
TATGGCTCGATTTCGAGAAATTCGCGGGTATATTCACTGCCCGCACGGGGAACTATTGAGTCCTA
GAACCTACGCGTCGTACGTGACTCAGATAATGGAACGGGGAACCCGACAAAGCGTTCCCTATCGC
CGGGTTCTTCAAGCAATCCAAAACTATGATATCCTTTTAGAACGAAGATGATATCATAGTTTGGG
TATTTGCCAGAACCGAAAGGGGGTAGAGGGGAAGGGGATGACCCGAAAGTACCAGTTGTCGTTGG
CAAGCAGCATGGGAAGGGGGTAGGCTAAGATAACTCAAGTGGGAG
Found at i:114129 original size:61 final size:60
Alignment explanation
Indices: 114034--114153 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 60
114024 CGCTAGGCGA
* *
114034 ACCAAGGAAGACGCTTCGCGTCACATTACTCACGCACAACGGCTTCATATTAACTATATAT
1 ACCAAGGAAGACGCGTAGCGTCACATTACTCACGCACAACGGCTTCATATTAAC-ATATAT
* *
114095 ACCAAGGAAGACGCGTAGCGTCACTTTACTCACGCACAACGGCTTCTTATTAACATATA
1 ACCAAGGAAGACGCGTAGCGTCACATTACTCACGCACAACGGCTTCATATTAACATATA
114154 GCTAAGTAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
60 5 0.09
61 50 0.91
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (60 bp):
ACCAAGGAAGACGCGTAGCGTCACATTACTCACGCACAACGGCTTCATATTAACATATAT
Left flanking sequence: Indices 113534 -- 114033
ATTGCGCTCCCTAGACCACTACCATGTAGTTAGGTAGGGACAATCAATCCGTAGTGACGGGAATC
TAGGAATGAATGGGGATCCCTATCAATATAAAAAGAATATCTAATTAGAGGTTTCTCCCTTTCTC
TCACTCAATAGATCTATCTGGTCTGATACGGCACAGTACAATACGAGACGATGGAATGAAATGGG
ATAGAAGGTAGAGGGCTGCCTGCGACGCCCAAAAGCGATGATTCACTTGTCCCCTTGTCCATAGG
GACCTCGTGGCATACAACCGAAACGACTCCCGCTAGATAGCCGCCCCTTTCTCTCTTTTTACAGC
CTCGTGGACGGACGAAAGAAGGGAAGTTACAGAACGGGGCAGCCAAGGCTCGCGCAGTAGACAGC
AAGCAGCAAGCAACAGCTTCTCAGCCCCCTCACCTTTCTATTAGTCAAGTTTATAAGCGGTTAAC
AAATAAAAAAGGCAAGCAACGCTTTATAATAGAGGCGCTAGGCGA
Right flanking sequence: Indices 114154 -- 114653
GCTAAGTAGCGTTAGAAGCCGTTGCTTGTTCGGTAGGGTAATATAAGCTTGAAGCCGTTGCTTGT
TCACCCCTTTTAATAAGAATAAGGTAAGCTTTGAAGCTGGCTGCTCTGCTATACTATACTAGTTG
TAGGGCGCTAGCGCTTGACTAATATAATAGAAAGTAAAGGGACTCTATTATGATCTTACGAATCT
AAAGATCTAAAAATTTAAGAACGAGCTCTTTTGCTCGCCCCTATCTCTAATGGGGCGTAAGCATT
TCACTCGCTAGGGGATGGGATTCATTCACTTGCATTTCTGCTAGCACTACAAAAAGCTCCGGTCT
TAACGCCCTTACTACTGCTGTGCAGCCTTTCCTCGGGTTCGTAGAGTCGGGTTTCCCGTTTACCC
ACAACGGAGGAGCCGCCCCCACCAGGCAGGCGGCCACGGGTCATAACGCATTCTTCGCACAACAA
ATCCACTTTGAAGTTGACTTATTCGCTCGGCCAATCGTCGGAATG
Found at i:126206 original size:19 final size:17
Alignment explanation
Indices: 126174--126224 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
126164 AGTCTACTAC
* *
126174 ATATATATATTATATAA
1 ATATAAATAGTATATAA
*
126191 TTATATAAATAGTATATCA
1 --ATATAAATAGTATATAA
126210 ATATAAATAGTATAT
1 ATATAAATAGTATAT
126225 CATTCGTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.52
19 14 0.48
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (17 bp):
ATATAAATAGTATATAA
Left flanking sequence: Indices 125674 -- 126173
AAGGGAAATACCTGGAGGCAAGGGATTGCTGCTGGAACTGCTTTTATTGATTTCTTACTTTCCCA
TGGGGCTCCTAAAGAAGTGAAATTGTATGAAGCAAGAAAACTCCTGCGCGTTGCTAACGCAGCAA
GAAAACTCCTGCAACAAGGACTTCTTTGGAGTTTGGACCTCGAGCATCCTCTGATGAAAACCTCA
TGGGCTAGCTCCGCCGTTGCTTGTTTCAGGTTGTTGCTTGTTGGATCTTTAGGTAGATTATTAGT
AGTGGGTGGCGAGCAGCCGTTGCTTGTTTGCTTAAAAGCTTAAAAATGAAGACTAATACAGGAGT
TTCGTGGAAAATAAAAAAGCCCTTTATCGGATTTGAAGCGATGACTTAAGCCTCTTTCTTATTCT
TATAGGGCGTTTAAAGAGCGTGACTCTTTACTTTAGTTTAATACATTTTAACTTAATTAGTTAAG
CCCATTTGATTCAATTCATGAATTAGCCCACTATGAGTCTACTAC
Right flanking sequence: Indices 126225 -- 126724
CATTCGTGTCTTTGTTACAACACGGCGAAACTAAATGGTTCGAATAAAAAGAATAAAATTCTAAT
TTCATTTTAGGCTGTACACCTAATTTTCCTGGGATTGTAGTTCAATCGGTTAGAGCACCGCCCTG
TCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGACGGATTAAATAAATATATAAATTCA
TCTCTCCATTTTCTGTGAAAAGGGGGACAGGGAGCATAATTGAATTCTCAACGGGGGATCTCTTT
TTTTCCTTTTTCGCTTCGCATTTCTCATCAAACAAAAAAGGGATTTTTTCATTACTTCAACTAGT
ACCGATTGATGGGAGAGAGACATATGTGGATTAGTACAATTATTGGCATATTCAGGATTCCAAGA
GAGACTGGGTCTGGTTTTTTGACCCGATCCATGTATGTAATGGAATAGAGTACCATATGTTTCTC
GGGAGCACATACACAAATGGAATTCGTTTCTTGTACGATACAAAA
Found at i:126224 original size:17 final size:17
Alignment explanation
Indices: 126193--126226 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
126183 TTATATAATT
126193 ATATAAATAGTATATCA
1 ATATAAATAGTATATCA
126210 ATATAAATAGTATATCA
1 ATATAAATAGTATATCA
126227 TTCGTGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (17 bp):
ATATAAATAGTATATCA
Left flanking sequence: Indices 125693 -- 126192
AAGGGATTGCTGCTGGAACTGCTTTTATTGATTTCTTACTTTCCCATGGGGCTCCTAAAGAAGTG
AAATTGTATGAAGCAAGAAAACTCCTGCGCGTTGCTAACGCAGCAAGAAAACTCCTGCAACAAGG
ACTTCTTTGGAGTTTGGACCTCGAGCATCCTCTGATGAAAACCTCATGGGCTAGCTCCGCCGTTG
CTTGTTTCAGGTTGTTGCTTGTTGGATCTTTAGGTAGATTATTAGTAGTGGGTGGCGAGCAGCCG
TTGCTTGTTTGCTTAAAAGCTTAAAAATGAAGACTAATACAGGAGTTTCGTGGAAAATAAAAAAG
CCCTTTATCGGATTTGAAGCGATGACTTAAGCCTCTTTCTTATTCTTATAGGGCGTTTAAAGAGC
GTGACTCTTTACTTTAGTTTAATACATTTTAACTTAATTAGTTAAGCCCATTTGATTCAATTCAT
GAATTAGCCCACTATGAGTCTACTACATATATATATTATATAATT
Right flanking sequence: Indices 126227 -- 126726
TTCGTGTCTTTGTTACAACACGGCGAAACTAAATGGTTCGAATAAAAAGAATAAAATTCTAATTT
CATTTTAGGCTGTACACCTAATTTTCCTGGGATTGTAGTTCAATCGGTTAGAGCACCGCCCTGTC
AAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGACGGATTAAATAAATATATAAATTCATC
TCTCCATTTTCTGTGAAAAGGGGGACAGGGAGCATAATTGAATTCTCAACGGGGGATCTCTTTTT
TTCCTTTTTCGCTTCGCATTTCTCATCAAACAAAAAAGGGATTTTTTCATTACTTCAACTAGTAC
CGATTGATGGGAGAGAGACATATGTGGATTAGTACAATTATTGGCATATTCAGGATTCCAAGAGA
GACTGGGTCTGGTTTTTTGACCCGATCCATGTATGTAATGGAATAGAGTACCATATGTTTCTCGG
GAGCACATACACAAATGGAATTCGTTTCTTGTACGATACAAAAGA
Found at i:168421 original size:24 final size:24
Alignment explanation
Indices: 168389--168435 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
168379 AAGCAGCGCG
* *
168389 TCGTGCTATAATCGGACACTTCCA
1 TCGTGCTATAAGCGGACAATTCCA
*
168413 TCGTGCTATGAGCGGACAATTCC
1 TCGTGCTATAAGCGGACAATTCC
168436 GAAGAAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (24 bp):
TCGTGCTATAAGCGGACAATTCCA
Left flanking sequence: Indices 167889 -- 168388
TAATTGAATCAGTCAAGATCAAATCTGTTTATCAAAGTGCTTCTCCGATTGCTCAAGACATCTCT
TTTCAACCGAGGAACAAAAAAAGATCATTTCGTTCCATTTTTAGTAAAATAGTGAAGGATATTCC
ATTAGTAATGAAAAAGGGGGTGGAGGGGATCCGTATATGTTGTTCAGGTCGATTAAAAGGTGCAG
AAATAGCTAGAACTGAATGCGGAAAGTATGGAAAAACATCTCGTAATGTATTTAACCAGAAAATA
GATTATGCTCCTGCGGAAGTATCTACTCGTTACGGAATCTCAGGTGTCAAAGTGTGGATTTCATA
TAGTTAAAAAAAAAGGGGACGTGCTATATCCGAAACGTACGAAATATAGTAAATATCGTAAAGGC
AGATGTAGTAGGGGTTGCAAACCGGACGGTACACAACTTGGTTTTGGAAGATATGGCACTAAAAG
TTGTAGAGCTGGTCGTCTTTCATATCGAGCCATTGAAGCAGCGCG
Right flanking sequence: Indices 168436 -- 168935
GAAGAAATGGTAAGATATGGGTAAGAGTTTTCGCAGATATCCCTATTACCGGGAAACCTACAGAA
GTAAGAATGGGAAGAGGAAAAGGAAATCCTACGGGTTGGATTGCTCGTGTGTCCACGGGACAAAT
CCTATTTGAAATGGCTGGTGTGAGTTTGTCAAATGCTCGACAAGCCGCTAGATTAGCGGCGCATA
AACTATGTTCGTCAACCAAGTTTGTTCAGTGGTCGTAAGCTAATTAGTTAGTGGGGAAATTCAAA
AGAATTAGGCGAAGTGTTTGTTCCTGAACGAGGGAAGTGGAAAGACACTAAGGGAGAGGGATATA
CTCCTTTTTAGAATCGCCGAAATTGTACGACTGTTCCAGGCGTACGACCCGGATACGTTAAGGTT
TCTTTCTTCCGGACCGGTTTATAAAGTTCTAGTAGTAAGAATAAATAAGAAAGAGAAGAGCTAAG
ATTCAGGAAAGGAAGTTGTTTCAGTCAAACTAAAGTAAGTGGGCT
Found at i:181541 original size:9 final size:9
Alignment explanation
Indices: 181527--181553 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
181517 ATTGTGGAAT
181527 GATGAAAAA
1 GATGAAAAA
181536 GATGAAAAA
1 GATGAAAAA
181545 GATGAAAAA
1 GATGAAAAA
181554 TCGTAAGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (9 bp):
GATGAAAAA
Left flanking sequence: Indices 181027 -- 181526
GGAAGAAATGTTCTTGGTGGATGCAGGACTTGGGACCCCCAGAATTTGTATGCAAGATGAGCCTA
CAGGAGTCCCAATCAACCGAGCCACCAGGTTTGAGAATAAGGTGGGATCCCTGGATCTAGTAGCC
GGTGAATCACTGATCAAAGAGCAGATTTTGGAGAGATTCTTCATCGATCTAGTGGCCGGTGAATC
ACTGATCAAAGAGCGAGCAGCCGCCAGGTTTAATGATTTGGTGGGATCTACAGATGTAGTGGCTG
GTGAACCGCTTCTTCTTCTTCCACGAAGATTCAGACAAAACCGAGCTTGGCTGGAACTGAACAAG
ATTTGGCGAACGAATACAAAGGTCAAAGGCTTTATTATTGAGAAAGTAAAAGGAGGTTCTTCAGT
AGCCATCGCAGGTTTCATTACTTTTCTTCCATTCCGTCGTCGTCAAAGAAGATCGAATGATCGAT
TCGCCATTGAGAGCATTAACCCCAAAAAGACGAATATTGTGGAAT
Right flanking sequence: Indices 181554 -- 182053
TCGTAAGCGTAAACTAGTAGACATTTATGCGACTACCAAGGCGGTTCTCCCTACTATAGGGAGAG
AACCCCAATCCCCCACTAGCAGCATTTCGGCTGCTCCAGCTGGAACAGGGACAGAAGTGGCTACA
ACCAATCACCTTGCTACCGTTGTTGAACAACAAAATTTCCCCTTGCAAGTTTTTGAGCTGGAGGA
AGAAAGTCTTTTTGATACCACTGACCTTATCTTTGATGGACTTTGTGAGCAGCTGATTTCACTTC
ACTCCATGAATCCCATCCCAAAATTGAGTCAATTTTCATCAGCACAAGCTGAAGAAGTGGTTGAG
TTGGCGGTTAACGCCATGTTAGAGAAATACACATTTTCCGTACCTTCCCTTCTACAGATGCAATT
GGATTTAATGACAGGGGGGGTCAATTCCGAATTTTATCACTTTTTTTTAGAAAGGATACTATAAG
TTATAATGTTTTCTAATTTGATTTCGAGGATGAGCCGGCCGATCC
Found at i:186125 original size:18 final size:18
Alignment explanation
Indices: 186102--186136 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
186092 TTCTTTGGTT
*
186102 TGTTGAGCTAATTCTTCA
1 TGTTGAGCGAATTCTTCA
186120 TGTTGAGCGAATTCTTC
1 TGTTGAGCGAATTCTTC
186137 TTTTAGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (18 bp):
TGTTGAGCGAATTCTTCA
Left flanking sequence: Indices 185602 -- 186101
TATCTGCTTCCTCTCACCTCTGCTCAGCAAACAAGGGTTGGGGCCCTCTTCAAGTGAGTGACTTC
CCTGGTGGAAGTAATAACGAATGATAACAACAAGGACTACCCTTTTACAACTCCTTAAGCTACTG
AAAGCAGTGAAGTGACCAATTGGTTGTAAGTGAACCTCTTGGTCTTCGATTTTTATTTAGGATTA
GCAACATAACTACTTACCTCGTGCTATCCGACCCTCGCTCGGGTACTTAGGATATGAATAAGACC
TTGTTTCCTCGGAAGAAGGTACCTCCTTCTAGTACTGACTGAGAGTGTAGGTACCCCTCTTTATA
TGGGTACCGAACGTTAGTAAAGTAAGTCTTAACGCCCGCACCGGACTTCCAATATGAATGAACTC
TTCCTATGGTTGGTTATCGGGATCCCTTTTCTCTTTTTATTCAGTCTTTATTAGGTGGTGGTTTC
TCACCCTTCCAAGGGTGATTCTGTGATATGGATTCTTCTTTGGTT
Right flanking sequence: Indices 186137 -- 186636
TTTTAGTCTTTTTATTTCGTTTTTCCATTCATTCATCATTCCATCATCTATGGTCTTCCGTTTAC
CTTCATACTTCATTTTACTTTTTTCTCAATCTTCTTCATGAGGAGTGGATGAAAGCGTCGTTGTG
CTTGCTTGATGGGCTTAGCATCTGGTTTGATATTAAGCCTGTGGACGGCGATTTCAGGGTCTAGC
CCAGGCATCTCAGCCTAACTCCAGGCCAAGCCCAAGTATTCATTCCTTAAGGAGCTGGACGTATT
GTTCAGCTTCCTATGAAGCTAGGCTGGCACTTAGGAAGATTGGACGAGGGTGGAGGGGGCACATC
TGGTGGTATCGTATATAAGAGAGAGCTTCTTTTAAGAATGATCTGAAACTAAAAATTTCATAAGA
GAAGAAAGAAAGTAGCCTAGTTCAGATGAAAAGGTATGCCACAATGCTATCCGAGTTCACAGGTG
TCGTTCCGTCTACTTTTCTTTCCAAACTTTTTCAAAATTCAGTTT
Found at i:211035 original size:42 final size:42
Alignment explanation
Indices: 210961--211106 Score: 229
Period size: 42 Copynumber: 3.5 Consensus size: 42
210951 GCTTCAGAAC
*
210961 TGTCGCCAGAACTGCTTCCCGGTACTGTTGTCCTTCCTTGGT
1 TGTCGCCAGAACTGCCTCCCGGTACTGTTGTCCTTCCTTGGT
* ** * *
211003 TGTCGCCAGAACTGCCTCCCAGTAAAGATGTCCATCCTTGGT
1 TGTCGCCAGAACTGCCTCCCGGTACTGTTGTCCTTCCTTGGT
*
211045 TGTCGCCAGAACTGCTTCCCGGTACTGTTGTCCTTCCTTGGT
1 TGTCGCCAGAACTGCCTCCCGGTACTGTTGTCCTTCCTTGGT
211087 TGTCGCCAGAACTGCCTCCC
1 TGTCGCCAGAACTGCCTCCC
211107 CCCTCCCCTC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.14, C:0.33, G:0.23, T:0.31
Consensus pattern (42 bp):
TGTCGCCAGAACTGCCTCCCGGTACTGTTGTCCTTCCTTGGT
Left flanking sequence: Indices 210461 -- 210960
AAAGTCAAAGCCCCCTAGAGACAAATGGGAATAACCGAACCCCGTCTACAAAATGCCAGTACCAT
GCAGCTGCTTCAAAGCCAACGTGGAGCTTCCGCCTTCGAGGTATATTTACCAATATCGCTTCATC
TTATATGGCGAATATATCTCCCTCATTAGGCTTGGCTCTCTTTCTAAGCGTGTGATCAACTCTCG
AATGTAGGGGATCTCTTCGGTTTCCACTTCTAGATCATTTTTGAGAATTAACGCCCCCACTTCAT
GAAAAAAGGCGTTATCAGGGGAGTGCCTCCAGGCTGGGAGATCGCGCTCACAATAATGTTTTAGT
TGATTGGAAACAAGCCTATGCAGGCGTCTCAGAAGATCTCCCCTCTCCCCCTCTTCTTGAAGGAA
TGGGATTAACGGGGCCGGCGGATTCCCTACATGGGTATCTTGTGCCGGGGGAACAGAGGGGCTAG
GATTCGAAGGGACAGGATGTGGCTGATTGACACTTGCTTCAGAAC
Right flanking sequence: Indices 211107 -- 211606
CCCTCCCCTCCAGCTGGAGCCATCATGTTCTCCGGGGCAAAGATATACCAAAGGGTTGGTAAAAA
AAGACCGCCCCATCCAAGCTGCCTAAGGAGGTAGAGGAGAGATTTTCTGACAAGCATGGATTGAA
CTCTTTCAAAAAAGAAATTCAAATCCAACCCCAAAAAACAAAATAAAAGGTAGAAAAATAAAAGA
AGAACAAACCAAAAAAGTCTTACCGAAATCGGATTTCCTTTGCGTGCCAAATGCGCCTTCACTTT
TTCCCCCCTTTTCTTACCCGTCCAATATTTGTTCTCGAAGGTCTTCGTTTTCGTGTAAAAGAAAA
CTCTCCAAATTTATGACCAACCTTTCCCTCAGTAATCTTACAATGAACAGGAGTTTTTCCATTGT
AAATTCGTACGGAGCAATCAACGAATTCCGGCGAAATAGAAGATCTACGTGACCAAATTTTCCTG
TTCAAAAGAGGATCTCTCTTCTTTTTCATTCTCAAGAGGAATGCA
Found at i:245608 original size:24 final size:24
Alignment explanation
Indices: 245572--245627 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
245562 ATATTGCCAC
* **
245572 CACTATAAAAATCATTATCAGAAT
1 CACTATCAAAATCAAAATCAGAAT
* **
245596 CACTATCAGAATCAAAATCATCAT
1 CACTATCAAAATCAAAATCAGAAT
245620 CACTATCA
1 CACTATCA
245628 TCATCAGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (24 bp):
CACTATCAAAATCAAAATCAGAAT
Left flanking sequence: Indices 245072 -- 245571
ATTTCATTTATTCGGGCCTATTAGAGCAGGATCCACTTTTTTGGGAATATTGGTCGAAGCAATAA
AAAGAATATTTCCAGTGTAACCTTTTTCCAAATCCCCTCTTTCCCCGGAGAAATTGTCCATTAAT
AGAGTGGACCAACCCCATTTTTCATAATCCCCGGAGAGATTGTTCGCTAATATACCAAGAGATAA
GGAATTCGACTCAGTCATATGCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTG
CTTTTGCTAATTCGAATTGAAGGTTGATAAAAAAAGGGTCTCTGTGTTCCGGTTCTAGCAGATCC
ACAGCCTCATTTATCACCTTTTCAAACTCCTGCTCCGCCTCAAGGGCACGGGCGATAGCGATCTC
GTAAACCACATCAGTAACGTCAATACCACAAATCTCTTCAATTTCCTTACTATCATCAATATCGT
CAATCATATCAAGATAAACATCGTCTTCTTCGTCAATATTGCCAC
Right flanking sequence: Indices 245628 -- 246127
TCATCAGAAACCTTAACCAGGTCCCGGTTCCGAAATACTGTAACGAAAGGAACATAGGAGTTTGT
TGCTAGGTATTTGACCAAATAGGATCGTCCAGTTTTTATAGAACCTATCACTAAAATACCCCTAG
AAGGGGATAGGGGTAAGCGGAGCGAAAAGGGTAGGTTAGGAGATGGGTAATGAAAACGATTCGAG
GTTTGTATTGTCTGATAATAAGCAAGGAATATCCGTCTTTCCGCTAAACAGAGTGTATTGAACTC
ATAATTCAGTAGATACTTTTTATGAATGTAAATGAAGTTTCGTAAGTAAATTACTCCCGGCTCTT
CATTCATTAGAGAACCAGAGTCAGTATTTGATAAATGATCACTCTGAGTCAGACTCAATAGAATT
TTATCAATCCTTTTTTCTGTCGTTAAGTTAGCGAACTTAATCAAGATTTTTTTTCTTTATCCTGA
AGCCAATCACAGCCCGTGATGAAGGATTCCATTTTCTCAGAAATC
Done.