Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_013765
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: 209482
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:9160 original size:81 final size:81
Alignment explanation
Indices: 9025--9174 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
9015 CTCAAGCTCA
*
9025 CTTGGTGAAAATGGTAAACACGACAGACTTAAAATCTGTTCCTATGGGTTATCGGTTC-AAGTCC
1 CTTGGTGAAAATGGTAAACACGACAGACTCAAAATCTGTTCCTATGGGTTATCGGTTCGAA-TCC
9089 GATAGTGAGCATACTCG
65 GATAGTGAGCATACTCG
* *
9106 CTTGGTGAAAATGGTAGACACGACAGCCTCAAAATCTGTTCCTATGGGTTATCGGTTCGAATCCG
1 CTTGGTGAAAATGGTAAACACGACAGACTCAAAATCTGTTCCTATGGGTTATCGGTTCGAATCCG
9171 ATAG
66 ATAG
9175 CGAGTATCTT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (81 bp):
CTTGGTGAAAATGGTAAACACGACAGACTCAAAATCTGTTCCTATGGGTTATCGGTTCGAATCCG
ATAGTGAGCATACTCG
Left flanking sequence: Indices 8525 -- 9024
TTTCGCAAACGAAAAGGAAAAATAAAAGAAGCGGCGCTTTTTCCTTAAACGTTTAGTTTTATTAT
TTATCTAGCCAAGAGAGTCTTCCGCGAGACTCCCATAGCTGATCTCTTCGAACGAACCTCTATTT
GATTTAAAGCCGTGTCATACAGAAGCCATTGCCAAGTGCACTCTTGCGACTTGTATCTTAAAATA
AACCGGTACAAATCAATAGAGAACAGGTTTTACAGGCTTTGAACACAAAGAAGCGCTTTACTATC
GACGCAGCCAACAAACAGGGGGTGCGCGAACGAAGTAGGGCGTCGTCAGCTCGCCCTACATCTTC
CTACCAAGAAAGGCAAGAAAAACATCTAGGGGTCGCAGCAGCCAGCAGGTCTGACCAAGCCAGAG
GGAGTCTCGTATGCCGAAGCCAAAGTAGCATGTCTAGAAAAAAAAATGGCGAAAAGAAAGCAAAA
CAGAAAGATTTTGTCTCCGTTCTGCGCTTTGCTTTCTCAAGCTCA
Right flanking sequence: Indices 9175 -- 9674
CGAGTATCTTAGTGTTTAAATTAGAAAGAAAGGCGGATATAACTTAATGGGTTGAAAGTGTCAGA
GTGTGAATTTGAAAACACGGGTTCGAATCCCGTTATTCGCCAAAAACACATCATGAATTAGCTTG
AATCTTTATAACTTTGAGTGAGGCGCTCAGAGAAGAAAACAAGTTTTCTTCTCTTGCCAAAGATT
CAGAGGAAGAAAGCATAACAAAAACAATTTCTGTTTCTTAGAAAAAAAAAATAGATGTTTTTTTG
CTCGCTAACGAAGTGCCGTGCACCTGACCAGTGAGCGGGTTCGCCGCTTGGTTGGTGGAAAAAAC
ATAATGCATTCCTTTATCTGAGCTTTGCCATGAACTACATGCCTCCGCTTACTGGGTCGCCCATC
AAGGTGCAAAGCACTTGATAGGCGACCCAGTGGCCTACTCCCCTCTTATGGATCCTCTGGTGACT
AAGTTACCTTTTCTGTATCCTCCTGTCGTTTTGGAGATAGGTAGG
Found at i:13608 original size:12 final size:12
Alignment explanation
Indices: 13591--13615 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13581 CCGCGCCTAC
13591 AACTAGATAATA
1 AACTAGATAATA
13603 AACTAGATAATA
1 AACTAGATAATA
13615 A
1 A
13616 GAGGAATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AACTAGATAATA
Left flanking sequence: Indices 13091 -- 13590
TTCCTATCAAGGTTAAGGAGTCAACTGAACGTCTCAGCGGCGGAATTGAAGACCCGAATTCAACC
AGAGCAGCGCGTAGGCGTGGCCTGAAAGCGATGATGGATGGTCACGCATAAGCCACCAAGTTGCA
CAGCAAACACCCAAGGTAGAGATGCAAACTCCTCCATGTTAAATTCTCATCTCCATGGGAGCTTT
TCGAAAGTCATGATCAACAGCAAGCAATCTGTAGGCTTAGTGAAACGCGGGCAATGAAGCATCTA
CTACAAGCAAAGCGCCAAGCGCTCACTTTATTATCACGAAAAAGCTTACCATAAAGAAAGCAGAA
AAGAAAAACCGTTGAGTAACTTATAGCTTTTTTCCTATCTCTCCTTCTTCTCGTTGTTCTTTTTT
CTTCGTTAGGCTAAAGCGCTCGGCGCTTTTTCCTCCGTGCCCGTTTAGTTTACGCGCTTCCATTT
ATTCCACCCCAATACGCCTCTTGTTCGCTAAGCTCCCGCGCCTAC
Right flanking sequence: Indices 13616 -- 14115
GAGGAATGTGCAAGGTACTAAAAAACAAGGCACACCGCATGCATAAAAATGGCAAATGTTACAAG
TCTCTCATTAATTTTGGAGAGATGTAACGAAAGAAAAAACGAATAAACGTTTTTTTTAGTTTTGG
GTGAGTCTTCTCCAATCATGTTGGGTAAGGAGTCTTGCTCTTACCAATTACCCTTCTTGCTCTGC
TTATAGAGCCTGAAAATTCCCGAGAATATATAAAGTGAGGCAGATGATTAAAATATATGAATAGG
TATTGTAGTGCAAAAGAAGAGCACCTAAACATATCTACTACTCACTAACATTGGAATGGTATGAG
TGCTGCGATGCCGTGAGGCACAACCATGAAAAGGAAAAAGCAGGCAGATAAAGTTCTGTACTTGA
ATCAGCTGCTCCATCTGTTTTTATGATCTCGCCGCCGTCTTCACGGAAAGGAGAATACGTTCTCT
TCTTCCGTGTTCACTCCGCGTTTTGGAGAACGCGTAGCGTTCTCT
Found at i:17237 original size:18 final size:18
Alignment explanation
Indices: 17214--17250 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17204 CGTCACTTTT
17214 TTTCTACGAAAGCTTCCC
1 TTTCTACGAAAGCTTCCC
17232 TTTCTACGAAAGCTTCCC
1 TTTCTACGAAAGCTTCCC
17250 T
1 T
17251 CGTCTATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.32, G:0.11, T:0.35
Consensus pattern (18 bp):
TTTCTACGAAAGCTTCCC
Left flanking sequence: Indices 16714 -- 17213
AAAGCCAAAACCAAAAAGAAAAGAAGAGAGGCCTAATTCCCTTCTTCGAACCCCGTGTAACCTCA
CGAAGAAAAACCATTTTGTTTTTCTCTTTCTTGATAATGGACAATAAGCTAGCTTAATGTCGATT
ACATACATGGCCTTAATTTGCGTTCGCAAAAAGTGGGAAAGTAGGCGACTGGTTGTTGCTCGCAC
TGTCTGCGTTGCAGATGGTAGGTAAGTCCAAAGATTGGTCAGGGTCTTTGGCCTCGAATAATAAG
TCAGCCTTGGAAACAGTATAGTTGTGGAGTAGGCTAAGGACGGATTCGAACCATCTTTCTAGGAT
TTGCAATCCAATACATTAACCTTATGTTACTTAGCCATTTCTTAGACTTTTCGGTACAAAAAGTA
TGAAAAAGGACCTTCAGCCTTATATTGAACATTGATAGAAGATGAAGAAGCGAAAGCTTCGCAAA
CAAAAACCTCAAAGAGAAACATATATAAAGCTCTTCGTCACTTTT
Right flanking sequence: Indices 17251 -- 17750
CGTCTATGATGTTATATTGTGTAGCAGTGCGGGGTTCAATTCCTATGGAGTCGCTATGACTGTAA
AGTAGTCGTGCGCTGAGACTTGTCTATGGAAGAAGCGCCTAAACCAAACTTCCAATGCCCTAACT
CTACAAAAGAGGGAAAAGCATCCGAGTTAGAAGGCAAAGGCCCGTGGGGCACCTGTGGCCTCTTT
CCTCCAGGTGAGAGAGCTTTGAAAAACAGAGATAGCGGAAAGGTACTAGCTAGTTTTAGCTAACG
AACTCCAACGAAAGCCGCCGCCCTTCACATAAAGATGGTCTGAAGTCCTTTAGGCACTATTCCCT
AAGCCGAGTGTAATAATTTTACGCCGGCCGGGGGGTGGGCTAAGCTTTCACTAAGCAAAACCAAA
CACCATAGATAGGCCGAAACAGCGGATCGCTCTACAACTTGGCCATGCCAAGGAGGCACTTCTTA
TCTCTCGAGTGGGCCTCCGCCGAGCTCACTCACAGCCGTTCTAAG
Found at i:50206 original size:40 final size:41
Alignment explanation
Indices: 50161--50244 Score: 134
Period size: 40 Copynumber: 2.0 Consensus size: 41
50151 CGGCGCGGAA
*
50161 GAAAGAATGTAGAAAAGGAA-AGAAATGTAGATATCAGCGC
1 GAAAGAATGTAGAAAAGGAAGAAAAATGTAGATATCAGCGC
50201 GAAAGAATGTAGAAAAGGAAGGCAAAAATGTAGATATCAGCGC
1 GAAAGAATGTAGAAAAGGAA-G-AAAAATGTAGATATCAGCGC
50244 G
1 G
50245 GGAATACGCG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 20 0.50
43 20 0.50
ACGTcount: A:0.49, C:0.08, G:0.29, T:0.14
Consensus pattern (41 bp):
GAAAGAATGTAGAAAAGGAAGAAAAATGTAGATATCAGCGC
Left flanking sequence: Indices 49661 -- 50160
GAAGAATACCGGGAAAGAGAAGTTGGTCCCCCGGAGACTTTTCTTGACTCGGTCAACTCACGAAG
TATGTCTCAAGACCGATTTATTTCGAGATTTCAAAGTTTTTAAGGATTTCATAGAAGGAAAGAAT
GTTTTTAATGAAAAGGACAATAATCCTAAAAGAAGGCCTTACAGGGAAGATTCTGAAGACCTCTG
AAGGTGAAAGACCTTTTGATTCGACCTAAAAGTCGAATCAATGACCATGTTTTGATGGAAGAATG
TAAGAAAAGAACGAAAGAGAGTGCCCATATAAGCCCAAAATTACGGACTAAATGTATGATTGTTA
AATATATGGAATTTTAATATGTAAAGACCAACTAAAAAGGAAAAGATTTCTCATGAAACTATGAA
ATCCAGCACTAAAAAGGGCGGGCGCCAAAGAAAGAAAAGAAAGGAAATAGGATAAACATCAAGGC
GAAAAATGTAGAAAAGGAAAGAAAATAAGGAAAATCGGCGCGGAA
Right flanking sequence: Indices 50245 -- 50744
GGAATACGCGGAAAATGTAGGATATGTAGGATAATTTGACTTTTCTTCCATTTAATTATATAATC
TTTTCATTTCGACTTTCTGAGGATAACTTAGACGCAAATCTCTCCGGATCCTATCTAATTCCTCA
TTAAAGCTAGAGAGAAAATGATCTTGTGAACCTTCAGGTATAACTAAGACATTTCCGTCATGAAA
GTGACCTATCACTTCGGCGGTTGGAAATCTCTTTAATGTCTGAATAGTACCTTGGGCTAAGAGGC
CAAATTCGAAAGATTGAAGATAATTTGAGTAGTTAGACCTAAAACTAGGTTCCGATATTCGATAA
GTATGACCCGTAGGCCCTATTAATAGCTGACCCAGATGCATATCTTGCATCATTTTGGAGACTGT
CCTGAACTCAGCTATTATACTGGATTGCTGCATTTCATATGTCACAGCTGTAGCCAGTTTTTCCA
TCTTAGGATAATCTGGATAATTCTTAAACTCAGTAGGTCTAATGC
Found at i:69053 original size:14 final size:15
Alignment explanation
Indices: 69026--69054 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
69016 TTTATTTATA
69026 TGAAATTGTATGATG
1 TGAAATTGTATGATG
69041 TGAAATT-TATGATG
1 TGAAATTGTATGATG
69055 CTGCAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (15 bp):
TGAAATTGTATGATG
Left flanking sequence: Indices 68526 -- 69025
TTCCTTGTCTTTACCCCGGCTCCTCGCTTAGCCCTTCTTAAAATCGACCGAATTCGAGGCACTTG
CTGCCCGCCGCCTCTTATCTCTTACCTAGGGTGAGCCAGCCAGGGCATTTAATAAGTAAGATGGA
GCTTCCTTTGTTGTGAGCAAGAAGTGGCCGCGGGCCGCGGCGGGCGGCCCTTAGCGAATGGGAGG
CTGTGTTCACCCGCAAGGCTTGTGTAGATTCTGATTCTCCTGATTCGAAAACAAGCTAACAACAA
AGTAAGGAGTAGAGCCTGAACAAGTATGCGTCTCATTAGTCTAATGGCTGCTGCGATATTTAGGA
AGGGGGCCTTGAGGAGGCTCGGTTGCAGTAGACGACTCAGAGGAAGACGGCTGCTCCGAAGAACT
CCGGCCAATTGCCAAGCGCCTCGTCTTTTGGCTCTTTTTACTACGGAATTGTATGATGCTGCAAG
CGGCTTTCAAATAATTATTAAAGGTATTAATAATATTTATTTATA
Right flanking sequence: Indices 69055 -- 69554
CTGCAACTTTCGAACAATTGGGGGAATTCGTTGTTGTATATGATGCTGCAAGCAGCCTTCAAAGA
AGTTGGCTTTCGAAAGAATAATTGAACAAGTATCATAATTACAAATTATATGTGATGATTCATTT
TAATTTATCTATGATAATTTTTTAATTACTATTAAGCAGATTAAGGATAATTTTGATATTATCCA
TAATTGATTTAATGGTCTTCAAAGTTAATACCTAAGACATGTTCTTAAGACACGCTCGAGAAAAA
AAAAGCCGCGCTGTTCGTAGGACATCTCGAGAGCAGTAAGACATACCTCTTCGTCTAATCTGTGT
CTTAGGGTCGCGTTTCAAGCGTGGCGTCTAAAGCATAACAACACAAGATCAGATTAAGACAAGGC
TTGTATAGAGTTTTAAGTCGAGCCGGTGGAAAAGCTTAAGTAGCTTATATAAGTAAGCACCTAAA
ACCAGGCGCTTCAGCGCGCGAGGAGATTGAACAATAGCACAGCCG
Found at i:81641 original size:31 final size:31
Alignment explanation
Indices: 81598--81657 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
81588 CACCGGCGCG
*
81598 CGCGCTCTGCGCCTTTCCTTCCAGCGAAGAA
1 CGCGCTCCGCGCCTTTCCTTCCAGCGAAGAA
*
81629 CGCGCTCCGCGCCTTTCCTTCTAGCGAAG
1 CGCGCTCCGCGCCTTTCCTTCCAGCGAAG
81658 CGCCGCCGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.13, C:0.40, G:0.23, T:0.23
Consensus pattern (31 bp):
CGCGCTCCGCGCCTTTCCTTCCAGCGAAGAA
Left flanking sequence: Indices 81098 -- 81597
TTTGAATGTTTTTGGTGCTGGAAGCGCGGCTAAAAGCCGCGCGTTTGATATGATATAATCGATTT
TTTGGATTTCTCCTCTCCGTTTACCGATTATAAAGAGATTTTGTACAAAATAATCCATTAGATGA
AAAAGAAAAAAACACATTTTCCTCCATAAAGGCTGATAGATTATCTCGTTTTGTCATCTCAGTTA
TAGACATAATAAAAGGATCAAGATCGCACTAACAATGCAGTTTTTCAAATGCTTTATCACCACGC
TTTACCGGTACAGCAAGAAAGCAACGCAACATCTATCTACTCCCAAACGAAAGCCTTAAAGGCTT
AAATTACCAAGCCATACGAGTCAGTCTTCGCATTATTTATAGGATGAATCCTTCTTCTGGCCAGA
ATAGAAAACAATTATTTTATTTTAGTTTTGGGAATGAAAGAAAAAGGTATTTTCGCTTTCTTCTC
CGCCGAGCTTTATAAAGCACTTTTCGCTTTATGGCCACCGGCGCG
Right flanking sequence: Indices 81658 -- 82157
CGCCGCCGCCGCTTCGCGCCTGGGGAACGCATTCTCCAACTCATAAAAAAAAATAATACGTTTGG
ATTTTTTTTTGGTGCCTAACCTCCCCTTCGAGGCGGCGGTTGCTGCCAAAAACAGCGCTTCATCG
CTATGCAATTAAAGTAGCCTGGAACGATCTTTTTTCCGAAGAAAGAGTGGATCGACAAAGAATGT
GGCGATGATAAGGTCTTGGCGGCTGGAGAAGAGGCTGGCTCCTTGCAAGCGTATTCCCCAGGCAC
GTTCAAAACCGGTGGATAAAGCAAGTCCTACCCTCTAAGGCTGTAGGGGCCGACACCAACAATCA
ACTACGTCTTTGCAGGGGAAAAGCCAATCAAAGCGTGTCGTTAAGTCGAAGATTCATAACACATT
GCTTCGCGCTTCGATTATGATGGATGATGAATTGTTGCGAACCATCAATCAACTTCGTTGATTGA
TCGAAACGTTTTGGAATCTGCGACAAGTCTTAGCATTAGTATGAG
Found at i:96989 original size:1 final size:1
Alignment explanation
Indices: 96983--97019 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
96973 AGAGGAAGGA
96983 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
97020 AAGGATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Left flanking sequence: Indices 96483 -- 96982
AGTAAGGTGCACCTTGTTAGCGAAGCCGGACTGCGGCGCATCTACGACGCATGATGATGCTTTGT
GAACGAAGTATAACCATGGCGTAGCAGTGGCTTGCTTCCGTTGCACCGAAAATAACAGAGCAGCA
AAGCAGAGAAAAACATATAGAAATCTATTTCTCTTTCTTCGCTCTTATGGCCGAAATGAAAAAAA
AGAGAAAGACCTAGAAAGTCTAATAGGCCGCAGGCCGTAAGAGAAAGCGCTTTGCGCTTTATCAA
ACCGGTCTCTTTTTCTGAGCATTTCCGCCGATCCGAGAACGCATACCTACGGCCGGCCACCAAAA
AGACTATCTCTTTTTCAGCCTCAACGCTTTTTTTCCCTTTCTGCCTGCCCGATGAGGGTAGCTTC
GTGTCTCTACGCTGATTTATGAAGCTCTTGAGGTTTCACCTCGCTTGAGGCTACTGCTTCGGGGC
CAAGGAAACCGCCCGCAAAAGAAGGTGTACAAGAAAGAGGAAGGA
Right flanking sequence: Indices 97020 -- 97519
AAGGATAAAAAGAGCTCCATTCGTATGGCGAAGCCTTACTAAGGGCGTAGTAGCCATCCATAATA
GGACCGGCCGCCTGGCCACTTTCTGGCTACCGCCCTAGGAGGCCCTTACTAGGAAGGAGCTTGGC
AACTTGATTTGGCTCTTCTACCTACGATGTGATAATGGCTTAGCGCCATGGCTCGTAATAAACGA
ACCATCTTTCACCCTCCACCCAAAAGCATCTACTTTTCCTGAAATTCTTCACCTAAAACAAGCGA
ATAATTCTATCTCTCATCTGGGAATATTTTTAAACCGAATGAGTTGCTAAGAAGCTCTGTGTAAA
TTTTTTGCAAAAGGTCGCAAGTTGACTGTTAATTTCCTCAGAGATGCTTTTTTATTTCACAATAA
CAAAAAGTATACTTGGATCAATAGGCTTCAATGGCTCATGTTCATATTCATTAATAATTGAAATA
GGAATTTCATCTAAATAACCTTTGACAGCTGCATGAATAACCACA
Found at i:107478 original size:19 final size:18
Alignment explanation
Indices: 107450--107494 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
107440 AATCGAGACA
*
107450 GGGA-GGGGGGAGGAGGAG
1 GGGAGGGGGGGAGGA-AAG
107468 GGGAGGGGGGGAGGAAAG
1 GGGAGGGGGGGAGGAAAG
107486 GGG-GGGGGG
1 GGGAGGGGGG
107495 AAAGGGGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 10 0.40
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (18 bp):
GGGAGGGGGGGAGGAAAG
Left flanking sequence: Indices 106950 -- 107449
ATAATTCCAGGGGCTTTAACTTCTACACGTCTTCATTCTACAGCGCCTAAGGCACCTTTTCCATC
AATAGGTACTCCTAAGGCATCAACTACACGACCTAATATGGCCTTTCCTACAGGAACATCCACAA
TAGATCCAGTGCGCCTTACAATATCTCCTTCTTTAATAGCGGTATCACTACCAAATACAACAATT
CCTACATTTTCCTTTTCTAGATTCAAAGCCATTCCTTTCACACCGCTGGCAAATTCGACCATTTC
CCCTGCCTAAATCTTGTTCAATCCATAAACACGTGCAATTCCATCTCCAACTGATACCACTCGAC
CAATCTCATCCACTTGCAATTTGGTGTAATAGTTAGTAATTCTTTGTTCTAATAACGTAGATGGT
TCCGTTCCAGCAAATTTGTTCGTGAATCAATCGAACCTTCTACCAATAAATAATTCCACAATCCG
AACCTATCGTGCTCAACTTATCATCGAAGATGATGAATCGAGACA
Right flanking sequence: Indices 107495 -- 107994
AAAGGGGGAGAGATGAGCAAAGCGCCCGAAAGCCAATAAACTGCAAAGGGAAGAGAAGAAGCTTC
GGCCTTCGCTTTAAGAGAATAGATTCTCTTTTCTGAGCTTTCTTCTTTGAACCTCTCATTCGTTC
GCCCACCGAAACGGGTTTCCAACCAGAGAAGCTACAAGCTAAAAAGGCTTCGACCCAAAAAACGA
ACTATCTTCTGCTTCGTTCTTCTTTTATTTGCCCTTGGATAGCGCTTCGCGTTTCCGGGGTGTAT
GTCGCAACAATAAGCTAAGCTTTTTTCTCTAAAAAAACAAAATACAAAAAATCTATCTTTCTTTG
CCTGAGCGCTGCTTCTTTTTAACCCCCCTTTCTCCTTCCTCGCGCTTGGCTCAAACAGGCAAAGC
GGATTATTCAGCATGCCGTAGAACCAGGCTAAGATGCAATTCCATAGTAATTGCATATTTTCAAA
ATGGCTTCGAGCAAATCCCGGTGCTTACTTGTCATTTGATTCGTA
Found at i:107496 original size:13 final size:13
Alignment explanation
Indices: 107471--107502 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
107461 GGAGGAGGGG
107471 AGGGGGGGAGGAA
1 AGGGGGGGAGGAA
*
107484 AGGGGGGGGGGAA
1 AGGGGGGGAGGAA
107497 AGGGGG
1 AGGGGG
107503 AGAGATGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (13 bp):
AGGGGGGGAGGAA
Left flanking sequence: Indices 106971 -- 107470
TCTACACGTCTTCATTCTACAGCGCCTAAGGCACCTTTTCCATCAATAGGTACTCCTAAGGCATC
AACTACACGACCTAATATGGCCTTTCCTACAGGAACATCCACAATAGATCCAGTGCGCCTTACAA
TATCTCCTTCTTTAATAGCGGTATCACTACCAAATACAACAATTCCTACATTTTCCTTTTCTAGA
TTCAAAGCCATTCCTTTCACACCGCTGGCAAATTCGACCATTTCCCCTGCCTAAATCTTGTTCAA
TCCATAAACACGTGCAATTCCATCTCCAACTGATACCACTCGACCAATCTCATCCACTTGCAATT
TGGTGTAATAGTTAGTAATTCTTTGTTCTAATAACGTAGATGGTTCCGTTCCAGCAAATTTGTTC
GTGAATCAATCGAACCTTCTACCAATAAATAATTCCACAATCCGAACCTATCGTGCTCAACTTAT
CATCGAAGATGATGAATCGAGACAGGGAGGGGGGAGGAGGAGGGG
Right flanking sequence: Indices 107503 -- 108002
AGAGATGAGCAAAGCGCCCGAAAGCCAATAAACTGCAAAGGGAAGAGAAGAAGCTTCGGCCTTCG
CTTTAAGAGAATAGATTCTCTTTTCTGAGCTTTCTTCTTTGAACCTCTCATTCGTTCGCCCACCG
AAACGGGTTTCCAACCAGAGAAGCTACAAGCTAAAAAGGCTTCGACCCAAAAAACGAACTATCTT
CTGCTTCGTTCTTCTTTTATTTGCCCTTGGATAGCGCTTCGCGTTTCCGGGGTGTATGTCGCAAC
AATAAGCTAAGCTTTTTTCTCTAAAAAAACAAAATACAAAAAATCTATCTTTCTTTGCCTGAGCG
CTGCTTCTTTTTAACCCCCCTTTCTCCTTCCTCGCGCTTGGCTCAAACAGGCAAAGCGGATTATT
CAGCATGCCGTAGAACCAGGCTAAGATGCAATTCCATAGTAATTGCATATTTTCAAAATGGCTTC
GAGCAAATCCCGGTGCTTACTTGTCATTTGATTCGTAACGACGCG
Found at i:111691 original size:23 final size:23
Alignment explanation
Indices: 111659--111704 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
111649 GTCACAGAAG
* *
111659 AGGGAGACTAAGTTAGGTTGGAA
1 AGGGAGACTAAGTAAGATTGGAA
*
111682 AGGGATACTAAGTAAGATTGGAA
1 AGGGAGACTAAGTAAGATTGGAA
111705 GAGGTAGGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.35, T:0.22
Consensus pattern (23 bp):
AGGGAGACTAAGTAAGATTGGAA
Left flanking sequence: Indices 111159 -- 111658
ATAACCTGCCATAGAATTACCTTATAGCTTCCTCTCCGGGCAGACCACAGCATAACAACCTCTTC
AAAATCCCAAATGACCAGGTCGAGAGAAAGCCGAGGACTTTAGAGCCCAGTGAGACTAATGATTC
CATGTACTATCTTCTTCGGAAAAGGAGTAATTCTATTTAGTTAGAGCTAATGCAGATTATTGTCA
GCACCACGGCTTTGGCATGAATCCTCAATAGCGGCATATCTTCATAAGAAAGGGGAATCGAGAAA
ATTCCTTAGCCGAAGCAAAGAAGGTCAAATAGCATGTGTATAAAGCAGAGCTGTTCCATACAAAT
AGAACGTATAGTAATCCTTGGAAAAAACTCAGACTCATTGCATAAATTGGTAAATTACCTACCGA
AATAATCATTACTATTGTCACTTAAAGCAACGACCATATATATGGTAATTATTTAAATAGTTGAG
ATGCTATATATGACTGTAGGAGTGAACACGGTCTCGTCACAGAAG
Right flanking sequence: Indices 111705 -- 112204
GAGGTAGGCTAGTGAGGGCGGCTTTCCCTTATCCCTTCTTCCCTCTCTCTCCCTTTCCCTAAAAA
CACAGGATCCTATCTATCATACGCCTCCAGTGTCGAAGAAGAGTTTAGGCCCTGGCAAAGGTCGC
CCCTTTTGGCTCCGGCGGGCGCTTATGCTATCACTAAAGCATTTTGCCACTCTGCCTGCGTGTTG
CGTATACCGCATGCGATTAACCCGCGCGCACCAAAAATGTGAATTTCGCGCCATATGAAGGGCTT
TTTTAGCCTCTTGTCAGCCATAATACAACAAGTCAAGACAAAAAATCTAGATTTCTGGTCGGCGA
CACACTTGGTGTTGCCTATCTTACTTCTCAGAAAGGAGCCTCGGCCTTTTTTTCTGCGCACTGCT
GAACGGTATCTGATCTCACGGCCAGACCTCTCTATGCTGGAGAGCTCCTTGGCTTGACTTGACAG
GTTGGGTCTAATGGCAGGCAAGATTTGGCGATCTTGTGCCTCACT
Found at i:112345 original size:19 final size:19
Alignment explanation
Indices: 112317--112355 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
112307 CACAGTTCAC
112317 TTCACCTACGTTGATAAAT
1 TTCACCTACGTTGATAAAT
* *
112336 TTCACTTACGTTGATGAAT
1 TTCACCTACGTTGATAAAT
112355 T
1 T
112356 CTTAGTCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (19 bp):
TTCACCTACGTTGATAAAT
Left flanking sequence: Indices 111817 -- 112316
GGCCCTGGCAAAGGTCGCCCCTTTTGGCTCCGGCGGGCGCTTATGCTATCACTAAAGCATTTTGC
CACTCTGCCTGCGTGTTGCGTATACCGCATGCGATTAACCCGCGCGCACCAAAAATGTGAATTTC
GCGCCATATGAAGGGCTTTTTTAGCCTCTTGTCAGCCATAATACAACAAGTCAAGACAAAAAATC
TAGATTTCTGGTCGGCGACACACTTGGTGTTGCCTATCTTACTTCTCAGAAAGGAGCCTCGGCCT
TTTTTTCTGCGCACTGCTGAACGGTATCTGATCTCACGGCCAGACCTCTCTATGCTGGAGAGCTC
CTTGGCTTGACTTGACAGGTTGGGTCTAATGGCAGGCAAGATTTGGCGATCTTGTGCCTCACTCC
GGTGATCATTTGCCGATCGAGGCACGCAATTGCCTATTATCCCCTTGCTTTGCGTTTACTCAATG
ACAGCTTGTAAGTGCACCTCAGCAAAATGTCGTCGCACAGTTCAC
Right flanking sequence: Indices 112356 -- 112855
CTTAGTCTCGCTACTCTTAGCAGGTTATATTTTGTATTATACACCTTTTCTATTTTTTTGTGCTT
TACATCTTGCCCATTACCAGGAACGCACAATAAGGTAGAAGCATCTCGTCGGCTGAGATGAACCT
ATAGCCCTCCCTACTAGGGCTATACACGCATGCTCGTCCTTCAGGTGGCACGGCAATACCGAAGT
GCCAAGGAAGGCCCCTTTATGTATTCTGGAAGAAAGTAACAAGTTTGTTCATTCTATGTAGATTT
TGGTTTCCATATAGACTGAGAGAGCACCATCTCAAGTCCAAGTTAGCCACTCATGAAGTGGATCC
AGACGCTACACCTGACATAAAAGCTGAGACGATCAGTACTTCGAGTAGTGCCCTATTGTTTATTG
CAATTCTTACAAAGCCTCATATATGGTGATTTATACGATGATTCATATGATGATTCATATGATGT
TTGGTCGTTGAAGCTATCTGCGGGCCAACAAAGAAGAAAGAAGGT
Found at i:113148 original size:18 final size:19
Alignment explanation
Indices: 113125--113163 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
113115 ATTTTGATAT
113125 TAGATT-TCCATCTGGAAC
1 TAGATTCTCCATCTGGAAC
**
113143 TAGATTCTTTATCTGGAAC
1 TAGATTCTCCATCTGGAAC
113162 TA
1 TA
113164 AATCCAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (19 bp):
TAGATTCTCCATCTGGAAC
Left flanking sequence: Indices 112625 -- 113124
TATAGACTGAGAGAGCACCATCTCAAGTCCAAGTTAGCCACTCATGAAGTGGATCCAGACGCTAC
ACCTGACATAAAAGCTGAGACGATCAGTACTTCGAGTAGTGCCCTATTGTTTATTGCAATTCTTA
CAAAGCCTCATATATGGTGATTTATACGATGATTCATATGATGATTCATATGATGTTTGGTCGTT
GAAGCTATCTGCGGGCCAACAAAGAAGAAAGAAGGTCAGAGTAGCTTCGCTCATAAGTAAAGCGC
GACATTTTGCTAAGAGCGGATGTGTTTCGAATCCCGGATGAATGATGATGCTAAAGACCTTATCC
AAGCTGCGCGTGCCTAAGATGTTTGCTCCACCAAAACTATGAACCAAGCTTAGTTTGCTTGATAA
CCGCCCCGCCTGAGATTAACCTTTCGGCCTCGTAACAGAACGCGAAGCTTGTTTGATACTTAATC
TTGATACTTTATACTAAACCTTTGTTTCTATCTTGATTTTGATAT
Right flanking sequence: Indices 113164 -- 113663
AATCCAAAACTAGAACTAGATGAAAGCATGTGTTGCGCGCCGCTTTGACAAGCTATCGCATGTCT
TCGGTTGCCGTAGGCTTGCCTCGGCATTCTCACGAAATTCTATCTGAGACTTTAACTTGAAGCCT
GAATTGTCAGCTTGAGGCAGAAGCGAACTTCTGTCATGAAATATGACAGTTTACGCAGAACCGGG
TGCTTGGTGTACTAAACATAACTCATGTTTTGTTTATTTGGTAGGTACATTTCTTCAAACAAATG
AAAGATAAAGATAAGGTCCCCTTTTAGTTTTTGGTATACTTGTCTCAATCAGCTTGAGCGTCCGT
CCTGTGCTGCTGTTTCTTGAAGGTTGGTATGTGCTCTCTTTAGCGTTTATAAATAAGTCTTTTAA
TCTGGGTCTATTGCAAGCATTTTAGCATAAGAAGGCTGCTGTCATCATTAGTCATTATAGATAAA
AAAACCTATTCAAAATTCATAATAAGGGGGACAGTCAAAAGTCAT
Found at i:134638 original size:16 final size:16
Alignment explanation
Indices: 134617--134647 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
134607 GTCAGACTAA
*
134617 AGCCAATTTTACAAAC
1 AGCCAATTTGACAAAC
134633 AGCCAATTTGACAAA
1 AGCCAATTTGACAAA
134648 AAACAATACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (16 bp):
AGCCAATTTGACAAAC
Left flanking sequence: Indices 134117 -- 134616
TGATTGGGCTGTGGAGAGCGCAGCGTTCTCTTCTTCCAATGTTTGATTTCGGTGTTGTCCATAAA
TCTCCCTAGGGATGGTGCACATGTGGCGGGAATGGTCTACACTCGGCGTTCAACGCTTACAGCGA
CTGTATCAAAAATCTATCTTTTTTGTTTGCTTTCAGGGTTGCGTCCTAAGATGGCAACAGTCGAG
ACAAGACCAAGGTAAAAGGGCCCTTCCATCTACAGCGAGTTTGCTTGTTCTCTGCGTTTATGAAA
ACGAGAGGATCATATTCGATATAACTAAACGAGCTGCACAGAATAACATAAAAATTCCGGAAGTA
TACACTTTAGATCATTCTAGAAAAGAACCCAGATCCCGCAATGAATGACGAACTCCATCACTCGT
GTAATAGCGCAACGCTAATGAAGTGAAATTGATTAAGCTTCAAATTAACCAATGTAAATAGAAAG
TTAGGAAGAATACGTAGCAGTGGAATTGGTGAAAAGTCAGACTAA
Right flanking sequence: Indices 134648 -- 135147
AAACAATACTAAACAAAACATAGTGGATAGAGTCGAGCTTCAGTCGGATCATTCACTCCCGCCAA
CTAAGTGCTCTACGAACCGTATGTGATAGTATCCAATCCGGCACACCAACTCTCCTTTCGTTTTC
GATCCGCGCGCGTTGTATGGTAGAAGGCGGGCTCCAAGGAAATTTGTTGCGAACCGATGTCCAAG
GAAGGCACCGATTATGCTCATGTATGATGCATAAAAATCAAGAATATAATGCGAATCCCGCCCGA
AGTTTTACCAAAAGACCATCCGCCTCAGCGCTTCGCGCCTCTTTTTCACTTCGCCCTCGTGGGTG
GGTGGCCTTGAATACATTTTCTTCCATTGGCTTTCAGAGAGTAAAACCTGCCACACCTGGCAAGT
ACATAAACCCCTTTGCCTTTTACTATTACTAGTGCTTTCCGTTCGCACGCTTTTTTGAAATTAGG
TAAGTGCAAGTAAAGTCCTCTGACTCCCAACTCGGTGGAACAAAG
Found at i:138828 original size:14 final size:15
Alignment explanation
Indices: 138809--138837 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
138799 AAAGTTGCAG
138809 CATCATA-AATTTCA
1 CATCATACAATTTCA
138823 CATCATACAATTTCA
1 CATCATACAATTTCA
138838 TATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (15 bp):
CATCATACAATTTCA
Left flanking sequence: Indices 138309 -- 138808
TCTTTAAAAATTCCTTGTTATACGTGCTTACTGAAACATTATGTTTTTTCTATTTCTGTGAAGTT
AGCATTTACTTCACCTACTGTTTATACATTTCCAAGCGTGGGCGCTAAACTTTGACTAATATTTG
GAAATGATCTGTGTGACCCATTTTTGTTTGCGCTAGCTGCCTTCAGCTCTTTGGCTTCTAGGTTT
CTTATTCCCTGACTTGGATCTCTCTGGGCTTTTGCTTGTGGGACAGAATGACACGAGGGACGCAG
TGATGAACAATCAATCAATCGCCCGATGATTTTAGGGGGATCAAGCCCTACTAAAGTCTCGCGTA
CCAAACTTGAAACAAAAGGCGCGCGCCGAAATCATAGATAAATCAAAATGAATCATCACATATAA
TTTGTAATTATGATACTTGTTCAATTATTCTTTCGAAAGCCAACTTCTTTGAAGGCTGCTTGCAG
CATCATATACAACAACGAATTCCCCCAATTGTTCGAAAGTTGCAG
Right flanking sequence: Indices 138838 -- 139337
TATAAATAAATATTATTAATACCTTTAATAATTATTTGAAAGCCGCTTGCAGCATCATACAATTC
CGTAGTAAAAAGAGCCAAAAGACGAGGCGCTTGGCAATTGGCCGGAGTTCTTCGGAGCAGCCGTC
TTCCTCTGAGTCGTCTACTGCAACCGAGCCTCCTCAAGGCCCCCTTCCTAAATATCGCAGCAGCC
ATTAGACTAATGAGACGCATACTTGTTCAGGCTCTACTCCTTACTTTGTTGTTAGCTTGTTTTCG
AATCAGGAGAATCAGAATCTACACAAGCCTTGCGGGTGAACACAGCCTCCCATTCGCTAAGGGCC
GCCCGCCGCGGCCCGCGGCCACTTCTTGCTCACAACAAATGTAGTTGTAGCTTCTTTGCCAACTA
GATGGAAAAGCTGACCCCACAGCGGCGATGCGCTTCGCCGCGCTTAGCGAAGAAGCCGCTATTGG
TTTTGGCATAAACGAAGCCTTGGTACAAGAAAAAGAGGTAATTTT
Done.