Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_031806
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: 495499
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:110418 original size:13 final size:13
Alignment explanation
Indices: 110400--110425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110390 GCGCCATCGT
110400 CTAACTATATATA
1 CTAACTATATATA
110413 CTAACTATATATA
1 CTAACTATATATA
110426 AGATAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAACTATATATA
Left flanking sequence: Indices 109900 -- 110399
TCCAAGTCCAGCACAGAAGCCGAGTACCTTCTGTTGAGTCATTTCTTTTTGCTTTGCTTATTTAG
AAGAGTAGTCGCAGAGTTCAGTCAAGCCTTAGCAAGGCTCTTTCAATATAAAAAAGGGACAAGGT
TGGCTTTCTAGTAATAAGTCGAGTAAGCGAACTCAAAATGAGCCTTGCTTGACACGCTGACTTGG
AACTATTTAAACACTACCTTTCCTGGAGAGTCAAGTTTTGAAAAAGAAGGTTCCAATGAATCCGA
GGAAAGATGTTCTACCAAAGTGGGTAGATGGAATCATTTGAAAGGTTCGAAGACCTTTCGATTCC
ATTCAGGTTCTTGTTCAAAAGCAAGGATAAAAGAAGAATTTGATAAAGACGGACTAGACCAATGA
AAGAGTAGATAAAGGATGGAATTCAGTGGATGGACAATTCTTGAACTCTACCCACACAATGGTTG
TTTGGACAGTATCCGTCGACGGGCAGAACCCCGGGGCGCCATCGT
Right flanking sequence: Indices 110426 -- 110925
AGATAATGATTGTTAATCACCCAAGGGCCAAGCCTGAGGGCATGAGTCATTGCTTCTTTGTCTTC
CATTCTAAGACAGAAGCAATTTGAACCCATGTCTATAAGTTCTATATCGCCGGAGGGCTTCCAGA
GGGTCTCATTGATCTGACTGACCTTCCTACTCAGTATGGAAGGACTCTTGACTGACTCTGAGACT
GAGTCTTCTGACTTGGATTGGTATACTGGGGTAAATTCTAGCCTATCTATGACGCTTTCAAAAAC
AAAAAAAAGGAAATGAATGGATTCGAGAATCCAATTAAATCTAATGGTTTACGTTATGGAAGAAA
GACATGTATATGTAATATTAGATATTGACTAGTTATATATGAACTAAAGATCTATTTCATTTTAC
CTACTACCGTGTGTGGGTTCAAATAGAAGTCCTCTCATATCGTTGTGGCTGTGAATTTGCTGAAT
AAAGAGATGAAATCAAGAAAAGATGAAAGAATTGAAATAAGAGTT
Found at i:237226 original size:24 final size:24
Alignment explanation
Indices: 237194--237259 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
237184 TGACGTATCA
237194 AAAAGATACAGGATATGATATTTC
1 AAAAGATACAGGATATGATATTTC
*
237218 AAAAGATACAGAATATGATATTTC
1 AAAAGATACAGGATATGATATTTC
*
237242 AGAAGATACAGGATATGA
1 AAAAGATACAGGATATGA
237260 AAAAGAAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (24 bp):
AAAAGATACAGGATATGATATTTC
Left flanking sequence: Indices 236694 -- 237193
GAACACCTTCAATAAAATAAAAAAAATCTTTTTTCGATTCGTTTTTTTTTATTACGACACGATAA
TCAAATCTGGATTCTCGGATTTGTCGAACAAAACACCAATCCACGTTTGAGTTCGGATTGGAATT
CTGATTCAAGTGAACAAAGAATAAGCTTATTTATTTCTAGTTCTAAGGCCCGCAGCTCGAGGGGT
CGGCTCGGTTCTTTCAAATTGTTTCTCATTATTGAGAAAGGGTAACAAAGATAAAATACGAGCTT
GTTTTATAGCAATAGTAATTAATCGTTGTTGTTTCAAGGTCAATCTATTCACCCGTCTAGATAAT
ATTTTTCCTTGTTCACTAATAAATCGACTAATTAAACTCATGTTTCTATAATCAATTCGATCCCC
CGATTGAATCGGGGGCAACCGTCCATGGTTTGTTTGTTTAGTTTATTTCTTATCCCGAAAATCCC
ATTTTTATTCTCAAAAAACTAAAAATCAACCAATATGACGTATCA
Right flanking sequence: Indices 237260 -- 237759
AAAAGAAACTCTCAATTCAATCAATTTCTTTCTTACTTTTCCCGACGCTCTCAAGAACTCTATGA
GTCATTTTATTAAGCCTCATGGGTCACAAATGAAGGAAGAGGATAAAATAGTGCTAGTCAATTTC
TGGTATGACTATTTTAAAGATAAACTAGAAATAATGGGTAGAACTGTATGTGAGTTGACTTCAGA
TGAAATCCCTCCGGAAGATAACTTACTTCAGAGTGATGGTAGAACACGTCGTAATGATGTAAGTA
AATCTGTTTTTACAAAAGTCTTTAAAGATAAAGTTTTCAAATTACTCGAAAAGTCTAAGAAAAAT
GAGCACCCTTCTTCTGGGGCTTTATATCGACTTCAGAAAGAGATCGAATCTCTGACTATGTATTT
CAATGAAGAAAATATCTATTCTAGAAGCCCTGCTCTGATGAAGGATATGATTTTAGAACATCAGC
TTTGTGCTAAGGAATATCTTATGTGTAAGTATAAATTGGATAAAA
Found at i:312375 original size:18 final size:18
Alignment explanation
Indices: 312354--312413 Score: 111
Period size: 18 Copynumber: 3.3 Consensus size: 18
312344 GTCACGATCG
312354 ATATCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
312372 ATATCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
*
312390 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
312408 ATATCG
1 ATATCG
312414 ATATCATCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (18 bp):
ATATCGTCACTAGCATCA
Left flanking sequence: Indices 311854 -- 312353
TCTGTGTAATACTAATCGATAGGGCCTCATTGGTAAGTGCTACAAGATCTCTTGCATTGGAACCC
ATGGTTATGGAACCGAATCCGTTAGTATGGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATA
TGAAAGAGTGAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCACGTAT
TTAATTTATTCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACA
AGAATATTTCGAGTGGAACATCTTTCAGAGAGATGGTTCACTAATAGACCGAAGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATCGGTCTATTTCCGACATCATATCCATAGTTAGCGCA
TTCATCATAGTTAGCAGTTCCAGCTCCGTATCAAGGTCACGATCG
Right flanking sequence: Indices 312414 -- 312913
ATATCATCAACAAGAAAACCTTTAGGCTTGTTATCCAGGAACTTGTTCAGAAATACCGTAATGAA
AGGAACATAGGAGTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTA
TCACTAAAATCCCCCTAGAGGGGGATAAGGCTAAGCGGAGCGAAAAGGGTTTTCCATGAGATGGG
AAATGCAAAGTATTAGTCCCACACGAAGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAA
TACCCTTCTTTCTGCTAAACAGGATGTATTGAACTCATAATTCAATAGATACTTTTTATGAATGT
CAACTAAGTATCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTTTTT
GATAAATGATCACTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGC
GGAGAACTGAACCAAGAATTCTCTTTCTTCATCATCAATCGAATC
Found at i:312418 original size:15 final size:17
Alignment explanation
Indices: 312354--312423 Score: 81
Period size: 18 Copynumber: 4.1 Consensus size: 17
312344 GTCACGATCG
*
312354 ATATCGTCACTAGCATCA
1 ATATCG-CACTATCATCA
*
312372 ATATCGTCACTAGCATCA
1 ATATCG-CACTATCATCA
312390 ATATCGTCACTATCATCA
1 ATATCG-CACTATCATCA
312408 ATATCG-A-TATCATCA
1 ATATCGCACTATCATCA
312423 A
1 A
312424 CAAGAAAACC
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
15 9 0.18
16 1 0.02
18 41 0.80
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.30
Consensus pattern (17 bp):
ATATCGCACTATCATCA
Left flanking sequence: Indices 311854 -- 312353
TCTGTGTAATACTAATCGATAGGGCCTCATTGGTAAGTGCTACAAGATCTCTTGCATTGGAACCC
ATGGTTATGGAACCGAATCCGTTAGTATGGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATA
TGAAAGAGTGAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCACGTAT
TTAATTTATTCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACA
AGAATATTTCGAGTGGAACATCTTTCAGAGAGATGGTTCACTAATAGACCGAAGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATCGGTCTATTTCCGACATCATATCCATAGTTAGCGCA
TTCATCATAGTTAGCAGTTCCAGCTCCGTATCAAGGTCACGATCG
Right flanking sequence: Indices 312424 -- 312923
CAAGAAAACCTTTAGGCTTGTTATCCAGGAACTTGTTCAGAAATACCGTAATGAAAGGAACATAG
GAGTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTATCACTAAAAT
CCCCCTAGAGGGGGATAAGGCTAAGCGGAGCGAAAAGGGTTTTCCATGAGATGGGAAATGCAAAG
TATTAGTCCCACACGAAGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAATACCCTTCTT
TCTGCTAAACAGGATGTATTGAACTCATAATTCAATAGATACTTTTTATGAATGTCAACTAAGTA
TCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTTTTTGATAAATGAT
CACTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGCGGAGAACTGA
ACCAAGAATTCTCTTTCTTCATCATCAATCGAATCACTGTTCGCG
Found at i:330804 original size:18 final size:18
Alignment explanation
Indices: 330781--330817 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
330771 TAGTTTCATT
*
330781 AGCTCCCGAGGTATTATA
1 AGCTCCCGAGCTATTATA
330799 AGCTCCCGAGCTATTATA
1 AGCTCCCGAGCTATTATA
330817 A
1 A
330818 AATAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (18 bp):
AGCTCCCGAGCTATTATA
Left flanking sequence: Indices 330281 -- 330780
GCCTATACGAACTCAATTTATTATTTTGGCATAAAAATGTAGAACCGGCAGAAATGGGTCTTGGG
ATGAAACAAAACCGCAGGTTTCTTTTTTTAGACAAACAATATTTCTTTTATTTTCTTCATCCAAA
GAATAGACTAAAAAATTGATATGATTCAACCTCAGACCCATTTAAATGTAGCGGATAACAGCGGG
GCTCGAGAATTGATGTGTATTCGAATTATAGGGGCTAGTAATCGTCGATATGCTCATATTGGTGA
CGTTATTGTTGCTGTGATCAAAGAAGCAGTACCAAACATGCCCCTAGAAAAATCAGAAGTAGTCA
GGGCTGTAATTGTTCGTACCTGTAAAGAACTTAAACGTGACAGCGGCATGATAATACGATATGAT
GACAATGCTGCAGTTGTGATTGATCAAGAAGGAAATCCAAAAGGAACTCGAATTTTTGGTGCAAT
CCCCCGGGAATTGAGACAATTAAATTTTACTAAAATAGTTTCATT
Right flanking sequence: Indices 330818 -- 331317
AATAAAATGAGATCGTAATATCTTTGAGGTATTTAAAAGAATTAGATTAATTGATTAAGAACTAG
ATTAATTCGTAGATTGTGTCTCACGCATATATCTTGAAAAATTCATATTCATAAACCAATAAAAA
CAAGAAAAACATGTTGATTATATCCAATTTTGAGAAACCAATAATTTTAGTTTATCATGGGTAGA
GACACTATTGCTGAGATAATAACCTCTATACGAAATGCTGATATGGATAGAAAAAGAGTTGTTCG
GATAGCATCTACTAATATTACCGAAAATATTGTTAAAATACTTTTCCGAGAAGGTTTTATCGAAA
ACGTCAGAAAACATCGAGCAAAAAACAACTCTTTTTTGGTTTTAACCCTGCGACATAGAAGGAAT
AGGAAAAGACCCTATAGAAATTTTTTAAATTTAAAACGGATCAGTCGACCCGGTCTACGAATCTA
TTCTAACTCTCAACGAATTCCTAGAATTTTAGGTGGGATGGGGAT
Found at i:332001 original size:15 final size:15
Alignment explanation
Indices: 331981--332011 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
331971 GGCTAATCAG
331981 ACTTACTATCACTAT
1 ACTTACTATCACTAT
331996 ACTTACTATCACTAT
1 ACTTACTATCACTAT
332011 A
1 A
332012 AAGGGCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (15 bp):
ACTTACTATCACTAT
Left flanking sequence: Indices 331481 -- 331980
CTAATGTCGTTTATCCTCCCTTAGTTGATACTTCAAGGAGGCTTGACCTGAAATGAAAGAACAAA
AATGGATCCATGAAGGTTTAATTACTGAATCGCTTCCCAACGGCATGTTCCGAGTTCGGTTAGAT
AATCAAGATCTGATTCTAGGTTATGTTTCAGGAAAGATCCGACGTAGTTTTATACGGATACTCAC
GGGAGATAAAGTAAAAATTGAAGTAAGTCGTTATGATTCAACCAGAGGACGTATAATTTATCGAC
TCCGAAACAAGGATTCGAAAGATTAGGTGGTTTTTAGTCAATACTATTCGAGATAAAAAATTTCA
AGAAACTTATTTTCTACCAATAAAATAGATTCAGAATTAAGATAAGGAATAACAAATATGAAAAT
AAGAGCTTCAGTTCGTAAAATTTGTGAAAAATGTCGACTAATCCGCAGGCGGGGACGCATTATAG
TAATTTGTTCCAACCCGAGACATAAACAAAGACAAGGCTAATCAG
Right flanking sequence: Indices 332012 -- 332511
AAGGGCTCAATGTGCAAATAAAGAATCTTTTTTGGCATGAAATGGATATATCCATATATTTCTGA
CTCATATTTATGAGATGATACAATATGGCAAAAGCTATACCGAGGACTGGTTCGCGTAGGAATGT
ACGTATTGGTTCACGTAAGAGTGCACGTAGAATACCAAAAGGAGTTATTCATGTTCAAGCAAGTT
TCAATAATACCATTGTCACGGTTACAGATGTACGGGGTCGGGTGGTTTCCTGGTCTTCGGCCGGT
ACTTGTGGATTCAAGGGTACTAGAAGAGGGACACCCTTTGCTGCTCAAACTGCAGCAGCAAATGC
TATTCGTACAGTTGTCGATCAAGGTATGCAACGAGCAGAAGTCATGATAAAGGGTCCCGGTCTAG
GAAGAGACGCAGCATTACGAGCTATTCGTAGAAGTGGGATACTATTAACTTTTGTACGGGATGTA
ACCCCTATGCCACATAATGGCTGCAGACCTCCGAAAAAAAGACGT
Found at i:332169 original size:24 final size:24
Alignment explanation
Indices: 332124--332170 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
332114 TACCGAGGAC
* * *
332124 TGGTTCGCGTAGGAATGTACGTAT
1 TGGTTCACGTAAGAATGCACGTAT
*
332148 TGGTTCACGTAAGAGTGCACGTA
1 TGGTTCACGTAAGAATGCACGTA
332171 GAATACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (24 bp):
TGGTTCACGTAAGAATGCACGTAT
Left flanking sequence: Indices 331624 -- 332123
TTCTAGGTTATGTTTCAGGAAAGATCCGACGTAGTTTTATACGGATACTCACGGGAGATAAAGTA
AAAATTGAAGTAAGTCGTTATGATTCAACCAGAGGACGTATAATTTATCGACTCCGAAACAAGGA
TTCGAAAGATTAGGTGGTTTTTAGTCAATACTATTCGAGATAAAAAATTTCAAGAAACTTATTTT
CTACCAATAAAATAGATTCAGAATTAAGATAAGGAATAACAAATATGAAAATAAGAGCTTCAGTT
CGTAAAATTTGTGAAAAATGTCGACTAATCCGCAGGCGGGGACGCATTATAGTAATTTGTTCCAA
CCCGAGACATAAACAAAGACAAGGCTAATCAGACTTACTATCACTATACTTACTATCACTATAAA
GGGCTCAATGTGCAAATAAAGAATCTTTTTTGGCATGAAATGGATATATCCATATATTTCTGACT
CATATTTATGAGATGATACAATATGGCAAAAGCTATACCGAGGAC
Right flanking sequence: Indices 332171 -- 332670
GAATACCAAAAGGAGTTATTCATGTTCAAGCAAGTTTCAATAATACCATTGTCACGGTTACAGAT
GTACGGGGTCGGGTGGTTTCCTGGTCTTCGGCCGGTACTTGTGGATTCAAGGGTACTAGAAGAGG
GACACCCTTTGCTGCTCAAACTGCAGCAGCAAATGCTATTCGTACAGTTGTCGATCAAGGTATGC
AACGAGCAGAAGTCATGATAAAGGGTCCCGGTCTAGGAAGAGACGCAGCATTACGAGCTATTCGT
AGAAGTGGGATACTATTAACTTTTGTACGGGATGTAACCCCTATGCCACATAATGGCTGCAGACC
TCCGAAAAAAAGACGTGTGTAGAAATGAACAATAAATAAATTTCAAAAGAAACAAGAGAAATAAA
TAATTCAATCAAATAAAATAATATTACTATGGTTCGAGAGAAAGTAACAGTATCTACTCGGACAC
TCCAGTGGAAGTGTGTTGAATCAAGAGCAGATAGTAAACGTTTTT
Found at i:350111 original size:24 final size:24
Alignment explanation
Indices: 350079--350144 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
350069 AAACAAGCTA
*
350079 GGGTTATCTCAACTATCTAATGTT
1 GGGTTATCTCCACTATCTAATGTT
350103 GGGTTATCTCCACTATCTAATGTT
1 GGGTTATCTCCACTATCTAATGTT
*
350127 GGATTATCTCCACTATCT
1 GGGTTATCTCCACTATCT
350145 GGGCTGTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (24 bp):
GGGTTATCTCCACTATCTAATGTT
Left flanking sequence: Indices 349579 -- 350078
TCAAAAAGTCCAACAGGGTTAGAACATCATAAAATCCCATTTTTATTCTCAAAAAACTATAAAGA
AATATCATGAACAATATAAGATCTATCTCTGCTAAGAAACATTTAGATGTATTAAAACTAACGGA
GCAGTTTAGTAGTTTGAAGATACAACAGCTAGGTTGGCTGCCATCTTCGTCTAGTTCGGCTTCAT
CGTCTTCTTCTTCTTCGACAAATTCCTGCATGGATTCTCCCGTGTATTCAGTTAGTAAAAGAGTT
TTAGATCGTTTTTATAAGAAAGAAAGTCAAAATTCAGATTTGACAGGACATGTGATTGAAAGAAC
TCGACCCGAGTTTATGAATATACCTACTAGTATATATGATATTGCTACTGCCATGTCTTCTGATT
TCTTTTTAAGACTTCGTTTTCGTTTTTTACCAGGCCAGGATTCTTTTATTACCCAGAATTTGTGT
TTGCCTAAAATGTTGGATAATCTAATTGATTTTAAAAACAAGCTA
Right flanking sequence: Indices 350145 -- 350644
GGGCTGTCTCCACTAGCTGGGCAATCTCCACTAGCTGGTCAATCTCCACTACCATTCTCTCCACT
ATCTAATCATAGTCTAAAAAATCGAATTGCAGAGAAAGCATCTGCGATCTATTCTCGAATTTGGA
TTGAAGCTATTACATATCATAATGGGTATTATGGTCGATTCTTGATTCTTGTTCAATTGGGTCTT
AAGTGTACTGTATGGTATGGTTTTCACCCTGGTGATGCACTAAGCATTCCAGCGGATGCATTATT
GTTTCATCCCATAGATTCATACGATCGTTTTCTATACCAGCCTGAAATTCATGTTCAGCCGGGTT
TTGAAAAACTCACATTAATTGAGAATGATGAGAATATCTTTCCTAAGTTAGCAGAAGCTTTTACG
CGTGAGAAACCGCTTATTGATATCAAGATTCCAAATGCAAGCGGCAGTGTTTGTATGAGCGTCGG
CCTCGGTTTAGCAATAGTGATATTACTATCATTGGGAATTAACCC
Found at i:350156 original size:18 final size:18
Alignment explanation
Indices: 350132--350195 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
350122 ATGTTGGATT
* *
350132 ATCTCCACTATCTGGGCT
1 ATCTCCACTAGCTGGGCA
*
350150 GTCTCCACTAGCTGGGCA
1 ATCTCCACTAGCTGGGCA
*
350168 ATCTCCACTAGCTGGTCA
1 ATCTCCACTAGCTGGGCA
350186 ATCTCCACTA
1 ATCTCCACTA
350196 CCATTCTCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.28
Consensus pattern (18 bp):
ATCTCCACTAGCTGGGCA
Left flanking sequence: Indices 349632 -- 350131
AAACTATAAAGAAATATCATGAACAATATAAGATCTATCTCTGCTAAGAAACATTTAGATGTATT
AAAACTAACGGAGCAGTTTAGTAGTTTGAAGATACAACAGCTAGGTTGGCTGCCATCTTCGTCTA
GTTCGGCTTCATCGTCTTCTTCTTCTTCGACAAATTCCTGCATGGATTCTCCCGTGTATTCAGTT
AGTAAAAGAGTTTTAGATCGTTTTTATAAGAAAGAAAGTCAAAATTCAGATTTGACAGGACATGT
GATTGAAAGAACTCGACCCGAGTTTATGAATATACCTACTAGTATATATGATATTGCTACTGCCA
TGTCTTCTGATTTCTTTTTAAGACTTCGTTTTCGTTTTTTACCAGGCCAGGATTCTTTTATTACC
CAGAATTTGTGTTTGCCTAAAATGTTGGATAATCTAATTGATTTTAAAAACAAGCTAGGGTTATC
TCAACTATCTAATGTTGGGTTATCTCCACTATCTAATGTTGGATT
Right flanking sequence: Indices 350196 -- 350695
CCATTCTCTCCACTATCTAATCATAGTCTAAAAAATCGAATTGCAGAGAAAGCATCTGCGATCTA
TTCTCGAATTTGGATTGAAGCTATTACATATCATAATGGGTATTATGGTCGATTCTTGATTCTTG
TTCAATTGGGTCTTAAGTGTACTGTATGGTATGGTTTTCACCCTGGTGATGCACTAAGCATTCCA
GCGGATGCATTATTGTTTCATCCCATAGATTCATACGATCGTTTTCTATACCAGCCTGAAATTCA
TGTTCAGCCGGGTTTTGAAAAACTCACATTAATTGAGAATGATGAGAATATCTTTCCTAAGTTAG
CAGAAGCTTTTACGCGTGAGAAACCGCTTATTGATATCAAGATTCCAAATGCAAGCGGCAGTGTT
TGTATGAGCGTCGGCCTCGGTTTAGCAATAGTGATATTACTATCATTGGGAATTAACCCAAGCGC
AGATTTAAACGATATTACAGCCTAAAATGATGATTATGATCATAA
Found at i:402597 original size:15 final size:15
Alignment explanation
Indices: 402577--402606 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
402567 ACCAATCTAT
402577 TCTATAGATATATAG
1 TCTATAGATATATAG
402592 TCTATAGATATATAG
1 TCTATAGATATATAG
402607 ATATTTGTAC
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:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
TCTATAGATATATAG
Left flanking sequence: Indices 402077 -- 402576
ATAATGAAACCAACCAGCAAAAAGCATTAACGCTGCAAAAACCAATGCACCGATTGCGGTACAAT
AGAGCTGTAATTCACTAGTTATTCCAGATGCTCGCCAAATCTGAAAAAAACAGAGGTATGACTGG
CATAAAATCCACGATTGGATTCAAAAAAGCATAGGCTTCGGGCAATTTGCCGAAGAAAAAACTAC
TCGAATAAAGGGCAGAATTAATACAGATCAAACTAACGGTATTAAGCATAACAGACATTTTGTTC
TTGGAGATAATTGCATTTTGATTGAGTTTTTGATATTAAGTAAAAAGGAAGAAAGTCAGTAAGGT
AGACAAAAAATCCTTATTTTTCTTTGAATCCACCCAATCAAAAATCCTCCAATTCTCAAAGGAGA
ATAGAAGAAATCATACTTTCATACAATATCTTAATTGAATTCTATGTAATGATCAATAAATTAAG
GTGAATTCTCTATCTATATGTATCAAAATCCCAGTACCAATCTAT
Right flanking sequence: Indices 402607 -- 403106
ATATTTGTACTAGAGTTGACAAACAACCAATACCAATATTATTGTTTCTTGGCGTAGATTAGAAA
TTCAAATGGGGCGTGGCCAAGTGGTAAGGCAACGGGTTTTGGTCCCGCTATTCGGAGGTTCGAAT
CCTTCCGTCCCAGAGCATATCCGTTTTTTATGCTCCATTATTCCCATAGAAAGAAGTAGAGGGGT
GGTAGGAATTAATCCATATTCATTTGAATATCTGTGTCTGTTTGAATCTCATTAAGAAATGATCA
AGTTCCATATCATTATCATATAGAAATATGTGATAGAGCCAATGTTTTTTCTTTGAATCTCGTTT
TATTTTTATTTAGGTATTTTGTGTTTGGCTCTAATTAAAAATGGGGAATCTATGTAACGATTGAG
GCAAGGGGTATTTAGCCTATAAAATGAATTTTATTCACTTTATGACAAGAGTCGATTATTGAAAT
ATTATCCAACCCCATTTTAAACAAAATACATATCAATCATTTAAT
Found at i:440318 original size:15 final size:15
Alignment explanation
Indices: 440298--440340 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 15
440288 TTTTGAGTGA
440298 TATTGCTTAGATTAT
1 TATTGCTTAGATTAT
440313 TATTGCTTATTTAGATTAT
1 TATTGC----TTAGATTAT
440332 TATTGCTTA
1 TATTGCTTA
440341 TAAGGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
15 9 0.38
19 15 0.62
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.56
Consensus pattern (15 bp):
TATTGCTTAGATTAT
Left flanking sequence: Indices 439798 -- 440297
TACCAAAGTGTTTCAAAGGTGGGGTTATCTTGACGTAGGTCTGCCTCTGGCCTAGATTGTTTTAA
GTTAAATGAAGTCTCTATCGTTCGGTTTACAAAATCAAATATGAAACTTCATACACCTTAAAGTT
CATAGGACGAAAAGAGATTTTTTGAGGACCTTATACTCATTATGCCTAGCATTAAATGTACTGGT
ATTCACCCTATCAATATCTCAAATCGACGATGGAGTCTGTTTGGTACCTAAATGGCAAAATCGGA
CCGAATCGTTTGTCAGGCTGTTGTTCCCTCAAAGTTATGGAGTAAGACATCGATTTCTCAATAGG
ATCCATTTTGTGGATTGTATGATGGACTCCCCCGAAAAACATTGGCGCGCGTGTAAACGAGTTGC
TCTACCAACTGAGCTATAGCCCTTAGTGCTTGTGATGGATATTTTAGCATGTATATCATTTGTTG
TCAAGATGAATATTCTATGATCTAACATCCTAAATTTTTGAGTGA
Right flanking sequence: Indices 440341 -- 440840
TAAGGAATATGATATTTATAATCCATCGACGGGATGGGTTCCCTTTAGTTCTTTTGGGGATGATA
AATGACCTACTTAACTCAGTGGTTAGAGTATTGCTTTCATACGGCGGGAGTCATTGGTTCAAATC
CAATAGTAGGTAGAACTTATTAGATACTATTGACTCCGGTATCTAATAAGTTTTTTGCCCCACCC
TCTTCTATTTTTAGAGATTTTGTATTTTTATTTATTTCATTTTTGAATTGCGTTGTATCAGAATT
GGATTCTGCTTGATTGGATTCACTCGGCAGAATCCAATTAAATATTAGGGTTTAGAATTAGAAAC
AGAACTTTTTTCGCCCGGCGGATTATAGTTTCGGGCGCCTGGCCCACTCGGCCTGTGCTGTGACC
GCGACCAGTTTTCTTCACCCCACGGACCAGTACCCATGGCCCACTCCAGACCATGAGATAGGTCA
AGGGGAGCAAGCGCGTTGATGACCAGGGTAGGCCGCCCTTTTAGC
Found at i:440328 original size:19 final size:19
Alignment explanation
Indices: 440304--440341 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
440294 GTGATATTGC
440304 TTAGATTATTATTGCTTAT
1 TTAGATTATTATTGCTTAT
440323 TTAGATTATTATTGCTTAT
1 TTAGATTATTATTGCTTAT
440342 AAGGAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (19 bp):
TTAGATTATTATTGCTTAT
Left flanking sequence: Indices 439804 -- 440303
AGTGTTTCAAAGGTGGGGTTATCTTGACGTAGGTCTGCCTCTGGCCTAGATTGTTTTAAGTTAAA
TGAAGTCTCTATCGTTCGGTTTACAAAATCAAATATGAAACTTCATACACCTTAAAGTTCATAGG
ACGAAAAGAGATTTTTTGAGGACCTTATACTCATTATGCCTAGCATTAAATGTACTGGTATTCAC
CCTATCAATATCTCAAATCGACGATGGAGTCTGTTTGGTACCTAAATGGCAAAATCGGACCGAAT
CGTTTGTCAGGCTGTTGTTCCCTCAAAGTTATGGAGTAAGACATCGATTTCTCAATAGGATCCAT
TTTGTGGATTGTATGATGGACTCCCCCGAAAAACATTGGCGCGCGTGTAAACGAGTTGCTCTACC
AACTGAGCTATAGCCCTTAGTGCTTGTGATGGATATTTTAGCATGTATATCATTTGTTGTCAAGA
TGAATATTCTATGATCTAACATCCTAAATTTTTGAGTGATATTGC
Right flanking sequence: Indices 440342 -- 440841
AAGGAATATGATATTTATAATCCATCGACGGGATGGGTTCCCTTTAGTTCTTTTGGGGATGATAA
ATGACCTACTTAACTCAGTGGTTAGAGTATTGCTTTCATACGGCGGGAGTCATTGGTTCAAATCC
AATAGTAGGTAGAACTTATTAGATACTATTGACTCCGGTATCTAATAAGTTTTTTGCCCCACCCT
CTTCTATTTTTAGAGATTTTGTATTTTTATTTATTTCATTTTTGAATTGCGTTGTATCAGAATTG
GATTCTGCTTGATTGGATTCACTCGGCAGAATCCAATTAAATATTAGGGTTTAGAATTAGAAACA
GAACTTTTTTCGCCCGGCGGATTATAGTTTCGGGCGCCTGGCCCACTCGGCCTGTGCTGTGACCG
CGACCAGTTTTCTTCACCCCACGGACCAGTACCCATGGCCCACTCCAGACCATGAGATAGGTCAA
GGGGAGCAAGCGCGTTGATGACCAGGGTAGGCCGCCCTTTTAGCC
Found at i:457295 original size:22 final size:22
Alignment explanation
Indices: 457267--457310 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
457257 CCCCGCTTTT
457267 AAGGCCTCCTGCACAGGCAAGA
1 AAGGCCTCCTGCACAGGCAAGA
*
457289 AAGGCCTCCTGCATAGGCAAGA
1 AAGGCCTCCTGCACAGGCAAGA
457311 GCAGATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.30, G:0.27, T:0.11
Consensus pattern (22 bp):
AAGGCCTCCTGCACAGGCAAGA
Left flanking sequence: Indices 456767 -- 457266
TCCTCAAGGCGACAGACCATATTCAGTAAGAGGATGGCGGAACCTTCCATTCAAGTCAAGGTGAG
GCAGTTTCTTCTTTACCTAATAAGAACCAATGGTTTAAGAATGGTTGATTCTCCGCACAGATCAA
AAGACCCTGCCGAAGCTTTCAATTGCTGCAGGAAATGGAAGCTTAGATAGAGGCTACGGCACAAG
AAGAAGATCAATTTTGGGGTCTCAACTCCTTAAGTCTTGAATCCGCTTCTTAGGTCCGTGTGAGA
AAGAGCTATTCTCAATATGAATGAGATCGACTAGAGTCTGCTGCTGATCCGCTTTTGCATAGATT
GGCTAGGGCGACCACTATCGGCGTCGTATTCAATCTCTCCCTGTACTAACTCATTGTATGAAACC
CTAGGATCTACACAATCCATTAGTACTGAGCCTTGAGCTCTTCTTCTCCTTATTAAAGTTTTACT
GGGTCTTCTTCTTCCATACTGGACCGGGGAAAACCCCCCGCTTTT
Right flanking sequence: Indices 457311 -- 457810
GCAGATTTTGCCCAACCAAAGGAGAGTAACGGTCTACCTTTCTATCTCATAGAAAGACTGATTCT
TTATATGATTTAGCCCGAAAGAGGCAATTCCTCCTCAGCCGATGGCTACACCCCTTCTATGAGCA
GGGATTTGAACCTCGGATGCAACTAATAAACTACTGAGTTCTTCTGTCAAGGAAAGGGGCTGGGA
GTGACTACTACTAAGTTACCAAAAAGCCTTTCTCGTCGTAGCCCTCTCCCATTGAGAATTGGATT
GATTTGCTTATTGCGGAACCAGCGTTCTCACTTTGCCAACTTTGTTTGAAAAGAGAGATCTATGA
TCCCCCTATTACCATAAAGGAAAGATCGGAAATATAGAATGTCTATGAGCCCTCCGATCCATTGA
TGTGATACTCGGATGAACGTGTGAATGAGGATTGACCGATCGCAAGTTCCACTCATCACTGGACC
CTTGACTTTATGTCGGACCGAAGCGGAGAACAGTGTAATTGTGTA
Found at i:481449 original size:12 final size:12
Alignment explanation
Indices: 481432--481456 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
481422 GTCGGGCTCC
481432 GGATTGCTCTCT
1 GGATTGCTCTCT
481444 GGATTGCTCTCT
1 GGATTGCTCTCT
481456 G
1 G
481457 ATAATGGATC
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:0.08, C:0.24, G:0.28, T:0.40
Consensus pattern (12 bp):
GGATTGCTCTCT
Left flanking sequence: Indices 480932 -- 481431
TAACCATGACATATTTGCTTGCTTGAACATAATTTCTTTCCAAAAGAAAGTAAATGATTAATTCC
ACAAAACAAAATTTAAAAGAATCCAAAAAATGGAAAAATTGGATCTATGTTCAACGGATCACACC
TAGCAAGAAAAAGTATTTTGTTTTGGTTCGACCTGTCATCACATATGAAATAACGGACGGTATAA
CTTTAACAACGCTTTTTCCCCCGGATCTGTTGCAGGAAAGGGATAATGTGAAACTTCAAGTTGCC
AATTATATCCTTTATGGAAATAGTAAACCAATTGGAGGAATTTCTGATACAAATATTCAATTAGT
TCGGACTTGTTTAGTATTGAATTGGGACCAAGACAAAAAAAGTTCTTCTAGTCAAGAAGCCCGCG
CTTCCTTTGTTGAAATAAGGGCAAAGGGTTTGATTCGACATTTCCTAAGAATCGACTTGGTGAAA
TCCATTATTTCATATATCGGAAAAAGGAATGATCTGTCGGGCTCC
Right flanking sequence: Indices 481457 -- 481956
ATAATGGATCAGATTGCACCAATATCAATCCGTTTTCTTCCATTTATTCCAAGGTAAGAATTCAA
CAACCCCTTAATCAAAATCAAAGAACTATTCATACGTTATTGAATAGAAATACGGGATTCCAATC
GTTGATAATTTTGTCATCATCCAATTGTTTTCGAATGGGTCCATTCAATGATGGAAAATATCACA
ATGTGATAAAAGAATCAATTAAAATTACAAAAGATCCTCTAATTCCAATTAATAATTTGCTGGGG
CCTTTAGGAACAGCCTTTCTAATTGCGAATGTTTATTCATTTTACCATTTAATAACTCATAACCA
GATCTTGGTAAATAACTATTTACAACTTGACAATTTCAATTTAAAACAGACTTTTCAAGTAATTA
AATATTATTTAATCGATGAAAATGAGCAAATTTATAACCCCGACCCATGCAGTAACATTATTTTC
AATTTGAATTGGTATTTTCTCCATCCCAATTATTGTCAAGAAACA
Done.