Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 27
Found at i:5563457 original size:181 final size:182
Alignment explanation
Indices: 5563122--5563594 Score: 741
Period size: 181 Copynumber: 2.6 Consensus size: 182
5563112 GATCCAAATT
* * * * **
5563122 AAAAATGTGTCGATCCAAAATGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
5563187 AAACCGGTAAAACGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
5563252 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
*
5563304 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
5563369 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
5563433 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
** *
5563485 AAAAAAATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
5563550 AAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
5563595 TGTAAGTACG
Statistics
Matches: 268, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
181 169 0.63
182 99 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:5563538 original size:20 final size:19
Alignment explanation
Indices: 5563515--5563561 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
5563505 CGATATAACA
5563515 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
5563535 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
5563555 GGTAAAA
1 GGTAAAA
5563562 CGATACCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:5563566 original size:17 final size:19
Alignment explanation
Indices: 5563526--5563566 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5563516 GTAAAAATAT
*
5563526 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
5563546 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
5563563 GATA
1 GATA
5563567 CCAGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:5565997 original size:19 final size:19
Alignment explanation
Indices: 5565973--5566021 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5565963 AATATAGGGT
5565973 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
* *
5565992 TAATTTTGTACACGATTTA
1 TAATTTTGTATAAGATTTA
5566011 TAATTTTGTAT
1 TAATTTTGTAT
5566022 GTGAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5566598 original size:200 final size:200
Alignment explanation
Indices: 5566255--5567217 Score: 1638
Period size: 200 Copynumber: 4.8 Consensus size: 200
5566245 AATTTACAAT
* * *
5566255 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAGAGCGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * * *
5566320 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATATAATCGGTACAAGTATACTGGTTTT
66 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
5566385 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5566450 AATGA
196 AATGA
*
5566455 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
5566520 CAAAACCCAGAAATATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
66 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
5566585 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5566650 AATGA
196 AATGA
* * * *
5566655 ATGGCAAACAGAGTGCAACAATAAAGTTTCGATCCATATATAAAAAGTGTCAATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
5566720 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGATTTT
66 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
5566785 ATGAGAGAATAGGTCTAAATAATGTTTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
5566850 AATGA
196 AATGA
*
5566855 ATGGCAAACAGGGTGAAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
5566920 CAAAACCCATAAGTATAATGTAATAGGTAATGTTTTCAATCTAACCGGTACAAGTATACCGGTTT
66 CAAAACCCATAAGTATAATGTAATAGGTAAT-TTTTCAATCTAACCGGTACAAGTATACCGGTTT
* * *
5566985 TATGAGAGAATAGGTCTAAATAATATGTCGACACTTTTGTAGTTTGTGTTGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
*
5567050 GATTGA
195 GAATGA
* * *
5567056 ATGGCAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAAAGTGTCAATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
5567121 CTAAACCCATAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
5567186 ATGAGAGAATAGGTCTAAATAATGTATCGACA
131 ATGAGAGAATAGGTCTAAATAATGTATCGACA
5567218 TTGTTTAATG
Statistics
Matches: 719, Mismatches: 43, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
200 532 0.74
201 187 0.26
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:5568740 original size:12 final size:12
Alignment explanation
Indices: 5568718--5568751 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5568708 CAAGCGGTCA
*
5568718 ATGAAGATGAAG
1 ATGACGATGAAG
*
5568730 CTGACGATGAAG
1 ATGACGATGAAG
5568742 ATGACGATGA
1 ATGACGATGA
5568752 TGATCCAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.32, T:0.18
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:5570260 original size:120 final size:120
Alignment explanation
Indices: 5570047--5570293 Score: 422
Period size: 120 Copynumber: 2.1 Consensus size: 120
5570037 ACATCGGAAC
*
5570047 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCTGTATAAATATACCGATTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGC
* *
5570112 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTGTTAATATTGTGTCGGTACTTTATGT
* * * *
5570167 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGC
*
5570232 GAATAGGTCTACAACCTATGTCGACACTTGTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTGTTAATATTGTGTCGGTACTTTATGT
5570287 CCAGAAT
1 CCAGAAT
5570294 GGAAGAAAAA
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTGTTAATATTGTGTCGGTACTTTATGT
Found at i:5570528 original size:303 final size:303
Alignment explanation
Indices: 5569981--5570761 Score: 1472
Period size: 303 Copynumber: 2.6 Consensus size: 303
5569971 TTTAATATTG
*
5569981 TGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
1 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
* *
5570046 CCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCTGTATAAATATACCGATTTTATGAG
66 CCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
5570111 CGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTA
131 CGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTA
5570176 TAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTC
196 TAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTC
5570241 TACAACCTATGTCGACACTTGTTAATATTGTGTCGGTACTTTA
261 TACAACCTATGTCGACACTTGTTAATATTGTGTCGGTACTTTA
*
5570284 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCAACATTTACACATCGGAA
1 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
5570349 CCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
66 CCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
*
5570414 CGAATATGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTA
131 CGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTA
5570479 TAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTC
196 TAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTC
*
5570544 TACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTA
261 TACAACCTATGTCGACACTTGTTAATATTGTGTCGGTACTTTA
5570587 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
1 TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
* *
5570652 CCCAGAATTATAATGTAATAGATAATTTTGTAATATAATCGGTATAAATATACCGGCTTTATGAG
66 CCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
* *
5570717 CGAATAGGTCTACAACCTATATCGACATTTTTTAATATTGTGTCG
131 CGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCG
5570762 CTAATTTTAA
Statistics
Matches: 466, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
303 466 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (303 bp):
TGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAA
CCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAG
CGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATTA
TAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTC
TACAACCTATGTCGACACTTGTTAATATTGTGTCGGTACTTTA
Found at i:5570563 original size:120 final size:120
Alignment explanation
Indices: 5570350--5570596 Score: 440
Period size: 120 Copynumber: 2.1 Consensus size: 120
5570340 ACATCGGAAC
5570350 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
* *
5570415 GAATATGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * *
5570470 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
5570535 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
5570590 CCAGAAT
1 CCAGAAT
5570597 GGAAGAAAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:5573517 original size:23 final size:23
Alignment explanation
Indices: 5573486--5573558 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
5573476 ATAGGTAAAA
*
5573486 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
5573509 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
5573532 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
5573555 ATAT
1 ATAT
5573559 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5574007 original size:23 final size:23
Alignment explanation
Indices: 5573976--5574048 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
5573966 ATAGGTAAAA
* *
5573976 ATATGATGTAATAGATAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
5573999 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
5574022 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
5574045 ATAT
1 ATAT
5574049 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5574224 original size:490 final size:489
Alignment explanation
Indices: 5573300--5574934 Score: 2987
Period size: 490 Copynumber: 3.4 Consensus size: 489
5573290 GACCCAAATT
* * *
5573300 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTTTGTAATTGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
5573365 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
66 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
*
5573430 AAAAGTATCGATCCTTTTTATAAAATGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
131 AAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
5573495 AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
196 AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
*
5573560 GTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAA
261 GTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAA
*
5573625 GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
326 GGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
*
5573690 TTACGTTACGGTATATATTATTATTAAATTAAAAATAATAAACATATATATTACATATTTATTAT
391 TTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
*
5573755 TATCTTTGGTTAATATTGTTAAATTTAAAATCTA
456 TATCTTTGGTTAATATTGTTAAATTTAAATTCTA
* *
5573789 AATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
5573854 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAA
66 ATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAA
*
5573919 AAAAAGTATCGATCCTTTTTATAAAAAGTATGGACTCTTTCAATATAATAGGTAAAAATATGATG
130 AAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATG
*
5573984 TAATAGATAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATAT
195 TAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATAT
5574049 TGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTA
260 TGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTA
*
5574114 AGGTTATCTTTTGAGTGAGCTTTAAGATATCAATTTAGTAATTATAGGCGTCTAATGATTTATTT
325 AGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATAGGCGTCTAATGATTTATTT
*
5574179 TTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTA
390 TTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTA
5574244 TTATCTTTGGTTAATATTGTTAAATTTAAATTCTA
455 TTATCTTTGGTTAATATTGTTAAATTTAAATTCTA
5574279 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
5574344 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAA
66 ATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAA
5574409 AAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATG
130 AAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATG
* *
5574474 TAATAGGTAGCGCTTATATAATGTAATAGGTAGTGTTTATATAATGTAATAGGTAGTGCTGATAT
195 TAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATAT
*
5574539 TGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCATTGTGGAAAACATTAATTTA
260 TGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTA
* **
5574604 AGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTT
325 AGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATAGGCGTCTAATGATTTATTT
* *
5574669 TTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTA
390 TTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTA
*
5574734 TTATCTTTGGTTAATATTGTTAAATTTAAATTCGA
455 TTATCTTTGGTTAATATTGTTAAATTTAAATTCTA
5574769 AATATTATTTTATAAAA-AT-----CAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
5574828 ATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAATTGAAACATAAATTACATAACTTTAAA
66 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
5574892 AAAAGTATCGATCCTTTTTATAAAAAGGTATGGACACTTTCAA
131 AAAAGTATCGATCCTTTTTATAAAAA-GTATGGACACTTTCAA
5574935 CATATTATAA
Statistics
Matches: 1117, Mismatches: 27, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
482 59 0.05
483 16 0.01
484 71 0.06
489 95 0.09
490 876 0.78
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (489 bp):
AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
AAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
GTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTAATTTAA
GGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
TTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
TATCTTTGGTTAATATTGTTAAATTTAAATTCTA
Found at i:5574497 original size:23 final size:23
Alignment explanation
Indices: 5574466--5574538 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
5574456 ATAGGTAAAA
* *
5574466 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5574489 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGTGCTT
*
5574512 ATATAATGTAATAGGTAGTGCTG
1 ATATAATGTAATAGGTAGTGCTT
5574535 ATAT
1 ATAT
5574539 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5575078 original size:23 final size:23
Alignment explanation
Indices: 5575008--5575066 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
5574998 AAATAGGTCA
5575008 ATATAAGCGCTACATATTACATT
1 ATATAAGCGCTACATATTACATT
5575031 ATATAAGCGCTACATATTACATT
1 ATATAAGCGCTACATATTACATT
5575054 ATATAAGCGCTAC
1 ATATAAGCGCTAC
5575067 CTAATATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (23 bp):
ATATAAGCGCTACATATTACATT
Found at i:5575639 original size:5 final size:5
Alignment explanation
Indices: 5575631--5576358 Score: 1440
Period size: 5 Copynumber: 145.8 Consensus size: 5
5575621 ATCGAAAATA
*
5575631 TATTA TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5575681 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5575731 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5575781 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5575831 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5575881 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5575931 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5575981 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5576031 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5576081 TA-TG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5576130 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5576180 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5576230 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5576280 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
5576330 TATTG TATTG TATTG TATTG TATTG TATT
1 TATTG TATTG TATTG TATTG TATTG TATT
5576359 ATTTTAAGTT
Statistics
Matches: 721, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
4 4 0.01
5 717 0.99
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TATTG
Found at i:5577708 original size:16 final size:16
Alignment explanation
Indices: 5577689--5577722 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5577679 CAATATACGA
5577689 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
5577705 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
5577721 AT
1 AT
5577723 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:5577795 original size:16 final size:18
Alignment explanation
Indices: 5577763--5577796 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5577753 TATTAATGTA
5577763 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
5577781 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
5577797 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:5578470 original size:130 final size:130
Alignment explanation
Indices: 5578266--5578513 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
5578256 AATTTTCTTC
* *
5578266 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** * *
5578331 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATCAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
5578396 TAATTAGGTGGTGACATGTGTCACCAATGACACGTATCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
5578461 CCTAATTAAATGATTAATTTATCAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATCAAATTCTATTTAATTTAGGACCAAATTGAT
5578514 TATATAAATG
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATCAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:5578950 original size:35 final size:35
Alignment explanation
Indices: 5578900--5578975 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
5578890 AATATGACAT
* *
5578900 AATTGAATTATTTTGG-AATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGA-GGTTTAGAATGA
5578935 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
5578970 AATTGA
1 AATTGA
5578976 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTGAGGTTTAGAATGA
Found at i:5580039 original size:22 final size:22
Alignment explanation
Indices: 5580014--5580077 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
5580004 ATATTTATTT
*
5580014 ATATTTTTAATAATATAATATA
1 ATATTTTTAATATTATAATATA
*
5580036 ATATTTTTAATATTATAATATT
1 ATATTTTTAATATTATAATATA
*
5580058 ATATTTTTTATATTATAATA
1 ATATTTTTAATATTATAATA
5580078 ATATTCAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTTTAATATTATAATATA
Found at i:5580381 original size:21 final size:22
Alignment explanation
Indices: 5580339--5580378 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5580329 ATATAATTTA
*
5580339 TAATATTTTTATTTCATAAACT
1 TAATATTTTTATTTAATAAACT
5580361 TAATA-TTTTA-TTAATAAA
1 TAATATTTTTATTTAATAAA
5580379 ACTATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATATTTTTATTTAATAAACT
Found at i:5580696 original size:20 final size:20
Alignment explanation
Indices: 5580672--5580736 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
5580662 GCGAATTTGT
*
5580672 AATTCGCGACGCTAATTCCC
1 AATTCGCGACGCTAATTCCA
* ** *
5580692 TATTCATGGCGCTAATTCCA
1 AATTCGCGACGCTAATTCCA
*
5580712 AATTCGCGACGCTAATTCCG
1 AATTCGCGACGCTAATTCCA
5580732 AATTC
1 AATTC
5580737 ACAATTCGCG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (20 bp):
AATTCGCGACGCTAATTCCA
Found at i:5580762 original size:27 final size:27
Alignment explanation
Indices: 5580703--5580767 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
5580693 ATTCATGGCG
*
5580703 CTAATTC-CAAATTCGCGACGCTAATTC
1 CTAATTCAC-AATTCGCGACGCGAATTC
* *
5580730 CGAATTCACAATTCGCGACGCGAATTT
1 CTAATTCACAATTCGCGACGCGAATTC
5580757 CTAATTCACAA
1 CTAATTCACAA
5580768 CACGAATCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (27 bp):
CTAATTCACAATTCGCGACGCGAATTC
Found at i:5581315 original size:20 final size:20
Alignment explanation
Indices: 5581292--5581343 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5581282 TTAGAAATTC
5581292 GCGTCGCGAATTCGGGATTA
1 GCGTCGCGAATTCGGGATTA
*
5581312 GCGTCGTGAATTCGGGATTA
1 GCGTCGCGAATTCGGGATTA
*
5581332 GCGTAGCGAATT
1 GCGTCGCGAATT
5581344 GTGAGTTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.35, T:0.27
Consensus pattern (20 bp):
GCGTCGCGAATTCGGGATTA
Found at i:5581461 original size:19 final size:19
Alignment explanation
Indices: 5581419--5581469 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5581409 TGGAACCTGT
* * *
5581419 GTTGCGAAATTGGAGTTCGC
1 GTTGC-AAATTTGAGATCGA
5581439 GTTGCAAATTTGAGATCGA
1 GTTGCAAATTTGAGATCGA
*
5581458 GTTGAAAATTTG
1 GTTGCAAATTTG
5581470 TTGGTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.33
Consensus pattern (19 bp):
GTTGCAAATTTGAGATCGA
Found at i:5584816 original size:64 final size:64
Alignment explanation
Indices: 5584713--5584832 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
5584703 GGATGTTACA
* * *
5584713 GTATCGATGCACATAAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGT
1 GTATCGATGCACATAAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGT
* *
5584777 GTATCGATGCACA-AGTAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATG
1 GTATCGATGCACATA-AAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATG
5584833 GGATTTATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
63 1 0.02
64 49 0.98
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (64 bp):
GTATCGATGCACATAAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGT
Found at i:5584850 original size:64 final size:64
Alignment explanation
Indices: 5584713--5584873 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
5584703 GGATGTTACA
* * * * * *
5584713 GTATCGATGCACATAAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGT
1 GTATCGATGCAAAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGT
* ** *
5584777 GTATCGATGCACAAG-TAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGGGATTTA-
1 GTATCGATGCA-AAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-TCAG
5584840 T
64 T
*
5584841 GTA-CTGATGCATAGATAGTGCATCGATGCACCC
1 GTATC-GATGCAAAGATAGTGCATCGATGCACCC
5584874 GTCAAGGGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.04
64 76 0.93
65 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (64 bp):
GTATCGATGCAAAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGT
Found at i:5591503 original size:20 final size:20
Alignment explanation
Indices: 5591458--5591503 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5591448 CGGTGGAGCT
**
5591458 TGGTCGACGGCAAAAAGTGA
1 TGGTCGACGGCAAAAAACGA
*
5591478 TAGTCGACGGCAAAAAACGA
1 TGGTCGACGGCAAAAAACGA
5591498 TGGTCG
1 TGGTCG
5591504 GCGTGGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.33, T:0.15
Consensus pattern (20 bp):
TGGTCGACGGCAAAAAACGA
Found at i:5592218 original size:22 final size:23
Alignment explanation
Indices: 5592193--5592236 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
5592183 AATATATTTT
*
5592193 ATTAAAATAATT-TTTTTTATAA
1 ATTAAAATAATTATTTATTATAA
* *
5592215 ATTACATTAATTATTTATTATA
1 ATTAAAATAATTATTTATTATA
5592237 TTAAGAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAAAATAATTATTTATTATAA
Found at i:5592276 original size:16 final size:17
Alignment explanation
Indices: 5592220--5592269 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5592210 TATAAATTAC
5592220 ATTAATTAT-TTATTA-T
1 ATTAATTATATTA-TACT
**
5592236 ATTAAGAATATTATACT
1 ATTAATTATATTATACT
5592253 ATTAATTATATTA-ACT
1 ATTAATTATATTATACT
5592269 A
1 A
5592270 CTTATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTAATTATATTATACT
Found at i:5592461 original size:23 final size:23
Alignment explanation
Indices: 5592434--5592478 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5592424 AAAATAAAAA
*
5592434 TATAATATCATATATTACTATAG
1 TATAATATAATATATTACTATAG
* *
5592457 TATAATTTAATATATTATTATA
1 TATAATATAATATATTACTATA
5592479 ACATTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TATAATATAATATATTACTATAG
Found at i:5592498 original size:22 final size:22
Alignment explanation
Indices: 5592473--5592515 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5592463 TTAATATATT
5592473 ATTATAACATTAAAAATATTAC
1 ATTATAACATTAAAAATATTAC
** *
5592495 ATTATATTATTAAAACTATTA
1 ATTATAACATTAAAAATATTA
5592516 ATAAATGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTATAACATTAAAAATATTAC
Found at i:5594669 original size:47 final size:47
Alignment explanation
Indices: 5594591--5594680 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
5594581 AAGTTTTGAA
*
5594591 GAAGAAGAAGAAGTTGCAAGAAAAAGAAGAAAAGAAGCTACCACGAG
1 GAAGAAGAAGAAGCTGCAAGAAAAAGAAGAAAAGAAGCTACCACGAG
* * * *
5594638 GAAGAAGAAGAAGCTGGAAGAAGATGGAGAAAAGAAGCTACCA
1 GAAGAAGAAGAAGCTGCAAGAAAAAGAAGAAAAGAAGCTACCA
5594681 TGTCAGAGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.53, C:0.10, G:0.30, T:0.07
Consensus pattern (47 bp):
GAAGAAGAAGAAGCTGCAAGAAAAAGAAGAAAAGAAGCTACCACGAG
Found at i:5597486 original size:16 final size:16
Alignment explanation
Indices: 5597461--5597518 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
5597451 CCGAATTTAA
*
5597461 CCGAACCGAAAGTAAC
1 CCGAACCGAAAGCAAC
*
5597477 CCGCACCGAAAGCAAC
1 CCGAACCGAAAGCAAC
*
5597493 CCAAACCGAAAGCAA-
1 CCGAACCGAAAGCAAC
5597508 CCGAACCGAAA
1 CCGAACCGAAA
5597519 ATAACCTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 10 0.27
16 27 0.73
ACGTcount: A:0.45, C:0.36, G:0.17, T:0.02
Consensus pattern (16 bp):
CCGAACCGAAAGCAAC
Found at i:5600031 original size:40 final size:40
Alignment explanation
Indices: 5599975--5600097 Score: 158
Period size: 40 Copynumber: 3.1 Consensus size: 40
5599965 TATCAGAGCC
* *
5599975 ATGCGAGGAGACGAATAGACCGGTGGCCAGAATATCGACG
1 ATGCGAGGAGATGAATAGACTGGTGGCCAGAATATCGACG
** *
5600015 ATGCGAGGAGATGAATACTCTGGTGACCAGAATATCGACG
1 ATGCGAGGAGATGAATAGACTGGTGGCCAGAATATCGACG
* * *
5600055 ATGCGAGGAGATGAAT-GCACTGGCGGCCATAATATGGACG
1 ATGCGAGGAGATGAATAG-ACTGGTGGCCAGAATATCGACG
5600095 ATG
1 ATG
5600098 TGAAATATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.32, C:0.18, G:0.33, T:0.17
Consensus pattern (40 bp):
ATGCGAGGAGATGAATAGACTGGTGGCCAGAATATCGACG
Found at i:5607763 original size:21 final size:22
Alignment explanation
Indices: 5607721--5607763 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
5607711 AATAAAAAAC
* **
5607721 AAAAAAAATAAATATACGATAT
1 AAAAAAAATAAATAAAAAATAT
5607743 AAAAAAAAT-AATAAAAAATAT
1 AAAAAAAATAAATAAAAAATAT
5607764 CGACTATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAAAATAAATAAAAAATAT
Found at i:5608625 original size:6 final size:6
Alignment explanation
Indices: 5608616--5608643 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5608606 CACGGATACG
5608616 GATATA GATATA GATATA GATATA GATA
1 GATATA GATATA GATATA GATATA GATA
5608644 CGAATACGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (6 bp):
GATATA
Found at i:5608655 original size:18 final size:20
Alignment explanation
Indices: 5608611--5608655 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
5608601 TGTTACACGG
5608611 ATACGGATATAGATATAGAT
1 ATACGGATATAGATATAGAT
*
5608631 ATA--GATATAGATA-CGA-
1 ATACGGATATAGATATAGAT
5608647 ATACGGATA
1 ATACGGATA
5608656 CGGATACGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.14
17 2 0.09
18 14 0.64
20 3 0.14
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (20 bp):
ATACGGATATAGATATAGAT
Found at i:5617275 original size:22 final size:23
Alignment explanation
Indices: 5617233--5617278 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
5617223 AATGTAGACC
*
5617233 TTAATTTGTTGTTTTAATTAAAA
1 TTAATTTGTTATTTTAATTAAAA
*
5617256 TTAATTT-TTATTTTATTTAAAA
1 TTAATTTGTTATTTTAATTAAAA
5617278 T
1 T
5617279 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TTAATTTGTTATTTTAATTAAAA
Found at i:5618290 original size:72 final size:72
Alignment explanation
Indices: 5618214--5618357 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
5618204 AATGCTTGCG
*
5618214 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAACTAGATATCATGCGGTTA
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAACTAGATATCATGAGGTTA
5618279 GGTTTAT
66 GGTTTAT
*
5618286 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAATTAGATATCATGAGGTTA
1 AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAACTAGATATCATGAGGTTA
5618351 GGTTTAT
66 GGTTTAT
5618358 TTTTCGAACA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.35
Consensus pattern (72 bp):
AACTAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAACTAGATATCATGAGGTTA
GGTTTAT
Found at i:5618297 original size:27 final size:27
Alignment explanation
Indices: 5618259--5618312 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5618249 CAAGCATGCG
5618259 AACTAGATATCATGCGGTTAGGTTTAT
1 AACTAGATATCATGCGGTTAGGTTTAT
5618286 AACTAGATATCATGCGGTTAGGTTTAT
1 AACTAGATATCATGCGGTTAGGTTTAT
5618313 TTTTCGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (27 bp):
AACTAGATATCATGCGGTTAGGTTTAT
Found at i:5618339 original size:45 final size:45
Alignment explanation
Indices: 5618289--5618407 Score: 211
Period size: 45 Copynumber: 2.6 Consensus size: 45
5618279 GGTTTATAAC
5618289 TAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAAT
1 TAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAAT
*
5618334 TAGATATCATGAGGTTAGGTTTATTTTTCGAACAAGCATGCGAAT
1 TAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAAT
*
5618379 TAGATATCATGCGGTTAGGATTTCTTTTT
1 TAGATATCATGCGGTTAGG-TTTATTTTT
5618408 GTGAATAACA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 62 0.89
46 8 0.11
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (45 bp):
TAGATATCATGCGGTTAGGTTTATTTTTCGAACAAGCATGCGAAT
Found at i:5624540 original size:8 final size:8
Alignment explanation
Indices: 5624527--5624554 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5624517 AGATCCTCCC
5624527 ATATGTAT
1 ATATGTAT
5624535 ATATGTAT
1 ATATGTAT
5624543 ATATGTAT
1 ATATGTAT
5624551 ATAT
1 ATAT
5624555 ATCTTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:5626689 original size:198 final size:202
Alignment explanation
Indices: 5626348--5626749 Score: 776
Period size: 198 Copynumber: 2.0 Consensus size: 202
5626338 AATCGGGGGC
5626348 AATTTTGGTCTCACCAGAAGGAGAACATTATCCTTTTACCAGTCGGATTAATTTTGATTGTACAA
1 AATTTTGGTCTCACCAGAAGGAGAACATTATCCTTTTACCAGTCGGATTAATTTTGATTGTACAA
5626413 ACAATATGGCCGAATATGAAGCTTGTGTTATGGGTCTTAGAGCTGTCGTTGATCGTAAAATAGAA
66 ACAATATGGCCGAATATGAAGCTTGTGTTATGGGTCTTAGAGCTGTCGTTGATCGTAAAATAGAA
5626478 ATGCTCAAAGTGTATGGGGATTCAGCTTTGGTAATTTACCAGCTCATAGGAGAAT-GGAGACAAA
131 ATGCTCAAAGTGTATGGGGATTCAGCTTTGGTAATTTACCAGCTCATAGGAGAATGGGAGACAAA
5626542 AGATCCT
196 AGATCCT
5626549 AATTTTGGTCTCACCAGAAGGAGAACA-TATCC-TTTACCAGTCGGATTAATTTTGATTGTACAA
1 AATTTTGGTCTCACCAGAAGGAGAACATTATCCTTTTACCAGTCGGATTAATTTTGATTGTACAA
5626612 AC-ATATGGCCGAATATGAAGCTTGTGTTATGGGTCTTAGAGCTGTCGTTGATCGTAAAATAGAA
66 ACAATATGGCCGAATATGAAGCTTGTGTTATGGGTCTTAGAGCTGTCGTTGATCGTAAAATAGAA
5626676 ATGCTCAAAGTGTATGGGGATTCAGCTTTGGTAATTTACCAGCTCATAGGAGAATGGGAGACAAA
131 ATGCTCAAAGTGTATGGGGATTCAGCTTTGGTAATTTACCAGCTCATAGGAGAATGGGAGACAAA
5626741 AGATCCT
196 AGATCCT
5626748 AA
1 AA
5626750 ACTTGTAGAA
Statistics
Matches: 200, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
198 117 0.58
199 51 0.25
200 5 0.03
201 27 0.14
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (202 bp):
AATTTTGGTCTCACCAGAAGGAGAACATTATCCTTTTACCAGTCGGATTAATTTTGATTGTACAA
ACAATATGGCCGAATATGAAGCTTGTGTTATGGGTCTTAGAGCTGTCGTTGATCGTAAAATAGAA
ATGCTCAAAGTGTATGGGGATTCAGCTTTGGTAATTTACCAGCTCATAGGAGAATGGGAGACAAA
AGATCCT
Found at i:5628228 original size:12 final size:12
Alignment explanation
Indices: 5628211--5628384 Score: 68
Period size: 12 Copynumber: 14.8 Consensus size: 12
5628201 ATTTCTCCTG
5628211 AAAAAGAAATGA
1 AAAAAGAAATGA
5628223 AAAAAGAAA--A
1 AAAAAGAAATGA
* *
5628233 AGAGAA-AAATAA
1 A-AAAAGAAATGA
5628245 AAAAAG-AA-GA
1 AAAAAGAAATGA
*
5628255 AAAGGAAAAAATGA
1 AAA--AAGAAATGA
5628269 AAAAA-AAATG-
1 AAAAAGAAATGA
5628279 AAAAA-AAATGA
1 AAAAAGAAATGA
5628290 AAAAA-AATGATGA
1 AAAAAGAA--ATGA
*
5628303 AAAAA-ATGATGA
1 AAAAAGA-AATGA
* *
5628315 AAAATGAAAAGA
1 AAAAAGAAATGA
*
5628327 AAAAA-ATAT-A
1 AAAAAGAAATGA
* * *
5628337 AAATATAAA-AA
1 AAAAAGAAATGA
5628348 AAAAAGATAAAATGA
1 AAAAAG---AAATGA
*
5628363 AAAAAGAAAAGAA
1 AAAAAGAAATG-A
5628376 AAAAAGAAA
1 AAAAAGAAA
5628385 AAGAAATAAA
Statistics
Matches: 125, Mismatches: 17, Indels: 39
0.69 0.09 0.22
Matches are distributed among these distances:
10 24 0.19
11 29 0.23
12 34 0.27
13 23 0.18
14 8 0.06
15 7 0.06
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (12 bp):
AAAAAGAAATGA
Found at i:5628246 original size:14 final size:14
Alignment explanation
Indices: 5628223--5628396 Score: 76
Period size: 14 Copynumber: 12.0 Consensus size: 14
5628213 AAAGAAATGA
*
5628223 AAAAAGAAAAAGAG
1 AAAAAGAAAAAAAG
*
5628237 AAAAATAAAAAAAG
1 AAAAAGAAAAAAAG
*
5628251 AAGAAAAGGAAAAAATG
1 -A-AAAA-GAAAAAAAG
5628268 AAAAA-AAAATGAAA-
1 AAAAAGAAAA--AAAG
5628282 AAAAATGAAAAAAA-
1 AAAAA-GAAAAAAAG
** *
5628296 ATGATGAAAAAAATG
1 AAAAAGAAAAAAA-G
**
5628311 ATGAAAA-ATGAAAAG
1 A--AAAAGAAAAAAAG
*
5628326 AAAAA-AATATAAAAT
1 AAAAAGAA-A-AAAAG
*
5628341 ATAAA-AAAAAAAG
1 AAAAAGAAAAAAAG
5628354 ATAAAATG-AAAAAAG
1 A-AAAA-GAAAAAAAG
5628369 -AAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
5628382 AAAAAGAAATAAAAG
1 AAAAAGAAA-AAAAG
5628397 GGGGGTTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 37
0.69 0.11 0.21
Matches are distributed among these distances:
12 1 0.01
13 33 0.27
14 34 0.28
15 32 0.26
16 14 0.11
17 8 0.07
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:5628258 original size:8 final size:7
Alignment explanation
Indices: 5628221--5628390 Score: 68
Period size: 7 Copynumber: 23.6 Consensus size: 7
5628211 AAAAAGAAAT
5628221 GAAAAAA
1 GAAAAAA
5628228 GAAAAAGA
1 GAAAAA-A
5628236 GAAAAATA
1 GAAAAA-A
5628244 -AAAAAA
1 GAAAAAA
5628250 GAAGAAAA
1 GAA-AAAA
5628258 GGAAAAAA
1 -GAAAAAA
5628266 TGAAAAAA
1 -GAAAAAA
5628274 -AAATGAAA
1 GAAA--AAA
*
5628282 -AAAAAT
1 GAAAAAA
5628288 GAAAAAA
1 GAAAAAA
** *
5628295 -AATGAT
1 GAAAAAA
5628301 GAAAAAAA
1 G-AAAAAA
5628309 TGATGAAAAA
1 -GA--AAAAA
*
5628319 TGAAAAGA
1 -GAAAAAA
5628327 -AAAAAA
1 GAAAAAA
* *
5628333 TATAAAA
1 GAAAAAA
* *
5628340 TATAAAA
1 GAAAAAA
5628347 -AAAAAA
1 GAAAAAA
*
5628353 GATAAAAT
1 GA-AAAAA
5628361 GAAAAAA
1 GAAAAAA
*
5628368 GAAAAGA
1 GAAAAAA
5628375 -AAAAAA
1 GAAAAAA
5628381 G-AAAAA
1 GAAAAAA
5628387 GAAA
1 GAAA
5628391 TAAAAGGGGG
Statistics
Matches: 128, Mismatches: 18, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
6 30 0.23
7 43 0.34
8 43 0.34
9 4 0.03
10 8 0.06
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (7 bp):
GAAAAAA
Found at i:5628273 original size:10 final size:10
Alignment explanation
Indices: 5628260--5628329 Score: 86
Period size: 10 Copynumber: 6.6 Consensus size: 10
5628250 GAAGAAAAGG
5628260 AAAAAATGAAA
1 AAAAAATG-AA
5628271 AAAAAATGAA
1 AAAAAATGAA
5628281 AAAAAATGAA
1 AAAAAATGAA
5628291 AAAAAATGATGA
1 AAAAAATGA--A
*
5628303 AAAAAATGAT
1 AAAAAATGAA
*
5628313 GAAAAATGAA
1 AAAAAATGAA
5628323 AAGAAAA
1 AA-AAAA
5628330 AAATATAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
10 30 0.58
11 12 0.23
12 10 0.19
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:5628283 original size:35 final size:34
Alignment explanation
Indices: 5628237--5628337 Score: 89
Period size: 35 Copynumber: 2.8 Consensus size: 34
5628227 AGAAAAAGAG
*
5628237 AAAAAT-AAAAAAAGAAGAAAAGGAAAA-AATGAAAA
1 AAAAATGAAAAAAA-ATGAAAA--AAAATAATGAAAA
*
5628272 AAAAATGAAAAAAAATGAAAAAAAATGATGAAAA
1 AAAAATGAAAAAAAATGAAAAAAAATAATGAAAA
* *
5628306 AAATGATGAAAAATGAAAAGAAAAAAATATAA
1 AAA-AATGAAAAA--AAATGAAAAAAA-ATAA
5628338 AATATAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
33 4 0.07
34 10 0.18
35 20 0.36
36 7 0.13
37 11 0.20
38 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (34 bp):
AAAAATGAAAAAAAATGAAAAAAAATAATGAAAA
Found at i:5628285 original size:20 final size:20
Alignment explanation
Indices: 5628260--5628395 Score: 87
Period size: 21 Copynumber: 7.2 Consensus size: 20
5628250 GAAGAAAAGG
5628260 AAAAAATGAAAAAAAAATGAA
1 AAAAAATGAAAAAAAAATG-A
5628281 AAAAAATGAAAAAAAATGATGA
1 AAAAAATGAAAAAAAA--ATGA
**
5628303 AAAAAATG-ATGAAAAATG-
1 AAAAAATGAAAAAAAAATGA
*
5628321 --AAAA-GAAAAAAATAT--
1 AAAAAATGAAAAAAAAATGA
* *
5628336 AAAATAT-AAAAAAAAAAG-
1 AAAAAATGAAAAAAAAATGA
* *
5628354 ATAAAATGAAAAAAGAAAAGA
1 AAAAAATGAAAAAA-AAATGA
*
5628375 AAAAAA-GAAAAAGAAAT-A
1 AAAAAATGAAAAAAAAATGA
5628393 AAA
1 AAA
5628396 GGGGGGTTCA
Statistics
Matches: 92, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
15 1 0.01
16 10 0.11
17 11 0.12
18 9 0.10
19 12 0.13
20 11 0.12
21 26 0.28
22 9 0.10
23 3 0.03
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAATGAAAAAAAAATGA
Found at i:5628285 original size:22 final size:21
Alignment explanation
Indices: 5628210--5628380 Score: 96
Period size: 25 Copynumber: 7.4 Consensus size: 21
5628200 TATTTCTCCT
*
5628210 GAAAAAGAAATGAAAAAAGAAA
1 GAAAAAAAAATGAAAAAA-AAA
*
5628232 -AAGAGAAAAAT-AAAAAAAGAA
1 GAA-AAAAAAATGAAAAAAA-AA
5628253 GAAAAGGAAAAAATGAAAAAAAAA
1 G-AAA--AAAAAATGAAAAAAAAA
5628277 TG-AAAAAAAATGAAAAAAAATGA
1 -GAAAAAAAAATGAAAAAAAA--A
*
5628300 TGAAAAAAATGATGAAAAATGAAAA
1 -GAAAAAAA-AATGAAAAA--AAAA
* *
5628325 GAAAAAAATATAAAATATAAAAA
1 GAAAAAAAAATGAAA-A-AAAAA
*
5628348 AAAAAGATAAAATGAAAAAAGAAAA
1 GAAAA-A-AAAATG-AAAAA-AAAA
5628373 GAAAAAAA
1 GAAAAAAA
5628381 GAAAAAGAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 39
0.71 0.06 0.23
Matches are distributed among these distances:
20 1 0.01
21 26 0.22
22 7 0.06
23 22 0.18
24 26 0.22
25 31 0.26
26 3 0.03
27 3 0.03
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (21 bp):
GAAAAAAAAATGAAAAAAAAA
Found at i:5629825 original size:55 final size:55
Alignment explanation
Indices: 5629750--5630187 Score: 424
Period size: 55 Copynumber: 8.1 Consensus size: 55
5629740 GAAGCAAAGT
*
5629750 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
** * * * * ** **
5629801 AATTCGTTGAAGATTGTTCAAGTCCCATACTCTCTGAAGAAATAGGGAGCATATA
1 CGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
** * * *
5629856 TATTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
* * * *
5629911 CGTTT-TATGAA-ATTGCTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACC
1 CGTTTGT-TGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
* * * * * *
5629965 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCTAAAGAAATAGAGAACGAACC
1 CGTTTGT-TGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
*
5630020 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
* * * * * * * * *
5630075 CGTTTATTAAAAATTGTTTGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
* * * * *
5630130 TGTTTGCTGAAGATTGTTCGAGTCTTATACTC-CTTGAATGAATAAGGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCCTATACTCTC-TGAAGGAATAGGGAGCGGACC
5630185 CGT
1 CGT
5630188 CATTTGAAGA
Statistics
Matches: 323, Mismatches: 56, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
51 10 0.03
54 55 0.17
55 257 0.80
56 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
Found at i:5630041 original size:164 final size:164
Alignment explanation
Indices: 5629765--5630161 Score: 446
Period size: 164 Copynumber: 2.4 Consensus size: 164
5629755 GTTGAAGATT
* * * * * * *
5629765 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAATTCGTTGAAGATTGTTCAAGTCCCATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTT-TTTGAAGATTGTTCGAGTTCTATA
* * * * * *
5629830 CTCTCTGAAGAAATAGGGAGCATATATATTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAT
65 CTCTCTAAAGAAATAGAGAACATACACATTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAG
*
5629895 GAATAGAGAGCGGACCCG-TT-TTATGAAATTGCTC
130 GAATAGAGAGCGGACCCGTTTATTA-AAAATTGCTC
* **
5629929 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTTTT-TGAAGATTGTTCGAGTTCTATA
* *
5629994 CTCTCTAAAGAAATAGAGAACGA-ACCCGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAA
65 CTCTCTAAAGAAATAGAGAAC-ATACACATTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAA
* * *
5630058 GGAATAGGGAGCGGACCCGTTTATTAAAAATTGTTT
129 GGAATAGAGAGCGGACCCGTTTATTAAAAATTGCTC
* * * *
5630094 GAG-TCTTATACTCCCTGAACGAATAGGGAGC-AGACATGTTTGCTGAAGATTGTTCGAG-TCTT
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGA-ACAAGTTT-TTGAAGATTGTTCGAGTTC-T
5630156 ATACTC
62 ATACTC
5630162 CTTGAATGAA
Statistics
Matches: 197, Mismatches: 28, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
163 1 0.01
164 130 0.66
165 63 0.32
166 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (164 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACAAGTTTTTGAAGATTGTTCGAGTTCTATAC
TCTCTAAAGAAATAGAGAACATACACATTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGG
AATAGAGAGCGGACCCGTTTATTAAAAATTGCTC
Found at i:5636825 original size:61 final size:61
Alignment explanation
Indices: 5636752--5636872 Score: 215
Period size: 61 Copynumber: 2.0 Consensus size: 61
5636742 GCCATATACC
*
5636752 TGAACCCATTTAAAAAATAATATATGAGCAAACTCGTCAATTGAGTGTGACGAGTTTGACT
1 TGAACCCATTTAAAAAATAATATATGAGCAAACTCGTCAATTAAGTGTGACGAGTTTGACT
* *
5636813 TGAACCCGTTTAAAAAATAATATATGAGCAAACTCGTCAATTAAGTGTGGCGAGTTTGAC
1 TGAACCCATTTAAAAAATAATATATGAGCAAACTCGTCAATTAAGTGTGACGAGTTTGAC
5636873 GTGCATTGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (61 bp):
TGAACCCATTTAAAAAATAATATATGAGCAAACTCGTCAATTAAGTGTGACGAGTTTGACT
Found at i:5638158 original size:3 final size:3
Alignment explanation
Indices: 5638150--5638180 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5638140 TACGGATGGA
5638150 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5638181 GCATGGATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5639471 original size:12 final size:12
Alignment explanation
Indices: 5639454--5639478 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5639444 ACAAAGCACC
5639454 ATTTGGTGCCTA
1 ATTTGGTGCCTA
5639466 ATTTGGTGCCTA
1 ATTTGGTGCCTA
5639478 A
1 A
5639479 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:5648003 original size:14 final size:13
Alignment explanation
Indices: 5647970--5647994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5647960 ATTTTTAAAG
5647970 AAATAAAAAAATA
1 AAATAAAAAAATA
5647983 AAATAAAAAAAT
1 AAATAAAAAAAT
5647995 TATATTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:5648272 original size:1 final size:1
Alignment explanation
Indices: 5648266--5648290 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5648256 TGAAGAAAAG
5648266 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
5648291 GGATGACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5656756 original size:21 final size:21
Alignment explanation
Indices: 5656727--5656779 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
5656717 TGATCAATGG
* *
5656727 TACTGACATGACA-ATTTACGA
1 TACTAACATGACAGA-TCACGA
* *
5656748 TACTAACATAACAGATCATGA
1 TACTAACATGACAGATCACGA
5656769 TACTAACATGA
1 TACTAACATGA
5656780 GAGTTCATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (21 bp):
TACTAACATGACAGATCACGA
Found at i:5659254 original size:45 final size:45
Alignment explanation
Indices: 5659073--5659256 Score: 314
Period size: 45 Copynumber: 4.1 Consensus size: 45
5659063 TGTCCAATGC
5659073 GATGGATTCGCTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
1 GATGGATTCGCTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
* *
5659118 GGTGGATTTGCTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
1 GATGGATTCGCTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
* *
5659163 GGTGGATTCGGTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
1 GATGGATTCGCTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
* *
5659208 GATGGATTCGGTAACATCTCTCGAGTATCCAAACTGTCTCTTCTA
1 GATGGATTCGCTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
5659253 GATG
1 GATG
5659257 CTGATGAAGA
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (45 bp):
GATGGATTCGCTAACATCTCTCGAGTCTCCAAACTGTCTCTTCTA
Found at i:5661868 original size:45 final size:45
Alignment explanation
Indices: 5661810--5661895 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
5661800 GGACTTGTCA
* ** *
5661810 TCGCATGTTTCCTTTCTCTCCGGTCCTATTGATGATGATTCATCT
1 TCGCAAGTTTCCTTTCTCTCCGACCCTATGGATGATGATTCATCT
5661855 TCGCAAGTTTCCTTTCTCTCCGACCCTATGGATGATGATTC
1 TCGCAAGTTTCCTTTCTCTCCGACCCTATGGATGATGATTC
5661896 GTCATCTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.41
Consensus pattern (45 bp):
TCGCAAGTTTCCTTTCTCTCCGACCCTATGGATGATGATTCATCT
Found at i:5661974 original size:45 final size:45
Alignment explanation
Indices: 5661910--5662043 Score: 241
Period size: 45 Copynumber: 3.0 Consensus size: 45
5661900 TCTTTAACCA
5661910 TTTCTTCAGCTGATGCCTTTACTTCAACTACTCCGGCCTTCACCG
1 TTTCTTCAGCTGATGCCTTTACTTCAACTACTCCGGCCTTCACCG
* *
5661955 TTTCTTCAACAGATGCCTTTACTTCAACTACTCCGGCCTTCACCG
1 TTTCTTCAGCTGATGCCTTTACTTCAACTACTCCGGCCTTCACCG
*
5662000 TTTCTTCAGCTGATGCCTTTACTTCAACTTCTCCGGCCTTCACC
1 TTTCTTCAGCTGATGCCTTTACTTCAACTACTCCGGCCTTCACC
5662044 ATCACATTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.16, C:0.36, G:0.12, T:0.36
Consensus pattern (45 bp):
TTTCTTCAGCTGATGCCTTTACTTCAACTACTCCGGCCTTCACCG
Found at i:5664231 original size:10 final size:10
Alignment explanation
Indices: 5664212--5664245 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5664202 TTTAAAAGAT
5664212 TTTCTCTCAC
1 TTTCTCTCAC
*
5664222 TTTCTTTCAC
1 TTTCTCTCAC
*
5664232 TTTCTCTCAT
1 TTTCTCTCAC
5664242 TTTC
1 TTTC
5664246 CTCTATCTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTCTCAC
Found at i:5664691 original size:22 final size:22
Alignment explanation
Indices: 5664641--5664693 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
5664631 TATATAATTA
*
5664641 TAAATTAGTTAAAATTTTAAAAG
1 TAAATTATTTAAAA-TTTAAAAG
*
5664664 TAAATTATTTAAAA-TTAAAGGG
1 TAAATTATTTAAAATTTAAA-AG
5664686 TAAATTAT
1 TAAATTAT
5664694 ACCACTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 9 0.33
23 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (22 bp):
TAAATTATTTAAAATTTAAAAG
Found at i:5665443 original size:22 final size:23
Alignment explanation
Indices: 5665418--5665467 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5665408 ACTAATATAG
5665418 TTTATCCTTT-AATTTTAAATAA
1 TTTATCCTTTAAATTTTAAATAA
* *
5665440 TTTA-CTTTTAAAATTTTAATTAA
1 TTTATCCTTT-AAATTTTAAATAA
5665463 TTTAT
1 TTTAT
5665468 AATTACACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 15 0.65
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATCCTTTAAATTTTAAATAA
Found at i:5667665 original size:31 final size:31
Alignment explanation
Indices: 5667621--5667688 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
5667611 TTAAAAAACA
*
5667621 TAAGATATAGACACTTTTATTTTTATTTAAT
1 TAAGATATAGACACTTTCATTTTTATTTAAT
* * *
5667652 TAAGTTATGGACACTTTCGTTTTTATTTAAT
1 TAAGATATAGACACTTTCATTTTTATTTAAT
*
5667683 AAAGAT
1 TAAGAT
5667689 GTGATCACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (31 bp):
TAAGATATAGACACTTTCATTTTTATTTAAT
Found at i:5668172 original size:39 final size:39
Alignment explanation
Indices: 5668071--5668176 Score: 119
Period size: 39 Copynumber: 2.7 Consensus size: 39
5668061 CATAATCCTC
* **
5668071 AAATTATTTCAC-TCTAACATTCTAAAATCTTAATTTCTT
1 AAATTATTTCACAT-TAACATTCTAAATTCACAATTTCTT
*
5668110 AAATT-TTGACACCA-TAACATTCTAAATTCACAATTTCTT
1 AAATTATT-TCA-CATTAACATTCTAAATTCACAATTTCTT
*
5668149 AAATTATTTCACATTAACGTTCTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
5668177 ATTTTTTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
38 4 0.07
39 49 0.88
40 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTCTAAATTCACAATTTCTT
Found at i:5668437 original size:23 final size:24
Alignment explanation
Indices: 5668411--5668486 Score: 86
Period size: 23 Copynumber: 3.1 Consensus size: 24
5668401 TGTATATATA
5668411 TATATTAACTTATTAAATAT-TTT
1 TATATTAACTTATTAAATATATTT
*
5668434 TATATTAGCTTATTAAATATATTT
1 TATATTAACTTATTAAATATATTT
5668458 TACTATTCAA-TTAATTTAAA-ATATTT
1 TA-TATT-AACTT-A-TTAAATATATTT
5668484 TAT
1 TAT
5668487 TTTCATTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
23 19 0.41
24 5 0.11
25 7 0.15
26 10 0.22
27 5 0.11
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (24 bp):
TATATTAACTTATTAAATATATTT
Found at i:5668497 original size:26 final size:26
Alignment explanation
Indices: 5668445--5668519 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 26
5668435 ATATTAGCTT
* *
5668445 ATTAAATATATTTTACTATTCA-ATTAA
1 ATTAAA-ATATTTTA-TTTTCATTTTAA
*
5668472 TTTAAAATATTTTATTTTCATTTTAA
1 ATTAAAATATTTTATTTTCATTTTAA
* * *
5668498 AAT-AAATAATTTATTTTAATTT
1 ATTAAAATATTTTATTTTCATTT
5668520 ATTAAAAGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 22 0.55
26 13 0.32
27 5 0.12
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTAAAATATTTTATTTTCATTTTAA
Found at i:5673913 original size:2 final size:2
Alignment explanation
Indices: 5673906--5673931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5673896 TTATGAGTTC
5673906 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5673932 GTGAACTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5682613 original size:29 final size:29
Alignment explanation
Indices: 5682571--5682732 Score: 200
Period size: 29 Copynumber: 5.6 Consensus size: 29
5682561 CATATTCAAA
*
5682571 AATTCCCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
** *
5682600 AATTCATAGCATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* *
5682629 AATTCCCAGAATATCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* *
5682658 ATTTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* * * *
5682687 ATTTCTCAGAATGTCACCTTTTCCATAAA-
1 AATTCCCAGAATGTCACATTTTTCA-AAAT
5682716 AATTCCCAGAATGTCAC
1 AATTCCCAGAATGTCAC
5682733 TGGGTCGGGT
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
29 114 0.97
30 3 0.03
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (29 bp):
AATTCCCAGAATGTCACATTTTTCAAAAT
Found at i:5682671 original size:87 final size:85
Alignment explanation
Indices: 5682565--5682732 Score: 223
Period size: 87 Copynumber: 2.0 Consensus size: 85
5682555 ATAGTTCATA
* *
5682565 TTCAAAAATTCCCAAAATGTCACATTTTTCAAAATAATTCAT-AGCATGTCACATTTTTCA-AAA
1 TTCAAAAATTCCCAAAATGTCACATTTTTCAAAATAATTC-TCAGAATGTCACATTTTCCATAAA
5682628 TAATTCCCAGAATATCACCTTT
65 -AATTCCCAGAATATCACCTTT
* * * *
5682650 TTCAAAATATTTCCCAGAATGTCACCTTTTTCAAAATATTTCTCAGAATGTCACCTTTTCCATAA
1 TTCAAAA-A-TTCCCAAAATGTCACATTTTTCAAAATAATTCTCAGAATGTCACATTTTCCATAA
*
5682715 AAATTCCCAGAATGTCAC
64 AAATTCCCAGAATATCAC
5682733 TGGGTCGGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
85 7 0.10
86 2 0.03
87 60 0.83
88 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (85 bp):
TTCAAAAATTCCCAAAATGTCACATTTTTCAAAATAATTCTCAGAATGTCACATTTTCCATAAAA
ATTCCCAGAATATCACCTTT
Found at i:5690151 original size:28 final size:29
Alignment explanation
Indices: 5690055--5690215 Score: 229
Period size: 29 Copynumber: 5.6 Consensus size: 29
5690045 AAAGGTCGAA
*
5690055 AATTCCCAAAATGTCACATTTTTTCAAAAT
1 AATTCCCAGAATGTCACA-TTTTTCAAAAT
* *
5690085 AATTCCCAGCATCTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
5690114 AATTCCCAGAATGTCAC-TTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* *
5690142 ATTTCTCAGAATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
*
5690171 ATTTCCCAGAATGTCACA-TTTTCACAAA-
1 AATTCCCAGAATGTCACATTTTTCA-AAAT
5690199 AATTCCCAGAATGTCAC
1 AATTCCCAGAATGTCAC
5690216 TGGGTCGGGT
Statistics
Matches: 120, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
28 48 0.40
29 57 0.47
30 15 0.12
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (29 bp):
AATTCCCAGAATGTCACATTTTTCAAAAT
Found at i:5690159 original size:57 final size:57
Alignment explanation
Indices: 5690055--5690215 Score: 225
Period size: 57 Copynumber: 2.8 Consensus size: 57
5690045 AAAGGTCGAA
* * *
5690055 AATTCCCAAAATGTCACATTTTTTCAAAATAATTCCCAGCATCTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCAC--TTTTTCAAAATAATTCCCAGAATGTCACATTTTTCAAAAT
* *
5690114 AATTCCCAGAATGTCACTTTTTCAAAATATTTCTCAGAATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACTTTTTCAAAATAATTCCCAGAATGTCACATTTTTCAAAAT
* *
5690171 ATTTCCCAGAATGTCACATTTTCACAAA-AATTCCCAGAATGTCAC
1 AATTCCCAGAATGTCACTTTTTCA-AAATAATTCCCAGAATGTCAC
5690216 TGGGTCGGGT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
57 73 0.79
58 3 0.03
59 16 0.17
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (57 bp):
AATTCCCAGAATGTCACTTTTTCAAAATAATTCCCAGAATGTCACATTTTTCAAAAT
Found at i:5690253 original size:23 final size:22
Alignment explanation
Indices: 5690211--5690257 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
5690201 TTCCCAGAAT
* **
5690211 GTCACTGGGTCGGGTTGGGTCGG
1 GTCACCGGGTCGGGCCGGGT-GG
5690234 GTCACCGGGTCGGGCCGGGTGG
1 GTCACCGGGTCGGGCCGGGTGG
5690256 GT
1 GT
5690258 TAACGGTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.04, C:0.21, G:0.53, T:0.21
Consensus pattern (22 bp):
GTCACCGGGTCGGGCCGGGTGG
Found at i:5693235 original size:17 final size:18
Alignment explanation
Indices: 5693196--5693241 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5693186 TCGCTATGAG
5693196 GGAATTGAAATCGGTGAA
1 GGAATTGAAATCGGTGAA
* *
5693214 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCGGTGAA
5693231 GGAATTGAAAT
1 GGAATTGAAAT
5693242 TCAATTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (18 bp):
GGAATTGAAATCGGTGAA
Found at i:5695703 original size:21 final size:21
Alignment explanation
Indices: 5695679--5695785 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 21
5695669 GCAAATTCGC
*
5695679 GTTGCATTTCGCGTTGAGATA
1 GTTGCATTTCGCGTTGCGATA
* ***
5695700 GTTGAAAACCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
5695720 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
5695741 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
5695761 TTTCCATTTCGCGTTGCTATA
1 GTTGCATTTCGCGTTGCGATA
5695782 GTTG
1 GTTG
5695786 AAAATCGCAA
Statistics
Matches: 60, Mismatches: 24, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:5695728 original size:41 final size:41
Alignment explanation
Indices: 5695683--5695824 Score: 221
Period size: 41 Copynumber: 3.5 Consensus size: 41
5695673 ATTCGCGTTG
* *
5695683 CATTTCGCGTTGAGATAGTTGAAAACCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
5695724 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *** *
5695765 CATTTCGCGTTGCTATAGTTGAAAATCGCAACGCGATTGTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
5695806 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
5695825 CTACAGTTGT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:5695734 original size:20 final size:20
Alignment explanation
Indices: 5695709--5695777 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
5695699 AGTTGAAAAC
5695709 CGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
* ** **
5695729 CGCGTTGCGATAGTTGAAAAT
1 CGCGTTGCGAT-TTTCCATTT
5695750 CGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
5695770 CGCGTTGC
1 CGCGTTGC
5695778 TATAGTTGAA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTTCCATTT
Found at i:5695858 original size:82 final size:81
Alignment explanation
Indices: 5695697--5695858 Score: 184
Period size: 82 Copynumber: 2.0 Consensus size: 81
5695687 TCGCGTTGAG
*** *
5695697 ATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
1 ATAGTTGAAAACCGCAACGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
* *
5695762 TTCCATTTCGCGTTGCT
66 TTCAAATTC-CGTTGCT
* * * *
5695779 ATAGTTGAAAATCGCAACGCGATTGTCCATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGA
1 ATAGTTGAAAACCGCAACGCGATTGTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGA
5695843 TTTTCTAAATT-CGTTG
64 TTTTC-AAATTCCGTTG
5695859 TGATAATTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 50 0.75
83 14 0.21
84 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (81 bp):
ATAGTTGAAAACCGCAACGCGATTGTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
TTCAAATTCCGTTGCT
Found at i:5695954 original size:6 final size:6
Alignment explanation
Indices: 5695943--5695980 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
5695933 GACACGTATT
5695943 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
5695981 CGAGACGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5696477 original size:5 final size:5
Alignment explanation
Indices: 5696463--5696499 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
5696453 CCGCCGCCGC
5696463 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
5696500 GGTCCTGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:5696686 original size:21 final size:21
Alignment explanation
Indices: 5696638--5696711 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
5696628 ACAACTGTAG
** *
5696638 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTGCA
* **
5696659 A-AATCGCATTGCGATTTGCA
1 ACTATCGCAACGCGATTTGCA
*
5696679 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTGCA
5696700 ACTATCGCAACG
1 ACTATCGCAACG
5696712 ACAACTGTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 14 0.33
21 28 0.67
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTGCA
Found at i:5697883 original size:2 final size:2
Alignment explanation
Indices: 5697878--5697905 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5697868 AAAAAAGGGA
5697878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5697906 CAATGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5699166 original size:16 final size:16
Alignment explanation
Indices: 5699109--5699168 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 16
5699099 AGAATTTATA
*
5699109 TTAAATTATTTTATAAT
1 TTAAATTTTTTTA-AAT
*
5699126 ATTATGATTTTTTTAAA-
1 -TTA-AATTTTTTTAAAT
*
5699143 -TAATTTTTTTTAAAT
1 TTAAATTTTTTTAAAT
5699158 TTAAATTTTTT
1 TTAAATTTTTT
5699169 ATTTGAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 9 0.26
18 5 0.15
19 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTAAATTTTTTTAAAT
Found at i:5699193 original size:23 final size:23
Alignment explanation
Indices: 5699167--5699210 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5699157 TTTAAATTTT
5699167 TTATTTGAAATAACATTATTTAA
1 TTATTTGAAATAACATTATTTAA
* *
5699190 TTATTTTAAATAATATTATTT
1 TTATTTGAAATAACATTATTT
5699211 TTAAAATGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTTGAAATAACATTATTTAA
Found at i:5700375 original size:14 final size:14
Alignment explanation
Indices: 5700358--5700387 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5700348 TAATTGGTTG
5700358 AATAAAATTAATTA
1 AATAAAATTAATTA
5700372 AATAAAATTAATTA
1 AATAAAATTAATTA
5700386 AA
1 AA
5700388 AATTTCGACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAAATTAATTA
Found at i:5700744 original size:2 final size:2
Alignment explanation
Indices: 5700737--5700779 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5700727 ATTAGAAATA
5700737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5700779 A
1 A
5700780 CCAGGTTGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5710583 original size:7 final size:7
Alignment explanation
Indices: 5710571--5710607 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
5710561 AATCTCAGTT
5710571 CTAGTAG
1 CTAGTAG
5710578 CTAGTAG
1 CTAGTAG
5710585 CTAGTAG
1 CTAGTAG
5710592 CTAGTAG
1 CTAGTAG
5710599 CTAGTAG
1 CTAGTAG
5710606 CT
1 CT
5710608 TTATCCTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (7 bp):
CTAGTAG
Found at i:5712321 original size:11 final size:11
Alignment explanation
Indices: 5712307--5712404 Score: 53
Period size: 11 Copynumber: 9.7 Consensus size: 11
5712297 AAATTGATAA
5712307 ATATATAATAT
1 ATATATAATAT
5712318 ATATATAATAT
1 ATATATAATAT
5712329 A-AGT-T--TAT
1 ATA-TATAATAT
5712337 ATATA-AACTAT
1 ATATATAA-TAT
5712348 ATATATAA-ACT
1 ATATATAATA-T
5712359 ATAT-T--TAT
1 ATATATAATAT
5712367 AT-TATAA-AT
1 ATATATAATAT
5712376 -TATATAAT-T
1 ATATATAATAT
5712385 AT-TATAAGTTAT
1 ATATATAA--TAT
5712397 ATATATAA
1 ATATATAA
5712405 ATTATGTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 36
0.65 0.00 0.35
Matches are distributed among these distances:
7 1 0.01
8 10 0.15
9 15 0.22
10 5 0.07
11 27 0.40
12 5 0.07
13 5 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
ATATATAATAT
Found at i:5712350 original size:13 final size:13
Alignment explanation
Indices: 5712307--5712452 Score: 70
Period size: 13 Copynumber: 11.1 Consensus size: 13
5712297 AAATTGATAA
5712307 ATATATAATA-TAT
1 ATATATAA-ACTAT
* *
5712320 ATATAATATAAGTTT
1 ATAT-ATA-AACTAT
5712335 ATATATAAACTAT
1 ATATATAAACTAT
5712348 ATATATAAACTAT
1 ATATATAAACTAT
* *
5712361 AT-T-TATATTAT
1 ATATATAAACTAT
*
5712372 AAATTATATAA-T-T
1 ATA-TATA-AACTAT
**
5712385 AT-TATAAGTTAT
1 ATATATAAACTAT
*
5712397 ATATATAAATTATGT
1 ATATATAAACTA--T
* *
5712412 TTATATGAACTAT
1 ATATATAAACTAT
5712425 ATATATAAACTAT
1 ATATATAAACTAT
* *
5712438 AAAAAATAAACTAT
1 -ATATATAAACTAT
5712452 A
1 A
5712453 ATTTATATTA
Statistics
Matches: 103, Mismatches: 17, Indels: 26
0.71 0.12 0.18
Matches are distributed among these distances:
10 1 0.01
11 12 0.12
12 4 0.04
13 47 0.46
14 21 0.20
15 18 0.17
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (13 bp):
ATATATAAACTAT
Found at i:5712381 original size:20 final size:19
Alignment explanation
Indices: 5712351--5712402 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
5712341 AAACTATATA
* *
5712351 TATAAACTATATTTA-TAT
1 TATAAATTATATATATTAT
5712369 TATAAATTATATA-ATTAT
1 TATAAATTATATATATTAT
*
5712387 TATAAGTTATATATAT
1 TATAAATTATATATAT
5712403 AAATTATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 1 0.03
18 26 0.90
19 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TATAAATTATATATATTAT
Found at i:5712479 original size:13 final size:13
Alignment explanation
Indices: 5712306--5712479 Score: 58
Period size: 13 Copynumber: 14.0 Consensus size: 13
5712296 AAAATTGATA
5712306 AATATATA-ATAT
1 AATATATATATAT
5712318 -ATATATA-ATAT
1 AATATATATATAT
*
5712329 AAGTTTATATATA-
1 AA-TATATATATAT
5712342 AACTATATATATA-
1 AA-TATATATATAT
*
5712355 AACTATATTTATAT
1 AA-TATATATATAT
* *
5712369 TATAAAT-TATAT
1 AATATATATATAT
5712381 AAT-TAT-TATA-
1 AATATATATATAT
*
5712391 AGT-TATATATAT
1 AATATATATATAT
* *
5712403 AAATTATGTTTATAT
1 -AA-TATATATATAT
5712418 GAACTATATATATA-
1 -AA-TATATATATAT
* *
5712432 AACTATA-AAAAAT
1 AA-TATATATATAT
5712445 AA-ACTATA-AT-T
1 AATA-TATATATAT
*
5712456 TATAT-TA-ATAT
1 AATATATATATAT
5712467 AATATATATATAT
1 AATATATATATAT
5712480 TATTCAAAGT
Statistics
Matches: 125, Mismatches: 21, Indels: 31
0.71 0.12 0.18
Matches are distributed among these distances:
10 9 0.07
11 30 0.24
12 17 0.14
13 47 0.38
14 5 0.04
15 17 0.14
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:5712607 original size:46 final size:44
Alignment explanation
Indices: 5712554--5712641 Score: 140
Period size: 46 Copynumber: 2.0 Consensus size: 44
5712544 ATTTATTTGG
*
5712554 GAATTTAGAGGGAAATTGAGAAATTTTGAGAATATAGGAAAATTGA
1 GAATTTAGAGGGAAATTGAGAAATTTAGAGAA-ATA-GAAAATTGA
*
5712600 GAATTTAGAGGGAAATTGAGAAATTTAGAGGAATAGAAAATT
1 GAATTTAGAGGGAAATTGAGAAATTTAGAGAAATAGAAAATT
5712642 TTGGAGGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 7 0.17
45 3 0.08
46 30 0.75
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.27
Consensus pattern (44 bp):
GAATTTAGAGGGAAATTGAGAAATTTAGAGAAATAGAAAATTGA
Found at i:5712615 original size:19 final size:19
Alignment explanation
Indices: 5712593--5712661 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
5712583 GAATATAGGA
5712593 AAATTGAGAATTTAGAGGG
1 AAATTGAGAATTTAGAGGG
5712612 AAATTGAGAAATTTAGA-GG
1 AAATTGAG-AATTTAGAGGG
* * *
5712631 -AATAGAAAATTTTGGAGGG
1 AAATTGAGAA-TTTAGAGGG
5712650 AAATTGAGAATT
1 AAATTGAGAATT
5712662 GAGATCTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.05
18 10 0.24
19 14 0.34
20 15 0.37
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (19 bp):
AAATTGAGAATTTAGAGGG
Found at i:5712853 original size:4 final size:4
Alignment explanation
Indices: 5712844--5713063 Score: 107
Period size: 4 Copynumber: 55.5 Consensus size: 4
5712834 TACTTTTAAT
* * ** * *
5712844 TATA TATA TATA TATA TATA TATA TGTA TGTA TATA GGTA TGTA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * * * *
5712892 TGTA TGTA TGTA TGTA TGTA TGTA TATA AACTA TATA TGTA TAAA CTATA
1 TATA TATA TATA TATA TATA TATA TATA TA-TA TATA TATA TATA -TATA
* * * * *
5712942 TA-A AATA TATA GTTTA TAAA T-TA TA-A TTTA TACTA -ATA TAGTA TATG
1 TATA TATA TATA -TATA TATA TATA TATA TATA TA-TA TATA TA-TA TATA
* * *
5712989 TATG TATA -ACTA -ATA TA-A GTA-A TCTA TAGA T-TA TATA TATA TATA
1 TATA TATA TA-TA TATA TATA -TATA TATA TATA TATA TATA TATA TATA
5713034 TATA TATA TATA TATA TATA TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TA
5713064 GAAACACTAT
Statistics
Matches: 176, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
3 15 0.09
4 146 0.83
5 15 0.09
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:5713300 original size:2 final size:2
Alignment explanation
Indices: 5713218--5713282 Score: 69
Period size: 2 Copynumber: 32.0 Consensus size: 2
5713208 ATAAGTAATG
* **
5713218 TA TA GTA TA TA TT TA TA TA TA TA TA TA TA GG T- 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 TA
*
5713260 TA TA TA AA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA
5713283 AAGTAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
1 1 0.02
2 48 0.91
3 4 0.08
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5715605 original size:51 final size:51
Alignment explanation
Indices: 5715501--5715606 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
5715491 CTACGTGGTG
**
5715501 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGTAAGCCATGTAATCA
1 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGTAAGCCAAATAATCA
*
5715552 TATAGCGCGGTAT-AGGGGGCGCGCTATACCCCACGTG-ATGCCAAATCAA-CA
1 TATAGCGCGG-ATCAGGGGGCGCGCTATA-CCCACGTGTAAGCCAAAT-AATCA
5715603 TATA
1 TATA
5715607 ACGTGTGGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
51 37 0.76
52 12 0.24
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (51 bp):
TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGTAAGCCAAATAATCA
Found at i:5715973 original size:19 final size:19
Alignment explanation
Indices: 5715939--5715975 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5715929 ATGACCAACA
*
5715939 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
5715958 AAATCGCAACGTGATCTC
1 AAATCGCAACGCGATCTC
5715976 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:5716962 original size:24 final size:24
Alignment explanation
Indices: 5716930--5716983 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5716920 GTATTCGAAA
5716930 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
5716954 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
5716978 TTTGAT
1 TTTGAT
5716984 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:5719254 original size:18 final size:18
Alignment explanation
Indices: 5719231--5719265 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5719221 AGAAAAAGAC
*
5719231 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
5719249 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
5719266 CAACCGGCTT
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:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:5719575 original size:140 final size:140
Alignment explanation
Indices: 5719323--5719605 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
5719313 GCAAACGTTG
5719323 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
5719388 TTAAACATTGCTATGATCTGTTCAGTTTTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTAAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
5719453 CGAATTTGAC
131 CGAATTTGAC
5719463 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
5719528 TTGAACATTGTTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTAAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
5719593 CGAATTTGAC
131 CGAATTTGAC
5719603 TAT
1 TAT
5719606 CGCAATGCGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTAAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:5719601 original size:20 final size:20
Alignment explanation
Indices: 5719576--5719726 Score: 179
Period size: 20 Copynumber: 7.8 Consensus size: 20
5719566 TTACACATTC
*
5719576 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
5719596 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
5719616 ATTTGACGATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
5719636 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
5719655 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
5719670 ATTTTACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
5719690 ATATGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
5719710 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
5719727 AGAAAATCGC
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.08
15 3 0.03
19 3 0.03
20 95 0.86
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:5719667 original size:34 final size:33
Alignment explanation
Indices: 5719624--5719738 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 33
5719614 GAATTTGACG
5719624 ATCGCAACGCGAATTTGACTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAAC-CAAAA
*
5719658 ATCGCAACGCGAATTTTACTATCGCAACACGAATATGA
1 ATCGCAACGCGAATTTGACTATCGCAAC-C-AA-A--A
* *
5719696 CTATCGCAACGGGAATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCGAATTTGACTATCGCAACCA-AAA
5719732 ATCGCAA
1 ATCGCAA
5719739 AGCACATTAG
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
34 35 0.51
35 2 0.03
36 2 0.03
38 3 0.04
39 1 0.01
40 26 0.38
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (33 bp):
ATCGCAACGCGAATTTGACTATCGCAACCAAAA
Found at i:5719705 original size:74 final size:74
Alignment explanation
Indices: 5719584--5719738 Score: 231
Period size: 74 Copynumber: 2.1 Consensus size: 74
5719574 TCATTTGAAT
** *
5719584 ATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGACGATCGCAACGCGAATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACGATCGCAACGCGAATTTGACTATCGC
5719649 AACTCA-AAA
66 AAC-CAGAAA
* * *
5719658 ATCGCAACGCGAATTTTACTATCGCAACACGAATATGACTATCGCAACGGGAATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACGATCGCAACGCGAATTTGACTATCGC
*
5719723 AACGAGAAA
66 AACCAGAAA
5719732 ATCGCAA
1 ATCGCAA
5719739 AGCACATTAG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 1 0.01
74 72 0.99
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACGATCGCAACGCGAATTTGACTATCGC
AACCAGAAA
Found at i:5719753 original size:74 final size:73
Alignment explanation
Indices: 5719584--5719775 Score: 210
Period size: 74 Copynumber: 2.6 Consensus size: 73
5719574 TCATTTGAAT
* * ** *
5719584 ATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGACGATCGCAACGCGAATTTGACTATCGC
1 ATCGCAAAGCGAATTAGACTATCGCAACACGAA-TTGACTATCGCAACGCGAATTTGACTATCGC
5719649 AACTCAAAA
65 AACTCAAAA
* ** *
5719658 ATCGCAACGCGAATTTTACTATCGCAACACGAATATGACTATCGCAACGGGAATTTGACTATCGC
1 ATCGCAAAGCGAATTAGACTATCGCAACACGAAT-TGACTATCGCAACGCGAATTTGACTATCGC
*
5719723 AAC-GAGAAA
65 AACTCA-AAA
* *
5719732 ATCGCAAAGC-ACATTAGACTATCCCAACGA-GAATTGACTTTCGC
1 ATCGCAAAGCGA-ATTAGACTATCGCAAC-ACGAATTGACTATCGC
5719776 GTTGCGATTT
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
73 12 0.12
74 90 0.87
75 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (73 bp):
ATCGCAAAGCGAATTAGACTATCGCAACACGAATTGACTATCGCAACGCGAATTTGACTATCGCA
ACTCAAAA
Found at i:5719828 original size:20 final size:20
Alignment explanation
Indices: 5719765--5719842 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
5719755 CCAACGAGAA
*
5719765 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
5719785 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
5719805 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
5719825 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
5719843 AAGTGTACCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:5719963 original size:14 final size:14
Alignment explanation
Indices: 5719944--5719980 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
5719934 CATCAATTAA
5719944 ACAAATCAACTTTT
1 ACAAATCAACTTTT
5719958 ACAAATCAACTTTT
1 ACAAATCAACTTTT
5719972 ACAAATCAA
1 ACAAATCAA
5719981 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5722007 original size:20 final size:20
Alignment explanation
Indices: 5721964--5722027 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
5721954 AATAGTTTCT
*
5721964 GAAACTTAAAATCGCAACAC-
1 GAAACTT-AAATCGCAACGCG
5721984 GAAACTTAAATCGCAACGCG
1 GAAACTTAAATCGCAACGCG
* *
5722004 GAAA-TCACTATCGCAACGCG
1 GAAACTTA-AATCGCAACGCG
5722024 GAAA
1 GAAA
5722028 TGACTATCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.14
Consensus pattern (20 bp):
GAAACTTAAATCGCAACGCG
Found at i:5722028 original size:20 final size:20
Alignment explanation
Indices: 5721993--5722035 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
5721983 CGAAACTTAA
5721993 ATCGCAACGCGGAAATCACT
1 ATCGCAACGCGGAAATCACT
*
5722013 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATCACT
5722033 ATC
1 ATC
5722036 TCAATGCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATCACT
Found at i:5722258 original size:20 final size:20
Alignment explanation
Indices: 5722190--5722246 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
5722180 GGGATTATCC
* *
5722190 CGTTGTGATAGTCAAATT-CG
1 CGTTGCGATAGTC-ATTTCCG
5722210 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
5722230 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
5722247 TTGTGTTGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:5724176 original size:20 final size:20
Alignment explanation
Indices: 5724153--5724267 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
5724143 TCTGAAACTT
*
5724153 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
5724173 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
5724193 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
5724213 ACTATCACAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
5724232 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
5724252 ACTATCGCAACACGAA
1 AAAATCGCAACACGAA
5724268 TTAAACTATC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
19 13 0.16
20 66 0.84
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:5724275 original size:20 final size:19
Alignment explanation
Indices: 5724176--5724278 Score: 61
Period size: 20 Copynumber: 5.2 Consensus size: 19
5724166 GAAAATGAAA
5724176 ATCGCAACACGAA-AATGACT
1 ATCGCAACACGAATAA--ACT
* **
5724196 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAA-TAAACT
* *
5724216 ATCACAACGCGAAATGAAA--
1 ATCGCAACACG-AAT-AAACT
5724235 ATCGCAACACGAA-AATGACT
1 ATCGCAACACGAATAA--ACT
5724255 ATCGCAACACGAATTAAACT
1 ATCGCAACACGAA-TAAACT
5724275 ATCG
1 ATCG
5724279 TTGCGATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
16 2 0.03
18 3 0.05
19 9 0.14
20 46 0.71
21 3 0.05
22 2 0.03
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.17
Consensus pattern (19 bp):
ATCGCAACACGAATAAACT
Found at i:5726784 original size:47 final size:44
Alignment explanation
Indices: 5726690--5726807 Score: 155
Period size: 47 Copynumber: 2.6 Consensus size: 44
5726680 GTAACCATGC
*
5726690 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGAA
* * * *
5726734 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGGAA
*
5726781 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
5726808 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
44 24 0.38
45 1 0.02
46 1 0.02
47 38 0.59
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGAA
Found at i:5727575 original size:22 final size:22
Alignment explanation
Indices: 5727545--5727591 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5727535 GATGGAGATA
*
5727545 GACGGATTTCATCGGAGATGGG
1 GACGAATTTCATCGGAGATGGG
* * *
5727567 GACGAATTTCGTTGGAGATTGG
1 GACGAATTTCATCGGAGATGGG
5727589 GAC
1 GAC
5727592 AGATGTCGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.38, T:0.26
Consensus pattern (22 bp):
GACGAATTTCATCGGAGATGGG
Found at i:5727600 original size:22 final size:22
Alignment explanation
Indices: 5727558--5727600 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5727548 GGATTTCATC
*
5727558 GGAGATGGGGACGAATTTCGTT
1 GGAGATGGGGACGAATGTCGTT
*
5727580 GGAGATTGGGAC-AGATGTCGT
1 GGAGATGGGGACGA-ATGTCGT
5727601 CGTAGAGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.23, C:0.09, G:0.42, T:0.26
Consensus pattern (22 bp):
GGAGATGGGGACGAATGTCGTT
Found at i:5728685 original size:23 final size:23
Alignment explanation
Indices: 5728659--5728731 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
5728649 ATATTTTACA
*
5728659 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
5728682 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
5728705 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
5728728 ATAT
1 ATAT
5728732 TTTTACCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:5729360 original size:41 final size:41
Alignment explanation
Indices: 5729315--5729412 Score: 196
Period size: 41 Copynumber: 2.4 Consensus size: 41
5729305 ATTCGCATTG
5729315 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
5729356 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
5729397 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
5729413 TTTCCATTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:5729365 original size:20 final size:20
Alignment explanation
Indices: 5729340--5729432 Score: 132
Period size: 20 Copynumber: 4.6 Consensus size: 20
5729330 TAGTTGAAAA
5729340 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
5729360 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
5729381 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
5729401 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
5729421 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5729433 AGTTGAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:5729502 original size:22 final size:21
Alignment explanation
Indices: 5729477--5729587 Score: 86
Period size: 19 Copynumber: 5.4 Consensus size: 21
5729467 TTACATTTCG
* **
5729477 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTTACAAAT-T
*
5729499 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTTTACAAATT
*
5729518 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTTTACAAATT
* **
5729537 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTTACAAAT-T
*
5729559 TGTTGCGATAGTTTACAAATT
1 CGTTGCGATAGTTTACAAATT
*
5729580 CATTGCGA
1 CGTTGCGA
5729588 AAATTCGTTG
Statistics
Matches: 72, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
19 29 0.40
20 5 0.07
21 12 0.17
22 26 0.36
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTTTACAAATT
Done.