Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, 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: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 2 of 10
Found at i:451308 original size:16 final size:15
Alignment explanation
Indices: 451287--451329 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
451277 AATCTTATTA
451287 ATATTTATAATATAAC
1 ATATTTA-AATATAAC
*
451303 ATATTTAAA-ATGAC
1 ATATTTAAATATAAC
451317 A-ATTTAAATATAA
1 ATATTTAAATATAA
451330 TAAACAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 7 0.29
14 8 0.33
15 2 0.08
16 7 0.29
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (15 bp):
ATATTTAAATATAAC
Found at i:453665 original size:33 final size:33
Alignment explanation
Indices: 453599--453668 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
453589 GTTGATATGG
* * *
453599 CATGCTAAAATATTATAATTTATTATAATATGA
1 CATGCTAAAATATTATAATTGATAATAACATGA
** *
453632 CATGCTAGTATATTATAATTGATAATGACATGA
1 CATGCTAAAATATTATAATTGATAATAACATGA
453665 CATG
1 CATG
453669 TTAATTAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (33 bp):
CATGCTAAAATATTATAATTGATAATAACATGA
Found at i:455503 original size:14 final size:12
Alignment explanation
Indices: 455461--455490 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
455451 AGTTCCACCC
*
455461 AAGAGGAAGAAA
1 AAGAGAAAGAAA
455473 AAGAGAAAGAAA
1 AAGAGAAAGAAA
455485 AAGAGA
1 AAGAGA
455491 GAGATCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
AAGAGAAAGAAA
Found at i:459682 original size:28 final size:26
Alignment explanation
Indices: 459628--459683 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
459618 ACATTAAATT
* **
459628 ATTCATCATTTAGAATTTTCATGAAA
1 ATTCATCATTGAGAATTTTCAAAAAA
459654 ATTCTATCATTGAGAAATTTTCAAAAAA
1 ATTC-ATCATTGAG-AATTTTCAAAAAA
459682 AT
1 AT
459684 CATATCCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 8 0.32
28 13 0.52
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (26 bp):
ATTCATCATTGAGAATTTTCAAAAAA
Found at i:459689 original size:28 final size:27
Alignment explanation
Indices: 459632--459689 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
459622 TAAATTATTC
* * *
459632 ATCATTTAGAATTTTCATGAAAATTCT
1 ATCATTGAGAATTTTCATAAAAAATCT
459659 ATCATTGAGAAATTTTCA-AAAAAATCAT
1 ATCATTGAG-AATTTTCATAAAAAATC-T
459687 ATC
1 ATC
459690 CACCAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (27 bp):
ATCATTGAGAATTTTCATAAAAAATCT
Found at i:468134 original size:3 final size:3
Alignment explanation
Indices: 468126--468161 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
468116 TTTTGGTTCT
468126 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
468162 TGTTATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:470527 original size:20 final size:20
Alignment explanation
Indices: 470499--470546 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
470489 ATTTTTTTTA
* * *
470499 ATTTATTATTACTATTATTT
1 ATTTTTTATTACTAATATAT
*
470519 ATTTTTTATTATTAATATAT
1 ATTTTTTATTACTAATATAT
470539 ATTTTTTA
1 ATTTTTTA
470547 AAACTAAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTTTATTACTAATATAT
Found at i:473167 original size:31 final size:30
Alignment explanation
Indices: 473142--473217 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
473132 TCTTGTATTT
473142 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAAAATATTTTATCTTGTCTA
* *
473172 AATTGAGACAAATATA-TTT-T-TTGTCTA
1 AATTAAGACAAAAATATTTTATCTTGTCTA
* *
473199 GATTAAGATGAAAAATATT
1 AATTAAGA-CAAAAATATT
473218 AAACATGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 13 0.34
28 7 0.18
29 4 0.11
30 14 0.37
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (30 bp):
AATTAAGACAAAAATATTTTATCTTGTCTA
Found at i:475929 original size:49 final size:51
Alignment explanation
Indices: 475834--475929 Score: 151
Period size: 49 Copynumber: 1.9 Consensus size: 51
475824 CCCCGACTCC
* * *
475834 TGCTGACCCTAGTACTTCCTCGGAACCCCCCGAGACCCCGGCTCCTGCTGA
1 TGCTGACCCTAGTACTTCCCCCGAACCCCCCGAGACCCCGACTCCTGCTGA
475885 TGCTGA-CCTAGTACTTCCCCCGAA-CCCCCGAGACCCCGACTCCTG
1 TGCTGACCCTAGTACTTCCCCCGAACCCCCCGAGACCCCGACTCCTG
475930 TTGACCCTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 20 0.48
50 16 0.38
51 6 0.14
ACGTcount: A:0.17, C:0.45, G:0.20, T:0.19
Consensus pattern (51 bp):
TGCTGACCCTAGTACTTCCCCCGAACCCCCCGAGACCCCGACTCCTGCTGA
Found at i:476725 original size:21 final size:22
Alignment explanation
Indices: 476692--476732 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
476682 GGTCAATAAA
*
476692 TATATCTAGCAAAT-AATTTGC
1 TATATCTAACAAATGAATTTGC
*
476713 TATATTTAACAAATGAATTT
1 TATATCTAACAAATGAATTT
476733 TCTTTTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (22 bp):
TATATCTAACAAATGAATTTGC
Found at i:478448 original size:28 final size:28
Alignment explanation
Indices: 478407--478469 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
478397 GTCTTTTCAT
* * *
478407 TATTTATCTACTTTTGGTGGATTAAAAG
1 TATTCATCAACTTTTAGTGGATTAAAAG
* *
478435 TATTCATCAACTTTTAGTGGGTTACAAG
1 TATTCATCAACTTTTAGTGGATTAAAAG
478463 TATTCAT
1 TATTCAT
478470 TTATTTCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (28 bp):
TATTCATCAACTTTTAGTGGATTAAAAG
Found at i:478598 original size:26 final size:26
Alignment explanation
Indices: 478517--478583 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
478507 TGGGTTAAGA
* *
478517 TATCCATTCACTTCTAATGGTAAAAT
1 TATCCATCCACTTCTAATAGTAAAAT
478543 TATCCATCCACTTCTAATAGTAAAAT
1 TATCCATCCACTTCTAATAGTAAAAT
*
478569 TATCGATCCACTTCT
1 TATCCATCCACTTCT
478584 GGTATCAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (26 bp):
TATCCATCCACTTCTAATAGTAAAAT
Found at i:478606 original size:26 final size:25
Alignment explanation
Indices: 478537--478625 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
478527 CTTCTAATGG
**
478537 TAAAATTATCCATCCACTTCTAATA
1 TAAAATTATCCATCCACTTCTGGTA
*
478562 GTAAAATTATCGATCCACTTCTGGTA
1 -TAAAATTATCCATCCACTTCTGGTA
* * * *
478588 TCAACATTATCCATTCACTTTTGTTA
1 T-AAAATTATCCATCCACTTCTGGTA
*
478614 GCAAAATTATCC
1 -TAAAATTATCC
478626 TTAAAATTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
25 1 0.02
26 50 0.98
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (25 bp):
TAAAATTATCCATCCACTTCTGGTA
Found at i:478763 original size:59 final size:59
Alignment explanation
Indices: 478666--478778 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
478656 GTCCATAGAT
* * *
478666 CATAATTATTAAATGTTGTTACATTTATTTCATGGAATGAATAGATTCATGATTATAAC
1 CATAATTATTAAATGGTGTTACATTCACTTCATGGAATGAATAGATTCATGATTATAAC
* * *
478725 CATAATTATTAAATGGTGTTACATTCACTTCA-GAGAATGGATGGATTTATGATT
1 CATAATTATTAAATGGTGTTACATTCACTTCATG-GAATGAATAGATTCATGATT
478779 TTTTATTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 1 0.02
59 46 0.98
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (59 bp):
CATAATTATTAAATGGTGTTACATTCACTTCATGGAATGAATAGATTCATGATTATAAC
Found at i:479346 original size:12 final size:12
Alignment explanation
Indices: 479329--479358 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
479319 AGCATAATTG
479329 AATATTCATAAA
1 AATATTCATAAA
*
479341 AATATTCATAAT
1 AATATTCATAAA
479353 AATATT
1 AATATT
479359 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATTCATAAA
Found at i:480460 original size:29 final size:29
Alignment explanation
Indices: 480396--480474 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
480386 TGTTTTTAAG
* *
480396 TTATTTAATAATATTTAAATAAATTTTTA
1 TTATTTTATTATATTTAAATAAATTTTTA
*
480425 TTATTTTATTATATTT-AATCAAGTTTTTA
1 TTATTTTATTATATTTAAAT-AAATTTTTA
480454 -TA-TTT-TTAT-TTTAAATTAAAT
1 TTATTTTATTATATTTAAA-TAAAT
480475 AGACGTGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
25 3 0.07
26 9 0.21
27 4 0.09
28 5 0.12
29 22 0.51
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (29 bp):
TTATTTTATTATATTTAAATAAATTTTTA
Found at i:487009 original size:30 final size:32
Alignment explanation
Indices: 486975--487036 Score: 110
Period size: 30 Copynumber: 2.0 Consensus size: 32
486965 CAATTAATTT
486975 TTTATTTATCGAAGAGGGTATT-TTT-TTTGA
1 TTTATTTATCGAAGAGGGTATTATTTGTTTGA
487005 TTTATTTATCGAAGAGGGTATTATTTGTTTGA
1 TTTATTTATCGAAGAGGGTATTATTTGTTTGA
487037 ACTATTAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 22 0.73
31 3 0.10
32 5 0.17
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52
Consensus pattern (32 bp):
TTTATTTATCGAAGAGGGTATTATTTGTTTGA
Found at i:503022 original size:39 final size:39
Alignment explanation
Indices: 502979--503055 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
502969 GTTGTAAAGA
* * *
502979 CACCAATCGTGGTGAGGTTAGAAACCCCATTTAGGTGAC
1 CACCAACCGTGGTGAGGTTAGAAACCCCACTAAGGTGAC
*
503018 CACCAACCTTGGTGAGGTTAGAAACCCCACTAAGGTGA
1 CACCAACCGTGGTGAGGTTAGAAACCCCACTAAGGTGA
503056 ATAATGGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (39 bp):
CACCAACCGTGGTGAGGTTAGAAACCCCACTAAGGTGAC
Found at i:510050 original size:27 final size:27
Alignment explanation
Indices: 510010--510062 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
510000 TAGTTTATAT
510010 TTAGTATCAAGTATGCTGTCATAAATG
1 TTAGTATCAAGTATGCTGTCATAAATG
**
510037 TTAGTATCTTGTATGCTGTCATAAAT
1 TTAGTATCAAGTATGCTGTCATAAAT
510063 ATGGCAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (27 bp):
TTAGTATCAAGTATGCTGTCATAAATG
Found at i:521071 original size:11 final size:12
Alignment explanation
Indices: 521048--521094 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 12
521038 CATAATTAAC
521048 ATATGATATTAT
1 ATATGATATTAT
521060 ATATGA-ATTAT
1 ATATGATATTAT
521071 ATAT-ATA-TAT
1 ATATGATATTAT
521081 ATAT-ATATT-T
1 ATATGATATTAT
521091 ATAT
1 ATAT
521095 TTAAAAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 16 0.48
11 11 0.33
12 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (12 bp):
ATATGATATTAT
Found at i:522677 original size:28 final size:28
Alignment explanation
Indices: 522645--522698 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
522635 CCAAAAGACT
522645 TTGCAGAAAACACACCACTAAAATTAGC
1 TTGCAGAAAACACACCACTAAAATTAGC
*
522673 TTGCAGAAAACATACCACTAAAATTA
1 TTGCAGAAAACACACCACTAAAATTA
522699 TCTTTCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.20
Consensus pattern (28 bp):
TTGCAGAAAACACACCACTAAAATTAGC
Found at i:524199 original size:74 final size:74
Alignment explanation
Indices: 524109--524350 Score: 308
Period size: 74 Copynumber: 3.3 Consensus size: 74
524099 TAGATAGAGT
*
524109 GCTCTTAGCTGACTAACCATACTTCTTAGTCGATTAAGTTTTCTCTATCTTATTATTGAATTCTC
1 GCTCTTAGTTGACTAACCATACTTCTTAGTCGATTAAGTTTTCTCTATCTTATTATTGAATTCTC
*
524174 TGGCAGTGA
66 TGGTAGTGA
* * * * * * *
524183 GCTCTTAGTTGACTAACCATTCTTTTTAATCGAGTAAGTCTTT-TCTGTCTTGTAATTGAATTCT
1 GCTCTTAGTTGACTAACCATACTTCTTAGTCGATTAAGT-TTTCTCTATCTTATTATTGAATTCT
524247 CTGGTAGTGA
65 CTGGTAGTGA
* * ** * *
524257 GCTTTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTCCCTCTATCTTA-TAGTTAAAGTCT
1 GCTCTTAGTTGACTAACCATACTTCTTAGTCGATTAAGTTTTCTCTATCTTATTA-TTGAATTCT
*
524321 CTAGTAGTGA
65 CTGGTAGTGA
524331 GCTCTTAGTTGACTAACCAT
1 GCTCTTAGTTGACTAACCAT
524351 NNNNNNNNNN
Statistics
Matches: 142, Mismatches: 23, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
73 2 0.01
74 137 0.96
75 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACCATACTTCTTAGTCGATTAAGTTTTCTCTATCTTATTATTGAATTCTC
TGGTAGTGA
Found at i:533320 original size:33 final size:32
Alignment explanation
Indices: 533283--533372 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
533273 GACTACTAAT
*
533283 TTTTTTTAGAAAAAGGAGTTTTTCTTGCATTTA
1 TTTTTTAAGAAAAA-GAGTTTTTCTTGCATTTA
* * *
533316 TTTTTTAAGAAAAAGATTTTTTCATGTATTTA
1 TTTTTTAAGAAAAAGAGTTTTTCTTGCATTTA
*
533348 TTTTTTAAGAAAAAGTGTTTTTCTT
1 TTTTTTAAGAAAAAGAGTTTTTCTT
533373 ATATTAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 37 0.74
33 13 0.26
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.53
Consensus pattern (32 bp):
TTTTTTAAGAAAAAGAGTTTTTCTTGCATTTA
Found at i:533767 original size:6 final size:6
Alignment explanation
Indices: 533756--533781 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
533746 TCAAATTGGG
533756 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
533782 GAGGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:534388 original size:31 final size:31
Alignment explanation
Indices: 534326--534391 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
534316 TTTCTCTCTC
*
534326 TTCCTCATTTCCCTCTTTCTCTCAATTGCTT
1 TTCCTCATTTCCCTCTTTCTCTCAATCGCTT
* * * *
534357 TTCCTCTTTTCCCTCTTTCTTTTAGTCGCTT
1 TTCCTCATTTCCCTCTTTCTCTCAATCGCTT
534388 TTCC
1 TTCC
534392 ACTATTTAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.06, C:0.35, G:0.05, T:0.55
Consensus pattern (31 bp):
TTCCTCATTTCCCTCTTTCTCTCAATCGCTT
Found at i:537598 original size:11 final size:11
Alignment explanation
Indices: 537578--537611 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
537568 AATGTTGATT
*
537578 GACATTTGTTA
1 GACATATGTTA
537589 GACATATGTTA
1 GACATATGTTA
537600 GACATATTGTTA
1 GACATA-TGTTA
537612 ATTGAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (11 bp):
GACATATGTTA
Found at i:543887 original size:23 final size:23
Alignment explanation
Indices: 543851--543929 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
543841 CCCTCCCTTT
*
543851 CCTTTTTCTTCTTCCCCTTTCTC
1 CCTTTCTCTTCTTCCCCTTTCTC
* *
543874 CCTTTCTCTCCTT--CCTTTCTT
1 CCTTTCTCTTCTTCCCCTTTCTC
*
543895 CCTTTC-CTTCTTCCTTCTTTCTTC
1 CCTTTCTCTTCTTCC-CCTTTC-TC
543919 TCCTTTCTCTT
1 -CCTTTCTCTT
543930 TTTCTTGGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.11
21 13 0.30
23 16 0.36
24 1 0.02
25 6 0.14
26 3 0.07
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (23 bp):
CCTTTCTCTTCTTCCCCTTTCTC
Found at i:543890 original size:13 final size:12
Alignment explanation
Indices: 543874--543926 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 12
543864 CCCCTTTCTC
543874 CCTTTCTCTCCTT
1 CCTTTCT-TCCTT
543887 CCTTTCTTCCTTT
1 CCTTTCTTCC-TT
543900 CC-TTCTTCCTT
1 CCTTTCTTCCTT
543911 -CTTTCTT-C-T
1 CCTTTCTTCCTT
543920 CCTTTCT
1 CCTTTCT
543927 CTTTTTCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 8 0.22
11 7 0.19
12 10 0.27
13 11 0.30
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
CCTTTCTTCCTT
Found at i:543909 original size:20 final size:20
Alignment explanation
Indices: 543866--543923 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
543856 TTCTTCTTCC
* *
543866 CCTTTCTCCCTTTCTCTCCTT
1 CCTTTCTTCCTTTC-CTTCTT
543887 CCTTTCTTCCTTTCCTTCTT
1 CCTTTCTTCCTTTCCTTCTT
*
543907 CC-TTCTTTCTTCTCCTT
1 CCTTTCTTCCTT-TCCTT
543924 TCTCTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.24
20 12 0.36
21 13 0.39
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (20 bp):
CCTTTCTTCCTTTCCTTCTT
Found at i:548166 original size:100 final size:100
Alignment explanation
Indices: 548039--548238 Score: 312
Period size: 100 Copynumber: 2.0 Consensus size: 100
548029 TTTGTCTTTT
* *
548039 CCGACGAATTTACATTAAAATAATTGAAAATATGGTAGCTTTTGT-CGATGGAATTTTGTAACTT
1 CCGACGAATTTACATTAAAATAATTGAAAATATGGTAGCTTTTGTCCAATGGAATTTGGTAACTT
548103 TTTCCATCAGAATTTTGAGAAAAAAGAATGACAGTG
66 TTTCCATCAGAATTTTGAG-AAAAAGAATGACAGTG
* * *
548139 CCGACGGATTTACATTAAAATAATTGAAAATATGGTAGGTTTTTTCCAATGGAATTTGGTAACTT
1 CCGACGAATTTACATTAAAATAATTGAAAATATGGTAGCTTTTGTCCAATGGAATTTGGTAACTT
** *
548204 TTTTTATCAGAATTTTGAGAAAAAGAATGATAGTG
66 TTTCCATCAGAATTTTGAGAAAAAGAATGACAGTG
548239 TTAATTATTA
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 57 0.63
101 34 0.37
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (100 bp):
CCGACGAATTTACATTAAAATAATTGAAAATATGGTAGCTTTTGTCCAATGGAATTTGGTAACTT
TTTCCATCAGAATTTTGAGAAAAAGAATGACAGTG
Found at i:556178 original size:22 final size:22
Alignment explanation
Indices: 556150--556225 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
556140 CAATTAGTTA
*
556150 TTAGGCATTGCAT-TTCTAATTT
1 TTAGGCATTGCATCAT-TAATTT
**
556172 TTAGGCATTGCATCATTGGTTT
1 TTAGGCATTGCATCATTAATTT
**
556194 TTAGGCATTGCATCATTGGTTT
1 TTAGGCATTGCATCATTAATTT
556216 TTAGGCATTG
1 TTAGGCATTG
556226 TATGACTTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
22 49 0.98
23 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.21, T:0.46
Consensus pattern (22 bp):
TTAGGCATTGCATCATTAATTT
Found at i:556556 original size:22 final size:22
Alignment explanation
Indices: 556531--556600 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
556521 ACGCATTAGG
*
556531 TGACTAGATTTTAGGCATTGCA
1 TGACTAGATTTTAGGAATTGCA
*
556553 TGACCTAG-TTTTAGAAATTG-A
1 TGA-CTAGATTTTAGGAATTGCA
* *
556574 GTGA-TTGATTTTTAGGTATTGCA
1 -TGACTAGA-TTTTAGGAATTGCA
556597 TGAC
1 TGAC
556601 ACATTTTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
20 2 0.05
21 1 0.03
22 29 0.78
23 5 0.14
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (22 bp):
TGACTAGATTTTAGGAATTGCA
Found at i:557746 original size:8 final size:8
Alignment explanation
Indices: 557733--557758 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
557723 TAGTGCGGTT
557733 AATGTTGA
1 AATGTTGA
557741 AATGTTGA
1 AATGTTGA
557749 AATGTTGA
1 AATGTTGA
557757 AA
1 AA
557759 AGTATTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (8 bp):
AATGTTGA
Found at i:564440 original size:10 final size:10
Alignment explanation
Indices: 564425--564455 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
564415 ATAATATAAG
564425 ATTGCAATGC
1 ATTGCAATGC
564435 ATTGCAATGC
1 ATTGCAATGC
564445 ATTGCAATGC
1 ATTGCAATGC
564455 A
1 A
564456 ATCACATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (10 bp):
ATTGCAATGC
Found at i:564661 original size:10 final size:10
Alignment explanation
Indices: 564638--564706 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
564628 ATAAGAATAA
*
564638 AAAATTAAAAT
1 AAAA-TAAATT
564649 AAAATAAATT
1 AAAATAAATT
*
564659 AAAAAAAATT
1 AAAATAAATT
**
564669 AAAATTTA-T
1 AAAATAAATT
* *
564678 ATAATATAAGT
1 AAAATA-AATT
564689 AAAATAAATT
1 AAAATAAATT
564699 AAAATAAA
1 AAAATAAA
564707 ATATATAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
9 5 0.11
10 31 0.67
11 10 0.22
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAATAAATT
Found at i:564741 original size:5 final size:5
Alignment explanation
Indices: 564592--564709 Score: 50
Period size: 5 Copynumber: 24.0 Consensus size: 5
564582 ATAATGTTAT
* * * **
564592 AAATA AAATA AAA-A ATATTC AAATA AAAT- ATATA GTATA AGAAT- AAA-A
1 AAATA AAATA AAATA A-AATA AAATA AAATA AAATA AAATA A-AATA AAATA
* * ** * *
564640 AATTA AAATA AAATA AATTA AAA-A AAATTA AAAT- TTATA TAATA TAAGTA
1 AAATA AAATA AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA -AAATA
*
564690 AAATA AATTA AAATA AAATA
1 AAATA AAATA AAATA AAATA
564710 TATAATATAA
Statistics
Matches: 83, Mismatches: 20, Indels: 20
0.67 0.16 0.16
Matches are distributed among these distances:
4 15 0.18
5 58 0.70
6 10 0.12
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (5 bp):
AAATA
Found at i:564750 original size:33 final size:33
Alignment explanation
Indices: 564699--564784 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
564689 AAAATAAATT
* *
564699 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAA-ATAAAATATAAAAAATTATAATAA
* *
564733 AAAATAAAAATAAAATATATAAGATTATAATAA
1 AAAATAAAAATAAAATATAAAAAATTATAATAA
* *
564766 TAAATGAAAATAAAATATA
1 AAAATAAAAATAAAATATA
564785 TGACATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 37 0.80
34 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (33 bp):
AAAATAAAAATAAAATATAAAAAATTATAATAA
Found at i:564759 original size:28 final size:28
Alignment explanation
Indices: 564728--564796 Score: 66
Period size: 33 Copynumber: 2.3 Consensus size: 28
564718 AAAAAATTAT
*
564728 ATTAAAAAATAAAAATAAAATATATAAG
1 ATTAAAAAATAAAAATAAAATATATAAC
* *
564756 ATTATAATAATAAATGAAAATAAAATATATGAC
1 A-T-T-A-AA-AAATAAAAATAAAATATATAAC
564789 ATTAAAAA
1 ATTAAAAA
564797 TATATTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
28 3 0.09
29 3 0.09
30 2 0.06
31 2 0.06
32 3 0.09
33 20 0.61
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (28 bp):
ATTAAAAAATAAAAATAAAATATATAAC
Found at i:565027 original size:15 final size:15
Alignment explanation
Indices: 565009--565062 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
564999 TATTGCTTGC
565009 AATCACATTACCTGT
1 AATCACATTACCTGT
*
565024 AATCACATTACCTGC
1 AATCACATTACCTGT
*
565039 AATCACATTACCTAT
1 AATCACATTACCTGT
565054 AATCACATT
1 AATCACATT
565063 GCATTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (15 bp):
AATCACATTACCTGT
Found at i:565042 original size:30 final size:30
Alignment explanation
Indices: 565006--565062 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
564996 TGATATTGCT
*
565006 TGCAATCACATTACCTGTAATCACATTACC
1 TGCAATCACATTACCTATAATCACATTACC
565036 TGCAATCACATTACCTATAATCACATT
1 TGCAATCACATTACCTATAATCACATT
565063 GCATTATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (30 bp):
TGCAATCACATTACCTATAATCACATTACC
Found at i:572747 original size:2 final size:2
Alignment explanation
Indices: 572740--572769 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
572730 ATAACTCTAT
572740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
572770 ATTGCTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:575014 original size:2 final size:2
Alignment explanation
Indices: 574991--575034 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
574981 ATTTAGGTAT
* * *
574991 TA TA -A TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
575032 TA T
1 TA T
575035 GGTTTCGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:579744 original size:29 final size:29
Alignment explanation
Indices: 579709--579772 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
579699 TTTAATCTTT
579709 TATTTAA-TTAATTATTAACAAACTTTTAA
1 TATTTAAGTTAATTATTAA-AAACTTTTAA
* *
579738 TATTTAAGTTTAATTCTTAAAAATTTTTAA
1 TATTTAAG-TTAATTATTAAAAACTTTTAA
579768 T-TTTA
1 TATTTA
579773 CCTCATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 11 0.35
30 10 0.32
31 10 0.32
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (29 bp):
TATTTAAGTTAATTATTAAAAACTTTTAA
Found at i:580176 original size:4 final size:4
Alignment explanation
Indices: 580167--580193 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
580157 CCAAGTTGGG
580167 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
580194 ATGTACCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:587366 original size:17 final size:18
Alignment explanation
Indices: 587344--587380 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
587334 TTAAGATATG
*
587344 AAAAATTAAATATT-TTT
1 AAAAATTAAAAATTATTT
587361 AAAAATTAAAAATTATTT
1 AAAAATTAAAAATTATTT
587379 AA
1 AA
587381 CTAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATTAAAAATTATTT
Found at i:592720 original size:13 final size:13
Alignment explanation
Indices: 592702--592726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
592692 CTTTTAATTT
592702 CAAAGAACAAAAG
1 CAAAGAACAAAAG
592715 CAAAGAACAAAA
1 CAAAGAACAAAA
592727 CATATTTAAA
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:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (13 bp):
CAAAGAACAAAAG
Found at i:594625 original size:2 final size:2
Alignment explanation
Indices: 594618--594650 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
594608 AAATGCAAAT
594618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
594651 TTCAGGTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:606413 original size:2 final size:2
Alignment explanation
Indices: 606406--606430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
606396 TAGATGGTCA
606406 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
606431 AATTGACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:620553 original size:70 final size:69
Alignment explanation
Indices: 620462--620646 Score: 199
Period size: 70 Copynumber: 2.7 Consensus size: 69
620452 TTTCCCTTTT
* * * * ** * *
620462 CAAGATCAACTATAAAAGGTCTATAGTCGATCTTGGACCAGAATTTTTATTTTTAATCGATTTTG
1 CAAGATCGACTATAAAGGGTCTATAGTCGATCTTGGACCAGAATGTTCACATTTAATCCATTTTC
620527 CTTC
66 CTTC
* * **
620531 ACAAGATCGACTATGAAGGGTCTATAGTCGATCTTGAACCAGAATGTTCACATTTCTTCCATTTT
1 -CAAGATCGACTATAAAGGGTCTATAGTCGATCTTGGACCAGAATGTTCACATTTAATCCATTTT
620596 CCTTC
65 CCTTC
* * * * *
620601 CTAAGATCGACCATAAAGGGCCCATAGTCGATCTTGGGCCTGAATG
1 C-AAGATCGACTATAAAGGGTCTATAGTCGATCTTGGACCAGAATG
620647 CATAACTTCT
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
69 1 0.01
70 94 0.99
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (69 bp):
CAAGATCGACTATAAAGGGTCTATAGTCGATCTTGGACCAGAATGTTCACATTTAATCCATTTTC
CTTC
Found at i:622299 original size:33 final size:33
Alignment explanation
Indices: 622230--622306 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
622220 CTTGCTTTTG
* * **
622230 TGAAAAGGTAATTGTGGGTTGTGCTTACTCTTA
1 TGAAAAGGCAATTGTGGGTTATGCTTACTCCCA
**
622263 TGAAAAGGCAATTGTGGGTTATGCTTGTTCCCA
1 TGAAAAGGCAATTGTGGGTTATGCTTACTCCCA
622296 TGAAAAGGCAA
1 TGAAAAGGCAA
622307 GTGCAGGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (33 bp):
TGAAAAGGCAATTGTGGGTTATGCTTACTCCCA
Found at i:627775 original size:27 final size:29
Alignment explanation
Indices: 627745--627802 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
627735 TTCATATCTC
*
627745 AAACTATTATG-TCATTATTAA-GAC-TTA
1 AAACT-TTATGATCATCATTAACGACATTA
*
627772 AAACTTTTTGATCATCATTAACGACATTA
1 AAACTTTATGATCATCATTAACGACATTA
627801 AA
1 AA
627803 TTTTATCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 14 0.54
28 3 0.12
29 5 0.19
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (29 bp):
AAACTTTATGATCATCATTAACGACATTA
Found at i:638048 original size:69 final size:69
Alignment explanation
Indices: 637975--638106 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 69
637965 AAGCTATATT
* * * * *
637975 CTATGTTTTTATTTTATATTATGATGATTCCATATA-TCATATGAGATAAGAATGAGCACATGAA
1 CTATGTTGTTATTATATATGATGATGATTCCACATACT-AGATGAGATAAGAATGAGCACATGAA
638039 GTATA
65 GTATA
* * *
638044 CTATGTTGTTATTATATGTGATGATGATTCCACATACTAGATGAGATAAGTATGAGTACATGA
1 CTATGTTGTTATTATATATGATGATGATTCCACATACTAGATGAGATAAGAATGAGCACATGA
638107 TTAAATGCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
69 53 0.98
70 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (69 bp):
CTATGTTGTTATTATATATGATGATGATTCCACATACTAGATGAGATAAGAATGAGCACATGAAG
TATA
Found at i:641325 original size:21 final size:22
Alignment explanation
Indices: 641296--641342 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
641286 ATGAAAGGAG
641296 AAAGAAGAAAGAAAAAAAGAGA
1 AAAGAAGAAAGAAAAAAAGAGA
* * *
641318 AAAG-AGAAGGAAGAAAGGAGA
1 AAAGAAGAAAGAAAAAAAGAGA
641339 AAAG
1 AAAG
641343 CAAAAAAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
AAAGAAGAAAGAAAAAAAGAGA
Found at i:642692 original size:27 final size:26
Alignment explanation
Indices: 642636--642692 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
642626 ACCTATGATA
*
642636 TATATACATGGCAAGGCCACGAGATG
1 TATATACATGGCAAGGCCACAAGATG
* * *
642662 -ATATACGTGGCTAGGCCACAAGTTG
1 TATATACATGGCAAGGCCACAAGATG
642687 TTATAT
1 -TATAT
642693 GTAGTTACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 21 0.84
27 4 0.16
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (26 bp):
TATATACATGGCAAGGCCACAAGATG
Found at i:658879 original size:2 final size:2
Alignment explanation
Indices: 658872--658908 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
658862 TAGAACAATC
658872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
658909 CCATGTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:659249 original size:14 final size:15
Alignment explanation
Indices: 659226--659258 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
659216 ACTTGGAAGC
659226 AAAAAGAGAAAGGAG
1 AAAAAGAGAAAGGAG
*
659241 AAAAA-AGAAATGAG
1 AAAAAGAGAAAGGAG
659255 AAAA
1 AAAA
659259 GCAAAACGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (15 bp):
AAAAAGAGAAAGGAG
Found at i:664651 original size:70 final size:71
Alignment explanation
Indices: 664538--664681 Score: 254
Period size: 70 Copynumber: 2.0 Consensus size: 71
664528 AATTGACTAT
664538 ACCCCAACAAGGAGCACGCCTCCCCACCCTATTCAGGTCAG-TTTTCTTTAAAAAAAAAAGGGGG
1 ACCCCAACAAGGAGCACGCCTCCCCACCCTATTCAGGTCAGTTTTTCTTTAAAAAAAAAAGGGGG
664602 CAGGGA
66 CAGGGA
* **
664608 ACCCCAACAAGGAGCACGCCTCCCCACCCTATTCAGGTCAGTTTTTTTTTTTAAAAAAAAGGGGG
1 ACCCCAACAAGGAGCACGCCTCCCCACCCTATTCAGGTCAGTTTTTCTTTAAAAAAAAAAGGGGG
664673 CAGGGA
66 CAGGGA
664679 ACC
1 ACC
664682 AGGATTTCCT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 41 0.59
71 29 0.41
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (71 bp):
ACCCCAACAAGGAGCACGCCTCCCCACCCTATTCAGGTCAGTTTTTCTTTAAAAAAAAAAGGGGG
CAGGGA
Found at i:668981 original size:205 final size:205
Alignment explanation
Indices: 668626--669036 Score: 673
Period size: 205 Copynumber: 2.0 Consensus size: 205
668616 AGCAGAAACC
668626 ATTGTACATTCTATCCAGAATCATCAAAGCTACATCAAAATGCTGAAAAAACTAGAAACTTCCAA
1 ATTGTACATTCTATCCAGAA-CATCAAAGCTACATCAAAATGCTGAAAAAACTAGAAACTTCCAA
* * * *
668691 GCCGTAGGACAATGAAATTTAAATATTGCCCACTAGTGCCACTGTTCTTAAAGCAGCAAAACCTA
65 ACCATAGGACAATGAAATTTAAATAGTGCCCACTAGGGCCACTGTTCTTAAAGCAGCAAAACCTA
* * *
668756 TTATAAGCAATTTTCTTTGGCTTAATAAGATTAAACAGAAAGTTGTACTTACAGCTAGTGTCCAA
130 TTATAAGCAATTTGCTTTGGCTTAACAAGA-T-AACAAAAAGTTGTACTTACAGCTAGTGTCCAA
668821 ACAACCAAAGAGA
193 ACAACCAAAGAGA
* * *
668834 ATTGTACGTTCTATCCAG-A-ATCAAAGCTACTTTAAAATGCTGAAAAAACTAGAAACTTCCAAA
1 ATTGTACATTCTATCCAGAACATCAAAGCTACATCAAAATGCTGAAAAAACTAGAAACTTCCAAA
668897 CCATAGGACAATGAAATTTAAATAGTGCCCACTAGGGCCACTGTTCTTAAAGCAGCAAAACCTAT
66 CCATAGGACAATGAAATTTAAATAGTGCCCACTAGGGCCACTGTTCTTAAAGCAGCAAAACCTAT
* *
668962 TATCAGTAATTTGCTTTGGCTTAACAAGATAACAAAAAGTTGTACTTACAGCTAGTGTCCAAACA
131 TATAAGCAATTTGCTTTGGCTTAACAAGATAACAAAAAGTTGTACTTACAGCTAGTGTCCAAACA
669027 ACCAAAGAGA
196 ACCAAAGAGA
669037 CTTTGATGGC
Statistics
Matches: 191, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
203 44 0.23
204 1 0.01
205 128 0.67
207 1 0.01
208 17 0.09
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (205 bp):
ATTGTACATTCTATCCAGAACATCAAAGCTACATCAAAATGCTGAAAAAACTAGAAACTTCCAAA
CCATAGGACAATGAAATTTAAATAGTGCCCACTAGGGCCACTGTTCTTAAAGCAGCAAAACCTAT
TATAAGCAATTTGCTTTGGCTTAACAAGATAACAAAAAGTTGTACTTACAGCTAGTGTCCAAACA
ACCAAAGAGA
Found at i:676787 original size:3 final size:3
Alignment explanation
Indices: 676779--676804 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
676769 GCTAGGGTTT
676779 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
676805 AATAACAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:696371 original size:33 final size:34
Alignment explanation
Indices: 696325--696390 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
696315 AGGAGGATTG
* *
696325 TAAAAAGGTATTAATGTAGTTAATAACATATATC
1 TAAAAAGGTATTAATATAGTGAATAACATATATC
696359 TAAAAA-GTATTAATATAGTGAATAACATATAT
1 TAAAAAGGTATTAATATAGTGAATAACATATAT
696391 TGTTGGAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.35
Consensus pattern (34 bp):
TAAAAAGGTATTAATATAGTGAATAACATATATC
Found at i:696421 original size:12 final size:12
Alignment explanation
Indices: 696404--696430 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
696394 TGGAGGAGTA
696404 TTGTAATCATGG
1 TTGTAATCATGG
696416 TTGTAATCATGG
1 TTGTAATCATGG
696428 TTG
1 TTG
696431 GAATGATGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (12 bp):
TTGTAATCATGG
Found at i:701312 original size:10 final size:10
Alignment explanation
Indices: 701286--701315 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
701276 TAATATCATT
*
701286 CATATAGATA
1 CATATATATA
701296 CATATATATA
1 CATATATATA
701306 CATATATATA
1 CATATATATA
701316 ATAAGCCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (10 bp):
CATATATATA
Found at i:701657 original size:15 final size:15
Alignment explanation
Indices: 701639--701681 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
701629 ATTAATATAT
701639 ATTTTA-AAAATAATA
1 ATTTTATAAAA-AATA
701654 ATTTTATAAAAAATA
1 ATTTTATAAAAAATA
701669 A-TTTATTAAAAAA
1 ATTTTA-TAAAAAA
701682 ATTAGAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTTATAAAAAATA
Found at i:701956 original size:35 final size:35
Alignment explanation
Indices: 701893--701960 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
701883 ACAAAATTTT
* * *
701893 AATATAAGAAAATCTCTTTTTCTTAAAAAAAAATA
1 AATACAAGAAAAGCTCTTTTTCTAAAAAAAAAATA
701928 AATACAAGAAAAGCTTCTTTTT-TAAAAAAAAAA
1 AATACAAGAAAAGC-TCTTTTTCTAAAAAAAAAA
701961 ATTAATAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (35 bp):
AATACAAGAAAAGCTCTTTTTCTAAAAAAAAAATA
Found at i:703335 original size:35 final size:35
Alignment explanation
Indices: 703233--703343 Score: 98
Period size: 35 Copynumber: 3.1 Consensus size: 35
703223 TGATGAAAGT
* * *
703233 CAAATGTAGAGGG-AAGAATACCACACAATTAAAGC
1 CAAATGTAG-GGGTAAGAATACTACACAAATATAGC
* * * * ***
703268 CTAGATGTGGGGGTAAAAATACTTCTTGAATATAGC
1 C-AAATGTAGGGGTAAGAATACTACACAAATATAGC
*
703304 CAAATGTAGGGGTAAGAATACTACACAAATATAAC
1 CAAATGTAGGGGTAAGAATACTACACAAATATAGC
703339 CAAAT
1 CAAAT
703344 ATAGAAGGCA
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
35 35 0.62
36 21 0.38
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (35 bp):
CAAATGTAGGGGTAAGAATACTACACAAATATAGC
Found at i:712904 original size:25 final size:25
Alignment explanation
Indices: 712876--712923 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
712866 TGAAATATGA
712876 TTTATGATTATACTTAAATGATTTT
1 TTTATGATTATACTTAAATGATTTT
*
712901 TTTATGATTGTACTTAAATGATT
1 TTTATGATTATACTTAAATGATT
712924 GGTTCAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (25 bp):
TTTATGATTATACTTAAATGATTTT
Found at i:712934 original size:25 final size:25
Alignment explanation
Indices: 712881--712935 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
712871 TATGATTTAT
* ** * *
712881 GATTATACTTAAATGATTTTTTTAT
1 GATTGTACTTAAATGATTGGTTCAA
712906 GATTGTACTTAAATGATTGGTTCAA
1 GATTGTACTTAAATGATTGGTTCAA
712931 GATTG
1 GATTG
712936 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.47
Consensus pattern (25 bp):
GATTGTACTTAAATGATTGGTTCAA
Found at i:714926 original size:35 final size:36
Alignment explanation
Indices: 714886--715030 Score: 102
Period size: 35 Copynumber: 4.1 Consensus size: 36
714876 NNNNNNNNNN
*
714886 CAATTAGGCCTAATAACTTAATTAAAT-AGTTTATT
1 CAATTAGGCCTAATAACTTAATTAAATAAGTTTAAT
* * * *
714921 TAATTAAG-CTGAACAACTTAATTAAATAATTTTAAT
1 CAATTAGGCCT-AATAACTTAATTAAATAAGTTTAAT
* *
714957 CAATTAGGCCCAATGAA-TTAATTAAACAA-TTTAAAT
1 CAATTAGGCCTAAT-AACTTAATTAAATAAGTTT-AAT
* ** * * * *
714993 -GATTAAACCCAACAACTTAATTAAACAATTTTAAT
1 CAATTAGGCCTAATAACTTAATTAAATAAGTTTAAT
715028 CAA
1 CAA
715031 GTACTTGAGA
Statistics
Matches: 87, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
34 4 0.05
35 48 0.55
36 32 0.37
37 3 0.03
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.34
Consensus pattern (36 bp):
CAATTAGGCCTAATAACTTAATTAAATAAGTTTAAT
Found at i:714978 original size:71 final size:71
Alignment explanation
Indices: 714886--715030 Score: 184
Period size: 71 Copynumber: 2.0 Consensus size: 71
714876 NNNNNNNNNN
* * * ** * ** *
714886 CAATTAGGCCTAATAACTTAATTAAATAGTTTATTTAATTAAGCTGAACAACTTAATTAAATAAT
1 CAATTAGGCCCAATAACTTAATTAAACAATTTAAATAATTAAACCCAACAACTTAATTAAACAAT
714951 TTTAAT
66 TTTAAT
*
714957 CAATTAGGCCCAATGAA-TTAATTAAACAATTTAAATGATTAAACCCAACAACTTAATTAAACAA
1 CAATTAGGCCCAAT-AACTTAATTAAACAATTTAAATAATTAAACCCAACAACTTAATTAAACAA
715021 TTTTAAT
65 TTTTAAT
715028 CAA
1 CAA
715031 GTACTTGAGA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 61 0.97
72 2 0.03
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.34
Consensus pattern (71 bp):
CAATTAGGCCCAATAACTTAATTAAACAATTTAAATAATTAAACCCAACAACTTAATTAAACAAT
TTTAAT
Found at i:716385 original size:19 final size:19
Alignment explanation
Indices: 716361--716403 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
716351 AAGTTTTCTC
* *
716361 AATTAGTATATAGCTTTAA
1 AATTAGCATAAAGCTTTAA
*
716380 AATTAGCATAAAGCTTTAT
1 AATTAGCATAAAGCTTTAA
716399 AATTA
1 AATTA
716404 CCTCTTCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (19 bp):
AATTAGCATAAAGCTTTAA
Found at i:729888 original size:31 final size:29
Alignment explanation
Indices: 729824--729959 Score: 143
Period size: 28 Copynumber: 4.6 Consensus size: 29
729814 TAACATGTTG
*
729824 GTCTTAATTTAGACAA-AAAAATATGTTT
1 GTCTTAATTTAGACAAGAAAAATATTTTT
*
729852 ATCTTAATTTAAGACAAGAAAAATATTTTTT
1 GTCTTAATTT-AGACAAGAAAAATA-TTTTT
*
729883 GTCTTAATTTAGATAAGAAAACATA--TTT
1 GTCTTAATTTAGACAAGAAAA-ATATTTTT
* * * *
729911 GTCTCAGTTTGGACAAGATAAAATTTTTTT
1 GTCTTAATTTAGACAAGA-AAAATATTTTT
729941 GTCTTAATTATAGACAAGA
1 GTCTTAATT-TAGACAAGA
729960 GTTGTCTTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
28 28 0.32
29 9 0.10
30 27 0.31
31 24 0.27
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (29 bp):
GTCTTAATTTAGACAAGAAAAATATTTTT
Found at i:731291 original size:20 final size:20
Alignment explanation
Indices: 731266--731307 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
731256 AAAAGGGAAA
731266 TAAGAC-TCACATTAATCAAT
1 TAAGACTTC-CATTAATCAAT
*
731286 TAAGACTTCCTTTAATCAAT
1 TAAGACTTCCATTAATCAAT
731306 TA
1 TA
731308 GAACATCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAGACTTCCATTAATCAAT
Found at i:745317 original size:2 final size:2
Alignment explanation
Indices: 745312--745338 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
745302 ATATAACTTG
745312 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
745339 GGTCAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:746229 original size:22 final size:22
Alignment explanation
Indices: 746203--746248 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
746193 CCAAGCTGAA
*
746203 CTTTCCTTCCTTT-CTCTCTTTT
1 CTTT-CTTCCTTTCCTCTCCTTT
*
746225 CTTTCTTTCTTTCCTCTCCTTT
1 CTTTCTTCCTTTCCTCTCCTTT
746247 CT
1 CT
746249 CTTTTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (22 bp):
CTTTCTTCCTTTCCTCTCCTTT
Found at i:750139 original size:12 final size:12
Alignment explanation
Indices: 750122--750148 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
750112 AAGATTGAAA
750122 CATATGAAAATC
1 CATATGAAAATC
750134 CATATGAAAATC
1 CATATGAAAATC
750146 CAT
1 CAT
750149 TCGAGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (12 bp):
CATATGAAAATC
Found at i:753283 original size:21 final size:21
Alignment explanation
Indices: 753259--753306 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
753249 ATGAATTTAC
753259 CTTGATCAATTTATATGACTA
1 CTTGATCAATTTATATGACTA
** * *
753280 CTTGATTGATTTATATGCCTG
1 CTTGATCAATTTATATGACTA
753301 CTTGAT
1 CTTGAT
753307 TGATTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (21 bp):
CTTGATCAATTTATATGACTA
Found at i:753307 original size:21 final size:21
Alignment explanation
Indices: 753267--753312 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
753257 ACCTTGATCA
753267 ATTTATATGACTACTTGATTG
1 ATTTATATGACTACTTGATTG
* *
753288 ATTTATATGCCTGCTTGATTG
1 ATTTATATGACTACTTGATTG
753309 ATTT
1 ATTT
753313 TATTATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (21 bp):
ATTTATATGACTACTTGATTG
Found at i:754061 original size:18 final size:17
Alignment explanation
Indices: 754030--754067 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
754020 CATTGAATCA
754030 CTTTCAAATTCA-TTTC
1 CTTTCAAATTCATTTTC
754046 CTTTCACAAGTTCATTTTC
1 CTTTCA-AA-TTCATTTTC
754065 CTT
1 CTT
754068 GGTCCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 4 0.21
19 7 0.37
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.50
Consensus pattern (17 bp):
CTTTCAAATTCATTTTC
Found at i:757826 original size:57 final size:56
Alignment explanation
Indices: 757753--758046 Score: 173
Period size: 58 Copynumber: 5.0 Consensus size: 56
757743 GGTAGCTTTT
*
757753 ACATGTTTGTCTTAATTTAAACCAA-AAAACATAATTTATCTTAACTTAGACAAGAAG
1 ACATATTTGTCTTAATTTAAA-CAAGAAAACAT-ATTTATCTTAACTTAGACAAGAAG
* * *
757810 ACATATTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAGTTTAGACAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAAACAAGAAAACATATTTATC-----TTA-AC---TTAGACAAGAAG
* * * * * * *
757875 ACATGTTTTATCTTAATTTAGATA-AAG-AAACATGTTTGTCTTTATTTAGACAAGAAA
1 ACAT-ATTTGTCTTAATTTA-A-ACAAGAAAACATATTTATCTTAACTTAGACAAGAAG
** * * * * * *
757932 ATGTATTTGTCTTAATTTAGACAAGAAAAACATGTTTTGTCTTAATTTAGATAAGAAA
1 ACATATTTGTCTTAATTTAAACAAG-AAAACAT-ATTTATCTTAACTTAGACAAGAAG
* * * * *
757990 ACATGTTTATCTTAATTCAAACAAGAAAA-ATATGTTTTGTCTTAACTTATACAAGAA
1 ACATATTTGTCTTAATTTAAACAAGAAAACATA---TTTATCTTAACTTAGACAAGAA
758047 AACTTGTTTG
Statistics
Matches: 189, Mismatches: 28, Indels: 39
0.74 0.11 0.15
Matches are distributed among these distances:
54 1 0.01
55 3 0.02
56 24 0.13
57 50 0.26
58 59 0.31
60 1 0.01
61 5 0.03
62 2 0.01
65 15 0.08
66 25 0.13
67 3 0.02
68 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (56 bp):
ACATATTTGTCTTAATTTAAACAAGAAAACATATTTATCTTAACTTAGACAAGAAG
Found at i:757829 original size:28 final size:28
Alignment explanation
Indices: 757753--757861 Score: 139
Period size: 28 Copynumber: 3.9 Consensus size: 28
757743 GGTAGCTTTT
* *
757753 ACATGTTTGTCTTAATTTAAACCAA-AAA
1 ACATATTTGTCTTAATTTAGA-CAAGAAA
* * *
757781 ACATAATTTATCTTAACTTAGACAAGAAG
1 ACAT-ATTTGTCTTAATTTAGACAAGAAA
757810 ACATATTTGTCTTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAA
*
757838 ACATATTTGTCTTAGTTTAGACAA
1 ACATATTTGTCTTAATTTAGACAA
757862 TTTAGACAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 51 0.73
29 19 0.27
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (28 bp):
ACATATTTGTCTTAATTTAGACAAGAAA
Found at i:757873 original size:37 final size:38
Alignment explanation
Indices: 757823--757896 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
757813 TATTTGTCTT
* *
757823 AATTTAGACAAGAAAACAT-ATTTGTCTTAGTTTAGAC
1 AATTTAGACAAGAAAACATGATTTATCTTAATTTAGAC
*
757860 AATTTAGACAAGAAAACATGTTTTATCTTAATTTAGA
1 AATTTAGACAAGAAAACATGATTTATCTTAATTTAGA
757897 TAAAGAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (38 bp):
AATTTAGACAAGAAAACATGATTTATCTTAATTTAGAC
Found at i:757884 original size:28 final size:28
Alignment explanation
Indices: 757860--758086 Score: 178
Period size: 28 Copynumber: 7.9 Consensus size: 28
757850 TAGTTTAGAC
*
757860 AATTTAGACAAGAAAACATGTTTTATCTT
1 AATTTAGACAAGAAAACATGTTTTGTC-T
*
757889 AATTTAGATAA-AGAAACATG-TTTGTCTT
1 AATTTAGACAAGA-AAACATGTTTTGTC-T
*
757917 TATTTAGACAAG-AAA-ATGTATTTGTCTT
1 AATTTAGACAAGAAAACATGT-TTTGTC-T
757945 AATTTAGACAAGAAAAACATGTTTTGTCTT
1 AATTTAGACAAG-AAAACATGTTTTGTC-T
* *
757975 AATTTAGATAAGAAAACATG-TTTATCTT
1 AATTTAGACAAGAAAACATGTTTTGTC-T
* * *
758003 AATTCAAACAAGAAAAATATGTTTTGTCTT
1 AATTTAGACAAG-AAAACATGTTTTGTC-T
* * *
758033 AACTTATACAAGAAAACTTGTTTGTGTC-
1 AATTTAGACAAGAAAACATGTTT-TGTCT
* * *
758061 AATATTAGACCAGATAATATGTTTTG
1 AAT-TTAGACAAGAAAACATGTTTTG
758087 CCTTAAGTAA
Statistics
Matches: 164, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.02
27 3 0.02
28 56 0.34
29 56 0.34
30 42 0.26
31 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (28 bp):
AATTTAGACAAGAAAACATGTTTTGTCT
Found at i:757906 original size:66 final size:65
Alignment explanation
Indices: 757798--757927 Score: 174
Period size: 66 Copynumber: 2.0 Consensus size: 65
757788 TTATCTTAAC
* * *
757798 TTAGACAAGAAGACATATTTGTCTTAATTTAGACAAGAAAACATATTTGTC-TTAGTTTAGACAA
1 TTAGACAAGAAAACATATTTATCTTAATTTAGAAAAGAAAACATATTTGTCTTTA-TTTAGACAA
757862 T
65 T
* *
757863 TTAGACAAGAAAACATGTTTTATCTTAATTTAGATAAAG-AAACATGTTTGTCTTTATTTAGACA
1 TTAGACAAGAAAACAT-ATTTATCTTAATTTAGA-AAAGAAAACATATTTGTCTTTATTTAGACA
757927 A
64 A
757928 GAAAATGTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
65 15 0.26
66 36 0.63
67 6 0.11
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (65 bp):
TTAGACAAGAAAACATATTTATCTTAATTTAGAAAAGAAAACATATTTGTCTTTATTTAGACAAT
Found at i:758014 original size:86 final size:87
Alignment explanation
Indices: 757860--758048 Score: 260
Period size: 86 Copynumber: 2.2 Consensus size: 87
757850 TAGTTTAGAC
* * * *
757860 AATTTAGACAAG-AAAACATGTTTTATCTTAATTTAGATAAAGAAACATGTTTGTCTTTATTTAG
1 AATTTAGACAAGAAAAACATGTTTTATCTTAATTTAGATAAAGAAACATGTTTATCTTAATTCAA
757924 ACAAG-AAA-ATGTATTTGTCTT
66 ACAAGAAAATATGT-TTTGTCTT
*
757945 AATTTAGACAAGAAAAACATGTTTTGTCTTAATTTAGAT-AAGAAAACATGTTTATCTTAATTCA
1 AATTTAGACAAGAAAAACATGTTTTATCTTAATTTAGATAAAG-AAACATGTTTATCTTAATTCA
758009 AACAAGAAAAATATGTTTTGTCTT
65 AACAAG-AAAATATGTTTTGTCTT
* *
758033 AACTTATACAAGAAAA
1 AATTTAGACAAGAAAA
758049 CTTGTTTGTG
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
85 15 0.16
86 48 0.52
88 25 0.27
89 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (87 bp):
AATTTAGACAAGAAAAACATGTTTTATCTTAATTTAGATAAAGAAACATGTTTATCTTAATTCAA
ACAAGAAAATATGTTTTGTCTT
Found at i:758049 original size:58 final size:58
Alignment explanation
Indices: 757860--758055 Score: 243
Period size: 58 Copynumber: 3.4 Consensus size: 58
757850 TAGTTTAGAC
* *
757860 AATTTAGACAAGAAAACATGTTTTATCTTAATTTAGATAA-AGAAACATG-TTTGTCTT
1 AATTTAGACAAGAAAACATG-TTTATCTTAATTTAGACAAGAAAAACATGTTTTGTCTT
* ** * *
757917 TATTTAGACAAGAAAATGTATTTGTCTTAATTTAGACAAGAAAAACATGTTTTGTCTT
1 AATTTAGACAAGAAAACATGTTTATCTTAATTTAGACAAGAAAAACATGTTTTGTCTT
* * * *
757975 AATTTAGATAAGAAAACATGTTTATCTTAATTCAAACAAGAAAAATATGTTTTGTCTT
1 AATTTAGACAAGAAAACATGTTTATCTTAATTTAGACAAGAAAAACATGTTTTGTCTT
* * *
758033 AACTTATACAAGAAAACTTGTTT
1 AATTTAGACAAGAAAACATGTTT
758056 GTGTCAATAT
Statistics
Matches: 117, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
56 17 0.15
57 24 0.21
58 76 0.65
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (58 bp):
AATTTAGACAAGAAAACATGTTTATCTTAATTTAGACAAGAAAAACATGTTTTGTCTT
Found at i:763705 original size:29 final size:29
Alignment explanation
Indices: 763672--763728 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
763662 ATTTAAGAAA
*
763672 ATTCAAATAAG-TCATTATATTTTTATTTC
1 ATTCAAATAAGCTC-GTATATTTTTATTTC
**
763701 ATTCAGTTAAGCTCGTATATTTTTATTT
1 ATTCAAATAAGCTCGTATATTTTTATTT
763729 TGAATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (29 bp):
ATTCAAATAAGCTCGTATATTTTTATTTC
Found at i:766322 original size:31 final size:31
Alignment explanation
Indices: 766287--766349 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
766277 AAGCAAAAAG
766287 CAAGTAGGATAAGTGA-CAACCAAAATGGAGC
1 CAAGTAGGATAAGT-ATCAACCAAAATGGAGC
766318 CAAGTAGGATAAGTATCAACCAAAATGGAGC
1 CAAGTAGGATAAGTATCAACCAAAATGGAGC
766349 C
1 C
766350 TTACACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.14
Consensus pattern (31 bp):
CAAGTAGGATAAGTATCAACCAAAATGGAGC
Found at i:766550 original size:2 final size:2
Alignment explanation
Indices: 766543--766584 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
766533 TTTTTGAAGG
* *
766543 TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
766585 ACACACACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:766611 original size:16 final size:16
Alignment explanation
Indices: 766590--766629 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
766580 CTCTCACACA
*
766590 CACACACACACGCACG
1 CACACACACACGCACC
**
766606 CACACACACATTCACC
1 CACACACACACGCACC
766622 CACACACA
1 CACACACA
766630 TGACTGCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.50, G:0.05, T:0.05
Consensus pattern (16 bp):
CACACACACACGCACC
Found at i:767643 original size:33 final size:33
Alignment explanation
Indices: 767601--767668 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
767591 AAAGGTAGGG
*
767601 CTATGTATAGCTATGGCTTTTTTCTCAGCATTT
1 CTATGTATAGCTATGGCTTTTTTCTCAACATTT
767634 CTATGTATAGCTATGGCTTTTTTCTCAACATTT
1 CTATGTATAGCTATGGCTTTTTTCTCAACATTT
767667 CT
1 CT
767669 TACATTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (33 bp):
CTATGTATAGCTATGGCTTTTTTCTCAACATTT
Found at i:773885 original size:47 final size:47
Alignment explanation
Indices: 773813--774323 Score: 430
Period size: 47 Copynumber: 10.9 Consensus size: 47
773803 CATGGCAAAA
* *
773813 TTCAGAGTTTGGTGACACGCCATGGAAGGAATCTGTGACACTCTAGAG
1 TTCAGAGTTT-GTGACACGCCATGGAGGGAATCTGTGACACGCTAGAG
* * * * **
773861 TTCAAAGTTTGTGACACGGCATGGAGGGAAACTATGACATACTAGAG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGAG
* * * *
773908 TTCAGAG-TT-TGACACGGCATGGATGGAATCTATGACACGGTAGTA-
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAG-AG
* * *
773953 TTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGC-AGGG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-GCTAGAG
* * * * *
774000 TTCAGGGTTTGTGACACGCCATTGAGGGAATTTGTGACACAAC-AGGG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-GCTAGAG
* * * *
774047 TTCAGGGTTTGTGACACACCATGGAGGGAATCTGTGACACGTTAGTG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGAG
* * * * * *
774094 TTCAGAGTTGGTGACACGACAAGGAGGGAATCCGTGACACGCCAAAG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGAG
* * * * *
774141 TTCAGAG-TT-TGACACGGCATGGATGGAATTTGTGACACGGTAGGG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGAG
* * * *
774186 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCCAGTG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGAG
* * * *** * * *
774233 TTCAGAATTGGTGACACGCCA-GCATTCAAGGTTTGTGACACGATAGCG
1 TTCAGAGTTTGTGACACGCCATGGAGGGAA--TCTGTGACACGCTAGAG
* * *
774281 TTCAG-GGTTGTGACACGCCACT-GAGAGAATCTGTGACATGCTA
1 TTCAGAGTTTGTGACACGCCA-TGGAGGGAATCTGTGACACGCTA
774324 TGTGTGTGTC
Statistics
Matches: 372, Mismatches: 79, Indels: 26
0.78 0.17 0.05
Matches are distributed among these distances:
45 69 0.19
46 23 0.06
47 250 0.67
48 30 0.08
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (47 bp):
TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCTAGAG
Found at i:773990 original size:23 final size:23
Alignment explanation
Indices: 773960--774087 Score: 93
Period size: 23 Copynumber: 5.5 Consensus size: 23
773950 GTATTCAGAG
*
773960 TTTGTGACACGGCATGGAGGGAA
1 TTTGTGACACGCCATGGAGGGAA
* *
773983 TTTGTGACACGGCAGGGTTCAGGG--
1 TTTGTGACACGCCATGG---AGGGAA
*
774007 TTTGTGACACGCCATTGAGGGAA
1 TTTGTGACACGCCATGGAGGGAA
** *
774030 TTTGTGACACAACAGGGTTCAGGG--
1 TTTGTGACACGCCATGG---AGGGAA
*
774054 TTTGTGACACACCATGGAGGGAA
1 TTTGTGACACGCCATGGAGGGAA
*
774077 TCTGTGACACG
1 TTTGTGACACG
774088 TTAGTGTTCA
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
21 8 0.10
23 38 0.46
24 29 0.35
26 8 0.10
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (23 bp):
TTTGTGACACGCCATGGAGGGAA
Found at i:774064 original size:24 final size:24
Alignment explanation
Indices: 773983--774064 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
773973 ATGGAGGGAA
**
773983 TTTGTGACACGGCAGGGTTCAGGG
1 TTTGTGACACAACAGGGTTCAGGG
** *
774007 TTTGTGACACGCCA---TTGAGGG
1 TTTGTGACACAACAGGGTTCAGGG
774028 AATTTGTGACACAACAGGGTTCAGGG
1 --TTTGTGACACAACAGGGTTCAGGG
774054 TTTGTGACACA
1 TTTGTGACACA
774065 CCATGGAGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
21 6 0.12
23 12 0.25
24 24 0.50
26 6 0.12
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (24 bp):
TTTGTGACACAACAGGGTTCAGGG
Found at i:774072 original size:94 final size:94
Alignment explanation
Indices: 773813--774318 Score: 411
Period size: 92 Copynumber: 5.4 Consensus size: 94
773803 CATGGCAAAA
* * * * *
773813 TTCAGAGTTTGGTGACACGCCATGGAAGGAATCTGTGACAC-TCTAGAGTTCAAAGTTTGTGACA
1 TTCAGGGTTT-GTGACACGCCATGGAGGGAATCTGTGACACAAC-AAAGTTCAGAGTTTGTGACA
** * *** *
773877 CGGCATGGAGGGAAACTATGACATACTAGAG
64 CGGCATGGAGGGAATTTGTGACACGGTAGGG
* * * * *** *
773908 TTCAGAG-TT-TGACACGGCATGGATGGAATCTATGACACGGTAGTA-TTCAGAGTTTGTGACAC
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACA-AAGTTCAGAGTTTGTGACAC
*
773970 GGCATGGAGGGAATTTGTGACACGGCAGGG
65 GGCATGGAGGGAATTTGTGACACGGTAGGG
* * ** * *
774000 TTCAGGGTTTGTGACACGCCATTGAGGGAATTTGTGACACAACAGGGTTCAGGGTTTGTGACACA
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACAAAGTTCAGAGTTTGTGACACG
* * * *
774065 CCATGGAGGGAATCTGTGACACGTTAGTG
66 GCATGGAGGGAATTTGTGACACGGTAGGG
* * * * * **
774094 TTCAGAGTTGGTGACACGACAAGGAGGGAATCCGTGACACGCCAAAGTTCAGAG-TT-TGACACG
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACAAAGTTCAGAGTTTGTGACACG
*
774157 GCATGGATGGAATTTGTGACACGGTAGGG
66 GCATGGAGGGAATTTGTGACACGGTAGGG
*** ** * *
774186 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCCAGTGTTCAGAATTGGTGACACG
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACAAAGTTCAGAGTTTGTGACACG
** * * *
774251 CCAGCATTCAAGG--TTTGTGACACGATAGCG
66 ---GCATGGAGGGAATTTGTGACACGGTAGGG
*
774281 TTCAGGG-TTGTGACACGCCACT-GAGAGAATCTGTGACA
1 TTCAGGGTTTGTGACACGCCA-TGGAGGGAATCTGTGACA
774319 TGCTATGTGT
Statistics
Matches: 333, Mismatches: 67, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
92 146 0.44
93 6 0.02
94 144 0.43
95 30 0.09
97 7 0.02
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (94 bp):
TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACAAAGTTCAGAGTTTGTGACACG
GCATGGAGGGAATTTGTGACACGGTAGGG
Found at i:774156 original size:186 final size:186
Alignment explanation
Indices: 773813--774224 Score: 517
Period size: 186 Copynumber: 2.2 Consensus size: 186
773803 CATGGCAAAA
* * *
773813 TTCAGAGTTTGGTGACACGCCATGGAAGGAATCTGTGACACTCTAGAGTTCAAAGTTTGTGACAC
1 TTCAGGGTTT-GTGACACGCCATGGAGGGAATCTGTGACACACTAGAGTTCAAAGTTTGTGACAC
** * * * * *
773878 GGCATGGAGGGAAACTATGACATACTAGAGTTCAGAGTTTGACACGGCATGGATGGAATCTATGA
65 ACCATGGAGGGAAACTATGACACACTAGAGTTCAGAGTTTGACACGACAAGGAGGGAATCCATGA
** *
773943 CACGGTAGTATTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
130 CACGCCAGAATTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
* * * **
774000 TTCAGGGTTTGTGACACGCCATTGAGGGAATTTGTGACACAAC-AGGGTTCAGGGTTTGTGACAC
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-ACTAGAGTTCAAAGTTTGTGACAC
* * ** * *
774064 ACCATGGAGGGAATCTGTGACACGTTAGTGTTCAGAGTTGGTGACACGACAAGGAGGGAATCCGT
65 ACCATGGAGGGAAACTATGACACACTAGAGTTCAGAGTT--TGACACGACAAGGAGGGAATCCAT
* *
774129 GACACGCCA-AAGTTCAGAG-TT-TGACACGGCATGGATGGAATTTGTGACACGGTAGGG
128 GACACGCCAGAA-TTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
774186 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACA
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACA
774225 TGCCAGTGTT
Statistics
Matches: 193, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
186 147 0.76
187 13 0.07
188 33 0.17
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (186 bp):
TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACACTAGAGTTCAAAGTTTGTGACACA
CCATGGAGGGAAACTATGACACACTAGAGTTCAGAGTTTGACACGACAAGGAGGGAATCCATGAC
ACGCCAGAATTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
Found at i:774178 original size:23 final size:23
Alignment explanation
Indices: 774150--774224 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
774140 GTTCAGAGTT
774150 TGACACGGCATGGATGGAATTTG
1 TGACACGGCATGGATGGAATTTG
* * * *
774173 TGACACGGTAGGGTTCAGG-GTTTG
1 TGACACGGCATGGAT--GGAATTTG
* * *
774197 TGACACGCCATGGAGGGAATCTG
1 TGACACGGCATGGATGGAATTTG
774220 TGACA
1 TGACA
774225 TGCCAGTGTT
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
22 2 0.05
23 20 0.53
24 14 0.37
25 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (23 bp):
TGACACGGCATGGATGGAATTTG
Found at i:774220 original size:139 final size:141
Alignment explanation
Indices: 773813--774250 Score: 506
Period size: 139 Copynumber: 3.1 Consensus size: 141
773803 CATGGCAAAA
* * * * *
773813 TTCAGAGTTTGGTGACACGCCATGGAAGGAATCTGTGACACTCTAGAGTTCAAAGTTTGTGACAC
1 TTCAGAG-TTGGTGACACGACATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTTTGTGACAC
** * * * * * * * *
773878 GGCATGGAGGGAAACTATGACATACTAGAGTTCAGAG-TT-TGACACGGCATGGATGGAATCTAT
65 GGCATGGAGGGAATTTGTGACACAATAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGT
* *
773941 GACACGGTAGTA
130 GACACGCTAGTG
* * * * * *
773953 TTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGGTTCAGGGTTTGTGACACG
1 TTCAGAGTTGGTGACACGACATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTTTGTGACACG
* * * *
774018 CCATTGAGGGAATTTGTGACACAACAGGGTTCAGGGTTTGTGACACACCATGGAGGGAATCTGTG
66 GCATGGAGGGAATTTGTGACACAATAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTG
*
774083 ACACGTTAGTG
131 ACACGCTAGTG
* * *
774094 TTCAGAGTTGGTGACACGACAAGGAGGGAATCCGTGACACGCCAAAGTTCAGAG-TT-TGACACG
1 TTCAGAGTTGGTGACACGACATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTTTGTGACACG
* **
774157 GCATGGATGGAATTTGTGACACGGTAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTG
66 GCATGGAGGGAATTTGTGACACAATAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTG
* *
774222 ACATGCCAGTG
131 ACACGCTAGTG
*
774233 TTCAGAATTGGTGACACG
1 TTCAGAGTTGGTGACACG
774251 CCAGCATTCA
Statistics
Matches: 250, Mismatches: 46, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
139 164 0.66
140 11 0.04
141 75 0.30
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (141 bp):
TTCAGAGTTGGTGACACGACATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTTTGTGACACG
GCATGGAGGGAATTTGTGACACAATAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTG
ACACGCTAGTG
Found at i:774249 original size:233 final size:233
Alignment explanation
Indices: 773813--774318 Score: 617
Period size: 233 Copynumber: 2.2 Consensus size: 233
773803 CATGGCAAAA
* * *
773813 TTCAGAGTTTGGTGACACGCCATGGAAGGAATCTGTGACACTCTAGAGTTCAAAGTTTGTGACAC
1 TTCAGGGTTT-GTGACACGCCATGGAGGGAATCTGTGACACTCTAGAGTTCAAAGTTGGTGACAC
* * * * * *
773878 GGCATGGAGGGAAACTATGACATACTAGAGTTCAGAGTTTGACACGGCATGGATGGAATCTATGA
65 GACAAGGAGGGAAACCATGACACACCAAAGTTCAGAGTTTGACACGGCATGGATGGAATCTATGA
* * * * **
773943 CACGGTAGTATTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGGTTCAGGGT
130 CACGGTAGGATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGGGTTCAGAAT
* * * *
774008 TTGTGACACG-C-CATTGAGGGAATTTGTGACACAACAGGG
195 TGGTGACACGCCACATTCAAGG--TTTGTGACACAACAGCG
* * *
774047 TTCAGGGTTTGTGACACACCATGGAGGGAATCTGTGACACGT-TAGTGTTCAGAGTTGGTGACAC
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-TCTAGAGTTCAAAGTTGGTGACAC
* * * * *
774111 GACAAGGAGGGAATCCGTGACACGCCAAAGTTCAGAGTTTGACACGGCATGGATGGAATTTGTGA
65 GACAAGGAGGGAAACCATGACACACCAAAGTTCAGAGTTTGACACGGCATGGATGGAATCTATGA
* * * *
774176 CACGGTAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCCAGTGTTCAGAAT
130 CACGGTAGGATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGGGTTCAGAAT
* *
774241 TGGTGACACGCCAGCATTCAAGGTTTGTGACACGATAGCG
195 TGGTGACACGCCA-CATTCAAGGTTTGTGACACAACAGCG
*
774281 TTCAGGG-TTGTGACACGCCACT-GAGAGAATCTGTGACA
1 TTCAGGGTTTGTGACACGCCA-TGGAGGGAATCTGTGACA
774319 TGCTATGTGT
Statistics
Matches: 232, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
233 192 0.83
234 33 0.14
236 7 0.03
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (233 bp):
TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCTAGAGTTCAAAGTTGGTGACACG
ACAAGGAGGGAAACCATGACACACCAAAGTTCAGAGTTTGACACGGCATGGATGGAATCTATGAC
ACGGTAGGATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGGGTTCAGAATT
GGTGACACGCCACATTCAAGGTTTGTGACACAACAGCG
Found at i:774270 original size:24 final size:23
Alignment explanation
Indices: 774243--774300 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
774233 TTCAGAATTG
*
774243 GTGACACGCCAGCATTCAAGGTTT
1 GTGACACGCCAGCATTC-AGGGTT
** *
774267 GTGACACGATAGCGTTCAGGGTT
1 GTGACACGCCAGCATTCAGGGTT
774290 GTGACACGCCA
1 GTGACACGCCA
774301 CTGAGAGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (23 bp):
GTGACACGCCAGCATTCAGGGTT
Found at i:774296 original size:186 final size:188
Alignment explanation
Indices: 773813--774297 Score: 468
Period size: 186 Copynumber: 2.6 Consensus size: 188
773803 CATGGCAAAA
* * * * *
773813 TTCAGAGTTTGGTGACACGCCATGGAAGGAATCTGTGACAC-TCTAGAGTTCA-AAGTTTGTGAC
1 TTCAGGGTTT-GTGACACGCCATGGAGGGAATCTGTGACACAAC-AGGGTTCAGAA-TTGGTGAC
** * * * * * * * * *
773876 ACGGCATGGAGGGAAACTATGACA-TACTAGAGTTCAGAGTT--TGACACGGCATGGATGGAATC
63 ACACCATGCAGGCAATCTGTGACACGA-TAGCGTTCAGAGTTGGTGACACGACAAGGAGGGAATC
** ** *
773938 TATGACACGGTAGTA-TTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
127 CGTGACACGCCA-AAGTTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
* * ** *
774000 TTCAGGGTTTGTGACACGCCATTGAGGGAATTTGTGACACAACAGGGTTCAGGGTTTGTGACACA
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACAGGGTTCAGAATTGGTGACACA
* * * *
774065 CCATGGAGGGAATCTGTGACACGTTAGTGTTCAGAGTTGGTGACACGACAAGGAGGGAATCCGTG
66 CCATGCAGGCAATCTGTGACACGATAGCGTTCAGAGTTGGTGACACGACAAGGAGGGAATCCGTG
* *
774130 ACACGCCAAAGTTCAGAG-TT-TGACACGGCATGGATGGAATTTGTGACACGGTAGGG
131 ACACGCCAAAGTTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
*** * *
774186 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCCAGTGTTCAGAATTGGTGACACG
1 TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACAGGGTTCAGAATTGGTGACACA
** * *
774251 CCA-GCATTCAAGGTTTGTGACACGATAGCGTTCAGGGTT-GTGACACG
66 CCATGCAGGCAA--TCTGTGACACGATAGCGTTCAGAGTTGGTGACACG
774298 CCACTGAGAG
Statistics
Matches: 247, Mismatches: 43, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
185 4 0.02
186 175 0.71
187 35 0.14
188 33 0.13
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (188 bp):
TTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACAACAGGGTTCAGAATTGGTGACACA
CCATGCAGGCAATCTGTGACACGATAGCGTTCAGAGTTGGTGACACGACAAGGAGGGAATCCGTG
ACACGCCAAAGTTCAGAGTTTGTGACACGGCATGGAGGGAATTTGTGACACGGCAGGG
Found at i:780695 original size:15 final size:14
Alignment explanation
Indices: 780681--780724 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
780671 AACAACAATT
780681 TTGAA-AAAAAAAA
1 TTGAATAAAAAAAA
780694 TTGAATAAAAAAAA
1 TTGAATAAAAAAAA
* *
780708 GTGCAAAAAAAAAAA
1 TTG-AATAAAAAAAA
780723 TT
1 TT
780725 TGTGGCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 5 0.19
14 10 0.38
15 11 0.42
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.18
Consensus pattern (14 bp):
TTGAATAAAAAAAA
Found at i:780703 original size:13 final size:13
Alignment explanation
Indices: 780681--780721 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
780671 AACAACAATT
780681 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
780694 TTGAATAAAAAAAA
1 TTGAA-AAAAAAAA
*
780708 GTGCAAAAAAAAAA
1 TTG-AAAAAAAAAA
780722 ATTTGTGGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 18 0.72
15 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:782592 original size:18 final size:18
Alignment explanation
Indices: 782569--782612 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
782559 CATTCATTCG
782569 GAAGCATTTGAAGATTGA
1 GAAGCATTTGAAGATTGA
*
782587 GAAGCATTAGAAGATTGA
1 GAAGCATTTGAAGATTGA
782605 G-AGCATTT
1 GAAGCATTT
782613 TAGAGATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (18 bp):
GAAGCATTTGAAGATTGA
Found at i:782619 original size:18 final size:19
Alignment explanation
Indices: 782569--782619 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
782559 CATTCATTCG
*
782569 GAAGCATTTGA-AGATTGA
1 GAAGCATTTTAGAGATTGA
782587 GAAGCA--TTAGAAGATTGA
1 GAAGCATTTTAG-AGATTGA
782605 G-AGCATTTTAGAGAT
1 GAAGCATTTTAGAGAT
782620 CAAGAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 2 0.07
17 4 0.14
18 18 0.64
19 4 0.14
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.27
Consensus pattern (19 bp):
GAAGCATTTTAGAGATTGA
Found at i:782677 original size:23 final size:23
Alignment explanation
Indices: 782649--782743 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
782639 TTAGGGTGAA
*
782649 GATCAAGCAACGGCGAAGTTTGT
1 GATCAAGCAACGGCGAAGTTCGT
*
782672 GATCAAGCGACGGCGAAGTTCGT
1 GATCAAGCAACGGCGAAGTTCGT
* **
782695 GATCAAGCGACAACGAAGTTCGT
1 GATCAAGCAACGGCGAAGTTCGT
* * * *
782718 GGTCAAGACAAAGTCCAAGTTCGT
1 GATCAAG-CAACGGCGAAGTTCGT
782742 GA
1 GA
782744 CTCTTGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
23 48 0.80
24 12 0.20
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (23 bp):
GATCAAGCAACGGCGAAGTTCGT
Found at i:792151 original size:26 final size:23
Alignment explanation
Indices: 792092--792145 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
792082 NNNNNNNNNN
792092 TGCTTGATCACGAACTTCGTTGT
1 TGCTTGATCACGAACTTCGTTGT
792115 TGCTTGATCACGAACTTCGTTGT
1 TGCTTGATCACGAACTTCGTTGT
792138 TGCTTGAT
1 TGCTTGAT
792146 GTTCACCCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (23 bp):
TGCTTGATCACGAACTTCGTTGT
Found at i:792210 original size:18 final size:18
Alignment explanation
Indices: 792183--792226 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
792173 TTGATCTTTG
792183 AAATGC-TCTCAATCTTC
1 AAATGCTTCTCAATCTTC
*
792200 GAATGCTTCTCAATCTTC
1 AAATGCTTCTCAATCTTC
792218 AAATGCTTC
1 AAATGCTTC
792227 CGAATGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (18 bp):
AAATGCTTCTCAATCTTC
Found at i:792659 original size:80 final size:81
Alignment explanation
Indices: 792516--792714 Score: 298
Period size: 80 Copynumber: 2.5 Consensus size: 81
792506 TTAAATTTTA
* *
792516 ATTGGTCAAAAATATGAAGATTATCTCTAAATTA-TTTGAATTTATTTAGAGATAAATTGGATGA
1 ATTGGTC-AAAATATAAATATTATCTCTAAATTATTTTGAATTTATTTAGAGATAAATTGGATGA
792580 CCAATAGCTAATATTTG
65 CCAATAGCTAATATTTG
* *
792597 ATTGGTCAAAATA-AAAT-TTGATCTCTAACATCATTTTG-ATTTGTTTAGAGATAAATTGGATG
1 ATTGGTCAAAATATAAATATT-ATCTCTAA-ATTATTTTGAATTTATTTAGAGATAAATTGGATG
792659 ACCAATAGCTAATATTTG
64 ACCAATAGCTAATATTTG
*
792677 ATTGGTCAAAATATCAATATTATCTCTAAATTATTTTG
1 ATTGGTCAAAATATAAATATTATCTCTAAATTATTTTG
792715 GGAGATAAAT
Statistics
Matches: 107, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
78 2 0.02
79 10 0.09
80 71 0.66
81 22 0.21
82 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (81 bp):
ATTGGTCAAAATATAAATATTATCTCTAAATTATTTTGAATTTATTTAGAGATAAATTGGATGAC
CAATAGCTAATATTTG
Found at i:796487 original size:16 final size:17
Alignment explanation
Indices: 796466--796499 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
796456 TTACACAATG
796466 GTTAAAT-ATATAAATA
1 GTTAAATAATATAAATA
*
796482 GTTAAATAATATTAATA
1 GTTAAATAATATAAATA
796499 G
1 G
796500 AAAAAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
GTTAAATAATATAAATA
Found at i:797280 original size:19 final size:19
Alignment explanation
Indices: 797256--797293 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
797246 CCATGCATCT
*
797256 CAATGCAATAAAAATAAAA
1 CAATGCAACAAAAATAAAA
*
797275 CAATGCAACAGAAATAAAA
1 CAATGCAACAAAAATAAAA
797294 AAAAACATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.66, C:0.13, G:0.08, T:0.13
Consensus pattern (19 bp):
CAATGCAACAAAAATAAAA
Found at i:797908 original size:40 final size:40
Alignment explanation
Indices: 797862--797954 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
797852 TTCACAAACT
*
797862 TTGCCTTTTCAAGAAGAGAAAGCACAACCTCATAATGTCA
1 TTGCCTTTTCAAGAAGAGAAAGCACAACCTCACAATGTCA
* * * *
797902 TTGCCTTTTCAATAGGAGCAAGTACAACCTCACAATGTCA
1 TTGCCTTTTCAAGAAGAGAAAGCACAACCTCACAATGTCA
797942 TTGCCTTTTCAAG
1 TTGCCTTTTCAAG
797955 GTTCAAGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (40 bp):
TTGCCTTTTCAAGAAGAGAAAGCACAACCTCACAATGTCA
Found at i:803352 original size:30 final size:31
Alignment explanation
Indices: 803294--803375 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
803284 AAAGTCAATC
* * *
803294 CCTTCTTTCTTTTTCTCCTCTCCTTTCTCTTT
1 CCTTCTTTCTTTTT-TCTTCTTCATTCTCTTT
* *
803326 TCTT-TTTTTTTTTTCTTCTTCATTCTCTTT
1 CCTTCTTTCTTTTTTCTTCTTCATTCTCTTT
803356 CCTTCTTTCTTTTTTCTTCT
1 CCTTCTTTCTTTTTTCTTCT
803376 CGGCTAAAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 17 0.40
31 22 0.52
32 3 0.07
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (31 bp):
CCTTCTTTCTTTTTTCTTCTTCATTCTCTTT
Found at i:816879 original size:14 final size:14
Alignment explanation
Indices: 816844--816884 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
816834 GAAACATTTT
816844 AATATTATTAATAA
1 AATATTATTAATAA
* *
816858 TATTTTATTAATAA
1 AATATTATTAATAA
816872 AATATTATATAAT
1 AATATTAT-TAAT
816885 TATAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATATTATTAATAA
Found at i:820078 original size:86 final size:86
Alignment explanation
Indices: 819933--820105 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
819923 GCAATAAGGA
819933 AGAGCATTTAGAAAAACACACTTTCAAAAATATGAAAATAGATGATTATCAATATTTGCAAAACT
1 AGAGCATTTAGAAAAACACACTTTCAAAAATATGAAAATAGATGATTATCAATATTTGCAAAACT
819998 TGCCTTATTAGGAATATTCAT
66 TGCCTTATTAGGAATATTCAT
820019 AGAGCATTTAGAAAAACACACTTTCAAAAATATGAAAATAGATGATTATCAATATTTGCAAAACT
1 AGAGCATTTAGAAAAACACACTTTCAAAAATATGAAAATAGATGATTATCAATATTTGCAAAACT
820084 TGCCTTATTAGGAATATTCAT
66 TGCCTTATTAGGAATATTCAT
820105 A
1 A
820106 AACCAAGCCT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.31
Consensus pattern (86 bp):
AGAGCATTTAGAAAAACACACTTTCAAAAATATGAAAATAGATGATTATCAATATTTGCAAAACT
TGCCTTATTAGGAATATTCAT
Found at i:834584 original size:18 final size:18
Alignment explanation
Indices: 834561--834610 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
834551 ATAAGTATCC
834561 ATCCACTTTTGGTGAGTG
1 ATCCACTTTTGGTGAGTG
* * * *
834579 ATCCACTTATGATTAGTT
1 ATCCACTTTTGGTGAGTG
834597 ATCCACTTTTGGTG
1 ATCCACTTTTGGTG
834611 GATTGTCCAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (18 bp):
ATCCACTTTTGGTGAGTG
Found at i:834904 original size:2 final size:2
Alignment explanation
Indices: 834892--834932 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
834882 AATGGAGAAA
834892 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
834933 CGATAGCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:835544 original size:20 final size:20
Alignment explanation
Indices: 835519--835586 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
835509 TACTCAAAAT
835519 AATATTTAAATTATAAATAA
1 AATATTTAAATTATAAATAA
* **
835539 AATA-TTAATATTTTAAAATTTT
1 AATATTTAA-ATTAT-AAA-TAA
*
835561 AATAATTAAATTATAAATAA
1 AATATTTAAATTATAAATAA
835581 AATATT
1 AATATT
835587 GATTTTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
19 4 0.11
20 14 0.38
21 6 0.16
22 9 0.24
23 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTAAATTATAAATAA
Found at i:835553 original size:43 final size:41
Alignment explanation
Indices: 835492--835595 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 41
835482 AAAAATTAAT
*
835492 TAAAATTATTAATATTTTACTCAAA-ATAATATTTAAATTATAAA
1 TAAAA-TATTAATATTTTA---AAATATAATAATTAAATTATAAA
*
835536 TAAAATATTAATATTTTAAAATTTTAATAATTAAATTATAAA
1 TAAAATATTAATATTTTAAAA-TATAATAATTAAATTATAAA
*
835578 TAAAATATTGAT-TTTTAA
1 TAAAATATTAATATTTTAA
835596 TTTATTAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
40 3 0.05
41 6 0.11
42 28 0.51
43 13 0.24
44 5 0.09
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (41 bp):
TAAAATATTAATATTTTAAAATATAATAATTAAATTATAAA
Found at i:835564 original size:42 final size:43
Alignment explanation
Indices: 835518--835641 Score: 141
Period size: 42 Copynumber: 2.9 Consensus size: 43
835508 TTACTCAAAA
835518 TAATATTTAAATTATAAATAAAATATTAATATTTTAAAATT-T
1 TAATATTTAAATTATAAATAAAATATTAATATTTTAAAATTAT
* * *
835560 TAATAATTAAATTATAAATAAAATATTGAT-TTTT-AATTTAT
1 TAATATTTAAATTATAAATAAAATATTAATATTTTAAAATTAT
* *
835601 TAATATTTCAAA-TA-AATTATAAATAGTTAATATTTAAAAAT
1 TAATATTT-AAATTATAAATA-AAATA-TTAATATTTTAAAAT
835642 AAAAATAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
40 8 0.12
41 19 0.28
42 35 0.51
43 3 0.04
44 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (43 bp):
TAATATTTAAATTATAAATAAAATATTAATATTTTAAAATTAT
Found at i:835631 original size:27 final size:27
Alignment explanation
Indices: 835599--835662 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
835589 TTTTTAATTT
* *
835599 ATTAATATTT-CAAATAAATTATAAATA
1 ATTAATATTTAAAAATAAA-AATAAATA
*
835626 GTTAATATTTAAAAATAAAAATAAATA
1 ATTAATATTTAAAAATAAAAATAAATA
835653 ATTATATATT
1 ATTA-ATATT
835663 ATAATGAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTAATATTTAAAAATAAAAATAAATA
Done.