Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, 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: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 8 of 18
Found at i:3843021 original size:2 final size:2
Alignment explanation
Indices: 3843016--3843042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3843006 ATATATATAT
3843016 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3843043 ATTATCATAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3844940 original size:2 final size:2
Alignment explanation
Indices: 3844933--3844961 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3844923 TCAGTCTAAG
3844933 AT AT 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 AT AT A
3844962 CATAGAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3858000 original size:16 final size:16
Alignment explanation
Indices: 3857976--3858006 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3857966 AAAGATATTT
3857976 GAATCAAAATAAATTC
1 GAATCAAAATAAATTC
*
3857992 GAATTAAAATAAATT
1 GAATCAAAATAAATT
3858007 TTTTTTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
GAATCAAAATAAATTC
Found at i:3865450 original size:22 final size:24
Alignment explanation
Indices: 3865425--3865480 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
3865415 ATTTAAAAAA
3865425 ATTTAAATAAATTT-T-TATTTTT
1 ATTTAAATAAATTTATATATTTTT
*
3865447 ATTTAATTAAATTTATATATTTTT
1 ATTTAAATAAATTTATATATTTTT
3865471 ATTTTAAATA
1 A-TTTAAATA
3865481 TAATATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.45
23 1 0.03
24 8 0.28
25 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTAAATAAATTTATATATTTTT
Found at i:3865450 original size:32 final size:30
Alignment explanation
Indices: 3865413--3865475 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
3865403 AGTTCTCAAA
3865413 TTATTTAAAAAAATTTAAATAAATTTTTATTT
1 TTATTTAAAAAAATTT--ATAAATTTTTATTT
** *
3865445 TTATTTAATTAAATTTATATATTTTTATTT
1 TTATTTAAAAAAATTTATAAATTTTTATTT
3865475 T
1 T
3865476 AAATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 14 0.50
32 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATTTAAAAAAATTTATAAATTTTTATTT
Found at i:3865489 original size:22 final size:21
Alignment explanation
Indices: 3865453--3865494 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3865443 TTTTATTTAA
* *
3865453 TTAAATTTATATATTTTTATT
1 TTAAATTAATATATTCTTATT
3865474 TTAAATATAATATATTCTTAT
1 TTAAAT-TAATATATTCTTAT
3865495 AATTAATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAATTAATATATTCTTATT
Found at i:3867747 original size:19 final size:21
Alignment explanation
Indices: 3867715--3867754 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3867705 CATAATACTC
*
3867715 AAAAAAACTCTTAAATTATTT
1 AAAAAAACTCTTAAATAATTT
3867736 AAAAAAA-T-TTAAATAATTT
1 AAAAAAACTCTTAAATAATTT
3867755 GTTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAAACTCTTAAATAATTT
Found at i:3871881 original size:2 final size:2
Alignment explanation
Indices: 3871874--3871900 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3871864 AAGCTAATCA
3871874 AT 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 AT A
3871901 GATCAATTGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3877084 original size:441 final size:431
Alignment explanation
Indices: 3876272--3877089 Score: 1314
Period size: 441 Copynumber: 1.9 Consensus size: 431
3876262 TTATAATGGT
* *
3876272 ATTTACATTGACAACTTTAGACCTGTTGTCAATAAATTCTTCAATACCCGCCTACCGCTTATGAA
1 ATTTACACTGACAACTTTAGACCTGTTGTCAATAAATTCTTCAATACCCGCCTACCACTTATGAA
* * *
3876337 TGTGTTCAAAGAGTTTAAAGAATGTCACTTGTCTCTGCACTGTAATCACAACATGACAATAAGAA
66 TGTGTTCAAAGAGTTTAAAGAATGTCACTTGTCTCTGCACTGTAATCACAAAAAGACAATAAAAA
*
3876402 TAAAAAACACATTATTGCATGGTATTGCAATCATTAACAATACAAAACAAGTAAAATGAATCATT
131 TAAAAAACACATTATTGCATGGTATCGCAATCATTAACAATACAAAACAAGTAAAATGAATCATT
3876467 TTTGTAGTATTACAATAAAAACACATATCAATTTCTTCCGATGTAGTGTAAAAGGTAAAAAACCA
196 TTTGTAGTATTACAATAAAAACACATATCAATTTCTTCCGATGTAGTGTAAAAGGTAAAAAACCA
* * *
3876532 CCTATATGTTTTGTTATGTAGACATGCTTCTTTGATAAATGGTTTTGATGGGCCTTGAGTGTGCG
261 CCTATATGTTTTGCTATGCAGACATGCTTCTCTGATAAATGGTTTTGATGGGCCTTGAGTGTGCG
*
3876597 TGTTTGTCACTCGGGCATGGACCATACGTTATCAACTAACTAGTCCCATATCCGAATTATTATGG
326 TGTTTGTCACTCAGGCATGGACCATACGTTATCAACTAACTAGTCCCATATCCGAATTATTATGG
3876662 TATTTAACTATTAAGCAACATATATAAGCACACCTATTATC
391 TATTTAACTATTAAGCAACATATATAAGCACACCTATTATC
* * * * ** * *
3876703 ATTTACACTGACAGCTTTAGACCTGTTGTCAATAAATTCTTTAGTATCCTTCTACTACTTATGAG
1 ATTTACACTGACAACTTTAGACCTGTTGTCAATAAATTCTTCAATACCCGCCTACCACTTATGAA
3876768 TGTGTTCAAAGAGTTTAAAGAATGTCACTTGTCTCTGCATGGCTTTGGACTGCAATCACAAAAAG
66 TGTGTTCAAAGAGTTTAAAGAATGTCACTTGTCTCTGCA---C--T-G--T--AATCACAAAAAG
*
3876833 ACAATAAAAATAAAAAACACATTATTGCATGGTATCGCAATCATTAACAATACAAAACAAGTAAT
121 ACAATAAAAATAAAAAACACATTATTGCATGGTATCGCAATCATTAACAATACAAAACAAGTAAA
3876898 ATGAATCATTTTTGTAG-ATTTACAATAAAAACACATATCAATTTCTTCCGATGTAGTGTAAAAG
186 ATGAATCATTTTTGTAGTA-TTACAATAAAAACACATATCAATTTCTTCCGATGTAGTGTAAAAG
* * * * *
3876962 GTCAAAAACCACCTGTATGTTTTGCTATGCAGCCATGCTTCTCTGTTAAATGGTTTTGTTGGGCC
250 GTAAAAAACCACCTATATGTTTTGCTATGCAGACATGCTTCTCTGATAAATGGTTTTGATGGGCC
3877027 TTGAGTGTGCGTGTTTGTCACTCAGGCATGGACCATACGTTATCAACTAACTAGTCCCATATC
315 TTGAGTGTGCGTGTTTGTCACTCAGGCATGGACCATACGTTATCAACTAACTAGTCCCATATC
3877090 TCTGCAGTGA
Statistics
Matches: 352, Mismatches: 24, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
431 94 0.27
434 1 0.00
436 1 0.00
437 1 0.00
439 1 0.00
440 1 0.00
441 253 0.72
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (431 bp):
ATTTACACTGACAACTTTAGACCTGTTGTCAATAAATTCTTCAATACCCGCCTACCACTTATGAA
TGTGTTCAAAGAGTTTAAAGAATGTCACTTGTCTCTGCACTGTAATCACAAAAAGACAATAAAAA
TAAAAAACACATTATTGCATGGTATCGCAATCATTAACAATACAAAACAAGTAAAATGAATCATT
TTTGTAGTATTACAATAAAAACACATATCAATTTCTTCCGATGTAGTGTAAAAGGTAAAAAACCA
CCTATATGTTTTGCTATGCAGACATGCTTCTCTGATAAATGGTTTTGATGGGCCTTGAGTGTGCG
TGTTTGTCACTCAGGCATGGACCATACGTTATCAACTAACTAGTCCCATATCCGAATTATTATGG
TATTTAACTATTAAGCAACATATATAAGCACACCTATTATC
Found at i:3877343 original size:25 final size:25
Alignment explanation
Indices: 3877288--3877353 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
3877278 CTCTCCCAGG
* * *
3877288 AAGCACCACTATTGGTGTTTCCCTTA
1 AAGCACTACGATTAGTG-TTCCCTTA
3877314 AAGCACTA-GATTAGTGTTCCCTTA
1 AAGCACTACGATTAGTGTTCCCTTA
* *
3877338 GGAGCATTACGATTAG
1 -AAGCACTACGATTAG
3877354 AAACACCAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 8 0.24
25 12 0.36
26 13 0.39
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (25 bp):
AAGCACTACGATTAGTGTTCCCTTA
Found at i:3883837 original size:20 final size:20
Alignment explanation
Indices: 3883808--3883848 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3883798 AAAATTAGCC
* *
3883808 ATTTAAAAATCTTAATGTAA
1 ATTTAAAAATATGAATGTAA
*
3883828 ATTTATAAATATGAATGTAA
1 ATTTAAAAATATGAATGTAA
3883848 A
1 A
3883849 AAATCATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
ATTTAAAAATATGAATGTAA
Found at i:3884368 original size:74 final size:74
Alignment explanation
Indices: 3884287--3884428 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 74
3884277 ACCTTTATAC
* * * *
3884287 TTATAAATATGTATTCATTAAATGACGATTATTGAAATATTTTTTATTATAATTATTATTAAGAT
1 TTATAAATATGTATTCATCAAATGACGATCATTGAAATATTTTTTATTATAATTATCAATAAGAT
3884352 TTAAATCTA
66 TTAAATCTA
* *
3884361 TTATAAATGTGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATCAATAAGAT
1 TTATAAATATGTATTCATCAAATGACGATCATTGAAATATTTTTTATTATAATTATCAATAAGAT
3884426 TTA
66 TTA
3884429 TTCCATTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATGACGATCATTGAAATATTTTTTATTATAATTATCAATAAGAT
TTAAATCTA
Found at i:3884538 original size:13 final size:13
Alignment explanation
Indices: 3884520--3884553 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3884510 ATTTAAATAA
3884520 TAATATTTTAAAT
1 TAATATTTTAAAT
*
3884533 TAATATTTTAATT
1 TAATATTTTAAAT
3884546 TAAGTATT
1 TAA-TATT
3884554 AATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TAATATTTTAAAT
Found at i:3884554 original size:20 final size:19
Alignment explanation
Indices: 3884526--3884596 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
3884516 ATAATAATAT
3884526 TTTAA-ATTAATATTTTAA
1 TTTAATATTAATATTTTAA
*
3884544 TTTAAGTATTAATATTTTTA
1 TTTAA-TATTAATATTTTAA
*
3884564 TTT--TTTTAATATTTTAA
1 TTTAATATTAATATTTTAA
*
3884581 GTTAAATATTAATATT
1 -TTTAATATTAATATT
3884597 CATCAAACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 12 0.28
18 7 0.16
20 24 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTAATATTAATATTTTAA
Found at i:3884728 original size:13 final size:14
Alignment explanation
Indices: 3884710--3884742 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3884700 AATCTGTTTG
3884710 ATAAATTAC-TTTT
1 ATAAATTACTTTTT
*
3884723 ATAAATTCCTTTTT
1 ATAAATTACTTTTT
3884737 ATAAAT
1 ATAAAT
3884743 AAGTTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATTACTTTTT
Found at i:3886030 original size:17 final size:17
Alignment explanation
Indices: 3886008--3886069 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
3885998 TATTTTAAGA
3886008 TAAAAATAGAATAAAAT
1 TAAAAATAGAATAAAAT
*
3886025 TAAAAATTAG-ATAACAT
1 TAAAAA-TAGAATAAAAT
*
3886042 TGAACATAAAATGAATAAAAT
1 T-AA-A-AATA-GAATAAAAT
3886063 TAAAAAT
1 TAAAAAT
3886070 TACTCATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
17 13 0.37
18 7 0.20
19 3 0.09
20 5 0.14
21 7 0.20
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
TAAAAATAGAATAAAAT
Found at i:3897108 original size:2 final size:2
Alignment explanation
Indices: 3897101--3897125 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3897091 TGTCTTTTAG
3897101 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
3897126 CATGTAATTA
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:3898050 original size:40 final size:41
Alignment explanation
Indices: 3897972--3898059 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 41
3897962 AATTCTAACT
*
3897972 TTTAATAAA-ATATTAATATTTTAAATTATGAATGATTAA-A
1 TTTAA-AAACATATTAATATTTTAAATTATCAATGATTAATA
*
3898012 TTATAAAAACATATTAATA-TTTAAATTATCAATTATTAATA
1 TT-TAAAAACATATTAATATTTTAAATTATCAATGATTAATA
3898053 TTTAAAA
1 TTTAAAA
3898060 TAAATTATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 28 0.65
41 15 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (41 bp):
TTTAAAAACATATTAATATTTTAAATTATCAATGATTAATA
Found at i:3898220 original size:94 final size:93
Alignment explanation
Indices: 3898026--3898209 Score: 216
Period size: 94 Copynumber: 2.0 Consensus size: 93
3898016 AAAAACATAT
* * * *
3898026 TAATATTTAAATTATCAATTATTAATATTTAAAATAAATTATAAATTATTAAACATAAATAAGCA
1 TAATAATTAAATTATCAACTAGTAATATTTAAAATAAATTATAAACTATTAAACATAAATAA-CA
* * *
3898091 TAATAACATTTAAATTATAAATGAAGTAT
65 TAATAACATTTAAATTAAAAATGAAATAA
* *
3898120 TAATAATTAAATTATCAACTAGTAATATTTCAAATAAATTATAAACTATTAATACTTAAA-AA-A
1 TAATAATTAAATTATCAACTAGTAATATTTAAAATAAATTATAAACTATTAA-ACATAAATAACA
3898183 TAAATTAA-A-TTAAATTAAAAAT-AAATA
65 T-AA-TAACATTTAAATTAAAAATGAAATA
3898210 GCCATAATAA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
91 4 0.05
92 14 0.18
93 3 0.04
94 52 0.66
95 6 0.08
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (93 bp):
TAATAATTAAATTATCAACTAGTAATATTTAAAATAAATTATAAACTATTAAACATAAATAACAT
AATAACATTTAAATTAAAAATGAAATAA
Found at i:3898298 original size:15 final size:15
Alignment explanation
Indices: 3898278--3898330 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3898268 ATTATAAAAA
3898278 TATCAATAATTAAAT
1 TATCAATAATTAAAT
*
3898293 TATCAATTATTAATAT
1 TATCAATAATTAA-AT
3898309 T-TC-A-AA-TAAAT
1 TATCAATAATTAAAT
3898320 TATCACATAAT
1 TATCA-ATAAT
3898331 AATATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
11 3 0.10
12 5 0.17
13 1 0.03
14 2 0.07
15 16 0.53
16 3 0.10
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (15 bp):
TATCAATAATTAAAT
Found at i:3898322 original size:27 final size:27
Alignment explanation
Indices: 3898288--3898345 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
3898278 TATCAATAAT
*
3898288 TAAATTATCA-ATTATTAATATTTCAAA
1 TAAATTATCACA-TAATAATATTTCAAA
*
3898315 TAAATTATCACATAATAATATTTTAAA
1 TAAATTATCACATAATAATATTTCAAA
3898342 -AAAT
1 TAAAT
3898346 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 23 0.82
28 1 0.04
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATTATCACATAATAATATTTCAAA
Found at i:3898372 original size:41 final size:43
Alignment explanation
Indices: 3898316--3898396 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
3898306 TATTTCAAAT
*
3898316 AAATTATCACATAATAATATTTTAAA-AAATAAA-ATAAAATAA
1 AAATTAACACATAATAATA-TTTAAATAAATAAATATAAAATAA
3898358 AAATTAAC-CATAATAATATTTAAATTAAATAAATATAAA
1 AAATTAACACATAATAATATTTAAA-TAAATAAATATAAA
3898397 TATTTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
40 6 0.17
41 10 0.29
42 14 0.40
43 5 0.14
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (43 bp):
AAATTAACACATAATAATATTTAAATAAATAAATATAAAATAA
Found at i:3898402 original size:152 final size:150
Alignment explanation
Indices: 3898100--3898663 Score: 623
Period size: 152 Copynumber: 3.6 Consensus size: 150
3898090 ATAATAACAT
* * *
3898100 TTAAATTATAAATGAAGTATTAATAATTAAATTATCAACTAGTAATATTTCAAATAAATTATAAA
1 TTAAATTATAAA--AA-TATTAATAATTAAATTATCAATTATTAATATTTCAAATAAATTATCAA
* * * *
3898165 CTATTAATACTTAAAAAATAAATTAAATTAAATTAAAAATAAATAGCCATAATAATATTTCAATT
63 CTATTAATATTTAAAAAAT--A--AAA-TAAAATAAAAAT---TAACCATAATAATATTT-AAAT
*
3898230 ATAAATAAATATTAATATTTTAAAATGTTAATGA
119 -TAAATAAATATTAATATTTT-AAATATTAATGA
*
3898264 TTAAATTATAAAAATATCAATAATTAAATTATCAATTATTAATATTTCAAATAAATTATC-ACAT
1 TTAAATTATAAAAATATTAATAATTAAATTATCAATTATTAATATTTCAAATAAATTATCAAC-T
*
3898328 AATAATATTTTAAAAAATAAAATAAAATAAAAATTAACCATAATAATATTTAAATTAAATAAATA
65 ATTAATA-TTTAAAAAATAAAATAAAATAAAAATTAACCATAATAATATTTAAATTAAATAAATA
* *
3898393 TAAATATTTTAAATATTAATTA
129 TTAATATTTTAAATATTAATGA
* * * *
3898415 TTAAATTATAATAAATATTAATATTTCAATTATCAATTATTAATATTTTAAATAAATTATCAATT
1 TTAAATTATAA-AAATATTAATAATTAAATTATCAATTATTAATATTTCAAATAAATTATCAACT
* * * * * *
3898480 ATTAGTATTT-AACAATAAAATAAAATGAACTAATTAATCATAATAATATTTAAGTTCAATAAAA
65 ATTAATATTTAAAAAATAAAATAAAAT-AA-AAATTAACCATAATAATATTTAAATTAAAT-AAA
*
3898544 TATTAATACTTTAAATATTAATGA
127 TATTAATATTTTAAATATTAATGA
* * * *
3898568 TTAAATTATAGAAAAATATTAATATTTAAATGATCAA-TATTAATATTTTAAATAAATTATCAAT
1 TTAAATTAT--AAAAATATTAATAATTAAATTATCAATTATTAATATTTCAAATAAATTATCAAC
* * * *
3898632 TATTACTATTTACAAAGTGAAAT-AAATAAAAA
64 TATTAATATTTAAAAAATAAAATAAAATAAAAA
3898664 AAGTAACATT
Statistics
Matches: 355, Mismatches: 35, Indels: 33
0.84 0.08 0.08
Matches are distributed among these distances:
150 15 0.04
151 28 0.08
152 98 0.28
153 78 0.22
154 45 0.13
155 2 0.01
157 11 0.03
158 3 0.01
160 3 0.01
161 49 0.14
162 11 0.03
164 12 0.03
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (150 bp):
TTAAATTATAAAAATATTAATAATTAAATTATCAATTATTAATATTTCAAATAAATTATCAACTA
TTAATATTTAAAAAATAAAATAAAATAAAAATTAACCATAATAATATTTAAATTAAATAAATATT
AATATTTTAAATATTAATGA
Found at i:3898438 original size:39 final size:39
Alignment explanation
Indices: 3898377--3898471 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 39
3898367 ATAATAATAT
* *
3898377 TTAAATTA-AATAAATATAAATATTTTAAATATTAATTA
1 TTAAATTATAATAAATATAAATATTTCAAATATCAATTA
* *
3898415 TTAAATTATAATAAATATTAATATTTCAATTATCAATTA
1 TTAAATTATAATAAATATAAATATTTCAAATATCAATTA
*
3898454 TTAATATTTTAAATAAAT
1 TTAA-ATTAT-AATAAAT
3898472 TATCAATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 8 0.16
39 30 0.61
40 4 0.08
41 7 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (39 bp):
TTAAATTATAATAAATATAAATATTTCAAATATCAATTA
Found at i:3898445 original size:24 final size:25
Alignment explanation
Indices: 3898402--3898467 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
3898392 ATAAATATTT
3898402 TAAATATTAAT-TATTAAATTAT-AA
1 TAAATATTAATAT-TTAAATTATCAA
*
3898426 TAAATATTAATATTTCAATTATCAA
1 TAAATATTAATATTTAAATTATCAA
3898451 T---TATTAATATTTTAAAT
1 TAAATATTAATA-TTTAAAT
3898468 AAATTATCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
22 8 0.22
23 6 0.16
24 19 0.51
25 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAATATTAATATTTAAATTATCAA
Found at i:3898474 original size:27 final size:28
Alignment explanation
Indices: 3898442--3898498 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
3898432 TTAATATTTC
*
3898442 AATTATCAATTATTAATATTTTA-AATA
1 AATTATCAATTATTAATATTTAACAATA
*
3898469 AATTATCAATTATTAGTATTTAACAATA
1 AATTATCAATTATTAATATTTAACAATA
3898497 AA
1 AA
3898499 ATAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTATCAATTATTAATATTTAACAATA
Found at i:3898764 original size:27 final size:27
Alignment explanation
Indices: 3898688--3898764 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
3898678 TTATAAATAA
* *
3898688 AATA-TTAATAATTAAATTATCAATTGGT
1 AATATTTAAAAATTAAATTA--AATTAGT
* * *
3898716 AATATTT-TAAATAAAATATAAATTATT
1 AATATTTAAAAATTAAAT-TAAATTAGT
3898743 AATATTTAAAAATTAAATTAAA
1 AATATTTAAAAATTAAATTAAA
3898765 AATAAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
27 16 0.41
28 19 0.49
29 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (27 bp):
AATATTTAAAAATTAAATTAAATTAGT
Found at i:3898772 original size:107 final size:105
Alignment explanation
Indices: 3898568--3898760 Score: 273
Period size: 107 Copynumber: 1.8 Consensus size: 105
3898558 ATATTAATGA
* * * *
3898568 TTAAATTATAGAAAAATATTAATATTTAAATGATCAATATTAATATTTTAAATAAATTATCAATT
1 TTAAATTATAAAAAAATATTAATAATTAAATGATCAATATTAATATTTTAAATAAAATATAAATT
* *
3898633 ATTACTATTTACAAAGTGAAATAAATAAAAAAAGTAACAT
66 ATTAATATTTACAAAATGAAATAAATAAAAAAAGTAACAT
*
3898673 TTAAATTATAAATAAAATATTAATAATTAAATTATCAAT-TGGTAATATTTTAAATAAAATATAA
1 TTAAATTATAAA-AAAATATTAATAATTAAATGATCAATAT--TAATATTTTAAATAAAATATAA
*
3898737 ATTATTAATATTTA-AAAATTAAAT
63 ATTATTAATATTTACAAAATGAAAT
3898761 TAAAAATAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
105 12 0.16
106 32 0.42
107 33 0.43
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (105 bp):
TTAAATTATAAAAAAATATTAATAATTAAATGATCAATATTAATATTTTAAATAAAATATAAATT
ATTAATATTTACAAAATGAAATAAATAAAAAAAGTAACAT
Found at i:3898963 original size:21 final size:21
Alignment explanation
Indices: 3898919--3898964 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3898909 TAAAAACTAA
* *
3898919 AATAAAATAAAAATTAATTGT
1 AATAAAATAAAAATTAAATAT
* *
3898940 AATAATATATAAATTAAATAT
1 AATAAAATAAAAATTAAATAT
3898961 AATA
1 AATA
3898965 TTAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AATAAAATAAAAATTAAATAT
Found at i:3898982 original size:419 final size:412
Alignment explanation
Indices: 3898274--3899066 Score: 1069
Period size: 419 Copynumber: 1.9 Consensus size: 412
3898264 TTAAATTATA
* * *
3898274 AAAATATCAATAATTAAATTATCAATTATTAATATTTCAAATAAATTATCACATAATAATATTTT
1 AAAATATCAATAATTAAATTATCAATTAGTAATATTTCAAATAAAATATCAAATAATAATATTTT
*
3898339 AAAAAATAAAATAAAATAAAAATTAACCATAATAATATTTAAATTAAATAAATATAAATATTTTA
66 AAAAAATAAAATAAAATAAAAATTAACCATAATAATATTCAAATTAAATAAATATAAATATTTTA
* * * * *
3898404 AATATTAATTATTAAATTATAATAAATATTAATATTTCAATTATCAATTATTAATATTTTAAATA
131 AATATTAATGATTAAATTATAATAAATATCAATAATTAAATTATCAATAATTAATATTTTAAATA
* * * * *
3898469 AATTATCAATTATTAGTATTTAACAATAAAATAAAATGAACTAATTAATCATAATAATATTTAAG
196 AATTATCAATTATTAATATTTAAAAATAAAATAAAATGAACAAATTAATCATAATAATATATAAA
*
3898534 TTCAATAAAATATTAATACTTTAAATATTAATGATTAAATTATAGA-AAAATATTAATATTTAAA
261 TTAAATAAAATATTAATACTTTAAATATTAATGATTAAATTATA-ATAAAATATTAATATTTAAA
*
3898598 TGATCAA-TATTAATATTTTAAATAAATTATCAATTATTACTATTTACAAAGTGAAATAAATAAA
325 TGATCAATTATTAATATTTTAAATAAAATATCAATTATTACTATTT-CAAAGTGAAATAAATAAA
3898662 AAAAGTAACATTTAAATTATAAAT
389 AAAAGTAACATTTAAATTATAAAT
* * * *
3898686 AAAATATTAATAATTAAATTATCAATTGGTAATATTTTAAATAAAATAT-AAATTATTAATA-TT
1 AAAATATCAATAATTAAATTATCAATTAGTAATATTTCAAATAAAATATCAAA-TAATAATATTT
* * * * *
3898749 TAAAAATTAAATTAAAAATAAAAATAAATAATCATAATAATATCTCAATTATAAATAAAATATTA
65 TAAAAAATAAAAT-AAAATAAAAAT---TAACCATAATAATAT-TCAAAT-TAAAT-AAATATAA
* * *
3898814 ATTTTTTAAAATGTTAATGATTAAATTATAAATAAAATATCAGTAATTAAATTATCAATAATTAA
123 ATATTTT-AAATATTAATGATTAAATTAT-AAT-AAATATCAATAATTAAATTATCAATAATTAA
* * **
3898879 TATTTTAAATATATTATGAA-TATTAATATTTAAAAACTAAAATAAAAT-AA-AAATTAATTGTA
185 TATTTTAAATAAATTATCAATTATTAATATTTAAAAA-TAAAATAAAATGAACAAATTAATCATA
* * *
3898941 ATAATATATAAATTAAATATAATATTAATATTTTAAATATTAATTATTAAATTATAATAAAATAT
249 ATAATATATAAATTAAATAAAATATTAATACTTTAAATATTAATGATTAAATTATAATAAAATAT
* * *
3899006 TAATATTTCAATTATCAATTATTAATATTTTAAATAAAATATCAATTATTAGTATTTCAAA
314 TAATATTTAAATGATCAATTATTAATATTTTAAATAAAATATCAATTATTACTATTTCAAA
3899067 AATAAAATAA
Statistics
Matches: 329, Mismatches: 38, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
411 15 0.05
412 62 0.19
415 14 0.04
416 4 0.01
417 5 0.02
418 14 0.04
419 105 0.32
420 55 0.17
421 55 0.17
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (412 bp):
AAAATATCAATAATTAAATTATCAATTAGTAATATTTCAAATAAAATATCAAATAATAATATTTT
AAAAAATAAAATAAAATAAAAATTAACCATAATAATATTCAAATTAAATAAATATAAATATTTTA
AATATTAATGATTAAATTATAATAAATATCAATAATTAAATTATCAATAATTAATATTTTAAATA
AATTATCAATTATTAATATTTAAAAATAAAATAAAATGAACAAATTAATCATAATAATATATAAA
TTAAATAAAATATTAATACTTTAAATATTAATGATTAAATTATAATAAAATATTAATATTTAAAT
GATCAATTATTAATATTTTAAATAAAATATCAATTATTACTATTTCAAAGTGAAATAAATAAAAA
AAGTAACATTTAAATTATAAAT
Found at i:3899007 original size:40 final size:40
Alignment explanation
Indices: 3898949--3899187 Score: 164
Period size: 40 Copynumber: 6.1 Consensus size: 40
3898939 TAATAATATA
*
3898949 TAAATTA-AATATAATATTAATATTTTAAATATTAATTAT
1 TAAATTATAATAAAATATTAATATTTTAAATATTAATTAT
* * *
3898988 TAAATTATAATAAAATATTAATATTTCAATTATCAATTAT
1 TAAATTATAATAAAATATTAATATTTTAAATATTAATTAT
* * * * *
3899028 TAATATTTTAAATAAAATATCAAT-TATT-AGTATT--TCA-
1 TAA-ATTAT-AATAAAATATTAATATTTTAAATATTAATTAT
* * * *
3899065 -AAAATAAAATAAAATA--AACTA-ATTAATCATAATAA-TATT
1 TAAATTATAATAAAATATTAA-TATTTTAA--ATATTAATTA-T
3899104 TAAATTA-AATAAAATATTAATATTTTAAAATATTAA-TAGT
1 TAAATTATAATAAAATATTAATATTTT-AAATATTAATTA-T
*
3899144 TAAATTATAACTAAAATATTAATA-TTTAAATTATCAATTAT
1 TAAATTATAA-TAAAATATTAATATTTTAAA-TATTAATTAT
3899185 TAA
1 TAA
3899188 TATTTTAAAT
Statistics
Matches: 157, Mismatches: 22, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
32 2 0.01
33 4 0.03
34 10 0.06
35 2 0.01
36 5 0.03
37 1 0.01
38 2 0.01
39 16 0.10
40 61 0.39
41 24 0.15
42 30 0.19
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (40 bp):
TAAATTATAATAAAATATTAATATTTTAAATATTAATTAT
Found at i:3899014 original size:573 final size:568
Alignment explanation
Indices: 3897975--3899234 Score: 1868
Period size: 573 Copynumber: 2.2 Consensus size: 568
3897965 TCTAACTTTT
*
3897975 AATAAAATATTAATATTTTAAATTATGAATGATTAAATTATAAAAACATATTAATATTTAAATTA
1 AATAAAATATTAATATTTTAAA-TATTAATGATTAAATTATAAAAA-ATATTAATATTTAAATTA
* * ** *
3898040 TCAATTATTAATATTTAAAATAAATTATAAATTATTA-A---AC--ATAAAT--AAGCATAATAA
64 TCAATTATTAATATTTTAAATAAATTATCAATTATTATATTTACAAATAAATAAAAAAAAAATAA
* * *
3898097 CATTTAAATTATAAATGAAGTATTAATAATTAAATTATCAACTAGTAATATTTCAAATAAATTAT
129 CATTTAAATTATAAATAAAATATTAATAATTAAATTATCAACTAGTAATATTTCAAATAAAATAT
* *
3898162 AAACTATTAATACTTAAAAAATAAATTAAATTAAATTAAAAATAAATAGCCATAATAATATTTCA
194 AAACTATTAATACTTAAAAAATAAATTAAA-TAAATTAAAAATAAATAACCATAATAATATCTCA
3898227 ATTATAAATAAATATTAATATTTTAAAATGTTAATGATTAAATTATAAAAATATCAATAATTAAA
258 ATTATAAATAAATATTAATATTTTAAAATGTTAATGATTAAATTATAAAAATATCAATAATTAAA
*
3898292 TTATCAATTATTAATATTTCAAATAAATTATCACATAATAATATTTTAAAAAATAAAATAAAATA
323 TTATCAATAATTAATATTTCAAATAAATTATCACATAATAATATTTTAAAAAATAAAATAAAATA
*
3898357 AAAATTAACCATAATAATATTTAAATTAAATAAATATAAATATTTTAAATATTAATTATTAAATT
388 AAAATTAACCATAATAATATATAAATTAAATAAATATAAATATTTTAAATATTAATTATTAAATT
*
3898422 ATAATAAATATTAATATTTCAATTATCAATTATTAATATTTTAAATAAATTATCAATTATTAGTA
453 ATAATAAATATTAATATTTCAATTATCAATTATTAATATTTTAAATAAAATATCAATTATTAGTA
* * * *
3898487 TTT-AACAATAAAATAAAATGAACTAATTAATCATAATAATATTTAAGTTC
518 TTTCAAAAATAAAATAAAATAAACTAATTAATCATAATAATATTTAAATTA
* *
3898537 AATAAAATATTAATACTTTAAATATTAATGATTAAATTATAGAAAAATATTAATATTTAAATGAT
1 AATAAAATATTAATATTTTAAATATTAATGATTAAATTATA-AAAAATATTAATATTTAAATTAT
3898602 CAA-TATTAATATTTTAAATAAATTATCAATTATTACTATTTACAAAGTGAAATAAATAAAAAAA
65 CAATTATTAATATTTTAAATAAATTATCAATTATTA-TATTTACAAA-T-AAATAAA-AAAAAAA
* * *
3898666 GTAACATTTAAATTATAAATAAAATATTAATAATTAAATTATCAATTGGTAATATTTTAAATAAA
126 -TAACATTTAAATTATAAATAAAATATTAATAATTAAATTATCAACTAGTAATATTTCAAATAAA
* * * *
3898731 ATATAAATTATTAATATTTAAAAATTAAATT-AA-AAA-TAAAAATAAATAATCATAATAATATC
190 ATATAAACTATTAATACTTAAAAAATAAATTAAATAAATTAAAAATAAATAACCATAATAATATC
* *
3898793 TCAATTATAAATAAAATATTAATTTTTTAAAATGTTAATGATTAAATTATAAATAAAATATCAGT
255 TCAATTATAAAT-AAATATTAATATTTTAAAATGTTAATGATTAAATTAT--A-AAAATATCAAT
* * * * *
3898858 AATTAAATTATCAATAATTAATATTTTAAATATATTATGA-ATATTAATA-TTTAAAAACTAAAA
316 AATTAAATTATCAATAATTAATATTTCAAATAAATTATCACATAATAATATTTTAAAAAATAAAA
*** *
3898921 TAAAATAAAAATTAATTGTAATAATATATAAATTAAATATAATATTAATATTTTAAATATTAATT
381 TAAAATAAAAATTAACCATAATAATATATAAATTAAATA-AATATAAATATTTTAAATATTAATT
3898986 ATTAAATTATAATAAAATATTAATATTTCAATTATCAATTATTAATATTTTAAATAAAATATCAA
445 ATTAAATTATAAT-AAATATTAATATTTCAATTATCAATTATTAATATTTTAAATAAAATATCAA
3899051 TTATTAGTATTTCAAAAATAAAATAAAATAAACTAATTAATCATAATAATATTTAAATTA
509 TTATTAGTATTTCAAAAATAAAATAAAATAAACTAATTAATCATAATAATATTTAAATTA
3899111 AATAAAATATTAATATTTTAAAATATTAAT-AGTTAAATTATAACTAAAATATTAATATTTAAAT
1 AATAAAATATTAATATTTT-AAATATTAATGA-TTAAATTATAA--AAAATATTAATATTTAAAT
*
3899175 TATCAATTATTAATATTTTAAATAAATTATCAATTATTAGTATTTAAAAATAAAATAAAA
62 TATCAATTATTAATATTTTAAATAAATTATCAATTATTA-TATTTACAAAT-AAATAAAA
3899235 TAACTAATCA
Statistics
Matches: 629, Mismatches: 43, Indels: 39
0.88 0.06 0.05
Matches are distributed among these distances:
560 30 0.05
561 39 0.06
562 26 0.04
565 2 0.00
567 1 0.00
568 1 0.00
569 39 0.06
570 39 0.06
571 49 0.08
572 52 0.08
573 194 0.31
574 63 0.10
575 21 0.03
576 32 0.05
577 41 0.07
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (568 bp):
AATAAAATATTAATATTTTAAATATTAATGATTAAATTATAAAAAATATTAATATTTAAATTATC
AATTATTAATATTTTAAATAAATTATCAATTATTATATTTACAAATAAATAAAAAAAAAATAACA
TTTAAATTATAAATAAAATATTAATAATTAAATTATCAACTAGTAATATTTCAAATAAAATATAA
ACTATTAATACTTAAAAAATAAATTAAATAAATTAAAAATAAATAACCATAATAATATCTCAATT
ATAAATAAATATTAATATTTTAAAATGTTAATGATTAAATTATAAAAATATCAATAATTAAATTA
TCAATAATTAATATTTCAAATAAATTATCACATAATAATATTTTAAAAAATAAAATAAAATAAAA
ATTAACCATAATAATATATAAATTAAATAAATATAAATATTTTAAATATTAATTATTAAATTATA
ATAAATATTAATATTTCAATTATCAATTATTAATATTTTAAATAAAATATCAATTATTAGTATTT
CAAAAATAAAATAAAATAAACTAATTAATCATAATAATATTTAAATTA
Found at i:3899131 original size:25 final size:25
Alignment explanation
Indices: 3898975--3899046 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
3898965 TTAATATTTT
*
3898975 AAATATTAAT-TATTAAATTATAATA
1 AAATATTAATATTTTAAATTA-AATA
* *
3899000 AAATATTAATA-TTTCAATT--ATC
1 AAATATTAATATTTTAAATTAAATA
* *
3899022 AATTATTAATATTTTAAATAAAATA
1 AAATATTAATATTTTAAATTAAATA
3899047 TCAATTATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
22 12 0.33
23 6 0.17
25 18 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATATTAATATTTTAAATTAAATA
Found at i:3899186 original size:22 final size:22
Alignment explanation
Indices: 3899160--3899222 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 22
3899150 ATAACTAAAA
3899160 TATTAATATTTAAATTATCAAT
1 TATTAATATTTAAATTATCAAT
3899182 TATTAATATTTTAAATAAATTATCAAT
1 TATTAATA--TT---TAAATTATCAAT
*
3899209 TATTAGTATTTAAA
1 TATTAATATTTAAA
3899223 AATAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 12 0.34
24 2 0.06
25 2 0.06
27 19 0.54
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTAATATTTAAATTATCAAT
Found at i:3899203 original size:27 final size:28
Alignment explanation
Indices: 3899170--3899228 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
3899160 TATTAATATT
*
3899170 TAAATTATCAATTATTAATATTT-TAAA
1 TAAATTATCAATTATTAATATTTAAAAA
*
3899197 TAAATTATCAATTATTAGTATTTAAAAA
1 TAAATTATCAATTATTAATATTTAAAAA
3899225 TAAA
1 TAAA
3899229 ATAAAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
TAAATTATCAATTATTAATATTTAAAAA
Found at i:3899298 original size:151 final size:152
Alignment explanation
Indices: 3898673--3899356 Score: 754
Period size: 151 Copynumber: 4.4 Consensus size: 152
3898663 AAAGTAACAT
* ** *
3898673 TTAAATTATAAATAAAATATTAATAATTAAATTATCAATTGGTAATATTTTAAATAAAATATAAA
1 TTAAATTAT-AATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAAATATCAA
* * * *
3898738 TTATTAATATTTAAAAATTAAATTAAAAATAAAAATAAATAATCATAATAATATCTCAATTATAA
65 TTATTAATATTT--AAA--AAACT-AAAAT-AAAATAACTAATCATAATAATAT-TTAAAT-TAA
*
3898803 ATAAAATATTAATTTTTTAAAAT-GTTAATGA
122 ATAAAATATTAATATTTTAAAATAG-TAATGA
* * * * * * *
3898834 TTAAATTATAAATAAAATATCAGTAATTAAATTATCAATAATTAATATTTTAAATATATTATGAA
1 TTAAATTAT-AATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAAATATCAA
* ** * *
3898899 -TATTAATATTT-AAAAACTAAAATAAAATAAAAATTAATTGTAATAATATATAAATTAAATATA
65 TTATTAATATTTAAAAAACTAAAATAAAAT---AACTAATCATAATAATATTTAAATTAAATAAA
* *
3898962 ATATTAATATTTT-AAATATTAATTA
127 ATATTAATATTTTAAAATAGTAATGA
*
3898987 TTAAATTATAATAAAATATTAATATTTCAATTATCAATTATTAATATTTTAAATAAAATATCAAT
1 TTAAATTATAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAAATATCAAT
* *
3899052 TATTAGTATTTCAAAAA-TAAAATAAAATAAACTAATTAATCATAATAATATTTAAATTAAATAA
66 TATTAATATTTAAAAAACTAAAATAAAAT-AAC----TAATCATAATAATATTTAAATTAAATAA
*
3899116 AATATTAATATTTTAAAATATTAAT-A
126 AATATTAATATTTTAAAATAGTAATGA
*
3899142 GTTAAATTATAACTAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATCA
1 -TTAAATTATAA-TAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAAATATCA
* *
3899207 ATTATTAGTATTT-AAAAA-TAAAATAAAATAACTAATCATTATAATATTTAAATTAAATAAAAT
64 ATTATTAATATTTAAAAAACTAAAATAAAATAACTAATCATAATAATATTTAAATTAAATAAAAT
* * **
3899270 ATTTATATTTTAAGATAGCGATGA
129 ATTAATATTTTAAAATAGTAATGA
* * * *
3899294 TTAAATTGTGAAGAAAATATTAATATTTAAGTTATCTATTATTAATATTTTAAAAATAAAATA
1 TTAAATTAT-AATAAAATATTAATATTTAAATTATCAATTATTAATATTTT--AAATAAAATA
3899357 AAATAAAATA
Statistics
Matches: 460, Mismatches: 46, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
151 94 0.20
152 50 0.11
153 53 0.12
154 29 0.06
155 49 0.11
156 52 0.11
157 65 0.14
160 11 0.02
161 57 0.12
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (152 bp):
TTAAATTATAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAAATATCAAT
TATTAATATTTAAAAAACTAAAATAAAATAACTAATCATAATAATATTTAAATTAAATAAAATAT
TAATATTTTAAAATAGTAATGA
Found at i:3899390 original size:21 final size:20
Alignment explanation
Indices: 3899366--3899430 Score: 87
Period size: 19 Copynumber: 3.1 Consensus size: 20
3899356 AAAATAAAAT
*
3899366 AATTAATTATAATAATATTTA
1 AATTAA-TATATTAATATTTA
3899387 AATTAA-ATATTAATATTTA
1 AATTAATATATTAATATTTA
3899406 AATTAATATTATTAATATTTTA
1 AATTAATA-TATTAATA-TTTA
3899428 AAT
1 AAT
3899431 AAATGATCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 18 0.45
20 1 0.03
21 14 0.35
22 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAATATATTAATATTTA
Found at i:3902617 original size:2 final size:2
Alignment explanation
Indices: 3902612--3902648 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3902602 TATGTGTGTG
*
3902612 TA TA TA TA TA TA TA TA TA TA TA TA TG 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
3902649 TTATGAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3916473 original size:18 final size:20
Alignment explanation
Indices: 3916450--3916488 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
3916440 ATTGATACTA
3916450 GTGCTGA-AATCTAT-TTTT
1 GTGCTGACAATCTATATTTT
3916468 GTGCTGACCAATCTATATTTT
1 GTGCTGA-CAATCTATATTTT
3916489 TAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
GTGCTGACAATCTATATTTT
Found at i:3918151 original size:16 final size:18
Alignment explanation
Indices: 3918122--3918158 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3918112 TTATTCAACA
3918122 TTTTATTTGATAG-TATC
1 TTTTATTTGATAGTTATC
*
3918139 TTTT-TTTGTTAGTTATC
1 TTTTATTTGATAGTTATC
3918156 TTT
1 TTT
3918159 CTTGGTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (18 bp):
TTTTATTTGATAGTTATC
Found at i:3919463 original size:10 final size:11
Alignment explanation
Indices: 3919439--3919463 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3919429 CTTAACTTAG
3919439 AAAAACAACTA
1 AAAAACAACTA
3919450 AAAAACAACTA
1 AAAAACAACTA
3919461 AAA
1 AAA
3919464 TGCTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAACAACTA
Found at i:3923531 original size:14 final size:13
Alignment explanation
Indices: 3923499--3923547 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
3923489 TTAATTTTTC
3923499 ATTTTAGTTTAA--
1 ATTTTAG-TTAATT
3923511 ATTTTAGTTAATT
1 ATTTTAGTTAATT
3923524 ATTTTTAGTTAATT
1 A-TTTTAGTTAATT
*
3923538 AATTTAGTTA
1 ATTTTAGTTA
3923548 TTTGATATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
11 4 0.12
12 7 0.21
13 9 0.27
14 13 0.39
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (13 bp):
ATTTTAGTTAATT
Found at i:3936348 original size:13 final size:13
Alignment explanation
Indices: 3936327--3936360 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3936317 ATTTTAGCTC
*
3936327 ATAAATTTTTTTA
1 ATAATTTTTTTTA
3936340 ATAATTTTTTTTA
1 ATAATTTTTTTTA
*
3936353 AAAATTTT
1 ATAATTTT
3936361 GAATATAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATAATTTTTTTTA
Found at i:3951259 original size:34 final size:30
Alignment explanation
Indices: 3951223--3951284 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3951213 TCATAATGAT
3951223 TTATTTGA-CTCAAAATAAAAGTATAAAGAC
1 TTATTT-ATCTCAAAATAAAAGTATAAAGAC
* *
3951253 TTATTTATCTCTAAATAAAAGTATAAATAC
1 TTATTTATCTCAAAATAAAAGTATAAAGAC
3951283 TT
1 TT
3951285 GATTAAACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (30 bp):
TTATTTATCTCAAAATAAAAGTATAAAGAC
Found at i:3951298 original size:30 final size:30
Alignment explanation
Indices: 3951230--3951309 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
3951220 GATTTATTTG
* *
3951230 ACTCAAAATAAAAGTATAAAGACTTATTTA
1 ACTCTAAATAAAAGTATAAAGACTTATTAA
* *
3951260 TCTCTAAATAAAAGTATAAATACTTGATTAA
1 ACTCTAAATAAAAGTATAAAGACTT-ATTAA
*
3951291 AC-GTAAATAAATA-TATAAA
1 ACTCTAAATAAA-AGTATAAA
3951310 AATTTATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 36 0.86
31 6 0.14
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (30 bp):
ACTCTAAATAAAAGTATAAAGACTTATTAA
Found at i:3953083 original size:22 final size:22
Alignment explanation
Indices: 3953055--3953102 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
3953045 TGCGATGAAA
3953055 ATTACCTATAATCACCATACAT
1 ATTACCTATAATCACCATACAT
3953077 ATTACCTATAATCACCATACAT
1 ATTACCTATAATCACCATACAT
3953099 ATTA
1 ATTA
3953103 TAAAATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (22 bp):
ATTACCTATAATCACCATACAT
Found at i:3953780 original size:2 final size:2
Alignment explanation
Indices: 3953773--3953798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3953763 AGACTAGTAC
3953773 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
3953799 GATTAGAGTA
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:3955654 original size:20 final size:20
Alignment explanation
Indices: 3955615--3955701 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
3955605 TTTTAATATG
* * *
3955615 TTTAAAATATTTTTTTATTT
1 TTTAAAAAATTTTATAATTT
3955635 TTTAAAAAATTTTATAATTT
1 TTTAAAAAATTTTATAATTT
3955655 TGCCTCTATAAAAATTTTA-AATTT
1 T---T-TA-AAAAATTTTATAATTT
* *
3955679 TTTATAAAATGTTT-TTATTT
1 TTTAAAAAAT-TTTATAATTT
3955699 TTT
1 TTT
3955702 TGAATTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
19 5 0.09
20 30 0.55
21 1 0.02
23 1 0.02
24 8 0.15
25 10 0.18
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTAAAAAATTTTATAATTT
Found at i:3956223 original size:141 final size:142
Alignment explanation
Indices: 3955967--3956223 Score: 358
Period size: 141 Copynumber: 1.8 Consensus size: 142
3955957 ATGCATCCAA
* * * * *
3955967 TTGGATCTATTTCAACTTGATATTCTTTATAATCAGGTTTTGAAAAAAATATATTTACACTTTTT
1 TTGGATCTATTTCAACTTGACATTCTTTATAATCAGGCTTTG-AAAAAATACATCTACACTTTTG
*
3956032 GAGCTATATCAAGTGTTGAAGAAGACGAAAATATCAAAAGTTTACTTTTTTGTAAACAGATTTCC
65 GAGCTATACCAAGTGTTGAAGAAGACGAAAATATCAAAAGTTTACTTTTTTGTAAACAGATTTCC
3956097 TCTAAGCTATCAG
130 TCTAAGCTATCAG
*
3956110 TTGGATCTATTT-AAGCTTGACATTCTTTATAATCAGGCTTTG-AAAAATGCATCTACACTTTTG
1 TTGGATCTATTTCAA-CTTGACATTCTTTATAATCAGGCTTTGAAAAAATACATCTACACTTTTG
* * * * *
3956173 GAGTTATGCCGAGTGTTGAAGGAGA-TAAGAATATCAAAAGTTTACTTTTTT
65 GAGCTATACCAAGTGTTGAAGAAGACGAA-AATATCAAAAGTTTACTTTTTT
3956224 ATTGATAGAT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
140 2 0.02
141 59 0.59
142 2 0.02
143 37 0.37
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (142 bp):
TTGGATCTATTTCAACTTGACATTCTTTATAATCAGGCTTTGAAAAAATACATCTACACTTTTGG
AGCTATACCAAGTGTTGAAGAAGACGAAAATATCAAAAGTTTACTTTTTTGTAAACAGATTTCCT
CTAAGCTATCAG
Found at i:3979962 original size:2 final size:2
Alignment explanation
Indices: 3979955--3979999 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
3979945 AAATGCCGTT
*
3979955 TA TA TA TA -A CTA T- TA TA CA 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 TA TA TA TA TA TA
3979996 TA TA
1 TA TA
3980000 GCCACAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3982054 original size:2 final size:2
Alignment explanation
Indices: 3982047--3982123 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
3982037 CTCAAATTCC
3982047 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
3982089 AT AT AT AT AT 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 AT AT AT AT AT A
3982124 GATGTGGGCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3986641 original size:32 final size:32
Alignment explanation
Indices: 3986604--3986668 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3986594 AACGATATTA
*
3986604 AATTTTTACAAAAAAGACAATAAAAACCTTAT
1 AATTTTCACAAAAAAGACAATAAAAACCTTAT
* *
3986636 AATTTTCACTAAAAAGACAATAAAACCCTTAT
1 AATTTTCACAAAAAAGACAATAAAAACCTTAT
3986668 A
1 A
3986669 TTTATTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (32 bp):
AATTTTCACAAAAAAGACAATAAAAACCTTAT
Found at i:3995941 original size:2 final size:2
Alignment explanation
Indices: 3995934--3995962 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3995924 TTATTGATTT
3995934 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 T
3995963 TATTTTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3996238 original size:2 final size:2
Alignment explanation
Indices: 3996231--3996271 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3996221 AGTATATGAG
3996231 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
3996272 ACATGATCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3997449 original size:68 final size:69
Alignment explanation
Indices: 3997340--3997479 Score: 221
Period size: 69 Copynumber: 2.0 Consensus size: 69
3997330 TTGAAAAATA
*
3997340 AAACTAATTATTAAATAAAAATTATTTTGAAAGCCATTAAAAA-AAGTATAATAAATAAAATTGT
1 AAACTAATTATTAAATAAAAAATATTTTGAAAGCCATTAAAAATAAGTATAATAAATAAAATTGT
3997404 ATTG
66 ATTG
***
3997408 AAACTAATTATTAAATCAAAAAATATTTTGAAAGCCA-TAAAAATTTTTATAATAAATAAAATTG
1 AAACTAATTATTAAAT-AAAAAATATTTTGAAAGCCATTAAAAATAAGTATAATAAATAAAATTG
3997472 TATTG
65 TATTG
3997477 AAA
1 AAA
3997480 GAAATACAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
68 22 0.33
69 44 0.67
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.34
Consensus pattern (69 bp):
AAACTAATTATTAAATAAAAAATATTTTGAAAGCCATTAAAAATAAGTATAATAAATAAAATTGT
ATTG
Found at i:4000636 original size:12 final size:12
Alignment explanation
Indices: 4000619--4000643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4000609 ATATTCATTG
4000619 ATAAATATATAA
1 ATAAATATATAA
4000631 ATAAATATATAA
1 ATAAATATATAA
4000643 A
1 A
4000644 CCAACATTGT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATATATAA
Found at i:4006215 original size:45 final size:45
Alignment explanation
Indices: 4006151--4006240 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
4006141 CAGTAAACCC
*
4006151 TTGCTTTAGGTCTCATAATTTGTAATAATATAATTAATTATATTA
1 TTGCTTTAGGTCCCATAATTTGTAATAATATAATTAATTATATTA
4006196 TTGCTTTAGGTCCCATAATTTGTAATAATATAATTAATTATATTA
1 TTGCTTTAGGTCCCATAATTTGTAATAATATAATTAATTATATTA
4006241 AAAATATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.48
Consensus pattern (45 bp):
TTGCTTTAGGTCCCATAATTTGTAATAATATAATTAATTATATTA
Found at i:4009194 original size:30 final size:30
Alignment explanation
Indices: 4009139--4009195 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4009129 AATTCTTATG
*
4009139 AAATTCTATTGGAAATGCTTATCCAACGGA
1 AAATTCTATTGGAAAAGCTTATCCAACGGA
4009169 AAATTCTATTGGAAAAGCATT-TCCAAC
1 AAATTCTATTGGAAAAGC-TTATCCAAC
4009196 AAAAATGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (30 bp):
AAATTCTATTGGAAAAGCTTATCCAACGGA
Found at i:4010524 original size:18 final size:17
Alignment explanation
Indices: 4010502--4010534 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4010492 TCGTAAAAAT
4010502 TTTTTTTAAAAAATAAC
1 TTTTTTTAAAAAATAAC
4010519 TTTTTTTAAAAAATAA
1 TTTTTTTAAAAAATAA
4010535 AATCTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTTTAAAAAATAAC
Found at i:4010549 original size:13 final size:14
Alignment explanation
Indices: 4010524--4010561 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4010514 ATAACTTTTT
*
4010524 TTAAAAAATAAAATC
1 TTAAAAAA-AAAAGC
4010539 -TAAAAAAAAAAGC
1 TTAAAAAAAAAAGC
4010552 TTAAAAAAAA
1 TTAAAAAAAA
4010562 GTTTCAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (14 bp):
TTAAAAAAAAAAGC
Found at i:4018522 original size:35 final size:33
Alignment explanation
Indices: 4018483--4018550 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
4018473 GTACGTGAAC
*
4018483 ATAAAAATGATCAAAGATGATTTAATTTTTTTTTA
1 ATAAAAATGA-AAAAGATG-TTTAATTTTTTTTTA
* **
4018518 ATAAAAATTAAAAAGATGTTTTCTTTTTTTTTA
1 ATAAAAATGAAAAAGATGTTTAATTTTTTTTTA
4018551 TTAATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 13 0.45
34 7 0.24
35 9 0.31
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (33 bp):
ATAAAAATGAAAAAGATGTTTAATTTTTTTTTA
Found at i:4019916 original size:26 final size:29
Alignment explanation
Indices: 4019864--4019916 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
4019854 TATTCTCATA
* *
4019864 ATAATGATATAAATTAATGTTTTAAATAT
1 ATAATGATATAAAATAATGTTTAAAATAT
4019893 ATAAT-ATATAAAAT-AT-TTTAAAAT
1 ATAATGATATAAAATAATGTTTAAAAT
4019917 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 2 0.09
28 8 0.36
29 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
ATAATGATATAAAATAATGTTTAAAATAT
Found at i:4027619 original size:14 final size:14
Alignment explanation
Indices: 4027600--4027630 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4027590 ACCTGTTTTA
*
4027600 ATAAAATAGATAAT
1 ATAAAAAAGATAAT
4027614 ATAAAAAAGATAAT
1 ATAAAAAAGATAAT
4027628 ATA
1 ATA
4027631 GAATTATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (14 bp):
ATAAAAAAGATAAT
Found at i:4030757 original size:24 final size:24
Alignment explanation
Indices: 4030721--4030772 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
4030711 CTAGGTTATG
*
4030721 AAAATTAATAACACACCACTTTTT
1 AAAATTAAAAACACACCACTTTTT
4030745 AAAATTAAAAACACACCACTTTTT
1 AAAATTAAAAACACACCACTTTTT
4030769 AAAA
1 AAAA
4030773 AAGTAACAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAATTAAAAACACACCACTTTTT
Found at i:4042910 original size:15 final size:15
Alignment explanation
Indices: 4042885--4042917 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4042875 AATCAAAAAT
4042885 AAAATAAGAGCAA-A
1 AAAATAAGAGCAAGA
4042899 AAAATCAAGAGCAAGA
1 AAAAT-AAGAGCAAGA
4042915 AAA
1 AAA
4042918 GTGTTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.70, C:0.09, G:0.15, T:0.06
Consensus pattern (15 bp):
AAAATAAGAGCAAGA
Found at i:4043901 original size:78 final size:78
Alignment explanation
Indices: 4043772--4044056 Score: 417
Period size: 78 Copynumber: 3.7 Consensus size: 78
4043762 AAGGCATGGG
* * *
4043772 CATGTGGCATTCCTATTATACATTAAGGTATAATGATGCTAATATGTAAATATCATCAAGGTCAA
1 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGCCAATATGTAAATAACATCAAGGTCAA
*
4043837 TGTGATAAGTGCA
66 TGTGATAAGTGGA
* * * *
4043850 CATGTAGCATTCTTATTATACATTAAGGTATAATGATGCCAATATGTAAATACCATCAAAGTCTA
1 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGCCAATATGTAAATAACATCAAGGTCAA
4043915 TGTGATAAGTGGA
66 TGTGATAAGTGGA
* * *
4043928 CATGTGGCATTCATATTATACATTAAGGTATAATGATGCCAATGTGTAAATAACATCAAGGTCCA
1 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGCCAATATGTAAATAACATCAAGGTCAA
*
4043993 TGTGATAAGTGGG
66 TGTGATAAGTGGA
* * * * *
4044006 CATGTGGCATTCTTATTATACATGAAAGTATAATGGTACCAATATATAAAT
1 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGCCAATATGTAAAT
4044057 TTAACATCTT
Statistics
Matches: 186, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 186 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (78 bp):
CATGTGGCATTCTTATTATACATTAAGGTATAATGATGCCAATATGTAAATAACATCAAGGTCAA
TGTGATAAGTGGA
Found at i:4050708 original size:8 final size:8
Alignment explanation
Indices: 4050694--4050725 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4050684 CTTTCTTCCC
4050694 CAAATAAA
1 CAAATAAA
*
4050702 TAAATAAA
1 CAAATAAA
4050710 CAAATAAA
1 CAAATAAA
4050718 CAAATAAA
1 CAAATAAA
4050726 ATTACTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (8 bp):
CAAATAAA
Found at i:4054021 original size:488 final size:490
Alignment explanation
Indices: 4053134--4054021 Score: 1044
Period size: 488 Copynumber: 1.8 Consensus size: 490
4053124 TGTAAATGTG
* *
4053134 TGAGATTTAATATAACAAATCAATTATGTCAAATAAACATAACTTTCGAGAAAATTAAACATTAA
1 TGAGATTTAACATAACAAATCAATTATATCAAATAAACATAACTTTCGAGAAAATTAAACATTAA
** ** * * *
4053199 AATTTTTTATTCTAGAGTTTAAAGTTTGTTACGGTTTACAAATTTTAATTTATGAATGAATAATA
66 AATTTTTTACCCTAGAGTTTAAAGTTTGTTACGACTTACAAATTTTAATCTATGAATAAACAATA
* **
4053264 ATAAGAATAAAAAAAATTATGATGAAAATTAGTAGTTGAAAGACCTTAATGTAAAACAGTAAAAA
131 ATAAGAATAAAAAAAATTATGATGAAAATTAGTAATT-AAAGACCTTAACATAAAACAGTAAAAA
* * *
4053329 TTAATGTAAAAAATTATAAAGGTGAAAAAAGAATTATCAAAATATTGACGTAAATATGTAAGATT
195 TTAATGTAAAAAATTATAAAGGAGAAAAAAGAATTATAAAAATATTGACGAAAATATGTAAGATT
* * * * *
4053394 TAATATAACAAGTCAATTATATCAAATAATCATAATTTTTGAAAAAATTAAATATTTAACTTTTT
260 TAACATAACAAATCAATGATATAAAATAATCATAATTTTTGAAAAAATTAAACATTTAACTTTTT
* * ** * ** *
4053459 ATTCTTGAGTTTAAAATATTTTATGATTGACAAATTTTAATCTATGGATAAATAATAGTAATGAT
325 ATTATTGAGTTTAAAATATTTAATGATTGACAAATTTTAATCTATAAATAAATAATAATAAAAAC
4053524 AAAATAATTATAATTTTAATTAATAGTTAAAAATCTTTGACACAAAGTGATAAGAATTAATGTAA
390 AAAATAATTATAATTTTAATTAATAGTTAAAAATCTTTGACACAAAGTGATAAGAATTAATGTAA
4053589 AATATTATAAAAGTGGAACAAGCATTAAAAAATGCA
455 AATATTATAAAAGTGGAACAAGCATTAAAAAATGCA
* * * * *
4053625 TGAGATTTAACATAACAAATCAATTATATTAAATAAACATAATTTTTTGAG-AAATTAAACTTTT
1 TGAGATTTAACATAACAAATCAATTATATCAAATAAACATAA-CTTTCGAGAAAATTAAACATTA
4053689 AAA-TTTTTACCCTCA-AGTTTAAAGTATT-TTACGACTTACAAATTTTAATCTATGTAA-AAAC
65 AAATTTTTTACCCT-AGAGTTTAAAGT-TTGTTACGACTTACAAATTTTAATCTATG-AATAAAC
* * * * *** *
4053750 AATAGTAAGTATAAAAAGAATTAT-AGTGAAAATT-TTAATT-TTTACCTTGACATAAAACCA-T
127 AATAATAAGAATAAAAAAAATTATGA-TGAAAATTAGTAATTAAAGACCTTAACATAAAA-CAGT
* * * * * * * * *
4053811 AAATATTAATGTAAAAAATTATAATGGAGGAATAAGCATTGTAAAAATATTGACGAAAATTTTTT
190 AAAAATTAATGTAAAAAATTATAAAGGAGAAAAAAGAATTATAAAAATATTGACGAAAATATGTA
* * * **
4053876 ATATTTAACGTAACAAATCAAATGAGT-TAAAATAGAT-TTAATTTTTGTTAAAATTAAACATTT
255 AGATTTAACATAACAAATC-AATGA-TATAAAATA-ATCATAATTTTTGAAAAAATTAAACATTT
* * * * * *
4053939 AATTTTTTATTATTGA-TTTAAAAATATTTAATGGTTTATAAATTTTAATTTATAAATGAATAAT
317 AACTTTTTATTATTGAGTTT-AAAATATTTAATGATTGACAAATTTTAATCTATAAATAAATAAT
4054003 AATAAAAACAAAATAATTA
381 AATAAAAACAAAATAATTA
4054022 AAGTTAAAAT
Statistics
Matches: 326, Mismatches: 61, Indels: 23
0.80 0.15 0.06
Matches are distributed among these distances:
487 83 0.25
488 99 0.30
489 8 0.02
490 72 0.22
491 58 0.18
492 6 0.02
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (490 bp):
TGAGATTTAACATAACAAATCAATTATATCAAATAAACATAACTTTCGAGAAAATTAAACATTAA
AATTTTTTACCCTAGAGTTTAAAGTTTGTTACGACTTACAAATTTTAATCTATGAATAAACAATA
ATAAGAATAAAAAAAATTATGATGAAAATTAGTAATTAAAGACCTTAACATAAAACAGTAAAAAT
TAATGTAAAAAATTATAAAGGAGAAAAAAGAATTATAAAAATATTGACGAAAATATGTAAGATTT
AACATAACAAATCAATGATATAAAATAATCATAATTTTTGAAAAAATTAAACATTTAACTTTTTA
TTATTGAGTTTAAAATATTTAATGATTGACAAATTTTAATCTATAAATAAATAATAATAAAAACA
AAATAATTATAATTTTAATTAATAGTTAAAAATCTTTGACACAAAGTGATAAGAATTAATGTAAA
ATATTATAAAAGTGGAACAAGCATTAAAAAATGCA
Found at i:4058079 original size:11 final size:11
Alignment explanation
Indices: 4058058--4058086 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4058048 AGTATTTTTT
4058058 ATTAA-TAATA
1 ATTAATTAATA
4058068 ATTAATTAATA
1 ATTAATTAATA
4058079 ATTAATTA
1 ATTAATTA
4058087 TAAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTAATTAATA
Found at i:4058912 original size:42 final size:42
Alignment explanation
Indices: 4058853--4058937 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
4058843 TTGTTAACCT
4058853 TCGACCCATCTCTTTCACCTGTATTCGGACAACATGATTTGG
1 TCGACCCATCTCTTTCACCTGTATTCGGACAACATGATTTGG
4058895 TCGACCCATCTCTTTCACCTGTATTCGGACAACATGATTTGG
1 TCGACCCATCTCTTTCACCTGTATTCGGACAACATGATTTGG
4058937 T
1 T
4058938 TGTGGCTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.34
Consensus pattern (42 bp):
TCGACCCATCTCTTTCACCTGTATTCGGACAACATGATTTGG
Found at i:4065626 original size:19 final size:20
Alignment explanation
Indices: 4065582--4065626 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4065572 AGAAAAATAT
*
4065582 AAGAGAAAGTATTTAGATGG
1 AAGAGAAAGTATTTAGAGGG
4065602 AA-AGAAAGTATTTAG-GGG
1 AAGAGAAAGTATTTAGAGGG
4065620 AAGAGAA
1 AAGAGAA
4065627 GAAATCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 17 0.74
20 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.20
Consensus pattern (20 bp):
AAGAGAAAGTATTTAGAGGG
Found at i:4069619 original size:27 final size:28
Alignment explanation
Indices: 4069544--4069619 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
4069534 ATCCATTTGG
* *
4069544 GTAAAAGTATTTATCCACGTTTGAGGAA
1 GTAAATGTATTTATCCACTTTTGAGGAA
*
4069572 -TAAATGTATTCATCCACTTTTG-GGAA
1 GTAAATGTATTTATCCACTTTTGAGGAA
*
4069598 GTAAATGTATTTATCCATTTTT
1 GTAAATGTATTTATCCACTTTT
4069620 TGTAGGTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.10
27 38 0.90
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (28 bp):
GTAAATGTATTTATCCACTTTTGAGGAA
Found at i:4069628 original size:27 final size:27
Alignment explanation
Indices: 4069478--4069629 Score: 84
Period size: 27 Copynumber: 5.8 Consensus size: 27
4069468 TCTTCACTAC
* * * *
4069478 TCATTCATTTTTGGTGGGTAAAGGTAT
1 TCATCCATTTTTTGTAGGTAAAAGTAT
* *
4069505 TCATCCATTTCTAGTAGGTAAAAGTAT
1 TCATCCATTTTTTGTAGGTAAAAGTAT
*
4069532 ACATCCA---TTTG--GGTAAAAGTAT
1 TCATCCATTTTTTGTAGGTAAAAGTAT
* ** *
4069554 TTATCCA-CGTTTG-AGGAATAAATGTAT
1 TCATCCATTTTTTGTAGG--TAAAAGTAT
* * * * *
4069581 TCATCCACTTTTGGGAAGTAAATGTAT
1 TCATCCATTTTTTGTAGGTAAAAGTAT
*
4069608 TTATCCATTTTTTGTAGGTAAA
1 TCATCCATTTTTTGTAGGTAAA
4069630 GATATATATT
Statistics
Matches: 97, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
22 16 0.16
24 6 0.06
25 2 0.02
27 68 0.70
28 3 0.03
29 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (27 bp):
TCATCCATTTTTTGTAGGTAAAAGTAT
Found at i:4069700 original size:81 final size:81
Alignment explanation
Indices: 4069613--4069764 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 81
4069603 TGTATTTATC
*
4069613 CATTTTTTGTAGGTAAAGATAT-ATATTCACTTCTAGTGAGTAAAGGTATAC-ATTTACTTCTAG
1 CATTTTTTGTAGGTAAAGATATCAT-TTCACTTCTAGTGAGTAAAGGTAT-CTATTCACTTCTAG
4069676 TGGGTAAAATTATCCATT
64 TGGGTAAAATTATCCATT
* * * * * * *
4069694 CATTTTTTGTATGTAAAGGTATCCTTTCATTTTTTGTGCGTAAAGGTATCTATTCACTTCTAGTG
1 CATTTTTTGTAGGTAAAGATATCATTTCACTTCTAGTGAGTAAAGGTATCTATTCACTTCTAGTG
*
4069759 GTTAAA
66 GGTAAA
4069765 TGTGCTTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
80 1 0.02
81 58 0.97
82 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (81 bp):
CATTTTTTGTAGGTAAAGATATCATTTCACTTCTAGTGAGTAAAGGTATCTATTCACTTCTAGTG
GGTAAAATTATCCATT
Found at i:4069764 original size:27 final size:26
Alignment explanation
Indices: 4069624--4069760 Score: 89
Period size: 27 Copynumber: 5.1 Consensus size: 26
4069614 ATTTTTTGTA
* *
4069624 GGTAAAGATATATATTCACTTCTAGT
1 GGTAAAGGTATCTATTCACTTCTAGT
*
4069650 GAGTAAAGGTATAC-ATTTACTTCTAGT
1 G-GTAAAGGTAT-CTATTCACTTCTAGT
** * * * *
4069677 GGGTAAAATTATCCATTCATTTTTTGT
1 -GGTAAAGGTATCTATTCACTTCTAGT
* * * *
4069704 ATGTAAAGGTATCCT-TTCATTTTTTGT
1 -GGTAAAGGTAT-CTATTCACTTCTAGT
4069731 GCGTAAAGGTATCTATTCACTTCTAGT
1 G-GTAAAGGTATCTATTCACTTCTAGT
4069758 GGT
1 GGT
4069761 TAAATGTGCT
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
26 6 0.07
27 78 0.91
28 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (26 bp):
GGTAAAGGTATCTATTCACTTCTAGT
Found at i:4075390 original size:30 final size:30
Alignment explanation
Indices: 4075317--4075410 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 30
4075307 AGAAAAATTT
* ** *
4075317 AAATAAGTCTTTATATTTTTATTACG-TTC
1 AAATAAGTTTTTATATTTTTATTTTGAGTC
*
4075346 -AATCAAGCTTTTATATTTTTATTTTGAGTC
1 AAAT-AAGTTTTTATATTTTTATTTTGAGTC
*
4075376 AAATAAGTTTTTATA-TTTTATTTTAAGTC
1 AAATAAGTTTTTATATTTTTATTTTGAGTC
4075405 AAATAA
1 AAATAA
4075411 ACCCTTATGA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 3 0.05
29 37 0.67
30 12 0.22
31 3 0.05
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (30 bp):
AAATAAGTTTTTATATTTTTATTTTGAGTC
Found at i:4075418 original size:29 final size:30
Alignment explanation
Indices: 4075356--4075418 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
4075346 AATCAAGCTT
* ****
4075356 TTATATTTTTATTTTGAGTCAAATAAGTTT
1 TTATATTTTTATTTTAAGTCAAATAAACCC
4075386 TTATA-TTTTATTTTAAGTCAAATAAACCC
1 TTATATTTTTATTTTAAGTCAAATAAACCC
4075415 TTAT
1 TTAT
4075419 GATTAATGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.52
Consensus pattern (30 bp):
TTATATTTTTATTTTAAGTCAAATAAACCC
Found at i:4077235 original size:22 final size:22
Alignment explanation
Indices: 4077176--4077226 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
4077166 AATTGAAAAG
4077176 TGATGTTTTGACTAATGACAAT
1 TGATGTTTTGACTAATGACAAT
4077198 TGATGTTTTGACTAATGACAAT
1 TGATGTTTTGACTAATGACAAT
4077220 TGATGTT
1 TGATGTT
4077227 AGTTATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (22 bp):
TGATGTTTTGACTAATGACAAT
Found at i:4080866 original size:26 final size:26
Alignment explanation
Indices: 4080813--4080886 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
4080803 CAGCCGGATT
* *
4080813 TGGTGCTCCCCCAATGGAGCACTGATC
1 TGGTGCT-CCCCAAGGGAGCACTAATC
4080840 TGGTGCTCCCCAAGGGAGC-CTCAATC
1 TGGTGCTCCCCAAGGGAGCACT-AATC
* * * *
4080866 TTGTGTTCTCCAGGGGAGCAC
1 TGGTGCTCCCCAAGGGAGCAC
4080887 GGCCAGATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 29 0.74
27 8 0.21
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (26 bp):
TGGTGCTCCCCAAGGGAGCACTAATC
Found at i:4088797 original size:15 final size:14
Alignment explanation
Indices: 4088761--4088798 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
4088751 TTTTTTTTTT
4088761 GGGG-GGGGT-TGG
1 GGGGTGGGGTGTGG
4088773 GGGGTGGGGTGTGG
1 GGGGTGGGGTGTGG
4088787 GGGGTGTGGGTG
1 GGGGTG-GGGTG
4088799 GCTCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 5 0.22
14 9 0.39
15 5 0.22
ACGTcount: A:0.00, C:0.00, G:0.79, T:0.21
Consensus pattern (14 bp):
GGGGTGGGGTGTGG
Found at i:4092639 original size:14 final size:15
Alignment explanation
Indices: 4092620--4092650 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4092610 TAATGTTATA
4092620 ATTAAAATAAAA-AT
1 ATTAAAATAAAATAT
4092634 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
4092649 AT
1 AT
4092651 AATATAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:4092672 original size:33 final size:34
Alignment explanation
Indices: 4092616--4092691 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
4092606 TTTATAATGT
4092616 TATAAT-TAA-AATAAAAATATTAAAATAAAATA
1 TATAATATAAGAATAAAAATATTAAAATAAAATA
*
4092648 TATAATATAAGAATCAAAA-ATTAAAATAAAATA
1 TATAATATAAGAATAAAAATATTAAAATAAAATA
4092681 -A-AATATAAGAA
1 TATAATATAAGAA
4092692 ATTAAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 10 0.24
32 7 0.17
33 17 0.41
34 7 0.17
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (34 bp):
TATAATATAAGAATAAAAATATTAAAATAAAATA
Found at i:4092776 original size:33 final size:32
Alignment explanation
Indices: 4092730--4092810 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 32
4092720 AAATTAAAAT
* * **
4092730 ATAATATATAATATAAAAAATTATAGTCAAGAA
1 ATAAAATAAAATATAAAAAATTATA-AAAAGAA
* * *
4092763 ATAAAATAAAATATATAAGATTATAAAAATAA
1 ATAAAATAAAATATAAAAAATTATAAAAAGAA
4092795 ATGAAAATAAAATATA
1 AT-AAAATAAAATATA
4092811 TGACATTACA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 6 0.15
33 34 0.85
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.28
Consensus pattern (32 bp):
ATAAAATAAAATATAAAAAATTATAAAAAGAA
Found at i:4093047 original size:15 final size:15
Alignment explanation
Indices: 4093027--4093068 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4093017 TTATTTTCAC
4093027 TACAATTACATTAAT
1 TACAATTACATTAAT
*
4093042 TACAATTACATTACT
1 TACAATTACATTAAT
* *
4093057 TGCAATCACATT
1 TACAATTACATT
4093069 GCATTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (15 bp):
TACAATTACATTAAT
Found at i:4099447 original size:17 final size:18
Alignment explanation
Indices: 4099425--4099463 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4099415 ATACATACTG
*
4099425 ATACTTTTAGTAT-ATAT
1 ATACTTTAAGTATAATAT
*
4099442 ATACTTTAATTATAATAT
1 ATACTTTAAGTATAATAT
4099460 ATAC
1 ATAC
4099464 ACCTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (18 bp):
ATACTTTAAGTATAATAT
Found at i:4101182 original size:36 final size:35
Alignment explanation
Indices: 4101140--4101262 Score: 158
Period size: 35 Copynumber: 3.5 Consensus size: 35
4101130 TTAATTGTTT
*
4101140 AATTTAATCAATTAGGCCTAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCTAATGACTTAATTAAAC
* * *
4101175 AATTTTAATCAACTAGGCCAAATGGCTTAATTAAAC
1 AA-TTTAATCAATTAGGCCTAATGACTTAATTAAAC
* *
4101211 AATTTAAT-ATATTAGGTCTAATGACTTAATTAAAT
1 AATTTAATCA-ATTAGGCCTAATGACTTAATTAAAC
*
4101246 AATTTAATTAATTAGGC
1 AATTTAATCAATTAGGC
4101263 ACAACTTAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
34 1 0.01
35 42 0.56
36 32 0.43
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCTAATGACTTAATTAAAC
Found at i:4103821 original size:20 final size:21
Alignment explanation
Indices: 4103793--4103831 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4103783 ATTAGATATA
*
4103793 TGGTATAAT-CTTGATTGAGT
1 TGGTATAATAATTGATTGAGT
*
4103813 TGGTGTAATAATTGATTGA
1 TGGTATAATAATTGATTGA
4103832 TAGGATGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.28, C:0.03, G:0.26, T:0.44
Consensus pattern (21 bp):
TGGTATAATAATTGATTGAGT
Found at i:4108925 original size:27 final size:28
Alignment explanation
Indices: 4108862--4108932 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
4108852 GATCATTAGC
* * *
4108862 AATTTATTTAATTTAAAATAAAATTTAAA
1 AATTTATTTAA-ATATAATAAAATATAAA
4108891 AATTTATTTAAATATAATAAAA-ATAAA
1 AATTTATTTAAATATAATAAAATATAAA
4108918 AATTTATTTAAATAT
1 AATTTATTTAAATAT
4108933 TAATTTATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 19 0.49
28 9 0.23
29 11 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTTATTTAAATATAATAAAATATAAA
Found at i:4109532 original size:29 final size:27
Alignment explanation
Indices: 4109500--4109562 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
4109490 TAATTTTAAA
*
4109500 AATTTATTTAATAAAAAATATAAAAAATT
1 AATTTATATAATAAAAAA-AT-AAAAATT
*
4109529 AATTAAATATAATAAAAAAATAAAAATT
1 AATT-TATATAATAAAAAAATAAAAATT
*
4109557 TATTTA
1 AATTTA
4109563 ACTATTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 10 0.34
29 6 0.21
30 12 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AATTTATATAATAAAAAAATAAAAATT
Found at i:4112672 original size:45 final size:45
Alignment explanation
Indices: 4112585--4112674 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
4112575 AAAAACTAGT
* *
4112585 TCCACAATAATTTAAAAATAGAATGATAGATAATGTAAAATTGAC
1 TCCACAATAATTTAAAAATAGAATAATAGATAATATAAAATTGAC
** * *
4112630 TCCACAATAATTT-AACTTAGAATAATAGTTAATATATTAATTGAC
1 TCCACAATAATTTAAAAATAGAATAATAGATAATATA-AAATTGAC
4112675 AGTTAATCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 18 0.47
45 20 0.53
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (45 bp):
TCCACAATAATTTAAAAATAGAATAATAGATAATATAAAATTGAC
Found at i:4131128 original size:49 final size:49
Alignment explanation
Indices: 4131074--4131303 Score: 219
Period size: 49 Copynumber: 4.7 Consensus size: 49
4131064 ACCTATGAGT
**
4131074 CGAAGTCTCCAAATCATTCGTTCAAGGTCAAGTTGAAAGACCCTTGAAG
1 CGAAGTCTCCAAATCATTCGTTCAAAATCAAGTTGAAAGACCCTTGAAG
* * * ** * *** *
4131123 TGAAGTCTCCAAATCCTTCTTTTGAGATCAAGTCCCAAGACTCTTGAAG
1 CGAAGTCTCCAAATCATTCGTTCAAAATCAAGTTGAAAGACCCTTGAAG
* * * * * * * *
4131172 CAAAGTTTCCAAATCGTTTGTTCAAAATCAAGTTGTCAAGGCCATTGAAA
1 CGAAGTCTCCAAATCATTCGTTCAAAATCAAGTTG-AAAGACCCTTGAAG
* *
4131222 CGAAGTCTCCAAATCATTCATTCAAAATCAAGTT-ACGAGACCCTTGAAG
1 CGAAGTCTCCAAATCATTCGTTCAAAATCAAGTTGA-AAGACCCTTGAAG
* *
4131271 TGAAGTCTCCAAATCATTCGATCAAAATCAAGT
1 CGAAGTCTCCAAATCATTCGTTCAAAATCAAGT
4131304 CATCAAGACT
Statistics
Matches: 141, Mismatches: 38, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
49 102 0.72
50 39 0.28
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (49 bp):
CGAAGTCTCCAAATCATTCGTTCAAAATCAAGTTGAAAGACCCTTGAAG
Found at i:4131252 original size:99 final size:99
Alignment explanation
Indices: 4131076--4131419 Score: 246
Period size: 99 Copynumber: 3.5 Consensus size: 99
4131066 CTATGAGTCG
* ** * * ** *
4131076 AAGTCTCCAAATCATTCGTTCAAGGTCAAGT--TGAAAGACCCTTGAAGTGAAGTCTCCAAATCC
1 AAGTCTCCAAATCATTCGATCAAAATCAAGTCAT-CAAGACCATTGAAACGAAGTCTCCAAATCA
* ** * * *
4131139 TTCTTTTGAGATCAAGTCCCAAGACTCTTGAAGCA
65 TTCATTCAAAATCAAGTCACAAGACCCTTGAAGCA
* * * * ** *
4131174 AAGTTTCCAAATCGTTTGTTCAAAATCAAGTTGTCAAGGCCATTGAAACGAAGTCTCCAAATCAT
1 AAGTCTCCAAATCATTCGATCAAAATCAAGTCATCAAGACCATTGAAACGAAGTCTCCAAATCAT
* * **
4131239 TCATTCAAAATCAAGTTACGAGACCCTTGAAGTG
66 TCATTCAAAATCAAGTCACAAGACCCTTGAAGCA
* * * **
4131273 AAGTCTCCAAATCATTCGATCAAAATCAAGTCATCAAGACTATTGAAACAAAGTCTCCGAATTGT
1 AAGTCTCCAAATCATTCGATCAAAATCAAGTCATCAAGACCATTGAAACGAAGTCTCCAAATCAT
* ** * *
4131338 TCGTTCAGGATTAAGT-AGTCAAGACCTTTGAAG-A
66 TCATTCAAAATCAAGTCA--CAAGACCCTTGAAGCA
* ** * * * *
4131372 GAAGTATCCAAATTGTTCGTTCAAGATCAAGTCGTCAAGACCTTTGAA
1 -AAGTCTCCAAATCATTCGATCAAAATCAAGTCATCAAGACCATTGAA
4131420 GTAAAGTCTT
Statistics
Matches: 193, Mismatches: 48, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
98 27 0.14
99 114 0.59
100 52 0.27
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (99 bp):
AAGTCTCCAAATCATTCGATCAAAATCAAGTCATCAAGACCATTGAAACGAAGTCTCCAAATCAT
TCATTCAAAATCAAGTCACAAGACCCTTGAAGCA
Found at i:4131435 original size:50 final size:50
Alignment explanation
Indices: 4131076--4131434 Score: 264
Period size: 50 Copynumber: 7.2 Consensus size: 50
4131066 CTATGAGTCG
* * * * **
4131076 AAGTCTCCAAATCATTCGTTCAAGGTCAAGTTG-AAAGACCCTTGAAGTG
1 AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGTCAAGACCTTTGAAGCA
* * ** *
4131125 AAGTCTCCAAATCCTTCTTTTGAGATCAAGTC-CCAAGA-CTCTTGAAGCA
1 AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGTCAAGACCT-TTGAAGCA
* * * * * * * * *
4131174 AAGTTTCCAAATCGTTTGTTCAAAATCAAGTTGTCAAGGCCATTGAAACG
1 AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGTCAAGACCTTTGAAGCA
* * * * **
4131224 AAGTCTCCAAATCATTCATTCAAAATCAAGT--TACGAGACCCTTGAAGTG
1 AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGT-CAAGACCTTTGAAGCA
* * * *
4131273 AAGTCTCCAAATCATTCGATCAAAATCAAGTCATCAAGA-CTATTGAAACA
1 AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGTCAAGACCT-TTGAAGCA
* ** * * *
4131323 AAGTCTCCGAATTGTTCGTTCAGGATTAAGTAGTCAAGACCTTTGAAG-A
1 AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGTCAAGACCTTTGAAGCA
* ** *
4131372 GAAGTATCCAAATTGTTCGTTCAAGATCAAGTCGTCAAGACCTTTGAAGTA
1 -AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGTCAAGACCTTTGAAGCA
*
4131423 AAGTCTTCAAAT
1 AAGTCTCCAAAT
4131435 TATAAGTCGT
Statistics
Matches: 243, Mismatches: 56, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
48 2 0.01
49 102 0.42
50 134 0.55
51 5 0.02
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (50 bp):
AAGTCTCCAAATCATTCGTTCAAGATCAAGTCGTCAAGACCTTTGAAGCA
Found at i:4131555 original size:49 final size:50
Alignment explanation
Indices: 4131438--4131600 Score: 147
Period size: 49 Copynumber: 3.3 Consensus size: 50
4131428 TTCAAATTAT
** * * **
4131438 AAGTCGTCAAGACCCTTGAAGCCAAA-TCTC-CAATCATTTTTTCAAGATC
1 AAGTCGTCAAGACCCTTGAA-ATAAAGTCTCTAAATTATTCCTTCAAGATC
* * *
4131487 -AGTAGTCAAGACCCTTGAAATGAAGTCTCTAAATTATTCGTTCAAGATC
1 AAGTCGTCAAGACCCTTGAAATAAAGTCTCTAAATTATTCCTTCAAGATC
* * * * *
4131536 AAGTCGTTAAGACTC-TGAAATAAAGTCTCTAAATTGTTCCTTTAAGATT
1 AAGTCGTCAAGACCCTTGAAATAAAGTCTCTAAATTATTCCTTCAAGATC
*
4131585 AAGTCAT-AAGACCCTT
1 AAGTCGTCAAGACCCTT
4131601 AAAGTGAATT
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
47 2 0.02
48 28 0.30
49 51 0.55
50 11 0.12
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (50 bp):
AAGTCGTCAAGACCCTTGAAATAAAGTCTCTAAATTATTCCTTCAAGATC
Found at i:4135141 original size:79 final size:79
Alignment explanation
Indices: 4135040--4135204 Score: 197
Period size: 79 Copynumber: 2.1 Consensus size: 79
4135030 TTTATCACTT
4135040 GAGATAATATCTAATTTGGACCAATAAAAATGCAAATATTGATCATCCAATTTATCCTTAAAGAA
1 GAGATAATATCTAATTTGGACCAATAAAAATGCAAATATTGATCATCCAATTTATCCTTAAAGAA
*
4135105 ATCAAGGTAATTTA
66 ATCAAGATAATTTA
* * * ** * * * * *
4135119 GAGATAATATTTAAATTT-GACCAATTAAATTTTACATGTTGGTCATCCAATTTATCTTTAAATA
1 GAGATAATATCT-AATTTGGACCAATAAAAATGCAAATATTGATCATCCAATTTATCCTTAAAGA
*
4135183 AATGAAGATAATTTA
65 AATCAAGATAATTTA
*
4135198 GATATAA
1 GAGATAA
4135205 AATCCAAATT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 67 0.93
80 5 0.07
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (79 bp):
GAGATAATATCTAATTTGGACCAATAAAAATGCAAATATTGATCATCCAATTTATCCTTAAAGAA
ATCAAGATAATTTA
Found at i:4135272 original size:57 final size:57
Alignment explanation
Indices: 4135163--4135274 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
4135153 CATGTTGGTC
** * *
4135163 ATCCAATTTATCTTTAAATAAATGAAGATAATTTAGATATAAAATCCAAATTTGATA
1 ATCCAATTTATCTCCAAATAAATCAAGATAATTTAGAGATAAAATCCAAATTTGATA
* *
4135220 ATCCAATTTATCTCCAAATAAATCAAGATAATTTATAGATAATACTCC-AATTTGA
1 ATCCAATTTATCTCCAAATAAATCAAGATAATTTAGAGATAA-AATCCAAATTTGA
4135275 CCAATCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 44 0.92
58 4 0.08
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (57 bp):
ATCCAATTTATCTCCAAATAAATCAAGATAATTTAGAGATAAAATCCAAATTTGATA
Found at i:4135478 original size:15 final size:16
Alignment explanation
Indices: 4135447--4135479 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4135437 GCCATTTGAT
4135447 GAACCATGGAGGAAAG
1 GAACCATGGAGGAAAG
*
4135463 GAACGATGGA-GAAAG
1 GAACCATGGAGGAAAG
4135478 GA
1 GA
4135480 GAACAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.09, G:0.39, T:0.06
Consensus pattern (16 bp):
GAACCATGGAGGAAAG
Found at i:4135606 original size:28 final size:28
Alignment explanation
Indices: 4135575--4135628 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4135565 ACCAAATTTG
4135575 AGAAAGAAGATTATGAAAATCAAAGCCT
1 AGAAAGAAGATTATGAAAATCAAAGCCT
* * *
4135603 AGAAGGAAGATTCTGAAGATCAAAGC
1 AGAAAGAAGATTATGAAAATCAAAGC
4135629 ATCAAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (28 bp):
AGAAAGAAGATTATGAAAATCAAAGCCT
Found at i:4136042 original size:50 final size:49
Alignment explanation
Indices: 4135812--4136237 Score: 214
Period size: 50 Copynumber: 8.7 Consensus size: 49
4135802 AAATCATTCA
* * * * ** *
4135812 TTCAAGATCAAGTC-CCAAGACCCTT-AGAGCGAAGTATTCAAATCATTCA
1 TTCAAGATCAAGTCGTCAAGACCCTTGA-AACAAAGT-CTCAAATTGTTCG
** * * *
4135861 TTCAAGATTGAGTCAT-AAGACTCTTGAAACAAAGTCTTTAAATAT-TT-G
1 TTCAAGATCAAGTCGTCAAGACCCTTGAAACAAAGTC-TCAAAT-TGTTCG
* * * * * * ** *
4135909 TTCAAAATCACGTTGTTAAGACCTTTGAAATAAAGTCTCTAAATCATTTG
1 TTCAAGATCAAGTCGTCAAGACCCTTGAAACAAAGTCTC-AAATTGTTCG
* * *
4135959 CTC-AGAGTCAAGTC--CCAGACCCTT-AAAGCAAAGTCTACAAATTGTTTG
1 TTCAAGA-TCAAGTCGTCAAGACCCTTGAAA-CAAAGTCT-CAAATTGTTCG
*
4136007 TTCAAGATCAAGTCGTCAAAACCCTTGAAACAAAGTCT-ATTAATTGTTCG
1 TTCAAGATCAAGTCGTCAAGACCCTTGAAACAAAGTCTCA--AATTGTTCG
* * * *** *
4136057 TTCAAGATCAAGTCATCAAGACCTTTGTAGTGAAGTCTCCAAATTGTTCA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAAACAAAGTCT-CAAATTGTTCG
* * ** *
4136107 TTC-A-ATTAAGTCGTCAAGACCCTTTAAGA-AAAGTCTCTAAATCATTCA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAA-ACAAAGTCTC-AAATTGTTCG
** ** * * *
4136155 TTCAAGATCAAGTTTTCAAGACATTTAAAACGAAGTCTCTAAATCGTTCG
1 TTCAAGATCAAGTCGTCAAGACCCTTGAAACAAAGTCTC-AAATTGTTCG
* *
4136205 TTCAAGATCAAGTCAT-AAGACCCTTGAAGCAAA
1 TTCAAGATCAAGTCGTCAAGACCCTTGAAACAAA
4136238 TTCAAGATCA
Statistics
Matches: 285, Mismatches: 68, Indels: 48
0.71 0.17 0.12
Matches are distributed among these distances:
47 4 0.01
48 78 0.27
49 77 0.27
50 122 0.43
51 3 0.01
52 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (49 bp):
TTCAAGATCAAGTCGTCAAGACCCTTGAAACAAAGTCTCAAATTGTTCG
Found at i:4136118 original size:98 final size:100
Alignment explanation
Indices: 4135989--4136233 Score: 239
Period size: 98 Copynumber: 2.5 Consensus size: 100
4135979 CCTTAAAGCA
** * **
4135989 AAGTCTACAAATTGTTTGTTCAAGATCAAGTCGTCAAAACCCTTGAA-ACAAAGTCTATTAATTG
1 AAGTCTACAAATTGTTCATTCAAGATCAAGTCGTCAAAACCCTTGAAGA-AAAGTCTATAAATCA
*
4136053 TTCGTTCAAGATCAAGTCATCAAGACCTTTGTAGTG
65 TTCATTCAAGATCAAGTCATCAAGACCTTTGTAGTG
* * * * *
4136089 AAGTCTCCAAATTGTTCATTC-A-ATTAAGTCGTCAAGACCCTTTAAGAAAAGTCTCTAAATCAT
1 AAGTCTACAAATTGTTCATTCAAGATCAAGTCGTCAAAACCCTTGAAGAAAAGTCTATAAATCAT
** * ** **
4136152 TCATTCAAGATCAAGTTTTCAAGACATTTAAAACG
66 TCATTCAAGATCAAGTCATCAAGACCTTTGTAGTG
* * * *
4136187 AAGTCT-CTAAATCGTTCGTTCAAGATCAAGTCAT-AAGACCCTTGAAG
1 AAGTCTAC-AAATTGTTCATTCAAGATCAAGTCGTCAAAACCCTTGAAG
4136234 CAAATTCAAG
Statistics
Matches: 118, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
97 1 0.01
98 76 0.64
99 15 0.13
100 26 0.22
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (100 bp):
AAGTCTACAAATTGTTCATTCAAGATCAAGTCGTCAAAACCCTTGAAGAAAAGTCTATAAATCAT
TCATTCAAGATCAAGTCATCAAGACCTTTGTAGTG
Found at i:4136265 original size:32 final size:33
Alignment explanation
Indices: 4136205--4136266 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
4136195 AAATCGTTCG
*
4136205 TTCAAGATCAAGTCATAAGACCCTTGAAGCAAA
1 TTCAAGATCAAGTCATAAAACCCTTGAAGCAAA
4136238 TTCAAGATCAAGTCA-AAAACCCTTGAAGC
1 TTCAAGATCAAGTCATAAAACCCTTGAAGC
4136267 GGAGTACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (33 bp):
TTCAAGATCAAGTCATAAAACCCTTGAAGCAAA
Found at i:4136530 original size:4 final size:4
Alignment explanation
Indices: 4136523--4136548 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4136513 AGAATGAATG
4136523 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
4136549 GATAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:4137634 original size:24 final size:24
Alignment explanation
Indices: 4137593--4137649 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
4137583 CCTACCATTA
* **
4137593 ATTTGTGGTTTTGATTGTTTGAAC
1 ATTTGAGGTTTTGATTGTTCAAAC
** *
4137617 ATTTGAGGTTTTTCTTGTTCAAAT
1 ATTTGAGGTTTTGATTGTTCAAAC
4137641 ATTTGAGGT
1 ATTTGAGGT
4137650 GTTAGTTGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.05, G:0.23, T:0.53
Consensus pattern (24 bp):
ATTTGAGGTTTTGATTGTTCAAAC
Found at i:4138344 original size:251 final size:250
Alignment explanation
Indices: 4138087--4138553 Score: 711
Period size: 251 Copynumber: 1.9 Consensus size: 250
4138077 TAAATAATTT
* * * *
4138087 AGTTAATTAAGTACTTTTATGTATTAATTACAAGTCTTAGTCATTAATCAAATAACTAAATGAGT
1 AGTTAATTAAGTAATGTAATGTATTAATTACAAGTATTAGTCATTAATCAAATAACTAAATGAGT
* *
4138152 TAATTGAAGATAATTAAAAATTATTTAAATTAATTAAGATTTTTACATAAATAATTAAATAGTTT
66 TAATTGAAGATAATTAAAAATTATTTAAATTAATTAAGATTCTTACATAAATAATTAAATAATTT
** * *
4138217 AACTAACGAAATGAATAAA-ATTTTTTAGTAATTAAGGAATCAAGAAAATTAGTAATATTATTGA
131 AACTAACGAAATGAA-AAATATTTTTTAGTAAAAAAGCAATCAACAAAATTAGTAATATTATTGA
*
4138281 ATTTTAAAAATATTTAAGTTAATGAGTTAACATGTTAATAATGTAGTTGGATGATTA
195 A-TTTAAAAATATTTAAATTAATGAGTTAACATGTTAATAATGTAGTTGGATGATTA
* * * *
4138338 AGTTAATTAAGTAATGTAATGTATTAATTATAAGTATTAGTCATTAGTCAAATAATTAAATTAGT
1 AGTTAATTAAGTAATGTAATGTATTAATTACAAGTATTAGTCATTAATCAAATAACTAAATGAGT
*
4138403 TAATTGAAGATAATTAAAAATTATTTAAATTAATTAAGGTTCTTACATAAATAATTAAATAATTT
66 TAATTGAAGATAATTAAAAATTATTTAAATTAATTAAGATTCTTACATAAATAATTAAATAATTT
* * * * * *
4138468 AACTAATGAAGTGAAAAATTTTTTTTAGTAAAAAAGCAATTAACAAAATTATTAATATTATTTAA
131 AACTAACGAAATGAAAAATATTTTTTAGTAAAAAAGCAATCAACAAAATTAGTAATATTATTGAA
4138533 TTTAAAAATATTTAAATTAAT
196 TTTAAAAATATTTAAATTAAT
4138554 TAATTTGTTA
Statistics
Matches: 193, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
250 23 0.12
251 170 0.88
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (250 bp):
AGTTAATTAAGTAATGTAATGTATTAATTACAAGTATTAGTCATTAATCAAATAACTAAATGAGT
TAATTGAAGATAATTAAAAATTATTTAAATTAATTAAGATTCTTACATAAATAATTAAATAATTT
AACTAACGAAATGAAAAATATTTTTTAGTAAAAAAGCAATCAACAAAATTAGTAATATTATTGAA
TTTAAAAATATTTAAATTAATGAGTTAACATGTTAATAATGTAGTTGGATGATTA
Found at i:4141190 original size:32 final size:32
Alignment explanation
Indices: 4141087--4141210 Score: 113
Period size: 32 Copynumber: 3.7 Consensus size: 32
4141077 GAAAAATACT
* * *
4141087 TTTTAAGGCTCAAGCATAACCTTTACAATGCC
1 TTTTAAGGATCAAGCACAACCTTCACAATGCC
* * *
4141119 TTTCAAGGATCAAGCACAATCTCTCAATATAATGCC
1 TTTTAAGGATCAAGCACAACCT-TC---ACAATGCC
*
4141155 TTTTATGGATCAAGCACAACCTTCACAATGCC
1 TTTTAAGGATCAAGCACAACCTTCACAATGCC
* * *
4141187 TTTTAAAGGCTAAAACACAACCTT
1 TTTT-AAGGATCAAGCACAACCTT
4141211 TTTCTCTCTT
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
32 29 0.40
33 16 0.22
35 2 0.03
36 26 0.36
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (32 bp):
TTTTAAGGATCAAGCACAACCTTCACAATGCC
Found at i:4141792 original size:21 final size:22
Alignment explanation
Indices: 4141741--4141803 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
4141731 TTCAAAATCA
*
4141741 AATGCAAAAAAGCTTT-AAAACT
1 AATGCAAACAAG-TTTAAAAACT
**
4141763 AATTTAAACAAGTTTAAAAACT
1 AATGCAAACAAGTTTAAAAACT
*
4141785 -ATGCAAACAAGTTCAAAAA
1 AATGCAAACAAGTTTAAAAA
4141804 TCATTCACAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.24
Consensus pattern (22 bp):
AATGCAAACAAGTTTAAAAACT
Found at i:4141839 original size:21 final size:21
Alignment explanation
Indices: 4141791--4141831 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4141781 AACTATGCAA
*
4141791 ACAAGTTCAAAAATCATTCAC
1 ACAATTTCAAAAATCATTCAC
*
4141812 ACAATTTCAAAACTCATTCA
1 ACAATTTCAAAAATCATTCA
4141832 AGTAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.27
Consensus pattern (21 bp):
ACAATTTCAAAAATCATTCAC
Found at i:4141984 original size:21 final size:21
Alignment explanation
Indices: 4141903--4141990 Score: 106
Period size: 21 Copynumber: 4.1 Consensus size: 21
4141893 TTTAAAAACT
4141903 ATTCAAACAAGTTCCAAA-ACTC
1 ATTCAAACAAGTT-CAAAGA-TC
* * *
4141925 ATTTAAACAACTTCAAAAATC
1 ATTCAAACAAGTTCAAAGATC
* *
4141946 ATTTAAACAAGTTGAAAGATC
1 ATTCAAACAAGTTCAAAGATC
4141967 ATTCAAACAAGTTCAAAGATC
1 ATTCAAACAAGTTCAAAGATC
4141988 ATT
1 ATT
4141991 GAAGCAATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
21 46 0.79
22 12 0.21
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (21 bp):
ATTCAAACAAGTTCAAAGATC
Found at i:4148647 original size:21 final size:22
Alignment explanation
Indices: 4148601--4148647 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
4148591 AGGGAGGTTT
*
4148601 AAAACTAATTTAAACAAGTTTA
1 AAAACTAATTTAAACAAGTTCA
*
4148623 AAAACT-ATTTAAATAAGTTCA
1 AAAACTAATTTAAACAAGTTCA
4148644 AAAA
1 AAAA
4148648 TCATTCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAACTAATTTAAACAAGTTCA
Found at i:4148756 original size:21 final size:22
Alignment explanation
Indices: 4148732--4148832 Score: 111
Period size: 21 Copynumber: 4.8 Consensus size: 22
4148722 TTAATTAAAA
* *
4148732 AAGTTTAAAAACT-ATTCAAAC
1 AAGTTCAAAGACTCATTCAAAC
*
4148753 AAGTTCAAAGACTCATTTAAAC
1 AAGTTCAAAGACTCATTCAAAC
* *
4148775 AACTTCAAAGA-TGATTCAAAC
1 AAGTTCAAAGACTCATTCAAAC
* *
4148796 AAGTTCAAAGA-TTACTCAAAC
1 AAGTTCAAAGACTCATTCAAAC
4148817 AAGTTCAAAGA-TCATT
1 AAGTTCAAAGACTCATT
4148833 AAAGCAATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
21 51 0.75
22 17 0.25
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.27
Consensus pattern (22 bp):
AAGTTCAAAGACTCATTCAAAC
Found at i:4152984 original size:14 final size:13
Alignment explanation
Indices: 4152941--4152977 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4152931 AAATCCGTTG
*
4152941 AAAATTTCCAACAA
1 AAAATTT-CATCAA
4152955 AAAATTTCATCAA
1 AAAATTTCATCAA
4152968 AAAATTTCAT
1 AAAATTTCAT
4152978 TGGAAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTCATCAA
Found at i:4153109 original size:28 final size:28
Alignment explanation
Indices: 4153014--4153109 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
4153004 ACCCTATAGT
*
4153014 AATTCCTTTGGAAAAGAATTTTG-AATGG
1 AATTCCGTTGGAAAAGAA-TTTGCAATGG
** * * *
4153042 AATTCTATT-G--AA-AATTTTCAACGA
1 AATTCCGTTGGAAAAGAATTTGCAATGG
*
4153066 AATTTCCGTTGAAAAAGAATTTGCAATGG
1 AA-TTCCGTTGGAAAAGAATTTGCAATGG
4153095 AATTCCGTTGGAAAA
1 AATTCCGTTGGAAAA
4153110 TTTTCATTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
23 3 0.06
24 7 0.14
25 7 0.14
27 1 0.02
28 21 0.42
29 11 0.22
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (28 bp):
AATTCCGTTGGAAAAGAATTTGCAATGG
Found at i:4153744 original size:12 final size:12
Alignment explanation
Indices: 4153727--4153752 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4153717 TGCATTCTTA
4153727 ATTTCTTCACGT
1 ATTTCTTCACGT
4153739 ATTTCTTCACGT
1 ATTTCTTCACGT
4153751 AT
1 AT
4153753 CTTGCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTTCTTCACGT
Found at i:4155750 original size:14 final size:14
Alignment explanation
Indices: 4155731--4155792 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
4155721 CATCTCCCTC
*
4155731 CATCTCATTTTTTT
1 CATCTCATCTTTTT
4155745 CATCTCATCTTTTT
1 CATCTCATCTTTTT
* *
4155759 CATTTTCATCTCTTTG
1 CA-TCTCATCT-TTTT
* *
4155775 CATGTCATCTTCTT
1 CATCTCATCTTTTT
4155789 CATC
1 CATC
4155793 CTCAATCAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 20 0.51
15 14 0.36
16 5 0.13
ACGTcount: A:0.15, C:0.27, G:0.03, T:0.55
Consensus pattern (14 bp):
CATCTCATCTTTTT
Found at i:4155791 original size:44 final size:45
Alignment explanation
Indices: 4155698--4155792 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 45
4155688 CGTCTTCAAT
* *
4155698 TTCATCTTCATCTTCATCATTTTCATCTCCCTCCATCTCATTTTT
1 TTCATCTTCATCTTCATCATTTTCATCTCCCTCCATCTCATCTTC
** ** * *
4155743 TTCATC-TCATCTTTTTCATTTTCATCTCTTTGCATGTCATCTTC
1 TTCATCTTCATCTTCATCATTTTCATCTCCCTCCATCTCATCTTC
4155787 TTCATC
1 TTCATC
4155793 CTCAATCAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 36 0.86
45 6 0.14
ACGTcount: A:0.15, C:0.31, G:0.02, T:0.53
Consensus pattern (45 bp):
TTCATCTTCATCTTCATCATTTTCATCTCCCTCCATCTCATCTTC
Found at i:4160126 original size:85 final size:84
Alignment explanation
Indices: 4159974--4160200 Score: 283
Period size: 85 Copynumber: 2.7 Consensus size: 84
4159964 AAGTAATACC
* * * * * * * *
4159974 CAAATATTAATTTCAATAATTAACTATAGCATATTGCCAATCATTTTAACTAAAAATTAATAAAA
1 CAAATATTATTTTTAATATTTAATTATAACATATTACCAATCATTTTAATTAAAAA-TAACAAAA
*
4160039 TAATTCTCAACATTAATTCT
65 TAATTCTAAACATTAATTCT
* *
4160059 CAAATATTATTTTTAATATTTAATTTTAACATATTACCAATCATTTTAATTAAAAATACACACAA
1 CAAATATTATTTTTAATATTTAATTATAACATATTACCAATCATTTTAATTAAAAATA-ACAAAA
4160124 TAATTCTAAACATTAATTCT
65 TAATTCTAAACATTAATTCT
* * * * * *
4160144 CAAACATAATTCTTAATGTTTAATTCTAACATATTACCAATCATTTTAATTACAAAT
1 CAAATATTATTTTTAATATTTAATTATAACATATTACCAATCATTTTAATTAAAAAT
4160201 TCAAATAATA
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
84 2 0.02
85 122 0.98
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (84 bp):
CAAATATTATTTTTAATATTTAATTATAACATATTACCAATCATTTTAATTAAAAATAACAAAAT
AATTCTAAACATTAATTCT
Found at i:4160142 original size:13 final size:13
Alignment explanation
Indices: 4160123--4160156 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
4160113 AATACACACA
4160123 ATAATTCT-AAAC
1 ATAATTCTCAAAC
4160135 ATTAATTCTCAAAC
1 A-TAATTCTCAAAC
4160149 ATAATTCT
1 ATAATTCT
4160157 TAATGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 14 0.70
14 5 0.25
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATTCTCAAAC
Found at i:4160211 original size:85 final size:85
Alignment explanation
Indices: 4160003--4160296 Score: 332
Period size: 85 Copynumber: 3.5 Consensus size: 85
4159993 TTAACTATAG
* * * * * *
4160003 CATATTGCCAATCATTTTAACTAAAAATT-AATAAAATAATTCTCAACATTAATTCTCAAATATT
1 CATATTACCAATCATTTTAATTAAAAATTCAA-ATAATAATTCTAAACATTAATTCTCAAACATA
* *
4160067 ATTTTTAATATTTAATTTTAA
65 ATTCTTAATATTTAATTCTAA
* * *
4160088 CATATTACCAATCATTTTAATTAAAAATACACACAATAATTCTAAACATTAATTCTCAAACATAA
1 CATATTACCAATCATTTTAATTAAAAATTCAAATAATAATTCTAAACATTAATTCTCAAACATAA
*
4160153 TTCTTAATGTTTAATTCTAA
66 TTCTTAATATTTAATTCTAA
* *
4160173 CATATTACCAATCATTTTAATTACAAATTCAAATAATAATTGC-AAATATTAATTC-CTAAACAT
1 CATATTACCAATCATTTTAATTAAAAATTCAAATAATAATT-CTAAACATTAATTCTC-AAACAT
* * *
4160236 AAATCTTCATATTTAATTCTAG
64 AATTCTTAATATTTAATTCTAA
** *
4160258 C--ATTA--AATCATTTTAATTAATTATCCAAATAATAATTCT
1 CATATTACCAATCATTTTAATTAAAAATTCAAATAATAATTCT
4160297 CAATGTTAAA
Statistics
Matches: 181, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
80 1 0.01
81 28 0.15
83 4 0.02
84 1 0.01
85 145 0.80
86 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (85 bp):
CATATTACCAATCATTTTAATTAAAAATTCAAATAATAATTCTAAACATTAATTCTCAAACATAA
TTCTTAATATTTAATTCTAA
Found at i:4161110 original size:24 final size:24
Alignment explanation
Indices: 4161083--4161128 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
4161073 ATGTCATTGT
*
4161083 ATCCTTAACAATTTTAGTCCATAG
1 ATCCTTAACAATTTTAGCCCATAG
*
4161107 ATCCTTAACTATTTTAGCCCAT
1 ATCCTTAACAATTTTAGCCCAT
4161129 TGAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (24 bp):
ATCCTTAACAATTTTAGCCCATAG
Found at i:4161222 original size:20 final size:20
Alignment explanation
Indices: 4161178--4161222 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4161168 CCATGGATCA
**
4161178 CAGCCCAAGTCAACCCATTT
1 CAGCCCAAGTCAACCCAAGT
*
4161198 TAGCCCAAGTCAACCCAAGT
1 CAGCCCAAGTCAACCCAAGT
4161218 CAGCC
1 CAGCC
4161223 TATTGATCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.40, G:0.13, T:0.16
Consensus pattern (20 bp):
CAGCCCAAGTCAACCCAAGT
Done.