Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 8 of 210
Found at i:2503705 original size:42 final size:42
Alignment explanation
Indices: 2503649--2503733 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
2503639 AAGATGGTGG
**
2503649 TGATGATAATAATAGGAGCTCAGGTGAGCATGGCCAGTTTGA
1 TGATGATAATAATAGGAGCTCAGGCAAGCATGGCCAGTTTGA
*
2503691 TGATGATAATAATAGGGGCTCAGGCAAGCATGGCCAGTTTGA
1 TGATGATAATAATAGGAGCTCAGGCAAGCATGGCCAGTTTGA
2503733 T
1 T
2503734 CCCGTCTCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (42 bp):
TGATGATAATAATAGGAGCTCAGGCAAGCATGGCCAGTTTGA
Found at i:2504030 original size:33 final size:33
Alignment explanation
Indices: 2503993--2504068 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
2503983 TTTGATGATT
2503993 ATGAAGATGATAGCGAATTCGTTGACGACCACA
1 ATGAAGATGATAGCGAATTCGTTGACGACCACA
* * * *
2504026 ATGAAGATGATAGCGAATTTGTTGATGACGACG
1 ATGAAGATGATAGCGAATTCGTTGACGACCACA
2504059 ATGAAGATGA
1 ATGAAGATGA
2504069 GGCTGACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.24
Consensus pattern (33 bp):
ATGAAGATGATAGCGAATTCGTTGACGACCACA
Found at i:2505577 original size:14 final size:14
Alignment explanation
Indices: 2505558--2505585 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2505548 TGCATGCATT
2505558 CATGCATGCAATGA
1 CATGCATGCAATGA
2505572 CATGCATGCAATGA
1 CATGCATGCAATGA
2505586 AGCAGGGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
CATGCATGCAATGA
Found at i:2506218 original size:3 final size:3
Alignment explanation
Indices: 2506210--2506236 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2506200 GGAAATGTTC
2506210 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2506237 CCTCAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2507504 original size:15 final size:16
Alignment explanation
Indices: 2507478--2507507 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2507468 AAATTACAAG
2507478 AAATTGTAAAAATATA
1 AAATTGTAAAAATATA
2507494 AAATT-TAAAAATAT
1 AAATTGTAAAAATAT
2507508 TTTAAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATTGTAAAAATATA
Found at i:2507567 original size:57 final size:58
Alignment explanation
Indices: 2507494--2507608 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 58
2507484 TAAAAATATA
2507494 AAATTTAAAAATATTTTAAACATTAAAGAATAAAAAGTTACGGGCCAATTTAAAAAAG
1 AAATTTAAAAATATTTTAAACATTAAAGAATAAAAAGTTACGGGCCAATTTAAAAAAG
2507552 AAATTT-AAAATATTTTAAACATTAAAGAATAAAAAGTTACGGGCCAATTTAAAAAAG
1 AAATTTAAAAATATTTTAAACATTAAAGAATAAAAAGTTACGGGCCAATTTAAAAAAG
2507609 TTACCAATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 51 0.89
58 6 0.11
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (58 bp):
AAATTTAAAAATATTTTAAACATTAAAGAATAAAAAGTTACGGGCCAATTTAAAAAAG
Found at i:2523532 original size:22 final size:23
Alignment explanation
Indices: 2523507--2523565 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
2523497 GGCGGAAAAC
*
2523507 AAACATGAAAAAAAAGG-AATTA
1 AAACATGAAAAAAAAGGAAATGA
*
2523529 AAACA-AAATAAAAAAGGAAATGA
1 AAACATGAA-AAAAAAGGAAATGA
*
2523552 AATCATAGAAAAAA
1 AAACAT-GAAAAAA
2523566 GGATGTGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 2 0.07
22 13 0.45
23 8 0.28
24 4 0.14
25 2 0.07
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (23 bp):
AAACATGAAAAAAAAGGAAATGA
Found at i:2530216 original size:19 final size:19
Alignment explanation
Indices: 2530192--2530235 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2530182 ATAGAGACCA
*
2530192 AATTTTAACAATAGAAAAT-
1 AATTTTAACAA-AAAAAATC
2530211 AATTTTTAACAAAAAAAATC
1 AA-TTTTAACAAAAAAAATC
2530231 AATTT
1 AATTT
2530236 ACTCTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTTTAACAAAAAAAATC
Found at i:2530217 original size:20 final size:20
Alignment explanation
Indices: 2530194--2530235 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2530184 AGAGACCAAA
*
2530194 TTTTAACAATAGAAAAT-AAT
1 TTTTAACAA-AAAAAATCAAT
2530214 TTTTAACAAAAAAAATCAAT
1 TTTTAACAAAAAAAATCAAT
2530234 TT
1 TT
2530236 ACTCTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (20 bp):
TTTTAACAAAAAAAATCAAT
Found at i:2533776 original size:13 final size:13
Alignment explanation
Indices: 2533722--2533786 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
2533712 TTAAACCAAT
2533722 CTTTTCAAAAGCA
1 CTTTTCAAAAGCA
* **
2533735 CTTCTCAAAAATA
1 CTTTTCAAAAGCA
* * * *
2533748 TTTTTCCACAGTA
1 CTTTTCAAAAGCA
*
2533761 CTTTTTAAAAGCA
1 CTTTTCAAAAGCA
2533774 CTTTTCAAAAGCA
1 CTTTTCAAAAGCA
2533787 ATGAAGAACT
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Found at i:2542616 original size:11 final size:12
Alignment explanation
Indices: 2542592--2542624 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2542582 GATTTATGCT
2542592 AAAAGAAGCAAC-
1 AAAAGAA-CAACA
2542604 AAAAGAACAACA
1 AAAAGAACAACA
2542616 AAAAGAACA
1 AAAAGAACA
2542625 CACACAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAACAACA
Found at i:2545120 original size:33 final size:33
Alignment explanation
Indices: 2545070--2545134 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2545060 TGTTTTTATC
*
2545070 CATGGGAGAGTGCATTTTGTTTTGATATTGGTA
1 CATGAGAGAGTGCATTTTGTTTTGATATTGGTA
* *
2545103 CATGAGAGAGTGTATTTTGTTTTGGTATTGGT
1 CATGAGAGAGTGCATTTTGTTTTGATATTGGT
2545135 TCTGTTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.20, C:0.05, G:0.31, T:0.45
Consensus pattern (33 bp):
CATGAGAGAGTGCATTTTGTTTTGATATTGGTA
Found at i:2550564 original size:208 final size:205
Alignment explanation
Indices: 2549938--2550616 Score: 1007
Period size: 205 Copynumber: 3.3 Consensus size: 205
2549928 AGAAATTAGA
* * * * * *
2549938 AAGTTGAATGCCTTAATAAGGATGTATGGTATGGTGTTTCTATCTTGTAATGCTTGAAAACTGTG
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
* * *
2550003 TATAAACCAGAATGGATGAAAGTATAATTGCATCT-TG---TGT-TTT-AAAATTATTAATATTT
66 TATAAACCAGAGTGGATGAAAGTATAATTGCATTTGTGTTTTGTGTTTCAAAATTAGTAATATTT
* * * *
2550062 CCGTCATTAACTGCTGATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATGATTTTACC
131 CTGTCATTAACTGCTGATTT-TATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACC
*
2550127 ATATATAATGT
195 ATATAAAATGT
*
2550138 AATTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTG--
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
* * *
2550201 TATAAACCAGAGTGGATTG-AAGTATTATTGCATCTTGTGTTTTGTGTATCAAAATTAGCAATAT
66 TATAAACCAGAGTGGA-TGAAAGTATAATTGCAT-TTGTGTTTTGTGTTTCAAAATTAGTAATAT
* * *
2550265 TTCTGTCATTAACTGCTAATTTTCATGTTCTGCTGCTCTCCCTTGTTTTCATTTGGATAGTTGTA
129 TTCTGTCATTAACTGCTGATTTT-ATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTA
*
2550330 CCATATAAGATGT
193 CCATATAAAATGT
2550343 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
2550408 TATAAACCAGAGTGGATGAAAGTATAATTGCATTTGTGTTTTGTGTTTCAAAAATTAGTAATATT
66 TATAAACCAGAGTGGATGAAAGTATAATTGCATTTGTGTTTTGTGTTTC-AAAATTAGTAATATT
*
2550473 TCTGTCATTGAACTGCTGATTTTATTGTTCTGCTGCCCTGCCTTGTTTTCATTTGGATAATTGTA
130 TCTGTCATT-AACTGCTGATTTTA-TGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTA
*
2550538 CCATATAAAATGC
193 CCATATAAAATGT
*
2550551 AAGTTGAATGCCTTAAGATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
2550616 T
66 T
2550617 GTTAACTGCT
Statistics
Matches: 432, Mismatches: 32, Indels: 22
0.89 0.07 0.05
Matches are distributed among these distances:
198 28 0.06
199 3 0.01
200 59 0.14
203 3 0.01
204 2 0.00
205 142 0.33
206 17 0.04
207 53 0.12
208 125 0.29
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (205 bp):
AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTTGAAAACTGTA
TATAAACCAGAGTGGATGAAAGTATAATTGCATTTGTGTTTTGTGTTTCAAAATTAGTAATATTT
CTGTCATTAACTGCTGATTTTATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACCA
TATAAAATGT
Found at i:2569448 original size:30 final size:30
Alignment explanation
Indices: 2569414--2569481 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
2569404 TAAATAAATT
2569414 TTAATTTGGTAC-AAT-TATACATATGAAACC
1 TTAATTTGGTACAAATGTATACATA--AAACC
* *
2569444 TTAATTGTGGTTCAAATGTATACATAAAACT
1 TTAATT-TGGTACAAATGTATACATAAAACC
2569475 TTAATTT
1 TTAATTT
2569482 TAATTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 7 0.21
31 15 0.45
32 3 0.09
33 8 0.24
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (30 bp):
TTAATTTGGTACAAATGTATACATAAAACC
Found at i:2578134 original size:4 final size:4
Alignment explanation
Indices: 2578121--2578150 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2578111 TTAATGTTCC
2578121 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2578151 CAAACATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2601885 original size:31 final size:31
Alignment explanation
Indices: 2601823--2601886 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2601813 TTAAGGGCCC
*
2601823 AATTTTTTTTACCAACTTTTAAAGGAACTAA
1 AATTTTTTTTACCAACTTTTAAAGAAACTAA
2601854 AATTTTTTTCT-CCAACTTTT-AAGAAACCTAA
1 AATTTTTTT-TACCAACTTTTAAAGAAA-CTAA
2601885 AA
1 AA
2601887 CCCCATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 5 0.17
31 24 0.80
32 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (31 bp):
AATTTTTTTTACCAACTTTTAAAGAAACTAA
Found at i:2602720 original size:27 final size:28
Alignment explanation
Indices: 2602689--2602751 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
2602679 TACATATTAA
*
2602689 TTATAATTT-A-TAAATTATATTCACTTT
1 TTATAATTTAATTAAATT-TAATCACTTT
*
2602716 TTAT-ATTTAATTATATTTAATCACTTT
1 TTATAATTTAATTAAATTTAATCACTTT
2602743 TTATGAATT
1 TTAT-AATT
2602752 ATTATAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.13
27 18 0.60
28 5 0.17
29 3 0.10
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (28 bp):
TTATAATTTAATTAAATTTAATCACTTT
Found at i:2603787 original size:21 final size:22
Alignment explanation
Indices: 2603743--2603787 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2603733 GTTGAATTTT
* **
2603743 TAAATATTTTTATTTATTTTTG
1 TAAATATTTTTATTAATTAATG
2603765 TAAA-ATTTTTATTAATTAATG
1 TAAATATTTTTATTAATTAATG
2603786 TA
1 TA
2603788 GTTAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TAAATATTTTTATTAATTAATG
Found at i:2604428 original size:43 final size:43
Alignment explanation
Indices: 2604364--2604724 Score: 478
Period size: 43 Copynumber: 8.4 Consensus size: 43
2604354 GCGTCGCTAA
* *
2604364 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACTAAGAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGAC
*
2604407 CTTTAGCGGCGCTTTTTCCACAAACGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGAC
* *
2604450 ATTTAGCCGCGC-TTTTCTCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTTC-CACAAACGCCGCTAAAGACCAAGAC
* *
2604493 CTTTAGCGGCGCCTTTTCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGAC
* *
2604536 CTTTAGCGGCGCTTTTTACCACAAACGCCGCTATAGACCATA-AT
1 CTTTAGCGGCGCTTTTT-CCACAAACGCCGCTAAAGACCA-AGAC
* * *
2604580 CTTTAGCGGCGCTTTTACCA-ATAACGCCGTTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCACA-AACGCCGCTAAAGACCAAGAC
* * *
2604623 CTTTAGTGACGCTTTTTCCACAAACGCCGCTAAAGACC-ATAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGAC
* *
2604665 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGAC
* * *
2604708 TTTTAGTGGCGTTTTTT
1 CTTTAGCGGCGCTTTTT
2604725 TTTTTAATGC
Statistics
Matches: 277, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
42 43 0.16
43 190 0.69
44 44 0.16
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGAC
Found at i:2604616 original size:130 final size:130
Alignment explanation
Indices: 2604364--2604713 Score: 491
Period size: 130 Copynumber: 2.7 Consensus size: 130
2604354 GCGTCGCTAA
* *
2604364 CTTTAGCGGCG-CTTTTCCCACAAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTTCCAC
1 CTTTAGCGGCGCCTTTT-CCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAC
*
2604428 AAACGCCACTAAAGACCA-AGACATTTAGCCGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGA
65 AAACGCCGCTAAAGACCATAGACATTTAGCCGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGA
2604492 C
130 C
2604493 CTTTAGCGGCGCCTTTTCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTACCAC
1 CTTTAGCGGCGCCTTTTCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTT-CCAC
* * *
2604558 AAACGCCGCTATAGACCATA-ATC-TTTAGCGGCGCTTTTAC-CA-ATAACGCCGTTAAAGACCA
65 AAACGCCGCTAAAGACCATAGA-CATTTAGCCGCGCTTTT-CTCACA-AACGCCGCTAAAGACCA
*
2604619 TGAC
127 AGAC
* * * *
2604623 CTTTAGTGACGCTTTTTCCACAAACGCCGCTAAAGACCAT-ACCTTTAGCGGCGCTTTTCCCACA
1 CTTTAGCGGCGCCTTTTCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCACA
*
2604687 AACGCCGCTAAAGACCAT-GACTTTTAG
66 AACGCCGCTAAAGACCATAGACATTTAG
2604714 TGGCGTTTTT
Statistics
Matches: 201, Mismatches: 12, Indels: 17
0.87 0.05 0.07
Matches are distributed among these distances:
127 1 0.00
128 28 0.14
129 71 0.35
130 98 0.49
131 3 0.01
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (130 bp):
CTTTAGCGGCGCCTTTTCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCACA
AACGCCGCTAAAGACCATAGACATTTAGCCGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
Found at i:2604946 original size:19 final size:19
Alignment explanation
Indices: 2604922--2604959 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2604912 TCCAAAAATG
*
2604922 TTAAAAGTTAAAATGATAA
1 TTAAAAGTCAAAATGATAA
2604941 TTAAAAGTCAAAATGATAA
1 TTAAAAGTCAAAATGATAA
2604960 AAATATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (19 bp):
TTAAAAGTCAAAATGATAA
Found at i:2606273 original size:17 final size:17
Alignment explanation
Indices: 2606251--2606283 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2606241 CGGGCATTTT
2606251 ATGTTATCGAGAGCTTA
1 ATGTTATCGAGAGCTTA
2606268 ATGTTATCGAGAGCTT
1 ATGTTATCGAGAGCTT
2606284 GGTTCTTGTT
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:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (17 bp):
ATGTTATCGAGAGCTTA
Found at i:2606553 original size:10 final size:11
Alignment explanation
Indices: 2606536--2606587 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
2606526 GGCCCATTTT
2606536 TATTTTAAAAA
1 TATTTTAAAAA
2606547 T-TTTT-AAAA
1 TATTTTAAAAA
**
2606556 -ATTAAAAAAA
1 TATTTTAAAAA
2606566 GTATTTTAAAAA
1 -TATTTTAAAAA
2606578 TATTTTAAAA
1 TATTTTAAAA
2606588 TTAAAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 6 0.18
10 8 0.24
11 11 0.33
12 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:2606574 original size:31 final size:31
Alignment explanation
Indices: 2606536--2606617 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
2606526 GGCCCATTTT
2606536 TATTTTAAAAAT-TTTTAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTT-AAAATTAAAAAAAG
2606567 TATTTTAAAAATATTTTAAAATTAAAAAAA-
1 TATTTTAAAAATATTTTAAAATTAAAAAAAG
* *
2606597 CA-TTAAAAAAGTATTTTAAAA
1 TATTTTAAAAA-TATTTTAAAA
2606618 ATATTTGACG
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 7 0.15
30 11 0.23
31 25 0.53
32 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAG
Found at i:2607469 original size:34 final size:34
Alignment explanation
Indices: 2607431--2607511 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
2607421 AAGTTTTATT
2607431 TTATGAAAGTTATATAA-TTGATGT-AG-GCTATGTA
1 TTATGAAAGTTATATAAGTTG-TGTAAGTG-T-TGTA
* *
2607465 TTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTA
1 TTATGAAAGTTATATAAGTTGTGTAAGTGTTGTA
*
2607499 TTATGTAAGTTAT
1 TTATGAAAGTTAT
2607512 GTATTATGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 34 0.83
35 6 0.15
36 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (34 bp):
TTATGAAAGTTATATAAGTTGTGTAAGTGTTGTA
Found at i:2607507 original size:16 final size:16
Alignment explanation
Indices: 2607339--2607768 Score: 144
Period size: 16 Copynumber: 25.4 Consensus size: 16
2607329 NNATGTAGGC
*
2607339 TATGTATTATGCAAGT
1 TATGTATTATGTAAGT
* *
2607355 TATTTAAGTTGTGTAAGT
1 TATGT-A-TTATGTAAGT
**
2607373 GCTGTATTATGTAAGT
1 TATGTATTATGTAAGT
*
2607389 TATGTATTATATAAGTTT
1 TATGTATTATGTAAG--T
*
2607407 TATGTAAAATATGTAAGT
1 TATGT--ATTATGTAAGT
* * * *
2607425 TTTATTTTATGAAAGT
1 TATGTATTATGTAAGT
* * *
2607441 TATATAATTGATGTAGGC
1 TATGT-ATT-ATGTAAGT
*
2607459 TATGTATTATGCAAGT
1 TATGTATTATGTAAGT
* *
2607475 TATTTAAGTTGTGTAAGT
1 TATGT-A-TTATGTAAGT
2607493 GT-TGTATTATGTAAGT
1 -TATGTATTATGTAAGT
2607509 TATGTATTATGT-A--
1 TATGTATTATGTAAGT
2607522 -A-G-A-TATGTAAGT
1 TATGTATTATGTAAGT
* *
2607534 TATATTTTATGTAAGT
1 TATGTATTATGTAAGT
* * * *
2607550 TCTGCATTATATATGT
1 TATGTATTATGTAAGT
* *
2607566 TATGCAAGTTGTGT-AG-
1 TATG-TA-TTATGTAAGT
* *
2607582 AATGTAAGCTATGTAAGT
1 TATGT-A-TTATGTAAGT
2607600 TATGTAAGTTATGTAAGT
1 TATGT-A-TTATGTAAGT
**
2607618 GGTGTATTATGTAAGT
1 TATGTATTATGTAAGT
2607634 TATGTAAGTTATTATGTAAGT
1 TA--T--G-TATTATGTAAGT
* *
2607655 TATGCAAGCTTCTATATAAGT
1 TATG-TA---T-TATGTAAGT
*
2607676 TATGTATTATGTTA-T
1 TATGTATTATGTAAGT
*
2607691 TATGTATTATGTAATTTAT
1 TATGTATTATGTAA---GT
*
2607710 TATGTTATTATATATAAGT
1 TATG-TA-T-TATGTAAGT
2607729 TATGTAAGTTATGTAAGT
1 TATGT-A-TTATGTAAGT
**
2607747 GGTGTATTATGTAAGT
1 TATGTATTATGTAAGT
2607763 TATGTA
1 TATGTA
2607769 AGTTATTATG
Statistics
Matches: 304, Mismatches: 69, Indels: 82
0.67 0.15 0.18
Matches are distributed among these distances:
9 5 0.02
10 2 0.01
11 1 0.00
12 1 0.00
13 1 0.00
15 16 0.05
16 125 0.41
17 18 0.06
18 75 0.25
19 14 0.05
20 13 0.04
21 27 0.09
22 6 0.02
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (16 bp):
TATGTATTATGTAAGT
Found at i:2607528 original size:25 final size:25
Alignment explanation
Indices: 2607500--2607548 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2607490 AGTGTTGTAT
*
2607500 TATGTAAGTTATGTATTATGTAAGA
1 TATGTAAGTTATATATTATGTAAGA
*
2607525 TATGTAAGTTATATTTTATGTAAG
1 TATGTAAGTTATATATTATGTAAG
2607549 TTCTGCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (25 bp):
TATGTAAGTTATATATTATGTAAGA
Found at i:2607629 original size:34 final size:32
Alignment explanation
Indices: 2607591--2607774 Score: 152
Period size: 34 Copynumber: 5.7 Consensus size: 32
2607581 GAATGTAAGC
2607591 TATGTAAGTTATGTAAGTTATGTAAGTGGTGTAT
1 TATGTAAGTTATGTAAGTTATGTAAGT-GT-TAT
*
2607625 TATGTAAGTTATGTAAGTTAT-T-A-TGTAAGT
1 TATGTAAGTTATGTAAGTTATGTAAGTGTTA-T
* *
2607655 TATGCAAGCTTCTATATAAGTTATGTATTA-TGTTAT
1 TATGTAAG--T-TATGTAAGTTATGTA--AGTGTTAT
*
2607691 TATGT-A-TTATGTAATTTAT-T-A-TGTTATT
1 TATGTAAGTTATGTAAGTTATGTAAGTGTTA-T
*
2607719 ATATATAAGTTATGTAAGTTATGTAAGTGGTGTAT
1 -TATGTAAGTTATGTAAGTTATGTAAGT-GT-TAT
2607754 TATGTAAGTTATGTAAGTTAT
1 TATGTAAGTTATGTAAGTTAT
2607775 TATGTAAGTT
Statistics
Matches: 123, Mismatches: 10, Indels: 34
0.74 0.06 0.20
Matches are distributed among these distances:
27 6 0.05
28 1 0.01
29 5 0.04
30 12 0.10
31 23 0.19
32 4 0.03
33 13 0.11
34 43 0.35
35 4 0.03
36 7 0.06
37 5 0.04
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.48
Consensus pattern (32 bp):
TATGTAAGTTATGTAAGTTATGTAAGTGTTAT
Found at i:2607647 original size:21 final size:21
Alignment explanation
Indices: 2607583--2607818 Score: 159
Period size: 21 Copynumber: 11.0 Consensus size: 21
2607573 GTTGTGTAGA
*
2607583 ATGTAAGCTATGTAAG---TT
1 ATGTAAGTTATGTAAGTTATT
2607601 ATGTAAGTTATGTAAGTGGTGTATT
1 ATGTAAGTTATGTAA---GT-TATT
2607626 ATGTAAGTTATGTAAGTTATT
1 ATGTAAGTTATGTAAGTTATT
* *
2607647 ATGTAAGTTATGCAAGCTT-CT
1 ATGTAAGTTATGTAAG-TTATT
*
2607668 ATATAAGTTATGTATTATGTTATT
1 ATGTAAGTTATGTA--A-GTTATT
*
2607692 ATGT-A-TTATGTAATTTATT
1 ATGTAAGTTATGTAAGTTATT
* * *
2607711 ATGTTA-TTATAT-A-TAAGTT
1 ATGTAAGTTATGTAAGTTA-TT
2607730 ATGTAAGTTATGTAAGTGGTGTATT
1 ATGTAAGTTATGTAA---GT-TATT
2607755 ATGTAAGTTATGTAAGTTATT
1 ATGTAAGTTATGTAAGTTATT
* *
2607776 ATGTAAGTTATGCAAGCTT-CT
1 ATGTAAGTTATGTAAG-TTATT
*
2607797 ATATAAGTTATGTCAAGCTTAT
1 ATGTAAGTTATGT-AAG-TTAT
2607819 ATATAATTAT
Statistics
Matches: 176, Mismatches: 18, Indels: 43
0.74 0.08 0.18
Matches are distributed among these distances:
18 16 0.09
19 17 0.10
20 12 0.07
21 65 0.37
22 21 0.12
23 4 0.02
24 5 0.03
25 35 0.20
26 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.46
Consensus pattern (21 bp):
ATGTAAGTTATGTAAGTTATT
Found at i:2607650 original size:12 final size:12
Alignment explanation
Indices: 2607599--2607786 Score: 62
Period size: 12 Copynumber: 17.1 Consensus size: 12
2607589 GCTATGTAAG
2607599 TTATGTAAGTTA
1 TTATGTAAGTTA
* *
2607611 TGTAAGT-GGTGTA
1 T-TATGTAAGT-TA
2607624 TTATGTAAG---
1 TTATGTAAGTTA
2607633 TTATGTAAGTTA
1 TTATGTAAGTTA
2607645 TTATGTAAG---
1 TTATGTAAGTTA
*
2607654 TTATGCAAGCTT-
1 TTATGTAAG-TTA
* *
2607666 CTATATAAGTTA
1 TTATGTAAGTTA
*
2607678 TGTAT-TATGTTA
1 T-TATGTAAGTTA
2607690 TTA--T--G-TA
1 TTATGTAAGTTA
*
2607697 TTATGTAATTTA
1 TTATGTAAGTTA
*
2607709 TTATGTTA-TTA
1 TTATGTAAGTTA
*
2607720 -TATATAAG---
1 TTATGTAAGTTA
2607728 TTATGTAAGTTA
1 TTATGTAAGTTA
* *
2607740 TGTAAGT-GGTGTA
1 T-TATGTAAGT-TA
2607753 TTATGTAAG---
1 TTATGTAAGTTA
2607762 TTATGTAAGTTA
1 TTATGTAAGTTA
2607774 TTATGTAAGTTA
1 TTATGTAAGTTA
2607786 T
1 T
2607787 GCAAGCTTCT
Statistics
Matches: 130, Mismatches: 19, Indels: 54
0.64 0.09 0.27
Matches are distributed among these distances:
7 5 0.04
8 1 0.01
9 34 0.26
10 6 0.05
11 7 0.05
12 58 0.45
13 19 0.15
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:2607693 original size:8 final size:7
Alignment explanation
Indices: 2607675--2607720 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
2607665 TCTATATAAG
2607675 TTATGTA
1 TTATGTA
2607682 TTATGTTA
1 TTATG-TA
2607690 TTATGTA
1 TTATGTA
2607697 TTATGTA
1 TTATGTA
*
2607704 --ATTTA
1 TTATGTA
2607709 TTATGTTA
1 TTATG-TA
2607717 TTAT
1 TTAT
2607721 ATATAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:2607695 original size:15 final size:15
Alignment explanation
Indices: 2607675--2607720 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
2607665 TCTATATAAG
2607675 TTATGTATTATGTTA
1 TTATGTATTATGTTA
2607690 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
2607704 --ATTTATTATGTTA
1 TTATGTATTATGTTA
2607717 TTAT
1 TTAT
2607721 ATATAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:2607733 original size:53 final size:57
Alignment explanation
Indices: 2607624--2607777 Score: 166
Period size: 56 Copynumber: 2.9 Consensus size: 57
2607614 AAGTGGTGTA
* * *
2607624 TTATGTAAGTTATGTAA--G-T-TATTATGTAAGTTATGCAAG--CTTCTATATAAG
1 TTATGTAAGTTATGTAAGTGATGTATTATGTAAGTTATGTAAGTTATTATATATAAG
* * * *
2607675 TTATGT-A-TTATGTTA-TTATGTATTATGTAATTTAT-TATGTTATTATATATAAG
1 TTATGTAAGTTATGTAAGTGATGTATTATGTAAGTTATGTAAGTTATTATATATAAG
*
2607728 TTATGTAAGTTATGTAAGTGGTGTATTATGTAAGTTATGTAAGTTATTAT
1 TTATGTAAGTTATGTAAGTGATGTATTATGTAAGTTATGTAAGTTATTAT
2607778 GTAAGTTATG
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
49 7 0.09
50 1 0.01
51 9 0.11
52 14 0.17
53 16 0.20
54 1 0.01
55 7 0.09
56 17 0.21
57 10 0.12
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (57 bp):
TTATGTAAGTTATGTAAGTGATGTATTATGTAAGTTATGTAAGTTATTATATATAAG
Found at i:2607787 original size:9 final size:9
Alignment explanation
Indices: 2607345--2607774 Score: 190
Period size: 9 Copynumber: 50.4 Consensus size: 9
2607335 AGGCTATGTA
*
2607345 TTATGCAAG
1 TTATGTAAG
*
2607354 TTATTTAAG
1 TTATGTAAG
*
2607363 TTGTGTAAG
1 TTATGTAAG
**
2607372 TGCTGT-A-
1 TTATGTAAG
2607379 TTATGTAAG
1 TTATGTAAG
2607388 TTATGT-A-
1 TTATGTAAG
*
2607395 TTATATAAG
1 TTATGTAAG
*
2607404 TTTTATGTAAA
1 --TTATGTAAG
*
2607415 ATATGTAAG
1 TTATGTAAG
**
2607424 TT-T-TATT
1 TTATGTAAG
*
2607431 TTATGAAAG
1 TTATGTAAG
*
2607440 TTATATAA-
1 TTATGTAAG
*
2607448 TTGATGTAGG
1 TT-ATGTAAG
*
2607458 CTATGT-A-
1 TTATGTAAG
*
2607465 TTATGCAAG
1 TTATGTAAG
*
2607474 TTATTTAAG
1 TTATGTAAG
*
2607483 TTGTGTAAG
1 TTATGTAAG
2607492 TGT-TGT-A-
1 T-TATGTAAG
2607499 TTATGTAAG
1 TTATGTAAG
2607508 TTATGT-A-
1 TTATGTAAG
2607515 TTATGTAAG
1 TTATGTAAG
*
2607524 ATATGTAAG
1 TTATGTAAG
**
2607533 TTA--TATT
1 TTATGTAAG
2607540 TTATGTAAG
1 TTATGTAAG
* *
2607549 TTCTG-CA-
1 TTATGTAAG
* *
2607556 TTATATATG
1 TTATGTAAG
*
2607565 TTATGCAAG
1 TTATGTAAG
*
2607574 TTGTGT-AG
1 TTATGTAAG
*
2607582 -AATGTAAG
1 TTATGTAAG
*
2607590 CTATGTAAG
1 TTATGTAAG
2607599 TTATGTAAG
1 TTATGTAAG
2607608 TTATGTAAG
1 TTATGTAAG
**
2607617 TGGTGT-A-
1 TTATGTAAG
2607624 TTATGTAAG
1 TTATGTAAG
2607633 TTATGTAAG
1 TTATGTAAG
2607642 TTATTATGTAAG
1 ---TTATGTAAG
*
2607654 TTATGCAAG
1 TTATGTAAG
*
2607663 CTTCTATATAAG
1 --T-TATGTAAG
2607675 TTATGT-A-
1 TTATGTAAG
*
2607682 TTATGTTA-
1 TTATGTAAG
2607690 TTATGT-A-
1 TTATGTAAG
*
2607697 TTATGTAAT
1 TTATGTAAG
*
2607706 TTAT-TATG
1 TTATGTAAG
2607714 TTAT-T-A-
1 TTATGTAAG
*
2607720 -TATATAAG
1 TTATGTAAG
2607728 TTATGTAAG
1 TTATGTAAG
2607737 TTATGTAAG
1 TTATGTAAG
**
2607746 TGGTGT-A-
1 TTATGTAAG
2607753 TTATGTAAG
1 TTATGTAAG
2607762 TTATGTAAG
1 TTATGTAAG
2607771 TTAT
1 TTAT
2607775 TATGTAAGTT
Statistics
Matches: 312, Mismatches: 68, Indels: 82
0.68 0.15 0.18
Matches are distributed among these distances:
5 3 0.01
6 2 0.01
7 60 0.19
8 38 0.12
9 183 0.59
10 3 0.01
11 8 0.03
12 15 0.05
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:2607828 original size:21 final size:22
Alignment explanation
Indices: 2607758--2607828 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 22
2607748 GTGTATTATG
*
2607758 TAAGTTATGT-AAG-TTATTATG
1 TAAGTTATGTCAAGCTTA-TATA
*
2607779 TAAGTTATG-CAAGCTTCTATA
1 TAAGTTATGTCAAGCTTATATA
2607800 TAAGTTATGTCAAGCTTATATA
1 TAAGTTATGTCAAGCTTATATA
2607822 TAA-TTAT
1 TAAGTTAT
2607829 TTATAAAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 28 0.64
22 16 0.36
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (22 bp):
TAAGTTATGTCAAGCTTATATA
Found at i:2607921 original size:45 final size:45
Alignment explanation
Indices: 2607855--2607954 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
2607845 ATTAATACTA
* *
2607855 ATAAATTTTATTACTAATAAATTTAGAACACTTATTTAGAAAACTT
1 ATAAA-TTTAATACTAATAAATTTAGAAAACTTATTTAGAAAACTT
2607901 ATAAATTTAATACTAATAAATTTAGAAAACTTATTTAGAAAACTT
1 ATAAATTTAATACTAATAAATTTAGAAAACTTATTTAGAAAACTT
2607946 ATAAATTTA
1 ATAAATTTA
2607955 GAAAACTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
45 47 0.90
46 5 0.10
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (45 bp):
ATAAATTTAATACTAATAAATTTAGAAAACTTATTTAGAAAACTT
Found at i:2607938 original size:13 final size:13
Alignment explanation
Indices: 2607920--2607947 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2607910 ATACTAATAA
2607920 ATTTAGAAAACTT
1 ATTTAGAAAACTT
2607933 ATTTAGAAAACTT
1 ATTTAGAAAACTT
2607946 AT
1 AT
2607948 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:2607955 original size:17 final size:17
Alignment explanation
Indices: 2607888--2608012 Score: 100
Period size: 17 Copynumber: 7.2 Consensus size: 17
2607878 TAGAACACTT
2607888 ATTTAGAAAACTTATAA
1 ATTTAGAAAACTTATAA
* *
2607905 ATTT--AATACTAATAA
1 ATTTAGAAAACTTATAA
2607920 ATTTAGAAAAC-T-T--
1 ATTTAGAAAACTTATAA
2607933 ATTTAGAAAACTTATAA
1 ATTTAGAAAACTTATAA
2607950 ATTTAGAAAACTTATATA
1 ATTTAGAAAACTTATA-A
* *
2607968 GATATTAAAACAATATTTATAA
1 -AT-TT-AGA-AA-ACTTATAA
2607990 TTATTTAGAAAACTTATAA
1 --ATTTAGAAAACTTATAA
2608009 ATTT
1 ATTT
2608013 TATAGTAATA
Statistics
Matches: 86, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
13 11 0.13
14 1 0.01
15 15 0.17
17 28 0.33
18 1 0.01
19 9 0.10
20 4 0.05
21 4 0.05
22 5 0.06
23 8 0.09
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (17 bp):
ATTTAGAAAACTTATAA
Found at i:2611089 original size:14 final size:15
Alignment explanation
Indices: 2611070--2611102 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2611060 CTTAAACCGA
2611070 AATCCCTAATT-CAT
1 AATCCCTAATTCCAT
2611084 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
2611099 AATC
1 AATC
2611103 TATAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:2611491 original size:20 final size:18
Alignment explanation
Indices: 2611458--2611495 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
2611448 ATTGAATTTT
2611458 AATTAATATAAATAAACA
1 AATTAATATAAATAAACA
2611476 AATTGAATAGTAAATAAACA
1 AATT-AATA-TAAATAAACA
2611496 GATAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AATTAATATAAATAAACA
Found at i:2611568 original size:41 final size:41
Alignment explanation
Indices: 2611507--2611732 Score: 186
Period size: 41 Copynumber: 5.5 Consensus size: 41
2611497 ATAAAATGTT
*
2611507 TTAGCGGCGCTTTTTTAAAAACGCCGCTAAAAGCCAGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCAGAGCA
* * * ** **
2611548 TTGGCGGCGCATTTTCAAAAATGCCGCT-GCAGCTCTTAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGC-CAGAGCA
* * * *
2611589 TTAGCGACGCTTTTTCAAAAACGCCGCTAAAAGCCCGATCT
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCAGAGCA
** * * * * *
2611630 TTAGCGGTACTTTTTTAGAACCGCCGCTAAAAGCCAGATCT
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCAGAGCA
* * * * *
2611671 TTAGCCGCGCTTTATCAAAAACACAGCT-AAAGCTCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGC-CAGAGCA
* *
2611712 TTAGCGGTGCTTTTTTAAAAA
1 TTAGCGGCGCTTTTTCAAAAA
2611733 AGCTCGAAAG
Statistics
Matches: 141, Mismatches: 41, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
40 8 0.06
41 130 0.92
42 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCAGAGCA
Found at i:2611725 original size:123 final size:123
Alignment explanation
Indices: 2611506--2611732 Score: 285
Period size: 123 Copynumber: 1.8 Consensus size: 123
2611496 GATAAAATGT
* * * **
2611506 TTTAGCGGCGCTTTTTTAAAAACGCCGCTAAAAGCCAGAGCATTGGCGGCGCATTTTCAAAAATG
1 TTTAGCGGCACTTTTTTAAAAACGCCGCTAAAAGCCAGAGCATTAGCCGCGCATTTTCAAAAACA
* ** *
2611571 CCGCTGCAGCTCTTAGCATTAGCGACGCTTTTTCAAAAACGCCGCTAAAAGCCCGATC
66 CAGCTAAAGCTCTGAGCATTAGCGACGCTTTTTCAAAAACGCCGCTAAAAGCCCGATC
* * * * *
2611629 TTTAGCGGTACTTTTTTAGAACCGCCGCTAAAAGCCAGATCTTTAGCCGCGC-TTTATCAAAAAC
1 TTTAGCGGCACTTTTTTAAAAACGCCGCTAAAAGCCAGAGCATTAGCCGCGCATTT-TCAAAAAC
** *
2611693 ACAGCTAAAGCTCTGAGCATTAGCGGTGCTTTTTTAAAAA
65 ACAGCTAAAGCTCTGAGCATTAGCGACGCTTTTTCAAAAA
2611733 AGCTCGAAAG
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
122 3 0.03
123 83 0.97
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (123 bp):
TTTAGCGGCACTTTTTTAAAAACGCCGCTAAAAGCCAGAGCATTAGCCGCGCATTTTCAAAAACA
CAGCTAAAGCTCTGAGCATTAGCGACGCTTTTTCAAAAACGCCGCTAAAAGCCCGATC
Found at i:2612735 original size:16 final size:17
Alignment explanation
Indices: 2612714--2612749 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2612704 GGTCAAGACT
2612714 AAAATTACA-AAACTAA
1 AAAATTACAGAAACTAA
*
2612730 AAAATTACAGGAACTAA
1 AAAATTACAGAAACTAA
2612747 AAA
1 AAA
2612750 TGATCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATTACAGAAACTAA
Found at i:2621951 original size:20 final size:20
Alignment explanation
Indices: 2621901--2621961 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
2621891 GGCATATTTT
2621901 AAATCAATAAAAAATTTAAA-
1 AAATCAATAAAAAA-TTAAAG
* * * *
2621921 ATATTATTAAAGAATTAAAG
1 AAATCAATAAAAAATTAAAG
*
2621941 AAATCAATAAAAAATTTAAG
1 AAATCAATAAAAAATTAAAG
2621961 A
1 A
2621962 TGTAGAATAA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAATCAATAAAAAATTAAAG
Found at i:2623126 original size:13 final size:11
Alignment explanation
Indices: 2623098--2623140 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2623088 AGTTCAATAT
2623098 TATTTTATTAA
1 TATTTTATTAA
2623109 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
2623122 TA-TTTATTAT
1 TATTTTATTAA
2623132 TATTTTATT
1 TATTTTATT
2623141 TAAAAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:2630186 original size:2 final size:2
Alignment explanation
Indices: 2630179--2630209 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2630169 TCCCTCATAT
2630179 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2630210 ATCTATTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2630330 original size:2 final size:2
Alignment explanation
Indices: 2630323--2630351 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2630313 ACAAACCCCT
2630323 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2630352 TTCTAGTTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2635480 original size:31 final size:32
Alignment explanation
Indices: 2635402--2635485 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 32
2635392 TGATACATGG
*
2635402 ACTTTAA-TTTGGTT-AAATTATACATATGGA
1 ACTTTAATTTTGGTTCAAATTATACATATGAA
* * *
2635432 ATTTTTATTGTGGTTCAAATGTATA-A-ATGAA
1 ACTTTAATTTTGGTTCAAAT-TATACATATGAA
2635463 ACTTTAATTTTGGTTC-AATTATA
1 ACTTTAATTTTGGTTCAAATTATA
2635486 TACATTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 4 0.09
30 8 0.18
31 23 0.52
32 5 0.11
33 4 0.09
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (32 bp):
ACTTTAATTTTGGTTCAAATTATACATATGAA
Found at i:2635646 original size:29 final size:30
Alignment explanation
Indices: 2635613--2635673 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
2635603 TTTGTGTATG
2635613 AAATTACACA-AAATCAAAATTCATATATA
1 AAATTACACATAAATCAAAATTCATATATA
2635642 AAATTACACATTAAATCAAAATTCATATATA
1 AAATTACACA-TAAATCAAAATTCATATATA
2635673 A
1 A
2635674 TTTTGAGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.33
31 20 0.67
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
AAATTACACATAAATCAAAATTCATATATA
Found at i:2635882 original size:7 final size:7
Alignment explanation
Indices: 2635870--2635896 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2635860 AATTTAGAAA
2635870 AATTATT
1 AATTATT
2635877 AATTATT
1 AATTATT
2635884 AATTATT
1 AATTATT
2635891 AATTAT
1 AATTAT
2635897 AAGTTAAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTATT
Found at i:2636549 original size:35 final size:34
Alignment explanation
Indices: 2636492--2636558 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
2636482 ATAATAGAAA
* *
2636492 TGAGAAAGAAAGAAACAGAGAAGCAAAACGAAAAT
1 TGAGAAAGAAAGAAACAAAGAAG-AAAAAGAAAAT
*
2636527 TGAGAAAGAAA-AAGAGAAAGAAGAAAAAGAAA
1 TGAGAAAGAAAGAA-ACAAAGAAGAAAAAGAAA
2636559 GAGAACACGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.04
Consensus pattern (34 bp):
TGAGAAAGAAAGAAACAAAGAAGAAAAAGAAAAT
Found at i:2637931 original size:32 final size:37
Alignment explanation
Indices: 2637855--2637931 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 37
2637845 AAATTTTTGT
2637855 TATATG-ATATTAGTGAGTAAAATTGCAATAGAATTG
1 TATATGAATATTAGTGAGTAAAATTGCAATAGAATTG
2637891 -ATATTGAATA-TAGTGA-T-AAATTG-AAT-GAATTG
1 TATA-TGAATATTAGTGAGTAAAATTGCAATAGAATTG
2637923 TATATGAAT
1 TATATGAAT
2637932 TAAAATGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
32 11 0.29
33 6 0.16
34 6 0.16
35 4 0.11
36 8 0.21
37 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.18, T:0.38
Consensus pattern (37 bp):
TATATGAATATTAGTGAGTAAAATTGCAATAGAATTG
Found at i:2642285 original size:18 final size:19
Alignment explanation
Indices: 2642262--2642297 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2642252 TACAATCCCA
2642262 ATCATATAATT-AACATCG
1 ATCATATAATTAAACATCG
2642280 ATCATATAATTAAACATC
1 ATCATATAATTAAACATC
2642298 TCAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (19 bp):
ATCATATAATTAAACATCG
Found at i:2647662 original size:104 final size:105
Alignment explanation
Indices: 2647535--2647744 Score: 413
Period size: 104 Copynumber: 2.0 Consensus size: 105
2647525 TTCAATTGAG
2647535 TAATGACTAAAAAACTCCCTTTTTTTGTAAAATAAATTATATCATTATATTTATCAAATATATAT
1 TAATGACTAAAAAACTCCCTTTTTTTGTAAAATAAATTATATCATTATATTTATCAAATATATAT
2647600 ATATCATTATAAGGTTTTTTTTTGTTTTTTGGTTTTCATA
66 ATATCATTATAAGGTTTTTTTTTGTTTTTTGGTTTTCATA
2647640 TAATGACT-AAAAACTCCCTTTTTTTGTAAAATAAATTATATCATTATATTTATCAAATATATAT
1 TAATGACTAAAAAACTCCCTTTTTTTGTAAAATAAATTATATCATTATATTTATCAAATATATAT
2647704 ATATCATTATAAGGTTTTTTTTTGTTTTTTGGTTTTCATA
66 ATATCATTATAAGGTTTTTTTTTGTTTTTTGGTTTTCATA
2647744 T
1 T
2647745 TTTTATATGA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 97 0.92
105 8 0.08
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.51
Consensus pattern (105 bp):
TAATGACTAAAAAACTCCCTTTTTTTGTAAAATAAATTATATCATTATATTTATCAAATATATAT
ATATCATTATAAGGTTTTTTTTTGTTTTTTGGTTTTCATA
Found at i:2661585 original size:22 final size:23
Alignment explanation
Indices: 2661545--2661589 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2661535 TAAGAGTACT
*
2661545 ATATATATAAATTATTATTAAATA
1 ATATATATAAA-TAGTATTAAATA
2661569 ATATATATAAA-AGTATTAAAT
1 ATATATATAAATAGTATTAAAT
2661590 TTTAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATATATAAATAGTATTAAATA
Found at i:2673621 original size:2 final size:2
Alignment explanation
Indices: 2673616--2673649 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2673606 ATATATATAT
2673616 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2673650 TCCGAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2674176 original size:22 final size:22
Alignment explanation
Indices: 2674132--2674194 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2674122 GACGGCGGAT
*
2674132 TGAACGAG-GAGA-AAAGA-AG
1 TGAAAGAGCGAGAGAAAGAGAG
2674151 TGAAATG-GCGAG-GAAAGGAGAG
1 TGAAA-GAGCGAGAGAAA-GAGAG
2674173 TGAAAGAGCGAGAGAAAGAGAG
1 TGAAAGAGCGAGAGAAAGAGAG
2674195 GAGAGCCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
19 5 0.14
20 7 0.19
21 3 0.08
22 17 0.47
23 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.41, T:0.06
Consensus pattern (22 bp):
TGAAAGAGCGAGAGAAAGAGAG
Found at i:2680875 original size:22 final size:22
Alignment explanation
Indices: 2680850--2680893 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2680840 AAAAAATTTT
*
2680850 AAATAATTTAATAATTTAATAA
1 AAATAATTGAATAATTTAATAA
* **
2680872 AAATTATTGAATCGTTTAATAA
1 AAATAATTGAATAATTTAATAA
2680894 TTATTTTATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATAATTGAATAATTTAATAA
Found at i:2699806 original size:30 final size:29
Alignment explanation
Indices: 2699771--2699845 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
2699761 AATATGTTGC
* *
2699771 TAATTATTTACTTTTATAAAATTTGAGATT
1 TAATTATTTACTTTTA-AAAATTTAAAATT
*
2699801 TAATTATTATA-TTTTAAAATTTTAAAATT
1 TAATTATT-TACTTTTAAAAATTTAAAATT
*
2699830 AAATTATTTCACTTTT
1 TAATTATTT-ACTTTT
2699846 CAATTTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 18 0.47
30 17 0.45
31 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.55
Consensus pattern (29 bp):
TAATTATTTACTTTTAAAAATTTAAAATT
Found at i:2704168 original size:2 final size:2
Alignment explanation
Indices: 2704161--2704195 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2704151 TAGTTTCAAG
*
2704161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2704196 AATAACCGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2704200 original size:10 final size:10
Alignment explanation
Indices: 2704161--2704200 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2704151 TAGTTTCAAG
*
2704161 ATATATATAT
1 ATATATATAA
*
2704171 ATATATATAT
1 ATATATATAA
2704181 ATATATATAA
1 ATATATATAA
*
2704191 ATATAAATAA
1 ATATATATAA
2704201 CCGTATTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAA
Found at i:2710934 original size:11 final size:11
Alignment explanation
Indices: 2710916--2710963 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
2710906 TATTCTTTAG
2710916 TAAATAAAATC
1 TAAATAAAATC
*
2710927 TGAATAAAATC
1 TAAATAAAATC
*
2710938 TAAATGAAATC
1 TAAATAAAATC
**
2710949 TTTATAAAA-C
1 TAAATAAAATC
2710959 TAAAT
1 TAAAT
2710964 TTCTATATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (11 bp):
TAAATAAAATC
Found at i:2710947 original size:22 final size:21
Alignment explanation
Indices: 2710916--2710963 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2710906 TATTCTTTAG
2710916 TAAATAAAATCTGAATAAAATC
1 TAAATAAAATCTGAATAAAA-C
* **
2710938 TAAATGAAATCTTTATAAAAC
1 TAAATAAAATCTGAATAAAAC
2710959 TAAAT
1 TAAAT
2710964 TTCTATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (21 bp):
TAAATAAAATCTGAATAAAAC
Found at i:2712160 original size:20 final size:20
Alignment explanation
Indices: 2712131--2712242 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
2712121 TTCGAAACTG
2712131 TACC-AAAATTATAAGAGAA
1 TACCAAAAATTATAAGAGAA
* **
2712150 TACCAAAAATTATAAAAGTG
1 TACCAAAAATTATAAGAGAA
*
2712170 TACCGAAAATTATGAAGA-AA
1 TACCAAAAATTAT-AAGAGAA
* * *
2712190 TATCAAACATTATAAGAGTA
1 TACCAAAAATTATAAGAGAA
* **
2712210 TATCAATTATTATGAAGA-AA
1 TACCAAAAATTAT-AAGAGAA
2712230 TACCAAAAATTAT
1 TACCAAAAATTAT
2712243 GCTAAATATT
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
19 8 0.11
20 57 0.79
21 7 0.10
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (20 bp):
TACCAAAAATTATAAGAGAA
Found at i:2712202 original size:40 final size:39
Alignment explanation
Indices: 2712129--2712242 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 39
2712119 AGTTCGAAAC
2712129 TGTACCAAAATTAT-AAGAGAATACCAAAAATTATAAAAG
1 TGTACCAAAATTATGAAGA-AATACCAAAAATTATAAAAG
* * *
2712168 TGTACCGAAAATTATGAAGAAATATCAAACATTATAAGAG
1 TGTACC-AAAATTATGAAGAAATACCAAAAATTATAAAAG
* * *
2712208 TATATCAATTATTATGAAGAAATACCAAAAATTAT
1 TGTACCAA-AATTATGAAGAAATACCAAAAATTAT
2712243 GCTAAATATT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
39 8 0.12
40 52 0.81
41 4 0.06
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.27
Consensus pattern (39 bp):
TGTACCAAAATTATGAAGAAATACCAAAAATTATAAAAG
Found at i:2715252 original size:27 final size:26
Alignment explanation
Indices: 2715222--2715354 Score: 99
Period size: 27 Copynumber: 5.0 Consensus size: 26
2715212 GCTCTTTTGT
2715222 TATTATTTATTTTAAGTTTTTTATATA
1 TATTATTTATTTTAA-TTTTTTATATA
* * **
2715249 TATTATTTATTCTAAACTATTTT-TACC
1 TATTATTTATT-TTAA-TTTTTTATATA
* *
2715276 TATTATTTATTTAAATTTTTTTTATTA
1 TATTATTTATTTTAATTTTTTATA-TA
* ** *
2715303 TATTACTTATTTTAAACTATTATATA
1 TATTATTTATTTTAATTTTTTATATA
* * *
2715329 TATTA-TCATTTAAAATTTTTATATA
1 TATTATTTATTTTAATTTTTTATATA
2715354 T
1 T
2715355 TATTTAAAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
25 22 0.26
26 13 0.15
27 42 0.49
28 8 0.09
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (26 bp):
TATTATTTATTTTAATTTTTTATATA
Found at i:2715339 original size:25 final size:23
Alignment explanation
Indices: 2715296--2715357 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
2715286 TTAAATTTTT
* *
2715296 TTTAT-TATATTACTTATTTTAAAC
1 TTTATATATATTA-TCA-TTTAAAA
2715320 TATTATATATATTATCATTTAAAA
1 T-TTATATATATTATCATTTAAAA
*
2715344 TTTTTATATATTAT
1 TTTATATATATTAT
2715358 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 12 0.36
24 8 0.24
25 6 0.18
26 7 0.21
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATATATATTATCATTTAAAA
Found at i:2715356 original size:54 final size:53
Alignment explanation
Indices: 2715222--2715357 Score: 143
Period size: 54 Copynumber: 2.5 Consensus size: 53
2715212 GCTCTTTTGT
* * * *
2715222 TATTATTTATTTTAAGTTTTTTATA-TATATTATTTATTCTAAACTATTTTTACC
1 TATTATTCA-TTTAAATTTTTTATATTATATTACTTATTCTAAACTATTTATA-C
* * *
2715276 TATTATTTATTTAAATTTTTTTTATTATATTACTTATTTTAAACTATTATATA-
1 TATTATTCATTTAAATTTTTTATATTATATTACTTATTCTAAACTATT-TATAC
2715329 TATTA-TCATTTAAAATTTTTATATATTAT
1 TATTATTCATTT-AAATTTTT-TATATTAT
2715358 TTAAAAAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
52 5 0.07
53 26 0.37
54 37 0.52
55 3 0.04
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (53 bp):
TATTATTCATTTAAATTTTTTATATTATATTACTTATTCTAAACTATTTATAC
Found at i:2715450 original size:26 final size:26
Alignment explanation
Indices: 2715382--2715455 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 26
2715372 TTATATGTTA
2715382 TTTTTATATTATTTATTTTAAACTGT
1 TTTTTATATTATTTATTTTAAACTGT
* * * * *
2715408 TTTGT-TATTATTCATTTTTAAGTTT
1 TTTTTATATTATTTATTTTAAACTGT
* *
2715433 TTTTTATATTGTTTATTTGAAAC
1 TTTTTATATTATTTATTTTAAAC
2715456 CTTTTATCAT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
25 20 0.56
26 16 0.44
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (26 bp):
TTTTTATATTATTTATTTTAAACTGT
Found at i:2715555 original size:29 final size:29
Alignment explanation
Indices: 2715523--2715581 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2715513 CTTTAAATTG
2715523 TTTCATATATTATTTTGGTTCGCTTTCCT
1 TTTCATATATTATTTTGGTTCGCTTTCCT
2715552 TTTCATATATTATTTTGGTTCGCTTTCCT
1 TTTCATATATTATTTTGGTTCGCTTTCCT
2715581 T
1 T
2715582 GATTGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.59
Consensus pattern (29 bp):
TTTCATATATTATTTTGGTTCGCTTTCCT
Found at i:2716846 original size:2 final size:2
Alignment explanation
Indices: 2716841--2716865 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2716831 AAACCGTGCC
2716841 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 T
2716866 GCATACATTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2716978 original size:2 final size:2
Alignment explanation
Indices: 2716971--2716995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2716961 NNNNNNNNNN
2716971 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 T
2716996 GTAAATGGGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2718229 original size:72 final size:73
Alignment explanation
Indices: 2718133--2718277 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 73
2718123 ATATTTTTGA
2718133 AGTCAGGTAAATATTTAAGTATAATTCTTTAAAAAATATTTAAACATAAAATATATAATTTTTTT
1 AGTCAGGTAAATATTTAAGTATAATTCTTTAAAAAATATTTAAACATAAAATATATAATTTTTTT
2718198 CTATATTC
66 CTATATTC
2718206 AGTCAGGT-AATATTTAAGTATAATTCTTTAAAAAATATTTAAACATAAAATATATAATTTTTTT
1 AGTCAGGTAAATATTTAAGTATAATTCTTTAAAAAATATTTAAACATAAAATATATAATTTTTTT
2718270 CTATATTC
66 CTATATTC
2718278 CATTATTATA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 64 0.89
73 8 0.11
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (73 bp):
AGTCAGGTAAATATTTAAGTATAATTCTTTAAAAAATATTTAAACATAAAATATATAATTTTTTT
CTATATTC
Found at i:2723253 original size:6 final size:6
Alignment explanation
Indices: 2723208--2723233 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2723198 GATATTTTAG
2723208 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
2723234 TTGATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:2730922 original size:3 final size:3
Alignment explanation
Indices: 2730916--2730957 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
2730906 TTTTATTTTT
* * *
2730916 TTA TTA TTA TTG TTA TTA TTA ATA TTA TTG TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2730958 GAAATAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2732777 original size:110 final size:109
Alignment explanation
Indices: 2732584--2732805 Score: 376
Period size: 110 Copynumber: 2.0 Consensus size: 109
2732574 AGAAGAAAAT
*
2732584 AAAAATGCGAAAACCAAATAAATGATCAAATTAAGCGGAACGCCGGATTTGAGTACTTCTGATCA
1 AAAAATGCGAAAACCAAATAAATGATCAAATTAAGCGGAACGCCGGATTTGAGTAC-TATGATCA
2732649 AGTAACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
65 AGTAACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
2732694 AAAAATGCGAAAACCAAATAAATGATCAAATTAAGCGGAACGCCGGATTTGAGTAC-ATGAT-AA
1 AAAAATGCGAAAACCAAATAAATGATCAAATTAAGCGGAACGCCGGATTTGAGTACTATGATCAA
*
2732757 GTGGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
66 ---GTAACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
2732804 AA
1 AA
2732806 GTGACAAAGT
Statistics
Matches: 107, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
107 2 0.02
108 4 0.04
110 101 0.94
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (109 bp):
AAAAATGCGAAAACCAAATAAATGATCAAATTAAGCGGAACGCCGGATTTGAGTACTATGATCAA
GTAACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:2739360 original size:2 final size:2
Alignment explanation
Indices: 2739355--2739385 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2739345 GTGTACACAC
2739355 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 A
2739386 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2739390 original size:2 final size:2
Alignment explanation
Indices: 2739385--2739417 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2739375 ATATATATAT
2739385 AG AG AG 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 AG AG AG A
2739418 CGCCCCCNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2745290 original size:21 final size:21
Alignment explanation
Indices: 2745241--2745292 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2745231 TTTTTTATAA
*
2745241 TCTGTTAGTTTAATTTTAGTT
1 TCTGTTATTTTAATTTTAGTT
*
2745262 TCTTTTATTTTATATTTTA-TT
1 TCTGTTATTTTA-ATTTTAGTT
*
2745283 TGTGTTATTT
1 TCTGTTATTT
2745293 AGAAGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.17, C:0.04, G:0.10, T:0.69
Consensus pattern (21 bp):
TCTGTTATTTTAATTTTAGTT
Found at i:2749267 original size:21 final size:23
Alignment explanation
Indices: 2749242--2749283 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2749232 AATCGGATAC
2749242 TAATTAGAACA-A-AAAGAAAAT
1 TAATTAGAACATAGAAAGAAAAT
*
2749263 TAATTTGAACATAGAAAGAAA
1 TAATTAGAACATAGAAAGAAA
2749284 TTTTAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (23 bp):
TAATTAGAACATAGAAAGAAAAT
Found at i:2749912 original size:3 final size:3
Alignment explanation
Indices: 2749904--2749941 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
2749894 CCATATCCTC
2749904 TCT TCT TCT TCT TCT TCT TCT TCT TCTT TCT TC- TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TC
2749942 ACAATCCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:2758350 original size:41 final size:41
Alignment explanation
Indices: 2758305--2758435 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
2758295 TCTCCAATTA
2758305 TATAATACTAAATAATTTTCTGATATCAAAATATTATTTCT
1 TATAATACTAAATAATTTTCTGATATCAAAATATTATTTCT
** * * * * * * *
2758346 TATAATA-TTTATATTTTTAATCATATTCTAAAATCTCAATT-A
1 TATAATACTAAATAATTTT-CTGATA-TC-AAAATATTATTTCT
2758388 TATAATACTAAATAATTTTCTGATATCAAAATATTATTTCT
1 TATAATACTAAATAATTTTCTGATATCAAAATATTATTTCT
2758429 TATAATA
1 TATAATA
2758436 TTTATATTTT
Statistics
Matches: 67, Mismatches: 18, Indels: 10
0.71 0.19 0.11
Matches are distributed among these distances:
40 17 0.25
41 20 0.30
42 13 0.19
43 17 0.25
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (41 bp):
TATAATACTAAATAATTTTCTGATATCAAAATATTATTTCT
Found at i:2758395 original size:83 final size:84
Alignment explanation
Indices: 2758288--2758455 Score: 329
Period size: 83 Copynumber: 2.0 Consensus size: 84
2758278 TCTTGAAGAG
2758288 TCTAAAATCTCCAATTATATAATACTAAATAATTTTCTGATATCAAAATATTATTTCTTATAATA
1 TCTAAAATCTCCAATTATATAATACTAAATAATTTTCTGATATCAAAATATTATTTCTTATAATA
2758353 TTTATATTTTTAATCATAT
66 TTTATATTTTTAATCATAT
2758372 TCTAAAATCT-CAATTATATAATACTAAATAATTTTCTGATATCAAAATATTATTTCTTATAATA
1 TCTAAAATCTCCAATTATATAATACTAAATAATTTTCTGATATCAAAATATTATTTCTTATAATA
2758436 TTTATATTTTTAATCATAT
66 TTTATATTTTTAATCATAT
2758455 T
1 T
2758456 TAATTAAAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 74 0.88
84 10 0.12
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.48
Consensus pattern (84 bp):
TCTAAAATCTCCAATTATATAATACTAAATAATTTTCTGATATCAAAATATTATTTCTTATAATA
TTTATATTTTTAATCATAT
Found at i:2759066 original size:22 final size:21
Alignment explanation
Indices: 2759031--2759072 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2759021 CCGAGGTGGT
2759031 TAAGCCCTAAAATAAATAATAA
1 TAAGCCCTAAAAT-AATAATAA
* *
2759053 TAAGCTCTACAATAATAATA
1 TAAGCCCTAAAATAATAATA
2759073 TTCCATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAGCCCTAAAATAATAATAA
Found at i:2760728 original size:23 final size:23
Alignment explanation
Indices: 2760685--2760729 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2760675 TTAAACTGAA
*
2760685 AAAAATTATATTTTATCTTTCAT
1 AAAAATTATATTTAATCTTTCAT
*
2760708 AAAAATTTTAATTTAAT-TTTCA
1 AAAAATTAT-ATTTAATCTTTCA
2760730 CCCTTTCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAAATTATATTTAATCTTTCAT
Found at i:2768293 original size:23 final size:22
Alignment explanation
Indices: 2768254--2768298 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2768244 CATTGTTTTT
2768254 AATTATTTTATTATTGTTCTAA
1 AATTATTTTATTATTGTTCTAA
* *
2768276 AATTGTTTATATTTTTGTTCTAA
1 AATTATTT-TATTATTGTTCTAA
2768299 TTATTGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (22 bp):
AATTATTTTATTATTGTTCTAA
Found at i:2768300 original size:21 final size:20
Alignment explanation
Indices: 2768253--2768303 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
2768243 ACATTGTTTT
2768253 TAATTATTTTATTATTGTTC
1 TAATTATTTTATTATTGTTC
* *
2768273 TAAAATTGTTTATATTTTTGTTC
1 T--AATTATTT-TATTATTGTTC
2768296 TAATTATT
1 TAATTATT
2768304 GTCAACTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 7 0.28
23 11 0.44
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (20 bp):
TAATTATTTTATTATTGTTC
Found at i:2768849 original size:32 final size:33
Alignment explanation
Indices: 2768813--2768875 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
2768803 TTTCACATGA
** *
2768813 TTGATTAAAGCCGTAAATAAAAAAA-TAAATAC
1 TTGATTAAAGCCAAAAAAAAAAAAACTAAATAC
*
2768845 TTGATTGAAGCCAAAAAAAAAAAAACTAAAT
1 TTGATTAAAGCCAAAAAAAAAAAAACTAAAT
2768876 TTTTTGATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (33 bp):
TTGATTAAAGCCAAAAAAAAAAAAACTAAATAC
Found at i:2769779 original size:15 final size:15
Alignment explanation
Indices: 2769759--2769788 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2769749 AGTGGACGGT
2769759 AACAGTTATTACATG
1 AACAGTTATTACATG
2769774 AACAGTTATTACATG
1 AACAGTTATTACATG
2769789 TGTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
AACAGTTATTACATG
Found at i:2769882 original size:22 final size:21
Alignment explanation
Indices: 2769843--2769911 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 21
2769833 ACTTAATATT
2769843 TAAGTAAATATATATAATATAATAA
1 TAAGTAAATATA-ATAA-AT-A-AA
2769868 TAAAGTAAATATAATAAAATAAA
1 T-AAGTAAATATAAT-AAATAAA
* *
2769891 TTAGTAAATGTAATAAATAAA
1 TAAGTAAATATAATAAATAAA
2769912 GAAAAGAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 7 0.17
22 11 0.28
23 3 0.08
24 1 0.03
25 5 0.12
26 13 0.32
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (21 bp):
TAAGTAAATATAATAAATAAA
Found at i:2770927 original size:37 final size:37
Alignment explanation
Indices: 2770877--2771007 Score: 181
Period size: 37 Copynumber: 3.5 Consensus size: 37
2770867 TAGATATATT
2770877 CGATGAGGCACTGGGTGCCAATTTACTTCGATTTAGC
1 CGATGAGGCACTGGGTGCCAATTTACTTCGATTTAGC
*
2770914 CGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAGC
1 CGATGAGGCACTGGGTGCCAATTTACTTCGATTTAGC
* * * * *
2770951 CGATGAGACACTGGGTGTCAAATTATCATTTCGAATTATC
1 CGATGAGGCACTGGGTG-CCAATT-T-ACTTCGATTTAGC
2770991 CGATGAGGCACTGGGTG
1 CGATGAGGCACTGGGTG
2771008 TCAAACTGGT
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
37 52 0.63
38 5 0.06
39 1 0.01
40 25 0.30
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (37 bp):
CGATGAGGCACTGGGTGCCAATTTACTTCGATTTAGC
Found at i:2775052 original size:19 final size:17
Alignment explanation
Indices: 2775024--2775099 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
2775014 AAATGTGAAC
2775024 TTATAAAAATTATAAACA
1 TTATAAAAATTATAAA-A
2775042 TTATCAAAAA-TATAAAA
1 TTAT-AAAAATTATAAAA
* * *
2775059 TTTCTAATAAATTCTAATATT
1 -TTATAA-AAATTATAA-A-A
2775080 TTATAAAAATTATAAAA
1 TTATAAAAATTATAAAA
2775097 TTA
1 TTA
2775100 ATAATACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
17 6 0.13
18 17 0.37
19 17 0.37
20 6 0.13
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TTATAAAAATTATAAAA
Found at i:2775098 original size:8 final size:9
Alignment explanation
Indices: 2775024--2775096 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 9
2775014 AAATGTGAAC
2775024 TTATAAAAA
1 TTATAAAAA
*
2775033 TTATAAACA
1 TTATAAAAA
2775042 TTATCAAAAA
1 TTAT-AAAAA
*
2775052 -TATAAAAT
1 TTATAAAAA
*
2775060 TTCTAATAAA
1 TTATAA-AAA
* **
2775070 TTCTAATATT
1 TTATAA-AAA
2775080 TTATAAAAA
1 TTATAAAAA
2775089 TTATAAAA
1 TTATAAAA
2775097 TTAATAATAC
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
8 4 0.08
9 28 0.55
10 19 0.37
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:2775105 original size:38 final size:38
Alignment explanation
Indices: 2775042--2775125 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
2775032 ATTATAAACA
** *
2775042 TTATCAAAAATATAAAATTTCTAATA-A-ATTCTAATATT
1 TTAT-AAAAATATAAAATTAATAATACATATT-TAAAATT
2775080 TTATAAAAATTATAAAATTAATAATACATATTTAAAATT
1 TTATAAAAA-TATAAAATTAATAATACATATTTAAAATT
2775119 TTATAAA
1 TTATAAA
2775126 TACATGTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 5 0.12
38 18 0.45
39 14 0.35
40 3 0.08
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (38 bp):
TTATAAAAATATAAAATTAATAATACATATTTAAAATT
Found at i:2775135 original size:21 final size:22
Alignment explanation
Indices: 2775102--2775146 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2775092 TAAAATTAAT
* *
2775102 AATACATATTTAAAATTTTATA
1 AATACATAGTTAAAATTCTATA
*
2775124 AATACAT-GTTAAAGTTCTATA
1 AATACATAGTTAAAATTCTATA
2775145 AA
1 AA
2775147 AATTATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (22 bp):
AATACATAGTTAAAATTCTATA
Found at i:2775862 original size:135 final size:134
Alignment explanation
Indices: 2775608--2775876 Score: 439
Period size: 135 Copynumber: 2.0 Consensus size: 134
2775598 ATAATATTCA
* * *
2775608 AGAAAACAACTCAAAAAACACCATTGAAGCCGATTGTGAAGCAAATTATTGTCAAGATTGAAGAT
1 AGAAAACAACTAAAAAAACACCATTGAAGCAGATTATGAAGCAAATTATTGTCAAGATTGAAGAT
* * * *
2775673 TCCTAGTTGATTTCTTAGGAATTTATCATGAGTTCCTTTATTTATTGTGGTTATACTGTATCTTG
66 TCCTAGTTGATTTCTTAGGAAATTATCATGAATTCCTTTATTTATTGTAGTTATACTGTATATTG
2775738 GATG
131 GATG
*
2775742 AGAAAACAACTAAAAAAAACACCATTGAAGCAGATTATGAAGCAAATTGTTGTCAAGATTGAAGA
1 AGAAAACAACT-AAAAAAACACCATTGAAGCAGATTATGAAGCAAATTATTGTCAAGATTGAAGA
* *
2775807 TTCCTAGTTGATTTCTTAGGAAATTATCATGAATTTCTTTATTTCTTGTAGTTATACTGTATATT
65 TTCCTAGTTGATTTCTTAGGAAATTATCATGAATTCCTTTATTTATTGTAGTTATACTGTATATT
2775872 GGATG
130 GGATG
2775877 CTTTTATTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
134 11 0.09
135 113 0.91
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (134 bp):
AGAAAACAACTAAAAAAACACCATTGAAGCAGATTATGAAGCAAATTATTGTCAAGATTGAAGAT
TCCTAGTTGATTTCTTAGGAAATTATCATGAATTCCTTTATTTATTGTAGTTATACTGTATATTG
GATG
Found at i:2776675 original size:24 final size:26
Alignment explanation
Indices: 2776638--2776686 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
2776628 GTTGAATCCA
2776638 TTTTTATTTCTTAATATTTT-TTTAT
1 TTTTTATTTCTTAATATTTTATTTAT
2776663 TTTTTATTT-TTAATATTTTATTTA
1 TTTTTATTTCTTAATATTTTATTTA
2776687 ATTGATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTATTTCTTAATATTTTATTTAT
Found at i:2776990 original size:19 final size:18
Alignment explanation
Indices: 2776965--2777034 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 18
2776955 AGTTAATATC
2776965 AATTTTAATATTTTTATA
1 AATTTTAATATTTTTATA
2776983 AATATTT-ATAATTTTTA-A
1 AAT-TTTAAT-ATTTTTATA
*
2777001 GAATTCTAATATGTTTT-TA
1 -AATTTTAATAT-TTTTATA
2777020 AATTTTAAATATTTT
1 AATTTT-AATATTTT
2777035 AAATAAGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
18 18 0.42
19 25 0.58
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTTTAATATTTTTATA
Found at i:2777011 original size:37 final size:36
Alignment explanation
Indices: 2776965--2777036 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
2776955 AGTTAATATC
*
2776965 AATTTTAATAT-TTTTATAAATATTTATAAT-TTTTAAG
1 AATTCTAATATGTTTT-TAAAT-TTTA-AATATTTTAAG
2777002 AATTCTAATATGTTTTTAAATTTTAAATATTTTAA
1 AATTCTAATATGTTTTTAAATTTTAAATATTTTAA
2777037 ATAAGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 3 0.09
36 10 0.31
37 15 0.47
38 4 0.12
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (36 bp):
AATTCTAATATGTTTTTAAATTTTAAATATTTTAAG
Found at i:2777257 original size:20 final size:19
Alignment explanation
Indices: 2777212--2777269 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 19
2777202 NNNNNNNNNN
*
2777212 TATTTTTTTATAATTTTAA
1 TATTTTTATATAATTTTAA
* *
2777231 AAATTTTATATCAATTTTAA
1 TATTTTTATAT-AATTTTAA
2777251 TATTTTTA-AT-A-TTTAA
1 TATTTTTATATAATTTTAA
2777267 TAT
1 TAT
2777270 ATCTATGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 8 0.24
17 1 0.03
19 10 0.30
20 14 0.42
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTTATATAATTTTAA
Found at i:2777983 original size:3 final size:3
Alignment explanation
Indices: 2777975--2778010 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2777965 AACCTACACA
2777975 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2778011 GGGAATATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2779215 original size:14 final size:15
Alignment explanation
Indices: 2779188--2779226 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
2779178 TATAAATCAG
2779188 TATATAATAAATATT
1 TATATAATAAATATT
2779203 TATATAA-AAATATT
1 TATATAATAAATATT
*
2779217 TAAATAATAA
1 TATATAATAA
2779227 TTATATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATAATAAATATT
Found at i:2779885 original size:37 final size:37
Alignment explanation
Indices: 2779835--2779909 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2779825 GTGAAGTTAA
2779835 CGGAGTAGTCAAAGAACGCTGTATACAATAGGGAAAG
1 CGGAGTAGTCAAAGAACGCTGTATACAATAGGGAAAG
*
2779872 CGGAGTAGTCAAAGAATGCTGTATACAATAGGGAAAG
1 CGGAGTAGTCAAAGAACGCTGTATACAATAGGGAAAG
2779909 C
1 C
2779910 CTCATCGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.17
Consensus pattern (37 bp):
CGGAGTAGTCAAAGAACGCTGTATACAATAGGGAAAG
Found at i:2792217 original size:31 final size:29
Alignment explanation
Indices: 2792177--2792276 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 29
2792167 ATAAGTTTGG
*
2792177 GTACCAAATTAGGAAAAAGTGTCAAATTCAA
1 GTACTAAATTAGGAAAAA-TGTCAAATTC-A
2792208 GTACTAAATT-GGACAAAA----AAACTT-A
1 GTACTAAATTAGGA-AAAATGTCAAA-TTCA
2792233 GATACTAAATTAGGAAAAATTGTCAAATTCGA
1 G-TACTAAATTAGGAAAAA-TGTCAAATTC-A
2792265 GTACTAAATTAG
1 GTACTAAATTAG
2792277 ACCCAAAAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 22
0.71 0.01 0.28
Matches are distributed among these distances:
25 2 0.04
26 16 0.28
27 5 0.09
30 5 0.09
31 27 0.47
32 2 0.04
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (29 bp):
GTACTAAATTAGGAAAAATGTCAAATTCA
Found at i:2792309 original size:57 final size:56
Alignment explanation
Indices: 2792176--2792301 Score: 155
Period size: 57 Copynumber: 2.2 Consensus size: 56
2792166 AATAAGTTTG
* *
2792176 GGTACCAAATTAGGAAAAAGTGTCAAATTCAAGTACTAAATTGGACAAAAAAACTTA
1 GGTA-CAAATTAGGAAAAATTGTCAAATTCAAGTACTAAATTAGACAAAAAAACTTA
* * **
2792233 GATACTAAATTAGGAAAAATTGTCAAATTCGAGTACTAAATTAGACCCAAAAA-TATA
1 GGTAC-AAATTAGGAAAAATTGTCAAATTCAAGTACTAAATTAGACAAAAAAACT-TA
2792290 GGTATCAAATTA
1 GGTA-CAAATTA
2792302 AAAAAAATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 2 0.03
57 56 0.95
58 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (56 bp):
GGTACAAATTAGGAAAAATTGTCAAATTCAAGTACTAAATTAGACAAAAAAACTTA
Found at i:2804367 original size:15 final size:15
Alignment explanation
Indices: 2804347--2804400 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
2804337 ATTGAGTATG
2804347 ATTAAGTTTTGATTA
1 ATTAAGTTTTGATTA
* *
2804362 ATTAAGGTTTAATTA
1 ATTAAGTTTTGATTA
*
2804377 CTTAA-TTTTGATTA
1 ATTAAGTTTTGATTA
*
2804391 ATTAAATTTT
1 ATTAAGTTTT
2804401 AAATTAAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (15 bp):
ATTAAGTTTTGATTA
Found at i:2804859 original size:32 final size:32
Alignment explanation
Indices: 2804817--2804877 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2804807 AAAATTTTAA
2804817 TAAATGAAAAA-ATATATAAA-ATTATTAAATAT
1 TAAATGAAAAATA-ATATAAATATT-TTAAATAT
*
2804849 TAAATTAAAAATAATATAAATATTTTAAA
1 TAAATGAAAAATAATATAAATATTTTAAA
2804878 AAAATTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (32 bp):
TAAATGAAAAATAATATAAATATTTTAAATAT
Found at i:2813330 original size:8 final size:8
Alignment explanation
Indices: 2813319--2813343 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2813309 TAAAATAATA
2813319 ATAAAGCG
1 ATAAAGCG
2813327 ATAAAGCG
1 ATAAAGCG
2813335 ATAAAGCG
1 ATAAAGCG
2813343 A
1 A
2813344 AGCTAGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.24, T:0.12
Consensus pattern (8 bp):
ATAAAGCG
Found at i:2815823 original size:29 final size:31
Alignment explanation
Indices: 2815767--2815847 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
2815757 AAAATTGATC
*
2815767 AAATTAAAATTT-TATGTATAAATCTACAC-A
1 AAATTAAAATTTATATATA-AAATCTACACGA
* *
2815797 AAATTAAGATTTATATATAAAAT-TACACGTT
1 AAATTAAAATTTATATATAAAATCTACACG-A
*
2815828 AAACTAAAATTTATATATAA
1 AAATTAAAATTTATATATAA
2815848 TTTTGAGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 5 0.12
30 15 0.35
31 23 0.53
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (31 bp):
AAATTAAAATTTATATATAAAATCTACACGA
Found at i:2837917 original size:2 final size:2
Alignment explanation
Indices: 2837910--2837935 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2837900 AGCTCACTAA
2837910 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
2837936 CTGTGGTTTG
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:2839385 original size:2 final size:2
Alignment explanation
Indices: 2839378--2839403 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2839368 AGCTCACTAA
2839378 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
2839404 CTGTGGTTTG
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:2854091 original size:249 final size:249
Alignment explanation
Indices: 2853653--2854141 Score: 951
Period size: 249 Copynumber: 2.0 Consensus size: 249
2853643 GCCGCTGCAC
2853653 TGCTTACTCGGTTGGCTCTTGGACGAAAAAGCTTGGATAACATCAGTGTCATAGTTGTTGATCTA
1 TGCTTACTCGGTTGGCTCTTGGACGAAAAAGCTTGGATAACATCAGTGTCATAGTTGTTGATCTA
2853718 AAGAAAAGTTGACAACAACCAAAACCAGAGGTAAAAACCAAGATGTTTTATATGAACCTTGCATG
66 AAGAAAAGTTGACAACAACCAAAACCAGAGGTAAAAACCAAGATGTTTTATATGAACCTTGCATG
2853783 TAAAATGACTCATGCATGAATCATGATGGTAAAAAGAAAACATGCATAGATACTGCAGTTGCTGA
131 TAAAATGACTCATGCATGAATCATGATGGTAAAAAGAAAACATGCATAGATACTGCAGTTGCTGA
*
2853848 CTTAGAATTGAATTAAATTGACTCGGATTTTATGATAAGACTATTGAATTAAAT
196 CTTAGAATTGAATTAAATTGACTCGGAGTTTATGATAAGACTATTGAATTAAAT
2853902 TGCTTACTCGGTTGGCTCTTGGACGAAAAAGCTTGGATAACATCAGTGTCATAGTTGTTGATCTA
1 TGCTTACTCGGTTGGCTCTTGGACGAAAAAGCTTGGATAACATCAGTGTCATAGTTGTTGATCTA
*
2853967 AAGAAAAGTTGACAACAACCAAAACCAGAGGTAAAAATCAAGATGTTTTATATGAACCTTGCATG
66 AAGAAAAGTTGACAACAACCAAAACCAGAGGTAAAAACCAAGATGTTTTATATGAACCTTGCATG
2854032 TAAAATGACTCATGCATGAATCATGATGGTAAAAAGAAAACATGCATAGATACTGCAGTTGCTGA
131 TAAAATGACTCATGCATGAATCATGATGGTAAAAAGAAAACATGCATAGATACTGCAGTTGCTGA
*
2854097 CTTAGAATTGAATTAAATTGACTCGGAGTTTATGATAAGATTATT
196 CTTAGAATTGAATTAAATTGACTCGGAGTTTATGATAAGACTATT
2854142 AAATGGGGGA
Statistics
Matches: 237, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
249 237 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (249 bp):
TGCTTACTCGGTTGGCTCTTGGACGAAAAAGCTTGGATAACATCAGTGTCATAGTTGTTGATCTA
AAGAAAAGTTGACAACAACCAAAACCAGAGGTAAAAACCAAGATGTTTTATATGAACCTTGCATG
TAAAATGACTCATGCATGAATCATGATGGTAAAAAGAAAACATGCATAGATACTGCAGTTGCTGA
CTTAGAATTGAATTAAATTGACTCGGAGTTTATGATAAGACTATTGAATTAAAT
Found at i:2854319 original size:1 final size:1
Alignment explanation
Indices: 2854313--2854343 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
2854303 ATATTTAAGC
2854313 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2854344 TGTTGTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2855005 original size:22 final size:22
Alignment explanation
Indices: 2854977--2855022 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2854967 CCATTAATTG
2854977 CTTTTCTTATTATAAAACAATC
1 CTTTTCTTATTATAAAACAATC
2854999 CTTTTCTTATTATAAAACAATC
1 CTTTTCTTATTATAAAACAATC
2855021 CT
1 CT
2855023 ACAATAATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.46
Consensus pattern (22 bp):
CTTTTCTTATTATAAAACAATC
Found at i:2856984 original size:60 final size:60
Alignment explanation
Indices: 2856912--2857028 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
2856902 GATCAATAGG
2856912 TCAAATGTTGGGGTTCGATAGCTGCAGGGTTAAGACAAGTTATGTCAATGGTACTTTGGT
1 TCAAATGTTGGGGTTCGATAGCTGCAGGGTTAAGACAAGTTATGTCAATGGTACTTTGGT
*
2856972 TCAAATGTTGGGGTTCGATAGCTGCAGGTTTAAGACAAGTTATGTCAATGGTACTTT
1 TCAAATGTTGGGGTTCGATAGCTGCAGGGTTAAGACAAGTTATGTCAATGGTACTTT
2857029 AGTATTATTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (60 bp):
TCAAATGTTGGGGTTCGATAGCTGCAGGGTTAAGACAAGTTATGTCAATGGTACTTTGGT
Found at i:2861375 original size:3 final size:3
Alignment explanation
Indices: 2861367--2861394 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2861357 ACTTGCGAAA
2861367 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2861395 GACAAGGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2870791 original size:4 final size:4
Alignment explanation
Indices: 2870782--2870806 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2870772 ATACAGCACT
2870782 TGGA TGGA TGGA TGGA TGGA TGGA T
1 TGGA TGGA TGGA TGGA TGGA TGGA T
2870807 TCATGCATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.28
Consensus pattern (4 bp):
TGGA
Found at i:2872635 original size:20 final size:20
Alignment explanation
Indices: 2872610--2872650 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2872600 GTAAAAATTT
*
2872610 TAAATTTCAAAGATAAAAAA
1 TAAATTTCAAAAATAAAAAA
* *
2872630 TAAATTTTAAAAATATAAAA
1 TAAATTTCAAAAATAAAAAA
2872650 T
1 T
2872651 CAAAATATAT
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:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAATTTCAAAAATAAAAAA
Found at i:2873170 original size:19 final size:18
Alignment explanation
Indices: 2873121--2873171 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2873111 ATTGTTTGGA
*
2873121 TATTGTATAATTATTGTTT
1 TATTGTATAATT-TTGTTC
*
2873140 TATTG-CTAATTTTGTTAC
1 TATTGTATAATTTTGTT-C
2873158 TATTGTATAATTTT
1 TATTGTATAATTTT
2873172 TTAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.19
18 10 0.37
19 12 0.44
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (18 bp):
TATTGTATAATTTTGTTC
Found at i:2876063 original size:3 final size:3
Alignment explanation
Indices: 2876055--2876150 Score: 192
Period size: 3 Copynumber: 32.0 Consensus size: 3
2876045 GTATATAGTA
2876055 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2876103 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2876151 ATGTGAATCT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.