Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008666.1 Hibiscus syriacus cultivar Beakdansim tig00111669_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 184521
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:393 original size:15 final size:15
Alignment explanation
Indices: 373--404 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
363 AGAATTTGAG
*
373 TCGAGTTGTTCGAGT
1 TCGAGTTATTCGAGT
388 TCGAGTTATTCGAGT
1 TCGAGTTATTCGAGT
403 TC
1 TC
405 TATACAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.41
Consensus pattern (15 bp):
TCGAGTTATTCGAGT
Found at i:1444 original size:90 final size:90
Alignment explanation
Indices: 1344--1513 Score: 252
Period size: 90 Copynumber: 1.8 Consensus size: 90
1334 TTTCTTTGAT
* *
1344 TTTAATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAG-GGACCTCTCAAATCTTTATCAATTA
1 TTTAATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGAGGACCTCTCAAACCTTTATCAATGA
1408 TTCTTACTATCTTCTTTAATTTTAG
66 TTCTTACTATCTTCTTTAATTTTAG
*
1433 TTTAATAAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTTAAGGACCTCTCAAGCCTTTAT
1 TTTAAT-AAAAAATTGAAAAGTATAAATAAAGAAAGAAAG-----AGGACCTCTCAAACCTTTAT
1498 CAATGATTCTTACTAT
60 CAATGATTCTTACTAT
1514 GTTTATTTGC
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
89 6 0.08
90 33 0.46
96 32 0.45
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (90 bp):
TTTAATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGAGGACCTCTCAAACCTTTATCAATGA
TTCTTACTATCTTCTTTAATTTTAG
Found at i:1951 original size:22 final size:22
Alignment explanation
Indices: 1926--1967 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1916 AAAAAAATAT
1926 AATTATAATTTATAAT-AATACA
1 AATTAT-ATTTATAATCAATACA
*
1948 AATTATATTTTTAATCAATA
1 AATTATATTTATAATCAATA
1968 TAGATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATATTTATAATCAATACA
Found at i:4457 original size:17 final size:17
Alignment explanation
Indices: 4435--4517 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 17
4425 AGTAGTTTGG
4435 ATTATTTTTATAATTAT
1 ATTATTTTTATAATTAT
4452 ATTA-TTTTATAA--AT
1 ATTATTTTTATAATTAT
* ***
4466 ATTATTTATA-AATGGG
1 ATTATTTTTATAATTAT
*
4482 ATCA--TTTAT--TTAT
1 ATTATTTTTATAATTAT
*
4495 ATTATTTTTCTAATTAT
1 ATTATTTTTATAATTAT
4512 ATTATT
1 ATTATT
4518 CTATAAATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
13 4 0.08
14 11 0.23
15 8 0.17
16 11 0.23
17 14 0.29
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
ATTATTTTTATAATTAT
Found at i:4467 original size:14 final size:14
Alignment explanation
Indices: 4435--4478 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 14
4425 AGTAGTTTGG
4435 ATTATTTTTATAATTAT
1 ATTA-TTTTATAA--AT
4452 ATTATTTTATAAAT
1 ATTATTTTATAAAT
4466 ATTA-TTTATAAAT
1 ATTATTTTATAAAT
4479 GGGATCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
16 8 0.30
17 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTTATAAAT
Found at i:14393 original size:73 final size:73
Alignment explanation
Indices: 14299--14443 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
14289 ACTTCAAACG
* * * *
14299 ACAATCTACAAATATATTAAAATGATAAATAGGATTTGATTTTTTGGTGTAGTAAAATATTAATT
1 ACAACCTACAAATACATTAAAATGATAAATAGAATTTGATTTTTTGGTATAGTAAAATATTAATT
14364 AATAATTA
66 AATAATTA
* *
14372 ACAACCTACAAATACATTAAAATGATAAATATAATTTGATTTTTTGGTATAGTAAAATATTAGTT
1 ACAACCTACAAATACATTAAAATGATAAATAGAATTTGATTTTTTGGTATAGTAAAATATTAATT
14437 AATAATT
66 AATAATT
14444 TATTTATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (73 bp):
ACAACCTACAAATACATTAAAATGATAAATAGAATTTGATTTTTTGGTATAGTAAAATATTAATT
AATAATTA
Found at i:14552 original size:16 final size:17
Alignment explanation
Indices: 14520--14552 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14510 ATTAAATTAG
*
14520 TAATTTTTTGAATAAAA
1 TAATTTTTTGAAGAAAA
14537 TAATTTTTT-AAGAAAA
1 TAATTTTTTGAAGAAAA
14553 AATAACTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TAATTTTTTGAAGAAAA
Found at i:14668 original size:19 final size:18
Alignment explanation
Indices: 14646--14726 Score: 63
Period size: 19 Copynumber: 4.1 Consensus size: 18
14636 GCAACACAGT
*
14646 TTTTAATTTCGCAACGTGA
1 TTTTAATTT-GCAACGCGA
14665 TTTTCAAATTTGCAACGCGA
1 TTTT--AATTTGCAACGCGA
**
14685 TCTCAAATTTGCAACGCGA
1 T-TTTAATTTGCAACGCGA
*
14704 TTTTCTAAATTCGCAACGCGA
1 -TTT-T-AATTTGCAACGCGA
14725 TT
1 TT
14727 CTCCAAATTC
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 19 0.38
20 12 0.24
21 19 0.38
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTTAATTTGCAACGCGA
Found at i:14755 original size:20 final size:20
Alignment explanation
Indices: 14629--14775 Score: 163
Period size: 20 Copynumber: 7.3 Consensus size: 20
14619 AAATAACTAA
*
14629 CAAATTCGCAACAC-AGTTTT
1 CAAATTCGCAACGCGA-TTTT
* * *
14649 TAATTTCGCAACGTGATTTT
1 CAAATTCGCAACGCGATTTT
* *
14669 CAAATTTGCAACGCGA-TCT
1 CAAATTCGCAACGCGATTTT
*
14688 CAAATTTGCAACGCGATTTT
1 CAAATTCGCAACGCGATTTT
*
14708 CTAAATTCGCAACGCGATTCTC
1 C-AAATTCGCAACGCGATT-TT
*
14730 CAAATTCGTAACGCGATTTT
1 CAAATTCGCAACGCGATTTT
*
14750 CAAATTCGCAACACGATTTT
1 CAAATTCGCAACGCGATTTT
14770 CAAATT
1 CAAATT
14776 AACCCTGTAC
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.17
20 54 0.50
21 33 0.31
22 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTT
Found at i:15499 original size:22 final size:22
Alignment explanation
Indices: 15471--15521 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
15461 GATGTAGATA
15471 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
15493 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
15515 GACGGAT
1 GACGGAT
15522 GTCGCCGCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:15710 original size:21 final size:21
Alignment explanation
Indices: 15684--15750 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
15674 ATATCACGTT
*
15684 GCGAATTTGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
**
15705 GCGAATTCAAAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
*
15726 GCGAATTCGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
15747 GCGA
1 GCGA
15751 TTTACATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.16
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:16346 original size:11 final size:11
Alignment explanation
Indices: 16332--16376 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
16322 TCGTTAAGGT
16332 CTCGAGTCGAG
1 CTCGAGTCGAG
16343 CTCGAGTTCGAG
1 CTCGAG-TCGAG
*
16355 -TCGAGTC-AA
1 CTCGAGTCGAG
16364 CTCGAGTCGAG
1 CTCGAGTCGAG
16375 CT
1 CT
16377 TTTACCGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 1 0.03
10 9 0.31
11 14 0.48
12 5 0.17
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:22295 original size:17 final size:17
Alignment explanation
Indices: 22273--22357 Score: 51
Period size: 17 Copynumber: 5.5 Consensus size: 17
22263 AATTTATTTA
22273 ATATTATTTTTATAATT
1 ATATTATTTTTATAATT
*
22290 ATATTA-ATTTATAA--
1 ATATTATTTTTATAATT
* **
22304 ATATTATTTATA-AACG
1 ATATTATTTTTATAATT
* *
22320 GTATCA--TTTAT--TT
1 ATATTATTTTTATAATT
*
22333 ATATTATTTTTCTAATT
1 ATATTATTTTTATAATT
22350 ATATTATT
1 ATATTATT
22358 CTATAAATAT
Statistics
Matches: 49, Mismatches: 11, Indels: 16
0.64 0.14 0.21
Matches are distributed among these distances:
13 4 0.08
14 11 0.22
15 7 0.14
16 11 0.22
17 16 0.33
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATTATTTTTATAATT
Found at i:22300 original size:16 final size:13
Alignment explanation
Indices: 22258--22376 Score: 58
Period size: 16 Copynumber: 8.1 Consensus size: 13
22248 AGTTTGGATT
* *
22258 AATATAATTTATTT
1 AATATTATTTA-TA
22272 AATATTATTTTTATA
1 AATATTA--TTTATA
22287 ATTATATTAATTTATA
1 A--ATATT-ATTTATA
22303 AATATTATTTATA
1 AATATTATTTATA
* *
22316 AACGGTATCATTTATT
1 AA---TATTATTTATA
* *
22332 TATATTATTTTTCTA
1 AATATTA--TTTATA
22347 ATTATATTATTCTATA
1 A--ATATTATT-TATA
22363 AATATTATTTATA
1 AATATTATTTATA
22376 A
1 A
22377 TTTTTTTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
13 18 0.22
14 19 0.23
15 8 0.10
16 25 0.30
17 11 0.13
18 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.55
Consensus pattern (13 bp):
AATATTATTTATA
Found at i:22314 original size:29 final size:29
Alignment explanation
Indices: 22262--22378 Score: 96
Period size: 32 Copynumber: 3.9 Consensus size: 29
22252 TGGATTAATA
*
22262 TAATTTATTTAATATTATTTTTATAATTATAT
1 TAATTTA-TAAATATTA--TTTATAATTATAT
*
22294 TAATTTATAAATATTATTTATAAACGGTATCAT
1 TAATTTATAAATATTATTTAT-AA--TTAT-AT
* * *
22327 TTATTTAT-ATTATT-TTTCTAATTATAT
1 TAATTTATAAATATTATTTATAATTATAT
22354 T-ATTCTATAAATATTATTTATAATT
1 TAATT-TATAAATATTATTTATAATT
22379 TTTTTTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
26 3 0.04
27 6 0.09
28 8 0.11
29 13 0.19
30 4 0.06
31 12 0.17
32 15 0.21
33 9 0.13
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (29 bp):
TAATTTATAAATATTATTTATAATTATAT
Found at i:22793 original size:17 final size:16
Alignment explanation
Indices: 22762--22817 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
22752 TAGTGTGAGG
*
22762 ATATTACAAAAATAAT
1 ATATTATAAAAATAAT
22778 AT-TTATAATTAAATAAAT
1 ATATTATAA--AAAT-AAT
22796 GATATTATAAAAATAAT
1 -ATATTATAAAAATAAT
22813 ATATT
1 ATATT
22818 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 7 0.21
18 7 0.21
19 2 0.06
20 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
ATATTATAAAAATAAT
Found at i:30200 original size:22 final size:21
Alignment explanation
Indices: 30158--30197 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30148 GAGTTTATTT
*
30158 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
30179 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
30198 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:32589 original size:23 final size:23
Alignment explanation
Indices: 32571--32631 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
32561 CTCGTATAAA
32571 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
32594 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
32617 TACACCGTAGTGCCA
1 TGCACCGAAGTGCCA
32632 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:33342 original size:63 final size:65
Alignment explanation
Indices: 33275--33432 Score: 184
Period size: 63 Copynumber: 2.5 Consensus size: 65
33265 ATCCCTTGAC
33275 GGGTGCATCGATGCACTATC-TATGCATCGATACA-TAA-ATCCTATTCGATGTTTGTA-TTTAA
1 GGGTGCATCGATGCACTATCATATGCATCGATACACTAATA-CC-ATTCGATGTTTGTATTTTAA
**
33336 GG
64 AA
* * * *
33338 GGGTGCATCGATACACTA-CTTATGCATCGATACACTGATAGCATTCGATGTTTGTATTTTAAAA
1 GGGTGCATCGATGCACTATCATATGCATCGATACACTAATACCATTCGATGTTTGTATTTTAAAA
* *
33402 GAGTGCATCGATGCACT-TCATGTGCATCGAT
1 GGGTGCATCGATGCACTATCATATGCATCGAT
33433 TCACCTTGAA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 45 0.56
64 34 0.42
65 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATATGCATCGATACACTAATACCATTCGATGTTTGTATTTTAAAA
Found at i:36772 original size:125 final size:125
Alignment explanation
Indices: 36538--36792 Score: 377
Period size: 125 Copynumber: 2.0 Consensus size: 125
36528 CTAGTACCGT
* *
36538 AACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCAACACCTCAGATTGTAAGGCTCACTC
1 AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTC
* * ***
36603 TCAATACCTTCTTGGTCTAAATCTTGTCATCTTGTCATGATGTGGGTTCAGTCGTGCCCC
66 TCAATACCTCCTTCGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC
* *
36663 AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTC
1 AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTC
* * * *
36728 TTC-ATGCCTCCTTCTTCTGAATCTTGTCATCTCAACATGTTGTGGGTTCAGTCGTGCCCC
66 -TCAATACCTCCTTCGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC
36788 AACAT
1 AACAT
36793 ATCCTAACTT
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
125 114 0.98
126 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (125 bp):
AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTC
TCAATACCTCCTTCGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC
Found at i:37756 original size:40 final size:39
Alignment explanation
Indices: 37702--37777 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
37692 TATTTAGATA
*
37702 AACTTGATTTAATTTGCCCTTGTCTGG-CTAGCTGAAATC
1 AACTTGATTTAATTTGCCCTTATC-GGCCTAGCTGAAATC
* *
37741 AACTTTATTATAATTTGCCTTTATCGGCCTAGCTGAA
1 AACTTGATT-TAATTTGCCCTTATCGGCCTAGCTGAA
37778 GGGTTCATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 10 0.31
40 22 0.69
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (39 bp):
AACTTGATTTAATTTGCCCTTATCGGCCTAGCTGAAATC
Found at i:40081 original size:6 final size:6
Alignment explanation
Indices: 40068--40110 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
40058 TAAAATGCTT
*
40068 ATGC-A ATGCAA ATGCAA ATGTAA ATGCCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
40111 AGGTGTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 4 0.12
6 25 0.74
7 5 0.15
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:41354 original size:24 final size:24
Alignment explanation
Indices: 41323--41368 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41313 TCGGTTTGCA
*
41323 AAAAAACCGGATTTTTT-TCCGGAT
1 AAAAAACCAG-TTTTTTATCCGGAT
41347 AAAAAACCAGTTTTTTATCCGG
1 AAAAAACCAGTTTTTTATCCGG
41369 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (24 bp):
AAAAAACCAGTTTTTTATCCGGAT
Found at i:49277 original size:43 final size:43
Alignment explanation
Indices: 49212--49306 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
49202 AGGAGCAGCT
* * * *
49212 AGCTCACATGGCAATCAATTACCAAAAGTCTTGCGAATATCAC
1 AGCTCACATGCCAATCAATTACCAAAAGCCTTGAGAAAATCAC
* *
49255 AGCTCACATGCCATTCATTTACCAAAAGCCTTGAGAAAATCAC
1 AGCTCACATGCCAATCAATTACCAAAAGCCTTGAGAAAATCAC
49298 AGCTCACAT
1 AGCTCACAT
49307 CGATTTGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (43 bp):
AGCTCACATGCCAATCAATTACCAAAAGCCTTGAGAAAATCAC
Found at i:49528 original size:21 final size:21
Alignment explanation
Indices: 49464--49535 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
49454 AAGTTGGGAG
* *
49464 AAAATAAATTTATAAATATTTTT
1 AAAATATATTT-TAAA-ATTTTA
**
49487 AAAAT-TATGATAAGAATTTTTA
1 AAAATATATTTTAA-AA-TTTTA
49509 AAAATATATTTTAAAATTTTA
1 AAAATATATTTTAAAATTTTA
*
49530 GAAATA
1 AAAATA
49536 AATAAAACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 14 0.36
22 14 0.36
23 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
AAAATATATTTTAAAATTTTA
Found at i:49704 original size:28 final size:29
Alignment explanation
Indices: 49672--49727 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
49662 CTTATTTTAC
49672 AAAAAATATAATTATAAT-ATATAATAAT
1 AAAAAATATAATTATAATAATATAATAAT
* *
49700 AAAAAATATATTTTTAATCAATATAATA
1 AAAAAATATAATTATAAT-AATATAATA
49728 GATATATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.67
30 8 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAAATATAATTATAATAATATAATAAT
Found at i:50531 original size:15 final size:15
Alignment explanation
Indices: 50513--50544 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
50503 GAAATTTGAG
*
50513 TCGAGTTGTTCGAGT
1 TCGAGTTATTCGAGT
50528 TCGAGTTATTCGAGT
1 TCGAGTTATTCGAGT
50543 TC
1 TC
50545 TATACAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.41
Consensus pattern (15 bp):
TCGAGTTATTCGAGT
Found at i:51608 original size:91 final size:91
Alignment explanation
Indices: 51404--51665 Score: 276
Period size: 91 Copynumber: 2.8 Consensus size: 91
51394 ATCAATTATC
* * * * * * * *
51404 ATAAAAATTTGAAAAATATAAATAAGGAAAGAAACACTAAGGACTTCTCCACTCTTAATCAATTA
1 ATAAAAAATTGAAAAGTATAAATAAAGAAAG-AA-A--GAGGACCTCTCAAATCTTTATCAATTA
* * *
51469 TTATTATTATCTTTCTTTGATTTTAATTTA
62 TTCTTACTATCTTTCTTTAATTTTAATTTA
51499 ATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAG-GGACCTCTCAAATCTTTATCAATTATTCT
1 ATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGAGGACCTCTCAAATCTTTATCAATTATTCT
*
51563 TACTATC-TTCTTTAATTTTAGTTTA
66 TACTATCTTTCTTTAATTTTAATTTA
**
51588 ATAAAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTTAAGGACCTCTCAAGCCTTTATCAA
1 AT--AAAAAATTGAAAAGTATAAATAAAGAAAGAAAG-----AGGACCTCTCAAATCTTTATCAA
*
51653 TGATTCTTACTAT
59 TTATTCTTACTAT
51666 GTTTATTTGC
Statistics
Matches: 144, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
89 18 0.12
90 30 0.21
91 33 0.23
93 1 0.01
94 2 0.01
95 28 0.19
97 32 0.22
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (91 bp):
ATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGAGGACCTCTCAAATCTTTATCAATTATTCT
TACTATCTTTCTTTAATTTTAATTTA
Found at i:52088 original size:21 final size:22
Alignment explanation
Indices: 52049--52089 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52039 ACCAAGAAAG
*
52049 AAAATATAATTACTTATTTAAA
1 AAAATATAATTACTAATTTAAA
52071 AAAATATAATTA-TAATTTA
1 AAAATATAATTACTAATTTA
52090 TAATAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATAATTACTAATTTAAA
Found at i:52103 original size:22 final size:22
Alignment explanation
Indices: 52078--52119 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52068 AAAAAAATAT
52078 AATTATAATTTATAAT-AATACA
1 AATTAT-ATTTATAATCAATACA
*
52100 AATTATATTTTTAATCAATA
1 AATTATATTTATAATCAATA
52120 TAATAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATATTTATAATCAATACA
Found at i:54614 original size:17 final size:17
Alignment explanation
Indices: 54592--54674 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 17
54582 AGTAGTTTGG
54592 ATTATTTTTATAATTAT
1 ATTATTTTTATAATTAT
54609 ATTA-TTTTATAA--AT
1 ATTATTTTTATAATTAT
* ***
54623 ATTATTTATA-AATGGG
1 ATTATTTTTATAATTAT
*
54639 ATCA--TTTAT--TTAT
1 ATTATTTTTATAATTAT
*
54652 ATTATTTTTCTAATTAT
1 ATTATTTTTATAATTAT
54669 ATTATT
1 ATTATT
54675 CTATAAATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
13 4 0.08
14 11 0.23
15 8 0.17
16 11 0.23
17 14 0.29
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
ATTATTTTTATAATTAT
Found at i:54618 original size:16 final size:16
Alignment explanation
Indices: 54592--54701 Score: 65
Period size: 16 Copynumber: 7.2 Consensus size: 16
54582 AGTAGTTTGG
54592 ATTATTTTTATAATTAT
1 ATTA-TTTTATAATTAT
54609 ATTATTTTATAA--AT
1 ATTATTTTATAATTAT
***
54623 ATTA-TTTATAAATGGG
1 ATTATTTTAT-AATTAT
*
54639 ATCA-TTTAT--TTAT
1 ATTATTTTATAATTAT
*
54652 ATTATTTTTCTAATTAT
1 ATTA-TTTTATAATTAT
* *
54669 ATTATTCTATAAATAT
1 ATTATTTTATAATTAT
*
54685 -TTA-TTTATAATTTT
1 ATTATTTTATAATTAT
54699 ATT
1 ATT
54702 TTTAAAAATA
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
13 9 0.13
14 16 0.23
15 9 0.13
16 25 0.35
17 12 0.17
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTATTTTATAATTAT
Found at i:54624 original size:14 final size:14
Alignment explanation
Indices: 54592--54635 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 14
54582 AGTAGTTTGG
54592 ATTATTTTTATAATTAT
1 ATTA-TTTTATAA--AT
54609 ATTATTTTATAAAT
1 ATTATTTTATAAAT
54623 ATTA-TTTATAAAT
1 ATTATTTTATAAAT
54636 GGGATCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
16 8 0.30
17 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTTATAAAT
Found at i:64554 original size:73 final size:73
Alignment explanation
Indices: 64460--64604 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
64450 ACTTCAAACG
* * * *
64460 ACAATCTACAAATATATTAAAATGATAAATAGGATTTGATTTTTTGGTGTAGTAAAATATTAATT
1 ACAACCTACAAATACATTAAAATGATAAATAGAATTTGATTTTTTGGTATAGTAAAATATTAATT
64525 AATAATTA
66 AATAATTA
* *
64533 ACAACCTACAAATACATTAAAATGATAAATATAATTTGATTTTTTGGTATAGTAAAATATTAGTT
1 ACAACCTACAAATACATTAAAATGATAAATAGAATTTGATTTTTTGGTATAGTAAAATATTAATT
64598 AATAATT
66 AATAATT
64605 TATTTATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (73 bp):
ACAACCTACAAATACATTAAAATGATAAATAGAATTTGATTTTTTGGTATAGTAAAATATTAATT
AATAATTA
Found at i:64714 original size:16 final size:17
Alignment explanation
Indices: 64682--64714 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
64672 ATTAAATTAG
*
64682 TAATTTTTTGAATAAAA
1 TAATTTTTTGAAGAAAA
64699 TAATTTTTT-AAGAAAA
1 TAATTTTTTGAAGAAAA
64715 AATAACTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TAATTTTTTGAAGAAAA
Found at i:64830 original size:19 final size:18
Alignment explanation
Indices: 64808--64888 Score: 63
Period size: 19 Copynumber: 4.1 Consensus size: 18
64798 GCAACACAGT
*
64808 TTTTAATTTCGCAACGTGA
1 TTTTAATTT-GCAACGCGA
64827 TTTTCAAATTTGCAACGCGA
1 TTTT--AATTTGCAACGCGA
**
64847 TCTCAAATTTGCAACGCGA
1 T-TTTAATTTGCAACGCGA
*
64866 TTTTCTAAATTCGCAACGCGA
1 -TTT-T-AATTTGCAACGCGA
64887 TT
1 TT
64889 CTCCAAATTC
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 19 0.38
20 12 0.24
21 19 0.38
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTTAATTTGCAACGCGA
Found at i:64917 original size:20 final size:20
Alignment explanation
Indices: 64791--64937 Score: 163
Period size: 20 Copynumber: 7.3 Consensus size: 20
64781 AAATAACTAA
*
64791 CAAATTCGCAACAC-AGTTTT
1 CAAATTCGCAACGCGA-TTTT
* * *
64811 TAATTTCGCAACGTGATTTT
1 CAAATTCGCAACGCGATTTT
* *
64831 CAAATTTGCAACGCGA-TCT
1 CAAATTCGCAACGCGATTTT
*
64850 CAAATTTGCAACGCGATTTT
1 CAAATTCGCAACGCGATTTT
*
64870 CTAAATTCGCAACGCGATTCTC
1 C-AAATTCGCAACGCGATT-TT
*
64892 CAAATTCGTAACGCGATTTT
1 CAAATTCGCAACGCGATTTT
*
64912 CAAATTCGCAACACGATTTT
1 CAAATTCGCAACGCGATTTT
64932 CAAATT
1 CAAATT
64938 AACCCTGTAC
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.17
20 54 0.50
21 33 0.31
22 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTT
Found at i:65662 original size:22 final size:22
Alignment explanation
Indices: 65634--65683 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
65624 ATGTAGATAA
65634 ACGGATTTCGTCGGAAATGGGG
1 ACGGATTTCGTCGGAAATGGGG
*
65656 ACGGATTTCGTCGGAGATGGGG
1 ACGGATTTCGTCGGAAATGGGG
65678 ACGGAT
1 ACGGAT
65684 GTCGCCGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.14, G:0.42, T:0.22
Consensus pattern (22 bp):
ACGGATTTCGTCGGAAATGGGG
Found at i:65872 original size:21 final size:21
Alignment explanation
Indices: 65846--65912 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
65836 ATATCACGTT
*
65846 GCGAATTTGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
**
65867 GCGAATTCAAAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
*
65888 GCGAATTCGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
65909 GCGA
1 GCGA
65913 TTTACATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.16
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:66507 original size:11 final size:11
Alignment explanation
Indices: 66493--66537 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
66483 TCGTTAAGGT
66493 CTCGAGTCGAG
1 CTCGAGTCGAG
66504 CTCGAGTTCGAG
1 CTCGAG-TCGAG
*
66516 -TCGAGTC-AA
1 CTCGAGTCGAG
66525 CTCGAGTCGAG
1 CTCGAGTCGAG
66536 CT
1 CT
66538 TTTACCGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 1 0.03
10 9 0.31
11 14 0.48
12 5 0.17
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:73593 original size:29 final size:26
Alignment explanation
Indices: 73545--73669 Score: 81
Period size: 28 Copynumber: 4.4 Consensus size: 26
73535 TTAATATAAT
*
73545 TTATTTAATATTATTTTTATAATTATA
1 TTATTTAA-AATATTTTTATAATTATA
*
73572 TTAATTTACAAATATTATTTATAAACGGTATCA
1 TT-ATTTA-AAATATT-TTTAT-AA--TTAT-A
* * *
73605 TTTATTTATATTATTTTTCTAATTATA
1 -TTATTTAAAATATTTTTATAATTATA
*
73632 TTATTCTATAAATATTATTTATAATTTTA
1 TTATT-TA-AAATATT-TTTATAATTATA
73661 TT-TTTAAAA
1 TTATTTAAAA
73670 ATAAATTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
26 8 0.10
27 7 0.09
28 20 0.26
29 18 0.23
30 4 0.05
31 4 0.05
32 8 0.10
33 6 0.08
34 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (26 bp):
TTATTTAAAATATTTTTATAATTATA
Found at i:73663 original size:12 final size:13
Alignment explanation
Indices: 73537--73668 Score: 50
Period size: 16 Copynumber: 9.2 Consensus size: 13
73527 AGTTTGGATT
* *
73537 AATATAATTTATTT
1 AATATTATTTA-TA
73551 AATATTATTTTTATA
1 AATATTA--TTTATA
*
73566 ATTATATTAATTTACA
1 A--ATATT-ATTTATA
73582 AATATTATTTATA
1 AATATTATTTATA
* *
73595 AACGGTATCATTTATT
1 AA---TATTATTTATA
* *
73611 TATATTATTTTTCTA
1 AATATTA--TTTATA
73626 ATTATATTATTCTATA
1 A--ATATTATT-TATA
73642 AATATTATTTAT-
1 AATATTATTTATA
* *
73654 AATTTTATTTTTA
1 AATATTATTTATA
73667 AA
1 AA
73669 AATAAATTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 29
0.68 0.11 0.22
Matches are distributed among these distances:
12 10 0.11
13 17 0.19
14 19 0.21
15 8 0.09
16 24 0.27
17 11 0.12
18 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (13 bp):
AATATTATTTATA
Found at i:74073 original size:17 final size:16
Alignment explanation
Indices: 74042--74099 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
74032 TAGTGTGAGG
*
74042 ATATTACAAAAATAAT
1 ATATTATAAAAATAAT
74058 AT-TTATAATTAAATAAAT
1 ATATTATAA--AAAT-AAT
74076 GATATTATAAAAATAAT
1 -ATATTATAAAAATAAT
74093 ATATTAT
1 ATATTAT
74100 TTTAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 5 0.14
16 9 0.25
17 7 0.19
18 7 0.19
19 2 0.06
20 6 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATATTATAAAAATAAT
Found at i:74105 original size:35 final size:34
Alignment explanation
Indices: 74041--74109 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
74031 TTAGTGTGAG
74041 GATATTACAAAAATAATATTTATAATTAAATAAAT
1 GATATTACAAAAATAATATTTATAATTAAA-AAAT
* *
74076 GATATTATAAAAATAATATATTAT-TTTAAAAAAT
1 GATATTACAAAAATAATAT-TTATAATTAAAAAAT
74110 TACTATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 4 0.13
35 23 0.74
36 4 0.13
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (34 bp):
GATATTACAAAAATAATATTTATAATTAAAAAAT
Found at i:79299 original size:43 final size:43
Alignment explanation
Indices: 79234--79329 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
79224 AGGAGCAGCT
* * * *
79234 AGCTCACATGGCAATCAATTACCAAAAGTCTTGCGAATATCAC
1 AGCTCACATGCCAATCAATTACCAAAAGCCTTGAGAAAATCAC
* *
79277 AGCTCACATGCCATTCATTTACCAAAAGCCTTGAGAAAATCAC
1 AGCTCACATGCCAATCAATTACCAAAAGCCTTGAGAAAATCAC
79320 AGCTCACATG
1 AGCTCACATG
79330 GATTTGATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (43 bp):
AGCTCACATGCCAATCAATTACCAAAAGCCTTGAGAAAATCAC
Found at i:79550 original size:21 final size:21
Alignment explanation
Indices: 79486--79557 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
79476 AAGTTGGGAG
* *
79486 AAAATAAATTTATAAATATTTTT
1 AAAATATATTT-TAAA-ATTTTA
**
79509 AAAAT-TATGATAAGAATTTTTA
1 AAAATATATTTTAA-AA-TTTTA
79531 AAAATATATTTTAAAATTTTA
1 AAAATATATTTTAAAATTTTA
*
79552 GAAATA
1 AAAATA
79558 AATAAAACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 14 0.36
22 14 0.36
23 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
AAAATATATTTTAAAATTTTA
Found at i:79726 original size:28 final size:29
Alignment explanation
Indices: 79694--79749 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
79684 CTTATTTTAC
79694 AAAAAATATAATTATAAT-ATATAATAAT
1 AAAAAATATAATTATAATAATATAATAAT
* * *
79722 AAAAATTATATTTTTAATCAATATAATA
1 AAAAAATATAATTATAAT-AATATAATA
79750 GATATATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
30 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAAAATATAATTATAATAATATAATAAT
Found at i:85356 original size:15 final size:15
Alignment explanation
Indices: 85338--85369 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
85328 GAAATTTGAG
*
85338 TCGAGTTGTTCGAGT
1 TCGAGTTATTCGAGT
85353 TCGAGTTATTCGAGT
1 TCGAGTTATTCGAGT
85368 TC
1 TC
85370 TATACAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.41
Consensus pattern (15 bp):
TCGAGTTATTCGAGT
Found at i:86431 original size:91 final size:91
Alignment explanation
Indices: 86227--86488 Score: 276
Period size: 91 Copynumber: 2.8 Consensus size: 91
86217 ATCAATTATC
* * * * * * * *
86227 ATAAAAATTTGAAAAATATAAATAAGGAAAGAAACACTAAGGACTTCTCCACTCTTAATCAATTA
1 ATAAAAAATTGAAAAGTATAAATAAAGAAAG-AA-A--GAGGACCTCTCAAATCTTTATCAATTA
* * *
86292 TTATTATTATCTTTCTTTGATTTTAATTTA
62 TTCTTACTATCTTTCTTTAATTTTAATTTA
86322 ATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAG-GGACCTCTCAAATCTTTATCAATTATTCT
1 ATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGAGGACCTCTCAAATCTTTATCAATTATTCT
*
86386 TACTATC-TTCTTTAATTTTAGTTTA
66 TACTATCTTTCTTTAATTTTAATTTA
**
86411 ATAAAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTTAAGGACCTCTCAAGCCTTTATCAA
1 AT--AAAAAATTGAAAAGTATAAATAAAGAAAGAAAG-----AGGACCTCTCAAATCTTTATCAA
*
86476 TGATTCTTACTAT
59 TTATTCTTACTAT
86489 GTTTATTTGC
Statistics
Matches: 144, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
89 18 0.12
90 30 0.21
91 33 0.23
93 1 0.01
94 2 0.01
95 28 0.19
97 32 0.22
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (91 bp):
ATAAAAAATTGAAAAGTATAAATAAAGAAAGAAAGAGGACCTCTCAAATCTTTATCAATTATTCT
TACTATCTTTCTTTAATTTTAATTTA
Found at i:86911 original size:21 final size:22
Alignment explanation
Indices: 86872--86912 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
86862 ACCAAGAAAG
*
86872 AAAATATAATTACTTATTTAAA
1 AAAATATAATTACTAATTTAAA
86894 AAAATATAATTA-TAATTTA
1 AAAATATAATTACTAATTTA
86913 TAATAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATAATTACTAATTTAAA
Found at i:86926 original size:22 final size:22
Alignment explanation
Indices: 86901--86942 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
86891 AAAAAAATAT
86901 AATTATAATTTATAAT-AATACA
1 AATTAT-ATTTATAATCAATACA
*
86923 AATTATATTTTTAATCAATA
1 AATTATATTTATAATCAATA
86943 TAATAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATATTTATAATCAATACA
Found at i:89406 original size:16 final size:16
Alignment explanation
Indices: 89380--89476 Score: 57
Period size: 16 Copynumber: 6.4 Consensus size: 16
89370 AGTAGTTTGG
89380 ATTATTTTTATAATTAT
1 ATTA-TTTTATAATTAT
89397 ATTATTTTATAA--AT
1 ATTATTTTATAATTAT
***
89411 ATTA-TTTATAAATGGG
1 ATTATTTTAT-AATTAT
*
89427 ATCA-TTTAT--TTAT
1 ATTATTTTATAATTAT
*
89440 A-TATTTTCTAATTAT
1 ATTATTTTATAATTAT
* *
89455 ATTATTCTATAAATAT
1 ATTATTTTATAATTAT
89471 -TTATTT
1 ATTATTT
89477 AATTTTTTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
12 1 0.02
13 11 0.18
14 8 0.13
15 10 0.16
16 27 0.44
17 4 0.07
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTATTTTATAATTAT
Found at i:89412 original size:14 final size:14
Alignment explanation
Indices: 89380--89423 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 14
89370 AGTAGTTTGG
89380 ATTATTTTTATAATTAT
1 ATTA-TTTTATAA--AT
89397 ATTATTTTATAAAT
1 ATTATTTTATAAAT
89411 ATTA-TTTATAAAT
1 ATTATTTTATAAAT
89424 GGGATCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
16 8 0.30
17 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTTATAAAT
Found at i:89420 original size:13 final size:13
Alignment explanation
Indices: 89382--89423 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
89372 TAGTTTGGAT
89382 TATT-TTTATAATTA
1 TATTATTTATAA--A
89396 TATTATTTTATAAA
1 TATTA-TTTATAAA
89410 TATTATTTATAAA
1 TATTATTTATAAA
89423 T
1 T
89424 GGGATCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.35
14 10 0.38
16 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTTATAAA
Found at i:99256 original size:72 final size:72
Alignment explanation
Indices: 99165--99307 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
99155 ACTTCAAACG
* * *
99165 ACAATCTACAAATATATTAAAATGATAAATAGGATTTGATTTTTTGGTGTAGT-AAATATTAATT
1 ACAACCTACAAATACATTAAAATGATAAATA-GATTTGATTTTTTGGTATAGTAAAATATTAATT
99229 AATAATTA
65 AATAATTA
* *
99237 ACAACCTACAAATACATTAAAATGATAAATATATTTGATTTTTTGGTATAGTAAAATATTAGTTA
1 ACAACCTACAAATACATTAAAATGATAAATAGATTTGATTTTTTGGTATAGTAAAATATTAATTA
99302 ATAATT
66 ATAATT
99308 TATTTTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 19 0.29
72 46 0.71
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.40
Consensus pattern (72 bp):
ACAACCTACAAATACATTAAAATGATAAATAGATTTGATTTTTTGGTATAGTAAAATATTAATTA
ATAATTA
Found at i:99553 original size:19 final size:20
Alignment explanation
Indices: 99515--99636 Score: 131
Period size: 21 Copynumber: 6.1 Consensus size: 20
99505 AGTTTTTAAT
* *
99515 TTCGC-ACGTGATTTTCAAA
1 TTCGCAACGCGATTCTCAAA
*
99534 TTTGCAACGCGA-TCTCAAA
1 TTCGCAACGCGATTCTCAAA
* *
99553 TTTGCAACGCGATTTTCTAAA
1 TTCGCAACGCGATTCTC-AAA
99574 TTCGCAACGCGATTCTCCAAA
1 TTCGCAACGCGATTCT-CAAA
* *
99595 TTCGTAACGCGATTTTCAAA
1 TTCGCAACGCGATTCTCAAA
* *
99615 TTCGCAACACGATTTTCAAA
1 TTCGCAACGCGATTCTCAAA
99635 TT
1 TT
99637 AACCCTGTAC
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
19 22 0.25
20 32 0.36
21 34 0.38
22 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (20 bp):
TTCGCAACGCGATTCTCAAA
Found at i:99616 original size:20 final size:20
Alignment explanation
Indices: 99515--99636 Score: 149
Period size: 20 Copynumber: 6.1 Consensus size: 20
99505 AGTTTTTAAT
*
99515 TTCGC-ACGTGATTTTCAAA
1 TTCGCAACGCGATTTTCAAA
* *
99534 TTTGCAACGCGA-TCTCAAA
1 TTCGCAACGCGATTTTCAAA
*
99553 TTTGCAACGCGATTTTCTAAA
1 TTCGCAACGCGATTTTC-AAA
*
99574 TTCGCAACGCGATTCTCCAAA
1 TTCGCAACGCGATT-TTCAAA
*
99595 TTCGTAACGCGATTTTCAAA
1 TTCGCAACGCGATTTTCAAA
*
99615 TTCGCAACACGATTTTCAAA
1 TTCGCAACGCGATTTTCAAA
99635 TT
1 TT
99637 AACCCTGTAC
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
19 22 0.25
20 33 0.37
21 32 0.36
22 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (20 bp):
TTCGCAACGCGATTTTCAAA
Found at i:100427 original size:21 final size:21
Alignment explanation
Indices: 100373--100436 Score: 89
Period size: 19 Copynumber: 3.2 Consensus size: 21
100363 TGATCACGTT
*
100373 GCGAATTTGG-AAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
100393 GCGAATTC--AAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
*
100412 GCGAATTCGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
100433 GCGA
1 GCGA
100437 TTACATATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 18 0.46
20 7 0.18
21 14 0.36
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:101013 original size:11 final size:11
Alignment explanation
Indices: 100999--101043 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
100989 TCGTTAAGGT
100999 CTCGAGTCGAG
1 CTCGAGTCGAG
101010 CTCGAGTTCGAG
1 CTCGAG-TCGAG
*
101022 -TCGAGTC-AA
1 CTCGAGTCGAG
101031 CTCGAGTCGAG
1 CTCGAGTCGAG
101042 CT
1 CT
101044 TTTACCGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 1 0.03
10 9 0.31
11 14 0.48
12 5 0.17
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:107420 original size:112 final size:117
Alignment explanation
Indices: 107256--107493 Score: 414
Period size: 112 Copynumber: 2.1 Consensus size: 117
107246 TCAATTATAT
*
107256 AAATTAAATTATATCTTTTAATAATAATAGATGGATTAAATAAACTTTTGATATAATACAAGAAT
1 AAATAAAATTATATCTTTT-ATAATAATAGATGGATTAAATAAACTTTTGATATAATACAAGAAT
107321 TTGGATTGCTATTAAACTTTAACTATAGTAAGAAAACGTATATATTATTATTA
65 TTGGATTGCTATTAAACTTTAACTATAGTAAGAAAACGTATATATTATTATTA
107374 AAATAAAATTATATC-TTT-TAATAATAGA-GGA-T-AATAAACTTTTGATATAATACAAGAATT
1 AAATAAAATTATATCTTTTATAATAATAGATGGATTAAATAAACTTTTGATATAATACAAGAATT
*
107434 TGGATTGCTATTAAACTTTAACTATAGTAAGAAAACTTATATATTATTATTA
66 TGGATTGCTATTAAACTTTAACTATAGTAAGAAAACGTATATATTATTATTA
107486 AAATAAAA
1 AAATAAAA
107494 ACTATCCAAT
Statistics
Matches: 118, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
112 87 0.74
113 1 0.01
114 3 0.03
115 10 0.08
117 3 0.03
118 14 0.12
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.39
Consensus pattern (117 bp):
AAATAAAATTATATCTTTTATAATAATAGATGGATTAAATAAACTTTTGATATAATACAAGAATT
TGGATTGCTATTAAACTTTAACTATAGTAAGAAAACGTATATATTATTATTA
Found at i:108680 original size:13 final size:13
Alignment explanation
Indices: 108643--108757 Score: 60
Period size: 13 Copynumber: 8.8 Consensus size: 13
108633 TATTTAATAT
108643 TATT-TTTATAATTA
1 TATTATTTATAA--A
108657 TATTAATTTATAAA
1 TATT-ATTTATAAA
108671 TATTATTTATAAA
1 TATTATTTATAAA
* **
108684 CGTATCATTTATTTA
1 --TATTATTTATAAA
* * *
108699 TATTTTTTCTAAT
1 TATTATTTATAAA
108712 TA-TATTCTATAAA
1 TATTATT-TATAAA
108725 TATTA-TTAT-AA
1 TATTATTTATAAA
*
108736 T-TTATTTTTAAA
1 TATTATTTATAAA
* *
108748 AATAATTTAT
1 TATTATTTAT
108758 TTTTCTAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 19
0.68 0.14 0.17
Matches are distributed among these distances:
10 3 0.04
11 6 0.08
12 8 0.11
13 31 0.41
14 11 0.14
15 10 0.13
16 7 0.09
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (13 bp):
TATTATTTATAAA
Found at i:109195 original size:135 final size:135
Alignment explanation
Indices: 108953--109225 Score: 521
Period size: 135 Copynumber: 2.0 Consensus size: 135
108943 CAAATTGATG
108953 TCAGAACTCTTCGACTTTCTTTGCCCTCAATCTATATCGTTCACTGTTGGATCTTCACCGTTTTG
1 TCAGAACTCTTCGACTTTCTTTGCCCTCAATCTATATCGTTCACTGTTGGATCTTCACCGTTTTG
109018 AAATATGTCAATCTTCTCACCAATGCACATCTCCTCACAATCCGAATATGTCATCTGAGCATCGA
66 AAATATGTCAATCTTCTCACCAATGCACATCTCCTCACAATCCGAATATGTCATCTGAGCATCGA
109083 AATCA
131 AATCA
*
109088 TCAGAACTCTTCGAC-TTCTTTGCCCTCCAATCTATATCGTTCACTGTTGGATCTTCACTGTTTT
1 TCAGAACTCTTCGACTTTCTTTGCCCT-CAATCTATATCGTTCACTGTTGGATCTTCACCGTTTT
109152 GAAATATGTCAATCTTCTCACCAATGCACATCTCCTCACAATCCGAATATGTCATCTGAGCATCG
65 GAAATATGTCAATCTTCTCACCAATGCACATCTCCTCACAATCCGAATATGTCATCTGAGCATCG
109217 AAATCA
130 AAATCA
109223 TCA
1 TCA
109226 TCATGGATTA
Statistics
Matches: 136, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
134 11 0.08
135 125 0.92
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (135 bp):
TCAGAACTCTTCGACTTTCTTTGCCCTCAATCTATATCGTTCACTGTTGGATCTTCACCGTTTTG
AAATATGTCAATCTTCTCACCAATGCACATCTCCTCACAATCCGAATATGTCATCTGAGCATCGA
AATCA
Found at i:109316 original size:21 final size:19
Alignment explanation
Indices: 109287--109328 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
109277 AAATAAATGA
109287 TATTATAAAAAATAATATATT
1 TATTATAAAAAAT--TATATT
*
109308 TATTTTAAAAAATTATATT
1 TATTATAAAAAATTATATT
109327 TA
1 TA
109329 ACATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTATAAAAAATTATATT
Found at i:110632 original size:25 final size:25
Alignment explanation
Indices: 110595--110653 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
110585 AATATTAATT
* * *
110595 ATTATATTAAATAAATATTATAAAAT
1 ATTAT-TTAAATAAAAATTAAAAAAA
*
110621 ATTTTTTAAATAAAAATTAAAAAAA
1 ATTATTTAAATAAAAATTAAAAAAA
110646 ATTATTTA
1 ATTATTTA
110654 GGTGTACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATTTAAATAAAAATTAAAAAAA
Found at i:116658 original size:22 final size:21
Alignment explanation
Indices: 116616--116655 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
116606 GAGTTTATTT
*
116616 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
116637 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
116656 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:119088 original size:23 final size:23
Alignment explanation
Indices: 119070--119130 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
119060 CTCGTATAAA
119070 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
119093 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
119116 TACACCGTAGTGCCA
1 TGCACCGAAGTGCCA
119131 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:119839 original size:63 final size:65
Alignment explanation
Indices: 119772--119933 Score: 192
Period size: 63 Copynumber: 2.6 Consensus size: 65
119762 ATCCCTTGAC
*
119772 GGGTGCATCGATGCACTATC-TATGAATCGATACA-TAA-ATCCTATTCGATGTTTGTA-TTTAA
1 GGGTGCATCGATGCACTATCATATGCATCGATACACTAATA-CC-ATTCGATGTTTGTATTTTAA
**
119833 GG
64 AA
* * *
119835 GGGTGCATCGATGCACTA-CTTATGCATCGATACACTGATAGCATTCGATGTTTGTATTTTAAAA
1 GGGTGCATCGATGCACTATCATATGCATCGATACACTAATACCATTCGATGTTTGTATTTTAAAA
* *
119899 GAGTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTATCATATGCATCGATACAC
119934 CTTGAACAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 45 0.52
64 39 0.45
65 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATATGCATCGATACACTAATACCATTCGATGTTTGTATTTTAAAA
Found at i:123249 original size:125 final size:125
Alignment explanation
Indices: 123030--123284 Score: 359
Period size: 125 Copynumber: 2.0 Consensus size: 125
123020 CTAGTGCCGT
* *
123030 AACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCAACACCTCAGATTGTAAGGCTCACTC
1 AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTC
* * * ***
123095 TCAATACCTTCTTGGTCTAAATCTTGTCATCTTGTCATGATGTGGGTTCAGTCGTGCCCC
66 TCAATACCTCCTTCGTCTAAATCTCGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC
* *
123155 AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTC
1 AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTC
* * * * *
123220 TTC-ATGCCTCCTTCTTCTGAATCTCGTCATCTCAACCTGTTGTGGGTTCAGTCGTGCCCC
66 -TCAATACCTCCTTCGTCTAAATCTCGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC
123280 AACAT
1 AACAT
123285 ATCCTAACTT
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
125 112 0.98
126 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (125 bp):
AACATTATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCACTC
TCAATACCTCCTTCGTCTAAATCTCGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCC
Found at i:126573 original size:6 final size:6
Alignment explanation
Indices: 126560--126602 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
126550 TAAAATGCTT
*
126560 ATGC-A ATGCAA ATGCAA ATGTAA ATGCCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
126603 AGGTATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 4 0.12
6 25 0.74
7 5 0.15
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:138441 original size:21 final size:21
Alignment explanation
Indices: 138377--138448 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
138367 AAGTTGGGAG
* *
138377 AAAATAAATTTATAAATATTTTT
1 AAAATATATTT-TAAA-ATTTTA
**
138400 AAAAT-TATGATAAGAATTTTTA
1 AAAATATATTTTAA-AA-TTTTA
138422 AAAATATATTTTAAAATTTTA
1 AAAATATATTTTAAAATTTTA
*
138443 GAAATA
1 AAAATA
138449 AATAAAACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 14 0.36
22 14 0.36
23 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
AAAATATATTTTAAAATTTTA
Found at i:139443 original size:15 final size:15
Alignment explanation
Indices: 139425--139456 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
139415 GAAATTTGAG
*
139425 TCGAGTTGTTCGAGT
1 TCGAGTTATTCGAGT
139440 TCGAGTTATTCGAGT
1 TCGAGTTATTCGAGT
139455 TC
1 TC
139457 TATACAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.41
Consensus pattern (15 bp):
TCGAGTTATTCGAGT
Found at i:143485 original size:3 final size:3
Alignment explanation
Indices: 143477--143501 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
143467 TCCAATGTTT
143477 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
143502 CCTTTGGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:146149 original size:22 final size:22
Alignment explanation
Indices: 146124--146169 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
146114 TCAAAAATTG
146124 AAAAGTATAAATAATAATAAAA
1 AAAAGTATAAATAATAATAAAA
146146 AAAAGTATAAATAATAATAAAA
1 AAAAGTATAAATAATAATAAAA
146168 AA
1 AA
146170 GACTAACGAC
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:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAGTATAAATAATAATAAAA
Found at i:147173 original size:6 final size:7
Alignment explanation
Indices: 147156--147192 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
147146 TGCATCCATT
147156 TTTTTTC
1 TTTTTTC
147163 TTTTTTC
1 TTTTTTC
147170 TTTTTTC
1 TTTTTTC
147177 TTTTTTC
1 TTTTTTC
147184 -TTTTTC
1 TTTTTTC
147190 TTT
1 TTT
147193 GGGTGGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:148720 original size:191 final size:191
Alignment explanation
Indices: 148178--148994 Score: 934
Period size: 194 Copynumber: 4.2 Consensus size: 191
148168 CTTATCCGTA
*
148178 CTTTTTATCTTTAAGTGTTCAAACTTCATCAAAATCCTCAATTTTAGCTCCAATACACCTCAGAC
1 CTTTTTCTCTTTAAGTGTTCAAACTTCATCAAAATCCTCAATTTTAGCTCCAATACACCTCAGAC
* * * * *
148243 ACATATATTGATCTGTAAAATACAAAGTTTAATAAGGGTTTAAATTGAAGATTACATTCGTTTGG
66 AC-TATATTGACCTATAAAATACAAAG-TCAATAAGAGTTTAAATTGAAGATTACATTCTTTTGG
* * ** * *
148308 TTTATCTTAGTATTATTAAAAAGTAGAGATAAAAGTTCTAATGGAAGTAGGAATGTCA-TCCGTC
129 TTTATCCTAATCCTATTAAAAAGTAAAGATAAGAGTTCTAAT-GAAGTAGGAATGTCATTCC-TC
* * * * * * * *
148372 CTTTTTCTCTTCAAGTGTCCAAACTTCATCAAAATCTTTAATTCTATCTCTAATACACCTTAGAC
1 CTTTTTCTCTTTAAGTGTTCAAACTTCATCAAAATCCTCAATTTTAGCTCCAATACACCTCAGAC
* * * *
148437 ACGTATATTGACCTATAAAATACAAAGTCTAATTAGAGTTTAAATTGAAGATTATATTGTTTTTG
66 AC-TATATTGACCTATAAAATACAAAGTC-AATAAGAGTTTAAATTGAAGATTACATTCTTTTGG
* * * *
148502 TTTATCCTAATTCTA--AAAAA-CAAAGATAAGAGTTCTAAT-AACGGTAGAAATGCCATTCCTC
129 TTTATCCTAATCCTATTAAAAAGTAAAGATAAGAGTTCTAATGAA--GTAGGAATGTCATTCCTC
* * *
148563 CTTTTTCTCTTTAAGTGTTCAAACTTCATTAAAATCGTCAATTTTAGCTCCAATACACCTCATAC
1 CTTTTTCTCTTTAAGTGTTCAAACTTCATCAAAATCCTCAATTTTAGCTCCAATACACCTCAGAC
* * *
148628 AC-ATACTGATCTATAAAATACAAAGTCCATAAGAGTTTAAATTGAAGATTACATTCTTTTGGTT
66 ACTATATTGACCTATAAAATACAAAGTCAATAAGAGTTTAAATTGAAGATTACATTCTTTTGGTT
*
148692 TATCCTAATCCTATTAAAAAGTAAAGATAAGATTTCTAACTGAAGTAGGAATGTCATCTGTCCT-
131 TATCCTAATCCTATTAAAAAGTAAAGATAAGAGTTCTAA-TGAAGTAGGAATGTCA--T-TCCTC
* * *
148756 TTTTTTCTCTTCAAGT-TTCCAAACTTCATCAAAAAATCCTCAATTTTAGCTTCAATACACCTCA
1 CTTTTTCTCTTTAAGTGTT-CAAACTTCATC--AAAATCCTCAATTTTAGCTCCAATACACCTCA
* * * * *
148820 GACACATATATTGACCTATAAAATACAAAGTGTAACAAGGGTTTAAATTGAAAATTACATTATTT
63 GACAC-TATATTGACCTATAAAATACAAAGT-CAATAAGAGTTTAAATTGAAGATTACATTCTTT
* * *
148885 TGGGTTATCCTAATCCTATTAAAAAATAATGATAAGAGTTCTAACAT-AAGTAGGAATGTCATTC
126 TGGTTTATCCTAATCCTATTAAAAAGTAAAGATAAGAGTTCT-A-ATGAAGTAGGAATGTCATTC
*
148949 GTC
189 CTC
* * *
148952 TTTTTTATCTTTGAGTG-TCTAAACTTCATCAAAATCCTCAATT
1 CTTTTTCTCTTTAAGTGTTC-AAACTTCATCAAAATCCTCAATT
148995 CTAGTTCTAA
Statistics
Matches: 528, Mismatches: 72, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
188 44 0.08
189 25 0.05
190 5 0.01
191 111 0.21
192 11 0.02
193 28 0.05
194 137 0.26
195 38 0.07
196 25 0.05
197 22 0.04
198 79 0.15
199 2 0.00
200 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (191 bp):
CTTTTTCTCTTTAAGTGTTCAAACTTCATCAAAATCCTCAATTTTAGCTCCAATACACCTCAGAC
ACTATATTGACCTATAAAATACAAAGTCAATAAGAGTTTAAATTGAAGATTACATTCTTTTGGTT
TATCCTAATCCTATTAAAAAGTAAAGATAAGAGTTCTAATGAAGTAGGAATGTCATTCCTC
Found at i:157095 original size:24 final size:24
Alignment explanation
Indices: 157063--157126 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
157053 AGAGTCCATG
* *
157063 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
157087 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
157111 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
157127 CTATTTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:157857 original size:29 final size:29
Alignment explanation
Indices: 157825--157947 Score: 106
Period size: 29 Copynumber: 4.3 Consensus size: 29
157815 CATTTTACAC
157825 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
** *** * * *
157854 AAATATTATTTTTTTCGAA-AAATTACTA
1 AAATAGCACCATTTTCGAATTAATTCCCA
157882 AAATAGCACCCA-TTTCGAATTAATTCCCA
1 AAATAGCA-CCATTTTCGAATTAATTCCCA
****
157911 AAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
*
157940 GAATAGCA
1 AAATAGCA
157948 TCGGTCAACG
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
28 22 0.31
29 49 0.69
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATAGCACCATTTTCGAATTAATTCCCA
Found at i:157982 original size:13 final size:12
Alignment explanation
Indices: 157950--157992 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
157940 GAATAGCATC
*
157950 GGTCAACGGTCAAC
1 GGTCAACGGTC--G
157964 GGTCAACGGGTCG
1 GGTCAAC-GGTCG
157977 GGTCAACGGTCG
1 GGTCAACGGTCG
157989 GGTC
1 GGTC
157993 GGGTAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 7 0.26
15 4 0.15
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:158007 original size:18 final size:17
Alignment explanation
Indices: 157970--158020 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
157960 CAACGGTCAA
*
157970 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
157987 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
158005 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
158021 GTAAACGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:158065 original size:11 final size:10
Alignment explanation
Indices: 158035--158086 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
158025 ACGGGTCGTG
158035 ACCGGTC-AA
1 ACCGGTCAAA
158044 ACCGGTCAAA
1 ACCGGTCAAA
158054 ACCGGTTCAAA
1 ACCGG-TCAAA
*
158065 ACCGGT-TAA
1 ACCGGTCAAA
158074 ACCGGTCAAA
1 ACCGGTCAAA
158084 ACC
1 ACC
158087 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:164364 original size:24 final size:24
Alignment explanation
Indices: 164332--164395 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
164322 AGAGTCCATG
* *
164332 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
164356 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
164380 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
164396 CTATTTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:165127 original size:29 final size:29
Alignment explanation
Indices: 165095--165217 Score: 106
Period size: 29 Copynumber: 4.3 Consensus size: 29
165085 CATTTTACAC
165095 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
** *** * * *
165124 AAATATTATTTTTTTCGAA-AAATTACTA
1 AAATAGCACCATTTTCGAATTAATTCCCA
165152 AAATAGCACCCA-TTTCGAATTAATTCCCA
1 AAATAGCA-CCATTTTCGAATTAATTCCCA
****
165181 AAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCATTTTCGAATTAATTCCCA
*
165210 GAATAGCA
1 AAATAGCA
165218 TCGGTCAACG
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
28 22 0.31
29 49 0.69
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATAGCACCATTTTCGAATTAATTCCCA
Found at i:165252 original size:13 final size:12
Alignment explanation
Indices: 165220--165262 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
165210 GAATAGCATC
*
165220 GGTCAACGGTCAAC
1 GGTCAACGGTC--G
165234 GGTCAACGGGTCG
1 GGTCAAC-GGTCG
165247 GGTCAACGGTCG
1 GGTCAACGGTCG
165259 GGTC
1 GGTC
165263 GGGTAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 7 0.26
15 4 0.15
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:165277 original size:18 final size:17
Alignment explanation
Indices: 165240--165290 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
165230 CAACGGTCAA
*
165240 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
165257 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
165275 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
165291 GTAAACGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:165335 original size:11 final size:10
Alignment explanation
Indices: 165305--165356 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
165295 ACGGGTCGTG
165305 ACCGGTC-AA
1 ACCGGTCAAA
165314 ACCGGTCAAA
1 ACCGGTCAAA
165324 ACCGGTTCAAA
1 ACCGG-TCAAA
*
165335 ACCGGT-TAA
1 ACCGGTCAAA
165344 ACCGGTCAAA
1 ACCGGTCAAA
165354 ACC
1 ACC
165357 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:167216 original size:16 final size:16
Alignment explanation
Indices: 167195--167227 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
167185 TCCAATGGTC
*
167195 AAAGTTCAATGGAGTA
1 AAAGTTCAATAGAGTA
167211 AAAGTTCAATAGAGTA
1 AAAGTTCAATAGAGTA
167227 A
1 A
167228 CTGTGGCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTTCAATAGAGTA
Found at i:168874 original size:32 final size:31
Alignment explanation
Indices: 168800--168876 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
168790 CTAATGTGAC
* *
168800 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
168831 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
168863 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
168877 CGTGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:181686 original size:96 final size:93
Alignment explanation
Indices: 181504--181783 Score: 330
Period size: 92 Copynumber: 3.0 Consensus size: 93
181494 AATTATCATC
** * * * * * *
181504 AAAAATTGAAAAAAATAAATAAGGAAAGAAAGACTAAGGACTTCTCCACTCTTAATCAATTATTA
1 AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTC
*
181569 TTATTATCTTTCTTTGATTTTAATTTAATA
66 TTACTATCTTTCTTTGATTTTAATTT-A-A
181599 AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTCAAGGACCTCTCAAGTCTTTATCAATTATT
1 AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACT-AAGGACCTCTCAAGTCTTTATCAATTATT
*
181664 CTTACTATCTTTCTTT-AGTTTTAGTTTAA
65 CTTACTATCTTTCTTTGA-TTTTAATTTAA
* * * * * * *
181693 AAGAATTGAAAAGTGTAAATAAATAAA-AAAGACAAAGGTCCTCTCAAGCCTTTATCAATGATTC
1 AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTC
* * *
181757 TTACTATGTTTCTTTGCTTTTAGTTTA
66 TTACTATCTTTCTTTGATTTTAATTTA
181784 GGCTCAGATA
Statistics
Matches: 163, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
92 51 0.31
93 6 0.04
94 25 0.15
95 34 0.21
96 47 0.29
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (93 bp):
AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTC
TTACTATCTTTCTTTGATTTTAATTTAA
Found at i:182174 original size:21 final size:22
Alignment explanation
Indices: 182135--182175 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
182125 ACCAAGAAAG
*
182135 AAAATATAATTACTTATTTAAA
1 AAAATATAATTACTAATTTAAA
182157 AAAATATAATTA-TAATTTA
1 AAAATATAATTACTAATTTA
182176 TAATATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATAATTACTAATTTAAA
Found at i:184133 original size:17 final size:16
Alignment explanation
Indices: 184109--184157 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
184099 AGGATGTAAC
184109 AAAAATAATAT-TTAT
1 AAAAATAATATATTAT
184124 AATTAAATAAATGATATTAT
1 AA--AAAT-AAT-ATATTAT
184144 AAAAATAATATATT
1 AAAAATAATATATT
184158 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 7 0.24
18 7 0.24
19 2 0.07
20 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAAATAATATATTAT
Done.