Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000402.1 Hibiscus syriacus cultivar Beakdansim tig00000738_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: 1701760
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1508412 original size:20 final size:20
Alignment explanation
Indices: 1508387--1508541 Score: 139
Period size: 20 Copynumber: 7.6 Consensus size: 20
1508377 ATTGTAGACT
1508387 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
1508407 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
1508427 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
1508448 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * **
1508468 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
* * **
1508489 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAA-ATGAAAA
*
1508510 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
1508530 ATCGCAACGCGA
1 ATCGCAACGCGA
1508542 TTTTCAATTA
Statistics
Matches: 109, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
20 60 0.55
21 49 0.45
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:1508453 original size:21 final size:21
Alignment explanation
Indices: 1508384--1508563 Score: 143
Period size: 21 Copynumber: 8.8 Consensus size: 21
1508374 GACATTGTAG
* *
1508384 ACTATCGCAACGCGAA-ATGA
1 ACTATCGCAACGCGAATTTCA
** * *
1508404 AAAATCGCAACGCGAA-ATGA
1 ACTATCGCAACGCGAATTTCA
** *
1508424 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
* **
1508445 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
1508466 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
1508486 ACTATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* **
1508507 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
1508528 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
* *
1508548 ATTATCGCAATGCGAA
1 ACTATCGCAACGCGAA
1508564 ATGCAACGCG
Statistics
Matches: 128, Mismatches: 29, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
20 63 0.49
21 65 0.51
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTTCA
Found at i:1508459 original size:41 final size:41
Alignment explanation
Indices: 1508407--1508501 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
1508397 GAAATGAAAA
1508407 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
*
1508448 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
1508489 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1508502 TTTCAACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
Found at i:1508506 original size:62 final size:62
Alignment explanation
Indices: 1508384--1508563 Score: 272
Period size: 62 Copynumber: 2.9 Consensus size: 62
1508374 GACATTGTAG
* ** * * *
1508384 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGA-AATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAAATATCGCAACGCGAATTTCA
*
1508445 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAAATATCGCAACGCGAATTTCA
* *
1508507 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAATTATCGCAATGCGAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAAATATCGCAACGCGAA
1508564 ATGCAACGCG
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
61 34 0.31
62 75 0.69
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAAATATCGCAACGCGAATTTCA
Found at i:1508534 original size:41 final size:42
Alignment explanation
Indices: 1508384--1508570 Score: 157
Period size: 41 Copynumber: 4.5 Consensus size: 42
1508374 GACATTGTAG
* * *
1508384 ACTATCGCAACGCGAAATG-AAAAATCGCAACGCGAA-ATGA
1 ACTATCGCAACGCGAAATGCAACAATCGCAACGCGAATTTCA
** ** * * * **
1508424 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCAACAATCGCAACGCGAATTTCA
* ** * *
1508466 A-AATCGCAACGCGATTTTCAACTATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGCAACAATCGCAACGCGAATTTCA
* *
1508507 ACTATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCAACAATCGCAACGCGAATTTCA
* *
1508548 ATTATCGCAATGCGAAATGCAAC
1 ACTATCGCAACGCGAAATGCAAC
1508571 GCGAATTTGC
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
40 14 0.12
41 89 0.74
42 18 0.15
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (42 bp):
ACTATCGCAACGCGAAATGCAACAATCGCAACGCGAATTTCA
Found at i:1508583 original size:103 final size:102
Alignment explanation
Indices: 1508338--1508566 Score: 295
Period size: 103 Copynumber: 2.2 Consensus size: 102
1508328 CAAAATCTTT
* * * *
1508338 TTTTTAACTATCGCAA--CGAATTTGGAAAATCGTAACGAC-ATTGT-AGACTATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGA
*
1508399 AATGAAAAATCGCAACGCGAAATGAAAAATCGCAACGCGA
63 AATCAAAAATCGCAACGCGAAATGAAAAATCGCAACGCGA
*
1508439 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAATT
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAA-A
** *
1508504 TCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
65 TCAAAAATCGCAACGCGAAATGAAAAATCGCAACGCGA
* *
1508542 TTTTCAATTATCGCAATGCGAAATG
1 TTTTCAACTATCGCAACGCGAAATG
1508567 CAACGCGAAT
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
101 16 0.14
102 34 0.30
103 62 0.55
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (102 bp):
TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAAT
CAAAAATCGCAACGCGAAATGAAAAATCGCAACGCGA
Found at i:1509345 original size:33 final size:33
Alignment explanation
Indices: 1509305--1509367 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
1509295 TATTTTGATT
1509305 AAAAATAACTTTAGATATTTATTTTACTAATTA
1 AAAAATAACTTTAGATATTTATTTTACTAATTA
1509338 AAAAATAACTTTAGATATTTATTTTACTAA
1 AAAAATAACTTTAGATATTTATTTTACTAA
1509368 AAAAATTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (33 bp):
AAAAATAACTTTAGATATTTATTTTACTAATTA
Found at i:1515380 original size:25 final size:25
Alignment explanation
Indices: 1515344--1515399 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
1515334 ATATTATTAC
* **
1515344 TTATTAATTATGTAATCTTAATTTG
1 TTATTAAGTATGTAATCCCAATTTG
1515369 TTATTAAGTATGTAATCCCAATTTG
1 TTATTAAGTATGTAATCCCAATTTG
1515394 TTATTA
1 TTATTA
1515400 CTTGTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (25 bp):
TTATTAAGTATGTAATCCCAATTTG
Found at i:1515413 original size:32 final size:32
Alignment explanation
Indices: 1515372--1515444 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
1515362 TAATTTGTTA
*
1515372 TTAAGTATGTAATCCCAATTTGTTATTACTTG
1 TTAATTATGTAATCCCAATTTGTTATTACTTG
* *
1515404 TTCATTATGTAATCTCAATTTGTTATTACTTG
1 TTAATTATGTAATCCCAATTTGTTATTACTTG
1515436 TTAATTATG
1 TTAATTATG
1515445 CAACTGATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (32 bp):
TTAATTATGTAATCCCAATTTGTTATTACTTG
Found at i:1520962 original size:185 final size:183
Alignment explanation
Indices: 1520638--1520969 Score: 409
Period size: 184 Copynumber: 1.8 Consensus size: 183
1520628 TAAAGTTTTT
* * *
1520638 AATTTTATAAAATAATCCTTACATTTATTTGTATAATTGAAGAACCATAATTTAATAATTTTCAT
1 AATTTTATAAAACAATCCCTACATTTATTTGTATAACTGAAGAACCATAATTTAATAATTTTCAT
** * * * * * *
1520703 GATTTGTTAACGTAATATTAAATTCATTGTTTAAAATAATATAGTCTTTTTTCGTTCTATAAGAC
66 GATTCATTAACGCAATATTAAATTCATTGTTTAAAATAATATAATATATTTCCGTTCTACAAGAC
1520768 CTATTTTTGAGTTTTCGCTCAAGATTTATAACTAAGGATCCCTAATTTGTTTC
131 CTATTTTTGAGTTTTCGCTCAAGATTTATAACTAAGGATCCCTAATTTGTTTC
* * *
1520821 AATTTTATAAAACAGTCCCTACATTCTACTTTG-ATAACT-AAGAGCCCATAATTTAATATTTTT
1 AATTTTATAAAACAATCCCTACATT-TA-TTTGTATAACTGAAGA-ACCATAATTTAATAATTTT
* * * *
1520884 TATGGTTCATTAATGCAATATTAAATT-AGTTTTTTCAAAATAATATAATATATTTCCGTTCTAC
63 CATGATTCATTAACGCAATATTAAATTCA-TTGTTT-AAAATAATATAATATATTTCCGTTCTAC
** *
1520948 AAGGTCTTTTTTTGAGTTTTCG
126 AAGACCTATTTTTGAGTTTTCG
1520970 AACGAGGTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
183 27 0.22
184 50 0.41
185 46 0.37
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (183 bp):
AATTTTATAAAACAATCCCTACATTTATTTGTATAACTGAAGAACCATAATTTAATAATTTTCAT
GATTCATTAACGCAATATTAAATTCATTGTTTAAAATAATATAATATATTTCCGTTCTACAAGAC
CTATTTTTGAGTTTTCGCTCAAGATTTATAACTAAGGATCCCTAATTTGTTTC
Found at i:1523277 original size:16 final size:16
Alignment explanation
Indices: 1523258--1523288 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1523248 ATACAAGGGT
*
1523258 TTTTTAATATTAAATA
1 TTTTTAATATCAAATA
1523274 TTTTTAATATCAAAT
1 TTTTTAATATCAAAT
1523289 CATGAGATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTAATATCAAATA
Found at i:1523459 original size:40 final size:40
Alignment explanation
Indices: 1523381--1523460 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1523371 TTTTGGATTT
* * *
1523381 GCAACGCTAATATGTAAATCGCAACGCAAATTTGTAAATC
1 GCAACGCAAATATGTAAATCGCAACGCAAATCTATAAATC
* **
1523421 GCAACGCAAATTTGTAAATCGCAACGTGAATCTATAAATC
1 GCAACGCAAATATGTAAATCGCAACGCAAATCTATAAATC
1523461 TGTAAATCGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (40 bp):
GCAACGCAAATATGTAAATCGCAACGCAAATCTATAAATC
Found at i:1523460 original size:20 final size:20
Alignment explanation
Indices: 1523381--1523446 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
1523371 TTTTGGATTT
* *
1523381 GCAACGCTAATATGTAAATC
1 GCAACGCAAATTTGTAAATC
1523401 GCAACGCAAATTTGTAAATC
1 GCAACGCAAATTTGTAAATC
1523421 GCAACGCAAATTTGTAAATC
1 GCAACGCAAATTTGTAAATC
1523441 GCAACG
1 GCAACG
1523447 TGAATCTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
GCAACGCAAATTTGTAAATC
Found at i:1523508 original size:20 final size:20
Alignment explanation
Indices: 1523482--1523652 Score: 121
Period size: 20 Copynumber: 8.6 Consensus size: 20
1523472 GCACAGAAGT
* *
1523482 CAAATTCGTAACGGGATTTC
1 CAAATTCGCAACGCGATTTC
* *
1523502 TAAATTCGCAATGCGATTTC
1 CAAATTCGCAACGCGATTTC
* * *
1523522 CAAATTCACAATGCAATTTC
1 CAAATTCGCAACGCGATTTC
* * *
1523542 CAAATTCACAACGTGATTTA
1 CAAATTCGCAACGCGATTTC
*** *
1523562 CAAATTCGCGTTGCGATTTA
1 CAAATTCGCAACGCGATTTC
*
1523582 CAAATTCGCAACACTGAATTT-
1 CAAATTCGCAACGC-G-ATTTC
*
1523603 CAAATTCGCAACTCGATTTC
1 CAAATTCGCAACGCGATTTC
** **
1523623 TGAATTCGCAACATGATTT-
1 CAAATTCGCAACGCGATTTC
*
1523642 CGAATTCGCAA
1 CAAATTCGCAA
1523653 AACGAATTTT
Statistics
Matches: 122, Mismatches: 26, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
19 14 0.11
20 90 0.74
21 14 0.11
22 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:1523620 original size:41 final size:39
Alignment explanation
Indices: 1523481--1523674 Score: 126
Period size: 40 Copynumber: 4.9 Consensus size: 39
1523471 TGCACAGAAG
* ** ***
1523481 TCAAATTCGTAACGGGATTTCTAAATTCGCAATGCGATT
1 TCAAATTCGCAACTCGATTTCTAAATTCGCAACATGATT
* * * * *
1523520 TCCAAATTCACAA-TGCAATTTCCAAATTCACAACGTGATT
1 T-CAAATTCGCAACT-CGATTTCTAAATTCGCAACATGATT
**
1523560 TACAAATTCGC-GTTGCGATTTAC-AAATTCGCAACACTGAATT
1 T-CAAATTCGCAACT-CGATTT-CTAAATTCGCAACA-TG-ATT
*
1523602 TCAAATTCGCAACTCGATTTCTGAATTCGCAACATGATT
1 TCAAATTCGCAACTCGATTTCTAAATTCGCAACATGATT
* ** *
1523641 TCGAATTCGCAAAACGAATTT-TAATTTCGCAACA
1 TCAAATTCGCAACTCG-ATTTCTAAATTCGCAACA
1523675 GGTTTTATTT
Statistics
Matches: 123, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
39 28 0.23
40 61 0.50
41 29 0.24
42 5 0.04
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (39 bp):
TCAAATTCGCAACTCGATTTCTAAATTCGCAACATGATT
Found at i:1523661 original size:20 final size:19
Alignment explanation
Indices: 1523584--1523657 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
1523574 GCGATTTACA
*
1523584 AATTCGCAACACTGAATTTCA
1 AATTCGCAACAC-G-ATTTCG
*
1523605 AATTCGCAACTCGATTTCTG
1 AATTCGCAACACGATTTC-G
*
1523625 AATTCGCAACATGATTTCG
1 AATTCGCAACACGATTTCG
*
1523644 AATTCGCAAAACGA
1 AATTCGCAACACGA
1523658 ATTTTAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 18 0.39
20 17 0.37
21 11 0.24
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (19 bp):
AATTCGCAACACGATTTCG
Found at i:1523670 original size:39 final size:41
Alignment explanation
Indices: 1523584--1523674 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 41
1523574 GCGATTTACA
**
1523584 AATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCGCAACACTGAATTTCAAATTCGCAAAACGATTTCTG
*
1523625 AATTCGCAACA-TG-ATTTCGAATTCGCAAAACGAATTT-T-
1 AATTCGCAACACTGAATTTCAAATTCGCAAAACG-ATTTCTG
1523663 AATTTCGCAACA
1 AA-TTCGCAACA
1523675 GGTTTTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 2 0.04
39 26 0.58
40 6 0.13
41 11 0.24
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (41 bp):
AATTCGCAACACTGAATTTCAAATTCGCAAAACGATTTCTG
Found at i:1526967 original size:18 final size:18
Alignment explanation
Indices: 1526944--1526979 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1526934 AAGTAAAAGG
1526944 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1526962 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1526980 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:1527437 original size:25 final size:25
Alignment explanation
Indices: 1527399--1527448 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1527389 AAATCAATTA
*
1527399 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1527424 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1527449 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:1529271 original size:29 final size:29
Alignment explanation
Indices: 1529214--1529271 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1529204 ATCAGATTTT
****
1529214 TTGTTGCGAAAGTCAAATTCGCGTTGCGA
1 TTGTTGCGAAAGTCAAATTCGAAACGCGA
1529243 TTGTTGCGAAAGTCAAATTCGAAACGCGA
1 TTGTTGCGAAAGTCAAATTCGAAACGCGA
1529272 AATCGTAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (29 bp):
TTGTTGCGAAAGTCAAATTCGAAACGCGA
Found at i:1529480 original size:64 final size:64
Alignment explanation
Indices: 1529378--1529528 Score: 223
Period size: 64 Copynumber: 2.4 Consensus size: 64
1529368 AATTTAAAAC
* * *
1529378 AACAAATCACCTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATTAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAAGAATTATTTACACATCAATTA
*** * *
1529442 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAAGAATTATTTACACATCAATTA
1529506 AACAAATCAAC-TTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
1529529 CTTTTACAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
63 12 0.15
64 67 0.85
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAAGAATTATTTACACATCAATTA
Found at i:1529523 original size:13 final size:14
Alignment explanation
Indices: 1529507--1529539 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1529497 CATCAATTAA
1529507 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
1529520 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1529534 ACAAAT
1 ACAAAT
1529540 ACATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1530973 original size:42 final size:42
Alignment explanation
Indices: 1530909--1531009 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
1530899 TGGGAGAGAA
* * *
1530909 CTCTTGAACGATGACAGAGGCCTCTTGAATGGTAGGAGGGGC
1 CTCTTGAACGATGACAGAGGCCTCTTGAACGATAGGAGAGGC
* * *
1530951 CTCTTGAAGGATGATAGGGGCCTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGACAGAGGCCTCTTGAACGATAGGAGAGGC
*
1530993 CTATTGAACGATGACAG
1 CTCTTGAACGATGACAG
1531010 GTGTTTTGGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATGACAGAGGCCTCTTGAACGATAGGAGAGGC
Found at i:1531001 original size:21 final size:21
Alignment explanation
Indices: 1530909--1531004 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
1530899 TGGGAGAGAA
*
1530909 CTCTTGAACGAT-GACAGAGGC
1 CTCTTGAACGATAG-GAGAGGC
* * *
1530930 CTCTTGAATGGTAGGAGGGGC
1 CTCTTGAACGATAGGAGAGGC
* * *
1530951 CTCTTGAAGGAT-GATAGGGGC
1 CTCTTGAACGATAG-GAGAGGC
1530972 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATAGGAGAGGC
*
1530993 CTATTGAACGAT
1 CTCTTGAACGAT
1531005 GACAGGTGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.02
21 58 0.95
22 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATAGGAGAGGC
Found at i:1531438 original size:21 final size:21
Alignment explanation
Indices: 1531414--1531463 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1531404 ACCATTGTCT
* *
1531414 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
1531435 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
1531456 TCACGTAA
1 TCACGTAA
1531464 CTCTCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1533730 original size:20 final size:20
Alignment explanation
Indices: 1533707--1533796 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
1533697 TGACTTCTGT
* *
1533707 GTTGCGAATTACAAATTTGC
1 GTTGCGAATTACAGATTCGC
* *
1533727 GTTG-TAATTTACAGACTCGC
1 GTTGCGAA-TTACAGATTCGC
*
1533747 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
* *
1533767 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAGATTCGC
1533787 GTTGCGAATT
1 GTTGCGAATT
1533797 TGGAAACTGA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 56 0.95
21 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCGC
Found at i:1533753 original size:40 final size:40
Alignment explanation
Indices: 1533707--1533796 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
1533697 TGACTTCTGT
* *
1533707 GTTGCGAATTACAAATTTGCGTTGTAATTTACAGACTCGC
1 GTTGCGAATTACAAATTCGCGTTGCAATTTACAGACTCGC
* * * * *
1533747 GTTGCGATTTACAGATTCGCGTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGCGTTGCAATTTACAGACTCGC
1533787 GTTGCGAATT
1 GTTGCGAATT
1533797 TGGAAACTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (40 bp):
GTTGCGAATTACAAATTCGCGTTGCAATTTACAGACTCGC
Found at i:1535599 original size:42 final size:42
Alignment explanation
Indices: 1535535--1535635 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
1535525 TGGGAGAGAA
* * *
1535535 CTCTTGAACGATGACAGAGGCCTCTTGAATGGTAGGAGGGGC
1 CTCTTGAACGATGACAGAGGCCTCTTGAACGATAGGAGAGGC
* * *
1535577 CTCTTGAAGGATGATAGGGGCCTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGACAGAGGCCTCTTGAACGATAGGAGAGGC
*
1535619 CTATTGAACGATGACAG
1 CTCTTGAACGATGACAG
1535636 GTGTTTTGGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATGACAGAGGCCTCTTGAACGATAGGAGAGGC
Found at i:1535627 original size:21 final size:21
Alignment explanation
Indices: 1535535--1535630 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
1535525 TGGGAGAGAA
*
1535535 CTCTTGAACGAT-GACAGAGGC
1 CTCTTGAACGATAG-GAGAGGC
* * *
1535556 CTCTTGAATGGTAGGAGGGGC
1 CTCTTGAACGATAGGAGAGGC
* * *
1535577 CTCTTGAAGGAT-GATAGGGGC
1 CTCTTGAACGATAG-GAGAGGC
1535598 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATAGGAGAGGC
*
1535619 CTATTGAACGAT
1 CTCTTGAACGAT
1535631 GACAGGTGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.02
21 58 0.95
22 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATAGGAGAGGC
Found at i:1536064 original size:21 final size:21
Alignment explanation
Indices: 1536040--1536089 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1536030 ACCATTGTCT
* *
1536040 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
1536061 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
1536082 TCACGTAA
1 TCACGTAA
1536090 CTCTCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1538359 original size:20 final size:20
Alignment explanation
Indices: 1538336--1538425 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
1538326 TGACTTCTGT
* *
1538336 GTTGCGAATTACAAATTTGC
1 GTTGCGAATTACAGATTCGC
* *
1538356 GTTG-TAATTTACAGACTCGC
1 GTTGCGAA-TTACAGATTCGC
*
1538376 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
* *
1538396 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAGATTCGC
1538416 GTTGCGAATT
1 GTTGCGAATT
1538426 TGGAAACTGA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 56 0.95
21 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCGC
Found at i:1538382 original size:40 final size:40
Alignment explanation
Indices: 1538336--1538425 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
1538326 TGACTTCTGT
* *
1538336 GTTGCGAATTACAAATTTGCGTTGTAATTTACAGACTCGC
1 GTTGCGAATTACAAATTCGCGTTGCAATTTACAGACTCGC
* * * * *
1538376 GTTGCGATTTACAGATTCGCGTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGCGTTGCAATTTACAGACTCGC
1538416 GTTGCGAATT
1 GTTGCGAATT
1538426 TGGAAACTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (40 bp):
GTTGCGAATTACAAATTCGCGTTGCAATTTACAGACTCGC
Found at i:1540602 original size:15 final size:16
Alignment explanation
Indices: 1540572--1540604 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1540562 TATGTTTTTT
*
1540572 ATTATTATTCTAATTA
1 ATTATTAATCTAATTA
1540588 ATTATTAAT-TAATTA
1 ATTATTAATCTAATTA
1540603 AT
1 AT
1540605 GTTGGTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATTAATCTAATTA
Found at i:1540773 original size:2 final size:2
Alignment explanation
Indices: 1540768--1540803 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1540758 TATTTTTTAT
1540768 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1540804 ACAGAATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1546343 original size:60 final size:61
Alignment explanation
Indices: 1546265--1546419 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 61
1546255 GTCCTCAAAT
* * * *
1546265 TATGACACTCATTTTAAATTAGTCCTTAAACTTTTTAATATTCTA-ATTTCA-CCCTTAAAC
1 TATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATT-TACATTTCATCCCTTAAAC
* *
1546325 TATGACTCTCATTCTAAATTAGTCCTTAGACTCTTGAACATTTACATTTCATCCCTTAAAC
1 TATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTACATTTCATCCCTTAAAC
* *
1546386 TATGAATCTCATTCTAAATT-GTTCCCTAAACTTT
1 TATGACTCTCATTCTAAATTAG-TCCTTAAACTTT
1546420 CAGAACTTCC
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.02
60 43 0.52
61 37 0.45
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (61 bp):
TATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTACATTTCATCCCTTAAAC
Found at i:1551259 original size:16 final size:17
Alignment explanation
Indices: 1551232--1551264 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1551222 TTAAAATAAA
*
1551232 TTTTTGATGTTTGAAAT
1 TTTTTGATGTTTAAAAT
1551249 TTTTTGA-GTTTAAAAT
1 TTTTTGATGTTTAAAAT
1551265 ATGTGTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (17 bp):
TTTTTGATGTTTAAAAT
Found at i:1552070 original size:15 final size:14
Alignment explanation
Indices: 1552034--1552119 Score: 52
Period size: 15 Copynumber: 6.0 Consensus size: 14
1552024 CGTGTTTAAG
*
1552034 ATATAATCATTAAAA
1 ATATAAT-ACTAAAA
1552049 ATAATAAGTACTAAAA
1 AT-ATAA-TACTAAAA
*
1552065 ATATAATATTATAAA
1 ATATAATACTA-AAA
**
1552080 ATATAA-AAGAAATA
1 ATATAATACTAAA-A
**
1552094 ATA-AATACTAACG
1 ATATAATACTAAAA
1552107 AT-TAATACTAAAA
1 ATATAATACTAAAA
1552120 TTGATGTCAC
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
13 14 0.25
14 13 0.24
15 15 0.27
16 12 0.22
17 1 0.02
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (14 bp):
ATATAATACTAAAA
Found at i:1552606 original size:15 final size:15
Alignment explanation
Indices: 1552561--1552607 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1552551 CTAAAAAGCA
1552561 ATATAAA-AATAAAT
1 ATATAAATAATAAAT
* * *
1552575 AAATAAATATTACAT
1 ATATAAATAATAAAT
*
1552590 ATATAATTAATAAAT
1 ATATAAATAATAAAT
1552605 ATA
1 ATA
1552608 GGTATTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATAAATAATAAAT
Found at i:1552643 original size:24 final size:25
Alignment explanation
Indices: 1552572--1552643 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 25
1552562 TATAAAAATA
1552572 AATAAATA-A-ATATTACATATATAATT
1 AATAAATATAGATATT--ATAT-TAATT
* *
1552598 AATAAATATAGGTATTAAATTAATT
1 AATAAATATAGATATTATATTAATT
1552623 AA-AAATAATAGAT-TTATATTA
1 AATAAAT-ATAGATATTATATTA
1552644 TAAATAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 11 0.28
25 12 0.31
26 11 0.28
27 1 0.03
28 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (25 bp):
AATAAATATAGATATTATATTAATT
Found at i:1561923 original size:16 final size:16
Alignment explanation
Indices: 1561902--1561939 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1561892 ACTCGAAACT
1561902 TTGCTTTGATATCAAG
1 TTGCTTTGATATCAAG
1561918 TTGCTTTGATATCAAG
1 TTGCTTTGATATCAAG
1561934 TTGCTT
1 TTGCTT
1561940 ATCACTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (16 bp):
TTGCTTTGATATCAAG
Found at i:1562414 original size:21 final size:21
Alignment explanation
Indices: 1562390--1562460 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
1562380 GAAAATCGCA
1562390 TTGCGATAGTCTAAGTTGTCG
1 TTGCGATAGTCTAAGTTGTCG
* *
1562411 TTGCGATAGTTTCCAA-AT-TCG
1 TTGCGATAG--TCTAAGTTGTCG
*
1562432 TTGCGACAGTCTACAGTTGTCG
1 TTGCGATAGTCTA-AGTTGTCG
1562454 TTGCGAT
1 TTGCGAT
1562461 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.08
20 1 0.03
21 21 0.54
22 10 0.26
23 4 0.10
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (21 bp):
TTGCGATAGTCTAAGTTGTCG
Found at i:1562475 original size:41 final size:41
Alignment explanation
Indices: 1562390--1562478 Score: 144
Period size: 41 Copynumber: 2.1 Consensus size: 41
1562380 GAAAATCGCA
*
1562390 TTGCGATAGTCTAAGTTGTCGTTGCGATAGTTTCCAAATTCG
1 TTGCGACAGTCTAAGTTGTCGTTGCGATA-TTTCCAAATTCG
1562432 TTGCGACAGTCTACAGTTGTCGTTGCGAT-TTTCCAAATTCG
1 TTGCGACAGTCTA-AGTTGTCGTTGCGATATTTCCAAATTCG
1562473 TTGCGA
1 TTGCGA
1562479 TAGTAAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 18 0.40
42 12 0.27
43 15 0.33
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
TTGCGACAGTCTAAGTTGTCGTTGCGATATTTCCAAATTCG
Found at i:1563600 original size:22 final size:22
Alignment explanation
Indices: 1563572--1563687 Score: 114
Period size: 22 Copynumber: 5.5 Consensus size: 22
1563562 GAATTTGGAA
1563572 AATCGCAACGACAACTGTAGAC
1 AATCGCAACGACAACTGTAGAC
** *
1563594 AATCGCAACGA-ATTTGTAAAC
1 AATCGCAACGACAACTGTAGAC
* *
1563615 TATCGCAACAACAACTGTAGAC
1 AATCGCAACGACAACTGTAGAC
* * * *
1563637 TATCGCAACG--AA-TTTGGAA
1 AATCGCAACGACAACTGTAGAC
1563656 AATCGCAACGACAACTGTAGAC
1 AATCGCAACGACAACTGTAGAC
*
1563678 TATCGCAACG
1 AATCGCAACG
1563688 CGAAATGCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
19 13 0.18
20 2 0.03
21 18 0.25
22 40 0.55
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (22 bp):
AATCGCAACGACAACTGTAGAC
Found at i:1563630 original size:43 final size:41
Alignment explanation
Indices: 1563555--1563687 Score: 221
Period size: 41 Copynumber: 3.2 Consensus size: 41
1563545 CAACAAATTT
*
1563555 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACAA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* *
1563596 TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
1 TCGCAACGAATTTGGAAA--ATCGCAACGACAACTGTAGACTA
1563639 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1563680 TCGCAACG
1 TCGCAACG
1563688 CGAAATGCAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
41 47 0.55
43 38 0.45
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:1566448 original size:15 final size:15
Alignment explanation
Indices: 1566411--1566450 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1566401 ATTTTACCCT
*
1566411 AAAATAAAATATTGA
1 AAAATAAAATATTAA
* *
1566426 AGATTAAAATATTAA
1 AAAATAAAATATTAA
1566441 AAAATAAAAT
1 AAAATAAAAT
1566451 GATAATTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAATAAAATATTAA
Found at i:1576348 original size:19 final size:21
Alignment explanation
Indices: 1576324--1576389 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 21
1576314 GGAGTGAAGT
1576324 ATGAAGTG-TT-GAGCTGAAA
1 ATGAAGTGTTTCGAGCTGAAA
1576343 ATGAAGTGATTTTCGAGCTGAAA
1 ATGAAGTG--TTTCGAGCTGAAA
1576366 ATGAAGTGATTTTCGAGCTGAAA
1 ATGAAGTG--TTTCGAGCTGAAA
1576389 A
1 A
1576390 ATATGATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.19
22 2 0.05
23 33 0.77
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (21 bp):
ATGAAGTGTTTCGAGCTGAAA
Found at i:1576362 original size:23 final size:23
Alignment explanation
Indices: 1576334--1576389 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
1576324 ATGAAGTGTT
1576334 GAGCTGAAAATGAAGTGATTTTC
1 GAGCTGAAAATGAAGTGATTTTC
1576357 GAGCTGAAAATGAAGTGATTTTC
1 GAGCTGAAAATGAAGTGATTTTC
1576380 GAGCTGAAAA
1 GAGCTGAAAA
1576390 ATATGATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (23 bp):
GAGCTGAAAATGAAGTGATTTTC
Found at i:1577872 original size:23 final size:23
Alignment explanation
Indices: 1577846--1577913 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1577836 ATTATTATAT
1577846 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1577869 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
1577892 GACACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1577914 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1580934 original size:21 final size:20
Alignment explanation
Indices: 1580906--1580949 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1580896 TGAGCTTAAC
1580906 TTTCAAATCA-AGATTTTCTT
1 TTTCAAATCATAGATTTT-TT
*
1580926 TTTCTAAATCATTGATTTTTT
1 TTTC-AAATCATAGATTTTTT
1580947 TTT
1 TTT
1580950 GAAAGCTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTCAAATCATAGATTTTTT
Found at i:1582958 original size:20 final size:20
Alignment explanation
Indices: 1582930--1583000 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1582920 TTTACTTTGG
*
1582930 ATATTGATACTATAAGAACA
1 ATATCGATACTATAAGAACA
* * *
1582950 ATATCGATACTGTTCATG-A-G
1 ATATCGATACT-AT-AAGAACA
* *
1582970 GTATCGATACTGTAAGAACA
1 ATATCGATACTATAAGAACA
1582990 ATATCGATACT
1 ATATCGATACT
1583001 TCTTCCCTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 30 0.79
21 2 0.05
22 2 0.05
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (20 bp):
ATATCGATACTATAAGAACA
Found at i:1604089 original size:38 final size:38
Alignment explanation
Indices: 1604044--1604116 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
1604034 CCGTACTCCT
*
1604044 TGAAAGAATGCCTATCGGTGTTTGCTGTACTCGGCTAG
1 TGAAAGAATGCCTATCGGTGTTGGCTGTACTCGGCTAG
* *
1604082 TGAAAGAATGCCTGTTGGTGTTGGCTGTACTCGGC
1 TGAAAGAATGCCTATCGGTGTTGGCTGTACTCGGC
1604117 GAGTTCAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.32
Consensus pattern (38 bp):
TGAAAGAATGCCTATCGGTGTTGGCTGTACTCGGCTAG
Found at i:1607084 original size:17 final size:18
Alignment explanation
Indices: 1607057--1607090 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1607047 TTTAGCTCAA
1607057 TTGATGTTCAAACTCGAG
1 TTGATGTTCAAACTCGAG
*
1607075 TTGA-GTTCAAGCTCGA
1 TTGATGTTCAAACTCGA
1607091 ATTCGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (18 bp):
TTGATGTTCAAACTCGAG
Found at i:1611426 original size:18 final size:18
Alignment explanation
Indices: 1611402--1611443 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1611392 TACCGTTAAT
1611402 CTCATCTGTTTATTTTCA
1 CTCATCTGTTTATTTTCA
*
1611420 TTCATCTGTTTATTTTCA
1 CTCATCTGTTTATTTTCA
1611438 CTCATC
1 CTCATC
1611444 CAACAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.24, G:0.05, T:0.55
Consensus pattern (18 bp):
CTCATCTGTTTATTTTCA
Found at i:1617670 original size:13 final size:13
Alignment explanation
Indices: 1617652--1617679 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1617642 GTGAGTTGGT
1617652 AGTAAAATGAACA
1 AGTAAAATGAACA
1617665 AGTAAAATGAACA
1 AGTAAAATGAACA
1617678 AG
1 AG
1617680 ATCAATCTTC
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:0.61, C:0.07, G:0.18, T:0.14
Consensus pattern (13 bp):
AGTAAAATGAACA
Found at i:1624973 original size:3 final size:3
Alignment explanation
Indices: 1624965--1625007 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1624955 AAACAAAAAC
1624965 ATT ATT ATT ATT ATT ATT A-T ATT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1625008 CTCCCGTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1627027 original size:35 final size:31
Alignment explanation
Indices: 1626988--1627058 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 31
1626978 TTCAAATTAT
1626988 ATAATATAAAAAATAAAATTATAACTAAATTTAAA
1 ATAATATAAAAAATAAAA-TA-AA-T-AATTTAAA
* * *
1627023 ATAAT-TTAAGATTAAAATAAATAATTTAAA
1 ATAATATAAAAAATAAAATAAATAATTTAAA
1627053 ATAATA
1 ATAATA
1627059 ATTTAAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
30 13 0.41
31 1 0.03
32 2 0.06
33 2 0.06
34 9 0.28
35 5 0.16
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (31 bp):
ATAATATAAAAAATAAAATAAATAATTTAAA
Found at i:1627060 original size:13 final size:13
Alignment explanation
Indices: 1627015--1627065 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
1627005 ATTATAACTA
1627015 AATTTAAAATAATTT
1 AATTTAAAATAA--T
*
1627030 AAGATTAAAATAAAT
1 AA-TTTAAAAT-AAT
1627045 AATTTAAAATAAT
1 AATTTAAAATAAT
1627058 AATTTAAA
1 AATTTAAA
1627066 TGTTAAAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 11 0.34
14 7 0.22
15 5 0.16
16 7 0.22
17 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
AATTTAAAATAAT
Found at i:1630941 original size:2 final size:2
Alignment explanation
Indices: 1630934--1630975 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1630924 GTGGTGCTGC
1630934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1630976 CTATCCTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1634912 original size:23 final size:23
Alignment explanation
Indices: 1634863--1634938 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
1634853 TACCCAGCAG
* * * * *
1634863 CAATAATAACTGCATTATGGTAG
1 CAATAATAGCAGCATTATTGCAA
* * *
1634886 CAATAATGGCTGCATTTTTGCAA
1 CAATAATAGCAGCATTATTGCAA
**
1634909 CAATAATAGCAGCATTATTGCGG
1 CAATAATAGCAGCATTATTGCAA
1634932 CAATAAT
1 CAATAAT
1634939 TGAACCCAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (23 bp):
CAATAATAGCAGCATTATTGCAA
Found at i:1641167 original size:16 final size:15
Alignment explanation
Indices: 1641142--1641171 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1641132 AGAGAGATAA
1641142 AGGAATGGATTTGAG
1 AGGAATGGATTTGAG
1641157 AGGACATGGATTTGA
1 AGGA-ATGGATTTGA
1641172 TAATGAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.03, G:0.37, T:0.27
Consensus pattern (15 bp):
AGGAATGGATTTGAG
Found at i:1641456 original size:31 final size:31
Alignment explanation
Indices: 1641421--1641486 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1641411 TAATACATAA
* *
1641421 TCACTTTCGTTTTTATTTAATTAAGATGTGG
1 TCACTTTCGTTTTTATTTAATTAACACGTGG
*
1641452 TCACTTTTGTTTTTATTTAATTAACACGTGG
1 TCACTTTCGTTTTTATTTAATTAACACGTGG
1641483 TCAC
1 TCAC
1641487 CCCGAGTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (31 bp):
TCACTTTCGTTTTTATTTAATTAACACGTGG
Found at i:1642062 original size:6 final size:6
Alignment explanation
Indices: 1642051--1642359 Score: 618
Period size: 6 Copynumber: 51.5 Consensus size: 6
1642041 AAAGATATAC
1642051 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1642099 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1642147 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1642195 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1642243 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1642291 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1642339 ATGTAT ATGTAT ATGTAT ATG
1 ATGTAT ATGTAT ATGTAT ATG
1642360 GTTGGAATAG
Statistics
Matches: 303, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 303 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:1647751 original size:20 final size:20
Alignment explanation
Indices: 1647726--1647780 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 20
1647716 CAACCTGATA
1647726 ATTTAAAAAAAATTATATAT
1 ATTTAAAAAAAATTATATAT
1647746 ATTTAAAAAAATAAAATTATATAT
1 ATTT---AAAA-AAAATTATATAT
1647770 -TTTAAAAAAAA
1 ATTTAAAAAAAA
1647781 AATACATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 4 0.13
20 8 0.26
23 7 0.23
24 12 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTAAAAAAAATTATATAT
Found at i:1647763 original size:24 final size:22
Alignment explanation
Indices: 1647730--1647782 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 22
1647720 CTGATAATTT
1647730 AAAAAAAATTATATATATTTAAA
1 AAAAAAAATTATATAT-TTTAAA
1647753 AAAATAAAATTATATATTTTAAA
1 AAAA-AAAATTATATATTTTAAA
1647776 AAAAAAA
1 AAAAAAA
1647783 TACATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.10
23 14 0.48
24 12 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAAAAATTATATATTTTAAA
Found at i:1647793 original size:22 final size:22
Alignment explanation
Indices: 1647730--1647794 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
1647720 CTGATAATTT
* *
1647730 AAAAAAAATTATATATATTTAA
1 AAAAAAAAATATATATATTTTA
1647752 AAAAATAAAAT-TATATATTTTA
1 AAAAA-AAAATATATATATTTTA
* *
1647774 AAAAAAAAATACATAAATTTT
1 AAAAAAAAATATATATATTTT
1647795 GAAATAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.14
22 28 0.76
23 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAAAAAATATATATATTTTA
Found at i:1653869 original size:11 final size:11
Alignment explanation
Indices: 1653853--1653883 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1653843 CAAAAAGCTC
1653853 AAACATATCCA
1 AAACATATCCA
1653864 AAACATATCCA
1 AAACATATCCA
*
1653875 AAGCATATC
1 AAACATATC
1653884 ACTTAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.26, G:0.03, T:0.19
Consensus pattern (11 bp):
AAACATATCCA
Found at i:1655218 original size:69 final size:69
Alignment explanation
Indices: 1655102--1655292 Score: 231
Period size: 69 Copynumber: 2.8 Consensus size: 69
1655092 ACACTCTGTA
* * * * * * *
1655102 ATATCTAAAATTGACAACTTTATCATGTCGAGAGAAGATGGTGGATAGTTAGACGAAAGAA-CTT
1 ATATCTAAAATTGATAACTTCATCATGTCAAGAGAAGATGATAGATAGTTAAACCAAA-AAGCTT
1655166 TCTTT
65 TCTTT
*
1655171 ATGTCTAAAATTGATAACTTCATCATGTCAAGAGAAGATGATAGATAGTTAAACCAAAAAGCTTT
1 ATATCTAAAATTGATAACTTCATCATGTCAAGAGAAGATGATAGATAGTTAAACCAAAAAGCTTT
*
1655236 TTTT
66 CTTT
* * * * * *
1655240 GTATCTAAAATTGATAACTTCATCATGCCAAAAGAAGACGGTGGATAGTTAAA
1 ATATCTAAAATTGATAACTTCATCATGTCAAGAGAAGATGATAGATAGTTAAA
1655293 TCGAAAAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
68 2 0.02
69 103 0.98
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (69 bp):
ATATCTAAAATTGATAACTTCATCATGTCAAGAGAAGATGATAGATAGTTAAACCAAAAAGCTTT
CTTT
Found at i:1666921 original size:24 final size:24
Alignment explanation
Indices: 1666889--1666941 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1666879 ACCAACCAAA
1666889 CATGAGAATGTGGAATTCTCATCT
1 CATGAGAATGTGGAATTCTCATCT
1666913 CATGAGAATGTGGAATTCTCATCT
1 CATGAGAATGTGGAATTCTCATCT
1666937 CATGA
1 CATGA
1666942 TAATCTCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (24 bp):
CATGAGAATGTGGAATTCTCATCT
Found at i:1668073 original size:35 final size:35
Alignment explanation
Indices: 1668026--1668102 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
1668016 AAAACAGTCA
* *
1668026 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
1668061 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1668096 TCAATTT
1 TCAATTT
1668103 AAGGTAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1668182 original size:18 final size:18
Alignment explanation
Indices: 1668156--1668194 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1668146 ACGAATAAAA
1668156 ATATATATATATAAATGT
1 ATATATATATATAAATGT
* * *
1668174 ATATTTATATTTAGATGT
1 ATATATATATATAAATGT
1668192 ATA
1 ATA
1668195 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
ATATATATATATAAATGT
Found at i:1668256 original size:16 final size:18
Alignment explanation
Indices: 1668224--1668257 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1668214 TATTAATGTA
1668224 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1668242 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1668258 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1675718 original size:32 final size:33
Alignment explanation
Indices: 1675682--1675744 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
1675672 TGTCCTCTCT
1675682 TCAAGTACTTGATCTTAGG-ACAATTCCATTGG
1 TCAAGTACTTGATCTTAGGAACAATTCCATTGG
*
1675714 TCAAGTACTTGATCTTGGGAACAATTCCATT
1 TCAAGTACTTGATCTTAGGAACAATTCCATT
1675745 TATGGATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (33 bp):
TCAAGTACTTGATCTTAGGAACAATTCCATTGG
Found at i:1685395 original size:35 final size:35
Alignment explanation
Indices: 1685349--1685460 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
1685339 AAAACAACCA
* * *
1685349 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* *
1685384 TCAATTTCATTCTAAACTCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
** * *
1685419 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1685454 TCAATTT
1 TCAATTT
1685461 AAGGTTTAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1687238 original size:69 final size:67
Alignment explanation
Indices: 1687146--1687285 Score: 208
Period size: 69 Copynumber: 2.1 Consensus size: 67
1687136 GTCTTGTGTT
* *
1687146 ATATTTTTAAATGATATTTTTAAAATATTTTATAATTAAATAAATTTATAAAATATCAAAACTTA
1 ATATTTTTAAATGATATTCTTAAAATATTTTATAATAAAATAAATTTATAAAATATCAAAACTTA
1687211 TC
66 TC
* * * *
1687213 ATATTATTTAAAATGGTATTCTTAAAATATTTTATAATAAAATAAATTTGTAAAATATCAATATT
1 ATATT-TTT-AAATGATATTCTTAAAATATTTTATAATAAAATAAATTTATAAAATATCAAAACT
1687278 TATC
64 TATC
1687282 ATAT
1 ATAT
1687286 ATGATTGCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 5 0.08
68 3 0.05
69 57 0.88
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (67 bp):
ATATTTTTAAATGATATTCTTAAAATATTTTATAATAAAATAAATTTATAAAATATCAAAACTTA
TC
Found at i:1690775 original size:1 final size:1
Alignment explanation
Indices: 1690771--1690803 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
1690761 AAAGGTTAGT
*
1690771 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1690804 TAAATGGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1690810 original size:124 final size:130
Alignment explanation
Indices: 1690675--1690913 Score: 373
Period size: 124 Copynumber: 1.9 Consensus size: 130
1690665 TTGATATAAT
*
1690675 AAAAAGAAATGGAAAATATAAACAAAAGTTAAAACAAAGGAAATATAAAATAATTAAAT-A-AA-
1 AAAAAGAAATGGAAAATATAAACAAAAGTTAAAACAAAGGAAATAGAAAATAATTAAATAATAAT
1690737 T-AAT-AAGAATAAGAAT-AATAATAAAAAGGTTAGTAAAAAACAAAAAAAAAAAAAAAAAAAAA
66 TAAATAAAGAATAAGAATAAATAATAAAAAGGTTAGTAAAAAACAAAAAAAAAAAAAAAAAAAAA
* *
1690799 AAAAATAAATGGGAAATATAAACAAAAGTTAAAACAAAGGAAATAGAAAATAATTAAATAATAAT
1 AAAAAGAAATGGAAAATATAAACAAAAGTTAAAACAAAGGAAATAGAAAATAATTAAATAATAAT
*
1690864 TAAATAAAATAATAAGAATAAGAATAATAAAAAGGTTAGTAAAAAACAAA
66 TAAAT-AAAGAATAAGAAT-A-AATAATAAAAAGGTTAGTAAAAAACAAA
1690914 TAATAAATAA
Statistics
Matches: 102, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
124 56 0.55
125 1 0.01
126 2 0.02
127 1 0.01
128 3 0.03
130 11 0.11
133 28 0.27
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.18
Consensus pattern (130 bp):
AAAAAGAAATGGAAAATATAAACAAAAGTTAAAACAAAGGAAATAGAAAATAATTAAATAATAAT
TAAATAAAGAATAAGAATAAATAATAAAAAGGTTAGTAAAAAACAAAAAAAAAAAAAAAAAAAAA
Found at i:1690992 original size:133 final size:134
Alignment explanation
Indices: 1690719--1691002 Score: 307
Period size: 133 Copynumber: 2.1 Consensus size: 134
1690709 CAAAGGAAAT
1690719 ATAA-AATAATTAAAT-AAATAATAAGAATAAGAATAATAATAAAAAGGTTAGTAAAAAACAAAA
1 ATAATAATAATTAAATAAAATAATAAGAATAAG-A-AATAATAAAAAGGTTAGTAAAAAAC-AAA
* ** * *
1690782 AAAAAAAAAAAAAAAAAAAAAATAAATGGGAAATATAAACAAAAGTTAAAACAAAGGAAATAGAA
63 AAAAAAAAAAAAAAAAAAAAAATAAATGGGAAATAGAAACAAAAGAAAAAACAAAGAAAACAGAA
*
1690847 AATAATT
128 AATAATA
*
1690854 A-AATAATAATTAAATAAAATAATAAGAATAAG-AATAATAAAAAGGTTAGTAAAAAAC-AAATA
1 ATAATAATAATTAAATAAAATAATAAGAATAAGAAATAATAAAAAGGTTAGTAAAAAACAAAAAA
* * * ** * * *
1690916 ATAAATAATAAAAAATTAA-AAA-GGGTAATAGAATACAATAA-AAAAAACAAATTAAAACAGTG
66 AAAAAAAAAAAAAAAAAAATAAATGGGAAATAGAA-ACAA-AAGAAAAAACAAA-GAAAACAG-A
1690978 AAATAATA
127 AAATAATA
1690986 ATAATAATAA-TAAATAA
1 ATAATAATAATTAAATAA
1691003 CATAGAAGAA
Statistics
Matches: 127, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
129 9 0.07
130 15 0.12
131 25 0.20
132 15 0.12
133 33 0.26
134 2 0.02
135 12 0.09
136 16 0.13
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.20
Consensus pattern (134 bp):
ATAATAATAATTAAATAAAATAATAAGAATAAGAAATAATAAAAAGGTTAGTAAAAAACAAAAAA
AAAAAAAAAAAAAAAAAAATAAATGGGAAATAGAAACAAAAGAAAAAACAAAGAAAACAGAAAAT
AATA
Found at i:1692034 original size:6 final size:6
Alignment explanation
Indices: 1692025--1692087 Score: 60
Period size: 6 Copynumber: 10.3 Consensus size: 6
1692015 AAAAGAAATG
*
1692025 AATAAA AAT--A AATAAA AATAAC AATAAA TGAATAATAA AATAAA AAT-AA
1 AATAAA AATAAA AATAAA AATAAA AATAAA --AAT-A-AA AATAAA AATAAA
1692074 AATAAA AATAAA AA
1 AATAAA AATAAA AA
1692088 AAAGAACATT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 29 0.60
7 1 0.02
8 6 0.12
9 1 0.02
10 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:1692072 original size:11 final size:11
Alignment explanation
Indices: 1692029--1692090 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
1692019 GAAATGAATA
*
1692029 AAAATAAATA-
1 AAAATAAAAAT
*
1692039 AAAATAACAAT
1 AAAATAAAAAT
*
1692050 -AAATGAATAAT
1 AAAAT-AAAAAT
1692061 AAAATAAAAAT
1 AAAATAAAAAT
1692072 AAAATAAAAAT
1 AAAATAAAAAT
1692083 AAAA-AAAA
1 AAAATAAAA
1692091 GAACATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.36
11 25 0.56
12 4 0.09
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:1692076 original size:33 final size:30
Alignment explanation
Indices: 1692008--1692085 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
1691998 ACCCTGAAAC
* * *
1692008 AAAAAGAAAAAGAAATGAATAAAAATAAAT
1 AAAAATAAAAATAAATGAATAAAAATAAAA
*
1692038 AAAAATAACAATAAATGAATAATAAAATAAAA
1 AAAAATAAAAATAAATGAAT-A-AAAATAAAA
1692070 ATAAAATAAAAATAAA
1 A-AAAATAAAAATAAA
1692086 AAAAAGAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 17 0.43
31 1 0.03
32 9 0.22
33 13 0.32
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (30 bp):
AAAAATAAAAATAAATGAATAAAAATAAAA
Found at i:1692189 original size:36 final size:35
Alignment explanation
Indices: 1692097--1692190 Score: 127
Period size: 35 Copynumber: 2.6 Consensus size: 35
1692087 AAAAGAACAT
1692097 TTTTAAATATTATACTATATATATGTTTAAAAAAATA
1 TTTTAAA-ATTATA-TATATATATGTTTAAAAAAATA
* * *
1692134 TTTTAAAATCATATA-ATATATGTTTTCAAATAATA
1 TTTTAAAATTATATATATATATG-TTTAAAAAAATA
1692169 TTTTAAAATTATATATATATAT
1 TTTTAAAATTATATATATATAT
1692191 ATATATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
34 7 0.14
35 26 0.51
36 11 0.22
37 7 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (35 bp):
TTTTAAAATTATATATATATATGTTTAAAAAAATA
Found at i:1692225 original size:36 final size:35
Alignment explanation
Indices: 1692185--1692336 Score: 113
Period size: 36 Copynumber: 4.3 Consensus size: 35
1692175 AATTATATAT
1692185 ATATATATATATATATTCTAAAAATGTTTCAAAATC
1 ATATATATATATATATTCTAAAAATGTTTCAAAA-C
* *
1692221 ATATATATA-GT-T-TTC--AAAATGTTTTAAAAC
1 ATATATATATATATATTCTAAAAATGTTTCAAAAC
* * *
1692251 -TATATATTATATATATTTTTCAAAATATTTTTAAAAACC
1 ATATATA-TATATATA-TTCT-AAAA-ATGTTTCAAAA-C
* *
1692290 ATATAT-TATATATATTTTAAAAATATTTTCAAAA-
1 ATATATATATATATATTCTAAAAAT-GTTTCAAAAC
1692324 ACTATATATATAT
1 A-TATATATATAT
1692337 TTCCAAAAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
29 6 0.06
30 3 0.03
31 14 0.15
32 1 0.01
33 3 0.03
34 4 0.04
35 8 0.08
36 26 0.27
37 7 0.07
38 17 0.18
39 1 0.01
40 5 0.05
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (35 bp):
ATATATATATATATATTCTAAAAATGTTTCAAAAC
Found at i:1692225 original size:38 final size:35
Alignment explanation
Indices: 1692184--1692336 Score: 129
Period size: 38 Copynumber: 4.3 Consensus size: 35
1692174 AAATTATATA
1692184 TATATATATATATATATTCTAAAAATGTTTCAAAA-
1 TATATATATATATAT-TTCTAAAAATGTTTCAAAAC
* *
1692219 TCATATATATA-GT-TTTC--AAAATGTTTTAAAAC
1 T-ATATATATATATATTTCTAAAAATGTTTCAAAAC
* * *
1692251 TATATATTATATATATTTTTCAAAATATTTTTAAAAAC
1 TATATA-TATATATATTTCT-AAAA-ATGTTTCAAAAC
* *
1692289 CATATATTATATATATTT-TAAAAATATTTTCAAAAAC
1 TATATA-TATATATATTTCTAAAAAT-GTTTC-AAAAC
1692326 TATATATATAT
1 TATATATATAT
1692337 TTCCAAAAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
31 18 0.18
32 5 0.05
33 4 0.04
34 4 0.04
35 4 0.04
36 22 0.22
37 14 0.14
38 27 0.28
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (35 bp):
TATATATATATATATTTCTAAAAATGTTTCAAAAC
Found at i:1692243 original size:31 final size:29
Alignment explanation
Indices: 1692191--1692257 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 29
1692181 ATATATATAT
1692191 ATATATATATTCTAAAAATGTTTCAAAATC
1 ATATATATATTCTAAAAATGTTTCAAAA-C
* * *
1692221 ATATATATAGTTTTCAAAATGTTTTAAAAC
1 ATATATATA-TTCTAAAAATGTTTCAAAAC
1692251 -TATATAT
1 ATATATAT
1692258 TATATATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 7 0.21
30 10 0.30
31 16 0.48
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (29 bp):
ATATATATATTCTAAAAATGTTTCAAAAC
Found at i:1692336 original size:21 final size:21
Alignment explanation
Indices: 1692312--1692357 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1692302 TATTTTAAAA
*
1692312 ATATTTTCAAAAACTATAT-AT
1 ATATTTCCAAAAA-TATATAAT
1692333 ATATTTCCAAAAATATATAAT
1 ATATTTCCAAAAATATATAAT
1692354 ATAT
1 ATAT
1692358 ATGTTTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATTTCCAAAAATATATAAT
Found at i:1692337 original size:58 final size:57
Alignment explanation
Indices: 1692283--1692393 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 57
1692273 AAATATTTTT
*
1692283 AAAAACCATATATTATATATATTTTAAAAATATTTTCAAAAACTATATA-TATATTTCC
1 AAAAA-CATATAATATATATATTTTAAAAATATTTT-AAAAACTATATATTATATTTCC
* * * * **
1692341 AAAAATATATAATATATATGTTTTCAAAATGTTTTTTAAACTATATATTATAT
1 AAAAACATATAATATATATATTTTAAAAATATTTTAAAAACTATATATTATAT
1692394 ATATTTTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
56 10 0.22
57 30 0.67
58 5 0.11
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (57 bp):
AAAAACATATAATATATATATTTTAAAAATATTTTAAAAACTATATATTATATTTCC
Found at i:1692344 original size:20 final size:21
Alignment explanation
Indices: 1692311--1692357 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1692301 ATATTTTAAA
*
1692311 AATAT-TTTCAAAAACTATAT
1 AATATATTTCAAAAAATATAT
*
1692331 -ATATATTTCCAAAAATATAT
1 AATATATTTCAAAAAATATAT
1692351 AATATAT
1 AATATAT
1692358 ATGTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATTTCAAAAAATATAT
Found at i:1692429 original size:21 final size:21
Alignment explanation
Indices: 1692404--1692447 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1692394 ATATTTTCAA
1692404 AATATTTTCAAAAATATTATT
1 AATATTTTCAAAAATATTATT
* *
1692425 AATATTTTTAAAAATATTCTT
1 AATATTTTCAAAAATATTATT
1692446 AA
1 AA
1692448 AAACTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATTTTCAAAAATATTATT
Found at i:1692430 original size:32 final size:33
Alignment explanation
Indices: 1692385--1692464 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 33
1692375 TTTAAACTAT
*
1692385 ATATTATATATA-TTTTCAAAATATT-TTCAAAA
1 ATATTATATATATTTTTAAAAATATTCTT-AAAA
1692417 ATATTAT-TAATATTTTTAAAAATATTCTTAAAA
1 ATATTATAT-ATATTTTTAAAAATATTCTTAAAA
1692450 ACTATATATATATAT
1 A-TAT-TATATATAT
1692465 ATATATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
31 1 0.02
32 10 0.24
33 17 0.41
34 5 0.12
35 7 0.17
36 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATTATATATATTTTTAAAAATATTCTTAAAA
Found at i:1692438 original size:93 final size:93
Alignment explanation
Indices: 1692242--1692441 Score: 271
Period size: 93 Copynumber: 2.1 Consensus size: 93
1692232 TTTCAAAATG
*
1692242 TTTTAAAACTATATATTATATATATTTTTCAAAATATTTTTAAAAACCATATATTATATATATTT
1 TTTTAAAA--ATATATAATATATATTTTTCAAAATATTTTTAAAAACCATATATTATATATATTT
1692307 TAAAAATATTTTCAAAAACTATATATATAT
64 TAAAAATATTTTCAAAAACTATATATATAT
** * * *
1692337 TTCCAAAAATATATAATATATATGTTTTCAAAATGTTTTT-TAAACTATATATTATATATATTTT
1 TTTTAAAAATATATAATATATAT-TTTTCAAAATATTTTTAAAAACCATATATTATATATATTTT
*
1692401 CAAAATATTTTCAAAAA-TAT-TATTAATAT
65 AAAAATATTTTCAAAAACTATATA-T-ATAT
1692430 TTTTAAAAATAT
1 TTTTAAAAATAT
1692442 TCTTAAAAAC
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
91 2 0.02
92 4 0.04
93 66 0.71
94 15 0.16
95 6 0.06
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (93 bp):
TTTTAAAAATATATAATATATATTTTTCAAAATATTTTTAAAAACCATATATTATATATATTTTA
AAAATATTTTCAAAAACTATATATATAT
Found at i:1692459 original size:2 final size:2
Alignment explanation
Indices: 1692452--1692480 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1692442 TCTTAAAAAC
1692452 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1692481 TTAAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1692789 original size:21 final size:22
Alignment explanation
Indices: 1692765--1692820 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1692755 CTATACGGTA
1692765 TGAA-AATAATGAACAATACCG
1 TGAACAATAATGAACAATACCG
* * *
1692786 TGAATAGTAAT-AACAGTACCG
1 TGAACAATAATGAACAATACCG
*
1692807 TGAACAATACTGAA
1 TGAACAATAATGAA
1692821 TGTTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.21
Consensus pattern (22 bp):
TGAACAATAATGAACAATACCG
Found at i:1694049 original size:16 final size:15
Alignment explanation
Indices: 1694021--1694050 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1694011 ATGTGCATTA
1694021 TTCATGTTTCATGTG
1 TTCATGTTTCATGTG
1694036 TTCATGTATTCATGT
1 TTCATGT-TTCATGT
1694051 CATTTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (15 bp):
TTCATGTTTCATGTG
Found at i:1699289 original size:14 final size:14
Alignment explanation
Indices: 1699266--1699299 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1699256 ATCCTAACCT
*
1699266 CATAACCTCTAAAA
1 CATAAACTCTAAAA
*
1699280 CATAAACTCTAAAT
1 CATAAACTCTAAAA
1699294 CATAAA
1 CATAAA
1699300 TCTTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (14 bp):
CATAAACTCTAAAA
Found at i:1700803 original size:24 final size:26
Alignment explanation
Indices: 1700773--1700824 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
1700763 CGACTCAAAT
1700773 ATAATTT-A-AAT-TTATTTATTTGAA
1 ATAATTTCATAATATTATTTATTT-AA
1700797 ATAATTTCATAATATTATTTATTTAA
1 ATAATTTCATAATATTATTTATTTAA
1700823 AT
1 AT
1700825 TGAATTTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.28
25 1 0.04
26 7 0.28
27 10 0.40
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
ATAATTTCATAATATTATTTATTTAA
Found at i:1701018 original size:34 final size:34
Alignment explanation
Indices: 1700975--1701042 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1700965 AAAATTGAAA
1700975 AAAAATAAGAATGTAAGAATGAACGTTAAATATT
1 AAAAATAAGAATGTAAGAATGAACGTTAAATATT
1701009 AAAAATAAGAATGTAAGAATGAACGTTAAATATT
1 AAAAATAAGAATGTAAGAATGAACGTTAAATATT
1701043 TTCAAAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (34 bp):
AAAAATAAGAATGTAAGAATGAACGTTAAATATT
Done.