Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009572.1 Hibiscus syriacus cultivar Beakdansim tig00116937_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: 2529503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1126128 original size:23 final size:25
Alignment explanation
Indices: 1126102--1126155 Score: 87
Period size: 23 Copynumber: 2.3 Consensus size: 25
1126092 AAATCCAGCA
1126102 AAGAAAATT-AAAGCACTC-AAAAG
1 AAGAAAATTGAAAGCACTCAAAAAG
1126125 AAG-AAATTGAAAGCACTCAAAAAG
1 AAGAAAATTGAAAGCACTCAAAAAG
1126149 AAGAAAA
1 AAGAAAA
1126156 AGAAAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.18
23 12 0.43
24 8 0.29
25 3 0.11
ACGTcount: A:0.63, C:0.11, G:0.15, T:0.11
Consensus pattern (25 bp):
AAGAAAATTGAAAGCACTCAAAAAG
Found at i:1126152 original size:24 final size:22
Alignment explanation
Indices: 1126106--1126154 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 22
1126096 CCAGCAAAGA
1126106 AAATTAAAGCACTCAAAAGAAG
1 AAATTAAAGCACTCAAAAGAAG
1126128 AAATTGAAAGCACTCAAAAAGAAG
1 AAATT-AAAGCACTC-AAAAGAAG
1126152 AAA
1 AAA
1126155 AAGAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.20
23 9 0.36
24 11 0.44
ACGTcount: A:0.61, C:0.12, G:0.14, T:0.12
Consensus pattern (22 bp):
AAATTAAAGCACTCAAAAGAAG
Found at i:1131063 original size:14 final size:14
Alignment explanation
Indices: 1131041--1131081 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1131031 CAGAATCCAC
*
1131041 CTTTCCTCTCTCTA
1 CTTTTCTCTCTCTA
1131055 CTTTTCTCTCTCTA
1 CTTTTCTCTCTCTA
*
1131069 CTTCTCTCTCTCT
1 CTTTTCTCTCTCT
1131082 CTCTCTCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (14 bp):
CTTTTCTCTCTCTA
Found at i:1131499 original size:17 final size:17
Alignment explanation
Indices: 1131477--1131510 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1131467 GGAACATGAC
1131477 TCGCTATGACAATTCCT
1 TCGCTATGACAATTCCT
1131494 TCGCTATGACAATTCCT
1 TCGCTATGACAATTCCT
1131511 CTTGGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (17 bp):
TCGCTATGACAATTCCT
Found at i:1134779 original size:24 final size:24
Alignment explanation
Indices: 1134752--1134858 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1134742 AAACGGAGTT
*
1134752 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1134776 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
1134800 GTTAGGACTCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
1134824 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1134848 ATCAGAAATCA
1 ATCAGAAATCA
1134859 GATAAAATAT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1136007 original size:18 final size:18
Alignment explanation
Indices: 1135986--1136021 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1135976 CTTCCATCCG
*
1135986 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1136004 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1136022 GTCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1137344 original size:7 final size:7
Alignment explanation
Indices: 1137332--1137364 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
1137322 TGGTCAACGT
1137332 CGGTCAA
1 CGGTCAA
1137339 CGGTCAA
1 CGGTCAA
1137346 CGGGTCAA
1 C-GGTCAA
1137354 CGGTCAA
1 CGGTCAA
1137361 CGGT
1 CGGT
1137365 TCGGGTCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:1137353 original size:15 final size:15
Alignment explanation
Indices: 1137323--1137363 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 15
1137313 GGTCAACAGT
1137323 GGTCAACGTCGGTCAAC
1 GGTCAACG--GGTCAAC
1137340 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
1137355 GGTCAACGG
1 GGTCAACGG
1137364 TTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 16 0.67
17 8 0.33
ACGTcount: A:0.24, C:0.27, G:0.34, T:0.15
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:1137378 original size:18 final size:18
Alignment explanation
Indices: 1137355--1137390 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1137345 ACGGGTCAAC
1137355 GGTCAAC-GGTTCGGGTCG
1 GGTCAACGGGTT-GGGTCG
1137373 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTTGGGTCG
1137391 AGTTGTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.11, C:0.19, G:0.47, T:0.22
Consensus pattern (18 bp):
GGTCAACGGGTTGGGTCG
Found at i:1140710 original size:23 final size:21
Alignment explanation
Indices: 1140671--1140713 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1140661 CATAATTATT
1140671 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
1140692 TAAAAATATTTAATCAAAAATA
1 TAAAAA-ATTAAAT-AAAAATA
1140714 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:1140921 original size:14 final size:14
Alignment explanation
Indices: 1140904--1140931 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1140894 ATCATAACAA
1140904 AATTATATAACTAT
1 AATTATATAACTAT
1140918 AATTATATAACTAT
1 AATTATATAACTAT
1140932 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:1155104 original size:164 final size:163
Alignment explanation
Indices: 1154779--1155105 Score: 629
Period size: 164 Copynumber: 2.0 Consensus size: 163
1154769 AATTAATAAT
1154779 TTATAAGTAGTTTATGGAACTTTTTGATTCTTGCTTCATTCCATCCAGACTAATCAAGCTTATGT
1 TTATAAGTAGTTTATGGAACTTTTTGATTCTTGCTTCATTCCATCCAGACTAATCAAGCTTATGT
1154844 AAAGAGCATCAGATACCTGCTTCATCTGAAACACGCTTCCCTCTACAGACATACAACCGTGTTTC
66 AAAGAGCATCAGATACCTGCTTCATCTGAAACACGCTTCCCTCTACAGACATACAACCGTGTTTC
1154909 AAACTCTTCTTCTTCTGGCTTTTTAAATCCAGA
131 AAACTCTTCTTCTTCTGGCTTTTTAAATCCAGA
1154942 TTATAAGTAGTTTATGGAAC-TTTTGATTCTTGCTTCATTCCATCCAGACTAATCAAGCTTATGT
1 TTATAAGTAGTTTATGGAACTTTTTGATTCTTGCTTCATTCCATCCAGACTAATCAAGCTTATGT
1155006 AAAGAGCATCAGATACCTGCTTCAATCTGACAACACGCTTCCCTCTACAGACATACAACCGTGTT
66 AAAGAGCATCAGATACCTGCTTC-ATCTGA-AACACGCTTCCCTCTACAGACATACAACCGTGTT
1155071 TCAAACTCTTCTTCTTCTGGCTTTTTAAATCCAGA
129 TCAAACTCTTCTTCTTCTGGCTTTTTAAATCCAGA
1155106 AGCAATACCA
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
162 67 0.41
163 26 0.16
164 69 0.43
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (163 bp):
TTATAAGTAGTTTATGGAACTTTTTGATTCTTGCTTCATTCCATCCAGACTAATCAAGCTTATGT
AAAGAGCATCAGATACCTGCTTCATCTGAAACACGCTTCCCTCTACAGACATACAACCGTGTTTC
AAACTCTTCTTCTTCTGGCTTTTTAAATCCAGA
Found at i:1158452 original size:40 final size:42
Alignment explanation
Indices: 1158397--1158479 Score: 134
Period size: 40 Copynumber: 2.0 Consensus size: 42
1158387 TTTTTTCGGT
1158397 CAACGTTACAAACATTACTA-TTTTATGTCTC-TTCGTAACG
1 CAACGTTACAAACATTACTATTTTTATGTCTCGTTCGTAACG
*
1158437 CAACGTTACAAACATTACTATTTTTTGTGTCTCGTTCGTAACG
1 CAACGTTACAAACATTACTA-TTTTTATGTCTCGTTCGTAACG
1158480 ACTATTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 20 0.51
42 10 0.26
43 9 0.23
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (42 bp):
CAACGTTACAAACATTACTATTTTTATGTCTCGTTCGTAACG
Found at i:1165158 original size:2 final size:2
Alignment explanation
Indices: 1165151--1165193 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1165141 TTATTTTTAT
1165151 TA TA TA 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 TA TA TA
1165193 T
1 T
1165194 CCGTCTCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1165643 original size:15 final size:15
Alignment explanation
Indices: 1165623--1165673 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1165613 AAAAACCGGG
1165623 TACCGGGTACCCGAT
1 TACCGGGTACCCGAT
* *
1165638 TACCGGATACCCGTAA
1 TACCGGGTACCCG-AT
*
1165654 AATCCGGGTACCCGAT
1 TA-CCGGGTACCCGAT
1165670 TACC
1 TACC
1165674 AAATACTCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 14 0.50
16 4 0.14
17 10 0.36
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (15 bp):
TACCGGGTACCCGAT
Found at i:1165685 original size:32 final size:32
Alignment explanation
Indices: 1165625--1165694 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1165615 AAACCGGGTA
**
1165625 CCGGGTACCCGATTACCGGATACCCGTAAAAT
1 CCGGGTACCCGATTACCAAATACCCGTAAAAT
* *
1165657 CCGGGTACCCGATTACCAAATACTCGTAACAT
1 CCGGGTACCCGATTACCAAATACCCGTAAAAT
*
1165689 TCGGGT
1 CCGGGT
1165695 CAAGACACGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (32 bp):
CCGGGTACCCGATTACCAAATACCCGTAAAAT
Found at i:1182376 original size:65 final size:63
Alignment explanation
Indices: 1182302--1182461 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
1182292 AATTAAATTG
* *
1182302 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATAA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-T-A
1182366 A
63 A
* * * *
1182367 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTAA
*
1182431 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1182462 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 31 0.36
65 49 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTAA
Found at i:1182461 original size:17 final size:19
Alignment explanation
Indices: 1182433--1182481 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1182423 TATTTTAAAA
1182433 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1182451 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1182470 CACCGATGCACT
1 CATCGATGCACT
1182482 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1182477 original size:64 final size:63
Alignment explanation
Indices: 1182302--1182481 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 63
1182292 AATTAAATTG
* *
1182302 AACATCGAATGCATTTCATGCATCGATGCACATACCA-TGCACCGATGCACTGAGGATTTTATAA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T--CAGTGCACCGATGCACTCAGGATTTTATAA
1182366 A
63 A
* * *
1182367 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTT-T-
1 AACATCGAATGCATTTGATGCATCGATGCACTCAG---TGCACCGATGCACTCAGGAT-TTTATA
1182429 AA
62 AA
*
1182431 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC--AGTGCACCGATGCACT
1182482 AAGGGTCCAA
Statistics
Matches: 100, Mismatches: 7, Indels: 17
0.81 0.06 0.14
Matches are distributed among these distances:
61 2 0.02
64 45 0.45
65 48 0.48
66 3 0.03
67 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGTGCACCGATGCACTCAGGATTTTATAAA
Found at i:1183655 original size:59 final size:61
Alignment explanation
Indices: 1183583--1183696 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 61
1183573 AAACTAAAGT
1183583 CACTCACGAAGGCA-CGACGAGGTAAAAGAATCTAAAA-TAGTCTTCTAACACATCTATGA
1 CACTCACGAAGGCACCGACGAGGTAAAAGAATCTAAAATTAGTCTTCTAACACATCTATGA
1183642 CACTCACGAAGGCACCGACGAGGTAAAAGAATCTAAAATTAGTCTTCTAACACAT
1 CACTCACGAAGGCACCGACGAGGTAAAAGAATCTAAAATTAGTCTTCTAACACAT
1183697 AGCTATGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
59 14 0.26
60 23 0.43
61 16 0.30
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (61 bp):
CACTCACGAAGGCACCGACGAGGTAAAAGAATCTAAAATTAGTCTTCTAACACATCTATGA
Found at i:1190013 original size:21 final size:21
Alignment explanation
Indices: 1189971--1190014 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1189961 ACCTCGAGAG
*
1189971 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1189992 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1190013 CT
1 CT
1190015 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1194549 original size:29 final size:29
Alignment explanation
Indices: 1194516--1194599 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 29
1194506 TAATTAATTG
1194516 AGTATGATCAAACTTTTCTAAATTAGCTA
1 AGTATGATCAAACTTTTCTAAATTAGCTA
**
1194545 AGTATTGA--AAA-TCAT-T-AATT-G---
1 AGTA-TGATCAAACTTTTCTAAATTAGCTA
*
1194566 AGTAGGATCAAACTTTTCTAAATTAGCTA
1 AGTATGATCAAACTTTTCTAAATTAGCTA
1194595 AGTAT
1 AGTAT
1194600 TGATTGGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 20
0.60 0.09 0.31
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 3 0.08
23 2 0.05
24 2 0.05
25 8 0.21
26 2 0.05
27 2 0.05
28 3 0.08
29 8 0.21
30 3 0.08
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (29 bp):
AGTATGATCAAACTTTTCTAAATTAGCTA
Found at i:1194575 original size:50 final size:50
Alignment explanation
Indices: 1194497--1194602 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
1194487 ATTACTACAA
*
1194497 TATTGAAAATAATTAATTGAGTATGATCAAACTTTTCTAAATTAGCTAAG
1 TATTGAAAATAATTAATTGAGTAGGATCAAACTTTTCTAAATTAGCTAAG
*
1194547 TATTGAAAATCATTAATTGAGTAGGATCAAACTTTTCTAAATTAGCTAAG
1 TATTGAAAATAATTAATTGAGTAGGATCAAACTTTTCTAAATTAGCTAAG
1194597 TATTGA
1 TATTGA
1194603 TTGGATACAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (50 bp):
TATTGAAAATAATTAATTGAGTAGGATCAAACTTTTCTAAATTAGCTAAG
Found at i:1202563 original size:15 final size:15
Alignment explanation
Indices: 1202543--1202571 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1202533 CAACCCGGAT
1202543 ATTTCGGGTACCCGG
1 ATTTCGGGTACCCGG
1202558 ATTTCGGGTACCCG
1 ATTTCGGGTACCCG
1202572 ATACCCAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (15 bp):
ATTTCGGGTACCCGG
Found at i:1202606 original size:22 final size:22
Alignment explanation
Indices: 1202551--1202598 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1202541 ATATTTCGGG
*
1202551 TACCCGGATTTCGGGTACCCGA
1 TACCCAGATTTCGGGTACCCGA
1202573 TACCCAGATTTCGGGTACCCGA
1 TACCCAGATTTCGGGTACCCGA
1202595 TACC
1 TACC
1202599 TTTTTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (22 bp):
TACCCAGATTTCGGGTACCCGA
Found at i:1203882 original size:20 final size:20
Alignment explanation
Indices: 1203857--1203926 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1203847 GATTGAAGTA
*
1203857 GTATCGATATTGTTATGGAG
1 GTATCGATACTGTTATGGAG
**** *
1203877 GTATCGATACCAAGA-GTAGG
1 GTATCGATACTGTTATGGA-G
1203897 GTATCGATACTGTTATGGAG
1 GTATCGATACTGTTATGGAG
1203917 GTATCGATAC
1 GTATCGATAC
1203927 CAAGAGTAGG
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (20 bp):
GTATCGATACTGTTATGGAG
Found at i:1203904 original size:40 final size:40
Alignment explanation
Indices: 1203857--1203949 Score: 177
Period size: 40 Copynumber: 2.3 Consensus size: 40
1203847 GATTGAAGTA
*
1203857 GTATCGATATTGTTATGGAGGTATCGATACCAAGAGTAGG
1 GTATCGATACTGTTATGGAGGTATCGATACCAAGAGTAGG
1203897 GTATCGATACTGTTATGGAGGTATCGATACCAAGAGTAGG
1 GTATCGATACTGTTATGGAGGTATCGATACCAAGAGTAGG
1203937 GTATCGATACTGT
1 GTATCGATACTGT
1203950 AATTGAAATC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (40 bp):
GTATCGATACTGTTATGGAGGTATCGATACCAAGAGTAGG
Found at i:1203939 original size:20 final size:20
Alignment explanation
Indices: 1203876--1203946 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1203866 TTGTTATGGA
1203876 GGTATCGATACCAAGAGTAG
1 GGTATCGATACCAAGAGTAG
**** *
1203896 GGTATCGATACTGTTA-TGG
1 GGTATCGATACCAAGAGTAG
1203915 AGGTATCGATACCAAGAGTAG
1 -GGTATCGATACCAAGAGTAG
1203936 GGTATCGATAC
1 GGTATCGATAC
1203947 TGTAATTGAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
19 2 0.05
20 35 0.90
21 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAAGAGTAG
Found at i:1204590 original size:15 final size:16
Alignment explanation
Indices: 1204579--1204609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1204569 GTGGTGAATA
1204579 TGTCATACGTGAAAAG
1 TGTCATACGTGAAAAG
*
1204595 TGTTATACGTGAAAA
1 TGTCATACGTGAAAA
1204610 ATGATCTACA
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:0.39, C:0.10, G:0.23, T:0.29
Consensus pattern (16 bp):
TGTCATACGTGAAAAG
Found at i:1210448 original size:21 final size:18
Alignment explanation
Indices: 1210406--1210479 Score: 103
Period size: 18 Copynumber: 3.9 Consensus size: 18
1210396 ACTGAATATT
*
1210406 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
1210424 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCAC---TA
*
1210445 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1210463 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1210480 GATATCCCTC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 33 0.66
21 17 0.34
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1210460 original size:39 final size:39
Alignment explanation
Indices: 1210406--1210484 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1210396 ACTGAATATT
1210406 TGTCCCGAAAGACCACTATGTCCCGAAGGACCACTGATA
1 TGTCCCGAAAGACCACTATGTCCCGAAGGACCACTGATA
* *
1210445 TGTCTCGAAGGACCACTATGTCCCGAAGGACCACTGATA
1 TGTCCCGAAAGACCACTATGTCCCGAAGGACCACTGATA
1210484 T
1 T
1210485 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (39 bp):
TGTCCCGAAAGACCACTATGTCCCGAAGGACCACTGATA
Found at i:1222859 original size:103 final size:103
Alignment explanation
Indices: 1222676--1222865 Score: 247
Period size: 103 Copynumber: 1.8 Consensus size: 103
1222666 TCATAGGCGC
* * * * * * *
1222676 ATTTTGTTTAATGCATTTTTTGCATTTTCGTATCAGTAATTTGTTTACTTTCGATAATATGTTTG
1 ATTTTGTTTAATGCATATGTTACATTTTCATATCAGTAATTTGTGTACTTTCGACAATATGTGTG
** * *
1222741 CATTGATGATGTTCATAATGAGCACTTGTTATCGATCG
66 CATCCACGATATTCATAATGAGCACTTGTTATCGATCG
*
1222779 ATTTTGTTTAATGCATATGTTACATTTTCATATCAGT-ATTATGTGTACTTTCGACACTATGTGT
1 ATTTTGTTTAATGCATATGTTACATTTTCATATCAGTAATT-TGTGTACTTTCGACAATATGTGT
*
1222843 GCATCCACGGTATTCATAATGAG
65 GCATCCACGATATTCATAATGAG
1222866 TTTGTGAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
102 3 0.04
103 70 0.96
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (103 bp):
ATTTTGTTTAATGCATATGTTACATTTTCATATCAGTAATTTGTGTACTTTCGACAATATGTGTG
CATCCACGATATTCATAATGAGCACTTGTTATCGATCG
Found at i:1223445 original size:2 final size:2
Alignment explanation
Indices: 1223438--1223488 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1223428 TTTTAAATGT
1223438 TA TA TA 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 TA TA TA
1223480 TA TA TA TA T
1 TA TA TA TA T
1223489 TTGAAGAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1225801 original size:21 final size:21
Alignment explanation
Indices: 1225734--1225787 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1225724 AGGGTTCTAC
*
1225734 GTGGTCCTTTGGAACATATAT
1 GTGGTACTTTGGAACATATAT
**
1225755 GTAATACTTTGGAACATATAT
1 GTGGTACTTTGGAACATATAT
1225776 GTGGTACTTTGG
1 GTGGTACTTTGG
1225788 TACACTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (21 bp):
GTGGTACTTTGGAACATATAT
Found at i:1232148 original size:104 final size:103
Alignment explanation
Indices: 1231964--1232154 Score: 303
Period size: 104 Copynumber: 1.8 Consensus size: 103
1231954 TCATAGGTTC
* * *
1231964 ATTTTGTTTAATGCATTTTTTGCATTTTTATATCAGTACTTTGTGTACTTTCGGCACTATGTGTG
1 ATTTTGTTTAATGCATATGTTACATTTTTATATCAGTACTTTGTGTACTTTCGGCACTATGTGTG
* *
1232029 CAGTGATGGTGTTCATAATGAGCACTTGTTATCGATCG
66 CAGTCATGGTATTCATAATGAGCACTTGTTATCGATCG
*
1232067 ATTTTGTTTAATGCATATGTTACATTTTTCATATCAGTACTTTGTGTACTTTCGGCACTATTTGT
1 ATTTTGTTTAATGCATATGTTACATTTTT-ATATCAGTACTTTGTGTACTTTCGGCACTATGTGT
1232132 GCA-TCCATGGTATTCATAATGAG
65 GCAGT-CATGGTATTCATAATGAG
1232155 TTTGTGAATT
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
103 27 0.34
104 53 0.66
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (103 bp):
ATTTTGTTTAATGCATATGTTACATTTTTATATCAGTACTTTGTGTACTTTCGGCACTATGTGTG
CAGTCATGGTATTCATAATGAGCACTTGTTATCGATCG
Found at i:1236366 original size:2 final size:2
Alignment explanation
Indices: 1236359--1236402 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1236349 TTAATTAATA
1236359 AT AT AT AT AT AT -T 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
1236400 AT A
1 AT A
1236403 ATTGTTGTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1237995 original size:2 final size:2
Alignment explanation
Indices: 1237988--1238065 Score: 128
Period size: 2 Copynumber: 41.0 Consensus size: 2
1237978 ATTCAAAACA
1237988 AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1238027 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
1238066 TGGAACGAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 4 0.06
2 68 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1238029 original size:31 final size:32
Alignment explanation
Indices: 1237988--1238064 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
1237978 ATTCAAAACA
1237988 ATAT-ATATATATATAATATA-ATATATATAT
1 ATATAATATATATATAATATATATATATATAT
1238018 ATATAATATATATAT-ATATATATATATATAT
1 ATATAATATATATATAATATATATATATATAT
1238049 ATATAATATATATATA
1 ATATAATATATATATA
1238065 TTGGAACGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
30 9 0.20
31 35 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATAATATATATATAATATATATATATATAT
Found at i:1238065 original size:31 final size:31
Alignment explanation
Indices: 1237989--1238065 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 31
1237979 TTCAAAACAA
1237989 TATATATATATATAATATA-ATATATATATA
1 TATATATATATATAATATATATATATATATA
1238019 TATAATATATATATATATATATATATATATATA
1 TAT-ATATATATATA-ATATATATATATATATA
1238052 TAATATATATATAT
1 T-ATATATATATAT
1238066 TGGAACGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
30 3 0.07
31 11 0.26
32 5 0.12
33 22 0.51
34 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TATATATATATATAATATATATATATATATA
Found at i:1243322 original size:249 final size:248
Alignment explanation
Indices: 1242877--1243372 Score: 910
Period size: 249 Copynumber: 2.0 Consensus size: 248
1242867 TTAGATAGGT
1242877 TAACTTGAAATTAAGGATGGGTAAAAAAAATTAACCCTAATTCATTTTCTCATTTTTGCCTTTCT
1 TAACTTGAAATTAAGGATGGGTAAAAAAAATTAACCCTAATTCATTTTCTCATTTTTGCCTTTCT
1242942 CTTTATGCCTCTATGTAGGCACCTCAACTTAATCGGAGATTGGATTGACAAGTTACATGGCTAAT
66 CTTTATGCCTCTATGTAGGCACCTCAACTTAATCGGAGATTGGATTGACAAGTTACATGGCTAAT
1243007 CGAAAATAATAAACTTTAATTAATTTTAATTATTGAATAATTAGTATTTATTTTATAAATTTTAG
131 CGAAAATAATAAACTTTAATTAATTTTAATTATTGAATAATTAGTATTTATTTTATAAATTTTAG
1243072 GGACTAAATGATATTTACAATATCATATCATACATCAAATCAACATATTGTGGAG
196 GGACTAAATGATATTTACAATATC--ATCATACATCAAATCAACATATTGTGGAG
1243127 TAACTTGAAATTAAGGATGGGTAAAAAAAA-TAACCCTAATTCATTTT-TCATTTTTGCCTTTCC
1 TAACTTGAAATTAAGGATGGGTAAAAAAAATTAACCCTAATTCATTTTCTCATTTTTGCCTTT-C
1243190 TCTTTATGCCTCTATGTAGGCACCTCAACTTAATCGGAGATTGGATTGACAATGTTACATGGCTA
65 TCTTTATGCCTCTATGTAGGCACCTCAACTTAATCGGAGATTGGATTGACAA-GTTACATGGCTA
*
1243255 ATCGAAAATAATAAACTTTAATTTAATTTTAATTATTGAATAATTAGTATTTATTTT-TATA-TT
129 ATCGAAAATAATAAACTTTAA-TTAATTTTAATTATTGAATAATTAGTATTTATTTTATAAATTT
1243318 TAGGGACTAAATGATATTTACAATATCATCATACATCAAATCAACATATTGTGGA
193 TAGGGACTAAATGATATTTACAATATCATCATACATCAAATCAACATATTGTGGA
1243373 AGAATTTCAT
Statistics
Matches: 242, Mismatches: 1, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
247 28 0.12
248 14 0.06
249 99 0.41
250 66 0.27
251 35 0.14
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (248 bp):
TAACTTGAAATTAAGGATGGGTAAAAAAAATTAACCCTAATTCATTTTCTCATTTTTGCCTTTCT
CTTTATGCCTCTATGTAGGCACCTCAACTTAATCGGAGATTGGATTGACAAGTTACATGGCTAAT
CGAAAATAATAAACTTTAATTAATTTTAATTATTGAATAATTAGTATTTATTTTATAAATTTTAG
GGACTAAATGATATTTACAATATCATCATACATCAAATCAACATATTGTGGAG
Found at i:1243398 original size:39 final size:38
Alignment explanation
Indices: 1243345--1243426 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 38
1243335 TTACAATATC
*
1243345 ATCATACATCAAATCAACATATTGTGGAAGAATTTCATT
1 ATCATACATCAAATCAACATATTGTGGAAGAA-TTCATA
*
1243384 ATCATACATCAAATCAACATATTGTGGAAGCATTCATA
1 ATCATACATCAAATCAACATATTGTGGAAGAATTCATA
1243422 ATCAT
1 ATCAT
1243427 CATTAATCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 10 0.24
39 31 0.76
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (38 bp):
ATCATACATCAAATCAACATATTGTGGAAGAATTCATA
Found at i:1248398 original size:132 final size:129
Alignment explanation
Indices: 1248165--1248411 Score: 451
Period size: 132 Copynumber: 1.9 Consensus size: 129
1248155 CACAGAAAAA
1248165 CAAAAATAACCACCAAAAGCTTTGATGCCAGTTTTTCGAAAAATCGAGTAATTTCTCTATAACCA
1 CAAAAATAACCACCAAAAGCTTTGATGCCAGTTTTTCGAAAAATCGAGTAATTTCTCTATAACCA
1248230 GATTAGTGAGAATGCGAAATAAAAAGTGGAAAAATAATACCC-AAAATTGATACAGAAAAAACG
66 GATTAGTGAGAATGCGAAATAAAAAGTGGAAAAATAATACCCGAAAATTGATACAGAAAAAACG
1248293 CAAAAATAACCACCAAAAGCTTTGATGCCAGTTTTTTCGGAAATAAATCGAGTAATTTCTCTATA
1 CAAAAATAACCACCAAAAGCTTTGATGCCAG-TTTTTC-G-AA-AAATCGAGTAATTTCTCTATA
1248358 ACCAGATTAGTGAGAATGCGAAATAAAAAGTGGAAAAATAATACCCGAAAATTG
62 ACCAGATTAGTGAGAATGCGAAATAAAAAGTGGAAAAATAATACCCGAAAATTG
1248412 TAACGGAGTT
Statistics
Matches: 114, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
128 31 0.27
129 6 0.05
130 1 0.01
131 2 0.02
132 67 0.59
133 7 0.06
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (129 bp):
CAAAAATAACCACCAAAAGCTTTGATGCCAGTTTTTCGAAAAATCGAGTAATTTCTCTATAACCA
GATTAGTGAGAATGCGAAATAAAAAGTGGAAAAATAATACCCGAAAATTGATACAGAAAAAACG
Found at i:1252975 original size:25 final size:29
Alignment explanation
Indices: 1252908--1252980 Score: 68
Period size: 28 Copynumber: 2.7 Consensus size: 29
1252898 TATATAAAAA
* *
1252908 TATTATAT-GATATTATGATATGATATATT
1 TATTATATAGA-AATATTATATGATATATT
1252937 TATTATATAGAAAT-TTATAT-ATATAATT
1 TATTATATAGAAATATTATATGATAT-ATT
1252965 TA-TAT-TA-AAATATTAT
1 TATTATATAGAAATATTAT
1252981 TTTAGTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 4 0.10
26 6 0.15
27 7 0.18
28 10 0.26
29 10 0.26
30 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (29 bp):
TATTATATAGAAATATTATATGATATATT
Found at i:1254217 original size:60 final size:59
Alignment explanation
Indices: 1254122--1254260 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 59
1254112 GGTAAAATAC
**
1254122 ACAAATGGTCTCCTGACTATAAGATGTTACTTTGTTGAGTCCATCGACTATTAAAAGTT
1 ACAAATGGTCTCCTGACTATAAGACATTACTTTGTTGAGTCCATCGACTATTAAAAGTT
* * * * *
1254181 ACGAAATGGTCTCCTGATTATAGGACATTGCTTTGTTGAGTCCTTTGACTATTAAAAGTT
1 AC-AAATGGTCTCCTGACTATAAGACATTACTTTGTTGAGTCCATCGACTATTAAAAGTT
* * *
1254241 ACAAATAGTCACCAGACTAT
1 ACAAATGGTCTCCTGACTAT
1254261 TCATATGTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 16 0.24
60 52 0.76
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (59 bp):
ACAAATGGTCTCCTGACTATAAGACATTACTTTGTTGAGTCCATCGACTATTAAAAGTT
Found at i:1255899 original size:35 final size:34
Alignment explanation
Indices: 1255860--1255934 Score: 132
Period size: 35 Copynumber: 2.2 Consensus size: 34
1255850 TTTGAAAACT
1255860 TATATAATATATGGTTTTTAAAAAACATTTTGAA
1 TATATAATATATGGTTTTTAAAAAACATTTTGAA
*
1255894 CTATATAATATATGGTTTTTTAAAAACATTTTGAA
1 -TATATAATATATGGTTTTTAAAAAACATTTTGAA
1255929 TATATA
1 TATATA
1255935 GTTTAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 6 0.15
35 33 0.85
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (34 bp):
TATATAATATATGGTTTTTAAAAAACATTTTGAA
Found at i:1255965 original size:34 final size:34
Alignment explanation
Indices: 1255927--1256073 Score: 158
Period size: 34 Copynumber: 4.2 Consensus size: 34
1255917 AAACATTTTG
* *
1255927 AATATATAGTTTAAAAAATATTTTGAAA-ATATAT
1 AATATATAGTTT-TAAAACATTTTGAAACATATAT
* * *
1255961 AATATATGGTTTTTAAAC-TTTTAAATACATATAT
1 AATATATAGTTTTAAAACATTTTGAA-ACATATAT
1255995 ATATTATATAGTTTTTAAAACATTTTGAAACTATATAT
1 A-A-TATATAG-TTTTAAAACATTTTGAAAC-ATATAT
1256033 AATATATAGTTTT-AAACA-TTTGAAACATATAT
1 AATATATAGTTTTAAAACATTTTGAAACATATAT
1256065 ATATATATA
1 A-ATATATA
1256074 TATTATATAG
Statistics
Matches: 97, Mismatches: 8, Indels: 17
0.80 0.07 0.14
Matches are distributed among these distances:
32 13 0.13
33 19 0.20
34 23 0.24
35 5 0.05
36 13 0.13
37 11 0.11
38 13 0.13
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (34 bp):
AATATATAGTTTTAAAACATTTTGAAACATATAT
Found at i:1255995 original size:36 final size:35
Alignment explanation
Indices: 1255955--1256075 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 35
1255945 TATTTTGAAA
* *
1255955 ATATATAATATATGGTTTTTAAACTTTTAAATACAT
1 ATATATAATATATAGTTTTTAAACTTTTGAA-ACAT
*
1255991 ATATATATTATATAGTTTTTAAAACATTTTGAAAC-T
1 ATATATAATATATAGTTTTT-AAAC-TTTTGAAACAT
*
1256027 ATATATAATATATAG-TTTTAAACATTTGAAACAT
1 ATATATAATATATAGTTTTTAAACTTTTGAAACAT
1256061 ATATATATATATATA
1 ATATATA-ATATATA
1256076 TTATATAGTT
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
33 8 0.11
34 12 0.16
35 11 0.14
36 33 0.43
37 6 0.08
38 6 0.08
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTAAACTTTTGAAACAT
Found at i:1256081 original size:42 final size:43
Alignment explanation
Indices: 1256026--1256113 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 43
1256016 ATTTTGAAAC
1256026 TATATATAATATATAG-TTTT-AAACA-TTTGAAACATATATATA
1 TATATATAATATATAGTTTTTAAAACATTTTGAAA-ATATAT-TA
*
1256068 TATATATATTATATAGTTTTTAAAACATTTTGAAAATATATTA
1 TATATATAATATATAGTTTTTAAAACATTTTGAAAATATATTA
1256111 TAT
1 TAT
1256114 TTTTTGAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 15 0.36
43 9 0.21
44 11 0.26
45 7 0.17
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (43 bp):
TATATATAATATATAGTTTTTAAAACATTTTGAAAATATATTA
Found at i:1256143 original size:30 final size:29
Alignment explanation
Indices: 1256077--1256143 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 29
1256067 ATATATATAT
*
1256077 TATATAGTTTTTAAAACATTTTGAAAATA
1 TATATATTTTTTAAAACATTTTGAAAATA
*
1256106 TATTATATTTTTTGAAAACATTTTGAAATTA
1 TA-TATATTTTTT-AAAACATTTTGAAAATA
1256137 TATATAT
1 TATATAT
1256144 GATTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 2 0.06
30 14 0.41
31 18 0.53
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (29 bp):
TATATATTTTTTAAAACATTTTGAAAATA
Found at i:1256265 original size:7 final size:7
Alignment explanation
Indices: 1256239--1256303 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
1256229 ATATATAATA
1256239 TTATTA-
1 TTATTAT
*
1256245 TTATTGT
1 TTATTAT
1256252 ATTATTAT
1 -TTATTAT
1256260 TTATTAT
1 TTATTAT
1256267 TTATTAT
1 TTATTAT
*
1256274 ATATTAAT
1 TTATT-AT
*
1256282 TTCTT-T
1 TTATTAT
1256288 TT-TTAT
1 TTATTAT
1256294 TT-TT-T
1 TTATTAT
1256299 TTATT
1 TTATT
1256304 TTCAATTCAG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
5 5 0.10
6 15 0.31
7 18 0.37
8 11 0.22
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (7 bp):
TTATTAT
Found at i:1256452 original size:38 final size:37
Alignment explanation
Indices: 1256404--1256606 Score: 153
Period size: 38 Copynumber: 5.1 Consensus size: 37
1256394 AGGGTTATAC
* *
1256404 ATATAATATATGGTTTTTAAAACATTTTAAATACATAT
1 ATATATTATATAGTTTTTAAAACATTTTAAATA-ATAT
1256442 ATATATTATATAGTTTTTAAAACATTTTGAAAACATATATATT
1 ATATATTATATAGTTTTTAAAACATTTT---AA-ATA-ATA-T
* *
1256485 ATATATATATATTATATAGTTTTTAAAACATTTTGAA-AATAT
1 ATATAT-TATA-TA-GT--TTTT-AAAACATTTTAAATAATAT
*
1256527 ATATATTATATAGTTTTTGAAAACATTTTGAA-AAT-T
1 ATATATTATATAGTTTTT-AAAACATTTTAAATAATAT
* * *
1256563 ATATAATATATGATTTTTTGAAAACGTTTTTAAAT-ATAT
1 ATATATTATAT-AGTTTTT-AAAAC-ATTTTAAATAATAT
1256602 ATATA
1 ATATA
1256607 GTTTCAAATA
Statistics
Matches: 139, Mismatches: 11, Indels: 29
0.78 0.06 0.16
Matches are distributed among these distances:
36 11 0.08
37 32 0.23
38 34 0.24
39 7 0.05
40 2 0.01
41 6 0.04
42 13 0.09
43 10 0.07
44 5 0.04
45 3 0.02
46 2 0.01
48 4 0.03
49 10 0.07
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
ATATATTATATAGTTTTTAAAACATTTTAAATAATAT
Found at i:1256494 original size:13 final size:13
Alignment explanation
Indices: 1256476--1256502 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1256466 TTTTGAAAAC
1256476 ATATATATTATAT
1 ATATATATTATAT
1256489 ATATATATTATAT
1 ATATATATTATAT
1256502 A
1 A
1256503 GTTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:1256521 original size:420 final size:407
Alignment explanation
Indices: 1255993--1256822 Score: 1204
Period size: 420 Copynumber: 2.0 Consensus size: 407
1255983 AAATACATAT
* *
1255993 ATATATTATATAGTTTTTAAAACATTTTGAAACTATATATAATATATAGTTTTAAACATTTGAAA
1 ATATAATATATAGTTTTTAAAACATTTTAAAACTATATATAATATATAGTTTTAAACATTTGAAA
1256058 CATATATATATATATATATTATATAGTTTTTAAAACATTTTG-AA-A-ATATATTATAT-TTTTT
66 CATATATATATATATATATTATATAGTTTTTAAAACATTTTGAAATATATATATTATATATTTTT
* *
1256119 GAAAACATTTTG-AAATTATAT-ATATGAT-TTTTTTGAAAACGTTTTTTAATCTATAATATAGT
131 GAAAACATTTTGAAAATTATATAATAT-ATATTTTTTGAAAACGTTTTTAAATATAT-ATATAGT
1256181 TTCAAATATTTTTGAAAATAT-TA-T-TATAGTTTTTGAAAATATTTGTATATATATAATATTAT
194 TTCAAATATTTTTGAAAATATATATTATATAGTTTTTGAAAATATTTG----TATAT-ATA--A-
1256243 TATTATTGTATTATTATTTATTATTTATTATATATTAATT-TCTTTTTTTATTTTTTTT-ATTTT
251 -ATTA-T-TATTATTA--T-TT-TTTATTATATATTAATTCT-TTTTTTTATTTTTTTTCATTTT
1256306 CAATTCAGTCCA-GTCCAAATGG-TAAGGAGGAGCCCCAACCGGGTAGGCAGGCCTGACCCAGCC
308 CAATTCAGTCCAGGTCCAAATGGCTAAGGAGGAG-CCCAACCGGGTAGGCAGGCCTGACCCAGCC
1256369 AGCCAACCCGGGTAA-CCAACAGATTAGGGTTATAC
372 AGCCAACCCGGGTAACCCAACAGATTAGGGTTATAC
* *
1256404 ATATAATATATGGTTTTTAAAACATTTTAAATACATATATATATTATATAGTTTTTAAAACATTT
1 ATATAATATATAGTTTTTAAAACATTTTAAA-AC-TATATATAATATATAG-TTTT-AAACA-TT
1256469 TGAAAACATATATATTATATATATATATTATATAGTTTTTAAAACATTTTGAAAATATATATATT
61 TG-AAAC--ATATA-TATATATATATATTATATAGTTTTTAAAACATTTTG-AAATATATATATT
1256534 ATATAGTTTTTGAAAACATTTTGAAAATTATATAATATATGATTTTTTGAAAACGTTTTTAAATA
121 ATATA-TTTTTGAAAACATTTTGAAAATTATATAATATAT-ATTTTTTGAAAACGTTTTTAAATA
1256599 TATATATAGTTTCAAATATTTTTGAAAATATATATTATATAGTTTTTGAAAATATTTGTATATAT
184 TATATATAGTTTCAAATATTTTTGAAAATATATATTATATAGTTTTTGAAAATATTTGTATATAT
*
1256664 AAATTATTATTATTATTTTTTATTATATATTAATTCTTTTTTTTATTTTTTTTCTTTTTCAATTC
249 AAATTATTATTATTATTTTTTATTATATATTAATTCTTTTTTTTATTTTTTTTCATTTTCAATTC
1256729 AGTCCAGGTCCAAATGGTCTAAGGAGGAGCCCAACCGGGTAGGCAGGCCTGACCCAGCCAGCCAA
314 AGTCCAGGTCCAAATGG-CTAAGGAGGAGCCCAACCGGGTAGGCAGGCCTGACCCAGCCAGCCAA
1256794 CCCGGGTAACCCAACAGATTAGGGTTATA
378 CCCGGGTAACCCAACAGATTAGGGTTATA
1256823 TATCTAAACA
Statistics
Matches: 384, Mismatches: 7, Indels: 47
0.88 0.02 0.11
Matches are distributed among these distances:
411 28 0.07
412 2 0.01
413 15 0.04
414 4 0.01
415 5 0.01
416 37 0.10
417 23 0.06
418 11 0.03
419 50 0.13
420 73 0.19
421 1 0.00
422 6 0.02
423 1 0.00
424 12 0.03
426 20 0.05
427 16 0.04
428 32 0.08
429 26 0.07
430 1 0.00
431 21 0.05
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.44
Consensus pattern (407 bp):
ATATAATATATAGTTTTTAAAACATTTTAAAACTATATATAATATATAGTTTTAAACATTTGAAA
CATATATATATATATATATTATATAGTTTTTAAAACATTTTGAAATATATATATTATATATTTTT
GAAAACATTTTGAAAATTATATAATATATATTTTTTGAAAACGTTTTTAAATATATATATAGTTT
CAAATATTTTTGAAAATATATATTATATAGTTTTTGAAAATATTTGTATATATAAATTATTATTA
TTATTTTTTATTATATATTAATTCTTTTTTTTATTTTTTTTCATTTTCAATTCAGTCCAGGTCCA
AATGGCTAAGGAGGAGCCCAACCGGGTAGGCAGGCCTGACCCAGCCAGCCAACCCGGGTAACCCA
ACAGATTAGGGTTATAC
Found at i:1256532 original size:49 final size:49
Alignment explanation
Indices: 1256438--1256538 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
1256428 TTTTAAATAC
1256438 ATATATATATTATATAGTTTTTAAAACATTTTGAAAACATATATATTAT
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAAACATATATATTAT
*
1256487 ATATATATATTATATAGTTTTTAAAACATTTTGAAAATATATATATTAT
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAAACATATATATTAT
1256536 ATA
1 ATA
1256539 GTTTTTGAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (49 bp):
ATATATATATTATATAGTTTTTAAAACATTTTGAAAACATATATATTAT
Found at i:1256555 original size:37 final size:37
Alignment explanation
Indices: 1256487--1256606 Score: 172
Period size: 37 Copynumber: 3.2 Consensus size: 37
1256477 TATATATTAT
1256487 ATATATATATTATATAGTTTTT-AAAACATTTTGAAA
1 ATATATATATTATATAGTTTTTGAAAACATTTTGAAA
1256523 ATATATATATTATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATATTATATAGTTTTTGAAAACATTTTGAAA
* * * *
1256560 AT-TATATAATATATGATTTTTTGAAAACGTTTTTAAA
1 ATATATATATTATAT-AGTTTTTGAAAACATTTTGAAA
1256597 TATATATATA
1 -ATATATATA
1256607 GTTTCAAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
36 33 0.43
37 35 0.46
38 2 0.03
39 6 0.08
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (37 bp):
ATATATATATTATATAGTTTTTGAAAACATTTTGAAA
Found at i:1256691 original size:30 final size:30
Alignment explanation
Indices: 1256657--1256714 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1256647 AAAATATTTG
1256657 TATATATAAATTATTATTATTATTTTTTAT
1 TATATATAAATTATTATTATTATTTTTTAT
* * * *
1256687 TATATATTAATTCTTTTTTTTATTTTTT
1 TATATATAAATTATTATTATTATTTTTT
1256715 TTCTTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (30 bp):
TATATATAAATTATTATTATTATTTTTTAT
Found at i:1257257 original size:22 final size:23
Alignment explanation
Indices: 1257221--1257264 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1257211 ATACAAATCG
*
1257221 AAAAACCAAATACAACACCACAA
1 AAAAACCAAATACAACAACACAA
*
1257244 AAAAACTAAA-ACAACAACACA
1 AAAAACCAAATACAACAACACA
1257265 GAAACAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.68, C:0.27, G:0.00, T:0.05
Consensus pattern (23 bp):
AAAAACCAAATACAACAACACAA
Found at i:1259617 original size:2 final size:2
Alignment explanation
Indices: 1259610--1259635 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1259600 AAACAGTAAC
1259610 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
1259636 CAATGTGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1260504 original size:2 final size:2
Alignment explanation
Indices: 1260497--1260562 Score: 71
Period size: 2 Copynumber: 32.5 Consensus size: 2
1260487 TTCTGAAATA
* * *
1260497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AG AT AA AGT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT
*
1260541 AC AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1260563 ATTCTTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
1 1 0.02
2 51 0.94
3 1 0.02
4 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1264866 original size:29 final size:29
Alignment explanation
Indices: 1264833--1264927 Score: 181
Period size: 29 Copynumber: 3.3 Consensus size: 29
1264823 AAAACTGTAC
1264833 AAATTGTATAGTTGGAAAGGAAGTATATA
1 AAATTGTATAGTTGGAAAGGAAGTATATA
1264862 AAATTGTATAGTTGGAAAGGAAGTATATA
1 AAATTGTATAGTTGGAAAGGAAGTATATA
*
1264891 AAATTGTATAGTTGGAAAGGAAGTACATA
1 AAATTGTATAGTTGGAAAGGAAGTATATA
1264920 AAATTGTA
1 AAATTGTA
1264928 GCGACAAACA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.45, C:0.01, G:0.23, T:0.31
Consensus pattern (29 bp):
AAATTGTATAGTTGGAAAGGAAGTATATA
Found at i:1266054 original size:23 final size:23
Alignment explanation
Indices: 1266028--1266073 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1266018 GGAGCCGTCG
*
1266028 GTGAGGTCGTCGATGAGCCACCA
1 GTGAGGTCATCGATGAGCCACCA
* *
1266051 GTGATGTCATCGGTGAGCCACCA
1 GTGAGGTCATCGATGAGCCACCA
1266074 TCCGTCAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.26, G:0.33, T:0.20
Consensus pattern (23 bp):
GTGAGGTCATCGATGAGCCACCA
Found at i:1267274 original size:196 final size:198
Alignment explanation
Indices: 1266984--1267370 Score: 460
Period size: 196 Copynumber: 2.0 Consensus size: 198
1266974 TATTGCGGTG
* * *
1266984 ATGGTTAACGTATAGTTGTTATTTTTAAAGATTTCAATCGGATTTAGATATAATATCTATAAAAT
1 ATGGTTAACGTATAGTTGTTATTATTAAAGATCTCAATCGGATTTAGATATAATATCTACAAAAT
** * * ***** *
1267049 GTTTGAGTATTTATTTTCAAACGATTAAAATTCTTTCAAATAAATATTACCACTGTAA-TCATCT
66 GTTTGAACATTTATTATCAAACAATTAAAAAAAAATCAAATAAATATTACCACTGTAATTC-CCT
* *
1267113 AATACTAATAAAAAAGAG-ATAACAATTTAAAACCCATA-TTTTGGGTCTATTTTCTATATATGT
130 AATACTAATAAAAAAGAGAATAACAATTTAAAACCCATATTTTTGGGTCCATTTTCCATATATGT
1267176 GGTA
195 GGTA
* * * * * *
1267180 ATGGTTAAGGTATGGTTTTTATTATTAAAGATCTCAATC-GAGTTT-GAATATGATATTTGCAAA
1 ATGGTTAACGTATAGTTGTTATTATTAAAGATCTCAATCGGA-TTTAG-ATATAATATCTACAAA
* * *
1267243 ATGTTTGAACATTTATTATCAAACAATTAAAAAAAAATCAAATAGATATTATCATTGTAATTCCC
64 ATGTTTGAACATTTATTATCAAACAATTAAAAAAAAATCAAATAAATATTACCACTGTAATTCCC
** *
1267308 TCGTACTAATAAAAAAGAGATATAACAATTTAAAACCTATATTTTTGGGTCCATTTTCCATAT
129 TAATACTAATAAAAAAGAGA-ATAACAATTTAAAACCCATATTTTTGGGTCCATTTTCCATAT
1267371 GAAATAATTC
Statistics
Matches: 158, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
195 3 0.02
196 115 0.73
197 2 0.01
198 19 0.12
199 19 0.12
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (198 bp):
ATGGTTAACGTATAGTTGTTATTATTAAAGATCTCAATCGGATTTAGATATAATATCTACAAAAT
GTTTGAACATTTATTATCAAACAATTAAAAAAAAATCAAATAAATATTACCACTGTAATTCCCTA
ATACTAATAAAAAAGAGAATAACAATTTAAAACCCATATTTTTGGGTCCATTTTCCATATATGTG
GTA
Found at i:1267753 original size:29 final size:30
Alignment explanation
Indices: 1267718--1267777 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1267708 TCATACAATT
1267718 TCTAAATAAGACAAC-CAAAATAAATTTTC
1 TCTAAATAAGACAACTCAAAATAAATTTTC
** * *
1267747 TCTAAATTTGACACCTCAATATAAATTTTC
1 TCTAAATAAGACAACTCAAAATAAATTTTC
1267777 T
1 T
1267778 AGCTCCGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.35
Consensus pattern (30 bp):
TCTAAATAAGACAACTCAAAATAAATTTTC
Found at i:1268022 original size:14 final size:14
Alignment explanation
Indices: 1268005--1268033 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1267995 TATAATTTAA
1268005 TTAAAATTTAATAT
1 TTAAAATTTAATAT
1268019 TTAAAATTTAATAT
1 TTAAAATTTAATAT
1268033 T
1 T
1268034 ATATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAAATTTAATAT
Found at i:1269721 original size:22 final size:22
Alignment explanation
Indices: 1269695--1269753 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1269685 AATTGATATC
1269695 AAATTATTA-TAAAATAATTATT
1 AAATTATTATTAAAAT-ATTATT
*
1269717 GAATT-TTATTAAAATATTATT
1 AAATTATTATTAAAATATTATT
*
1269738 AAATAATTATTAAAAT
1 AAATTATTATTAAAAT
1269754 TTTTATCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTATTATTAAAATATTATT
Found at i:1269794 original size:18 final size:18
Alignment explanation
Indices: 1269771--1269809 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1269761 AAGTGATTAT
1269771 CTTTAATATACTCTCCAA
1 CTTTAATATACTCTCCAA
1269789 CTTTAATATACTCTCCAA
1 CTTTAATATACTCTCCAA
1269807 CTT
1 CTT
1269810 ATTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (18 bp):
CTTTAATATACTCTCCAA
Found at i:1270643 original size:25 final size:25
Alignment explanation
Indices: 1270608--1270668 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
1270598 TGTAAAAAAT
1270608 AAAAATAA-TTTATAAATTATT-TTA
1 AAAAATAATTTTAT-AATTATTATTA
1270632 AAAAATAGATTTTATAATTATTATTA
1 AAAAATA-ATTTTATAATTATTATTA
*
1270658 ATAAATTAATT
1 A-AAAATAATT
1270669 AATTAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.22
25 8 0.25
26 12 0.38
27 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AAAAATAATTTTATAATTATTATTA
Found at i:1270658 original size:26 final size:24
Alignment explanation
Indices: 1270608--1270668 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 24
1270598 TGTAAAAAAT
1270608 AAAAATAATTTATAAATTATTTTA
1 AAAAATAATTTATAAATTATTTTA
1270632 AAAAATAGATTT-TATAATTATTATTA
1 AAAAATA-ATTTATA-AATTATT-TTA
*
1270658 ATAAATTAATT
1 A-AAAATAATT
1270669 AATTAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 9 0.28
25 11 0.34
26 7 0.22
27 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AAAAATAATTTATAAATTATTTTA
Found at i:1270924 original size:17 final size:17
Alignment explanation
Indices: 1270902--1270943 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1270892 TCAATAAATT
*
1270902 AAATATTAATAATTTA-A
1 AAATATT-ATAATCTACA
1270919 AAATATT-TAATCTACA
1 AAATATTATAATCTACA
1270935 AAATATTAT
1 AAATATTAT
1270944 TCTTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 8 0.36
17 8 0.36
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTATAATCTACA
Found at i:1271293 original size:2 final size:2
Alignment explanation
Indices: 1271286--1271313 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1271276 AAAATTAAGA
1271286 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
1271314 TTGTGATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1272043 original size:2 final size:2
Alignment explanation
Indices: 1272004--1272028 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1271994 ATAAAACTTT
1272004 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1272029 CTAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1273500 original size:22 final size:22
Alignment explanation
Indices: 1273475--1273530 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1273465 TATTGAATTA
1273475 TTTATTCCTAAAATATAT-AAGT
1 TTTA-TCCTAAAATATATAAAGT
* *
1273497 TTTACCCTAATATATATAAAGT
1 TTTATCCTAAAATATATAAAGT
*
1273519 TCTATCCTAAAA
1 TTTATCCTAAAA
1273531 GCCAATGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTATCCTAAAATATATAAAGT
Found at i:1278647 original size:26 final size:26
Alignment explanation
Indices: 1278596--1278648 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1278586 TTGTATAAAA
*
1278596 AAATTAAATATAATTTGTTATAAATT
1 AAATTAAATATAATTTGATATAAATT
*
1278622 AAATTAAATTATAATTT-ATATTAATT
1 AAATTAAA-TATAATTTGATATAAATT
1278648 A
1 A
1278649 GTAAATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AAATTAAATATAATTTGATATAAATT
Found at i:1279516 original size:30 final size:30
Alignment explanation
Indices: 1279480--1279541 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
1279470 GAAGTTCAAA
* *
1279480 GATTAAAATAATATTCTATCCACAATTTAG
1 GATTAAAATAATATTATATCCAAAATTTAG
* *
1279510 GATTAAATTAATATTATATCTAAAATTTAG
1 GATTAAAATAATATTATATCCAAAATTTAG
1279540 GA
1 GA
1279542 CCACTTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (30 bp):
GATTAAAATAATATTATATCCAAAATTTAG
Found at i:1280569 original size:13 final size:12
Alignment explanation
Indices: 1280539--1280573 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
1280529 TATTGTATAA
1280539 TTTAAAA-TATT
1 TTTAAAAGTATT
1280550 TTTAAAAGTATT
1 TTTAAAAGTATT
1280562 TTTGAAAAGTAT
1 TTT-AAAAGTAT
1280574 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 7 0.32
13 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (12 bp):
TTTAAAAGTATT
Found at i:1285727 original size:23 final size:22
Alignment explanation
Indices: 1285682--1285745 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
1285672 AATATGAAAA
* * *
1285682 AGAATAAAAAAAT-ATTAATGT
1 AGAATAATAAAATAAATAAAGT
1285703 AGTAATAATAAAATAAATAAAGT
1 AG-AATAATAAAATAAATAAAGT
1285726 AG-ATAAATAAAGATAAATAA
1 AGAAT-AATAAA-ATAAATAA
1285746 GATTGAGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 4 0.11
22 16 0.44
23 16 0.44
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (22 bp):
AGAATAATAAAATAAATAAAGT
Found at i:1285775 original size:13 final size:13
Alignment explanation
Indices: 1285757--1285803 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
1285747 ATTGAGTAAA
1285757 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
1285770 AAAAT-AACAAAT
1 AAAATAAAAAAAT
**
1285782 AAAATAACGAAAT
1 AAAATAAAAAAAT
1285795 AAAATAAAA
1 AAAATAAAA
1285804 CAAGCAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:1285783 original size:12 final size:13
Alignment explanation
Indices: 1285766--1285801 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
1285756 AAAAATAAAA
1285766 AAATAAAATAAC-
1 AAATAAAATAACG
1285778 AAATAAAATAACG
1 AAATAAAATAACG
1285791 AAATAAAATAA
1 AAATAAAATAA
1285802 AACAAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (13 bp):
AAATAAAATAACG
Found at i:1286734 original size:3 final size:3
Alignment explanation
Indices: 1286726--1286763 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1286716 TGGGGTGCAA
1286726 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1286764 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1287377 original size:124 final size:124
Alignment explanation
Indices: 1287181--1287847 Score: 907
Period size: 124 Copynumber: 5.4 Consensus size: 124
1287171 ATTTGAGTTA
* * * * *
1287181 GATATCATTCATCGTAAAGTTGAAATCCAATCTAGAGATGGATGTTGCTTGTGGACACGATAT-C
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTA-AGATGAATGTTGCTGGTGGGCACGAT-TCC
* * * * *
1287245 TTTCGTCGTGAAGTTGAAATCGTTGA-GAGCCCCTTCTTTGTGAAGTTGAGCCTTAAATTG
64 CTTCGTCGTGAAGTTGAAACCGTGGATGAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
* * *
1287305 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGGTATGATTCCC
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCT-AAGATGAATGTTGCTGGTGGGCACGATTCCC
* * *
1287370 TTTGTCGTGAAGTTGAAACTGTGGATGA-CCCATTCGTTGTGAAGTTGAGCCTTGAATTG
65 TTCGTCGTGAAGTTGAAACCGTGGATGAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
* * * *
1287429 GATATCCTTCGTCGTGAAGTTGATATCCAATCTAA-ATTAATGTTGTTGGTGGGCACGATTCCCT
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTAAGATGAATGTTGCTGGTGGGCACGATTCCCT
* * * *
1287493 TCGTCGTAAAGTTGAAACCGTGGAT-AACCCTTTCGTTGTGAAGTTGAGCCTTGAATTT
66 TCGTCGTGAAGTTGAAACCGTGGATGAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
* * *
1287551 GATATCATTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCC
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCT-AAGATGAATGTTGCTGGTGGGCACGATTCCC
*
1287616 TTCGTCGTGAAGTTGAAACCGTCGATG-GCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
65 TTCGTCGTGAAGTTGAAACCGTGGATGAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
* * * *
1287675 GATATCATTCGTCGTGAAGTTGAAATTCAATCTAAATATGAATGTTACTGGTGAGCACGATTCCC
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCT-AAGATGAATGTTGCTGGTGGGCACGATTCCC
* *
1287740 TTCGTCATGACGTTGAAACCGTGGATG-GCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
65 TTCGTCGTGAAGTTGAAACCGTGGATGAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
* *
1287799 GATATCCTTCGTCGTGAAGTTGAAATCCAATATAATGATGAATGTTGCT
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTAA-GATGAATGTTGCT
1287848 TCGAGTCCAA
Statistics
Matches: 486, Mismatches: 49, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
121 1 0.00
122 106 0.22
123 7 0.01
124 369 0.76
125 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (124 bp):
GATATCATTCGTCGTGAAGTTGAAATCCAATCTAAGATGAATGTTGCTGGTGGGCACGATTCCCT
TCGTCGTGAAGTTGAAACCGTGGATGAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
Found at i:1287680 original size:246 final size:246
Alignment explanation
Indices: 1287181--1287844 Score: 918
Period size: 246 Copynumber: 2.7 Consensus size: 246
1287171 ATTTGAGTTA
* * ** *
1287181 GATATCATTCATCGTAAAGTTGAAATCCAATCTAGAGATGGATGTTGCTT-GTGGACACGATAT-
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTA-A-ATTAATGTTG-TTGGTGGGCACGAT-TC
* * * * * *
1287244 CTTTCGTCGTGAAGTTGAAATCGTTGAGAGCCCCTTCTTTGTGAAGTTGAGCCTTAAATTGGATA
62 CCTTCGTCGTGAAGTTGAAACCGTGGATAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * * * * *
1287309 TCCTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGGTATGATTCCCTTTG
127 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCG
* *
1287374 TCGTGAAGTTGAAACTGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
192 TCGTGAAGTTGAAACCGTCGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
* *
1287429 GATATCCTTCGTCGTGAAGTTGATATCCAATCTAAATTAATGTTGTTGGTGGGCACGATTCCCTT
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTAAATTAATGTTGTTGGTGGGCACGATTCCCTT
* * * * *
1287494 CGTCGTAAAGTTGAAACCGTGGATAACCCTTTCGTTGTGAAGTTGAGCCTTGAATTTGATATCAT
66 CGTCGTGAAGTTGAAACCGTGGATAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCT
*
1287559 TCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCGTCGT
131 TCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCGTCGT
* *
1287624 GAAGTTGAAACCGTCGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
196 GAAGTTGAAACCGTCGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
* ** *
1287675 GATATCATTCGTCGTGAAGTTGAAATTCAATCTAAATATGAATGTTACTGGTGAGCACGATTCCC
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAT-T-AATGTTGTTGGTGGGCACGATTCCC
* * *
1287740 TTCGTCATGACGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATC
64 TTCGTCGTGAAGTTGAAACCGTGGATAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATC
* *
1287805 CTTCGTCGTGAAGTTGAAATCCAATATAATGATGAATGTT
129 CTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTT
1287845 GCTTCGAGTC
Statistics
Matches: 366, Mismatches: 46, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
245 3 0.01
246 215 0.59
247 2 0.01
248 146 0.40
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (246 bp):
GATATCATTCGTCGTGAAGTTGAAATCCAATCTAAATTAATGTTGTTGGTGGGCACGATTCCCTT
CGTCGTGAAGTTGAAACCGTGGATAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCT
TCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTCCCTTCGTCGT
GAAGTTGAAACCGTCGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
Found at i:1288051 original size:110 final size:110
Alignment explanation
Indices: 1287905--1288315 Score: 349
Period size: 110 Copynumber: 3.6 Consensus size: 110
1287895 AACTGGGAAA
* * * * *
1287905 CCCCTTCGCCGTGAAATTGAGCTTTGAATTGGATATCCTTTGTCATGAAGTTGAAATCCAATCTA
1 CCCCTTCGCCGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
*
1287970 GAGTTGGCACGATATCCTTTGTCGTGAAGTTGAAATTGTGGATGG
66 GAGTTGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGG
** * *
1288015 CCCCTTCGTTGTGAATTTGAGCCTT-AACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT
1 CCCCTTCGCCGTGAAGTTGAGCCTTGAA-TTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCT
* * *
1288079 TGTATTGTTTCGAGTC-CAATATCCTTCGACGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGA
65 AG-A--G-TT-G-G-CACGATATCCTTCGTCGTGAAGTTGAAATT-G---TG---G--A-T--G-
1288143 AG
110 -G
* * ** *
1288145 CCCCTTCGCCGTGAAGTTGAGCTTTGAATTGGATATAATTCATCGTGAAGTTGAAATCCAATCTA
1 CCCCTTCGCCGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
* * * *
1288210 GAGTTGGCACGATATCATTCATCGTGAAGTTGAAATCGTGGATAG
66 GAGTTGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGG
* * ** * * *
1288255 TCCATTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCTTTGTCCTGAAGTTGAAATCCAA
1 CCCCTTCGCCGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
1288316 GTATTTTATG
Statistics
Matches: 237, Mismatches: 40, Indels: 48
0.73 0.12 0.15
Matches are distributed among these distances:
109 2 0.01
110 104 0.44
111 1 0.00
113 1 0.00
114 3 0.01
115 2 0.01
116 26 0.11
117 3 0.01
120 4 0.02
123 3 0.01
124 24 0.10
125 2 0.01
126 3 0.01
127 1 0.00
128 1 0.00
129 1 0.00
130 54 0.23
131 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (110 bp):
CCCCTTCGCCGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
GAGTTGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGG
Found at i:1288167 original size:240 final size:244
Alignment explanation
Indices: 1287729--1288364 Score: 854
Period size: 240 Copynumber: 2.6 Consensus size: 244
1287719 TTACTGGTGA
* * *
1287729 GCACGAT-TCCCTTCGTCATGACGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTT
1 GCACGATAT-CCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTT
* *
1287793 GAA-TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAATGATGAATGTTGCTTCGAGTCCA
65 -AACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGAT-ATGAT-AA-GTTGCTTCGAGTCCA
* *
1287857 ATATCCTTTGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAACCCCTTCGCCGTGAAAT
126 ATATCCTTCGACGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAACCCCTTCGCCGTGAAAT
** **
1287922 TGAGCTTTGAATTGGATATCCTTTGTCATGAAGTTGAAATCCAATCTAGAGTTG
191 TGAGCTTTGAATTGGATATAATTCATCATGAAGTTGAAATCCAATCTAGAGTTG
* * *
1287976 GCACGATATCCTTTGTCGTGAAGTTGAAATTGTGGATGGCCCCTTCGTTGTGAATTTGAGCCTTA
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTA
* *
1288041 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT-TG-T-A-TTGTTTCGAGTCCAATATC
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGATATGATAAGTTGCTTCGAGTCCAATATC
* *
1288102 CTTCGACGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCCGTGAAGTTGAGC
131 CTTCGACGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAACCCCTTCGCCGTGAAATTGAGC
*
1288167 TTTGAATTGGATATAATTCATCGTGAAGTTGAAATCCAATCTAGAGTTG
196 TTTGAATTGGATATAATTCATCATGAAGTTGAAATCCAATCTAGAGTTG
* * * * * *
1288216 GCACGATATCATTCATCGTGAAGTTGAAATCGTGGATAGTCCATTCGTTGTGAAGTTGAGCCTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTA
* * ** * * ***
1288281 ACTTGAATATCCTTTGTCCTGAAGTTGAAATCCAAG-TATTTTATGTTGCTTTGAGTTGGATATC
66 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGATATGATAAGTTGCTTCGAGTCCAATATC
**
1288345 CTTCGTTGTGAAGTTGAAAT
131 CTTCGACGTGAAGTTGAAAT
1288365 CTAATATCGA
Statistics
Matches: 344, Mismatches: 39, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
239 1 0.00
240 214 0.62
241 1 0.00
242 1 0.00
243 32 0.09
244 1 0.00
245 2 0.01
246 2 0.01
247 89 0.26
248 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (244 bp):
GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTA
ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGATATGATAAGTTGCTTCGAGTCCAATATC
CTTCGACGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAACCCCTTCGCCGTGAAATTGAGC
TTTGAATTGGATATAATTCATCATGAAGTTGAAATCCAATCTAGAGTTG
Found at i:1289545 original size:94 final size:94
Alignment explanation
Indices: 1289354--1289552 Score: 283
Period size: 95 Copynumber: 2.1 Consensus size: 94
1289344 CATTGTATAG
* * * *
1289354 ATATTATAATCACCTTTACAGGCTAGTTGAATATTATCCATAAAGCCGGGGTGTTTAACTAATTG
1 ATATTATAATCACCTTTACAGGCTAGCTGAATATTATCCATAAAGACGGGGCGTTTAACCAATTG
* *
1289419 CTCTAGAGGGACAACTCAAACTTTATTGT
66 CTCTAGAGGGACAAATCAAACTTTATTAT
*
1289448 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGACGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTA-CAGGCTAGCTGAATATTATCCATAAAGACGGGGCGTTTAACCAATT
* * *
1289513 GCTTTATA-GGACAAATCAAGCTTTATTAT
65 GCTCTAGAGGGACAAATCAAACTTTATTAT
1289542 ATATATATAAT
1 ATAT-TATAAT
1289553 ATTATAATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 40 0.43
95 53 0.57
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (94 bp):
ATATTATAATCACCTTTACAGGCTAGCTGAATATTATCCATAAAGACGGGGCGTTTAACCAATTG
CTCTAGAGGGACAAATCAAACTTTATTAT
Found at i:1291657 original size:39 final size:39
Alignment explanation
Indices: 1291603--1291682 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
1291593 CAATGACTAT
1291603 ATGAATCGTCGAAACCAAAGACATTCGATGGAGATCGCC
1 ATGAATCGTCGAAACCAAAGACATTCGATGGAGATCGCC
*
1291642 ATGAATCGTCGAAACCGAAGACATTCGATGGAGATCGCC
1 ATGAATCGTCGAAACCAAAGACATTCGATGGAGATCGCC
1291681 AT
1 AT
1291683 CGACATGTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (39 bp):
ATGAATCGTCGAAACCAAAGACATTCGATGGAGATCGCC
Found at i:1293942 original size:31 final size:31
Alignment explanation
Indices: 1293894--1294046 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
1293884 CCCGAAGGAC
* *
1293894 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1293925 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1293956 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1293987 CAGTCCATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1294017 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1294047 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
30 30 0.26
31 85 0.73
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1294028 original size:61 final size:62
Alignment explanation
Indices: 1293894--1294046 Score: 256
Period size: 61 Copynumber: 2.5 Consensus size: 62
1293884 CCCGAAGGAC
* *
1293894 CAGTCCATA-GATTCCGAAGAACCTAGGTAAACAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAATCCATATGTCCCGAAGAACATAGGTAAA
*
1293956 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCGAAGAACATAGGTAAA
1294017 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1294047 CCCTCGACCC
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
61 48 0.55
62 38 0.44
63 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (62 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1294751 original size:21 final size:21
Alignment explanation
Indices: 1294721--1294765 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1294711 ATTCTGTCGT
* *
1294721 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1294742 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1294763 TTG
1 TTG
1294766 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1298597 original size:31 final size:31
Alignment explanation
Indices: 1298559--1298712 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
1298549 CCCGAAGGAC
* *
1298559 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1298590 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1298621 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1298652 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1298683 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1298713 CCCTCGACCC
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1299415 original size:21 final size:21
Alignment explanation
Indices: 1299385--1299429 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1299375 ATTCTGTCGT
* *
1299385 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1299406 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1299427 TTG
1 TTG
1299430 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1300349 original size:20 final size:19
Alignment explanation
Indices: 1300319--1300359 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1300309 TTTTATCACA
*
1300319 CTAAATTCTCTCAAATTCT
1 CTAAATTCTCTCAAATACT
1300338 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTCTCAAATACT
1300358 CT
1 CT
1300360 CTTTTTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (19 bp):
CTAAATTCTCTCAAATACT
Found at i:1300361 original size:12 final size:10
Alignment explanation
Indices: 1300321--1300360 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1300311 TTATCACACT
1300321 AAATTCTCTC
1 AAATTCTCTC
1300331 AAATTCTCT-
1 AAATTCTCTC
1300340 AAATTTCTCTC
1 AAA-TTCTCTC
*
1300351 AAATACTCTC
1 AAATTCTCTC
1300361 TTTTTAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:1300624 original size:114 final size:111
Alignment explanation
Indices: 1300486--1300708 Score: 320
Period size: 114 Copynumber: 2.0 Consensus size: 111
1300476 GAAATCATAT
*
1300486 ATCTCTACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAATAGTAATA
1 ATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAATAGTAATA
* * * * *
1300551 TTTAGTAGTTATTTATTTAATGAATGATTATTTATATTAATAATTAAAC
66 ATTAGT--TGATTCATTTAATGAATGATTA-TTAGATTAAGAATTAAAC
* * * *
1300600 ATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTATTAATA
1 ATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAATAGTAATA
*
1300665 ATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 ATTAGTTGATTCATTTAATGAATGATTATTAGATTAAGAATTAA
1300709 TTTTTGTAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
111 14 0.14
112 19 0.19
114 65 0.66
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (111 bp):
ATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTAATAGTAATA
ATTAGTTGATTCATTTAATGAATGATTATTAGATTAAGAATTAAAC
Found at i:1306119 original size:16 final size:16
Alignment explanation
Indices: 1306100--1306130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1306090 ATTTTTTTCA
*
1306100 AATAATTATAATAAAC
1 AATAAATATAATAAAC
1306116 AATAAATATAATAAA
1 AATAAATATAATAAA
1306131 AAATTATAAC
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAATATAATAAAC
Found at i:1306138 original size:13 final size:14
Alignment explanation
Indices: 1306099--1306145 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
1306089 TATTTTTTTC
1306099 AAATAATTATAATAA
1 AAATAATTATAAT-A
*
1306114 ACAATAAATATAATA
1 A-AATAATTATAATA
*
1306129 AAA-AATTATAACA
1 AAATAATTATAATA
1306142 AAAT
1 AAAT
1306146 TACCTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 11 0.41
14 2 0.07
15 3 0.11
16 11 0.41
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATTATAATA
Found at i:1306419 original size:47 final size:49
Alignment explanation
Indices: 1306312--1306433 Score: 160
Period size: 47 Copynumber: 2.5 Consensus size: 49
1306302 TTATACAAAA
*
1306312 CGCGGTACTTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTC--GAGTAAAGGTATGT
*
1306363 CGCGATACCTGCCCCGCGCTATATAAAATTATG-C-AGTAAAGGTATAG-
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCGAGTAAAGGTAT-GT
**
1306410 CGCGGTACCTGATCCGCGCTATAT
1 CGCGGTACCTGCCCCGCGCTATAT
1306434 CCCTACGTGG
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
47 32 0.49
48 1 0.02
50 1 0.02
51 31 0.48
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (49 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCGAGTAAAGGTATGT
Found at i:1306568 original size:51 final size:50
Alignment explanation
Indices: 1306444--1306568 Score: 133
Period size: 51 Copynumber: 2.5 Consensus size: 50
1306434 CCCTACGTGG
* * * **
1306444 CGTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCACTATACCCACGTGGCGCCAAATCAC
* * * * *
1306494 CGTATAGCGCTGTGCAAGAGGCGCACTATACCCCACGTTGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCACTATA-CCCACGTGGCGCCAAATCAC
* *
1306545 CGTATAGTGCGGTACAGGGGGCGC
1 CGTATAGCGCGGTGCAGGGGGCGC
1306569 GCTTTACTGT
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
50 24 0.41
51 35 0.59
ACGTcount: A:0.20, C:0.32, G:0.31, T:0.17
Consensus pattern (50 bp):
CGTATAGCGCGGTGCAGGGGGCGCACTATACCCACGTGGCGCCAAATCAC
Found at i:1306965 original size:7 final size:7
Alignment explanation
Indices: 1306953--1306991 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
1306943 TAGTGGGTGC
1306953 AAAAATA
1 AAAAATA
1306960 AAAAATA
1 AAAAATA
1306967 AAAAATA
1 AAAAATA
1306974 ATAATAATA
1 A-AA-AATA
*
1306983 ATAAATA
1 AAAAATA
1306990 AA
1 AA
1306992 TATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 20 0.71
8 3 0.11
9 5 0.18
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAAATA
Found at i:1315646 original size:2 final size:2
Alignment explanation
Indices: 1315639--1315667 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1315629 TGAGAGTCTT
1315639 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
1315668 TTGTATAACA
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:1317930 original size:2 final size:2
Alignment explanation
Indices: 1317923--1317951 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1317913 TAAAAATAAC
1317923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1317952 AATTGCAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1319101 original size:21 final size:21
Alignment explanation
Indices: 1319068--1319111 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1319058 TGGTACTGAT
*
1319068 GTGACAGGTCACAGTACTAAC
1 GTGACAGGTCACACTACTAAC
*
1319089 GTGACA-GTCCACACTATTAAC
1 GTGACAGGT-CACACTACTAAC
1319110 GT
1 GT
1319112 AATAATTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
GTGACAGGTCACACTACTAAC
Found at i:1319325 original size:20 final size:19
Alignment explanation
Indices: 1319300--1319338 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1319290 TATTATAATT
* *
1319300 TAAAATTTTAGAAATGTTTA
1 TAAAATATTAAAAAT-TTTA
1319320 TAAAATATTAAAAATTTTA
1 TAAAATATTAAAAATTTTA
1319339 AACACTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TAAAATATTAAAAATTTTA
Found at i:1320272 original size:38 final size:37
Alignment explanation
Indices: 1320182--1320285 Score: 199
Period size: 37 Copynumber: 2.8 Consensus size: 37
1320172 TTTTGTTCGG
1320182 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1320219 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1320256 GTCGGGTCGGGTTTTTTTAAGTGTGATATT
1 GTCGGGTCGGG-TTTTTTAAGTGTGATATT
1320286 TGGGCCGTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
37 48 0.73
38 18 0.27
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1320505 original size:291 final size:292
Alignment explanation
Indices: 1320003--1320560 Score: 960
Period size: 291 Copynumber: 1.9 Consensus size: 292
1319993 TTCAGTTCGG
* * * * *
1320003 GTTCGGGTTTAGAGTGATAAAAATCGTACCGACCCGAAAATATATATAATTCAGGTCAGGTCGGA
1 GTTCGGGTTTAGAGTGAAAAAAACCGGACCAACCCAAAAATATATATAATTCAGGTCAGGTCGGA
* *
1320068 TTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGATCGGGTCGGGTTGGATT
66 TTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGATCGGGTCAGGTCGGATT
*
1320133 TCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTT
131 TCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGAGTCGGGTTTTT
*
1320198 TAAGTGTGATATTCGGGTCGAGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC-GAGTCGG
196 TAAGTGTGACATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAG-GTCGG
1320261 GTCGGGTTTTTTTAAGTGTGATATTTGGGCCGT
260 GTCGGGTTTTTTTAAGTGTGATATTTGGGCCGT
* * *
1320294 GTTCGGGTTTAGGGTGAAAAAAACCGGACCAACCCAAAAATATATATAATTCGGGTCGGGTCGGA
1 GTTCGGGTTTAGAGTGAAAAAAACCGGACCAACCCAAAAATATATATAATTCAGGTCAGGTCGGA
1320359 TTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGG-TCGGGTCAGGTCGGAT
66 TTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTC-GGATCGGGTCAGGTCGGAT
1320423 TTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGAGTCGGGTTTT
130 TTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGAGTCGGGTTTT
*
1320488 TTAAGTGTGACATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTTGG
195 TTAAGTGTGACATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGG
1320553 GTCGGGTT
260 GTCGGGTT
1320561 CGGGTTTAGG
Statistics
Matches: 251, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
291 212 0.84
292 38 0.15
293 1 0.00
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (292 bp):
GTTCGGGTTTAGAGTGAAAAAAACCGGACCAACCCAAAAATATATATAATTCAGGTCAGGTCGGA
TTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGATCGGGTCAGGTCGGATT
TCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGAGTCGGGTTTTT
TAAGTGTGACATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGG
TCGGGTTTTTTTAAGTGTGATATTTGGGCCGT
Found at i:1320533 original size:38 final size:38
Alignment explanation
Indices: 1320472--1320560 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
1320462 ATTTTGTTCG
*
1320472 GGTCGAGTCGGG-TTTTTTAAGTGTGACATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTTAAGTGTGACATTCGGGTCA
*
1320508 GAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCGGGTCGGGTTTTTTTAAGTGTGACATTCGGGTCA
*
1320547 GGTTGGGTCGGGTT
1 GGTCGGGTCGGGTT
1320561 CGGGTTTAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
36 1 0.02
37 10 0.21
38 35 0.74
39 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.37
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGACATTCGGGTCA
Found at i:1321152 original size:16 final size:18
Alignment explanation
Indices: 1321131--1321176 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1321121 TATGGAATTG
1321131 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
1321147 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1321165 GATTCCAATTCC
1 GATTCCAATTCC
1321177 CTCATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 15 0.54
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1321541 original size:3 final size:3
Alignment explanation
Indices: 1321533--1321964 Score: 486
Period size: 3 Copynumber: 143.7 Consensus size: 3
1321523 AACAAAACCT
1321533 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
1321581 AAG AAG AAG -AG AAAG AAG AAG AAG AGG AAG AAG AAG AAG AGG AAG
1 AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
1321626 AAG AAG AAG AGG AAG AAG AAG AAG AGG AAG AAG AAG AAG AGG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
1321674 AAG AAG AGG AAG AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *** * * * * * * *
1321722 AAG AATC CTC CAT AATTT CAG -AT AAC AA- AACCT AAG AAG AAG AAG
1 AAG AA-G AAG AAG AA--G AAG AAG AAG AAG AA--G AAG AAG AAG AAG
1321767 AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * *
1321813 AAG AAG AAG AAG AAAG AAG AAG AAG AAG -AG AGAG GAG GAG GAG GAG
1 AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG
* * *
1321859 GAG AGG AGG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1321906 AAG AAG AAG AAG AAG AAAG AA- AAG AAG AAG AA- AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1321950 AAG AAG AAAG AAG AA
1 AAG AAG -AAG AAG AA
1321965 AATTTTGCAA
Statistics
Matches: 381, Mismatches: 29, Indels: 38
0.85 0.06 0.08
Matches are distributed among these distances:
2 17 0.04
3 347 0.91
4 13 0.03
5 4 0.01
ACGTcount: A:0.63, C:0.02, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1322584 original size:2 final size:2
Alignment explanation
Indices: 1322577--1322699 Score: 178
Period size: 2 Copynumber: 61.5 Consensus size: 2
1322567 ATACCTCCTA
* *
1322577 AT AT AT AT AT AT AT AT AT CT CCT A- 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
1322619 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
* *
1322661 AT AT AT AT AT AT AT AT AT CT CCT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT A
1322700 AAAGGATAAG
Statistics
Matches: 113, Mismatches: 4, Indels: 8
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.02
2 107 0.95
3 4 0.04
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1324088 original size:24 final size:24
Alignment explanation
Indices: 1324067--1324113 Score: 51
Period size: 24 Copynumber: 2.0 Consensus size: 24
1324057 GTTTAAAATA
**
1324067 TAAAAATATTAATATTCAAAAA-AT
1 TAAAAATAACAATATT-AAAAATAT
*
1324091 TAAATATAACAATATTAAAAATA
1 TAAAAATAACAATATTAAAAATA
1324114 AATATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAAAATAACAATATTAAAAATAT
Found at i:1324107 original size:15 final size:14
Alignment explanation
Indices: 1324062--1324142 Score: 60
Period size: 15 Copynumber: 5.5 Consensus size: 14
1324052 TTTGAGTTTA
1324062 AAATATAAAAATATT
1 AAATAT-AAAATATT
*
1324077 -AATATTCAAAAAATT
1 AAATA-T-AAAATATT
1324092 AAATATAACAATATT
1 AAATATAA-AATATT
*
1324107 AAAAAT-AAATATT
1 AAATATAAAATATT
1324120 AAATTACTAAAA-ATT
1 AAA-TA-TAAAATATT
1324135 AATATATA
1 AA-ATATA
1324143 TATATATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 9 0.17
14 10 0.19
15 27 0.50
16 8 0.15
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAAATATT
Found at i:1324115 original size:21 final size:20
Alignment explanation
Indices: 1324085--1324140 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
1324075 TTAATATTCA
*
1324085 AAAAATTAAATATAACAATATT
1 AAAAA-TAAATATAA-AATACT
*
1324107 AAAAATAAATATTAAATTACT
1 AAAAATAAATA-TAAAATACT
*
1324128 AAAAATTAATATA
1 AAAAATAAATATA
1324141 TATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 20 0.67
22 8 0.27
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATAAATATAAAATACT
Found at i:1324853 original size:24 final size:23
Alignment explanation
Indices: 1324826--1324878 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1324816 ATTAAATAAT
1324826 TATTTATATATTTTATAAAATCAA
1 TATTTATATATTTTA-AAAATCAA
* * *
1324850 TATTAATTTATTTTAAAAATTAA
1 TATTTATATATTTTAAAAATCAA
1324873 -ATTTAT
1 TATTTAT
1324879 GAGATTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 5 0.20
23 7 0.28
24 13 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTTATATATTTTAAAAATCAA
Found at i:1324874 original size:28 final size:27
Alignment explanation
Indices: 1324843--1324924 Score: 69
Period size: 28 Copynumber: 3.0 Consensus size: 27
1324833 ATATTTTATA
1324843 AAATCAATATTAATTTATTTTAAAAATT
1 AAAT-AATATTAATTTATTTTAAAAATT
* * *
1324871 AAAT-TTATGAGATTTATTTATAAAAGAAT
1 AAATAATATTA-ATTTATTT-TAAAA-ATT
* *
1324900 AAAAAATA-TAAATTATTTTAAAAAT
1 AAATAATATTAATTTATTTTAAAAAT
1324925 AAAAAATCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
26 5 0.12
27 13 0.31
28 16 0.38
29 6 0.14
30 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (27 bp):
AAATAATATTAATTTATTTTAAAAATT
Found at i:1324983 original size:8 final size:8
Alignment explanation
Indices: 1324970--1325029 Score: 54
Period size: 8 Copynumber: 7.4 Consensus size: 8
1324960 AAATTATATG
1324970 TATTTAAT
1 TATTTAAT
1324978 TATTTAAT
1 TATTTAAT
1324986 TATTTAA-
1 TATTTAAT
*
1324993 AATTTAA-
1 TATTTAAT
1325000 -ATTTAAGTT
1 TATTTAA--T
1325009 TATTTATATT
1 TATTTA-A-T
1325019 TATTTAAT
1 TATTTAAT
1325027 TAT
1 TAT
1325030 AAATTTATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
6 6 0.13
7 6 0.13
8 19 0.41
9 1 0.02
10 13 0.28
11 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
TATTTAAT
Found at i:1325044 original size:32 final size:30
Alignment explanation
Indices: 1324974--1325045 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 30
1324964 TATATGTATT
1324974 TAATTATTTAATTATTTAAAATTTAAATTTA
1 TAATTATTTAATTATTT-AAATTTAAATTTA
*
1325005 -AGTTTATTTATATTTATTT-AATTATAAATTTA
1 TA-ATTATTTA-A-TTATTTAAATT-TAAATTTA
1325037 TAATTATTT
1 TAATTATTT
1325046 GTGAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 1 0.03
31 11 0.32
32 15 0.44
33 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TAATTATTTAATTATTTAAATTTAAATTTA
Found at i:1327855 original size:7 final size:7
Alignment explanation
Indices: 1327843--1327873 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1327833 GGTCAAGAAA
1327843 GTCAACG
1 GTCAACG
1327850 GTCAACG
1 GTCAACG
1327857 GTCAACG
1 GTCAACG
1327864 GTCAACG
1 GTCAACG
1327871 GTC
1 GTC
1327874 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1327918 original size:9 final size:9
Alignment explanation
Indices: 1327900--1327999 Score: 83
Period size: 9 Copynumber: 10.3 Consensus size: 9
1327890 ACGTCGGTCG
*
1327900 GGTCAGACC
1 GGTCAAACC
1327909 GGTCAAACC
1 GGTCAAACC
*
1327918 GGTTTCAGACC
1 GG--TCAAACC
1327929 GGTCAAACC
1 GGTCAAACC
*
1327938 GGTTCGAACC
1 GG-TCAAACC
*
1327948 GGTTGAAACC
1 GG-TCAAACC
1327958 GGTCAAACC
1 GGTCAAACC
1327967 GGTCAGAACC
1 GGTCA-AACC
*
1327977 GGTTGAAAACC
1 GG-T-CAAACC
*
1327988 GGTTAAACC
1 GGTCAAACC
1327997 GGT
1 GGT
1328000 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
9 37 0.49
10 23 0.30
11 15 0.20
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1327927 original size:20 final size:20
Alignment explanation
Indices: 1327902--1328002 Score: 93
Period size: 20 Copynumber: 5.1 Consensus size: 20
1327892 GTCGGTCGGG
1327902 TCAGACCGGTCAAACCGGTT
1 TCAGACCGGTCAAACCGGTT
1327922 TCAGACCGGTCAAACCGG-T
1 TCAGACCGGTCAAACCGGTT
*
1327941 TC-GAACCGGTTGAAACCGG--
1 TCAG-ACCGG-TCAAACCGGTT
*
1327960 TCAAACCGGTCAGAACCGGTT
1 TCAGACCGGTCA-AACCGGTT
** * *
1327981 GAAAACCGGTTAAACCGGTT
1 TCAGACCGGTCAAACCGGTT
1328001 TC
1 TC
1328003 CAGCAGCCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
18 3 0.04
19 21 0.31
20 34 0.51
21 9 0.13
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (20 bp):
TCAGACCGGTCAAACCGGTT
Found at i:1327933 original size:29 final size:29
Alignment explanation
Indices: 1327900--1327999 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
1327890 ACGTCGGTCG
* *
1327900 GGTCAGACCGGTCAAACCGGTTTCAGACC
1 GGTCAAACCGGTCAAACCGGTTTCAAACC
* *
1327929 GGTCAAACCGGTTCGAACCGG-TTGAAACC
1 GGTCAAACCGG-TCAAACCGGTTTCAAACC
**
1327958 GGTCAAACCGGTCAGAACCGGTTGAAAACC
1 GGTCAAACCGGTCA-AACCGGTTTCAAACC
*
1327988 GGTTAAACCGGT
1 GGTCAAACCGGT
1328000 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.03
29 33 0.55
30 25 0.42
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (29 bp):
GGTCAAACCGGTCAAACCGGTTTCAAACC
Found at i:1334863 original size:22 final size:21
Alignment explanation
Indices: 1334838--1334878 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
1334828 GAAAGTCAAC
1334838 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTC-GGTCGGGTCGG
1334860 GTCAACGGTCGGTCGGGTC
1 GTCAACGGTCGGTCGGGTC
1334879 AGACCGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.10, C:0.24, G:0.46, T:0.20
Consensus pattern (21 bp):
GTCAACGGTCGGTCGGGTCGG
Done.