Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 105 of 311
Found at i:34482246 original size:22 final size:24
Alignment explanation
Indices: 34482212--34482261 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
34482202 ATACTTATTA
*
34482212 TTTATATAAAATATAT-ATTTTCT
1 TTTATATAAAATAAATAATTTTCT
* *
34482235 TTTATAT-CAATAAATAATTTTTT
1 TTTATATAAAATAAATAATTTTCT
34482258 TTTA
1 TTTA
34482262 AGATCTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATATAAAATAAATAATTTTCT
Found at i:34486259 original size:20 final size:20
Alignment explanation
Indices: 34486234--34486280 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
34486224 GTTTTGATAT
34486234 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
34486254 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
34486274 ACATGAT
1 ACATGAT
34486281 GTATTCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:34486362 original size:25 final size:25
Alignment explanation
Indices: 34486328--34486410 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
34486318 AGGAAGTGCA
34486328 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
* *
34486353 AAAAGGGCTTTTGCCCCAATTTATC
1 AAAAGGGCTTTTGCCCCAGTTTATT
* *
34486378 AAAAAGGC-TTTACCCCAG-TTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
34486401 AAAAGAGGCT
1 AAAAG-GGCT
34486411 AGGCCTCCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
23 8 0.16
24 11 0.22
25 30 0.61
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (25 bp):
AAAAGGGCTTTTGCCCCAGTTTATT
Found at i:34486654 original size:31 final size:31
Alignment explanation
Indices: 34486619--34486682 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
34486609 CGTTTATAAT
* *
34486619 AAAGGCTTCGGCTCAGTAATATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
34486650 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
34486681 AA
1 AA
34486683 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:34494288 original size:20 final size:20
Alignment explanation
Indices: 34494262--34494328 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
34494252 GTTTTGATAT
34494262 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
* *
34494282 GCATGATATGTATGATATGT
1 ACATGATATGTATGATATGC
*
34494302 ACATGATATGTATGATATAC
1 ACATGATATGTATGATATGC
34494322 ACATGAT
1 ACATGAT
34494329 GTATTCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:34494296 original size:9 final size:9
Alignment explanation
Indices: 34494284--34494319 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
34494274 TGATATGCGC
34494284 ATGATATGT
1 ATGATATGT
34494293 ATGATATGT
1 ATGATATGT
34494302 ACATGATATGT
1 --ATGATATGT
34494313 ATGATAT
1 ATGATAT
34494320 ACACATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 16 0.64
11 9 0.36
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (9 bp):
ATGATATGT
Found at i:34494307 original size:11 final size:11
Alignment explanation
Indices: 34494261--34494313 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
34494251 GGTTTTGATA
34494261 TACATGAT-TG
1 TACATGATATG
*
34494271 -ATATGATATG
1 TACATGATATG
**
34494281 CGCATGATATG
1 TACATGATATG
34494292 T--ATGATATG
1 TACATGATATG
34494301 TACATGATATG
1 TACATGATATG
34494312 TA
1 TA
34494314 TGATATACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 15 0.43
10 2 0.06
11 18 0.51
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (11 bp):
TACATGATATG
Found at i:34494442 original size:24 final size:25
Alignment explanation
Indices: 34494376--34494458 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
34494366 AGGAAGTGCA
34494376 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
* *
34494401 GAAAGGGCTTTTGCCCCAGTTTATC
1 AAAAGGGCTTTTGCCCCAGTTTATT
34494426 AAAAGGGC-TTTGCCCCAG-TTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
34494449 AAAAGAGGCT
1 AAAAG-GGCT
34494459 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.17
24 13 0.25
25 30 0.58
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (25 bp):
AAAAGGGCTTTTGCCCCAGTTTATT
Found at i:34494469 original size:49 final size:50
Alignment explanation
Indices: 34494376--34494470 Score: 124
Period size: 49 Copynumber: 1.9 Consensus size: 50
34494366 AGGAAGTGCA
* **
34494376 AAAAGGGCTTTTGCCCCAGTTTATTGAAAGGGCTTTTGCCCCAGTTTATC
1 AAAAGGGCTTTTGCCCCAGTTTATTAAAAGGGCTTAGGCCCCAGTTTATC
34494426 AAAAGGGC-TTTGCCCCAG-TTATTAAAAGAGGC-TAGGCCTCCAGTT
1 AAAAGGGCTTTTGCCCCAGTTTATTAAAAG-GGCTTAGGCC-CCAGTT
34494471 ATATGATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
48 13 0.32
49 19 0.47
50 8 0.20
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.29
Consensus pattern (50 bp):
AAAAGGGCTTTTGCCCCAGTTTATTAAAAGGGCTTAGGCCCCAGTTTATC
Found at i:34494706 original size:31 final size:31
Alignment explanation
Indices: 34494666--34494729 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
34494656 CGTTTACAAT
*
34494666 AAAGGCTTCGGCCCAATAATATAAAATATGA
1 AAAGACTTCGGCCCAATAATATAAAATATGA
* ** *
34494697 AAAGACTTCGGCCCAGTGTTATGAAATATGA
1 AAAGACTTCGGCCCAATAATATAAAATATGA
34494728 AA
1 AA
34494730 TATGAAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (31 bp):
AAAGACTTCGGCCCAATAATATAAAATATGA
Found at i:34496125 original size:30 final size:30
Alignment explanation
Indices: 34496075--34496137 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
34496065 AAAACTTTTT
*
34496075 ATTTTCCCCCAAAATTTTTACTCCC-TCCC
1 ATTTTCCCCCAAAACTTTTACTCCCTTCCC
*
34496104 ATTTTCTCCCTAAAACTTTTACTCCCTTCCC
1 ATTTTC-CCCCAAAACTTTTACTCCCTTCCC
34496135 ATT
1 ATT
34496138 CCACCTCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 17 0.57
31 7 0.23
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (30 bp):
ATTTTCCCCCAAAACTTTTACTCCCTTCCC
Found at i:34496282 original size:20 final size:18
Alignment explanation
Indices: 34496221--34496283 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
34496211 TATTTACTTT
34496221 CCCTCAAACTTTTATTC-C
1 CCCT-AAACTTTTATTCTC
* *
34496239 CCCAAAACTTTTTAATTTTC
1 CCCTAAAC-TTTT-ATTCTC
34496259 CCCTAAACTTTTACTTCTC
1 CCCTAAACTTTTA-TTCTC
34496278 ACCCTA
1 -CCCTA
34496284 CTCTCAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
17 4 0.11
18 8 0.22
19 11 0.31
20 13 0.36
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (18 bp):
CCCTAAACTTTTATTCTC
Found at i:34496413 original size:17 final size:17
Alignment explanation
Indices: 34496359--34496417 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
34496349 TTATATCTAC
*
34496359 TATTTATATTATTAAGT
1 TATTTATATTATTAAAT
* *
34496376 TAAATTTCACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
34496395 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
34496412 TATTTA
1 TATTTA
34496418 GTCATATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 16 0.48
19 9 0.27
20 4 0.12
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:34522474 original size:21 final size:21
Alignment explanation
Indices: 34522435--34522475 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
34522425 GGTACGGTTG
34522435 ATATTGTTTTATTATGTTAAA
1 ATATTGTTTTATTATGTTAAA
34522456 ATATATGTTTTATTA-GTTAA
1 ATAT-TGTTTTATTATGTTAA
34522476 TAAAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
ATATTGTTTTATTATGTTAAA
Found at i:34523597 original size:13 final size:14
Alignment explanation
Indices: 34523573--34523604 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
34523563 TGGTTGTTCT
34523573 TTTAATTTGGAGGC
1 TTTAATTTGGAGGC
34523587 TTTAA-TTGGAGGC
1 TTTAATTTGGAGGC
34523600 TTTAA
1 TTTAA
34523605 GTTGCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (14 bp):
TTTAATTTGGAGGC
Found at i:34524894 original size:50 final size:50
Alignment explanation
Indices: 34524835--34525035 Score: 314
Period size: 50 Copynumber: 4.0 Consensus size: 50
34524825 GAGCTAAATG
* *
34524835 ACCTTGTGTATTCGGCCATGTAGGTAAGTATTTATGCGATGATATATTGA
1 ACCTTGTGTATTCGGCCATATAGGTAAGTATTTATGTGATGATATATTGA
* *
34524885 ACCTTGTGTATTCGACCATGTAGGTAAGTATTTATGTGATGATATATTGA
1 ACCTTGTGTATTCGGCCATATAGGTAAGTATTTATGTGATGATATATTGA
*
34524935 ACCTTGTGTATTCGGCCATATAGGTAAGTATTCATGTGATGATATATTGA
1 ACCTTGTGTATTCGGCCATATAGGTAAGTATTTATGTGATGATATATTGA
* *
34524985 ACCTTGTATATTTGGCCATAT-GAGTAAGTATTTATGTGATGATATACTTGA
1 ACCTTGTGTATTCGGCCATATAG-GTAAGTATTTATGTGATGATATA-TTGA
34525036 TCTTGCATAT
Statistics
Matches: 141, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
49 1 0.01
50 136 0.96
51 4 0.03
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (50 bp):
ACCTTGTGTATTCGGCCATATAGGTAAGTATTTATGTGATGATATATTGA
Found at i:34525059 original size:50 final size:51
Alignment explanation
Indices: 34524835--34525058 Score: 287
Period size: 50 Copynumber: 4.5 Consensus size: 51
34524825 GAGCTAAATG
* * *
34524835 ACCTTGTGTATTCGGCCATGT-AGGTAAGTATTTATGCGATGATATATTGA
1 ACCTTGTATATTCGGCCATATGAGGTAAGTATTTATGTGATGATATATTGA
* * *
34524885 ACCTTGTGTATTCGACCATGT-AGGTAAGTATTTATGTGATGATATATTGA
1 ACCTTGTATATTCGGCCATATGAGGTAAGTATTTATGTGATGATATATTGA
* *
34524935 ACCTTGTGTATTCGGCCATAT-AGGTAAGTATTCATGTGATGATATATTGA
1 ACCTTGTATATTCGGCCATATGAGGTAAGTATTTATGTGATGATATATTGA
*
34524985 ACCTTGTATATTTGGCCATATGA-GTAAGTATTTATGTGATGATATACTTG-
1 ACCTTGTATATTCGGCCATATGAGGTAAGTATTTATGTGATGATATA-TTGA
* * * *
34525035 ATCTTGCATATTCAGCCAAATGAG
1 ACCTTGTATATTCGGCCATATGAG
34525059 TGGTGATGGT
Statistics
Matches: 158, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
50 154 0.97
51 4 0.03
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.38
Consensus pattern (51 bp):
ACCTTGTATATTCGGCCATATGAGGTAAGTATTTATGTGATGATATATTGA
Found at i:34526278 original size:26 final size:26
Alignment explanation
Indices: 34526249--34526311 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
34526239 CTTGAATAGC
34526249 AGGCTTTGAGCCGATGATTACTTAGT
1 AGGCTTTGAGCCGATGATTACTTAGT
* * * *
34526275 AGGCTATGGGCCGATGTTTATTTAGT
1 AGGCTTTGAGCCGATGATTACTTAGT
34526301 AGGCTTTGAGC
1 AGGCTTTGAGC
34526312 TGGTGAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
AGGCTTTGAGCCGATGATTACTTAGT
Found at i:34527625 original size:49 final size:49
Alignment explanation
Indices: 34527553--34527651 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
34527543 TGTTATCTAT
34527553 TAATGTGTTATGTTTTAAAAATGCAGTGGGACCATGAGGTGATATAATA
1 TAATGTGTTATGTTTTAAAAATGCAGTGGGACCATGAGGTGATATAATA
34527602 TAATGTGTTATGTTTTAAAAATGCAGTGGGACCATGAGGTGATATAATA
1 TAATGTGTTATGTTTTAAAAATGCAGTGGGACCATGAGGTGATATAATA
34527651 T
1 T
34527652 GGAGCTCAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.35
Consensus pattern (49 bp):
TAATGTGTTATGTTTTAAAAATGCAGTGGGACCATGAGGTGATATAATA
Found at i:34530117 original size:36 final size:36
Alignment explanation
Indices: 34530070--34530141 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
34530060 TTTTTAGGAA
34530070 GTTAAAGTTTAAGATTATACGAGCTTACTAAGCACT
1 GTTAAAGTTTAAGATTATACGAGCTTACTAAGCACT
34530106 GTTAAAGTTTAAGATTATACGAGCTTACTAAGCACT
1 GTTAAAGTTTAAGATTATACGAGCTTACTAAGCACT
34530142 ATTTGCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (36 bp):
GTTAAAGTTTAAGATTATACGAGCTTACTAAGCACT
Found at i:34533822 original size:27 final size:26
Alignment explanation
Indices: 34533746--34533857 Score: 107
Period size: 27 Copynumber: 4.2 Consensus size: 26
34533736 AGGAAGTGTC
* * *
34533746 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
34533773 CTGATGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
* *
34533800 CTGGTGGCTCTGGCAGGATTATCTGTAT
1 CTGGTGGCTCTGCCA-CATTATCTGT-T
* * *
34533828 CTGGTGACTCTGTCACATTATCTGTC
1 CTGGTGGCTCTGCCACATTATCTGTT
34533854 CTGG
1 CTGG
34533858 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.07
27 50 0.70
28 16 0.23
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:34541445 original size:24 final size:23
Alignment explanation
Indices: 34541402--34541446 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
34541392 TACATCAGTG
*
34541402 AAAGATTTGTTGATTAGAAGCGT
1 AAAGATTTCTTGATTAGAAGCGT
34541425 AAAGAGTTTCTTGAGTT-GAAGC
1 AAAGA-TTTCTTGA-TTAGAAGC
34541447 AGGGCAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (23 bp):
AAAGATTTCTTGATTAGAAGCGT
Found at i:34542937 original size:22 final size:22
Alignment explanation
Indices: 34542912--34542961 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
34542902 GAGATTGTAT
34542912 GTTGACTATCGGTAATAAACAA
1 GTTGACTATCGGTAATAAACAA
34542934 GTTGACTATCGGTAATAAACAA
1 GTTGACTATCGGTAATAAACAA
*
34542956 GGTGAC
1 GTTGAC
34542962 AATGAAGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (22 bp):
GTTGACTATCGGTAATAAACAA
Found at i:34556637 original size:31 final size:31
Alignment explanation
Indices: 34556594--34556658 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
34556584 ACTGTCCAAG
*
34556594 GACTTAAATGAAATGTTTTGAATAGTTCAAT
1 GACTTAAATGAAATCTTTTGAATAGTTCAAT
*
34556625 GACTTAAGTGAAATCTTTTGAATAGTTCAAT
1 GACTTAAATGAAATCTTTTGAATAGTTCAAT
34556656 GAC
1 GAC
34556659 CATTTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (31 bp):
GACTTAAATGAAATCTTTTGAATAGTTCAAT
Found at i:34558171 original size:8 final size:8
Alignment explanation
Indices: 34558158--34558182 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34558148 TTTTTGTCAA
34558158 AATTTATC
1 AATTTATC
34558166 AATTTATC
1 AATTTATC
34558174 AATTTATC
1 AATTTATC
34558182 A
1 A
34558183 TGTTTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTATC
Found at i:34563813 original size:31 final size:31
Alignment explanation
Indices: 34563746--34563833 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
34563736 TTTGGATCAA
* *
34563746 GACTAAACTTGGCCAATTC-AAAAGTATAGG
1 GACTAAACTTGACCAATTCAAAAAGTAAAGG
34563776 GACTAAACTTGACCAATTCAAAAAGTACAAGG
1 GACTAAACTTGACCAATTCAAAAAGTA-AAGG
*
34563808 G-CTAAACTTGACCAATTTAAAAAGTA
1 GACTAAACTTGACCAATTCAAAAAGTA
34563834 TAGTGTAACA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 18 0.34
31 31 0.58
32 4 0.08
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (31 bp):
GACTAAACTTGACCAATTCAAAAAGTAAAGG
Found at i:34565410 original size:38 final size:36
Alignment explanation
Indices: 34565381--34565470 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 36
34565371 GCCTCGGGAC
34565381 TTAACCCGGATTTA-TAACTCAACAAAATGCCTTCGG
1 TTAA-CCGGATTTAGTAACTCAACAAAATGCCTTCGG
* *
34565417 TTAACCGGATTTAGTAACT-ACGCACAATGCCTTCGGG
1 TTAACCGGATTTAGTAACTCA-ACAAAATGCCTTC-GG
* *
34565454 CTTAGCCGGAATTAGTA
1 -TTAACCGGATTTAGTA
34565471 TTCGCACAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 10 0.22
36 20 0.43
37 2 0.04
38 14 0.30
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (36 bp):
TTAACCGGATTTAGTAACTCAACAAAATGCCTTCGG
Found at i:34565435 original size:36 final size:38
Alignment explanation
Indices: 34565365--34565470 Score: 114
Period size: 38 Copynumber: 2.8 Consensus size: 38
34565355 TAGATAATCG
34565365 CAAAATGCC-TCGGGACTTAACCCGGATTTA-TAACT-CAA
1 CAAAATGCCTTCGGG-CTTAA-CCGGATTTAGTAACTAC-A
*
34565403 CAAAATGCCTTC-GG-TTAACCGGATTTAGTAACTACG
1 CAAAATGCCTTCGGGCTTAACCGGATTTAGTAACTACA
* * *
34565439 CACAATGCCTTCGGGCTTAGCCGGAATTAGTA
1 CAAAATGCCTTCGGGCTTAACCGGATTTAGTA
34565471 TTCGCACAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
35 9 0.15
36 20 0.34
37 3 0.05
38 25 0.42
39 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (38 bp):
CAAAATGCCTTCGGGCTTAACCGGATTTAGTAACTACA
Found at i:34573281 original size:40 final size:40
Alignment explanation
Indices: 34573236--34573460 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
34573226 GCTCCTCGTT
* *
34573236 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
* *
34573276 AAAATGCCTTCGGGACTTAACCCGGATTGAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
34573316 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
34573356 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * ** *
34573395 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCATTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
34573436 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
34573461 CATCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 112 0.70
41 15 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:34573420 original size:119 final size:120
Alignment explanation
Indices: 34573238--34573460 Score: 276
Period size: 119 Copynumber: 1.9 Consensus size: 120
34573228 TCCTCGTTCA
* *
34573238 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCAAAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCAAAAATACCTTCGGGACTTAACCCGGAT
*
34573303 -TGAGT-AACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATG-GTCAACTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
34573358 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCAAAAATACCTTCGGGA-CTTAACCCGG
** *
34573420 ATATGGTCATTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATGGTCAACTAGCACAAAGCCTTCGGGACTTAACCCGGA
34573461 CATCATTCAA
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
118 4 0.05
119 61 0.69
120 23 0.26
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCAAAAATACCTTCGGGACTTAACCCGGAT
ATGGTCAACTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:34576364 original size:10 final size:10
Alignment explanation
Indices: 34576349--34576395 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
34576339 GAACATGTTG
34576349 AATTTTAATT
1 AATTTTAATT
*
34576359 AATTTTATATCA
1 AATTTTA-AT-T
34576371 AATTTTAATT
1 AATTTTAATT
*
34576381 AATTTTGATT
1 AATTTTAATT
34576391 -ATTTT
1 AATTTT
34576396 CGATAGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 5 0.16
10 16 0.50
11 4 0.12
12 7 0.22
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
AATTTTAATT
Found at i:34579327 original size:13 final size:13
Alignment explanation
Indices: 34579311--34579335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34579301 ATAAATTAAA
34579311 TTATATATAATTT
1 TTATATATAATTT
34579324 TTATATATAATT
1 TTATATATAATT
34579336 CACTAATCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATATAATTT
Found at i:34581370 original size:49 final size:47
Alignment explanation
Indices: 34581213--34581382 Score: 171
Period size: 49 Copynumber: 3.5 Consensus size: 47
34581203 TTCCAACGTT
* *
34581213 ATGTCCTAGACATGGTCTTACACTGGCTCACAC-ATCAAAGTCGATGCC
1 ATGTCCTAGACA-GGTCTTACACTGGCTCTCACTATC-AGGTCGATGCC
* * * * * *
34581261 ATGTCCTAAACAGGTCTTACACTGACTTTCACATATCGAGGCCGATACT
1 ATGTCCTAGACAGGTCTTACACTGGCTCTCAC-TATC-AGGTCGATGCC
* * *
34581310 GTGTCTTAGACAGGTCTTACACTGGCTCTCATCTATTAGTGTCGATGCC
1 ATGTCCTAGACAGGTCTTACACTGGCTCTCA-CTATCAG-GTCGATGCC
*
34581359 ATGTCCCAGACAGGTCTTACACTG
1 ATGTCCTAGACAGGTCTTACACTG
34581383 ACACACAACA
Statistics
Matches: 97, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
47 17 0.18
48 13 0.13
49 66 0.68
50 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (47 bp):
ATGTCCTAGACAGGTCTTACACTGGCTCTCACTATCAGGTCGATGCC
Found at i:34581493 original size:48 final size:47
Alignment explanation
Indices: 34581411--34581524 Score: 165
Period size: 48 Copynumber: 2.4 Consensus size: 47
34581401 CCATATCCTA
* * *
34581411 GACAGGTCTTACACTAGCTTGTATACCTCGAGGCCGATGCATGTCCC
1 GACATGTCTTACACTGGCTTGTATACCTCAAGGCCGATGCATGTCCC
* *
34581458 ATACATGTCTTACACTGGCTTGTATATCTCAAGGCCGATGCATGTCCC
1 -GACATGTCTTACACTGGCTTGTATACCTCAAGGCCGATGCATGTCCC
*
34581506 GACATATCTTACACTGGCT
1 GACATGTCTTACACTGGCT
34581525 CTCATAATGT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
47 17 0.29
48 42 0.71
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (47 bp):
GACATGTCTTACACTGGCTTGTATACCTCAAGGCCGATGCATGTCCC
Found at i:34586741 original size:42 final size:42
Alignment explanation
Indices: 34586662--34586766 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 42
34586652 TTAATTATGG
* **
34586662 GCACTTAGTGTGCGAAATCGGGATAGCTTTGGATATATATTT
1 GCACTTAGTGTGCGAAATCGAGATAGCTTCAGATATATATTT
*
34586704 GCACTTAGTGTGTGAGAA-CGAGATAGCTTCAGCTATATATATATATAT
1 GCACTTAGTGTGCGA-AATCGAGATAGCTTCAG----ATATATAT-T-T
34586752 GCACTTAGTGTGCGA
1 GCACTTAGTGTGCGA
34586767 GATTAATACA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
42 25 0.49
43 2 0.04
46 8 0.16
47 1 0.02
48 15 0.29
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (42 bp):
GCACTTAGTGTGCGAAATCGAGATAGCTTCAGATATATATTT
Found at i:34608991 original size:25 final size:25
Alignment explanation
Indices: 34608952--34609040 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
34608942 AGACACACTA
* *
34608952 CAGCTCATATGAGCTTACCGATTCT
1 CAGCTCGTGTGAGCTTACCGATTCT
* *
34608977 CAGCTCGTGTTAGCTTATCGATTCT
1 CAGCTCGTGTGAGCTTACCGATTCT
* *
34609002 CTGCTCATGTGAGCTTACCGATT-T
1 CAGCTCGTGTGAGCTTACCGATTCT
*
34609026 ACAGCTCGTGAGAGC
1 -CAGCTCGTGTGAGC
34609041 ATACTAATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 1 0.02
25 51 0.98
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (25 bp):
CAGCTCGTGTGAGCTTACCGATTCT
Found at i:34609058 original size:50 final size:51
Alignment explanation
Indices: 34608953--34609065 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 51
34608943 GACACACTAC
** * * *
34608953 AGCTCATATGAGCTTACCGATTCTCAGCTCGTGTTAGCTTATCGATTCTCT
1 AGCTCATATGAGCTTACCGATTCTCAGCTCGTGAGAGCATATCAATTCTAT
*
34609004 -GCTCATGTGAGCTTACCGATT-TACAGCTCGTGAGAGCATA-CTAATT-TAT
1 AGCTCATATGAGCTTACCGATTCT-CAGCTCGTGAGAGCATATC-AATTCTAT
34609053 AGCTCATATGAGC
1 AGCTCATATGAGC
34609066 ACACATGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
49 4 0.08
50 48 0.92
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (51 bp):
AGCTCATATGAGCTTACCGATTCTCAGCTCGTGAGAGCATATCAATTCTAT
Found at i:34611622 original size:26 final size:24
Alignment explanation
Indices: 34611569--34611623 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
34611559 AATTTTTATG
* *
34611569 TTTTTATCTTTCTTTATTTCTTTT
1 TTTTTATCTTTCTTTATTTATTTC
*
34611593 TTTTTATACTTATCTTTCTTTATTTC
1 TTTTTAT-CTT-TCTTTATTTATTTC
34611619 TTTTT
1 TTTTT
34611624 TTATACTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 7 0.27
25 3 0.12
26 16 0.62
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTATCTTTCTTTATTTATTTC
Found at i:34619297 original size:60 final size:60
Alignment explanation
Indices: 34619162--34619300 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
34619152 ATCAGAGTTA
* *
34619162 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAATAAAAGAGTAT
1 ACTGGGCCTT-GCCCATATCAATATCAATCTGGGCCATAGCCCATTACAATAAAAGAGTAT
* * * * **
34619223 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGTCGTAGCCCTATTACAAGT-CGAGA-TAT
1 ACTGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAA-TAAAAGAGTAT
*
34619283 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTTGCCCATAT
34619301 TAACACAGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
60 47 0.71
61 18 0.27
62 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (60 bp):
ACTGGGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAATAAAAGAGTAT
Found at i:34619318 original size:20 final size:20
Alignment explanation
Indices: 34619293--34619338 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34619283 ATTGGGCCTT
34619293 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
34619313 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
34619332 GCCCATA
1 GCCCATA
34619339 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:34619347 original size:19 final size:20
Alignment explanation
Indices: 34619305--34619348 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
34619295 CCATATTAAC
** *
34619305 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
34619325 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
34619344 ACAGT
1 ACAGT
34619349 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:34620975 original size:185 final size:185
Alignment explanation
Indices: 34620663--34621031 Score: 738
Period size: 185 Copynumber: 2.0 Consensus size: 185
34620653 GGAGTAGAAG
34620663 ATTAAGCTTGGTGAAGAAAAGATGAACAAAAAGAATGAAGGTCGATCTCAAAAATAATAATAGAT
1 ATTAAGCTTGGTGAAGAAAAGATGAACAAAAAGAATGAAGGTCGATCTCAAAAATAATAATAGAT
34620728 GTGAATGGCCCCAACCTAAATTGACTAACACTTAAAAATTCCCGAAACTAAACAAAGAAGAAAAA
66 GTGAATGGCCCCAACCTAAATTGACTAACACTTAAAAATTCCCGAAACTAAACAAAGAAGAAAAA
34620793 CAACCCATACAAGCCAAAATTTTGGTCCTTCGCGCACACAGCAAACTCAAACTCA
131 CAACCCATACAAGCCAAAATTTTGGTCCTTCGCGCACACAGCAAACTCAAACTCA
34620848 ATTAAGCTTGGTGAAGAAAAGATGAACAAAAAGAATGAAGGTCGATCTCAAAAATAATAATAGAT
1 ATTAAGCTTGGTGAAGAAAAGATGAACAAAAAGAATGAAGGTCGATCTCAAAAATAATAATAGAT
34620913 GTGAATGGCCCCAACCTAAATTGACTAACACTTAAAAATTCCCGAAACTAAACAAAGAAGAAAAA
66 GTGAATGGCCCCAACCTAAATTGACTAACACTTAAAAATTCCCGAAACTAAACAAAGAAGAAAAA
34620978 CAACCCATACAAGCCAAAATTTTGGTCCTTCGCGCACACAGCAAACTCAAACTC
131 CAACCCATACAAGCCAAAATTTTGGTCCTTCGCGCACACAGCAAACTCAAACTC
34621032 CAGACCTCAT
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
185 184 1.00
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.19
Consensus pattern (185 bp):
ATTAAGCTTGGTGAAGAAAAGATGAACAAAAAGAATGAAGGTCGATCTCAAAAATAATAATAGAT
GTGAATGGCCCCAACCTAAATTGACTAACACTTAAAAATTCCCGAAACTAAACAAAGAAGAAAAA
CAACCCATACAAGCCAAAATTTTGGTCCTTCGCGCACACAGCAAACTCAAACTCA
Found at i:34623090 original size:43 final size:42
Alignment explanation
Indices: 34622993--34623110 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 42
34622983 AATTTGTAAT
* * * *
34622993 TTACGTGTAAGACCATGTCTGCGACATTGGCATCGTATATGA
1 TTACGTGTAAGACCCTATCTGGGACAGTGGCATCGTATATGA
* * *
34623035 TTTCGTATAAGACCCTATCTGGGACAGTGGCATCGATATTTGA
1 TTACGTGTAAGACCCTATCTGGGACAGTGGCATCG-TATATGA
*
34623078 TTACATGTAAGACCAC-ATCTGGGAC-GTTGGCAT
1 TTACGTGTAAGACC-CTATCTGGGACAG-TGGCAT
34623111 TGTACGAGCT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 30 0.48
43 32 0.51
44 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (42 bp):
TTACGTGTAAGACCCTATCTGGGACAGTGGCATCGTATATGA
Found at i:34627839 original size:46 final size:46
Alignment explanation
Indices: 34627701--34627919 Score: 196
Period size: 46 Copynumber: 4.7 Consensus size: 46
34627691 GGGTTATTGT
** * *
34627701 GAGCTAGTGTAAGACATGTCTTAGACATGCATCAGCCAC-ATTACAA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GACAA
* * * * * *
34627747 GAACCAGTGTAAGGCCATGTCTGGGGCATGGCATCAGCATTGAGACAA
1 GAGCTAGTGTAA-GACATGTCTGGGACAT-GCATCAGCCTCGAGACAA
34627795 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACATA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACA-A
* * * **
34627842 -AGCCAGTGTAAAACATGTCTGGGACATGCATC-GACTACGAG--TT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGACAA
*
34627885 GAGCTAGTGTAAGACCATGTCCGGGACATGGCATC
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
34627920 GGCATCCTAC
Statistics
Matches: 141, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
44 11 0.08
45 16 0.11
46 64 0.45
47 27 0.19
48 22 0.16
49 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.21
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACAA
Found at i:34630867 original size:26 final size:26
Alignment explanation
Indices: 34630837--34630888 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
34630827 TGGCAAGGAC
34630837 TATGAATATTTCAAAAGCTTTAATCG
1 TATGAATATTTCAAAAGCTTTAATCG
34630863 TATGAATATTTCAAAAGCTTTAATCG
1 TATGAATATTTCAAAAGCTTTAATCG
34630889 AGACTAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (26 bp):
TATGAATATTTCAAAAGCTTTAATCG
Found at i:34640647 original size:17 final size:17
Alignment explanation
Indices: 34640614--34640647 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34640604 AATGATGAAA
* *
34640614 AAAAAGAAAAGAGAAAG
1 AAAAAGAAAAAAAAAAG
34640631 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
34640648 GAAAGGCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:34641966 original size:40 final size:40
Alignment explanation
Indices: 34641907--34642124 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
34641897 TTGATGATAA
* * * *
34641907 CCGGGCTAAGTCCCGAAGGCGTTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
34641947 CCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
34641987 TCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
34642027 CCGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
34642067 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
34642107 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
34642125 TACTTGGCTT
Statistics
Matches: 158, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
39 16 0.10
40 142 0.90
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:34649258 original size:15 final size:15
Alignment explanation
Indices: 34649238--34649271 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
34649228 AAGCTACGTG
34649238 GAACGAGTTTGGGAA
1 GAACGAGTTTGGGAA
34649253 GAACGAGTTTGGGAA
1 GAACGAGTTTGGGAA
34649268 GAAC
1 GAAC
34649272 AAGAAGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.38, T:0.18
Consensus pattern (15 bp):
GAACGAGTTTGGGAA
Found at i:34651572 original size:19 final size:19
Alignment explanation
Indices: 34651548--34651589 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
34651538 CGAGTTTTGA
34651548 GTTTTGCTCTTTTAAGGTT
1 GTTTTGCTCTTTTAAGGTT
34651567 GTTTTGCTCTTTTAAGGTT
1 GTTTTGCTCTTTTAAGGTT
34651586 GTTT
1 GTTT
34651590 CTATCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.60
Consensus pattern (19 bp):
GTTTTGCTCTTTTAAGGTT
Found at i:34657703 original size:17 final size:17
Alignment explanation
Indices: 34657663--34657712 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
34657653 ATATTATTTT
34657663 TATAT-TATTATAATTGTG
1 TATATATATTAT-A-TGTG
*
34657681 TGTATATATTATATGTG
1 TATATATATTATATGTG
34657698 TATATATATTATATG
1 TATATATATTATATG
34657713 CATATCAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 18 0.62
18 5 0.17
19 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (17 bp):
TATATATATTATATGTG
Found at i:34658713 original size:16 final size:18
Alignment explanation
Indices: 34658694--34658726 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
34658684 CATACGAATT
34658694 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
34658710 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
34658727 GCGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:34659353 original size:43 final size:43
Alignment explanation
Indices: 34659291--34659406 Score: 189
Period size: 43 Copynumber: 2.7 Consensus size: 43
34659281 CTGAACTCAT
*
34659291 TCACCGGCATTA-CGCCTGCTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
* *
34659333 TCACTGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
*
34659376 TTACCGGCATTATAGCCTGCTAGGCTCGAAG
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAG
34659407 GCCTGAATAG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 11 0.16
43 57 0.84
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
Found at i:34662289 original size:42 final size:42
Alignment explanation
Indices: 34662230--34662389 Score: 149
Period size: 42 Copynumber: 3.7 Consensus size: 42
34662220 GGGTTATGTG
* *
34662230 TGATTTCGTGTAAGACCATATCTGAGATATGGCATCGATATT
1 TGATTTCATGTAAGACCATATCTGGGATATGGCATCGATATT
* * **
34662272 TGATTTCATGTAAGACCATGTCTGGGACATGGCATCGATACG
1 TGATTTCATGTAAGACCATATCTGGGATATGGCATCGATATT
* * * * *
34662314 AGATATCGTGTAAGACCATAGCTGGGCTATCGGCATCGATATAT
1 TGATTTCATGTAAGACCATATCTGGGATAT-GGCATCGATAT-T
** * * *
34662358 GTGATCCCATGTAAGACTATATATAGGATATG
1 -TGATTTCATGTAAGACCATATCTGGGATATG
34662390 ACATTGGCAT
Statistics
Matches: 91, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
42 59 0.65
43 10 0.11
44 1 0.01
45 21 0.23
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
TGATTTCATGTAAGACCATATCTGGGATATGGCATCGATATT
Found at i:34665768 original size:27 final size:26
Alignment explanation
Indices: 34665731--34665842 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
34665721 AGCATGACTG
* *
34665731 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
34665757 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
34665785 CCAGAACAGATATATGTGGCAAAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
34665812 CCAGATCA-AGTATTTGTGGCATAGCCA
1 CCAGAACAGA-TA-ATGTGGCAGAGCCA
34665839 CCAG
1 CCAG
34665843 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:34665794 original size:54 final size:54
Alignment explanation
Indices: 34665731--34665842 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
34665721 AGCATGACTG
* *
34665731 CCAGAACAGATA-ATGTGACAGAGTCACCAGAT-ACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAAAGCCACCAGATCA-AG-TAATCGTGGCAGAGCCA
* * * *
34665785 CCAGAACAGATATATGTGGCAAAGCCACCAGATCAAGTATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAAAGCCACCAGATCAAGTAATCGTGGCAGAGCCA
34665839 CCAG
1 CCAG
34665843 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
54 30 0.60
55 19 0.38
56 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAAAGCCACCAGATCAAGTAATCGTGGCAGAGCCA
Found at i:34673106 original size:17 final size:17
Alignment explanation
Indices: 34673084--34673117 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34673074 TGTTTGATAT
34673084 GAGCTGCATCTTAGCAC
1 GAGCTGCATCTTAGCAC
34673101 GAGCTGCATCTTAGCAC
1 GAGCTGCATCTTAGCAC
34673118 CTAGATGCAT
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:0.24, T:0.24
Consensus pattern (17 bp):
GAGCTGCATCTTAGCAC
Found at i:34675273 original size:20 final size:20
Alignment explanation
Indices: 34675248--34675288 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
34675238 ATTCTAATTC
34675248 TAAAAAAT-ATAAAATATATT
1 TAAAAAATCATAAAA-ATATT
*
34675268 TAAAAAATCTTAAAAATATT
1 TAAAAAATCATAAAAATATT
34675288 T
1 T
34675289 TTGCATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAATCATAAAAATATT
Found at i:34679112 original size:42 final size:42
Alignment explanation
Indices: 34679060--34679157 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
34679050 GGGATTTCAC
* * * * *
34679060 ATCGATGCCATATCCCAGATATGGTCTTATACGGATTCTCAT
1 ATCGACGCCATATCCCAGATATAGTCTTACACGAAATCTCAT
* * * *
34679102 TTCGACGCCATGTCCTAGATGTAGTCTTACACGAAATCTCAT
1 ATCGACGCCATATCCCAGATATAGTCTTACACGAAATCTCAT
*
34679144 ATCAACGCCATATC
1 ATCGACGCCATATC
34679158 GTCTTACATG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (42 bp):
ATCGACGCCATATCCCAGATATAGTCTTACACGAAATCTCAT
Found at i:34683049 original size:43 final size:43
Alignment explanation
Indices: 34682986--34683152 Score: 205
Period size: 43 Copynumber: 3.9 Consensus size: 43
34682976 AGCTTGTACA
* * * *
34682986 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * *
34683028 ATGCCAATTTCCCAGACATGGTCTTACACGAAATCATATAAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAT-ATCG
*
34683071 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATAT-CG
* *
34683114 ATGTCAATGTCCCAGACATGGTCTTACATGTAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAT
34683153 CTTGGCAATC
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
43 99 0.92
44 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:34684255 original size:27 final size:26
Alignment explanation
Indices: 34684220--34684331 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
34684210 AGCATGGCTG
* *
34684220 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
34684246 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
34684274 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
34684301 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
34684328 CCAG
1 CCAG
34684332 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:34684312 original size:54 final size:54
Alignment explanation
Indices: 34684220--34684331 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
34684210 AGCATGGCTG
* *
34684220 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
34684274 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
34684328 CCAG
1 CCAG
34684332 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:34685551 original size:24 final size:24
Alignment explanation
Indices: 34685524--34685570 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
34685514 CTAGATTTCC
**
34685524 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
34685548 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
34685571 CTCCTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:34688503 original size:13 final size:13
Alignment explanation
Indices: 34688485--34688509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34688475 CTAAAAGTGC
34688485 AAAAATCATCAAG
1 AAAAATCATCAAG
34688498 AAAAATCATCAA
1 AAAAATCATCAA
34688510 AATCACTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:34694735 original size:41 final size:41
Alignment explanation
Indices: 34694688--34694772 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
34694678 AATGTGACAC
34694688 TAAAACAAGATCAAAGAGTCCTATACATGCCATAATCAAAA
1 TAAAACAAGATCAAAGAGTCCTATACATGCCATAATCAAAA
34694729 TAAAACAAGATCAAAGAGTCCTATACATGCCATAATCAAAA
1 TAAAACAAGATCAAAGAGTCCTATACATGCCATAATCAAAA
34694770 TAA
1 TAA
34694773 GAGATCTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.52, C:0.19, G:0.09, T:0.20
Consensus pattern (41 bp):
TAAAACAAGATCAAAGAGTCCTATACATGCCATAATCAAAA
Found at i:34695286 original size:49 final size:46
Alignment explanation
Indices: 34695173--34695332 Score: 137
Period size: 49 Copynumber: 3.4 Consensus size: 46
34695163 TGTAATGCCG
* * *
34695173 ATGCCATGTCCCAGACATGGTCTTACACTAGCACATCTATCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-GCACATCAATCAAGCCA
** * *
34695220 ATGCCATGTCCTGGACATGGTCTTACACTG-ACTATCGAAATTGAGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGCAC-ATC--AA-TCAAGCCA
* * ** *
34695269 ATGCCATGTCCCAGACATGGTCTTATACTGGCACATC-TTGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-GCACATCAATCAAGCCA
34695315 ATG-CATGTCCCAGACATG
1 ATGCCATGTCCCAGACATG
34695333 TTTCACACTG
Statistics
Matches: 93, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
45 17 0.18
46 12 0.13
47 27 0.29
48 1 0.01
49 30 0.32
50 4 0.04
51 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (46 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGCACATCAATCAAGCCA
Found at i:34695428 original size:47 final size:46
Alignment explanation
Indices: 34695169--34695480 Score: 194
Period size: 46 Copynumber: 6.7 Consensus size: 46
34695159 AGGGTGTAAT
* *
34695169 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACATCTATCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATCAA
* ** * * * * *
34695216 GTCGATGCCATGTCCTGGACATGGTCTTACACTGACTATCGAAATTGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--TA-TCAA
* * * **
34695265 GCCAATGCCATGTCCCAGACATGGTCTTATACTGGCACATCT-TGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATCAA
* *
34695311 GCCGATG-CATGTCCCAGACAT-GT-TTCACACTGGCT-TACATCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTT-ACACTGGCTCT-C-TATC-AA
* * * * *
34695357 GCTGATG-CATGTCCCAAACAT-GTCTTAAACTAGCTCTCGTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-TATCAA
***
34695402 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-T-ATCAA
* *
34695450 GCCGATG-CATGTCCCTGACA-CGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
34695481 AGCACACAAT
Statistics
Matches: 207, Mismatches: 43, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 10 0.05
45 16 0.08
46 71 0.34
47 70 0.34
48 2 0.01
49 32 0.15
50 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTATCAA
Found at i:34695457 original size:93 final size:92
Alignment explanation
Indices: 34695169--34695486 Score: 312
Period size: 93 Copynumber: 3.4 Consensus size: 92
34695159 AGGGTGTAAT
* **
34695169 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACATCTATCAAGTCGATGCCATGTCCTGG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACATCT-TCAAGCCGATGCCATGTCCCAG
*
34695234 ACATGGTCTTACACTGACTATCGA-AATTGAG
65 ACAT-GTCTTACACTGGCT-TC-ATAA-TGAG
* * * **
34695265 GCCAATGCCATGTCCCAGACATGGTCTTATACTGGCACATCTTGTAGCCGATG-CATGTCCCAGA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACATCTTCAAGCCGATGCCATGTCCCAGA
*
34695329 CATGT-TTCACACTGGCTTACAT-CTCGAG
66 CATGTCTT-ACACTGGCTT-CATAAT-GAG
* * * *
34695357 GCTGATG-CATGTCCCAAACAT-GTCTTAAACTAGCTC-TCGTCTCAATGCCGATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACATC-T-TCAA-GCCGATGCCATGTCCC
*
34695419 AGACATGTCTTACACTGGCTCTCATAATGTG
63 AGACATGTCTTACACTGGCT-TCATAATGAG
* *
34695450 GCCGATG-CATGTCCCTGACA-CGTCTTACACTAGCACA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACA
34695487 CAATTAACCC
Statistics
Matches: 184, Mismatches: 25, Indels: 28
0.78 0.11 0.12
Matches are distributed among these distances:
89 2 0.01
90 13 0.07
91 16 0.09
92 19 0.10
93 71 0.39
94 16 0.09
95 8 0.04
96 39 0.21
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (92 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACATCTTCAAGCCGATGCCATGTCCCAGA
CATGTCTTACACTGGCTTCATAATGAG
Found at i:34695983 original size:20 final size:20
Alignment explanation
Indices: 34695954--34696002 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
34695944 AAATTCTCAA
*
34695954 TATTTCACACATTTATAACC
1 TATTTTACACATTTATAACC
*
34695974 TATTTTACACATTTATTACC
1 TATTTTACACATTTATAACC
34695994 TATTTTACA
1 TATTTTACA
34696003 ACTTATGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTTACACATTTATAACC
Found at i:34703970 original size:21 final size:21
Alignment explanation
Indices: 34703946--34703990 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
34703936 GGAGTTGGGT
34703946 GGAGAGAATCTAAGAGAGTGC
1 GGAGAGAATCTAAGAGAGTGC
34703967 GGAGAGAATCTAAGAGAGTGC
1 GGAGAGAATCTAAGAGAGTGC
34703988 GGA
1 GGA
34703991 TATGGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.40, T:0.13
Consensus pattern (21 bp):
GGAGAGAATCTAAGAGAGTGC
Found at i:34705371 original size:56 final size:56
Alignment explanation
Indices: 34705284--34705394 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
34705274 TTAGGGCCTA
34705284 ATCGGAATAGTGGTTTCATGACCACAAATTCGAGATAGAAATAATTGTTTTATAATT
1 ATCGGAATAGTGGTTTCATGACCACAAATTCGAGATAGAAATAATTG-TTTATAATT
34705341 ATCGGAATAGTGG-TTCATGACCACAAATTCGAGATAGAAATAATTGTTTATAAT
1 ATCGGAATAGTGGTTTCATGACCACAAATTCGAGATAGAAATAATTGTTTATAAT
34705395 GATTTTGGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 8 0.15
56 33 0.61
57 13 0.24
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (56 bp):
ATCGGAATAGTGGTTTCATGACCACAAATTCGAGATAGAAATAATTGTTTATAATT
Found at i:34721813 original size:21 final size:21
Alignment explanation
Indices: 34721773--34721815 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
34721763 TCACACTATC
**
34721773 ACATGTTATGAAATTTCATGT
1 ACATGTTATGAAATGACATGT
34721794 ACATGTTATGAAATGACATGT
1 ACATGTTATGAAATGACATGT
34721815 A
1 A
34721816 TTACTGGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
ACATGTTATGAAATGACATGT
Found at i:34723158 original size:46 final size:46
Alignment explanation
Indices: 34723084--34723205 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 46
34723074 CAACTCGTAT
* *
34723084 GAGCTTACCGATTCATCTCG-TAAGAGCTTACTGTTTTAGCTCATTG
1 GAGCTTACCGATTCAACTCGATAA-AGCTTACTGTTTCAGCTCATTG
*
34723130 GAGCTTACCGATTCAGCTCGATAAAGCTTACTGTTTCAGCTCATTG
1 GAGCTTACCGATTCAACTCGATAAAGCTTACTGTTTCAGCTCATTG
* * *
34723176 GAGCTTACTGATTCAACTCAATAGAGCTTA
1 GAGCTTACCGATTCAACTCGATAAAGCTTA
34723206 TTGTCCATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
46 66 0.96
47 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (46 bp):
GAGCTTACCGATTCAACTCGATAAAGCTTACTGTTTCAGCTCATTG
Found at i:34723195 original size:23 final size:23
Alignment explanation
Indices: 34723084--34723205 Score: 111
Period size: 23 Copynumber: 5.3 Consensus size: 23
34723074 CAACTCGTAT
* * * *
34723084 GAGCTTACCGATTCATCTCGTAA
1 GAGCTTACTGATTCAGCTCATTA
* * *
34723107 GAGCTTACTGTTTTAGCTCATTG
1 GAGCTTACTGATTCAGCTCATTA
*
34723130 GAGCTTACCGATTCAGCTCGA-TA
1 GAGCTTACTGATTCAGCTC-ATTA
* * *
34723153 AAGCTTACTGTTTCAGCTCATTG
1 GAGCTTACTGATTCAGCTCATTA
* *
34723176 GAGCTTACTGATTCAACTCAATA
1 GAGCTTACTGATTCAGCTCATTA
34723199 GAGCTTA
1 GAGCTTA
34723206 TTGTCCATCA
Statistics
Matches: 77, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
22 1 0.01
23 75 0.97
24 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (23 bp):
GAGCTTACTGATTCAGCTCATTA
Found at i:34733157 original size:17 final size:17
Alignment explanation
Indices: 34733135--34733211 Score: 74
Period size: 17 Copynumber: 4.7 Consensus size: 17
34733125 CTTTTAATAG
*
34733135 ATTTAATATTAAATTTA
1 ATTTAATATTTAATTTA
*
34733152 ATTTAATACTT-ATCTTA
1 ATTTAATATTTAAT-TTA
*
34733169 A--TAGTATTTTAA--TA
1 ATTTAATA-TTTAATTTA
34733183 ATTTAATATTTAATTTA
1 ATTTAATATTTAATTTA
34733200 ATTTAATATTTA
1 ATTTAATATTTA
34733212 TCTTGTAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
14 3 0.06
15 9 0.19
16 8 0.17
17 28 0.58
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (17 bp):
ATTTAATATTTAATTTA
Found at i:34735713 original size:19 final size:19
Alignment explanation
Indices: 34735684--34735738 Score: 101
Period size: 19 Copynumber: 2.8 Consensus size: 19
34735674 TTTGATATTT
34735684 TGGGCTTAATGGGCCAAAAC
1 TGGG-TTAATGGGCCAAAAC
34735704 TGGGTTAATGGGCCAAAAC
1 TGGGTTAATGGGCCAAAAC
34735723 TGGGTTAATGGGCCAA
1 TGGGTTAATGGGCCAA
34735739 CGGTCCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 31 0.89
20 4 0.11
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (19 bp):
TGGGTTAATGGGCCAAAAC
Found at i:34735868 original size:28 final size:28
Alignment explanation
Indices: 34735836--34735900 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
34735826 ATTTACTAGA
* *
34735836 ATACCCCTACATATGCAAAATTACCATT
1 ATACCCCTACATATACAAAATGACCATT
** * *
34735864 ATACCCCTATGTATACTAAATGACCTTT
1 ATACCCCTACATATACAAAATGACCATT
34735892 ATACCCCTA
1 ATACCCCTA
34735901 GGGTTAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (28 bp):
ATACCCCTACATATACAAAATGACCATT
Found at i:34736094 original size:29 final size:27
Alignment explanation
Indices: 34736006--34736096 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
34735996 AGGAAGCGTC
34736006 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGCT-TGCCACAAATTATCTGTT
* *
34736034 CTCGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGG-CTTGCCACAAATTATCTGTT
* *
34736062 CTGGTGGCATTGCCACAAAATATATGTAT
1 CTGGTGGC-TTGCCACAAATTATCTGT-T
34736091 CTGGTG
1 CTGGTG
34736097 AATCTCTCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 1 0.02
28 45 0.83
29 8 0.15
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTTGCCACAAATTATCTGTT
Found at i:34737205 original size:11 final size:10
Alignment explanation
Indices: 34737177--34737211 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
34737167 AGCCTGTAAG
34737177 TATTCTGAAT
1 TATTCTGAAT
*
34737187 TTTTCTGAAT
1 TATTCTGAAT
34737197 ATATTCTGAAT
1 -TATTCTGAAT
34737208 TATT
1 TATT
34737212 TGTCTGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:34739845 original size:28 final size:28
Alignment explanation
Indices: 34739813--34739877 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
34739803 ATTTACTAGA
* *
34739813 ATACCCCTATGTCTGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
34739841 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
34739869 ATACCCCTA
1 ATACCCCTA
34739878 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:34740024 original size:28 final size:28
Alignment explanation
Indices: 34739983--34740073 Score: 130
Period size: 28 Copynumber: 3.2 Consensus size: 28
34739973 AGGAAGCGTC
34739983 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
34740011 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
* *
34740039 CTGGTAGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
34740068 CTGGTG
1 CTGGTG
34740074 ACTCTGTCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
28 50 0.89
29 6 0.11
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:34740084 original size:29 final size:28
Alignment explanation
Indices: 34739993--34740084 Score: 114
Period size: 28 Copynumber: 3.2 Consensus size: 28
34739983 CTGGTGGCTA
* *
34739993 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAATTATCTGTTCTGGTGACAC
34740021 TGCCACAAATTATCTGTTCTGGT-AGCAC
1 TGCCACAAATTATCTGTTCTGGTGA-CAC
* *
34740049 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAATTATCTGT-TCTGGTGACAC
*
34740078 TGTCACA
1 TGCCACA
34740085 TTTTCTGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
28 41 0.73
29 14 0.25
30 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (28 bp):
TGCCACAAATTATCTGTTCTGGTGACAC
Found at i:34740098 original size:56 final size:55
Alignment explanation
Indices: 34739993--34740098 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 55
34739983 CTGGTGGCTA
* *
34739993 TGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTTCTGGTAGCAC
1 TGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTTCTGGTAGCAC
* * *
34740049 TGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTATCTGG
1 TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-TCTGG
34740099 CAGCCATGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
55 8 0.19
56 21 0.49
57 14 0.33
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.35
Consensus pattern (55 bp):
TGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTTCTGGTAGCAC
Found at i:34740566 original size:18 final size:18
Alignment explanation
Indices: 34740527--34740567 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
34740517 TAATAAGGCC
* *
34740527 TTTTAATTATTTTTATGG
1 TTTTAATTACTTTTATGA
*
34740545 TTTTAATTACTTTTATTA
1 TTTTAATTACTTTTATGA
34740563 TTTTA
1 TTTTA
34740568 TTTTACTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTACTTTTATGA
Found at i:34741747 original size:46 final size:45
Alignment explanation
Indices: 34741694--34741869 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
34741684 GGGCTATTGT
* * *
34741694 GAGCTAGTGTAAGACATGTCTTGGACATGCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCA-GATGA
* *
34741740 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTTGAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCC-TCAGATGA
* * * * *
34741788 GTGCTAGTGTAAGACATGTCTAGGACATACATTGGCCTCGAGACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTC-AGATG-A
34741835 -AG-TCAGTGTAAGACATGTCTGGGACATGCATCGGC
1 GAGCT-AGTGTAAGACATGTCTGGGACATGCATCGGC
34741870 TACAAGATGT
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
45 2 0.02
46 53 0.49
47 27 0.25
48 25 0.23
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAGATGA
Found at i:34744744 original size:73 final size:74
Alignment explanation
Indices: 34744667--34744819 Score: 188
Period size: 73 Copynumber: 2.1 Consensus size: 74
34744657 TATATAACGA
* * *
34744667 GAAGCTCATA-ATAGCCATAT-TCAGGAAGCTCATGCGAGCCAATAACGGGTAGCTCT-GAAGAG
1 GAAGCTCATAGATAGCCATATATCAGGAAGCTCAAGAGAGCCAATAACGGGAAGCT-TAG-AGAG
34744729 CCATTAATCAG
64 CCATTAATCAG
* ** * *
34744740 GAAGCT-TTAGATAGCCATATATTGGGAAGTTCAAGAGAGCCAATATCGGGAAGCTTAGAGAGCC
1 GAAGCTCATAGATAGCCATATATCAGGAAGCTCAAGAGAGCCAATAACGGGAAGCTTAGAGAGCC
34744804 ATTAATCAG
66 ATTAATCAG
34744813 GAAGCTC
1 GAAGCTC
34744820 TTAAAGAGCC
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
72 2 0.03
73 38 0.56
74 28 0.41
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (74 bp):
GAAGCTCATAGATAGCCATATATCAGGAAGCTCAAGAGAGCCAATAACGGGAAGCTTAGAGAGCC
ATTAATCAG
Found at i:34744827 original size:26 final size:26
Alignment explanation
Indices: 34744702--34744871 Score: 115
Period size: 26 Copynumber: 6.8 Consensus size: 26
34744692 AAGCTCATGC
* * *
34744702 GAGCCAATAA-CGGGTAGCTC-TGAA
1 GAGCCATTAATCGGGAAGCTCTTAAA
* *
34744726 GAGCCATTAATCAGGAAGCT-TTAGA
1 GAGCCATTAATCGGGAAGCTCTTAAA
* * *
34744751 TAGCCA-TATATTGGGAAG-T-TCAAGA
1 GAGCCATTA-ATCGGGAAGCTCTTAA-A
* *
34744776 GAGCCAAT-ATCGGGAAG--CTTAGA
1 GAGCCATTAATCGGGAAGCTCTTAAA
*
34744799 GAGCCATTAATCAGGAAGCTCTTAAA
1 GAGCCATTAATCGGGAAGCTCTTAAA
* **
34744825 GAGCCTTTAATCGGGAAGCTCACAAA
1 GAGCCATTAATCGGGAAGCTCTTAAA
* *
34744851 AAGCCTTTAATCGGGAAGCTC
1 GAGCCATTAATCGGGAAGCTC
34744872 ACGAAGAGCC
Statistics
Matches: 115, Mismatches: 22, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
23 8 0.07
24 32 0.28
25 27 0.23
26 48 0.42
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (26 bp):
GAGCCATTAATCGGGAAGCTCTTAAA
Found at i:34744881 original size:26 final size:26
Alignment explanation
Indices: 34744798--34744881 Score: 114
Period size: 26 Copynumber: 3.2 Consensus size: 26
34744788 GGAAGCTTAG
* * **
34744798 AGAGCCATTAATCAGGAAGCTCTTAA
1 AGAGCCTTTAATCGGGAAGCTCACAA
34744824 AGAGCCTTTAATCGGGAAGCTCACAA
1 AGAGCCTTTAATCGGGAAGCTCACAA
* *
34744850 AAAGCCTTTAATCGGGAAGCTCACGA
1 AGAGCCTTTAATCGGGAAGCTCACAA
34744876 AGAGCC
1 AGAGCC
34744882 ATATAATAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (26 bp):
AGAGCCTTTAATCGGGAAGCTCACAA
Found at i:34745026 original size:24 final size:23
Alignment explanation
Indices: 34744945--34745026 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 23
34744935 ACAACCAATT
* * *
34744945 GGGATGCTCAAAAGAGCTATTAAT
1 GGGAAGCTC-AAAGAGCTAATAAC
* *
34744969 GGGAAGCTCACAAGAACCATATAAC
1 GGGAAGCTCA-AAGAGCTA-ATAAC
*
34744994 AGGAAGCTCAAGAGAGCTAATAAC
1 GGGAAGCTCAA-AGAGCTAATAAC
*
34745018 GGGACGCTC
1 GGGAAGCTC
34745027 TTTCGAGCTA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
23 1 0.02
24 27 0.60
25 17 0.38
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (23 bp):
GGGAAGCTCAAAGAGCTAATAAC
Found at i:34749918 original size:11 final size:11
Alignment explanation
Indices: 34749904--34749937 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
34749894 CAAAATTTGG
34749904 AATAAATAAAT
1 AATAAATAAAT
34749915 AATAAATAAAT
1 AATAAATAAAT
*
34749926 AA-AAATTAAT
1 AATAAATAAAT
34749936 AA
1 AA
34749938 ATATAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:34749922 original size:15 final size:15
Alignment explanation
Indices: 34749904--34749945 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
34749894 CAAAATTTGG
34749904 AATAAATAAATAATA
1 AATAAATAAATAATA
*
34749919 AATAAATAAA-AATT
1 AATAAATAAATAATA
34749933 AATAAATATAATA
1 AATAAATA-AATA
34749946 TTGGGCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 11 0.46
15 12 0.50
16 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAATAAATAATA
Found at i:34751928 original size:37 final size:37
Alignment explanation
Indices: 34751875--34751977 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
34751865 CGAATAGTCC
*
34751875 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
34751912 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
34751949 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
34751978 ATATATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:34752179 original size:48 final size:48
Alignment explanation
Indices: 34752118--34752899 Score: 1314
Period size: 48 Copynumber: 16.3 Consensus size: 48
34752108 ATATACACAC
*
34752118 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
34752166 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
34752214 ATCTCATACATATTTCCCACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
34752262 ATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * * *
34752310 ATCTCATATATATTTCGCATTAGCCATTCGGCTTTACCACATGTACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * * *
34752358 ATCTCATACATATTTCGCATTAGCCGTTCGGATTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
34752406 ATCTCATACATATTTCGCATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
34752454 ATCTCATACATATTTCGCACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
34752502 ATCTCATACATATTTCGCACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
34752550 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
34752598 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
34752646 ATCTCATACATATTTCACACTAGCCATTCGG-TTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
34752693 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * * *
34752741 ATCTCATACATATTTCGCATTAGCCGTTCGGATTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
34752789 ATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
34752837 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
34752885 ATCTCATATATATTT
1 ATCTCATACATATTT
34752900 ATCTTGTACA
Statistics
Matches: 705, Mismatches: 28, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 0.07
48 658 0.93
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:34757634 original size:39 final size:40
Alignment explanation
Indices: 34757557--34757703 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
34757547 TAGCTCCTCG
* * *
34757557 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
34757597 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
34757636 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
34757676 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
34757704 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:34757714 original size:80 final size:80
Alignment explanation
Indices: 34757603--34757783 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
34757593 CTCATTCAAT
* * *
34757603 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
34757666 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
34757682 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
34757746 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
34757763 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
34757784 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:34757743 original size:40 final size:40
Alignment explanation
Indices: 34757600--34757783 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
34757590 TAACTCATTC
* *
34757600 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
34757640 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
34757680 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
34757720 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
34757761 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34757784 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:34765482 original size:39 final size:40
Alignment explanation
Indices: 34765405--34765511 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
34765395 TAGCTCCTCG
* * *
34765405 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
34765445 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
34765484 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
34765512 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:34765510 original size:79 final size:80
Alignment explanation
Indices: 34765411--34765631 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
34765401 CTCGTTCAAG
* * * ** * *
34765411 TGCCTTCGGGACATAGCCCGG-TTATATTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
34765474 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
34765490 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
34765555 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
34765570 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
34765632 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
79 36 0.31
80 75 0.64
81 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:34765547 original size:80 final size:80
Alignment explanation
Indices: 34765451--34765631 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
34765441 CTCATTCAAT
* * *
34765451 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA
*
34765513 TTAGT-A-TCTCGCACAAA
64 -TAGTCACT-TAGCACAAA
**
34765530 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATAT
34765595 AGTCACTTAGCACAAA
65 AGTCACTTAGCACAAA
*
34765611 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
34765632 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:34765591 original size:40 final size:40
Alignment explanation
Indices: 34765448--34765631 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
34765438 TAACTCATTC
* *
34765448 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
34765488 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
34765528 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
34765568 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
34765609 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
34765632 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:34767201 original size:11 final size:11
Alignment explanation
Indices: 34767187--34767223 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
34767177 AACTGCCTTC
*
34767187 GACCATCGTCA
1 GACCATCGCCA
34767198 GACCATCGCCA
1 GACCATCGCCA
34767209 GACCATCGCCA
1 GACCATCGCCA
34767220 -ACCA
1 GACCA
34767224 CTATCGACCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 4 0.16
11 21 0.84
ACGTcount: A:0.30, C:0.43, G:0.16, T:0.11
Consensus pattern (11 bp):
GACCATCGCCA
Found at i:34776214 original size:17 final size:19
Alignment explanation
Indices: 34776192--34776237 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
34776182 ACATACATGC
34776192 AATAAT-ATTTT-TCTAAT
1 AATAATAATTTTATCTAAT
*
34776209 AATAATAATTTTATCTCAT
1 AATAATAATTTTATCTAAT
*
34776228 AATACTAATT
1 AATAATAATT
34776238 AAAATTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 14 0.56
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATAATTTTATCTAAT
Found at i:34778778 original size:25 final size:25
Alignment explanation
Indices: 34778750--34778799 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
34778740 TAAAGTATGT
34778750 GAAATTGAACAATATTGATTGATAC
1 GAAATTGAACAATATTGATTGATAC
*
34778775 GAAATTGAACGATATTGATTGATAC
1 GAAATTGAACAATATTGATTGATAC
34778800 CAACTCAATG
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:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (25 bp):
GAAATTGAACAATATTGATTGATAC
Found at i:34786718 original size:47 final size:48
Alignment explanation
Indices: 34786649--34786860 Score: 199
Period size: 46 Copynumber: 4.5 Consensus size: 48
34786639 TAAGGTACCA
* * *
34786649 ATGCCATGTCCTAGACACGGTCTTACACAGGCTAAT-ATCTC-AAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCT-ATCATCTCGAAGCCG
* * * *
34786696 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTAGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCTATCATCTCGAAGCCG
* * * *
34786744 ATG-CATATCCCAGACAT-GTCTTACACTGGCT-TACGTCTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCTAT-CATCTCGAAGCCG
* * *
34786790 ATG-CATGTCCCAGACAT-GTCTTACACTA-GCTTTCGTCTC-AATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACAC-AGGCTATCATCTCGAA-GCCG
34786836 ATGCCATGTCCCAGACATGGTCTTA
1 ATGCCATGTCCCAGACATGGTCTTA
34786861 AATTAGCTCT
Statistics
Matches: 140, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
45 2 0.01
46 64 0.46
47 62 0.44
48 12 0.09
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACAGGCTATCATCTCGAAGCCG
Found at i:34786891 original size:47 final size:49
Alignment explanation
Indices: 34786694--34786901 Score: 131
Period size: 46 Copynumber: 4.4 Consensus size: 49
34786684 TATCTCAAGT
* *
34786694 CGATGCCATGTCCCAGACATGGTCTTACACT-GACTATC--ATC--TCGTAGC
1 CGATG-CATGTCCCAGACATGGTCTTAAACTAG-CT-TCGTATCAAT-GTGGC
* * * * * *
34786742 CAATGCATATCCCAGACAT-GTCTTACACTGGCTTACGTCTC---GAGGC
1 CGATGCATGTCCCAGACATGGTCTTAAACTAGCTT-CGTATCAATGTGGC
* *
34786788 CGATGCATGTCCCAGACAT-GTCTTACACTAGCTTTCGTCTCAATGT---
1 CGATGCATGTCCCAGACATGGTCTTAAACTAGC-TTCGTATCAATGTGGC
* *
34786834 CGATGCCATGTCCCAGACATGGTCTTAAATTAGC-TCTTAT-AATGTGGC
1 CGATG-CATGTCCCAGACATGGTCTTAAACTAGCTTCGTATCAATGTGGC
*
34786882 CGATGCATGTCCTAGACATG
1 CGATGCATGTCCCAGACATG
34786902 TATTACATTA
Statistics
Matches: 133, Mismatches: 14, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
45 6 0.05
46 60 0.45
47 44 0.33
48 22 0.17
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (49 bp):
CGATGCATGTCCCAGACATGGTCTTAAACTAGCTTCGTATCAATGTGGC
Found at i:34788450 original size:33 final size:31
Alignment explanation
Indices: 34788408--34788492 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 31
34788398 TCACACAAGG
34788408 TAGGTGCAACTTTATACTTAAAT-AACATTAAGA
1 TAGGTGCAACTTTA-AC--AAATAAACATTAAGA
*
34788441 TAGGTGCAAC-TTAACAAGTAAACATTAAGA
1 TAGGTGCAACTTTAACAAATAAACATTAAGA
*
34788471 TAGGTGCAAC-TTAACAAGTAAA
1 TAGGTGCAACTTTAACAAATAAA
34788493 TGCCTATAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
29 3 0.06
30 32 0.64
31 2 0.04
32 3 0.06
33 10 0.20
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (31 bp):
TAGGTGCAACTTTAACAAATAAACATTAAGA
Found at i:34788467 original size:30 final size:30
Alignment explanation
Indices: 34788431--34788492 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
34788421 ATACTTAAAT
34788431 AACATTAAGATAGGTGCAACTTAACAAGTA
1 AACATTAAGATAGGTGCAACTTAACAAGTA
34788461 AACATTAAGATAGGTGCAACTTAACAAGTA
1 AACATTAAGATAGGTGCAACTTAACAAGTA
34788491 AA
1 AA
34788493 TGCCTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (30 bp):
AACATTAAGATAGGTGCAACTTAACAAGTA
Found at i:34789474 original size:31 final size:31
Alignment explanation
Indices: 34789436--34789495 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
34789426 TTGTATGTAT
* *
34789436 TGTTATTTTAAATGTCGGTATAATTTTTTTA
1 TGTTATTTTAAAAGTCGATATAATTTTTTTA
*
34789467 TGTTATTTTAAAAGTTGATATAATTTTTT
1 TGTTATTTTAAAAGTCGATATAATTTTTT
34789496 AACTCATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (31 bp):
TGTTATTTTAAAAGTCGATATAATTTTTTTA
Found at i:34789752 original size:17 final size:17
Alignment explanation
Indices: 34789732--34789765 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34789722 AATAAATTAT
*
34789732 AAATCAATAAAAATATA
1 AAATAAATAAAAATATA
*
34789749 AAATAAATACAAATATA
1 AAATAAATAAAAATATA
34789766 CCTTAATAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAAAATATA
Found at i:34789754 original size:21 final size:20
Alignment explanation
Indices: 34789709--34789757 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
34789699 TTTTTACTCC
*
34789709 AATAAATATTAAAAATAAAT
1 AATAAATAATAAAAATAAAT
*
34789729 TATAAATCAATAAAAATATAA-
1 AATAAAT-AATAAAAATA-AAT
34789750 AATAAATA
1 AATAAATA
34789758 CAAATATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.29
21 15 0.62
22 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAATAATAAAAATAAAT
Found at i:34789819 original size:7 final size:7
Alignment explanation
Indices: 34789807--34789857 Score: 102
Period size: 7 Copynumber: 7.3 Consensus size: 7
34789797 TTATAAAAAT
34789807 AAAATTA
1 AAAATTA
34789814 AAAATTA
1 AAAATTA
34789821 AAAATTA
1 AAAATTA
34789828 AAAATTA
1 AAAATTA
34789835 AAAATTA
1 AAAATTA
34789842 AAAATTA
1 AAAATTA
34789849 AAAATTA
1 AAAATTA
34789856 AA
1 AA
34789858 TTCAAATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:34789831 original size:21 final size:21
Alignment explanation
Indices: 34789800--34789857 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
34789790 TAATACCTTA
34789800 TAAAAA-T-AAAATTAAAAAT
1 TAAAAATTAAAAATTAAAAAT
34789819 TAAAAATTAAAAATTAAAAAT
1 TAAAAATTAAAAATTAAAAAT
34789840 TAAAAATTAAAAATTAAA
1 TAAAAATTAAAAATTAAA
34789858 TTCAAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.16
20 1 0.03
21 30 0.81
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATTAAAAATTAAAAAT
Found at i:34790099 original size:37 final size:34
Alignment explanation
Indices: 34790029--34790101 Score: 83
Period size: 37 Copynumber: 2.1 Consensus size: 34
34790019 TATTATTTTT
*
34790029 TTCCTTATTTTTCTTTTTCCTTCCCTCCCTCTTC
1 TTCCTTATTTTTCTTTTTCCTTCCCGCCCTCTTC
* **
34790063 TTCCTTTTTTTTCTTTCTTTCCTTTCCCGCTGTCTTC
1 TTCCTTATTTTTC-TT-TTTCC-TTCCCGCCCTCTTC
34790100 TT
1 TT
34790102 TTTCTTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 12 0.38
35 2 0.06
36 5 0.16
37 13 0.41
ACGTcount: A:0.01, C:0.34, G:0.03, T:0.62
Consensus pattern (34 bp):
TTCCTTATTTTTCTTTTTCCTTCCCGCCCTCTTC
Found at i:34793867 original size:47 final size:47
Alignment explanation
Indices: 34793798--34793891 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
34793788 AAGAGTCAAG
34793798 GTAATCTCAACATAACCTTTTAGTGCTTAGTCTATCAATATAATTCA
1 GTAATCTCAACATAACCTTTTAGTGCTTAGTCTATCAATATAATTCA
34793845 GTAATCTCAACATAACCTTTTAGTGCTTAGTCTATCAATATAATTCA
1 GTAATCTCAACATAACCTTTTAGTGCTTAGTCTATCAATATAATTCA
34793892 TTCTTTTACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (47 bp):
GTAATCTCAACATAACCTTTTAGTGCTTAGTCTATCAATATAATTCA
Found at i:34799451 original size:34 final size:34
Alignment explanation
Indices: 34799404--34799468 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
34799394 AATGTATAGG
* *
34799404 ATCCATCCAAACACTAGAGAGCACATAAGTGTTA
1 ATCCATCCAAACACCAGAGAACACATAAGTGTTA
*
34799438 ATCC-TCCAAAACACCAGAGAACACGTAAGTG
1 ATCCATCC-AAACACCAGAGAACACATAAGTG
34799469 CTAAGGTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 24 0.89
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (34 bp):
ATCCATCCAAACACCAGAGAACACATAAGTGTTA
Found at i:34799574 original size:36 final size:36
Alignment explanation
Indices: 34799510--34799609 Score: 89
Period size: 36 Copynumber: 2.8 Consensus size: 36
34799500 AGCCCGAAGG
* * *
34799510 CAACAAAATTCCAGATGATAAT-AGAACTCTAA-ATCA
1 CAACAAAATTCCATATCAT-ATCAAAACTC-AATATCA
34799546 CAACAAAATTCCATATCATATCAAAACTCAATATCA
1 CAACAAAATTCCATATCATATCAAAACTCAATATCA
* * * *
34799582 GAAC-AGATCTTCATATCATAACAAAACT
1 CAACAAAAT-TCCATATCATATCAAAACT
34799610 TCATATCTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 7 0.13
36 47 0.87
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (36 bp):
CAACAAAATTCCATATCATATCAAAACTCAATATCA
Found at i:34799597 original size:18 final size:18
Alignment explanation
Indices: 34799542--34799616 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
34799532 AGAACTCTAA
*
34799542 ATCACAACAAAA-TTCCAT
1 ATCAGAACAAAACTT-CAT
* *
34799560 ATCATATCAAAAC-TCAAT
1 ATCAGAACAAAACTTC-AT
* *
34799578 ATCAGAACAGATCTTCAT
1 ATCAGAACAAAACTTCAT
*
34799596 ATCATAACAAAACTTCAT
1 ATCAGAACAAAACTTCAT
34799614 ATC
1 ATC
34799617 TAAACTATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
17 1 0.02
18 42 0.93
19 2 0.04
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.27
Consensus pattern (18 bp):
ATCAGAACAAAACTTCAT
Found at i:34810879 original size:71 final size:71
Alignment explanation
Indices: 34810793--34810955 Score: 281
Period size: 71 Copynumber: 2.3 Consensus size: 71
34810783 AGCATAAATT
*
34810793 AGGTTCATGTATTAATTGGATTATGACCAAACGTGAAGCGATCATTAGTACGTGTGAATACCTAA
1 AGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGATCATTAGTACGTGTGAATACCTAA
34810858 GGAATC
66 GGAATC
* * *
34810864 AGGTTCACATATTAATTGGATTATGACCAAACGTGAAGCGATTATTAGTACGTGTGAATGCCTAA
1 AGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGATCATTAGTACGTGTGAATACCTAA
*
34810929 GGAATT
66 GGAATC
34810935 AGGTTCACGTATTAATTGGAT
1 AGGTTCACGTATTAATTGGAT
34810956 GAAAATTCAT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 86 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (71 bp):
AGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGATCATTAGTACGTGTGAATACCTAA
GGAATC
Found at i:34812547 original size:718 final size:718
Alignment explanation
Indices: 34810841--34812985 Score: 3976
Period size: 718 Copynumber: 3.0 Consensus size: 718
34810831 CGATCATTAG
* *
34810841 TACGTGTGAATACCTAAGGAATCAGGTTCACATATTAATTGGATTATGACCAAACGTGAAGCGAT
1 TACGTGTGAATACCTAAGGAATTAGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGAT
34810906 TATTAGTACGTGTGAATGCCTAAGGAATTAGGTTCACGTATTAATTGGATGAAAATTCATTTTCT
66 TATTAGTACGTGTGAATGCCTAAGGAATTAGGTTCACGTATTAATTGGATGAAAATTCATTTTCT
34810971 TACTAGTTGATTAAGATTGCCCTAAGGTGATTTAATTCAATGAGTATAGGGATTATCATTGCAAT
131 TACTAGTTGATTAAGATTGCCCTAAGGTGATTTAATTCAATGAGTATAGGGATTATCATTGCAAT
*
34811036 GACTTACAAATATTTTCCAAGATTTAATGTCAGACGCATGCATTATCTTAATGCATATCGTTTGT
196 GACTTACAAATATTTTCCAAGATTTAATGTAAGACGCATGCATTATCTTAATGCATATCGTTTGT
34811101 TGCAAAAGGTTTTATAATATTTCCTTAATACAAAAATATTAATGAATGGATGTTTTATTTTTAGT
261 TGCAAAAGGTTTTATAATATTTCCTTAATACAAAAATATTAATGAATGGATGTTTTATTTTTAGT
34811166 TCAAAAAAATGACACCTACTCTCTTACTAAACATACTTATTGAGAACAAACTAAACGAAAATAAC
326 TCAAAAAAATGACACCTACTCTCTTACTAAACATACTTATTGAGAACAAACTAAACGAAAATAAC
*
34811231 TATAATGAATGGAAAAAGGAACATCATGATTGTCCTAAGCTATGAGAAACTCAAAACATGTCTTG
391 TATAATGAATGG-AAAAGGAACATCATGATTGTCCTAAGCTATGAGAAACTCAAAACATTTCTTG
34811296 ATAATAGATGCCCACGACCACTCAAAATAAGGCTAGAAAACATTGGGAGGAGTTTGATGGGATAG
455 ATAATAGATGCCCACGACCACTCAAAATAAGGCTAGAAAACATTGGGAGGAGTTTGATGGGATAG
34811361 CTCGCTGTCATATGCTGGCAAGTGTGACCAACACTCTTTATAAGAAATTGGAGAAATGTAAGGTT
520 CTCGCTGTCATATGCTGGCAAGTGTGACCAACACTCTTTATAAGAAATTGGAGAAATGTAAGGTT
34811426 GCCAAAGTTATTCTAGACAAACTAGAGGACATGTTTGGAGGCCAAACTGCCTTGGCAT-ACAGTC
585 GCCAAAGTTATTCTAGACAAACTAGAGGACATGTTTGGAGGCCAAACTGCCTTGGCATGACAGTC
34811490 GGCTATAATTAGTTTGATGAATGCCCAACAAAAACCTAGTACTCTAGTCAAAGACCATATGATTG
650 GGCTATAATTAGTTTGATGAATGCCCAACAAAAACCTAGTACTCTAGTCAAAGACCATATGATTG
34811555 CTCT
715 CTCT
* * *
34811559 TAC----GAATACCTAAGAAATTAGGTTCAAGTATTAATTGGATTATGACCAAACGTGGAGCGAT
1 TACGTGTGAATACCTAAGGAATTAGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGAT
*
34811620 TATTAGTACATGTGAATGCCTAAGGAATTAGGTTCACGTATTAATTGGATGAAAATTCATTTTCT
66 TATTAGTACGTGTGAATGCCTAAGGAATTAGGTTCACGTATTAATTGGATGAAAATTCATTTTCT
* *
34811685 TACTAATTGATTAAGATTGCCCTAAGGTGACTTAATTCAATGAGTATAGGGATTATCATTGCAAT
131 TACTAGTTGATTAAGATTGCCCTAAGGTGATTTAATTCAATGAGTATAGGGATTATCATTGCAAT
*
34811750 GACTTACAAATATTTTCCCAGATTTAATGTAAGACGCATGCATTATCTTAATGCATATCGTTTGT
196 GACTTACAAATATTTTCCAAGATTTAATGTAAGACGCATGCATTATCTTAATGCATATCGTTTGT
34811815 TGCAAAAGGTTTTATAATATTTCCTTAATACAAAAATATTAATGAATGGATGTTTTATTTTTAGT
261 TGCAAAAGGTTTTATAATATTTCCTTAATACAAAAATATTAATGAATGGATGTTTTATTTTTAGT
* *
34811880 TCAAAAAAATGACACCTACTCTCTTACTAAACATACTTATTGAGAATAAACTAAATGAAAATAAC
326 TCAAAAAAATGACACCTACTCTCTTACTAAACATACTTATTGAGAACAAACTAAACGAAAATAAC
*
34811945 TATAATGAATGGAAAAGGAAAATCATGATTGTCCTAAGCTATGAGAAACTCAAAACATTTCTTGA
391 TATAATGAATGGAAAAGGAACATCATGATTGTCCTAAGCTATGAGAAACTCAAAACATTTCTTGA
* *
34812010 TAATAGATGCCCACAACCACTCAAAATAATGCTAGAAAACATTGGGAGGAGTTTGATGGGATAGC
456 TAATAGATGCCCACGACCACTCAAAATAAGGCTAGAAAACATTGGGAGGAGTTTGATGGGATAGC
* * *
34812075 TCGTTGTCATATGCTGGAAAGTGTGACCAACACTCTTTATAAGAAATTAGAGAAATGTAAGGTTG
521 TCGCTGTCATATGCTGGCAAGTGTGACCAACACTCTTTATAAGAAATTGGAGAAATGTAAGGTTG
*
34812140 CCAAAGTTATTCTAGACAAACTATAGGACATGTTTGGAGGCCAAACTGCCTTGGCATGACAGTCG
586 CCAAAGTTATTCTAGACAAACTAGAGGACATGTTTGGAGGCCAAACTGCCTTGGCATGACAGTCG
*
34812205 ACTATAATTAGTTTGATGAATGCCCAACAAAAACCTAGTACTCTAGTCAAAGACCATATGATTGC
651 GCTATAATTAGTTTGATGAATGCCCAACAAAAACCTAGTACTCTAGTCAAAGACCATATGATTGC
34812270 TCT
716 TCT
34812273 TACGTGTGAATACCTAAGGAATTAGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGAT
1 TACGTGTGAATACCTAAGGAATTAGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGAT
34812338 TATTAGTACGTGTGAATGCCTAAGGAATTAGGTTCACGTATTAATTGGATGAAAATTCATTTTCT
66 TATTAGTACGTGTGAATGCCTAAGGAATTAGGTTCACGTATTAATTGGATGAAAATTCATTTTCT
34812403 TACTAGTTGATTAAGATTGCCCTAAGGTGATTTAATTCAATGAGTATAGGGATTATCATTGCAAT
131 TACTAGTTGATTAAGATTGCCCTAAGGTGATTTAATTCAATGAGTATAGGGATTATCATTGCAAT
34812468 GACTTACAAATATTTTCCAAGATTTAATGTAAGACGCATGCATTATCTTAATGCATATCGTTTGT
196 GACTTACAAATATTTTCCAAGATTTAATGTAAGACGCATGCATTATCTTAATGCATATCGTTTGT
*
34812533 TGCAAAAAGTTTTATAATATTTCCTTAATACAAAAATATTAATGAATGGATGTTTTATTTTTAGT
261 TGCAAAAGGTTTTATAATATTTCCTTAATACAAAAATATTAATGAATGGATGTTTTATTTTTAGT
34812598 TCAAAAAAATGACACCTACTCTCTTACTAAACATACTTATTGAGAACAAACTAAACGAAAATAAC
326 TCAAAAAAATGACACCTACTCTCTTACTAAACATACTTATTGAGAACAAACTAAACGAAAATAAC
*
34812663 TATAATGAATGGAAAATGAACATCATGATTGTCCTAAGCTATGAGAAACTCAAAACATTTCTTGA
391 TATAATGAATGGAAAAGGAACATCATGATTGTCCTAAGCTATGAGAAACTCAAAACATTTCTTGA
* *
34812728 TAATAGATTCCCACGACCACTCAAAATAAGGCTAGAAAACATTAGGAGGAGTTTGATGGGATAGC
456 TAATAGATGCCCACGACCACTCAAAATAAGGCTAGAAAACATTGGGAGGAGTTTGATGGGATAGC
* * *
34812793 TCGCTATCATATGCTGGCAAGTGTGACCAGCACTCTTTATAAGCAATTGGAGAAATGTAAGGTTG
521 TCGCTGTCATATGCTGGCAAGTGTGACCAACACTCTTTATAAGAAATTGGAGAAATGTAAGGTTG
*
34812858 CCAAAGTTATTCTAGATAAACTAGAGGACATGTTTGGAGGCCAAACTGCCTTGGCATGACAGTCG
586 CCAAAGTTATTCTAGACAAACTAGAGGACATGTTTGGAGGCCAAACTGCCTTGGCATGACAGTCG
*
34812923 GCTATAATTAGTTTGATGAATGCCCAACAAAAACCTGGTACTCTAGTCAAAGACCATATGATT
651 GCTATAATTAGTTTGATGAATGCCCAACAAAAACCTAGTACTCTAGTCAAAGACCATATGATT
34812986 AAGGACTGCA
Statistics
Matches: 1375, Mismatches: 47, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
713 232 0.17
714 460 0.33
718 683 0.50
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (718 bp):
TACGTGTGAATACCTAAGGAATTAGGTTCACGTATTAATTGGATTATGACCAAACGTGAAGCGAT
TATTAGTACGTGTGAATGCCTAAGGAATTAGGTTCACGTATTAATTGGATGAAAATTCATTTTCT
TACTAGTTGATTAAGATTGCCCTAAGGTGATTTAATTCAATGAGTATAGGGATTATCATTGCAAT
GACTTACAAATATTTTCCAAGATTTAATGTAAGACGCATGCATTATCTTAATGCATATCGTTTGT
TGCAAAAGGTTTTATAATATTTCCTTAATACAAAAATATTAATGAATGGATGTTTTATTTTTAGT
TCAAAAAAATGACACCTACTCTCTTACTAAACATACTTATTGAGAACAAACTAAACGAAAATAAC
TATAATGAATGGAAAAGGAACATCATGATTGTCCTAAGCTATGAGAAACTCAAAACATTTCTTGA
TAATAGATGCCCACGACCACTCAAAATAAGGCTAGAAAACATTGGGAGGAGTTTGATGGGATAGC
TCGCTGTCATATGCTGGCAAGTGTGACCAACACTCTTTATAAGAAATTGGAGAAATGTAAGGTTG
CCAAAGTTATTCTAGACAAACTAGAGGACATGTTTGGAGGCCAAACTGCCTTGGCATGACAGTCG
GCTATAATTAGTTTGATGAATGCCCAACAAAAACCTAGTACTCTAGTCAAAGACCATATGATTGC
TCT
Found at i:34816590 original size:22 final size:22
Alignment explanation
Indices: 34816562--34816606 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
34816552 GAACCACTTG
34816562 GAATACTAAAGGATATTTAGGA
1 GAATACTAAAGGATATTTAGGA
34816584 GAATACTAAAGGATATTTAGGA
1 GAATACTAAAGGATATTTAGGA
34816606 G
1 G
34816607 CCCCGTACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.27
Consensus pattern (22 bp):
GAATACTAAAGGATATTTAGGA
Found at i:34816744 original size:42 final size:42
Alignment explanation
Indices: 34816631--34816784 Score: 211
Period size: 42 Copynumber: 3.7 Consensus size: 42
34816621 TACCATACCA
* * *
34816631 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
34816673 ATGCCAATAGCCTAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
34816716 ATGTCATATCCCAGATATGGTCTTACACGAAGTCTCATATCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
34816758 ATGCCATAT-CCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
34816785 ATAATCCTCG
Statistics
Matches: 98, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
41 18 0.18
42 45 0.46
43 35 0.36
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Done.