Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 91 of 135
Found at i:34518293 original size:12 final size:12
Alignment explanation
Indices: 34518259--34518297 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
34518249 TAAAATATAT
34518259 TAAATTTATTT-
1 TAAATTTATTTA
34518270 TATAATTT-TTTA
1 TA-AATTTATTTA
34518282 TAAATTTATTTA
1 TAAATTTATTTA
34518294 TAAA
1 TAAA
34518298 CAACATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATTTATTTA
Found at i:34523247 original size:15 final size:15
Alignment explanation
Indices: 34523227--34523257 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34523217 TTTTCAAATG
*
34523227 AACAACAATGAACAA
1 AACAACAAAGAACAA
34523242 AACAACAAAGAACAA
1 AACAACAAAGAACAA
34523257 A
1 A
34523258 GGCCCTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.19, G:0.06, T:0.03
Consensus pattern (15 bp):
AACAACAAAGAACAA
Found at i:34524609 original size:22 final size:23
Alignment explanation
Indices: 34524581--34524630 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
34524571 TTACGGAAGG
*
34524581 CTCAATGTCTCAAGACATGAA-C
1 CTCAATGTCTCAAGACATCAAGC
34524603 CTCAATGTCTCAAGACATCAAGC
1 CTCAATGTCTCAAGACATCAAGC
34524626 CTCAA
1 CTCAA
34524631 AGCTAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (23 bp):
CTCAATGTCTCAAGACATCAAGC
Found at i:34527385 original size:23 final size:24
Alignment explanation
Indices: 34527341--34527386 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
34527331 TTCAAACTCG
34527341 AGCCTAACCCATATTTTTAAACAA
1 AGCCTAACCCATATTTTTAAACAA
34527365 AGCCTAACCCATA-TTTTAAACA
1 AGCCTAACCCATATTTTTAAACA
34527387 TACATTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.28
Consensus pattern (24 bp):
AGCCTAACCCATATTTTTAAACAA
Found at i:34529981 original size:6 final size:6
Alignment explanation
Indices: 34529970--34530001 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
34529960 CATATATATC
34529970 TAGATA TAGATA TAGATA TAGATA TAGATA TA
1 TAGATA TAGATA TAGATA TAGATA TAGATA TA
34530002 ATTATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
TAGATA
Found at i:34532599 original size:14 final size:16
Alignment explanation
Indices: 34532565--34532602 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
34532555 TTTCTAATAT
*
34532565 AAATTTAGCACTTATA
1 AAATTTAGCACGTATA
34532581 AAATTTAGCA-GTA-A
1 AAATTTAGCACGTATA
34532595 AAATTTAG
1 AAATTTAG
34532603 TATTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 2 0.10
16 10 0.48
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (16 bp):
AAATTTAGCACGTATA
Found at i:34533596 original size:2 final size:2
Alignment explanation
Indices: 34533589--34533625 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
34533579 TAAATATCTC
*
34533589 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34533626 CCACATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34534640 original size:27 final size:28
Alignment explanation
Indices: 34534609--34534670 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
34534599 GTAGGTGGTG
34534609 CCTATCTAG-TAGGCGCCACTA-GTGACT
1 CCTATCTAGATAGGCGCCAC-AGGTGACT
34534636 CCTATCT-GATAGGCGCCACAGGTGACT
1 CCTATCTAGATAGGCGCCACAGGTGACT
34534663 CCTATCTA
1 CCTATCTA
34534671 ATATGTGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (28 bp):
CCTATCTAGATAGGCGCCACAGGTGACT
Found at i:34535152 original size:108 final size:108
Alignment explanation
Indices: 34534833--34535163 Score: 434
Period size: 102 Copynumber: 3.1 Consensus size: 108
34534823 ATTCAATTTA
* ** *
34534833 AAAAAATTACAAAATACTAAACTAAACACTAACAACTTATATAACCTAAT--CATAAATTACTAA
1 AAAAAATAACAAAACCCTAAACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATTACTAA
* * * *
34534896 C---A-AAATAACTATAAAATTATTTAAAAAAAAATTACATTACT
64 CAAAATAAATAACTATAACATTTTTTTAAAAGAAATTACATTACT
*
34534937 AAAAAATCACAAAACCCTAAACTAAACACTAACAATTTG-----TAA-CCCATAAATTACTAACA
1 AAAAAATAACAAAACCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTACTAACA
*
34534996 AAATAAATAACTATAACATTTTTTTAAAAGAAATTACATCACT
66 AAATAAATAACTATAACATTTTTTTAAAAGAAATTACATTACT
* *
34535039 AAAAAATAACAAAGCCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTAATAACA
1 AAAAAATAACAAAACCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTACTAACA
34535104 AAATAAATAACTATAACATTTTTTTTAAAAGAAATTACATTACT
66 AAATAAATAACTATAACA-TTTTTTTAAAAGAAATTACATTACT
34535148 AAAAAAATAACAAAAC
1 -AAAAAATAACAAAAC
34535164 ACAAAACACT
Statistics
Matches: 199, Mismatches: 14, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
97 3 0.02
98 14 0.07
101 1 0.01
102 72 0.36
103 2 0.01
104 32 0.16
107 3 0.02
108 34 0.17
109 24 0.12
110 14 0.07
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (108 bp):
AAAAAATAACAAAACCCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTACTAACA
AAATAAATAACTATAACATTTTTTTAAAAGAAATTACATTACT
Found at i:34535314 original size:72 final size:71
Alignment explanation
Indices: 34535219--34535357 Score: 269
Period size: 72 Copynumber: 1.9 Consensus size: 71
34535209 TATATTTTTA
34535219 AATTTTCATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAA
1 AATTTTCATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAA
34535284 CAAAAT
66 CAAAAT
34535290 AATTTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTA
1 AATTTT-CATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTA
34535355 ACA
65 ACA
34535358 CAACCAGTGG
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 6 0.09
72 61 0.91
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (71 bp):
AATTTTCATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAA
CAAAAT
Found at i:34535328 original size:34 final size:34
Alignment explanation
Indices: 34535219--34535328 Score: 98
Period size: 34 Copynumber: 3.1 Consensus size: 34
34535209 TATATTTTTA
34535219 AATTTT-CATTACTAAAAACTCACAAAACACAAC
1 AATTTTACATTACTAAAAACTCACAAAACACAAC
* * *** * *
34535252 AATTTATAATAAATTACTAACAAAAT-ATTTAACAAAAT
1 AA-TT-T--TACATTACTAA-AAACTCACAAAACACAAC
34535290 AATTTTACATTACTAAAAACTCACAAAACACAAC
1 AATTTTACATTACTAAAAACTCACAAAACACAAC
34535324 AATTT
1 AATTT
34535329 ATAATAAATT
Statistics
Matches: 56, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
33 6 0.11
34 24 0.43
35 1 0.02
36 1 0.02
37 3 0.05
38 17 0.30
39 4 0.07
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (34 bp):
AATTTTACATTACTAAAAACTCACAAAACACAAC
Found at i:34535358 original size:38 final size:38
Alignment explanation
Indices: 34535244--34535361 Score: 129
Period size: 38 Copynumber: 3.2 Consensus size: 38
34535234 AAACTCACAA
34535244 AACACAACAATTTATAATAAATTACTAACAAAATATTT
1 AACACAACAATTTATAATAAATTACTAACAAAATATTT
* * * * ***
34535282 AACAAAATAA-TT-T--TACATTACTAA-AAACTCACAA
1 AACACAACAATTTATAATAAATTACTAACAAAAT-ATTT
34535316 AACACAACAATTTATAATAAATTACTAACAAAATATTT
1 AACACAACAATTTATAATAAATTACTAACAAAATATTT
34535354 AACACAAC
1 AACACAAC
34535362 CAGTGGCGCC
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
33 4 0.07
34 19 0.32
35 2 0.03
36 2 0.03
37 2 0.03
38 27 0.45
39 4 0.07
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (38 bp):
AACACAACAATTTATAATAAATTACTAACAAAATATTT
Found at i:34535416 original size:27 final size:27
Alignment explanation
Indices: 34535363--34535417 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
34535353 TAACACAACC
* *
34535363 AGTGGCGCCTATCAGATAGGAGTCACT
1 AGTGGCGCCTACCAGATAGGAGCCACT
34535390 AGTGGCGCCTACCAGATAGGCA-CCACT
1 AGTGGCGCCTACCAGATAGG-AGCCACT
34535417 A
1 A
34535418 ACCCCATACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (27 bp):
AGTGGCGCCTACCAGATAGGAGCCACT
Found at i:34536049 original size:24 final size:25
Alignment explanation
Indices: 34536017--34536071 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
34536007 CACTTTTTTT
* *
34536017 AATAATATTTTTTTACTTT-TAAAA
1 AATATTATTATTTTACTTTATAAAA
*
34536041 AATATTATTATTTTATTTTATAAAA
1 AATATTATTATTTTACTTTATAAAA
34536066 AATATT
1 AATATT
34536072 TAAATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTATTATTTTACTTTATAAAA
Found at i:34536243 original size:7 final size:7
Alignment explanation
Indices: 34536231--34536267 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
34536221 CACAGCCCCT
34536231 CCCTCTG
1 CCCTCTG
34536238 CCCTCTG
1 CCCTCTG
34536245 CCCTCTG
1 CCCTCTG
34536252 CCCTCTG
1 CCCTCTG
34536259 CCCTCTG
1 CCCTCTG
34536266 CC
1 CC
34536268 GTGGACTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.59, G:0.14, T:0.27
Consensus pattern (7 bp):
CCCTCTG
Found at i:34536578 original size:11 final size:11
Alignment explanation
Indices: 34536564--34536648 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
34536554 TTTTTTTGTT
34536564 TTTTATAATTA
1 TTTTATAATTA
*
34536575 TTTTAAAATTA
1 TTTTATAATTA
* * *
34536586 TTTTGTTAGTA
1 TTTTATAATTA
* **
34536597 ATTTAGGATTA
1 TTTTATAATTA
* *
34536608 TGTTATAAATTG
1 TTTTAT-AATTA
34536620 TGTTTATAATTA
1 T-TTTATAATTA
*
34536632 TTTTAAAATTA
1 TTTTATAATTA
*
34536643 ATTTAT
1 TTTTAT
34536649 TAGTAATTTA
Statistics
Matches: 52, Mismatches: 20, Indels: 4
0.68 0.26 0.05
Matches are distributed among these distances:
11 39 0.75
12 9 0.17
13 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TTTTATAATTA
Found at i:34536709 original size:53 final size:57
Alignment explanation
Indices: 34536566--34536725 Score: 238
Period size: 57 Copynumber: 2.9 Consensus size: 57
34536556 TTTTTGTTTT
* * *
34536566 TTATAATTATTTTAAAATTATTTTGTTAGTAATTTAGGATTATGTTATAAATTGTGT
1 TTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTGA
34536623 TTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAA-T-T-A
1 TTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTGA
* * *
34536677 TTGT-GTTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAA
1 TTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAA
34536726 GTTTGTGTGT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
53 43 0.44
54 3 0.03
55 1 0.01
56 1 0.01
57 49 0.51
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (57 bp):
TTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTGA
Found at i:34536735 original size:53 final size:54
Alignment explanation
Indices: 34536572--34536736 Score: 226
Period size: 53 Copynumber: 3.0 Consensus size: 54
34536562 TTTTTTATAA
* * * * *
34536572 TTATTTTAAAATTATTTTGTTAGTAATTTAGGATTATGTTATAAATTGTGTTTATAA
1 TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTATG--TGT-G
34536629 TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTAT-TGTG
1 TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTATGTGTG
* *
34536682 TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAGTT-TGTGTG
1 TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTATGTGTG
34536735 TT
1 TT
34536737 TAGTTTAATA
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
52 1 0.01
53 51 0.51
54 2 0.02
57 46 0.46
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTATGTGTG
Found at i:34536935 original size:60 final size:59
Alignment explanation
Indices: 34536803--34536916 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 59
34536793 ATGGTAAATC
**
34536803 ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGTAAAATTATTTTGTTAGTAATTT
1 ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGT-AAATTATTTTGTTAAAAATTT
* *
34536863 ATTATAAATTGTTGTGTTTTGTTAGTTTTTAGTAATGT-AATTATTTT-TTAAAAA
1 ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGTAAATTATTTTGTTAAAAA
34536917 ATTTTATGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 5 0.10
58 9 0.18
60 36 0.72
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (59 bp):
ATTATAAATTGTTGTATTTTGTGAGTTTTTAGTAATGTAAATTATTTTGTTAAAAATTT
Found at i:34537166 original size:103 final size:100
Alignment explanation
Indices: 34536876--34537211 Score: 382
Period size: 103 Copynumber: 3.3 Consensus size: 100
34536866 ATAAATTGTT
* ** * *
34536876 GTGTTTTGTTAGTTTTTAGTAATGTAATTATTTTTTAAAAAATTTTATGGTTATTTTGTTAGTAG
1 GTGTTTTGTGA-TTTTTAGTAATGTAATT-TTTTAAAAAAAATTTTATAGTTATTTTGTTAGTAA
34536941 TTTATGATTAGGTTATAAATTGTTAGTG--T--TTT-
64 TTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTA
* * * *
34536973 GTGTTTTGTTATTTTTAGTAATTTAATTTCTTTTAAAAAAATGTTATAGTTATTTATTTTGTTAG
1 GTGTTTTGTGATTTTTAGTAATGTAATTT-TTTAAAAAAAAT-TT-TA--TAGTTATTTTGTTAG
*
34537038 TAATTTATGGGATTAGGTTAGAAATTGTTAGTGTTTAGTTTA
61 TAATTTAT--GATTAGGTTATAAATTGTTAGTGTTTAGTTTA
* *
34537080 GGGTTTTGTGATTTTTTAGTAATGTAA-TTTTTAAAAAATAATTTTATAGTTGTTTTGTTAGTAA
1 GTGTTTTGTGA-TTTTTAGTAATGTAATTTTTTAAAAAA-AATTTTATAGTTATTTTGTTAGTAA
34537144 TTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
64 TTTATGATTAGG-T-TATAAATTGTTAGTGTTTAGTTTA
*
34537183 GTGTCTTGTGATTTTT--TAATGTAATTTTT
1 GTGTTTTGTGATTTTTAGTAATGTAATTTTT
34537212 ATATAATGCA
Statistics
Matches: 207, Mismatches: 15, Indels: 30
0.82 0.06 0.12
Matches are distributed among these distances:
95 1 0.00
96 27 0.13
97 13 0.06
98 2 0.01
100 28 0.14
101 11 0.05
102 28 0.14
103 53 0.26
104 1 0.00
105 2 0.01
106 13 0.06
107 14 0.07
108 14 0.07
ACGTcount: A:0.27, C:0.01, G:0.17, T:0.55
Consensus pattern (100 bp):
GTGTTTTGTGATTTTTAGTAATGTAATTTTTTAAAAAAAATTTTATAGTTATTTTGTTAGTAATT
TATGATTAGGTTATAAATTGTTAGTGTTTAGTTTA
Found at i:34539691 original size:76 final size:77
Alignment explanation
Indices: 34539577--34539869 Score: 416
Period size: 76 Copynumber: 3.8 Consensus size: 77
34539567 AATAATTTCA
* * *
34539577 TATTTATATAATGACTTTTTTTCCATTTTA-GTATTTAATTTTATGGTTTTTTTTTGCTATTTAA
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTA-TTAATTTTATGGTTTTTTTTTGCAATTTAA
34539641 ATAGTCAACTTTG
65 ATAGTCAACTTTG
* * *
34539654 TATTTATGTAATGA-TTTTTTTCCATTTTATTTATTAATTTTAAGGGTTTTTTTTACAATTTAAA
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTATTAATTTTATGGTTTTTTTTTGCAATTTAAA
34539718 TAGTCAACTTTG
66 TAGTCAACTTTG
34539730 TATTTATGTAATGACTTTTTTGT-CATTTTATTTATTAATTTTATGGGTTTTTTTTTGCAATTTA
1 TATTTATGTAATGACTTTTTT-TCCATTTTATTTATTAATTTTAT-GGTTTTTTTTTGCAATTTA
34539794 AATAGTCAACTTTG
64 AATAGTCAACTTTG
** * * * *
34539808 TATTTATGTAATGACTTTTTCGCTATTTCAGTTATTAATTTTA-GG-ATTTTTTTGCAATTTAA
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTATTAATTTTATGGTTTTTTTTTGCAATTTAA
34539870 TAATAAAATT
Statistics
Matches: 196, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
75 16 0.08
76 70 0.36
77 41 0.21
78 69 0.35
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (77 bp):
TATTTATGTAATGACTTTTTTTCCATTTTATTTATTAATTTTATGGTTTTTTTTTGCAATTTAAA
TAGTCAACTTTG
Found at i:34542985 original size:27 final size:27
Alignment explanation
Indices: 34542938--34542994 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
34542928 ACCTATTAGG
* *
34542938 TAGGAGTCACCAGTAGTGCCTACCAGA
1 TAGGAGTCACCAATAGCGCCTACCAGA
* *
34542965 TAGGAGTCACCAATGGCGCCTACTAGA
1 TAGGAGTCACCAATAGCGCCTACCAGA
34542992 TAG
1 TAG
34542995 ATACCACCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (27 bp):
TAGGAGTCACCAATAGCGCCTACCAGA
Found at i:34544425 original size:29 final size:31
Alignment explanation
Indices: 34544365--34544426 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
34544355 TCCGCCACTA
34544365 ATCACAATTAAAATTTCATATATATAATTAT
1 ATCACAATTAAAATTTCATATATATAATTAT
34544396 ATCA-AATTAAAATTTC-TATATCA-AATTAT
1 ATCACAATTAAAATTTCATATAT-ATAATTAT
34544425 AT
1 AT
34544427 ATTCAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 13 0.43
30 13 0.43
31 4 0.13
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (31 bp):
ATCACAATTAAAATTTCATATATATAATTAT
Found at i:34545097 original size:23 final size:25
Alignment explanation
Indices: 34545067--34545121 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
34545057 ATTTTATTTG
34545067 ATAT-AAATTAAA-AAT-TATCTACA
1 ATATAAAATTAAATAATATAT-TACA
34545090 A-ATAAAATTAAATAATATATTACA
1 ATATAAAATTAAATAATATATTACA
34545114 ATATAAAA
1 ATATAAAA
34545122 AAACCAGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.07
23 9 0.32
24 8 0.29
25 9 0.32
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAAAATTAAATAATATATTACA
Found at i:34545310 original size:20 final size:20
Alignment explanation
Indices: 34545285--34545323 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34545275 ATTCAACTAT
34545285 TATTAT-TATTTTATAAAATA
1 TATTATATATTTT-TAAAATA
34545305 TATTATAATATTTTTAAAA
1 TATTAT-ATATTTTTAAAA
34545324 AAAACTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATATATTTTTAAAATA
Found at i:34547673 original size:60 final size:60
Alignment explanation
Indices: 34547601--34547722 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
34547591 AAATAAATAT
34547601 ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
1 ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
* * *
34547661 ATCCTATAATTTCATATGTTCTTAGGAGCTCCGTTTACCTACGGTACTTTGAGGAGACAA
1 ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
34547721 AT
1 AT
34547723 TTAGGCAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (60 bp):
ATCCTATAATTTCATATGTTCTTAAGAGCTCCGATTACCCACGGTACTTTGAGGAGACAA
Found at i:34550651 original size:3 final size:3
Alignment explanation
Indices: 34550589--34550636 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
34550579 AACTAATATA
* * * *
34550589 AAT AAT AAC ACT AGT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34550637 GGTAGTAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34551634 original size:14 final size:16
Alignment explanation
Indices: 34551612--34551649 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
34551602 TTCGCTCTTA
*
34551612 TTTTATTTTATTT-C-
1 TTTTCTTTTATTTGCT
34551626 TTTTCTTTTATTTGCT
1 TTTTCTTTTATTTGCT
34551642 TTTTCTTT
1 TTTTCTTT
34551650 GTCTGTGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTATTTGCT
Found at i:34558157 original size:43 final size:43
Alignment explanation
Indices: 34557829--34558146 Score: 392
Period size: 43 Copynumber: 7.4 Consensus size: 43
34557819 TCACCGCTAA
* * ** **
34557829 CTTTAGCGGCG-TTTTTCGAAATAAACGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGCTTTTTC--CACAAACGCCGCTAAAGACCATGAC
**
34557873 CTTTAGCGGCG-TTTTTGGA-AAAGCGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCACAAA-CGCCGCTAAAGACCATGAC
34557915 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
*
34557958 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
*
34558001 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
* * * * *
34558044 CTTTAGCGGCGC-TTTTCCTAAAAACGCCGCTAGAGACCCTAAT
1 CTTTAGCGGCGCTTTTTCC-ACAAACGCCGCTAAAGACCATGAC
* * * *
34558087 CTTTAGCGGCGCTTTTTCTACAAACGCCGCTAAAGACCCTAAT
1 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
*
34558130 CTTTAGCGGTGCTTTTT
1 CTTTAGCGGCGCTTTTT
34558147 TAAAAAACGC
Statistics
Matches: 250, Mismatches: 19, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
41 3 0.01
42 32 0.13
43 191 0.76
44 24 0.10
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCATGAC
Found at i:34560163 original size:25 final size:25
Alignment explanation
Indices: 34560129--34560177 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
34560119 ATACAAATAT
*
34560129 AAGTTGTGTATAATGTAAGTTATGA
1 AAGTTATGTATAATGTAAGTTATGA
*
34560154 AAGTTATGTATTATGTAAGTTATG
1 AAGTTATGTATAATGTAAGTTATG
34560178 TATTATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (25 bp):
AAGTTATGTATAATGTAAGTTATGA
Found at i:34560167 original size:16 final size:16
Alignment explanation
Indices: 34560148--34560242 Score: 86
Period size: 16 Copynumber: 5.8 Consensus size: 16
34560138 ATAATGTAAG
*
34560148 TTATGAAAGTTATGTA
1 TTATGTAAGTTATGTA
34560164 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
34560180 TTATGTAAGTTATTTAA
1 TTATGTAAGTTATGT-A
*
34560197 GTTGTGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
* * *
34560213 GTCATGTAGGCTATGTA
1 -TTATGTAAGTTATGTA
34560230 TTATGTAAGTTAT
1 TTATGTAAGTTAT
34560243 AATAAGTAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
16 51 0.80
17 3 0.05
18 10 0.16
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:34560176 original size:9 final size:9
Alignment explanation
Indices: 34560141--34560487 Score: 103
Period size: 9 Copynumber: 42.2 Consensus size: 9
34560131 GTTGTGTATA
34560141 ATGTAAGTT
1 ATGTAAGTT
*
34560150 ATGAAAGTT
1 ATGTAAGTT
34560159 ATGT-A-TT
1 ATGTAAGTT
34560166 ATGTAAGTT
1 ATGTAAGTT
34560175 ATGT-A-TT
1 ATGTAAGTT
34560182 ATGTAAGTT
1 ATGTAAGTT
*
34560191 ATTTAAGTT
1 ATGTAAGTT
*
34560200 GTGT-A-TT
1 ATGTAAGTT
*
34560207 ATGTAAGTC
1 ATGTAAGTT
* *
34560216 ATGTAGGCT
1 ATGTAAGTT
34560225 ATGT-A-TT
1 ATGTAAGTT
34560232 ATGTAAGTT
1 ATGTAAGTT
34560241 A--TAA--T
1 ATGTAAGTT
*
34560246 AAGTAAGTT
1 ATGTAAGTT
*
34560255 ATGAAAGTTAT
1 ATGTAAG-T-T
*
34560266 ATATAAGTTTAT
1 ATGTAAG--T-T
*
34560278 ATATAAGTT
1 ATGTAAGTT
34560287 ATGTAAGTT
1 ATGTAAGTT
34560296 A--T-A--T
1 ATGTAAGTT
34560300 ATGTAAGTT
1 ATGTAAGTT
34560309 ATGT--GTT
1 ATGTAAGTT
*
34560316 GTGTAAGTT
1 ATGTAAGTT
*
34560325 -TAT-A-TAT
1 ATGTAAGT-T
*
34560332 AT-TAAATTT
1 ATGT-AAGTT
34560341 AT-TCAAGTT
1 ATGT-AAGTT
34560350 ATG--A---
1 ATGTAAGTT
34560354 ATGTAAGTT
1 ATGTAAGTT
*
34560363 ATGTAAATT
1 ATGTAAGTT
* *
34560372 GTGT-A-TA
1 ATGTAAGTT
*
34560379 ACGTAAGTT
1 ATGTAAGTT
* *
34560388 AAGAAAGTT
1 ATGTAAGTT
34560397 ATGT-A-TT
1 ATGTAAGTT
34560404 ATGTAAGTT
1 ATGTAAGTT
*
34560413 ATTTAAGTT
1 ATGTAAGTT
*
34560422 GTGT-A-TT
1 ATGTAAGTT
34560429 ATGTAAGTCT
1 ATGTAAGT-T
* *
34560439 -TGTAGGCT
1 ATGTAAGTT
34560447 ATGT--GTT
1 ATGTAAGTT
34560454 ATGTAAGTT
1 ATGTAAGTT
34560463 AT-T-A--T
1 ATGTAAGTT
34560468 ATGTAAGTT
1 ATGTAAGTT
*
34560477 ATGAAAGTT
1 ATGTAAGTT
34560486 AT
1 AT
34560488 ATATAAGTTT
Statistics
Matches: 252, Mismatches: 39, Indels: 94
0.65 0.10 0.24
Matches are distributed among these distances:
4 5 0.02
5 5 0.02
6 5 0.02
7 62 0.25
8 18 0.07
9 136 0.54
10 4 0.02
11 6 0.02
12 11 0.04
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:34560186 original size:41 final size:41
Alignment explanation
Indices: 34560128--34560220 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
34560118 AATACAAATA
*
34560128 TAAGTTGTGTATAATGTAAGTTATGAAAGTTATGTATTATG
1 TAAGTTATGTATAATGTAAGTTATGAAAGTTATGTATTATG
* ** *
34560169 TAAGTTATGTATTATGTAAGTTATTTAAGTTGTGTATTATG
1 TAAGTTATGTATAATGTAAGTTATGAAAGTTATGTATTATG
*
34560210 TAAGTCATGTA
1 TAAGTTATGTA
34560221 GGCTATGTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (41 bp):
TAAGTTATGTATAATGTAAGTTATGAAAGTTATGTATTATG
Found at i:34560192 original size:25 final size:25
Alignment explanation
Indices: 34560128--34560211 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
34560118 AATACAAATA
* *
34560128 TAAGTTGTGTATAATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
*
34560153 AAAGTTATGTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* *
34560178 T-A-TTATGTAAGTTATTTAAGTTGTG
1 TAAGTTATGT-A-TTATGTAAGTTATG
34560203 T-A-TTATGTA
1 TAAGTTATGTA
34560212 AGTCATGTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.12
24 3 0.06
25 42 0.82
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:34560229 original size:25 final size:25
Alignment explanation
Indices: 34560166--34560239 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
34560156 GTTATGTATT
* *
34560166 ATGTAAGTTATGTATTATGTAAGTT
1 ATGTAAGCTATGTATTATGTAAGTC
* * *
34560191 ATTTAAGTTGTGTATTATGTAAGTC
1 ATGTAAGCTATGTATTATGTAAGTC
*
34560216 ATGTAGGCTATGTATTATGTAAGT
1 ATGTAAGCTATGTATTATGTAAGT
34560240 TATAATAAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.46
Consensus pattern (25 bp):
ATGTAAGCTATGTATTATGTAAGTC
Found at i:34560239 original size:41 final size:41
Alignment explanation
Indices: 34560141--34560242 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
34560131 GTTGTGTATA
* * *
34560141 ATGTAAGTTATGAAAGTTATGTATTATGTAAGTTATGTATT
1 ATGTAAGTTATGTAAGTTATGTATTATGTAAGTCATGTACT
* *
34560182 ATGTAAGTTATTTAAGTTGTGTATTATGTAAGTCATGTAGGCT
1 ATGTAAGTTATGTAAGTTATGTATTATGTAAGTCATGTA--CT
34560225 ATGT-A-TTATGTAAGTTAT
1 ATGTAAGTTATGTAAGTTAT
34560243 AATAAGTAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 46 0.88
42 1 0.02
43 5 0.10
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (41 bp):
ATGTAAGTTATGTAAGTTATGTATTATGTAAGTCATGTACT
Found at i:34560273 original size:34 final size:34
Alignment explanation
Indices: 34560234--34560310 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 34
34560224 TATGTATTAT
34560234 GTAAGTTATA-ATAAGTAAGTTATGAAAGTTATATA
1 GTAAGTTATATAT-A-TAAGTTATGAAAGTTATATA
*
34560269 -TAAGTT-TATATATAAGTTATGTAAGTTATATA
1 GTAAGTTATATATATAAGTTATGAAAGTTATATA
34560301 TGTAAGTTAT
1 -GTAAGTTAT
34560311 GTGTTGTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
32 19 0.51
33 3 0.08
34 14 0.38
35 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.43
Consensus pattern (34 bp):
GTAAGTTATATATATAAGTTATGAAAGTTATATA
Found at i:34560280 original size:10 final size:11
Alignment explanation
Indices: 34560259--34560301 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
34560249 TAAGTTATGA
34560259 AAGTTATATAT
1 AAGTTATATAT
34560270 AAGTTTATATAT
1 AAG-TTATATAT
*
34560282 AAG-T-TATGT
1 AAGTTATATAT
34560291 AAGTTATATAT
1 AAGTTATATAT
34560302 GTAAGTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 7 0.26
12 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (11 bp):
AAGTTATATAT
Found at i:34560304 original size:13 final size:13
Alignment explanation
Indices: 34560286--34560310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34560276 ATATATAAGT
34560286 TATGTAAGTTATA
1 TATGTAAGTTATA
34560299 TATGTAAGTTAT
1 TATGTAAGTTAT
34560311 GTGTTGTGTA
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TATGTAAGTTATA
Found at i:34560384 original size:25 final size:25
Alignment explanation
Indices: 34560354--34560436 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
34560344 CAAGTTATGA
*
34560354 ATGTAAGTTATGTAAATTGTGTATA
1 ATGTAAGTTATGTAAATTGTGTATT
* * *
34560379 ACGTAAGTTAAG-AAAGTTATGTATT
1 ATGTAAGTTATGTAAA-TTGTGTATT
* *
34560404 ATGTAAGTTATTTAAGTTGTGTATT
1 ATGTAAGTTATGTAAATTGTGTATT
34560429 ATGTAAGT
1 ATGTAAGT
34560437 CTTGTAGGCT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
24 3 0.06
25 42 0.89
26 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.43
Consensus pattern (25 bp):
ATGTAAGTTATGTAAATTGTGTATT
Found at i:34560413 original size:16 final size:16
Alignment explanation
Indices: 34560392--34560479 Score: 51
Period size: 16 Copynumber: 5.5 Consensus size: 16
34560382 TAAGTTAAGA
34560392 AAGTTATGTATTATGT
1 AAGTTATGTATTATGT
* *
34560408 AAGTTATTTAAGTTGTGT
1 AAGTTATGT-A-TTATGT
34560426 -A-TTATGTAAGTCT-TGT
1 AAGTTATGT-A-T-TATGT
* * *
34560442 AGGCTATGTGTTATGT
1 AAGTTATGTATTATGT
34560458 AAGTTAT-TA-TATGT
1 AAGTTATGTATTATGT
34560472 AAGTTATG
1 AAGTTATG
34560480 AAAGTTATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
14 12 0.21
15 2 0.04
16 29 0.52
17 3 0.05
18 10 0.18
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (16 bp):
AAGTTATGTATTATGT
Found at i:34561599 original size:18 final size:18
Alignment explanation
Indices: 34561551--34561599 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
34561541 GACATTCGCA
*
34561551 TATCAATTTATCAAATAC
1 TATCAATTTATCCAATAC
34561569 TATCAATTTATCCAATAC
1 TATCAATTTATCCAATAC
34561587 TATCAATTTATCC
1 TATCAATTTATCC
34561600 TTCCCACCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (18 bp):
TATCAATTTATCCAATAC
Found at i:34561975 original size:36 final size:32
Alignment explanation
Indices: 34561899--34561960 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
34561889 NNNNNNNNNN
*
34561899 TTATTCAAACAAACCGGATAAATGACTGGAAA
1 TTATTCAAACAAACCGGATAAATGACAGGAAA
34561931 TTATTCAAACAAACCGGATAAATGACAGGA
1 TTATTCAAACAAACCGGATAAATGACAGGA
34561961 TTATCTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (32 bp):
TTATTCAAACAAACCGGATAAATGACAGGAAA
Found at i:34563611 original size:22 final size:22
Alignment explanation
Indices: 34563570--34563623 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
34563560 TGTATGTTTC
* *
34563570 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
34563593 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
34563614 -TAAAAGTTTT
1 ATTAAAGTTTT
34563624 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:34563638 original size:21 final size:21
Alignment explanation
Indices: 34563572--34563638 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
34563562 TATGTTTCAT
*
34563572 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
34563594 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
34563614 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
34563635 TAAA
1 TAAA
34563639 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:34563671 original size:21 final size:20
Alignment explanation
Indices: 34563645--34563689 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
34563635 TAAATTTTAG
34563645 TTTTTTTATTTCCTTT-TTATA
1 TTTTTTTATTT--TTTCTTATA
34563666 TTTTTTTATTTTTTCTTATA
1 TTTTTTTATTTTTTCTTATA
34563686 TTTT
1 TTTT
34563690 GGTCTTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.13
20 9 0.39
21 11 0.48
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTATTTTTTCTTATA
Found at i:34563884 original size:2 final size:2
Alignment explanation
Indices: 34563877--34563905 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34563867 TAAAGTGATC
34563877 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
34563906 CTTAAATAAT
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:34564551 original size:7 final size:7
Alignment explanation
Indices: 34564541--34564573 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
34564531 CTCTTAACAT
34564541 CTAACCC
1 CTAACCC
34564548 CTAA--C
1 CTAACCC
34564553 CTAACCC
1 CTAACCC
34564560 CTAACCC
1 CTAACCC
34564567 CTAACCC
1 CTAACCC
34564574 ATAAACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.21
7 19 0.79
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAACCC
Found at i:34564558 original size:12 final size:12
Alignment explanation
Indices: 34564541--34564565 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34564531 CTCTTAACAT
34564541 CTAACCCCTAAC
1 CTAACCCCTAAC
34564553 CTAACCCCTAAC
1 CTAACCCCTAAC
34564565 C
1 C
34564566 CCTAACCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:34564629 original size:14 final size:15
Alignment explanation
Indices: 34564607--34564640 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34564597 CTTAAACAAA
*
34564607 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
34564621 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
34564636 AATCT
1 AATCT
34564641 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:34565106 original size:41 final size:40
Alignment explanation
Indices: 34565046--34565323 Score: 351
Period size: 41 Copynumber: 6.8 Consensus size: 40
34565036 AAATGTTTTT
* * *
34565046 GCGGCGCTTCTTCACAAACGCCGCTAAAGGCCTCAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCC-GAGCATTA
* * *
34565087 GCGGCGCTTCTTCAAAAACGCCGCTAACGGCCCGAGCAGTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
34565128 GCGGCGCATT-TTCAAAAACGCCGCTAAAGGTCCGAGCATTA
1 GCGGCGC-TTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
* * *
34565169 CCGGCGCTTATGCAAAAACGCCGCTACAGGTCCGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
*
34565210 GCGGCGCTTATGCAAAAACGCCGCTAAAGGTCCGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGG-CCGAGCATTA
*** *
34565251 GCGGCGCTTATTCAAAATTTCCGCTAAAGACCTGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCC-GAGCATTA
*
34565292 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCC
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCC
34565324 CCAAAAACTC
Statistics
Matches: 211, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 4 0.02
41 203 0.96
42 4 0.02
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (40 bp):
GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCGAGCATTA
Found at i:34565431 original size:39 final size:40
Alignment explanation
Indices: 34565377--34565495 Score: 143
Period size: 40 Copynumber: 3.0 Consensus size: 40
34565367 GGCGCTTTCC
*
34565377 AAAAAACGCCACTAATGCTT-ATTTTTAGCGGCGTTTTTT
1 AAAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
* * ** *
34565416 AAAAATCGCCGCTAATTCTTGACCTTTAGCGGCGTTTTTG
1 AAAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
* *
34565456 AAAAAGA-GCCGCTACTGCTTGATTTTTAGTGGCGTTTTTT
1 AAAAA-ACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
34565496 GTCCAAATGC
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 17 0.26
40 48 0.74
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (40 bp):
AAAAAACGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTT
Found at i:34567233 original size:113 final size:113
Alignment explanation
Indices: 34567090--34567907 Score: 838
Period size: 113 Copynumber: 7.2 Consensus size: 113
34567080 CGTTTATTGT
* *
34567090 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTCGA-GGTATATTAGAATTAGTGGC
34567155 GTTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
65 GTTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
* * * *
34567204 AAGCGCCGC-AAATATCTTAACGAAAACGCAGCGTTTGGTCTCGAGGTAGATTAGTATTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TCGAGGTATATTAGAATTAGTGGC
* * * * ****
34567268 GTTTT-TAAACAAACGCCG-TAAAAGAACA-TCATTAGTGGCG-TTTATTTGT
65 GTTTTCGATA-AAACGCCGCT-AAAGAATAGT-ATTAGCGGCGTTTTA-CAAA
* *
34567317 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTCGA-GGTATATTAGAATTAGTGGC
34567382 GTTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
65 GTTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
* * * * *
34567431 AAGCGCCGC-AAATATCTTAACGAAAATGCAGCGTTTGGTCTCGAGGTAGATTAGTATTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TCGAGGTATATTAGAATTAGTGGC
* * * * * ****
34567495 ATTTT-TAAACAAACGCCG-TAAAAGAACA-TCATTAGTGGCG-TTTATTTGT
65 GTTTTCGATA-AAACGCCGCT-AAAGAATAGT-ATTAGCGGCGTTTTA-CAAA
* *
34567544 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGCTTGGTTTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGG-TTCGAGGTATATTAGAATTAGTGGC
34567609 GTTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
65 GTTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
* * * * * **
34567658 AAGCGCCGC-AAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTGTTAGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGT-TCGAGGTATATTAGAATTAGTGGC
** * * * ***
34567722 GTTTTTAAAAAAACGCCG-TAAAAGAACA-TAATTAGTGGCG-TTTACTTTT
65 GTTTTCGATAAAACGCCGCT-AAAGAATAGT-ATTAGCGGCGTTTTAC-AAA
* * * * * *
34567771 AAGCACCGCAAAATACCTTAACCAAAACGTAGCGTTTGGATCAATTGTATATTAGAATTCGTGGC
1 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTCGA-GGTATATTAGAATTAGTGGC
* * * * *
34567836 GTTTTCTATAAAACACCGCTAAAGAATAGTATTAGCGGCGTATCACAAG
65 GTTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
*
34567885 AAGCGCCGC-AAATATCTTAACCA
1 AAGCGCCGCAAAATACCTTAACCA
34567908 GAGGTAGATT
Statistics
Matches: 572, Mismatches: 101, Indels: 63
0.78 0.14 0.09
Matches are distributed among these distances:
112 24 0.04
113 267 0.47
114 259 0.45
115 22 0.04
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (113 bp):
AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTCGAGGTATATTAGAATTAGTGGCG
TTTTCGATAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAA
Found at i:34567429 original size:227 final size:227
Alignment explanation
Indices: 34567035--34568062 Score: 1598
Period size: 227 Copynumber: 4.6 Consensus size: 227
34567025 CCTGAACAAC
* * *
34567035 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
34567099 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
34567164 AAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
34567229 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
34567261 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
34567326 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
34567391 AAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
*
34567456 ATGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
*
34567488 TAGTGGCATTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
* ** *
34567553 AAAATACCTTAACCAAAACGCAGCGCTTGGTTTTGA-GGTATATTAGAATTAGTGGCGTTTTCGA
66 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAATTAGTGGCGTTTTCGA
34567617 TAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAA
130 TAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAA
* * *
34567682 AACGCACCGTTTGGTCTTGAGGTAGATTAGTGT
195 AACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
* * *
34567715 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTACTTT-TAAGCACCG
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTA-TTTGTAAGCGCCG
* * * *
34567779 CAAAATACCTTAACCAAAACGTAGCGTTTGGATCAATTGTATATTAGAATTCGTGGCGTTTTCTA
65 CAAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGA
* * * *
34567844 TAAAACACCGCTAAAGAATAGTATTAGCGGCGTATCACAAGAAGCGCCGCAAATATCTT------
130 TAAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAA
34567903 AAC-CA------------GAGGTAGATTAGTAT
195 AACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
* *
34567923 TAGTGGCGTTTTTAAACAAACGCAGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGAGCCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
* ** * *
34567988 AAAATACCTTAACCAAAACGCAACGTTTGGTTTTGA-GGTATATTAGAATTAGTGGCGTTTACGA
66 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAATTAGTGGCGTTTTCGA
34568052 TAAAACGCCGC
130 TAAAACGCCGC
34568063 AAATATCTTA
Statistics
Matches: 751, Mismatches: 45, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
207 3 0.00
208 132 0.18
209 2 0.00
220 2 0.00
221 3 0.00
226 50 0.07
227 553 0.74
228 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (227 bp):
TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
AAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
Found at i:34568637 original size:14 final size:15
Alignment explanation
Indices: 34568604--34568637 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
34568594 TAAGTTTTAT
34568604 AGATTATGGAATTAG
1 AGATTATGGAATTAG
34568619 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
34568633 GGATT
1 AGATT
34568638 TTTGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:34569064 original size:7 final size:7
Alignment explanation
Indices: 34569052--34569127 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
34569042 TAAATAAGGT
34569052 TTAGGGG
1 TTAGGGG
34569059 TTAGGGG
1 TTAGGGG
*
34569066 TTAGAGG
1 TTAGGGG
* **
34569073 TCATAGG
1 TTAGGGG
*
34569080 TTAAGGGT
1 TT-AGGGG
*
34569088 TTAGGGT
1 TTAGGGG
34569095 TTA-GGG
1 TTAGGGG
*
34569101 TTAAGGG
1 TTAGGGG
*
34569108 TTAAGGG
1 TTAGGGG
34569115 TTAGGGG
1 TTAGGGG
34569122 TTAGGG
1 TTAGGG
34569128 ATTGGGTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
6 5 0.09
7 49 0.84
8 4 0.07
ACGTcount: A:0.21, C:0.01, G:0.46, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:34569122 original size:21 final size:21
Alignment explanation
Indices: 34569046--34569124 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
34569036 ATATATTAAA
* *
34569046 TAAGGTTTAGGGGTTAGGGGT
1 TAAGGGTTAGGGGTTAAGGGT
* **
34569067 T-AGAGGTCATAGGTTAAGGGT
1 TAAG-GGTTAGGGGTTAAGGGT
*
34569088 TTAGGGTTTA-GGGTTAAGGGT
1 TAAGGG-TTAGGGGTTAAGGGT
34569109 TAAGGGTTAGGGGTTA
1 TAAGGGTTAGGGGTTA
34569125 GGGATTGGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 5 0.11
21 37 0.80
22 4 0.09
ACGTcount: A:0.23, C:0.01, G:0.43, T:0.33
Consensus pattern (21 bp):
TAAGGGTTAGGGGTTAAGGGT
Found at i:34569225 original size:89 final size:89
Alignment explanation
Indices: 34569105--34569275 Score: 218
Period size: 89 Copynumber: 1.9 Consensus size: 89
34569095 TTAGGGTTAA
* * * * * **
34569105 GGGTTAAGGGTTAGGGGTTAGGGATTGGGTTATGGTTTAAGGTTTAGATTAATTAGTGTTTTTTA
1 GGGTTAAGGGTTAGGGATTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTACTTTTTA
* *
34569170 ATTTATATATTAAATAAAGTTTAG
66 ATTAACATATTAAATAAAGTTTAG
* * *
34569194 GGGTTAAGGGTTATGGATT-TGGAGTCGGGTTAGGGATTAAGATTTGGATTAATTAGTACTTTTT
1 GGGTTAAGGGTTAGGGATTAGGGA-TCGGGTTAGGGATTAAGATTTAGATTAATTAGTACTTTTT
34569258 AATTAACATATTAAATAA
65 AATTAACATATTAAATAA
34569276 GTTCTTTATA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
88 3 0.04
89 66 0.96
ACGTcount: A:0.30, C:0.02, G:0.27, T:0.42
Consensus pattern (89 bp):
GGGTTAAGGGTTAGGGATTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTACTTTTTA
ATTAACATATTAAATAAAGTTTAG
Found at i:34569377 original size:21 final size:21
Alignment explanation
Indices: 34569324--34569377 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
34569314 TAAAGATTAT
34569324 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
34569345 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
34569366 TAATTTAAAATT
1 TAATTTAAAATT
34569378 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:34569412 original size:20 final size:20
Alignment explanation
Indices: 34569372--34569415 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34569362 ATAATAATTT
**
34569372 AAAATTGTAAAAATTGTAAA
1 AAAATTGTAAAAATTACAAA
*
34569392 AAAATTGTCAAAATTACAAA
1 AAAATTGTAAAAATTACAAA
34569412 AAAA
1 AAAA
34569416 AATGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAATTGTAAAAATTACAAA
Found at i:34569423 original size:19 final size:18
Alignment explanation
Indices: 34569401--34569449 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
34569391 AAAAATTGTC
*
34569401 AAAATTACAAAAAAAAATG
1 AAAATTA-AAAAAAAAAAG
*
34569420 AAAATAAAAAATAAAAAAG
1 AAAATTAAAAA-AAAAAAG
34569439 -AAATTAAAAAA
1 AAAATTAAAAAA
34569450 CTAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 13 0.50
19 12 0.46
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAATTAAAAAAAAAAAG
Found at i:34569448 original size:13 final size:12
Alignment explanation
Indices: 34569401--34569449 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
34569391 AAAAATTGTC
34569401 AAAATTACAAAAA
1 AAAATTA-AAAAA
*
34569414 AAAATGAAAATAA
1 AAAATTAAAA-AA
34569427 AAAA-TAAAAAA
1 AAAATTAAAAAA
*
34569438 GAAATTAAAAAA
1 AAAATTAAAAAA
34569450 CTAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 5 0.16
12 14 0.45
13 12 0.39
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (12 bp):
AAAATTAAAAAA
Found at i:34569455 original size:19 final size:20
Alignment explanation
Indices: 34569412--34569455 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
34569402 AAATTACAAA
34569412 AAAAAATGAAAATAAAAAAT
1 AAAAAATGAAAATAAAAAAT
*
34569432 AAAAAA-GAAATTAAAAAACT
1 AAAAAATGAAAATAAAAAA-T
34569452 AAAA
1 AAAA
34569456 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAAAATGAAAATAAAAAAT
Found at i:34569494 original size:47 final size:47
Alignment explanation
Indices: 34569442--34569535 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
34569432 AAAAAAGAAA
** *
34569442 TTAAAAAACTAAAATTTTTATTTTTACCTAATTTTTATAAATATTAC
1 TTAAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTAC
* * * *
34569489 TTAAAAAACTGAGATTGATAATTTTATCTAATTTTTTTAAATATTAC
1 TTAAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTAC
34569536 CGAAATTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (47 bp):
TTAAAAAACTAAAATTGATAATTTTACCTAATTTTTATAAATATTAC
Found at i:34570237 original size:198 final size:198
Alignment explanation
Indices: 34569899--34570324 Score: 773
Period size: 198 Copynumber: 2.2 Consensus size: 198
34569889 GCCTAATATT
* * * * *
34569899 TAGTGGCGCTTATGTATAAATGCCACAATTTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
1 TAGTGGCGCTTGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
34569964 TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCGCAAAATGGTTTTAATTTTTATGGAGACGATG
66 TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCGCAAAATGGTTTTAATTTTTATGGAGACGATG
34570029 CCGTTTTCTCTAAAATGCCATGAGTTTTAGTTAACTAATCTGGAAACGATAGCGTTTGATCATAT
131 CCGTTTTCTCTAAAATGCCATGAGTTTTAGTTAACTAATCTGGAAACGATAGCGTTTGATCATAT
34570094 TAC
196 TAC
* *
34570097 TAGTGGCGCTGGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTTCGTTTTCT
1 TAGTGGCGCTTGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
34570162 TATTT-ACTTTTAGTGGCGCTTTTAGTAAACGCCGCAAAATGGTTTTAATTTTTATGGAGACGAT
66 TATTTAAC-TTTAGTGGCGCTTTTAGTAAACGCCGCAAAATGGTTTTAATTTTTATGGAGACGAT
34570226 GCCGTTTTCTCTAAAATGCCATGAGTTTTAGTTAACTAATCTGGAAACGATAGCGTTTGATCATA
130 GCCGTTTTCTCTAAAATGCCATGAGTTTTAGTTAACTAATCTGGAAACGATAGCGTTTGATCATA
34570291 TTAC
195 TTAC
34570295 TAGTGGCGCTTGTATATAAACGCCGCAAAT
1 TAGTGGCGCTTGTATATAAACGCCGCAAAT
34570325 GGGTTAATTA
Statistics
Matches: 219, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
197 2 0.01
198 217 0.99
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (198 bp):
TAGTGGCGCTTGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCGCAAAATGGTTTTAATTTTTATGGAGACGATG
CCGTTTTCTCTAAAATGCCATGAGTTTTAGTTAACTAATCTGGAAACGATAGCGTTTGATCATAT
TAC
Found at i:34576258 original size:43 final size:41
Alignment explanation
Indices: 34576205--34576328 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 41
34576195 ATTTCTGAAC
* *
34576205 AAGCACCGCTATAGAACATTA-CTTTTAAAGGCGTTTTCTTCCA
1 AAGCGCCGCTA-AGAACATGATC-TTTAAAGGCGTTTT-TTCCA
** *
34576248 AAGCGCCGCTAAGTAACATGATCTTTAGCGGCGTTTTTTCCT
1 AAGCGCCGCTAAG-AACATGATCTTTAAAGGCGTTTTTTCCA
**
34576290 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 AAGCGCCGCT-AAGAACATGATCTTTAAAGGCGTTTTTT
34576329 TCTGTAAGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
42 41 0.56
43 31 0.42
44 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (41 bp):
AAGCGCCGCTAAGAACATGATCTTTAAAGGCGTTTTTTCCA
Found at i:34576308 original size:42 final size:43
Alignment explanation
Indices: 34576234--34576348 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 43
34576224 TACTTTTAAA
*
34576234 GGCGTTTTCTTCCAAAGCGCCGCT-AAGTAACATGATCTTTAGC
1 GGCGTTTT-TTCCTAAGCGCCGCTAAAGTAACATGATCTTTAGC
34576277 GGCGTTTTTTCCTAAGCGCCGCTAAAG-AACATGATCTTTAGC
1 GGCGTTTTTTCCTAAGCGCCGCTAAAGTAACATGATCTTTAGC
* *
34576319 GGCGTTTTTTTCTGTAAGCGCCGCAAAAGT
1 GGCG-TTTTTTC-CTAAGCGCCGCTAAAGT
34576349 TAGCGACGTT
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
42 33 0.51
43 18 0.28
44 14 0.22
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (43 bp):
GGCGTTTTTTCCTAAGCGCCGCTAAAGTAACATGATCTTTAGC
Found at i:34576602 original size:182 final size:182
Alignment explanation
Indices: 34576295--34576658 Score: 683
Period size: 182 Copynumber: 2.0 Consensus size: 182
34576285 TTCCTAAGCG
* *
34576295 CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
34576360 TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
66 TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
34576425 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
131 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
* *
34576477 CCGCTAAAGAACATGATCTTTTGCGGTATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
*
34576542 TTGTTAGCGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
66 TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
34576607 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
131 CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
34576659 TTTACGGGAA
Statistics
Matches: 177, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
182 177 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (182 bp):
CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCCTGTAAGCGCCGCAAAAGTTAGCGACGTTG
TTGTTAACGGCATTTTTTGTGGCGCTTCTTCAAGCGCCGGAAATGGATTTAGTGGCGTTAAAAAG
CGCCGCTAAAGGCCTAAAAAACGCCGCTAAAAACCTGTTCTGGTGTAGTGTT
Found at i:34579644 original size:68 final size:64
Alignment explanation
Indices: 34579520--34579649 Score: 163
Period size: 68 Copynumber: 2.0 Consensus size: 64
34579510 TGATTAAACT
* * *
34579520 TAATCATTTTAATATTAAAATAATATAATGTTAGATAAACATTAAATTAAATTTAATATTAAGA
1 TAATCACTTTAATATTAAAATAAAATAATGTTAGATAAACATTAAATTAAAATTAATATTAAGA
* *
34579584 TAATCACTTTAATATTAATTTAATAAAATACTTTTAAGATAAGA-ATTAAATTAAAATTAATATT
1 TAATCACTTTAATATTAA---AATAAAATAATGTT-AGATAA-ACATTAAATTAAAATTAATATT
34579648 AA
61 AA
34579650 AATATTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
64 17 0.30
67 11 0.20
68 27 0.48
69 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (64 bp):
TAATCACTTTAATATTAAAATAAAATAATGTTAGATAAACATTAAATTAAAATTAATATTAAGA
Found at i:34586525 original size:45 final size:45
Alignment explanation
Indices: 34586474--34586564 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
34586464 AACATGCATG
* * *
34586474 ACAAAGACAATAATAAGAGTACAAATAATAATATGGGGAACAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
* * * *
34586519 ACAAAGAGAATAATAACAATATAAATGATAATATGGAGAATAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
34586564 A
1 A
34586565 GAGCGATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (45 bp):
ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
Found at i:34589397 original size:44 final size:44
Alignment explanation
Indices: 34589335--34589522 Score: 209
Period size: 44 Copynumber: 4.3 Consensus size: 44
34589325 TCAGAGAGAT
* * * *
34589335 AAGATCTGTTTTCTTCGATCTACTTCGCCACCAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCCACTTC-CCACCAATATAGGAAGAC
*
34589380 AAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGAC
1 AAGATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGAC
* * * * * *
34589423 -AGAACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
1 AAG-ATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGAC
* *
34589467 AAGATCTGCTTTCTTCGATCCACTTCCTACCAATATAGGAAGAC
1 AAGATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGAC
* *
34589511 AGGACCTGCTAT
1 AAGATCTGCTAT
34589523 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
42 2 0.02
43 21 0.18
44 84 0.72
45 10 0.09
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (44 bp):
AAGATCTGCTATCTTCGATCCACTTCCCACCAATATAGGAAGAC
Found at i:34589495 original size:88 final size:88
Alignment explanation
Indices: 34589346--34589522 Score: 275
Period size: 88 Copynumber: 2.0 Consensus size: 88
34589336 AGATCTGTTT
* **
34589346 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGACACCAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
34589411 ATATAGGAAGACAGAACCTGCTA
66 ATATAGGAAGACAGAACCTGCTA
* * *
34589434 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCACTTCCTACC
1 TCTTCGATCTACTTCGACACCAATACAGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACC
*
34589498 AATATAGGAAGACAGGACCTGCTA
65 AATATAGGAAGACAGAACCTGCTA
34589522 T
1 T
34589523 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 22 0.27
88 59 0.73
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTACTTCGACACCAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCA
ATATAGGAAGACAGAACCTGCTA
Found at i:34590227 original size:43 final size:43
Alignment explanation
Indices: 34590178--34590315 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 43
34590168 CAAGATCTGT
34590178 TGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
* * * * * *
34590221 TGTCTTCGATCTGCTTCACTG-T-CAA-TGCAG-GAAGGCAAGATCTG
1 TGTCTTCAACCAGC-T--CTGCTACAACCG-AGAG-AGGCAAGGTTTG
34590265 TTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
1 -TGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
34590309 TGTCTTC
1 TGTCTTC
34590316 GATCTGCTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
42 3 0.04
43 21 0.29
44 32 0.44
45 14 0.19
46 3 0.04
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTG
Found at i:34590257 original size:44 final size:43
Alignment explanation
Indices: 34590209--34590434 Score: 124
Period size: 44 Copynumber: 5.2 Consensus size: 43
34590199 CAACCGAGAG
34590209 AGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAA-GCAGGA
* * * * * *
34590253 AGGCAAGATCTGTTGTCTTCAACCAGC-T--CTGCTACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCACTG-T-CAAGCAG-GA
**
34590296 GAGGCAAGGTTTGTGTCTTCGATCTGCTTTGCTGTCAAGGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAA-GCAGGA
* * * ** * * * * *
34590341 AGGCAAGATCTGCTATCTTTAACCAGCTCCACTG-CAACCGATGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCACTGTCAAGC-AGGA
* *
34590385 AGGCAAGGCTTTGT-T-TTCGATCTGCTTCACTGTTAATGCATGA
1 AGGCAAGG-TTTGTGTCTTCGATCTGCTTCACTGTCAA-GCAGGA
34590428 AGGCAAG
1 AGGCAAG
34590435 ATCTGCTATC
Statistics
Matches: 134, Mismatches: 33, Indels: 31
0.68 0.17 0.16
Matches are distributed among these distances:
42 17 0.13
43 29 0.22
44 53 0.40
45 30 0.22
46 5 0.04
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTCACTGTCAAGCAGGA
Found at i:34590440 original size:87 final size:88
Alignment explanation
Indices: 34590159--34590526 Score: 460
Period size: 88 Copynumber: 4.2 Consensus size: 88
34590149 NNNNNNNNNN
* * **
34590159 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGT
1 GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGT
34590224 CTTCGATCTGCTTCACTGTCAAT
66 CTTCGATCTGCTTCACTGTCAAT
* * **
34590247 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGT
1 GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGT
** *
34590312 CTTCGATCTGCTTTGCTGTCAAG
66 CTTCGATCTGCTTCACTGTCAAT
* *
34590335 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGA-AGGCAAGGCTTTGT
1 GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGT
*
34590399 -T-TTCGATCTGCTTCACTGTTAAT
64 GTCTTCGATCTGCTTCACTGTCAAT
* * *
34590422 GCATGAAGGCAAGATCTGCTATCTTTAACCATCTCCACTACAACCGATG-GAGGCAAGGCTTTGT
1 GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGT
* * *
34590486 -T-TTCGATCTGCTTCGCTGTTAAC
64 GTCTTCGATCTGCTTCACTGTCAAT
* *
34590509 ACAAGAAGGCAAGATCTG
1 GCAGGAAGGCAAGATCTG
34590527 ATGTATTAAT
Statistics
Matches: 257, Mismatches: 20, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
87 115 0.45
88 135 0.53
89 7 0.03
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (88 bp):
GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGT
CTTCGATCTGCTTCACTGTCAAT
Found at i:34590468 original size:175 final size:175
Alignment explanation
Indices: 34590159--34590526 Score: 485
Period size: 175 Copynumber: 2.1 Consensus size: 175
34590149 NNNNNNNNNN
* * **
34590159 GCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACCGAGAGAGGCAAGGTTTGTGT
1 GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGT
* * **
34590224 CTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTGCTACA
66 CTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACA
* *
34590289 ACCGA-GAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTTGCTGTCAAG
131 ACCGATG-GAGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTCAAC
* *
34590335 GCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGA-AGGCAAGGCTTTGT
1 GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGT
* * * *
34590399 -T-TTCGATCTGCTTCACTGTTAATGCATGAAGGCAAGATCTGCTATCTTTAACCATCTCCACTA
64 GTCTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTA
*
34590462 CAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAAC
129 CAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAAC
* *
34590509 ACAAGAAGGCAAGATCTG
1 GCAGGAAGGCAAGATCTG
34590527 ATGTATTAAT
Statistics
Matches: 169, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
174 35 0.21
175 71 0.42
176 56 0.33
177 7 0.04
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (175 bp):
GCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGT
CTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACA
ACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAAC
Found at i:34591553 original size:6 final size:6
Alignment explanation
Indices: 34591498--34591545 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
34591488 TTGGCCTCTC
* * *
34591498 CTTTTT CTTTTT -TTGTT CTTCTT CTCTTTT CTTTTT CTTTTT GTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTTT
34591546 TTCTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
7 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:34592003 original size:9 final size:8
Alignment explanation
Indices: 34591977--34592030 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
34591967 AGGTCTTTTC
34591977 TTTTATTT
1 TTTTATTT
* *
34591985 TTGGTCTTT
1 TT-TTATTT
34591994 TTTTATTT
1 TTTTATTT
34592002 TTTTACTTT
1 TTTTA-TTT
34592011 TTTTATTT
1 TTTTATTT
*
34592019 TTTTGTTT
1 TTTTATTT
34592027 TTTT
1 TTTT
34592031 TGTTTTTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
8 25 0.64
9 14 0.36
ACGTcount: A:0.07, C:0.04, G:0.06, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:34592011 original size:25 final size:25
Alignment explanation
Indices: 34591977--34592030 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
34591967 AGGTCTTTTC
* *
34591977 TTTTATTTTTGGTCTTTTTTTATTT
1 TTTTACTTTTGGTATTTTTTTATTT
** *
34592002 TTTTACTTTTTTTATTTTTTTGTTT
1 TTTTACTTTTGGTATTTTTTTATTT
34592027 TTTT
1 TTTT
34592031 TGTTTTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.07, C:0.04, G:0.06, T:0.83
Consensus pattern (25 bp):
TTTTACTTTTGGTATTTTTTTATTT
Found at i:34592031 original size:17 final size:17
Alignment explanation
Indices: 34591972--34592040 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
34591962 CGGTGAGGTC
*
34591972 TTTTCTTTTA-TTTTTGG
1 TTTT-TTTTATTTTTTTG
*
34591989 TCTTTTTTTATTTTTTTA
1 T-TTTTTTTATTTTTTTG
*
34592007 CTTTTTTTATTTTTTTG
1 TTTTTTTTATTTTTTTG
*
34592024 TTTTTTTTGTTTTTTTG
1 TTTTTTTTATTTTTTTG
34592041 CCTCCACTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.06, C:0.04, G:0.07, T:0.83
Consensus pattern (17 bp):
TTTTTTTTATTTTTTTG
Found at i:34592036 original size:8 final size:8
Alignment explanation
Indices: 34591991--34592040 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
34591981 ATTTTTGGTC
*
34591991 TTTTTTTA
1 TTTTTTTG
*
34591999 TTTTTTTAC
1 TTTTTTT-G
*
34592008 TTTTTTTA
1 TTTTTTTG
34592016 TTTTTTTG
1 TTTTTTTG
34592024 TTTTTTTTG
1 -TTTTTTTG
34592033 TTTTTTTG
1 TTTTTTTG
34592041 CCTCCACTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 22 0.59
9 15 0.41
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:34595541 original size:45 final size:45
Alignment explanation
Indices: 34595490--34595580 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
34595480 AACATGCATG
* * *
34595490 ACAAAGACAATAATAAGAGTACAAATAATAATATGGGGAACAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
* * * *
34595535 ACAAAGAGAATAATAACAATATAAATGATAATATGGAGAATAATA
1 ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
34595580 A
1 A
34595581 GAGCGATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (45 bp):
ACAAAGACAATAATAACAATACAAATAATAATATGGAGAACAATA
Found at i:34597954 original size:24 final size:25
Alignment explanation
Indices: 34597908--34597954 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
34597898 CAATCATATC
* * *
34597908 AATTTTTAACAGTACAAATGGATAA
1 AATTTTTAACAGAAAAAAAGGATAA
34597933 AATTTTTAACA-AAAAAAAGGAT
1 AATTTTTAACAGAAAAAAAGGAT
34597955 TAATTTGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.30
Consensus pattern (25 bp):
AATTTTTAACAGAAAAAAAGGATAA
Found at i:34598098 original size:22 final size:20
Alignment explanation
Indices: 34598066--34598109 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
34598056 TTTACGGTGC
34598066 AAATTATATATTAACATATCAAA
1 AAATTATATA-TAA-ATAT-AAA
34598089 AAATT-TATATAAATATAAA
1 AAATTATATATAAATATAAA
34598108 AA
1 AA
34598110 TACGATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 3 0.14
22 4 0.19
23 5 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTATATATAAATATAAA
Found at i:34600152 original size:14 final size:14
Alignment explanation
Indices: 34600129--34600162 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34600119 TACAATATCT
34600129 AAATAATAACAATA
1 AAATAATAACAATA
*
34600143 AAATAGTAACAATA
1 AAATAATAACAATA
*
34600157 TAATAA
1 AAATAA
34600163 CGAAATGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:34600189 original size:11 final size:11
Alignment explanation
Indices: 34600173--34600211 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
34600163 CGAAATGACA
34600173 ACAAAACAATG
1 ACAAAACAATG
34600184 ACAAAACAA-G
1 ACAAAACAATG
34600194 AGCAAAACAATG
1 A-CAAAACAATG
*
34600206 GCAAAA
1 ACAAAA
34600212 TAGAATTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 2 0.08
11 22 0.88
12 1 0.04
ACGTcount: A:0.64, C:0.18, G:0.13, T:0.05
Consensus pattern (11 bp):
ACAAAACAATG
Found at i:34601148 original size:15 final size:16
Alignment explanation
Indices: 34601093--34601149 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
34601083 ACAATTGGAT
34601093 GAAGAAAAAAAGGAAAA
1 GAAGAAAAAAA-GAAAA
34601110 -AAGAACAAAAAGAAATA
1 GAAGAA-AAAAAGAAA-A
* *
34601127 GATGAAAAAAA-TAAA
1 GAAGAAAAAAAGAAAA
34601142 GAAGAAAA
1 GAAGAAAA
34601150 GGAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 11 0.32
18 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (16 bp):
GAAGAAAAAAAGAAAA
Found at i:34605529 original size:32 final size:32
Alignment explanation
Indices: 34605488--34605554 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
34605478 CTCACAAAAT
34605488 TTATTATATCTCATGATTTACAATTCTGTTAC
1 TTATTATATCTCATGATTTACAATTCTGTTAC
34605520 TTATTATATCTCATGATTTACAATTCTGTTAC
1 TTATTATATCTCATGATTTACAATTCTGTTAC
34605552 TTA
1 TTA
34605555 CACCGTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (32 bp):
TTATTATATCTCATGATTTACAATTCTGTTAC
Found at i:34608528 original size:40 final size:40
Alignment explanation
Indices: 34608469--34608547 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
34608459 TAACCTATTT
*
34608469 GTACTTCAGTACCTCTGATTGCACATACGTGCCCTTGTTC
1 GTACTTCAGTACCTCTGATTGCACATACGTGCCCCTGTTC
* * *
34608509 GTACTTCCGTATCCT-TGATTGCACTTATGTGCCCCTGTT
1 GTACTTCAGTA-CCTCTGATTGCACATACGTGCCCCTGTT
34608548 TACATTTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (40 bp):
GTACTTCAGTACCTCTGATTGCACATACGTGCCCCTGTTC
Found at i:34609935 original size:14 final size:15
Alignment explanation
Indices: 34609898--34609935 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
34609888 GATTCAATTG
34609898 AATAAAT-TATTAAA
1 AATAAATATATTAAA
*
34609912 AATAAAAATATTTAAA
1 AATAAATATA-TTAAA
34609928 AATAAATA
1 AATAAATA
34609936 AAATCAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 6 0.30
15 2 0.10
16 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAATATATTAAA
Found at i:34612551 original size:5 final size:5
Alignment explanation
Indices: 34612541--34612591 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
34612531 AGACATATTT
34612541 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
34612591 T
1 T
34612592 GTCCTACTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (5 bp):
TATCA
Found at i:34613374 original size:33 final size:31
Alignment explanation
Indices: 34613337--34613410 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 31
34613327 GAGCCCTATT
34613337 CAGTAACAGTACAGTGAGGGCCTTAGCCAAATA
1 CAGTAACAGTACAGT--GGGCCTTAGCCAAATA
*
34613370 CAGTAACAGT---GTGGGCCTTAGCCCAATA
1 CAGTAACAGTACAGTGGGCCTTAGCCAAATA
* *
34613398 CTGTATCAGTACA
1 CAGTAACAGTACA
34613411 ATGTAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
28 23 0.66
30 2 0.06
33 10 0.29
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (31 bp):
CAGTAACAGTACAGTGGGCCTTAGCCAAATA
Found at i:34613385 original size:28 final size:28
Alignment explanation
Indices: 34613342--34613407 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
34613332 CTATTCAGTA
34613342 ACAGT-ACAGTGAGGGCCTTAGCCAAAT
1 ACAGTAACAGTGAGGGCCTTAGCCAAAT
* *
34613369 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGAGGGCCTTAGCCAAAT
* *
34613397 ACTGTATCAGT
1 ACAGTAACAGT
34613408 ACAATGTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (28 bp):
ACAGTAACAGTGAGGGCCTTAGCCAAAT
Found at i:34613571 original size:26 final size:26
Alignment explanation
Indices: 34613537--34613616 Score: 115
Period size: 26 Copynumber: 3.1 Consensus size: 26
34613527 CAGAAGTAGC
* *
34613537 ATCGCAGCAAAGCTGCTAGTAACAGT
1 ATCGAAGCAAAGCTGCCAGTAACAGT
*
34613563 ATTGAAGCAAAGCTGCCAGTAACAGT
1 ATCGAAGCAAAGCTGCCAGTAACAGT
* *
34613589 ATCGCAGCAAAGTTGCCAGTAACAGT
1 ATCGAAGCAAAGCTGCCAGTAACAGT
34613615 AT
1 AT
34613617 ACTCCCTCCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
ATCGAAGCAAAGCTGCCAGTAACAGT
Found at i:34613798 original size:27 final size:27
Alignment explanation
Indices: 34613750--34613896 Score: 160
Period size: 27 Copynumber: 5.5 Consensus size: 27
34613740 AAGGCCATAA
* **
34613750 CAGTCATTTTGACTCT-TAGGGGTATAA
1 CAGTCATTTT-ACCCTATAGGGGTATTT
*
34613777 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* *
34613804 C-GATCATTGTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTATAGGGGTATTT
*
34613831 CAGACATTTTACCCTAT-GGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
*
34613857 TAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
34613884 C-GATCA-TTTACCC
1 CAG-TCATTTTACCC
34613897 AGAAATGGCA
Statistics
Matches: 105, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
26 37 0.35
27 67 0.64
28 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (27 bp):
CAGTCATTTTACCCTATAGGGGTATTT
Found at i:34613827 original size:54 final size:53
Alignment explanation
Indices: 34613766--34613881 Score: 153
Period size: 53 Copynumber: 2.2 Consensus size: 53
34613756 TTTTGACTCT
*
34613766 TAGGGGTATAACAGTCATTTTACCCTATGGGGGTATTTCGA-TCATTGTACCCTA
1 TAGGGGTATAACAGACATTTTACCCTAT-GGGGTATTT-GAGTCATTGTACCCTA
* ** * *
34613820 TGGGGGTATTTCAGACATTTTACCCTATGGGGTATTTTAGTCATTTTACCCTA
1 TAGGGGTATAACAGACATTTTACCCTATGGGGTATTTGAGTCATTGTACCCTA
34613873 TAGGGGTAT
1 TAGGGGTAT
34613882 TTCGATCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.02
53 29 0.54
54 24 0.44
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (53 bp):
TAGGGGTATAACAGACATTTTACCCTATGGGGTATTTGAGTCATTGTACCCTA
Found at i:34613893 original size:26 final size:27
Alignment explanation
Indices: 34613780--34613896 Score: 161
Period size: 27 Copynumber: 4.4 Consensus size: 27
34613770 GGTATAACAG
34613780 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
34613807 TCATTGTACCCTATGGGGGTATTTCAGA
1 TCATTTTACCCTATGGGGGTATTTC-GA
*
34613835 -CATTTTACCCTAT-GGGGTATTT-TA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
34613859 GTCATTTTACCCTATAGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTCGA
34613887 TCA-TTTACCC
1 TCATTTTACCC
34613897 AGAAATGGCA
Statistics
Matches: 81, Mismatches: 4, Indels: 11
0.84 0.04 0.11
Matches are distributed among these distances:
24 1 0.01
26 29 0.36
27 48 0.59
28 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:34616257 original size:5 final size:5
Alignment explanation
Indices: 34616247--34616271 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34616237 TTGATAGACT
34616247 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
34616272 ATAGCAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:34617973 original size:19 final size:20
Alignment explanation
Indices: 34617949--34617986 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34617939 TAGATCAAAA
34617949 TTTATTAAAT-ATATAATTT
1 TTTATTAAATGATATAATTT
*
34617968 TTTATTATATGATATAATT
1 TTTATTAAATGATATAATT
34617987 AGTGACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTATTAAATGATATAATTT
Found at i:34618315 original size:26 final size:27
Alignment explanation
Indices: 34618265--34618316 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
34618255 TTAAAATATG
* *
34618265 TTTTTTATGTTTTATAATTTTTAATAC
1 TTTTTTATGTTTTATAATATATAATAC
*
34618292 TTTTTTAT-TTTTTTAATATATAATA
1 TTTTTTATGTTTTATAATATATAATA
34618317 AAATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTTTATGTTTTATAATATATAATAC
Found at i:34625051 original size:9 final size:9
Alignment explanation
Indices: 34625015--34625051 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
34625005 ATATGTTTGA
34625015 ATTATTTAT
1 ATTATTTAT
34625024 A-T-TTTAT
1 ATTATTTAT
*
34625031 ATAATTTAT
1 ATTATTTAT
34625040 ATTATTTAT
1 ATTATTTAT
34625049 ATT
1 ATT
34625052 TAGGCGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.25
8 1 0.04
9 17 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTATTTAT
Found at i:34625481 original size:228 final size:228
Alignment explanation
Indices: 34625084--34625535 Score: 823
Period size: 228 Copynumber: 2.0 Consensus size: 228
34625074 TATAATTTAT
** *
34625084 ATTTTTTTTACTTGACAAGGAACCTTAAAAAATTGTTATATATTTTTAATTTTAATATTTTACGA
1 ATTTTTTTTACTCCACAAGCAACCTTAAAAAATTGTTATATATTTTTAATTTTAATATTTTACGA
* *
34625149 TATCTTTATAAAATATTTGTTAACCTCTGACCCTACTTATGAAATCTAAAATTTTTATTGATAGT
66 TATCCTTATAAAATATTTGTCAACCTCTGACCCTACTTATGAAATCTAAAATTTTTATTGATAGT
34625214 GTACCAAATATTATTTCTTTATATATTATAAAAGTAAAATTTCATAAATTTAAGAAAATCAAAAT
131 GTACCAAATATTATTTCTTTATATATTATAAAAGTAAAATTTCATAAATTTAAGAAAATCAAAAT
34625279 TTTATATAATTTTTAAAAATTCATTTTGAGTGC
196 TTTATATAATTTTTAAAAATTCATTTTGAGTGC
* * *
34625312 ATTTTTTTTACTCCATAAGCAACCTTAAAAAATTGTTATATATTTTTATTTTTAATATTTTATGA
1 ATTTTTTTTACTCCACAAGCAACCTTAAAAAATTGTTATATATTTTTAATTTTAATATTTTACGA
*
34625377 TATCCTTATAAAATATTTGTCAATCTCTGACCCTACTTATGAAATCTAAAATTTTTATTGATAGT
66 TATCCTTATAAAATATTTGTCAACCTCTGACCCTACTTATGAAATCTAAAATTTTTATTGATAGT
34625442 GTACCAAATATTATTTCTTTATATATTATAAAAGTAAAATTTCATAAATTTAAGAAAATCAAAAT
131 GTACCAAATATTATTTCTTTATATATTATAAAAGTAAAATTTCATAAATTTAAGAAAATCAAAAT
34625507 TTTATATAATTTTTAAAAATTCATTTTGA
196 TTTATATAATTTTTAAAAATTCATTTTGA
34625536 ATTTGAAATT
Statistics
Matches: 215, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
228 215 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.46
Consensus pattern (228 bp):
ATTTTTTTTACTCCACAAGCAACCTTAAAAAATTGTTATATATTTTTAATTTTAATATTTTACGA
TATCCTTATAAAATATTTGTCAACCTCTGACCCTACTTATGAAATCTAAAATTTTTATTGATAGT
GTACCAAATATTATTTCTTTATATATTATAAAAGTAAAATTTCATAAATTTAAGAAAATCAAAAT
TTTATATAATTTTTAAAAATTCATTTTGAGTGC
Found at i:34625585 original size:21 final size:21
Alignment explanation
Indices: 34625544--34625587 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34625534 GAATTTGAAA
*
34625544 TTAAAACTTTTAATATTTATT
1 TTAAAACTTTTAATATATATT
*
34625565 TTAAAA-TTTTGATATAATATT
1 TTAAAACTTTTAATAT-ATATT
34625586 TT
1 TT
34625588 TAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAAAACTTTTAATATATATT
Found at i:34632135 original size:13 final size:13
Alignment explanation
Indices: 34632117--34632145 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
34632107 TACAGATGCC
34632117 GCTAATTCATCAG
1 GCTAATTCATCAG
34632130 GCTAATTCATCAG
1 GCTAATTCATCAG
34632143 GCT
1 GCT
34632146 GCGTCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (13 bp):
GCTAATTCATCAG
Found at i:34633103 original size:20 final size:20
Alignment explanation
Indices: 34633071--34633108 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34633061 TTGAAACATG
*
34633071 TTTAAAATAAAAATTATCGT
1 TTTAAAATAAAAAGTATCGT
34633091 TTTATAAAT-AAAAGTATC
1 TTTA-AAATAAAAAGTATC
34633109 ATGAAAACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTAAAATAAAAAGTATCGT
Found at i:34636048 original size:221 final size:222
Alignment explanation
Indices: 34635665--34636107 Score: 870
Period size: 221 Copynumber: 2.0 Consensus size: 222
34635655 CGATCCTCAG
34635665 TTTTTTCAGTGTAATAGACACACTATCCTCAGGAAGGGATTTGATATTAGAACAACCAGAGATAG
1 TTTTTTCAGTGTAATAGACACACTATCCTCAGGAAGGGATTTGATATTAGAACAACCAGAGATAG
34635730 TTAACTTGTCGAGATGAGTGCAGTGTTGCAACATCTGTTCCAATATGGAATCATTCATATTCGAA
66 TTAACTTGTCGAGATGAGTGCAGTGTTGCAACATCTGTTCCAATATGGAATCATTCATATTCGAA
34635795 CCTCCAATTTCCAACTCTCGAAGCCCACAAGGCAATGGCTCCAATTGCAATGCGTTGCATTTCTT
131 CCTCCAATTTCCAACTCTCGAAGCCCACAAGGCAATGGCTCCAATTGCAATGCGTTGCATTTCTT
*
34635860 TAACTGCAGTTCAC-AATGCTTGGTGT
196 TAACTGAAGTTCACAAATGCTTGGTGT
34635886 TTTTTTCAGTGTAATAGACACACTATCCTCAGGAAGGGATTTGATATTAGAACAACCAGAGATAG
1 TTTTTTCAGTGTAATAGACACACTATCCTCAGGAAGGGATTTGATATTAGAACAACCAGAGATAG
34635951 TTAACTTGTCGAGATGAGTGCAGTGTTGCAACATCTGTTCCAATATGGAATCATTCATATTCGAA
66 TTAACTTGTCGAGATGAGTGCAGTGTTGCAACATCTGTTCCAATATGGAATCATTCATATTCGAA
34636016 CCTCCAATTTCCAACTCTCGAAGCCCACAAGGCAATGGCTCCAATTGCAATGCGTTGCATTTCTT
131 CCTCCAATTTCCAACTCTCGAAGCCCACAAGGCAATGGCTCCAATTGCAATGCGTTGCATTTCTT
34636081 TAACTGAAGTTCACAAATGCTTGGTGT
196 TAACTGAAGTTCACAAATGCTTGGTGT
34636108 CCTTGGGAGA
Statistics
Matches: 220, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
221 208 0.95
222 12 0.05
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (222 bp):
TTTTTTCAGTGTAATAGACACACTATCCTCAGGAAGGGATTTGATATTAGAACAACCAGAGATAG
TTAACTTGTCGAGATGAGTGCAGTGTTGCAACATCTGTTCCAATATGGAATCATTCATATTCGAA
CCTCCAATTTCCAACTCTCGAAGCCCACAAGGCAATGGCTCCAATTGCAATGCGTTGCATTTCTT
TAACTGAAGTTCACAAATGCTTGGTGT
Found at i:34639700 original size:17 final size:16
Alignment explanation
Indices: 34639658--34639713 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
34639648 TTATACTACA
34639658 AAATATTTATTATTAAT
1 AAATATTTATTA-TAAT
* *
34639675 ACATTTTTAATTATAAT
1 AAATATTT-ATTATAAT
34639692 AAATATTTATTAT--T
1 AAATATTTATTATAAT
34639706 AAATATTT
1 AAATATTT
34639714 TAGAAGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.26
16 5 0.15
17 16 0.47
18 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTTATTATAAT
Found at i:34647958 original size:28 final size:27
Alignment explanation
Indices: 34647908--34647960 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
34647898 TACATGATGA
* *
34647908 AATTAAATAATAATATATGATAAAAAG
1 AATTAAATAATAATACATAATAAAAAG
*
34647935 AATTAAAATAATAGTACATAATAAAA
1 AATT-AAATAATAATACATAATAAAA
34647961 TAAAATAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (27 bp):
AATTAAATAATAATACATAATAAAAAG
Found at i:34647968 original size:23 final size:21
Alignment explanation
Indices: 34647938--34647981 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
34647928 TAAAAAGAAT
34647938 TAAAATAATAGTACATAATAAAA
1 TAAAATAAT-GTACAT-ATAAAA
*
34647961 TAAAATAATGTATATATAAAA
1 TAAAATAATGTACATATAAAA
34647982 AGGTAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 5 0.25
23 9 0.45
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAATAATGTACATATAAAA
Found at i:34648016 original size:3 final size:3
Alignment explanation
Indices: 34648008--34648078 Score: 54
Period size: 3 Copynumber: 22.7 Consensus size: 3
34647998 AAACTAATAC
* * * * *
34648008 AAT AAT AAT ACCT -AT AAT AAT AAC AAC AAC AAT AAT AAT AGT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34648053 AAT AAT AAT AATT AATT AATT AAT AA
1 AAT AAT AAT AA-T AA-T AA-T AAT AA
34648079 AAAAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 46 0.78
4 12 0.20
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34648139 original size:30 final size:30
Alignment explanation
Indices: 34648103--34648163 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
34648093 AAAAAGGATT
34648103 AAATCGCAATTAAAACTGAATTAACAGGAA
1 AAATCGCAATTAAAACTGAATTAACAGGAA
34648133 AAATCGCAATTAAAACTGAATTAACAGGAA
1 AAATCGCAATTAAAACTGAATTAACAGGAA
34648163 A
1 A
34648164 CAAATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (30 bp):
AAATCGCAATTAAAACTGAATTAACAGGAA
Found at i:34651893 original size:27 final size:27
Alignment explanation
Indices: 34651855--34651915 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
34651845 CACATTGCTA
34651855 ACATTTACCCAATAGAAAGAAGAGTTC
1 ACATTTACCCAATAGAAAGAAGAGTTC
34651882 ACATTTACCCAATAGAAAGAAGAGTTC
1 ACATTTACCCAATAGAAAGAAGAGTTC
34651909 ACATTTA
1 ACATTTA
34651916 TGAAAGTACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (27 bp):
ACATTTACCCAATAGAAAGAAGAGTTC
Found at i:34651920 original size:21 final size:23
Alignment explanation
Indices: 34651866--34651921 Score: 62
Period size: 27 Copynumber: 2.3 Consensus size: 23
34651856 CATTTACCCA
34651866 ATAGAAAGAAGAGTTCACATTTACCC
1 ATAGAAAGAAGAGTTCACATTT---C
34651892 AATAGAAAGAAGAGTTCACATTT-
1 -ATAGAAAGAAGAGTTCACATTTC
34651915 AT-GAAAG
1 ATAGAAAG
34651922 TACGCAGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
27 22 0.76
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.23
Consensus pattern (23 bp):
ATAGAAAGAAGAGTTCACATTTC
Found at i:34659479 original size:13 final size:13
Alignment explanation
Indices: 34659461--34659488 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34659451 TAACCATTAC
34659461 AATAGTCACTCAA
1 AATAGTCACTCAA
34659474 AATAGTCACTCAA
1 AATAGTCACTCAA
34659487 AA
1 AA
34659489 CTGATTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAGTCACTCAA
Found at i:34660935 original size:19 final size:20
Alignment explanation
Indices: 34660892--34660934 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
34660882 ACACAAACGG
*
34660892 AAAACATCAACTTAATACAA
1 AAAACATAAACTTAATACAA
34660912 AAAACATAAACTTAATACAA
1 AAAACATAAACTTAATACAA
34660932 AAA
1 AAA
34660935 CCAAAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAACATAAACTTAATACAA
Found at i:34667403 original size:50 final size:50
Alignment explanation
Indices: 34667347--34667475 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
34667337 GGTCTCATGG
* ** *
34667347 AAGACCATATTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGA
1 AAGACCATATTTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACGA
* * * * *
34667397 AAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGT
1 AAGACCATATTTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACGA
* *
34667447 AAGACCATATCTGGGATATGGCATTGGCA
1 AAGACCATATTTGGGACATGGCATTGGCA
34667476 GTACAAGAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
AAGACCATATTTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACGA
Found at i:34668190 original size:16 final size:17
Alignment explanation
Indices: 34668169--34668203 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34668159 AGACGAAAAA
*
34668169 GAAAG-AAAGAAAAGGG
1 GAAAGAAAAGAAAAAGG
34668185 GAAAGAAAAGAAAAAGG
1 GAAAGAAAAGAAAAAGG
34668202 GA
1 GA
34668204 GAATTAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAGAAAAAGG
Found at i:34668974 original size:6 final size:6
Alignment explanation
Indices: 34668963--34668994 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
34668953 GGATTGAATG
34668963 AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
34668995 TAAACATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:34669089 original size:2 final size:2
Alignment explanation
Indices: 34669084--34669129 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
34669074 TATATATATA
34669084 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
34669126 TG TG
1 TG TG
34669130 AATTGAGTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34669738 original size:39 final size:38
Alignment explanation
Indices: 34669658--34669785 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 38
34669648 ACTTGTCGGC
* *
34669658 TTACTGATCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATC-GGCACTTTGTGTGCCGAATACTGTTACTG
*
34669696 TTACTGATTCGGCACTTTGTGTGTCGAGTACTGTTACTGTTACTG
1 TTACTGA-TCGGCACTTTGTGTGCCGA--A----TACTGTTACTG
* *
34669741 TTACCGACTCGGCACTTTGTGTGCCGAATACTGTTACCG
1 TTACTGA-TCGGCACTTTGTGTGCCGAATACTGTTACTG
34669780 TTACTG
1 TTACTG
34669786 TTACAGGTTC
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
38 12 0.16
39 26 0.35
43 1 0.01
45 35 0.47
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (38 bp):
TTACTGATCGGCACTTTGTGTGCCGAATACTGTTACTG
Done.