Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 90 of 325
Found at i:30080749 original size:19 final size:20
Alignment explanation
Indices: 30080725--30080762 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
30080715 GATTTGATTA
30080725 AATAAATTA-TTTAAAAAAT
1 AATAAATTATTTTAAAAAAT
30080744 AATAAATTATTTTAAAAAA
1 AATAAATTATTTTAAAAAA
30080763 ACTACTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATAAATTATTTTAAAAAAT
Found at i:30084971 original size:2 final size:2
Alignment explanation
Indices: 30084964--30084988 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30084954 ACTTTGAAAC
30084964 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30084989 TATTCTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30086141 original size:19 final size:19
Alignment explanation
Indices: 30086117--30086174 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
30086107 TATAATATTA
30086117 TTTTTAAAAATTTAATAAT
1 TTTTTAAAAATTTAATAAT
*
30086136 TTTTTAATAATTTAATAAT
1 TTTTTAAAAATTTAATAAT
30086155 TTATATATAAAAATTTAATA
1 TT-T-T-TAAAAATTTAATA
30086175 CTAATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 20 0.59
20 1 0.03
21 1 0.03
22 12 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTAAAAATTTAATAAT
Found at i:30088582 original size:110 final size:110
Alignment explanation
Indices: 30088389--30088613 Score: 441
Period size: 110 Copynumber: 2.0 Consensus size: 110
30088379 ATATAGGACT
*
30088389 ATTACATTTGGTACCAAAGCAATCTTAGCTAGACACTAGGTAAATTGAACATTTTACGACTAAAT
1 ATTACATTTGGTACCAAAGCAATCTTAGCTAGACACTAGGTAAATTGAACATTTTACGACTAAAA
30088454 TTTAACATTTAGAACTCATTAATGTCATTACTTATTTTTTGAAAC
66 TTTAACATTTAGAACTCATTAATGTCATTACTTATTTTTTGAAAC
30088499 ATTACATTTGGTACCAAAGCAATCTTAGCTAGACACTAGGTAAATTGAACATTTTACGACTAAAA
1 ATTACATTTGGTACCAAAGCAATCTTAGCTAGACACTAGGTAAATTGAACATTTTACGACTAAAA
30088564 TTTAACATTTAGAACTCATTAATGTCATTACTTATTTTTTGAAAC
66 TTTAACATTTAGAACTCATTAATGTCATTACTTATTTTTTGAAAC
30088609 ATTAC
1 ATTAC
30088614 CTATTAACAG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 114 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (110 bp):
ATTACATTTGGTACCAAAGCAATCTTAGCTAGACACTAGGTAAATTGAACATTTTACGACTAAAA
TTTAACATTTAGAACTCATTAATGTCATTACTTATTTTTTGAAAC
Found at i:30088805 original size:20 final size:20
Alignment explanation
Indices: 30088780--30088832 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
30088770 AACTTTATGT
30088780 AGGTATTGATACCTATGCC-A
1 AGGTATTGATACCT-TGCCTA
*
30088800 AGGTATTGATACCTTGCCTT
1 AGGTATTGATACCTTGCCTA
*
30088820 AGGTACTGATACC
1 AGGTATTGATACC
30088833 AAAGCATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
AGGTATTGATACCTTGCCTA
Found at i:30093544 original size:16 final size:15
Alignment explanation
Indices: 30093503--30093548 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
30093493 CTTTATTATT
30093503 ATAATTTACTAAAAAA
1 ATAATTTAC-AAAAAA
30093519 ATTAA-TTACAAAAAA
1 A-TAATTTACAAAAAA
30093534 ATAATTATACAAAAA
1 ATAATT-TACAAAAA
30093549 GTTAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.11
15 8 0.30
16 13 0.48
17 3 0.11
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATTTACAAAAAA
Found at i:30093548 original size:15 final size:15
Alignment explanation
Indices: 30093508--30093540 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
30093498 TTATTATAAT
30093508 TTACTAAAAAAATTAA
1 TTAC-AAAAAAATTAA
30093524 TTACAAAAAAA-TAA
1 TTACAAAAAAATTAA
30093538 TTA
1 TTA
30093541 TACAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
TTACAAAAAAATTAA
Found at i:30093610 original size:23 final size:23
Alignment explanation
Indices: 30093522--30093610 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 23
30093512 TAAAAAAATT
**
30093522 AATTACAAAAAAATAATTATACAAA
1 AATTAC-AAAAAA-AATTATTTAAA
* *
30093547 AAGTTAAAAAATAAAATGA-TTAAA
1 AA-TTACAAAA-AAAATTATTTAAA
* **
30093571 AATT-TATTAAAAA-TATTTAAA
1 AATTACAAAAAAAATTATTTAAA
30093592 AATTACAAAAAAAATTATT
1 AATTACAAAAAAAATTATT
30093611 ATTTTGAAGG
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
22 8 0.17
23 6 0.12
24 5 0.10
25 10 0.21
26 5 0.10
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.30
Consensus pattern (23 bp):
AATTACAAAAAAAATTATTTAAA
Found at i:30099256 original size:26 final size:24
Alignment explanation
Indices: 30099226--30099273 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
30099216 AATAAAAAAA
*
30099226 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAACATAA-AAA-CAAATATAT
30099252 TTAAAAACATAAAAACAAATAT
1 TTAAAAACATAAAAACAAATAT
30099274 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAAAACATAAAAACAAATATAT
Found at i:30099285 original size:22 final size:21
Alignment explanation
Indices: 30099252--30099302 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
30099242 TCAAATATAT
*
30099252 TTAAAA-ACATAAAAACAAATA
1 TTAAAACAAATAAAAACAAA-A
**
30099273 TTAAAACAAATAAAAATGAAA
1 TTAAAACAAATAAAAACAAAA
30099294 TTAAAACAA
1 TTAAAACAA
30099303 TTCTTAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.20
Consensus pattern (21 bp):
TTAAAACAAATAAAAACAAAA
Found at i:30105699 original size:39 final size:39
Alignment explanation
Indices: 30105670--30105855 Score: 273
Period size: 39 Copynumber: 4.7 Consensus size: 39
30105660 TAGTACCAAT
* * *
30105670 ACGAAGCCTACGGACCTTAAGTCCGGATATAGTACCAGC
1 ACGAAGCCTGCGGACCTTAAGTCCGGATACAGTTCCAGC
*
30105709 ACGAAGCCTGCGGATCTTAAGTCCGGATACAGTTCCAGC
1 ACGAAGCCTGCGGACCTTAAGTCCGGATACAGTTCCAGC
* * * *
30105748 ACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGC
1 ACGAAGCCTGC-GGACCTTAAGTCCGGATACAGTTCCAGC
* *
30105788 ATGAAGCCTGCGGACCTTAAGTCCGGATACAATTCCAGC
1 ACGAAGCCTGCGGACCTTAAGTCCGGATACAGTTCCAGC
30105827 ACGAAGCCTGCGGACCTTAAGTCCGGATA
1 ACGAAGCCTGCGGACCTTAAGTCCGGATA
30105856 TACATCAAAT
Statistics
Matches: 132, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
39 99 0.75
40 33 0.25
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (39 bp):
ACGAAGCCTGCGGACCTTAAGTCCGGATACAGTTCCAGC
Found at i:30105775 original size:79 final size:78
Alignment explanation
Indices: 30105670--30105857 Score: 277
Period size: 79 Copynumber: 2.4 Consensus size: 78
30105660 TAGTACCAAT
* * *
30105670 ACGAAGCCTACGGACCTTAAGTCCGGATATAGTACCAGCACGAAGCCTGCGGATCTTAAGTCCGG
1 ACGAAGCCTGCGGACCTTAAGTCCGGATATAATACCAGCACGAAGCCTGCGGACCTTAAGTCCGG
*
30105735 ATACAGTTCCAGC
66 ATACAATTCCAGC
* * * * * *
30105748 ACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATGAAGCCTGCGGACCTTAAGTCCG
1 ACGAAGCCTGC-GGACCTTAAGTCCGGATATAATACCAGCACGAAGCCTGCGGACCTTAAGTCCG
30105813 GATACAATTCCAGC
65 GATACAATTCCAGC
30105827 ACGAAGCCTGCGGACCTTAAGTCCGGATATA
1 ACGAAGCCTGCGGACCTTAAGTCCGGATATA
30105858 CATCAAATAT
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
78 26 0.27
79 69 0.73
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (78 bp):
ACGAAGCCTGCGGACCTTAAGTCCGGATATAATACCAGCACGAAGCCTGCGGACCTTAAGTCCGG
ATACAATTCCAGC
Found at i:30105920 original size:24 final size:24
Alignment explanation
Indices: 30105893--30105938 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
30105883 ATATATTAAT
30105893 ACATCTCATTTAACATATCACAAC
1 ACATCTCATTTAACATATCACAAC
30105917 ACATCTCATTTAACATATCACA
1 ACATCTCATTTAACATATCACA
30105939 TTAGTAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.30
Consensus pattern (24 bp):
ACATCTCATTTAACATATCACAAC
Found at i:30106620 original size:24 final size:24
Alignment explanation
Indices: 30106608--30106699 Score: 157
Period size: 24 Copynumber: 3.8 Consensus size: 24
30106598 TTGACATTCC
30106608 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
30106632 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
* *
30106656 AATTCGCACACATAGTGCCATTCA
1 AATCCGCACACATAGTGCCATACA
*
30106680 AATTCGCACACATAGTGCCA
1 AATCCGCACACATAGTGCCA
30106700 AAATCATTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.20
Consensus pattern (24 bp):
AATCCGCACACATAGTGCCATACA
Found at i:30106669 original size:72 final size:72
Alignment explanation
Indices: 30106563--30106699 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
30106553 CCATGTTAAC
* ** * * *
30106563 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCCAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
30106628 TACAAAT
66 TACAAAT
* * *
30106635 CCGCACACATAGTGCCATACAAATTCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
30106700 AAATCATTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.23
Consensus pattern (72 bp):
CCGCACACATAGTGCCATACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
TACAAAT
Found at i:30106697 original size:48 final size:48
Alignment explanation
Indices: 30106563--30106699 Score: 161
Period size: 48 Copynumber: 2.9 Consensus size: 48
30106553 CCATGTTAAC
* * * * * *
30106563 CCGCACACATAGTGCC-TT-AGTAATTCACATACATATTGACATTCCAAT
1 CCGCACACATAGTGCCATTCA--AATTCGCACACATAGTGCCATACAAAT
* *
30106611 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCATACAAAT
*
30106659 TCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
30106700 AAATCATTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 74 0.97
49 1 0.01
50 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.23
Consensus pattern (48 bp):
CCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCATACAAAT
Found at i:30107899 original size:17 final size:17
Alignment explanation
Indices: 30107877--30107910 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30107867 CCCCACTTAA
*
30107877 TATATTATAACTTATTT
1 TATATTATAACATATTT
30107894 TATATTATAACATATTT
1 TATATTATAACATATTT
30107911 CAATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:30111112 original size:19 final size:19
Alignment explanation
Indices: 30111088--30111134 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
30111078 TGTTGTTTTC
30111088 CCTTTTGATTCATAGCCTT
1 CCTTTTGATTCATAGCCTT
*
30111107 CCTTTTGATTCGTAGCCTT
1 CCTTTTGATTCATAGCCTT
*
30111126 CTTTTTGAT
1 CCTTTTGAT
30111135 CTTGTTCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.51
Consensus pattern (19 bp):
CCTTTTGATTCATAGCCTT
Found at i:30124333 original size:50 final size:50
Alignment explanation
Indices: 30124264--30124398 Score: 180
Period size: 50 Copynumber: 2.7 Consensus size: 50
30124254 GCAGATGTAA
* * *
30124264 AGCCTACGAGCTTAGCACTTGGTGCCTAGGTATGTTTTTAGAGGGATGTT
1 AGCCTACGGGCTTAGCACTTGGTGCCTAGGCATGTCTTTAGAGGGATGTT
* * *
30124314 AGCCTACGGGCTTGGCACTTGGTGCTTAGGCGTGTCTTTAGAGGGATGTT
1 AGCCTACGGGCTTAGCACTTGGTGCCTAGGCATGTCTTTAGAGGGATGTT
* * * *
30124364 AGTCTACGGGCTAAGCACTTGGTGCCCAAGCATGT
1 AGCCTACGGGCTTAGCACTTGGTGCCTAGGCATGT
30124399 TCTTGGTTAG
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (50 bp):
AGCCTACGGGCTTAGCACTTGGTGCCTAGGCATGTCTTTAGAGGGATGTT
Found at i:30125077 original size:2 final size:2
Alignment explanation
Indices: 30125070--30125099 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30125060 TGGGATGTAG
*
30125070 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30125100 GATGGAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30129734 original size:23 final size:23
Alignment explanation
Indices: 30129691--30129757 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
30129681 ATCCCAATAT
* *
30129691 TTTTTTCGTTTTGA-GTAATTTAA
1 TTTTTTC-TTTTCATGTTATTTAA
*
30129714 TTTTTTCTTTTTATGTTATTTTAA
1 TTTTTTCTTTTCATGTTA-TTTAA
* *
30129738 CTTTTT-TTTTCATTTTATTT
1 TTTTTTCTTTTCATGTTATTT
30129758 TGCTTCTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 8 0.22
23 19 0.51
24 10 0.27
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (23 bp):
TTTTTTCTTTTCATGTTATTTAA
Found at i:30129758 original size:23 final size:24
Alignment explanation
Indices: 30129709--30129758 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
30129699 TTTTGAGTAA
* *
30129709 TTTAATTTTTTCTTTTTATGTTAT
1 TTTAACTTTTTCTTTTCATGTTAT
*
30129733 TTTAACTTTTT-TTTTCATTTTAT
1 TTTAACTTTTTCTTTTCATGTTAT
30129756 TTT
1 TTT
30129759 GCTTCTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTAACTTTTTCTTTTCATGTTAT
Found at i:30131094 original size:20 final size:20
Alignment explanation
Indices: 30131066--30131170 Score: 78
Period size: 20 Copynumber: 5.4 Consensus size: 20
30131056 AAAATAAAAA
*
30131066 TATAGAAAAATTATTAAATTT
1 TATA-AAAAATTATAAAATTT
30131087 TAATAAAAAATTA-AAAATTT
1 T-ATAAAAAATTATAAAATTT
* *
30131107 TAT-TAAAATTAT-AATTTT
1 TATAAAAAATTATAAAATTT
* *
30131125 TTTATAAAAATCATAAAA---
1 TATA-AAAAATTATAAAATTT
* *
30131143 AATAAAAAATTACAAAATTT
1 TATAAAAAATTATAAAATTT
30131163 TATAAAAA
1 TATAAAAA
30131171 TCATAAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
17 11 0.17
18 16 0.25
19 2 0.03
20 21 0.33
21 11 0.17
22 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (20 bp):
TATAAAAAATTATAAAATTT
Found at i:30131966 original size:49 final size:49
Alignment explanation
Indices: 30131907--30132011 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
30131897 TTTTTTTATG
*
30131907 AAATTTATATTTCTTTACATTTTGTATA-ATTTTCTTACGA-CTTTATAA
1 AAATTTATATTTCTATACATTTT-TATATATTTTCTTACGATCTTTATAA
* * * *
30131955 AAATTCTATATTTCTATATATTTTTTTATATTTTTTTACGATTTTTATAA
1 AAATT-TATATTTCTATACATTTTTATATATTTTCTTACGATCTTTATAA
*
30132005 AATTTTA
1 AAATTTA
30132012 CAATTTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
48 8 0.17
49 29 0.60
50 11 0.23
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (49 bp):
AAATTTATATTTCTATACATTTTTATATATTTTCTTACGATCTTTATAA
Found at i:30131988 original size:10 final size:10
Alignment explanation
Indices: 30131961--30132038 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 10
30131951 ATAAAAATTC
* *
30131961 TATATTTCTA
1 TATATTTTTT
30131971 TATATTTTTT
1 TATATTTTTT
30131981 TATATTTTTT
1 TATATTTTTT
* *
30131991 TACGATTTTTA
1 TA-TATTTTTT
* * *
30132002 TAAAATTTTA
1 TATATTTTTT
*
30132012 CA-ATTTTTT
1 TATATTTTTT
*
30132021 TATATTTTCT
1 TATATTTTTT
30132031 TACTATTT
1 TA-TATTT
30132039 ATATATATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
9 6 0.11
10 35 0.65
11 13 0.24
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.65
Consensus pattern (10 bp):
TATATTTTTT
Found at i:30132001 original size:19 final size:19
Alignment explanation
Indices: 30131977--30132044 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
30131967 TCTATATATT
*
30131977 TTTTTATATTTTTTTACGA
1 TTTTTATATTTTTTTACAA
***
30131996 TTTTTATAAAATTTTACAA
1 TTTTTATATTTTTTTACAA
* *
30132015 TTTTTTTATATTTTCTTACTA
1 --TTTTTATATTTTTTTACAA
*
30132036 TTTATATAT
1 TTTTTATAT
30132045 ATATATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
19 23 0.62
21 14 0.38
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTATATTTTTTTACAA
Found at i:30139805 original size:86 final size:86
Alignment explanation
Indices: 30139658--30139815 Score: 253
Period size: 86 Copynumber: 1.8 Consensus size: 86
30139648 ATAAGCCCAA
* * *
30139658 CTAGTTAGAAGTAGATCCTCTAAGTTTATTTTAGCTTCCTACTATTCACAAGAACAGTCCTTTGT
1 CTAGTTAGAAGCAGATCCTCTAAGTTCATTTTAGCTTCCTACTATTCACAAGAACAATCCTTTGT
30139723 AACATGAGATGATCAAAAAAG
66 AACATGAGATGATCAAAAAAG
* * *
30139744 CTAGTTAGAAGCAGATCCTCTAAGTTCGTTTTAGTTTCTTACTATTCACAAGAACAATCCTTTGT
1 CTAGTTAGAAGCAGATCCTCTAAGTTCATTTTAGCTTCCTACTATTCACAAGAACAATCCTTTGT
*
30139809 AATATGA
66 AACATGA
30139816 TATATCCATC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (86 bp):
CTAGTTAGAAGCAGATCCTCTAAGTTCATTTTAGCTTCCTACTATTCACAAGAACAATCCTTTGT
AACATGAGATGATCAAAAAAG
Found at i:30142527 original size:37 final size:37
Alignment explanation
Indices: 30142477--30142551 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
30142467 CACATTAGTC
30142477 ATCATACATAATTCATGTATTTATGCAAATATAATTA
1 ATCATACATAATTCATGTATTTATGCAAATATAATTA
*
30142514 ATCATACATAATTCATGTTTTTATGCAAATATAATTA
1 ATCATACATAATTCATGTATTTATGCAAATATAATTA
30142551 A
1 A
30142552 ATACCACTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (37 bp):
ATCATACATAATTCATGTATTTATGCAAATATAATTA
Found at i:30146312 original size:25 final size:25
Alignment explanation
Indices: 30146279--30146334 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
30146269 AATTATAAAT
30146279 AAATAAATTTAAAAGAAAATATATA
1 AAATAAATTTAAAAGAAAATATATA
* **
30146304 TAATAAATTTAAAAGAATTTATATA
1 AAATAAATTTAAAAGAAAATATATA
30146329 AAATAA
1 AAATAA
30146335 CACGAAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (25 bp):
AAATAAATTTAAAAGAAAATATATA
Found at i:30148233 original size:27 final size:27
Alignment explanation
Indices: 30148195--30148252 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
30148185 ATTTTTACAG
*
30148195 TAAGATATTATCTTTGATATAGTAAAA
1 TAAGATATTATCCTTGATATAGTAAAA
30148222 TAAGATATTATCCTTGATATAGTAAAA
1 TAAGATATTATCCTTGATATAGTAAAA
30148249 TAAG
1 TAAG
30148253 GAAATAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (27 bp):
TAAGATATTATCCTTGATATAGTAAAA
Found at i:30148405 original size:30 final size:31
Alignment explanation
Indices: 30148371--30148440 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
30148361 TTACACAAGA
* * * **
30148371 GTAAATATTCAAAATTTGAGGGGTTAA-AGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
*
30148401 GTAAATATGAAAAAGTTGAAGGACTAATAGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
30148432 GTAAATATT
1 GTAAATATT
30148441 TTAAGAGTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (31 bp):
GTAAATATTAAAAAGTTGAAGGACTAATAGT
Found at i:30148677 original size:20 final size:21
Alignment explanation
Indices: 30148643--30148696 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
30148633 TGATGATATT
*
30148643 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
30148664 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
30148684 TTTTATTATTTTA
1 TTATATTATTTTA
30148697 TTATTATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:30148700 original size:3 final size:3
Alignment explanation
Indices: 30148682--30148730 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
30148672 TTTAATGAGA
*
30148682 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
30148727 TAT T
1 TAT T
30148731 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:30148702 original size:11 final size:11
Alignment explanation
Indices: 30148686--30148724 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
30148676 ATGAGATATT
30148686 TTATTATTTTA
1 TTATTATTTTA
*
30148697 TTATTATTTCA
1 TTATTATTTTA
30148708 TTATTATTTTA
1 TTATTATTTTA
30148719 TTATTA
1 TTATTA
30148725 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:30148710 original size:19 final size:19
Alignment explanation
Indices: 30148682--30148723 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
30148672 TTTAATGAGA
*
30148682 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
30148701 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
30148720 TATT
1 TATT
30148724 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:30157090 original size:18 final size:18
Alignment explanation
Indices: 30157064--30157254 Score: 160
Period size: 18 Copynumber: 10.6 Consensus size: 18
30157054 AATTGATCGG
*
30157064 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
*
30157082 TTATTCAGTAA-AATCAGA
1 TTATTCAGTAACAGTCA-A
*
30157100 -TATTCAGTAACTA-TTAA
1 TTATTCAGTAAC-AGTCAA
*
30157117 GTTATTCAGTAGCAGTC-A
1 -TTATTCAGTAACAGTCAA
* * *
30157135 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAA
*
30157154 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAA
* * *
30157172 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAA
30157190 TTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTC-AA
*
30157209 -TATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
* *
30157226 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
30157244 TTATTCAGTAA
1 TTATTCAGTAA
30157255 TAATTAGTTA
Statistics
Matches: 138, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
17 19 0.14
18 104 0.75
19 15 0.11
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:30157133 original size:54 final size:53
Alignment explanation
Indices: 30157064--30157254 Score: 183
Period size: 54 Copynumber: 3.5 Consensus size: 53
30157054 AATTGATCGG
*
30157064 TTATCCAGTAACAGTCAATTATTCAGTAAAATCAGATATTCAGTAACTATTAA
1 TTATCCAGTAACAGTCAATTATTCAGTAAAATCAGATATTCAGTAACTATCAA
* * * *
30157117 GTTATTCAGTAGCAGTC-ATTCATTCAGTGACAATCAGTTATTCAGTAA-TGATCAA
1 -TTATCCAGTAACAGTCAATT-ATTCAGT-AAAATCAGATATTCAGTAACT-ATCAA
* * * * * *
30157172 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA-ATATCCAGTAAC-AGTCAA
1 TTATCCAGTAACAGTCAATTATTCAGTAA-AATC-AGATATTCAGTAACTA-TCAA
*
30157226 TTATCCGGTAACAGTCAATTATTCAGTAA
1 TTATCCAGTAACAGTCAATTATTCAGTAA
30157255 TAATTAGTTA
Statistics
Matches: 111, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
53 5 0.05
54 82 0.74
55 24 0.22
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (53 bp):
TTATCCAGTAACAGTCAATTATTCAGTAAAATCAGATATTCAGTAACTATCAA
Found at i:30157199 original size:72 final size:70
Alignment explanation
Indices: 30157065--30157266 Score: 219
Period size: 72 Copynumber: 2.8 Consensus size: 70
30157055 ATTGATCGGT
* *
30157065 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTCAGTAACTATTAAGTTATTCAGTAG
1 TATCCAGTAACAATCAATTATTCAGTAAAATCA-ATTATTCAGTAA-TATT-AGTTATTCAGTAA
*
30157129 CAGTC-AT
63 CAGTCTAA
* * * *
30157136 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATT-AGTTATTCAGTAA
30157201 CAGTCTAA
63 CAGTCTAA
* * * *
30157209 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATTAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAAT-ATTAGTTATT
30157267 TTATACCTTT
Statistics
Matches: 109, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
71 1 0.01
72 89 0.82
73 19 0.17
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (70 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTAGTTATTCAGTAACAG
TCTAA
Found at i:30157469 original size:45 final size:45
Alignment explanation
Indices: 30157428--30157577 Score: 192
Period size: 45 Copynumber: 3.3 Consensus size: 45
30157418 ATCTGAAATA
* *
30157428 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCG
1 GTAACGGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCG
* * *
30157473 GTAACGGTAACAGTAACAATATTCGACACACACAGTGCCGAATCG
1 GTAACGGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCG
* * * * *
30157518 GTAACGGTAACAGTAACAATATTCGATACATACAGTGCCGAATCG
1 GTAACGGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCG
* *
30157563 GTAACAGTAGCAGTA
1 GTAACGGTAACAGTA
30157578 GCGTTAATAG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 96 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (45 bp):
GTAACGGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCG
Found at i:30157997 original size:5 final size:5
Alignment explanation
Indices: 30157986--30158037 Score: 68
Period size: 5 Copynumber: 10.2 Consensus size: 5
30157976 AATTAATCAT
* * *
30157986 AATTC CATTC CATTC CATTC AATTC AATTC AATTC AATTC AATTC AAATTC
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC -AATTC
30158037 A
1 A
30158038 CTTTTCCACT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 39 0.89
6 5 0.11
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTC
Found at i:30159446 original size:23 final size:23
Alignment explanation
Indices: 30159418--30159470 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
30159408 ATTTCTTTAT
30159418 TTTATTA-TTAAACTAT-TATAATA
1 TTTATTATTTAAAC-ATGTAT-ATA
*
30159441 TTTATTATTTATACATGTATATA
1 TTTATTATTTAAACATGTATATA
30159464 TTTATTA
1 TTTATTA
30159471 ATACACATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTATTATTTAAACATGTATATA
Found at i:30159481 original size:22 final size:23
Alignment explanation
Indices: 30159438--30159490 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
30159428 AACTATTATA
* *
30159438 ATATTTATTATTTATACATGTAT
1 ATATTTATTATATACACATGTAT
30159461 ATATTTATTA-ATACACATGTAT
1 ATATTTATTATATACACATGTAT
30159483 -TAATTTAT
1 AT-ATTTAT
30159491 CACCTTACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.59
23 10 0.37
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATTTATTATATACACATGTAT
Found at i:30163238 original size:25 final size:25
Alignment explanation
Indices: 30163173--30163232 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
30163163 ACTATCGGGA
* *
30163173 AAGCTCACAAAGAGTCAATTTAATGGG
1 AAGCTCACCAAGAG-C-CTTTAATGGG
30163200 AAGCTCACCAAGAGCCTTTAATTGGG
1 AAGCTCACCAAGAGCCTTTAA-TGGG
*
30163226 ATGCTCA
1 AAGCTCA
30163233 TAAGAGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 11 0.38
27 13 0.45
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (25 bp):
AAGCTCACCAAGAGCCTTTAATGGG
Found at i:30178815 original size:38 final size:38
Alignment explanation
Indices: 30178726--30178814 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
30178716 AAAAATTATA
* * **
30178726 TTTAATACAATAAAATATTTATTATATTTTTTTTGTTT
1 TTTAATATAATAAAATATTTATTATATTTGTAGTGTTT
30178764 TTTAATATAATAAAATATTTATTATATTTAAGGTAGTGTTT
1 TTTAATATAATAAAATATTTATTATATTT---GTAGTGTTT
30178805 TTTAATATAA
1 TTTAATATAA
30178815 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.64
41 16 0.36
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (38 bp):
TTTAATATAATAAAATATTTATTATATTTGTAGTGTTT
Found at i:30182025 original size:31 final size:31
Alignment explanation
Indices: 30181987--30182049 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
30181977 AATTAAAGTG
30181987 TAAGACCATGTCTGGGACATTGGTATCGTAT
1 TAAGACCATGTCTGGGACATTGGTATCGTAT
30182018 TAAGACCATGTCTGGGACATTGGTATCGTAT
1 TAAGACCATGTCTGGGACATTGGTATCGTAT
30182049 T
1 T
30182050 TGATTTTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (31 bp):
TAAGACCATGTCTGGGACATTGGTATCGTAT
Found at i:30182107 original size:43 final size:42
Alignment explanation
Indices: 30182018--30182110 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
30182008 GGTATCGTAT
* * * ***
30182018 TAAGACCATGTCTGGGACATTGGTATCGTATTTGATTTTGTG
1 TAAGACCATATCTGGGACAATGGCATCGTATTTGATTACATG
*
30182060 TAAGACCCTATCTGGGACAATGGCATCGATATTTGATTACATG
1 TAAGACCATATCTGGGACAATGGCATCG-TATTTGATTACATG
30182103 TAAGACCA
1 TAAGACCA
30182111 CGTCTAGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 24 0.57
43 18 0.43
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (42 bp):
TAAGACCATATCTGGGACAATGGCATCGTATTTGATTACATG
Found at i:30182127 original size:43 final size:42
Alignment explanation
Indices: 30182018--30182128 Score: 116
Period size: 43 Copynumber: 2.6 Consensus size: 42
30182008 GGTATCGTAT
* * ***
30182018 TAAGACCATGTCTGGGACATTGGTATCGTATTTGATTTTGTG
1 TAAGACCACGTCTGGGACATTGGCATCGTATTTGATTACATG
* *
30182060 TAAGACC-CTATCTGGGACAATGGCATCGATATTTGATTACATG
1 TAAGACCAC-GTCTGGGACATTGGCATCG-TATTTGATTACATG
* *
30182103 TAAGACCACGTCTAGGACGTTGGCAT
1 TAAGACCACGTCTGGGACATTGGCAT
30182129 TGTACGAGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
42 23 0.42
43 31 0.56
44 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (42 bp):
TAAGACCACGTCTGGGACATTGGCATCGTATTTGATTACATG
Found at i:30184073 original size:17 final size:17
Alignment explanation
Indices: 30184051--30184084 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30184041 TATAGAAACA
*
30184051 TAATCTTCGAAGATATG
1 TAATCTTAGAAGATATG
30184068 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
30184085 ATTTTGTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:30189136 original size:18 final size:18
Alignment explanation
Indices: 30189115--30189244 Score: 64
Period size: 18 Copynumber: 6.7 Consensus size: 18
30189105 TAATAGTCAG
*
30189115 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
30189133 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
*
30189151 TTATTCAGTATCAATCAACTGA
1 TTATTCAGTAACAATC-A---A
* *
30189173 TCGGTTATCCAGTAACAGTCAA
1 ----TTATTCAGTAACAATCAA
*
30189195 TTATTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCA-A
* * *
30189214 -TATACAGTAAAAATTAAA
1 TTATTCAGTAACAA-TCAA
30189232 TTATTCAGTAACA
1 TTATTCAGTAACA
30189245 GTCGGTCTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
18 54 0.65
19 14 0.17
22 1 0.01
25 1 0.01
26 13 0.16
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:30189240 original size:19 final size:19
Alignment explanation
Indices: 30189193--30189242 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
30189183 AGTAACAGTC
30189193 AATTATTCAGTAAAAATCA
1 AATTATTCAGTAAAAATCA
* * *
30189212 GA-TATACAGTAAAAATTA
1 AATTATTCAGTAAAAATCA
30189230 AATTATTCAGTAA
1 AATTATTCAGTAA
30189243 CAGTCGGTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTATTCAGTAAAAATCA
Found at i:30189491 original size:45 final size:45
Alignment explanation
Indices: 30189419--30189527 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
30189409 ACAAATCCGG
* *
30189419 AACAGTAACAGTAACAGTATTCAACACACAAATTGCTGAATCGAT
1 AACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGAT
* * *
30189464 AACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGT
1 AACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGAT
30189509 AACAGTAAC-GATAACAGTA
1 AACAGTAACAG-TAACAGTA
30189528 ATAGTAGTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.02
45 56 0.98
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (45 bp):
AACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGAT
Found at i:30190588 original size:4 final size:4
Alignment explanation
Indices: 30190575--30190618 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
30190565 TGAATTTTCC
*
30190575 CTTT -TTT CTTT CTTT -TCTC CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT CTTT CTTT C
30190619 CCTGCTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 4 0.11
4 30 0.86
5 1 0.03
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:30190604 original size:20 final size:18
Alignment explanation
Indices: 30190569--30190609 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 18
30190559 AAACCTTGAA
30190569 TTTTCCCTTTTTTCTTTC
1 TTTTCCCTTTTTTCTTTC
30190587 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTT-TTTCTTTC
30190607 TTT
1 TTT
30190610 CTTTCTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCCCTTTTTTCTTTC
Found at i:30190609 original size:12 final size:11
Alignment explanation
Indices: 30190575--30190683 Score: 53
Period size: 11 Copynumber: 9.5 Consensus size: 11
30190565 TGAATTTTCC
30190575 CTTTTTTCTTT
1 CTTTTTTCTTT
*
30190586 CTTTTCTCCTTT
1 CTTTT-TTCTTT
30190598 CTTTCTTTCTTT
1 CTTT-TTTCTTT
* *
30190610 CTTTCTTTCCCTG
1 CTTT-TTT-CTTT
*
30190623 CTTTTCTCTTT
1 CTTTTTTCTTT
* * *
30190634 GCCTATTCTGTTT
1 --CTTTTTTCTTT
*
30190647 C-TATTTCTATT
1 CTTTTTTCT-TT
*
30190658 C-TATTTCTTT
1 CTTTTTTCTTT
30190668 CTTTTTTCTTT
1 CTTTTTTCTTT
30190679 -TTTTT
1 CTTTTT
30190684 CATTAAACCA
Statistics
Matches: 77, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
10 11 0.14
11 26 0.34
12 24 0.31
13 16 0.21
ACGTcount: A:0.04, C:0.24, G:0.03, T:0.70
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:30193938 original size:26 final size:23
Alignment explanation
Indices: 30193889--30193938 Score: 55
Period size: 23 Copynumber: 2.0 Consensus size: 23
30193879 CTCCAAAAAA
* *
30193889 AAAAAAAGAATCTGAATTCCATG
1 AAAAAAAGAATCTGAAATCAATG
30193912 AAAAAAAGAATCTAGAACATCTAATG
1 AAAAAAAGAATCT-GAA-ATC-AATG
30193938 A
1 A
30193939 CCTAGCCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 3 0.14
25 2 0.09
26 4 0.18
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (23 bp):
AAAAAAAGAATCTGAAATCAATG
Found at i:30203866 original size:27 final size:30
Alignment explanation
Indices: 30203825--30203881 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 30
30203815 CTATGTCTTC
*
30203825 ATTATCATTGGTA-T-TTTATT-ATCTATT
1 ATTATCATTAGTATTATTTATTCATCTATT
*
30203852 ATTATCATTATTATTATTTATTCATCTATT
1 ATTATCATTAGTATTATTTATTCATCTATT
30203882 TATTTATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 1 0.04
29 6 0.24
30 7 0.28
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (30 bp):
ATTATCATTAGTATTATTTATTCATCTATT
Found at i:30203882 original size:12 final size:11
Alignment explanation
Indices: 30203839--30203885 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
30203829 TCATTGGTAT
30203839 TTTATTATCTA
1 TTTATTATCTA
30203850 -TTATTATC-A
1 TTTATTATCTA
30203859 -TTATTAT-TA
1 TTTATTATCTA
30203868 TTTATTCATCTA
1 TTTATT-ATCTA
30203880 TTTATT
1 TTTATT
30203886 TATTACCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.28
10 13 0.41
11 2 0.06
12 8 0.25
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATTATCTA
Found at i:30204149 original size:6 final size:7
Alignment explanation
Indices: 30204134--30204158 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30204124 GTCTTTGCTA
30204134 TTTTATT
1 TTTTATT
30204141 TTTTATT
1 TTTTATT
30204148 TTTTATT
1 TTTTATT
30204155 TTTT
1 TTTT
30204159 TTACATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:30205060 original size:35 final size:35
Alignment explanation
Indices: 30205014--30205083 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
30205004 AAAATCAAAT
30205014 CGACCGTTTTCAAAAAATGGTTTCGACAGTTGCCC
1 CGACCGTTTTCAAAAAATGGTTTCGACAGTTGCCC
30205049 CGACCGTTTTCAAAAAATGGTTTCGACAGTTGCCC
1 CGACCGTTTTCAAAAAATGGTTTCGACAGTTGCCC
30205084 TTACCCATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (35 bp):
CGACCGTTTTCAAAAAATGGTTTCGACAGTTGCCC
Found at i:30205189 original size:27 final size:30
Alignment explanation
Indices: 30205132--30205195 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 30
30205122 TTCAACATCC
30205132 AACAAGCTTAAAACATAATAAATCCAATATCT
1 AACAAGCTTAAAAC--AATAAATCCAATATCT
*
30205164 AACAAGCTTAAAAC-AT-AAT-CAGTATCT
1 AACAAGCTTAAAACAATAAATCCAATATCT
30205191 AACAA
1 AACAA
30205196 ATTCAAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 12 0.39
28 3 0.10
29 2 0.06
32 14 0.45
ACGTcount: A:0.53, C:0.19, G:0.05, T:0.23
Consensus pattern (30 bp):
AACAAGCTTAAAACAATAAATCCAATATCT
Found at i:30205422 original size:18 final size:15
Alignment explanation
Indices: 30205378--30205431 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 15
30205368 AAACCCTAGC
30205378 CCCAAAACCCAACAA
1 CCCAAAACCCAACAA
30205393 CCCACTAAACCCAACAGAA
1 CCCA--AAACCCAAC--AA
30205412 GCCCAAAACCCAACTAA
1 -CCCAAAACCCAAC-AA
30205429 CCC
1 CCC
30205432 TTAACCCCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 11 0.33
18 9 0.27
19 2 0.06
20 4 0.12
ACGTcount: A:0.46, C:0.46, G:0.04, T:0.04
Consensus pattern (15 bp):
CCCAAAACCCAACAA
Found at i:30205485 original size:18 final size:18
Alignment explanation
Indices: 30205445--30205485 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
30205435 ACCCCATTAC
* *
30205445 ATTAGCCCAATCCCAAAA
1 ATTACCCCAAACCCAAAA
30205463 A-TACCCCAAACCCAAAA
1 ATTACCCCAAACCCAAAA
30205480 ATTACC
1 ATTACC
30205486 AAGCCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.46, C:0.37, G:0.02, T:0.15
Consensus pattern (18 bp):
ATTACCCCAAACCCAAAA
Found at i:30206841 original size:28 final size:28
Alignment explanation
Indices: 30206810--30206870 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
30206800 ACATATTAAC
*
30206810 ATTATA-CCATGTATATATTTTTATAAAT
1 ATTATATCCATATATATATTTTTA-AAAT
** *
30206838 ATTATATGTATATATATATTTTTAATAT
1 ATTATATCCATATATATATTTTTAAAAT
30206866 ATTAT
1 ATTAT
30206871 GTATACTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (28 bp):
ATTATATCCATATATATATTTTTAAAAT
Found at i:30207333 original size:3 final size:3
Alignment explanation
Indices: 30207288--30207353 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
30207278 TAATACTATA
* * * * *
30207288 TAT TA- TAT TCT TAC TAT TAT CAT TAC TA- TATT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
30207332 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
30207354 GTAGCGACGT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:30208628 original size:19 final size:21
Alignment explanation
Indices: 30208600--30208657 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
30208590 ACATATATAT
* **
30208600 AAATATATATAATGGTATTAG
1 AAATATATATAGTAATATTAG
30208621 AAATATATATAGTAATATTAG
1 AAATATATATAGTAATATTAG
*
30208642 AAATATACAT-GTAATA
1 AAATATATATAGTAATA
30208658 GTTCAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 6 0.18
21 27 0.82
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATATATAGTAATATTAG
Found at i:30215497 original size:25 final size:25
Alignment explanation
Indices: 30215459--30215508 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
30215449 GTAAGAGAAG
30215459 ATGAAGAACAGAAGAAGGAAAAAGA
1 ATGAAGAACAGAAGAAGGAAAAAGA
* * *
30215484 ATGAAGAACGGAAGATGGAGAAAGA
1 ATGAAGAACAGAAGAAGGAAAAAGA
30215509 GCCTTACCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.32, T:0.06
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGGAAAAAGA
Found at i:30215757 original size:16 final size:16
Alignment explanation
Indices: 30215736--30215766 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30215726 CATGTTAGAG
30215736 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
30215752 CATATATATTTGAAA
1 CATATAAATTTGAAA
30215767 ACTCTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:30215945 original size:22 final size:23
Alignment explanation
Indices: 30215920--30215962 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
30215910 AATTATTATT
30215920 GTTTAGCT-TTAGTTTT-TCTTAG
1 GTTT-GCTCTTAGTTTTCTCTTAG
*
30215942 GTTTTCTCTTAGTTTTCTCTT
1 GTTTGCTCTTAGTTTTCTCTT
30215963 CTAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 2 0.11
22 12 0.67
23 4 0.22
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (23 bp):
GTTTGCTCTTAGTTTTCTCTTAG
Found at i:30215953 original size:12 final size:11
Alignment explanation
Indices: 30215928--30215962 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
30215918 TTGTTTAGCT
30215928 TTAGTTTT-TC
1 TTAGTTTTCTC
30215938 TTAGGTTTTCTC
1 TTA-GTTTTCTC
30215950 TTAGTTTTCTC
1 TTAGTTTTCTC
30215961 TT
1 TT
30215963 CTAATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.13
11 15 0.65
12 5 0.22
ACGTcount: A:0.09, C:0.14, G:0.11, T:0.66
Consensus pattern (11 bp):
TTAGTTTTCTC
Found at i:30219980 original size:13 final size:13
Alignment explanation
Indices: 30219962--30219990 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
30219952 GACGTCATCA
30219962 ACAAATTGAAGTC
1 ACAAATTGAAGTC
30219975 ACAAATTGAAGTC
1 ACAAATTGAAGTC
30219988 ACA
1 ACA
30219991 TGCCCGTGTG
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:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (13 bp):
ACAAATTGAAGTC
Found at i:30223158 original size:29 final size:30
Alignment explanation
Indices: 30223094--30223164 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
30223084 TATTAATTTA
30223094 TAATTTCATTATTTTTGAAGGGGTTAAATAG
1 TAATTTCATTA-TTTTGAAGGGGTTAAATAG
*
30223125 -AATTTTATTATTTT-AAGGGGTTAAAGT-G
1 TAATTTCATTATTTTGAAGGGGTTAAA-TAG
30223153 TAATTTCATTAT
1 TAATTTCATTAT
30223165 ATTTTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 12 0.33
29 15 0.42
30 9 0.25
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (30 bp):
TAATTTCATTATTTTGAAGGGGTTAAATAG
Found at i:30234598 original size:52 final size:52
Alignment explanation
Indices: 30234536--30234641 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
30234526 GACGTTACAC
30234536 ATGATAGTATGTTTGTCGCATTAGATTCTAAAAGTAGTAAAATTTTAACTTA
1 ATGATAGTATGTTTGTCGCATTAGATTCTAAAAGTAGTAAAATTTTAACTTA
30234588 ATGATAGTATGTTTGTCGCATTAGATTCTAAAAGTAGTAAAATTTTAACTTA
1 ATGATAGTATGTTTGTCGCATTAGATTCTAAAAGTAGTAAAATTTTAACTTA
30234640 AT
1 AT
30234642 AAATTTAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.41
Consensus pattern (52 bp):
ATGATAGTATGTTTGTCGCATTAGATTCTAAAAGTAGTAAAATTTTAACTTA
Found at i:30237064 original size:20 final size:20
Alignment explanation
Indices: 30237022--30237060 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
30237012 TTTATGTGTG
*
30237022 TAAAAATCATATATTTAGAA
1 TAAAAATCATATATTTAAAA
30237042 TAAAAAT-ATATATTTAAAA
1 TAAAAATCATATATTTAAAA
30237061 ATAACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAAATCATATATTTAAAA
Found at i:30237069 original size:17 final size:19
Alignment explanation
Indices: 30237022--30237070 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
30237012 TTTATGTGTG
30237022 TAAAAATCATATATTTAGAA
1 TAAAAA-CATATATTTAGAA
*
30237042 TAAAAATATATATTTA-AA
1 TAAAAACATATATTTAGAA
*
30237060 -AATAACATATA
1 TAAAAACATATA
30237071 ATAAATAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 9 0.35
18 2 0.08
19 9 0.35
20 6 0.23
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAAACATATATTTAGAA
Found at i:30238064 original size:18 final size:18
Alignment explanation
Indices: 30238001--30238064 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
30237991 TAATAAAGTG
*
30238001 TGTACAATAAAATTAAAA
1 TGTATAATAAAATTAAAA
*
30238019 TGTATAA-AAATATCTAGAGTA
1 TGTATAATAAA-AT-TA-A-AA
*
30238040 TGCATAATAAAATTAAAA
1 TGTATAATAAAATTAAAA
30238058 TGTATAA
1 TGTATAA
30238065 AATTATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
17 3 0.08
18 15 0.42
19 3 0.08
20 3 0.08
21 9 0.25
22 3 0.08
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (18 bp):
TGTATAATAAAATTAAAA
Found at i:30241603 original size:21 final size:22
Alignment explanation
Indices: 30241579--30241625 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
30241569 CATTGTTTAG
*
30241579 AATTAGAT-G-AATTAGGCTTGA
1 AATTAGATAGAAATTAAGCTT-A
30241600 AATT-GATAGAAATTAAGCTTA
1 AATTAGATAGAAATTAAGCTTA
30241621 AATTA
1 AATTA
30241626 TGAAAATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 3 0.14
21 10 0.45
22 9 0.41
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (22 bp):
AATTAGATAGAAATTAAGCTTA
Found at i:30243776 original size:24 final size:26
Alignment explanation
Indices: 30243743--30243797 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
30243733 GATATTGCAC
*
30243743 AAAATGTTAACATAATATG-ACAAA-A
1 AAAATGTTAAAATAAT-TGCACAAATA
30243768 AAAAT-TTAAAATAATTGCACAAATA
1 AAAATGTTAAAATAATTGCACAAATA
30243793 AAAAT
1 AAAAT
30243798 AAAGCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 2 0.07
24 14 0.52
25 11 0.41
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (26 bp):
AAAATGTTAAAATAATTGCACAAATA
Found at i:30245388 original size:14 final size:14
Alignment explanation
Indices: 30245369--30245398 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30245359 AGCTCTTAAT
*
30245369 CTGCTCTACTGCAA
1 CTGCTCCACTGCAA
30245383 CTGCTCCACTGCAA
1 CTGCTCCACTGCAA
30245397 CT
1 CT
30245399 TTAGGAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.13, T:0.27
Consensus pattern (14 bp):
CTGCTCCACTGCAA
Found at i:30245499 original size:44 final size:43
Alignment explanation
Indices: 30245431--30245903 Score: 358
Period size: 44 Copynumber: 10.6 Consensus size: 43
30245421 TTTTTTATCT
* * *
30245431 TGCTCTACTGCAACTTTAGAGAGATAAGGATTGTGACTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAA-GATTGTGACTTCGATC
* *
30245475 TGCTCCACTGCAACTTCAGGGAGATAAGATCTACTAACTTC-AGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAT-T-GTGACTTCGA-TC
* ** **
30245520 TGTTCCACTGCAACTTCAGAAAGATAAGGATTGTGGTTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAA-GATTGTGACTTCGATC
* * *
30245564 TGCTCTACTGCAACTTCAAGGAGATAAGATCTGCTAACTTC-AGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-TGACTTCGA-TC
* * * * **
30245609 TGCTCTACTGCAACTTTAGGGAGATAAAACTTAGAT-AATTTTATCC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-TT-G-TGACTTCGAT-C
* * *
30245655 TGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAA-GATTGTGACTTCGATC
* * * * **
30245699 TGCTCCACTACAATTTTAGGGAGATAAGGGTTGTGGTTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAA-GATTGTGACTTCGATC
* * * * * *
30245743 TACTCCATTGTAACTTCGGGGAGATAAGATCTGCTAACTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-TGACTTCGATC
* * * **
30245788 TACTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTATCC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTG-ACTTCGAT-C
* * *
30245834 TGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATC
1 TGCTCCACTGCAACTTCAGGGAGATAA-GATTGTGACTTCGATC
*
30245878 TGCTCCACTGCGACTTCAGGGAGATA
1 TGCTCCACTGCAACTTCAGGGAGATA
30245904 GAACCTGCAG
Statistics
Matches: 338, Mismatches: 71, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
43 8 0.02
44 142 0.42
45 120 0.36
46 65 0.19
47 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTCGATC
Found at i:30245552 original size:89 final size:89
Alignment explanation
Indices: 30245431--30245903 Score: 424
Period size: 89 Copynumber: 5.3 Consensus size: 89
30245421 TTTTTTATCT
* * * *
30245431 TGCTCTACTGCAACTTTAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGG
1 TGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGAATTCGATCTGCTCTACTGCAACTTCAGGG
*
30245496 AGATAAGATCTACTAACTTCAGTC
66 AGATAAGATCTGCTAACTTCAGTC
* * ** ** *
30245520 TGTTCCACTGCAACTTCAGAAAGATAAGGATTGTGGTTTCGATCTGCTCTACTGCAACTTCAAGG
1 TGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGAATTCGATCTGCTCTACTGCAACTTCAGGG
30245585 AGATAAGATCTGCTAACTTCAGTC
66 AGATAAGATCTGCTAACTTCAGTC
* * **
30245609 TGCTCTACTGCAACTTTAGGGAGATAA-AACTTAGAT-AATTTTATCCTGCTCTACTGCAACTTC
1 TGCTCCACTGCAACTTTAGGGAGATAAGGA-TT-G-TGAATTCGAT-CTGCTCTACTGCAACTTC
* **
30245672 AGAGAGATAAGGAT-TG-TGGCTTC-GATC
62 AGGGAGATAA-GATCTGCTAACTTCAG-TC
* * * ** * * * * *
30245699 TGCTCCACTACAATTTTAGGGAGATAAGGGTTGTGGTTTCGATCTACTCCATTGTAACTTCGGGG
1 TGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGAATTCGATCTGCTCTACTGCAACTTCAGGG
*
30245764 AGATAAGATCTGCTAACTTCAATC
66 AGATAAGATCTGCTAACTTCAGTC
* * * **
30245788 TACTCCACTGCAACTTCAGGGAGATAA-GACTTGGGTAATTTTATCCTGCTCTACTGCAACTTCA
1 TGCTCCACTGCAACTTTAGGGAGATAAGGA-TTGTG-AATTCGAT-CTGCTCTACTGCAACTTCA
* **
30245852 GAGAGATAAGGAT-TG-TGGCTTC-GATC
63 GGGAGATAA-GATCTGCTAACTTCAG-TC
* *
30245878 TGCTCCACTGCGACTTCAGGGAGATA
1 TGCTCCACTGCAACTTTAGGGAGATA
30245904 GAACCTGCAG
Statistics
Matches: 306, Mismatches: 62, Indels: 31
0.77 0.16 0.08
Matches are distributed among these distances:
87 3 0.01
88 27 0.09
89 144 0.47
90 73 0.24
91 53 0.17
92 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (89 bp):
TGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGAATTCGATCTGCTCTACTGCAACTTCAGGG
AGATAAGATCTGCTAACTTCAGTC
Found at i:30245813 original size:224 final size:225
Alignment explanation
Indices: 30245423--30245860 Score: 503
Period size: 224 Copynumber: 2.0 Consensus size: 225
30245413 TTCGTGTATT
* * *
30245423 TTTTATCTTGCTCTACTGCAACTTTAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAA
1 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTACAA
**
30245488 CTTCAGGGAGATAAGATCTACTAACTTCAGTCTGTTCCACTGCAACTTCAGAAAGATAAGGATTG
66 CTTCAGGGAGATAAGATCTACTAACTTCAGTCTACTCCACTGCAACTTCAGAAAGATAAGGATTG
*** * * *
30245553 TGGTTTCGATCTGCTCTACTGCAACTTCAAGGAGATAAGA-TCT-GCTAACTTCAGT-CTGCTCT
131 TAACTTCAATCTACTCCACTGCAACTTCAAGGAGATAAGACT-TGGCTAACTTCA-TCCTGCTCT
* *
30245615 ACTGCAACTTTAGGGAGATAAAACTTAGATAA
194 ACTGCAACTTCAGAGAGATAAAACTTAGATAA
*
30245647 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTACAA
1 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTACAA
* * * * *** * * * **
30245712 TTTTAGGGAGATAAGGGT-T-GTGGTTTC-GATCTACTCCATTGTAACTTCGGGGAGATAA-GAT
66 CTTCAGGGAGATAA-GATCTACTAACTTCAG-TCTACTCCACTGCAACTTCAGAAAGATAAGGAT
* * * *
30245773 CTGCTAACTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTATCCTGCT
129 -TG-TAACTTCAATCTACTCCACTGCAACTTCAAGGAGATAAGACTTGGCTAACTTCATCCTGCT
30245838 CTACTGCAACTTCAGAGAGATAA
192 CTACTGCAACTTCAGAGAGATAA
30245861 GGATTGTGGC
Statistics
Matches: 177, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
222 4 0.02
223 28 0.16
224 109 0.62
225 36 0.20
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (225 bp):
TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTACAA
CTTCAGGGAGATAAGATCTACTAACTTCAGTCTACTCCACTGCAACTTCAGAAAGATAAGGATTG
TAACTTCAATCTACTCCACTGCAACTTCAAGGAGATAAGACTTGGCTAACTTCATCCTGCTCTAC
TGCAACTTCAGAGAGATAAAACTTAGATAA
Found at i:30245837 original size:135 final size:136
Alignment explanation
Indices: 30245423--30245957 Score: 348
Period size: 135 Copynumber: 4.0 Consensus size: 136
30245413 TTCGTGTATT
* * * * * *
30245423 TTTTATCTTGCTCTACTGCAACTTTAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAA
1 TTTTATCCTGCTCCACTACAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTACTCCACTGCAA
* * * ** * **
30245488 CTTCAGGGAGATA-AGATCTAC-TAACTTCAGTCTGTTCCACTGCAACTTCAGAAAGATAAGGA-
66 CTTCAGGGAGATAGA-ACCTGCATAACTTCAATCTACTCCACTACAACTTCAGGGAGATAA-GAC
30245550 TTGTGGT--
129 TTG-GGTAA
** * * ** * *
30245557 TTCGAT-CTGCTCTACTGCAACTTCA-AGGAGATAA-GATCTGCTAACTTC-AGTCTGCTCTACT
1 TTTTATCCTGCTCCACTACAACTTCAGA-GAGATAAGGAT-TG-TGGCTTCGA-TCTACTCCACT
* * * ** * * * *
30245618 GCAACTTTAGGGAGATAAAACTTAG-ATAA-TTTTATCCTGCTCTACTGCAACTTCAGAGAGATA
62 GCAACTTCAGGGAGATAGAACCT-GCATAACTTCAAT-CTACTCCACTACAACTTCAGGGAGATA
*
30245681 AGGA-TTGTGG--C
125 A-GACTTG-GGTAA
** * * * * * * *
30245692 TTCGAT-CTGCTCCACTACAATTTTAGGGAGATAAGGGTTGTGGTTTCGATCTACTCCATTGTAA
1 TTTTATCCTGCTCCACTACAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTACTCCACTGCAA
* * *
30245756 CTTCGGGGAGATA-AGATCTGC-TAACTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACT
66 CTTCAGGGAGATAGA-ACCTGCATAACTTCAATCTACTCCACTACAACTTCAGGGAGATAAGACT
30245819 TGGGTAA
130 TGGGTAA
* * * *
30245826 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTGCGA
1 TTTTATCCTGCTCCACTACAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTACTCCACTGCAA
** * * * *
30245891 CTTCAGGGAGATAGAACCTGCAGTTTCTTCAGTCTGCTCCATTACAACTTTAGGGAGATAAGACT
66 CTTCAGGGAGATAGAACCTGCA-TAACTTCAATCTACTCCACTACAACTTCAGGGAGATAAGACT
30245956 TG
130 TG
30245958 TTACTTTACT
Statistics
Matches: 318, Mismatches: 61, Indels: 41
0.76 0.15 0.10
Matches are distributed among these distances:
132 8 0.03
133 60 0.19
134 77 0.24
135 133 0.42
136 3 0.01
137 37 0.12
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (136 bp):
TTTTATCCTGCTCCACTACAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTACTCCACTGCAA
CTTCAGGGAGATAGAACCTGCATAACTTCAATCTACTCCACTACAACTTCAGGGAGATAAGACTT
GGGTAA
Found at i:30245901 original size:179 final size:179
Alignment explanation
Indices: 30245474--30245903 Score: 585
Period size: 179 Copynumber: 2.4 Consensus size: 179
30245464 TGACTTCGAT
* * * ** *
30245474 CTGCTCCACTGCAACTTCAGGGAGATAA-GATCTACTAACTTC-AGTCTGTTCCACTGCAACTTC
1 CTGCTCTACTGCAACTTCAGAGAGATAAGGAT-T-GTGGCTTCGA-TCTGCTCCACTGCAACTTC
** * *
30245537 AGAAAGATAAGGATTGTGGTTTCGATCTGCTCTACTGCAACTTCAAGGAGATAAGATCTGCTAAC
63 AGGGAGATAAGGATTGTGGTTTCGATCTACTCCACTGCAACTTCAAGGAGATAAGATCTGCTAAC
* * * *
30245602 TTCAGTCTGCTCTACTGCAACTTTAGGGAGATAAAACTTAGATAATTTTATC
128 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAAACTTAGATAATTTTATC
* * *
30245654 CTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTACAATTTTAGG
1 CTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTGCAACTTCAGG
* * * **
30245719 GAGATAAGGGTTGTGGTTTCGATCTACTCCATTGTAACTTCGGGGAGATAAGATCTGCTAACTTC
66 GAGATAAGGATTGTGGTTTCGATCTACTCCACTGCAACTTCAAGGAGATAAGATCTGCTAACTTC
* * *
30245784 AATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTATC
131 AATCTACTCCACTGCAACTTCAGGGAGATAAAACTTAGATAATTTTATC
*
30245833 CTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTGCGACTTCAGG
1 CTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTGCAACTTCAGG
30245898 GAGATA
66 GAGATA
30245904 GAACCTGCAG
Statistics
Matches: 219, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
179 188 0.86
180 28 0.13
181 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (179 bp):
CTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTGCAACTTCAGG
GAGATAAGGATTGTGGTTTCGATCTACTCCACTGCAACTTCAAGGAGATAAGATCTGCTAACTTC
AATCTACTCCACTGCAACTTCAGGGAGATAAAACTTAGATAATTTTATC
Found at i:30259080 original size:20 final size:20
Alignment explanation
Indices: 30259055--30259093 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30259045 TTTCATTATT
*
30259055 GAACACCAAAATTAAATTGG
1 GAACACCAAAAGTAAATTGG
*
30259075 GAACACCGAAAGTAAATTG
1 GAACACCAAAAGTAAATTG
30259094 AAACTACCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (20 bp):
GAACACCAAAAGTAAATTGG
Found at i:30261305 original size:3 final size:3
Alignment explanation
Indices: 30261299--30261369 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
30261289 CAGCAGCAGC
* *
30261299 AGA AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
30261346 AGA AGA AGA AGA AGA AGA ATGA AG
1 AGA AGA AGA AGA AGA AGA A-GA AG
30261370 CCACTTCACC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:30261414 original size:21 final size:21
Alignment explanation
Indices: 30261390--30261429 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30261380 AACGTGGCAA
30261390 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
*
30261411 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
30261430 AATCCAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:30262828 original size:23 final size:23
Alignment explanation
Indices: 30262783--30262829 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
30262773 AGGTGATTCA
* *
30262783 AGTTTTCAGTTTTTTTTTCTTTT
1 AGTTTTCAGTCTTGTTTTCTTTT
30262806 AGTTTTCAGATCTTGTTTT-TTTT
1 AGTTTTCAG-TCTTGTTTTCTTTT
30262829 A
1 A
30262830 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.13, C:0.09, G:0.11, T:0.68
Consensus pattern (23 bp):
AGTTTTCAGTCTTGTTTTCTTTT
Found at i:30265388 original size:61 final size:61
Alignment explanation
Indices: 30265293--30265414 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
30265283 TTGACGTTAT
30265293 AAACATATCATCAACAGAAAAGAAGAGATAAATAAAATATCCATATTGTAGCTTTTGCAAA
1 AAACATATCATCAACAGAAAAGAAGAGATAAATAAAATATCCATATTGTAGCTTTTGCAAA
30265354 AAACATATCATCAACAGAAAAGAAGAGATAAATAAAATATCCATATTGTAGCTTTTGCAAA
1 AAACATATCATCAACAGAAAAGAAGAGATAAATAAAATATCCATATTGTAGCTTTTGCAAA
30265415 CACACACAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (61 bp):
AAACATATCATCAACAGAAAAGAAGAGATAAATAAAATATCCATATTGTAGCTTTTGCAAA
Found at i:30269410 original size:34 final size:35
Alignment explanation
Indices: 30269346--30269416 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
30269336 TATGAAAAGA
30269346 TTTTCACGTAAAATCTATGCATATTTTATTTTTCTT
1 TTTTCACGTAAAATCTATG-ATATTTTATTTTTCTT
* *
30269382 TTTTCATGTAAAATCTGTG-TATTTTATTTTTCTT
1 TTTTCACGTAAAATCTATGATATTTTATTTTTCTT
30269416 T
1 T
30269417 CTCATTGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 16 0.48
36 17 0.52
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (35 bp):
TTTTCACGTAAAATCTATGATATTTTATTTTTCTT
Found at i:30272049 original size:6 final size:6
Alignment explanation
Indices: 30272040--30272089 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
30272030 CACCGATCTT
* *
30272040 CCCTTT CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
30272088 CC
1 CC
30272090 TTGACACCTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CCCTTC
Found at i:30275114 original size:22 final size:25
Alignment explanation
Indices: 30275064--30275121 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 25
30275054 TTGTAATGCT
30275064 TTTATAT-TTTAATAATTGAGTATTA
1 TTTATATATTTAAT-ATTGAGTATTA
30275089 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATATATTTAATATTGAGTATTA
*
30275110 TTTATTTATTTA
1 TTTATATATTTA
30275122 TAAATAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.10
22 11 0.37
23 4 0.13
24 6 0.20
25 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTATATATTTAATATTGAGTATTA
Found at i:30275222 original size:13 final size:13
Alignment explanation
Indices: 30275204--30275228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30275194 AAAAATAATT
30275204 TTTTCAGAAAATA
1 TTTTCAGAAAATA
30275217 TTTTCAGAAAAT
1 TTTTCAGAAAAT
30275229 CTGCCAAACA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTTCAGAAAATA
Found at i:30275541 original size:31 final size:31
Alignment explanation
Indices: 30275505--30275567 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
30275495 CTCAAAAGAC
30275505 TTTATTATGATAGATCATAATAATAGTGATA
1 TTTATTATGATAGATCATAATAATAGTGATA
30275536 TTTATTATGATAGATCATAATAATAGTGATA
1 TTTATTATGATAGATCATAATAATAGTGATA
30275567 T
1 T
30275568 ATTCGAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTATTATGATAGATCATAATAATAGTGATA
Found at i:30276749 original size:17 final size:17
Alignment explanation
Indices: 30276727--30276760 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
30276717 GTTTCAACCA
30276727 CACTTCTCTCATTTCTT
1 CACTTCTCTCATTTCTT
30276744 CACTTCTCTCATTTCTT
1 CACTTCTCTCATTTCTT
30276761 TGATTTTTAT
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:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (17 bp):
CACTTCTCTCATTTCTT
Found at i:30286418 original size:12 final size:12
Alignment explanation
Indices: 30286401--30286433 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
30286391 TTTCCTGTAA
30286401 AATAGTAAAAAT
1 AATAGTAAAAAT
30286413 AATAGTAAAAAT
1 AATAGTAAAAAT
30286425 AATAGTAAA
1 AATAGTAAA
30286434 GGGGAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:30287351 original size:10 final size:10
Alignment explanation
Indices: 30287323--30287370 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
30287313 TAAATTCTAA
30287323 AAAGATAAAT
1 AAAGATAAAT
* **
30287333 ACATTTAAAT
1 AAAGATAAAT
30287343 AAAGATAAAT
1 AAAGATAAAT
*
30287353 AAAGATAATT
1 AAAGATAAAT
30287363 AAA-ATAAA
1 AAAGATAAA
30287371 ATCCTAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 4 0.13
10 26 0.87
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:30287414 original size:15 final size:15
Alignment explanation
Indices: 30287394--30287423 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30287384 ATAATCCTAA
*
30287394 TAATTATCTTAATAT
1 TAATTATCCTAATAT
30287409 TAATTATCCTAATAT
1 TAATTATCCTAATAT
30287424 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:30290918 original size:32 final size:32
Alignment explanation
Indices: 30290881--30290942 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
30290871 GCTTACCATA
30290881 CCCATCATCCATTAACTATTAAAATGCTAATG
1 CCCATCATCCATTAACTATTAAAATGCTAATG
30290913 CCCATCATCCATTAACTATTAAAATGCTAA
1 CCCATCATCCATTAACTATTAAAATGCTAA
30290943 AATGCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.31
Consensus pattern (32 bp):
CCCATCATCCATTAACTATTAAAATGCTAATG
Found at i:30294371 original size:14 final size:14
Alignment explanation
Indices: 30294344--30294377 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
30294334 TGAAAATAAT
*
30294344 AAAT-AATAAGATA
1 AAATAAATAAAATA
30294357 AAATAAATAAAATA
1 AAATAAATAAAATA
30294371 AAATAAA
1 AAATAAA
30294378 AATAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:30297151 original size:12 final size:12
Alignment explanation
Indices: 30297134--30297166 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
30297124 TTCCCTGTAA
30297134 AATAGTAAAAAT
1 AATAGTAAAAAT
30297146 AATAGTAAAAAT
1 AATAGTAAAAAT
30297158 AATAGTAAA
1 AATAGTAAA
30297167 GGGGAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:30298094 original size:20 final size:20
Alignment explanation
Indices: 30298056--30298103 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
30298046 TAAATTCTAA
* **
30298056 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
30298076 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
30298096 AAA-ATAAA
1 AAAGATAAA
30298104 ATCCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:30298147 original size:15 final size:15
Alignment explanation
Indices: 30298127--30298156 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30298117 ATAATCCTAA
*
30298127 TAATTATCTTAATAT
1 TAATTATCCTAATAT
30298142 TAATTATCCTAATAT
1 TAATTATCCTAATAT
30298157 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:30300034 original size:20 final size:20
Alignment explanation
Indices: 30300009--30300046 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30299999 GGTGAAAAAA
*
30300009 ATATATTTCTTTAAAAATTT
1 ATATATTTATTTAAAAATTT
*
30300029 ATATATTTATTTATAAAT
1 ATATATTTATTTAAAAAT
30300047 AATTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTTATTTAAAAATTT
Found at i:30304400 original size:21 final size:21
Alignment explanation
Indices: 30304376--30304416 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30304366 AAAAAATGAC
*
30304376 AACTATTTATATAAAAAAAAG
1 AACTATTTACATAAAAAAAAG
*
30304397 AACTATTTACATTAAAAAAA
1 AACTATTTACATAAAAAAAA
30304417 TACTGTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (21 bp):
AACTATTTACATAAAAAAAAG
Found at i:30305976 original size:23 final size:24
Alignment explanation
Indices: 30305934--30305986 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
30305924 AATTAAATAA
**
30305934 TAAAATAAAATTACTAAAATGTAC
1 TAAAATAAAATTACTAAAATAAAC
* *
30305958 TAAAATTAACTTA-TAAAATAAAC
1 TAAAATAAAATTACTAAAATAAAC
30305981 TAAAAT
1 TAAAAT
30305987 CCTACTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (24 bp):
TAAAATAAAATTACTAAAATAAAC
Found at i:30306926 original size:88 final size:88
Alignment explanation
Indices: 30306761--30306977 Score: 251
Period size: 88 Copynumber: 2.5 Consensus size: 88
30306751 TTCAATTTCC
* * *
30306761 AACAGGCTGAAG-ATATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGGCAACGAGC
1 AACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACAACGAGC
* *
30306825 TTTAACCCCCTAAGTAATAGGGT
66 TTTAACCCCCTAAGCAATAGAGT
* * ** *
30306848 AACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAGGGAAATAGATCGAAGATGATGAGC
1 AACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACAACGAGC
* *
30306913 TTTAACCCTCTAAGCAGTAGAGT
66 TTTAACCCCCTAAGCAATAGAGT
* * * * *
30306936 AACAAGC-CAAATTTACAGACCTTGA-CCCCCTAAGCAGTAGGG
1 AACAAGCTGAAGTTTATAGATCTT-ATCACCCTAAGCAGTAGGG
30306978 TAATGGGCTG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
87 39 0.35
88 72 0.65
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (88 bp):
AACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCAAAGACAACGAGC
TTTAACCCCCTAAGCAATAGAGT
Found at i:30307199 original size:43 final size:42
Alignment explanation
Indices: 30307137--30307246 Score: 114
Period size: 43 Copynumber: 2.6 Consensus size: 42
30307127 GATAGGCTTC
* * *
30307137 AACCCCATGAGCAATAGGGTAACAAGCCAAATTTTCAAACCTTA
1 AACCCCATAAGCAGTAGGGTAACAAGCCAAATTTCCAAA--TTA
* ** *
30307181 AACCCC-TAAGCAGTAGGGTAACAGGCTGAATTTCCAAATTT
1 AACCCCATAAGCAGTAGGGTAACAAGCCAAATTTCCAAATTA
* *
30307222 AACCCCTTAAGCAGTAGGGAAACAA
1 AACCCCATAAGCAGTAGGGTAACAA
30307247 ATCGAAGACG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 8 0.14
42 16 0.29
43 26 0.46
44 6 0.11
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (42 bp):
AACCCCATAAGCAGTAGGGTAACAAGCCAAATTTCCAAATTA
Found at i:30307279 original size:86 final size:85
Alignment explanation
Indices: 30307176--30307418 Score: 319
Period size: 86 Copynumber: 2.8 Consensus size: 85
30307166 AATTTTCAAA
* *
30307176 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAAAT-TTAACCCCTTAAGCAGTAGG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTCCAGATATTAACCCC-TAAGCAGTAGG
30307240 GAAACAAATCGAAGACGAAGGG
65 G-AACAAATCGAAGACGAAGGG
* * * *
30307262 CCTTAAACCCCTAAGCAGTAGGGTAACAGACCAAA-TTGCAGATATTATCTCCCTAAGCAGTAGT
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTCCAGATATTAAC-CCCTAAGCAGTAG-
* * *
30307326 GGAGCAGATCGAAGATGAAGGG
64 GGAACAAATCGAAGACGAAGGG
* *
30307348 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTCTAGATCTTAACCCCCTAAGCAGTAGG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTCCAGATATTAA-CCCCTAAGCAGTAGG
30307413 GTAACA
65 G-AACA
30307419 GACCAAATTG
Statistics
Matches: 135, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
85 6 0.04
86 98 0.73
87 30 0.22
88 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (85 bp):
CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTCCAGATATTAACCCCTAAGCAGTAGGG
AACAAATCGAAGACGAAGGG
Found at i:30307323 original size:42 final size:42
Alignment explanation
Indices: 30307270--30307636 Score: 253
Period size: 43 Copynumber: 8.5 Consensus size: 42
30307260 GGCCTTAAAC
* *
30307270 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCT
1 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTAACT
* * * **
30307312 CCCTAAGCAGTAGTGG-AGCAGATCGAAGA-TGAAGGGCCTTAAAC-
1 CCCTAAGCAGTAG-GGTAACAGA-CCAA-ATTGCA-GATCTT-AACT
* * * *
30307356 CCCTAAGCAGTAGGGTAACAGGCTAAATTTCTAGATCTTAACC
1 CCCTAAGCAGTAGGGTAACAGACCAAATTGC-AGATCTTAACT
*
30307399 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTAACT
* * * ** * * *
30307441 CCCTAAGTAGTAGTGG-AGCAGATCAAAGACGAAGGGTCTTGAACC
1 CCCTAAGCAGTAG-GGTAACAGACCAAA-TTGCA-GATCTT-AACT
*
30307486 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTAACT
* * * *
30307528 CCCTAAGCAGTAGTGG-AGCAGATCGAAGA-TGAAAGGTCTTAAAC-
1 CCCTAAGCAGTAG-GGTAACAGA-CCAA-ATTG-CAGATCTT-AACT
* * * * * *
30307572 CCCTAAGCAATAGGGTAACAGGCTGAATTTCCAGATCTTAACC
1 CCCTAAGCAGTAGGGTAACAGAC-CAAATTGCAGATCTTAACT
*
30307615 CCCTAAGCAGTAGGGAAACAGA
1 CCCTAAGCAGTAGGGTAACAGA
30307637 TCGAAGACGA
Statistics
Matches: 250, Mismatches: 52, Indels: 45
0.72 0.15 0.13
Matches are distributed among these distances:
42 75 0.30
43 90 0.36
44 58 0.23
45 27 0.11
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (42 bp):
CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTAACT
Found at i:30307396 original size:129 final size:129
Alignment explanation
Indices: 30307263--30307540 Score: 425
Period size: 129 Copynumber: 2.2 Consensus size: 129
30307253 GACGAAGGGC
30307263 CTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTAGTGG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTAGTGG
* * * * *
30307328 AGCAGATCGAAGATGAAGGGCCTT-AAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTCTAGAT
66 AGCAGATCAAAGACGAAGGGCCTTGAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGC-AGAT
* * *
30307392 CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGTAGTAGTGG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTAGTGG
* *
30307457 AGCAGATCAAAGACGAAGGGTCTTGAACCCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
66 AGCAGATCAAAGACGAAGGGCCTTGAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
*
30307521 CTT-ATCTCCCTAAGCAGTAG
1 CTTAAAC-CCCTAAGCAGTAG
30307541 TGGAGCAGAT
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
128 2 0.01
129 103 0.76
130 31 0.23
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (129 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTAGTGG
AGCAGATCAAAGACGAAGGGCCTTGAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
Found at i:30307405 original size:43 final size:42
Alignment explanation
Indices: 30307177--30307635 Score: 223
Period size: 43 Copynumber: 10.7 Consensus size: 42
30307167 ATTTTCAAAC
* * * *
30307177 CTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAAAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAATTGCAGAT
* * ** * * * **
30307220 -TTAACCCCTTAAGCAGTAGGGAAACAAATCGAAGA-CGAAGGGC
1 CTTAACCCCCTAAGCAGTAGGGTAAC-AGGCTAA-ATTGCA-GAT
* * *
30307263 CTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTGCAGAT
* * * * * * * **
30307305 ATTATCTCCCTAAGCAGTAGTGG-AGCAGATCGAAGA-TGAAGGGC
1 CTTAACCCCCTAAGCAGTAG-GGTAACAG-GCTAA-ATTGCA-GAT
* *
30307349 CTTAAACCCCTAAGCAGTAGGGTAACAGGCTAAATTTCTAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTGC-AGAT
* *
30307392 CTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTGCAGAT
* * * * * ** * *
30307434 CTTATCTCCCTAAGTAGTAGTGG-AGCA-GATCAAAGACGAAGGGT
1 CTTAACCCCCTAAGCAGTAG-GGTAACAGGCT-AAA-TTGCA-GAT
* *
30307478 CTTGAACCCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
1 CTT-AACCCCCTAAGCAGTAGGGTAACAGGCTAAATTGCAGAT
* * * * * * *
30307521 CTTATCTCCCTAAGCAGTAGTGG-AGCAGATCGAAGA-TGAAAGGT
1 CTTAACCCCCTAAGCAGTAG-GGTAACAG-GCTAA-ATTG-CAGAT
* * * *
30307565 CTTAAACCCCTAAGCAATAGGGTAACAGGCTGAATTTCCAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAATTGCAGAT
*
30307608 CTTAACCCCCTAAGCAGTAGGGAAACAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAG
30307636 ATCGAAGACG
Statistics
Matches: 299, Mismatches: 91, Indels: 52
0.68 0.21 0.12
Matches are distributed among these distances:
42 94 0.31
43 104 0.35
44 81 0.27
45 20 0.07
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (42 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAATTGCAGAT
Found at i:30307539 original size:216 final size:213
Alignment explanation
Indices: 30307099--30307636 Score: 692
Period size: 216 Copynumber: 2.5 Consensus size: 213
30307089 ATCTAACCCT
* * * *
30307099 CTAAGCAGTAG-GGAAACAGATCGAA-AGTGATAGGCTTCAACCCCATGAGCAATAGGGTAACAA
1 CTAAGCAGTAGTGG-AGCAGATCGAAGA-TGA-AGGCTTAAACCCC-TAAGCAATAGGGTAACAG
* * * * * * *
30307162 GCCAAATTT-TCAAACCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTCCAAATTTAACC
62 GCTAAATTTCT-AGATCTTAACCCCCTAAGCAGTAGGGTAACAGACTCAAATTCCAAATTTAACC
*
30307226 CCTTAAGCAGTAGGGAAACAAATCGAAGACGAAGGGCCTTAAACCCCTAAGCAGTAGGGTAACAG
126 CCTTAAGCAGTAGGGAAACAAATCAAAGACGAAGGGCCTTAAACCCCTAAGCAGTAGGGTAACAG
30307291 ACCAAATTGCAGATATTATCTCC
191 ACCAAATTGCAGATATTATCTCC
*
30307314 CTAAGCAGTAGTGGAGCAGATCGAAGATGAAGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGC
1 CTAAGCAGTAGTGGAGCAGATCGAAGATGAA-GG-CTTAAACCCCTAAGCAATAGGGTAACAGGC
* * *
30307379 TAAATTTCTAGATCTTAACCCCCTAAGCAGTAGGGTAACAGAC-CAAATTGCAGATCTTATCTCC
64 TAAATTTCTAGATCTTAACCCCCTAAGCAGTAGGGTAACAGACTCAAATTCCAAAT-TTAAC-CC
* * * * *
30307443 C-TAAGTAGTAGTGG-AGCAGATCAAAGACGAAGGGTCTTGAACCCCCTAAGCAGTAGGGTAACA
127 CTTAAGCAGTAG-GGAAACAAATCAAAGACGAAGGGCCTT-AAACCCCTAAGCAGTAGGGTAACA
*
30307506 GACCAAATTGCAGATCTTATCTCC
190 GACCAAATTGCAGATATTATCTCC
30307530 CTAAGCAGTAGTGGAGCAGATCGAAGATGAAAGGTCTTAAACCCCTAAGCAATAGGGTAACAGGC
1 CTAAGCAGTAGTGGAGCAGATCGAAGATG-AAGG-CTTAAACCCCTAAGCAATAGGGTAACAGGC
* * *
30307595 TGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAACAGA
64 TAAATTTCTAGATCTTAACCCCCTAAGCAGTAGGGTAACAGA
30307637 TCGAAGACGA
Statistics
Matches: 286, Mismatches: 27, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
214 9 0.03
215 112 0.39
216 163 0.57
217 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (213 bp):
CTAAGCAGTAGTGGAGCAGATCGAAGATGAAGGCTTAAACCCCTAAGCAATAGGGTAACAGGCTA
AATTTCTAGATCTTAACCCCCTAAGCAGTAGGGTAACAGACTCAAATTCCAAATTTAACCCCTTA
AGCAGTAGGGAAACAAATCAAAGACGAAGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGACCAA
ATTGCAGATATTATCTCC
Found at i:30307685 original size:87 final size:86
Alignment explanation
Indices: 30307391--30307675 Score: 383
Period size: 87 Copynumber: 3.3 Consensus size: 86
30307381 AATTTCTAGA
* *
30307391 TCTTAACCCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGTAGTAGTG
1 TCTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
*
30307456 GAGCAGATCAAAGACGAAGGG
66 GAGCAGATCGAAGACGAAGGG
*
30307477 TCTTGAACCCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGT
1 TCTT-AAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGT
* *
30307542 GGAGCAGATCGAAGATGAAAGG
65 GGAGCAGATCGAAGACGAAGGG
* * * * * * *
30307564 TCTTAAACCCCTAAGCAATAGGGTAACAGGCTGAATTTCCAGATCTTAACCCCCTAAGCAGTAG-
1 TCTTAAACCCCTAAGCAGTAGGGTAACAGAC-CAAATTGCAGATCTTATCTCCCTAAGCAGTAGT
* *
30307628 GGAAACAGATCGAAGACGACGGG
65 GG-AGCAGATCGAAGACGAAGGG
* *
30307651 CCTTAAACCTCTAAGCAGTAGGGTA
1 TCTTAAACCCCTAAGCAGTAGGGTA
30307676 CCAGGCTGAA
Statistics
Matches: 177, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
86 30 0.17
87 147 0.83
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (86 bp):
TCTTAAACCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGACGAAGGG
Found at i:30308709 original size:20 final size:21
Alignment explanation
Indices: 30308684--30308728 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
30308674 GGTTTATTGT
30308684 TTTTTTATT-TCTTTTCTTCC
1 TTTTTTATTATCTTTTCTTCC
* *
30308704 TTTTTTATTATTTTTTCTTTC
1 TTTTTTATTATCTTTTCTTCC
30308725 TTTT
1 TTTT
30308729 CAAAACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTATTATCTTTTCTTCC
Found at i:30308709 original size:21 final size:22
Alignment explanation
Indices: 30308683--30308728 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
30308673 AGGTTTATTG
30308683 TTTTTTTATT-TCTTTTCTTCC
1 TTTTTTTATTATCTTTTCTTCC
* *
30308704 -TTTTTTATTATTTTTTCTTTC
1 TTTTTTTATTATCTTTTCTTCC
30308725 TTTT
1 TTTT
30308729 CAAAACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 9 0.43
21 9 0.43
22 3 0.14
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTATTATCTTTTCTTCC
Found at i:30309515 original size:3 final size:3
Alignment explanation
Indices: 30309509--30309578 Score: 106
Period size: 3 Copynumber: 23.0 Consensus size: 3
30309499 TTGTTATCAC
*
30309509 TAT TAT T-T CTAT TAT TTT TAT TAT TACT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
30309555 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
30309579 CAATATTTAC
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
2 1 0.02
3 57 0.92
4 4 0.06
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30309841 original size:3 final size:3
Alignment explanation
Indices: 30309796--30309829 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
30309786 TATTGCTACA
*
30309796 ATT ATT ATT ATT ATT ATT ATT AATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
30309830 TGATATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:30316593 original size:66 final size:66
Alignment explanation
Indices: 30316482--30316610 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
30316472 ATTCATATAT
30316482 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCTATCATAACATCCTAATTATTTGAC
1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCTATCATAACATCCTAATTATTTGAC
30316547 A
66 A
* * * *
30316548 CATTCATAACGCATCTAATTAGGAGCATTTGGTTCATTT-TGATCATAGCATCCTAATTCTTTG
1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCT-ATCATAACATCCTAATTATTTG
30316611 GCATAAGCAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 1 0.02
66 57 0.98
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (66 bp):
CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCTATCATAACATCCTAATTATTTGAC
A
Found at i:30316840 original size:87 final size:88
Alignment explanation
Indices: 30316722--30316925 Score: 277
Period size: 88 Copynumber: 2.3 Consensus size: 88
30316712 TTCACAAGCC
* *
30316722 TTAACCTCC-TAAACAGTAGGGTAACAGGCTGAAG-ATATAGATCTTATCACCCTAAGCAGTAGA
1 TTAACC-CCTTAAGCAGTAGGGTAACAAGCTGAAGTATATAGATCTTATCACCCTAAGCAGTAGA
*
30316785 GAAACAGATCAAAGGCAACGAGCT
65 GAAACAGATCAAAGACAACGAGCT
* *
30316809 TTAACCCCTTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAGGG
1 TTAACCCCTTAAGCAGTAGGGTAACAAGCTGAAGTATATAGATCTTATCACCCTAAGCAGTAGAG
* * ** *
30316874 AAATAGATCGAAGATGATGAGCT
66 AAACAGATCAAAGACAACGAGCT
* *
30316897 TTAACCCTTTAAGCAGTAGAGTAACAAGC
1 TTAACCCCTTAAGCAGTAGGGTAACAAGC
30316926 CAAATTTACA
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
86 2 0.02
87 29 0.28
88 72 0.70
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (88 bp):
TTAACCCCTTAAGCAGTAGGGTAACAAGCTGAAGTATATAGATCTTATCACCCTAAGCAGTAGAG
AAACAGATCAAAGACAACGAGCT
Found at i:30316866 original size:44 final size:43
Alignment explanation
Indices: 30316729--30316873 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 43
30316719 GCCTTAACCT
* *
30316729 CCTAAACAGTAGGGTAACAGGCTGAAGATATAGATCTTATCAC
1 CCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCAC
* * * * ** * *
30316772 CCTAAGCAGTAGAGAAAC-AGATCAAAGGCA-ACGAGCTT-TAACC
1 CCTAAGCAGTAGGGTAACAAGCT-GAAGATATA-GATCTTATCA-C
*
30316815 CCTTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATCTTATCAC
1 CC-TAAGCAGTAGGGTAACAAGCTGAAG-ATATAGATCTTATCAC
30316860 CCTAAGCAGTAGGG
1 CCTAAGCAGTAGGG
30316874 AAATAGATCG
Statistics
Matches: 76, Mismatches: 18, Indels: 15
0.70 0.17 0.14
Matches are distributed among these distances:
42 5 0.07
43 27 0.36
44 29 0.38
45 12 0.16
46 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (43 bp):
CCTAAGCAGTAGGGTAACAAGCTGAAGATATAGATCTTATCAC
Done.