Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 148 of 202
Found at i:46106542 original size:108 final size:113
Alignment explanation
Indices: 46106327--46106586 Score: 365
Period size: 117 Copynumber: 2.3 Consensus size: 113
46106317 TCAATCATAT
* * *
46106327 TTTAACATAATTGTTATAAAATATAATTTAATAA-AATATATAATTTAATAAAATTGTTAATAAA
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAA-T-TTAAT--A
46106391 TATTCTTATATGAATTTACTAATAAAATCATAATATATAATACT-AAAATATAA
62 TATTCTTATATGAATTTAC--ATAAAATCATAATATATAATACTAAAAATATAA
*
46106444 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAA-TT-CT-TATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTTAATATATT
46106506 CTTATATGAATTTAC-TAAAATCATAATATATAATACTACAAAATATAA
66 CTTATATGAATTTACATAAAATCATAATATATAATACTA-AAAATATAA
46106554 TTT-AAATAATTATTATTAAATATAATTT-ATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAT
46106587 CTACTTTATT
Statistics
Matches: 136, Mismatches: 4, Indels: 15
0.88 0.03 0.10
Matches are distributed among these distances:
108 27 0.20
109 25 0.18
110 12 0.09
111 19 0.14
114 1 0.01
115 2 0.01
117 31 0.23
118 19 0.14
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (113 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTTAATATATT
CTTATATGAATTTACATAAAATCATAATATATAATACTAAAAATATAA
Found at i:46108140 original size:64 final size:64
Alignment explanation
Indices: 46108031--46108246 Score: 364
Period size: 64 Copynumber: 3.4 Consensus size: 64
46108021 TAGAATCAAG
* *
46108031 TTGATTATATCTAATGATCCAA--TTAATATATTATCGATATGTTTTTTAATCAAGTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
*
46108093 TTGATTATATCTAATGATTCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
* *
46108157 TTGATTATATGTAATGATCCAATTTTAATATATTATCCATATCTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
*
46108221 TTGATTATATGTAATGATCCAATTTT
1 TTGATTATATCTAATGATCCAATTTT
46108247 TATTTTATTT
Statistics
Matches: 146, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
62 21 0.14
64 125 0.86
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (64 bp):
TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
Found at i:46110435 original size:13 final size:13
Alignment explanation
Indices: 46110417--46110441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46110407 AACATTCGGC
46110417 CGGTGGGAATAAT
1 CGGTGGGAATAAT
46110430 CGGTGGGAATAA
1 CGGTGGGAATAA
46110442 ACAAATAAAA
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:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (13 bp):
CGGTGGGAATAAT
Found at i:46112707 original size:5 final size:5
Alignment explanation
Indices: 46112697--46112732 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
46112687 TAGGAGGCAT
*
46112697 ATCTA ATCTA ATCTA ATCTA ATCTA TTCTA ATCTA A
1 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA A
46112733 CATACAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (5 bp):
ATCTA
Found at i:46123466 original size:14 final size:15
Alignment explanation
Indices: 46123447--46123489 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
46123437 TGGTAGCTGG
46123447 TTCGGTTC-ACTAGA
1 TTCGGTTCAACTAGA
46123461 TTCGGTTCAACTA-A
1 TTCGGTTCAACTAGA
*
46123475 TGCGGTTCAACTAGA
1 TTCGGTTCAACTAGA
46123490 CCCCTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (15 bp):
TTCGGTTCAACTAGA
Found at i:46123738 original size:12 final size:11
Alignment explanation
Indices: 46123711--46123748 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
46123701 GAAAATAGTC
46123711 AAAATTAATA-
1 AAAATTAATAT
46123721 AAAATTAACTAT
1 AAAATTAA-TAT
46123733 AAAATTAAT-T
1 AAAATTAATAT
46123743 AAAATT
1 AAAATT
46123749 CATCATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:46134641 original size:15 final size:16
Alignment explanation
Indices: 46134621--46134679 Score: 77
Period size: 15 Copynumber: 3.8 Consensus size: 16
46134611 TATAGTCTCA
*
46134621 TATAGTGTCACAA-TC
1 TATAGTTTCACAAGTC
*
46134636 TATAGTTTTCACAATTC
1 TATAG-TTTCACAAGTC
46134653 TATAGTTTCA-AAGTC
1 TATAGTTTCACAAGTC
46134668 TATAGTTTCACA
1 TATAGTTTCACA
46134680 TCTAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
15 19 0.49
16 13 0.33
17 7 0.18
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (16 bp):
TATAGTTTCACAAGTC
Found at i:46135703 original size:22 final size:21
Alignment explanation
Indices: 46135654--46135704 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
46135644 TGGATAAGCC
*
46135654 ACCACATAATTGCCGATAACG
1 ACCACATAATTGCCAATAACG
*
46135675 ACCACATAATTG-CAATTAAACT
1 ACCACATAATTGCCAA-T-AACG
46135697 ACCACATA
1 ACCACATA
46135705 GCTTCCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 11 0.42
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (21 bp):
ACCACATAATTGCCAATAACG
Found at i:46147667 original size:67 final size:67
Alignment explanation
Indices: 46147555--46147695 Score: 246
Period size: 67 Copynumber: 2.1 Consensus size: 67
46147545 ATACTATGGA
*
46147555 TTAGGGATTAATTGTGAAAATAAGCTTGTTTTAGTTTTAGAGACTAAATTAAACAAATTGAAAAA
1 TTAGGGATTAATTGTGAAAATAAGCTTGTTTCAGTTTTAGAGACTAAATTAAACAAATTGAAAAA
46147620 CT
66 CT
* * *
46147622 TTAGGGATTGATTGTGAAAATAAGCTTGTTTCAGTTTTTGGGACTAAATTAAACAAATTGAAAAA
1 TTAGGGATTAATTGTGAAAATAAGCTTGTTTCAGTTTTAGAGACTAAATTAAACAAATTGAAAAA
46147687 CT
66 CT
46147689 TTAGGGA
1 TTAGGGA
46147696 AATTATGAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (67 bp):
TTAGGGATTAATTGTGAAAATAAGCTTGTTTCAGTTTTAGAGACTAAATTAAACAAATTGAAAAA
CT
Found at i:46161961 original size:34 final size:34
Alignment explanation
Indices: 46161923--46161995 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
46161913 CACATTCGAG
* *
46161923 CCAATATTGGACGTTATGTCACCACATAGGAGAT
1 CCAATATTGGACATTATGTCACCACATAGGAGAC
*
46161957 CCAATATTGGACATTATGTCACCACATGGGAGAC
1 CCAATATTGGACATTATGTCACCACATAGGAGAC
46161991 CCAAT
1 CCAAT
46161996 GTCGCAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (34 bp):
CCAATATTGGACATTATGTCACCACATAGGAGAC
Found at i:46166781 original size:17 final size:17
Alignment explanation
Indices: 46166736--46166783 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
46166726 CATTGTCCCC
*
46166736 AATGCATTGAC-ATGAA
1 AATGCAATGACAATGAA
* * *
46166752 TATGTAATTACAATGAA
1 AATGCAATGACAATGAA
46166769 AATGCAATGACAATG
1 AATGCAATGACAATG
46166784 TATACTTATC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (17 bp):
AATGCAATGACAATGAA
Found at i:46200453 original size:19 final size:19
Alignment explanation
Indices: 46200429--46200468 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
46200419 ATCTCACCTC
46200429 ATTCA-TTGCATTTAGATTA
1 ATTCATTTGCATTTAG-TTA
46200448 ATTCATTTGCATTTAGTTA
1 ATTCATTTGCATTTAGTTA
46200467 AT
1 AT
46200469 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTCATTTGCATTTAGTTA
Found at i:46205816 original size:29 final size:29
Alignment explanation
Indices: 46205774--46205832 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
46205764 TGTATCATGA
*
46205774 TGTGCTTTCAATGTTACTATATGTTACTT
1 TGTGCTTTCAATGTTACTATATCTTACTT
46205803 TGTGCTTTCAATGTTACTATATCTTACTT
1 TGTGCTTTCAATGTTACTATATCTTACTT
46205832 T
1 T
46205833 TGTTGGTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (29 bp):
TGTGCTTTCAATGTTACTATATCTTACTT
Found at i:46213694 original size:58 final size:58
Alignment explanation
Indices: 46213566--46213701 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 58
46213556 AGTGATCATC
* *
46213566 TTAAAT-TTAAATTTAATTTAATATTTATTTTCTTGATGAATATTATATTAATATAATAGA
1 TTAAATATTAAATTTAATCTAATATTTA--TTCTTGATAAATATTATATTAATATAATA-A
* *
46213626 TTTAATATTAAATTTAATCTAATATTTA-TCTTGATAAATATTATATTAATTTAAT-A
1 TTAAATATTAAATTTAATCTAATATTTATTCTTGATAAATATTATATTAATATAATAA
*
46213682 TTAAAGTGATTAAGTTTAAT
1 TTAAA-T-ATTAAATTTAAT
46213702 TATAGTTGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
56 5 0.07
57 1 0.01
58 36 0.54
60 5 0.07
61 20 0.30
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (58 bp):
TTAAATATTAAATTTAATCTAATATTTATTCTTGATAAATATTATATTAATATAATAA
Found at i:46214613 original size:24 final size:23
Alignment explanation
Indices: 46214586--46214640 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
46214576 TTTATGGACA
*
46214586 ATTTTTACTTAAGTTTTATTTT-T
1 ATTTTTACTT-AGTTCTATTTTCT
*
46214609 CATTTCCTACTTAGTTCTATTTTCT
1 -ATTT-TTACTTAGTTCTATTTTCT
46214634 ATTTTTA
1 ATTTTTA
46214641 GTTTAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 2 0.08
24 18 0.69
25 6 0.23
ACGTcount: A:0.20, C:0.13, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTTTTACTTAGTTCTATTTTCT
Found at i:46217568 original size:31 final size:32
Alignment explanation
Indices: 46217530--46217618 Score: 119
Period size: 31 Copynumber: 2.8 Consensus size: 32
46217520 AACTTTGGAC
46217530 ATAGGTATCGATACCCAGATCAGGTACT-GAT
1 ATAGGTATCGATACCCAGATCAGGTACTCGAT
*
46217561 ATAGGTATCGATACACAGATCAGGTA-TCGAT
1 ATAGGTATCGATACCCAGATCAGGTACTCGAT
* * * *
46217592 ATCGGTATCGATAGCCAAATCAAGTAC
1 ATAGGTATCGATACCCAGATCAGGTAC
46217619 CAATATCGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (32 bp):
ATAGGTATCGATACCCAGATCAGGTACTCGAT
Found at i:46217787 original size:20 final size:19
Alignment explanation
Indices: 46217745--46217792 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
46217735 AAGTCAATTC
*
46217745 GTATTGATACCTTTATAAA
1 GTATTGATACCTTGATAAA
46217764 GTATTGAT-CCTTGATGATAA
1 GTATTGATACCTTGAT-A-AA
*
46217784 GTATCGATA
1 GTATTGATA
46217793 TTGTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (19 bp):
GTATTGATACCTTGATAAA
Found at i:46223169 original size:23 final size:23
Alignment explanation
Indices: 46223143--46223193 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
46223133 TTTGTTGAAG
*
46223143 TTAAATGAAAATATTCGTGAACA
1 TTAAATGAAAATATTCGTAAACA
* * *
46223166 TTAAATTAATATGTTCGTAAACA
1 TTAAATGAAAATATTCGTAAACA
46223189 TTAAA
1 TTAAA
46223194 CAAATATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
TTAAATGAAAATATTCGTAAACA
Found at i:46223199 original size:23 final size:23
Alignment explanation
Indices: 46223156--46223203 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
46223146 AATGAAAATA
* **
46223156 TTCGTGAACATTAAATTAATATG
1 TTCGTAAACATTAAACAAATATG
46223179 TTCGTAAACATTAAACAAATATG
1 TTCGTAAACATTAAACAAATATG
46223202 TT
1 TT
46223204 TAGTAACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (23 bp):
TTCGTAAACATTAAACAAATATG
Found at i:46223212 original size:23 final size:23
Alignment explanation
Indices: 46223162--46223209 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
46223152 AATATTCGTG
** *
46223162 AACATTAAATTAATATGTTCGTA
1 AACATTAAACAAATATGTTAGTA
46223185 AACATTAAACAAATATGTTTAGTA
1 AACATTAAACAAATATG-TTAGTA
46223209 A
1 A
46223210 CATATTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (23 bp):
AACATTAAACAAATATGTTAGTA
Found at i:46232285 original size:59 final size:59
Alignment explanation
Indices: 46232202--46232765 Score: 589
Period size: 59 Copynumber: 9.7 Consensus size: 59
46232192 AACAGAGGTA
*
46232202 GCCACGAAA-GCTTT-CTTTTCAGAGATTTGCCACAAAGGCATCATTTTTATTCAGTACTC
1 GCCAC-AAAGGCTTTCCTTTT-AGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * *
46232261 ACTAAAAAGGCTTCCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * *
46232320 GCGAAAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAATACTC
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * * *
46232379 CCCACAAAGGCTTT-CTTTTAAGTGATTTTCCACAAAATGCATCATTTTTATTTAGTACTC
1 GCCACAAAGGCTTTCCTTTT-AGAGATTTGCCAC-AAAGGCATCATTTTCATTCAGTACTC
* * * * *
46232439 GTCACAAAGGCTTTCCTTTAAGAGATTTTCCACAAAGGTATCCTTTTCATTCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * *
46232498 GCCACAAAGGCTTTCCTTTCA-ATGATTTTCCACAAAGGCATCCTTTTCATTCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGA-GATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * *
46232557 GCCACAAAGGCTTTCCTTTAAGAGATTCT-CCACAAAGGCATCCTTTTCATTCAATATTC
1 GCCACAAAGGCTTTCCTTTTAGAGATT-TGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * * *
46232616 GCCACAAAGGCTCTCCTTTCAAAGATTTGCCACAAAGACATCCTTTTCATTCAGTACTT
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * *
46232675 GCCACAAA-G--TT-C----A-ATGATTTTCTACAAATGAATCATTTTCTTTCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGA-GATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * *
46232726 GCCAAAAAGGCTTTCCTTTTTGTAGGTTTGCCACAAAGGC
1 GCCACAAAGGCTTTCCTTTTAG-AGATTTGCCACAAAGGC
46232766 TTTCCTTTTC
Statistics
Matches: 427, Mismatches: 58, Indels: 39
0.81 0.11 0.07
Matches are distributed among these distances:
50 1 0.00
51 36 0.08
52 1 0.00
54 2 0.00
55 2 0.00
56 1 0.00
58 11 0.03
59 304 0.71
60 64 0.15
61 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (59 bp):
GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
Found at i:46232473 original size:28 final size:29
Alignment explanation
Indices: 46232441--46232652 Score: 116
Period size: 28 Copynumber: 7.2 Consensus size: 29
46232431 TAGTACTCGT
* *
46232441 CACAAAGGCTTTCCTTT-AAGAGATTTTC
1 CACAAAGGCTTTCCTTTCAACAGATTCTC
* * * *
46232469 CACAAAGG-TATCCTTTTCATTCAGTACTCGC
1 CACAAAGGCTTTCC-TTTCA-ACAG-ATTCTC
* *
46232500 CACAAAGGCTTTCCTTTCAA-TGATTTTC
1 CACAAAGGCTTTCCTTTCAACAGATTCTC
* * * *
46232528 CACAAAGGC-ATCCTTTTCATTCAGTACTCGC
1 CACAAAGGCTTTCC-TTTCA-ACAG-ATTCTC
*
46232559 CACAAAGGCTTTCCTTT-AAGAGATTCTC
1 CACAAAGGCTTTCCTTTCAACAGATTCTC
* * * *
46232587 CACAAAGGC-ATCCTTTTCATTCAATATTCGC
1 CACAAAGGCTTTCC-TTTCA-AC-AGATTCTC
*
46232618 CACAAAGGCTCTCCTTTCAA-AGATT-TGC
1 CACAAAGGCTTTCCTTTCAACAGATTCT-C
46232646 CACAAAG
1 CACAAAG
46232653 ACATCCTTTT
Statistics
Matches: 136, Mismatches: 32, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
27 10 0.07
28 56 0.41
29 5 0.04
30 4 0.03
31 51 0.38
32 10 0.07
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (29 bp):
CACAAAGGCTTTCCTTTCAACAGATTCTC
Found at i:46232504 original size:31 final size:31
Alignment explanation
Indices: 46232468--46232683 Score: 143
Period size: 31 Copynumber: 7.3 Consensus size: 31
46232458 AAGAGATTTT
*
46232468 CCACAAAGGTATCCTTTTCATTCAGTACTCG
1 CCACAAAGGTATCCTTTTCATTCAGTATTCG
* * **
46232499 CCACAAAGGCTTTCC-TTTCAAT--G-ATTTT
1 CCACAAAGG-TATCCTTTTCATTCAGTATTCG
* *
46232527 CCACAAAGGCATCCTTTTCATTCAGTACTCG
1 CCACAAAGGTATCCTTTTCATTCAGTATTCG
* ** *
46232558 CCACAAAGGCTTTCC-TTT-A-AGAG-ATTCT
1 CCACAAAGG-TATCCTTTTCATTCAGTATTCG
* *
46232586 CCACAAAGGCATCCTTTTCATTCAATATTCG
1 CCACAAAGGTATCCTTTTCATTCAGTATTCG
* * *
46232617 CCACAAAGGCTCTCC-TTTCA--AAG-ATTTG
1 CCACAAAGG-TATCCTTTTCATTCAGTATTCG
**
46232645 CCACAAAGACATCCTTTTCATTCAGTACTT-G
1 CCACAAAGGTATCCTTTTCATTCAGTA-TTCG
46232676 CCACAAAG
1 CCACAAAG
46232684 TTCAATGATT
Statistics
Matches: 137, Mismatches: 32, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
27 9 0.07
28 49 0.36
29 5 0.04
30 5 0.04
31 57 0.42
32 12 0.09
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (31 bp):
CCACAAAGGTATCCTTTTCATTCAGTATTCG
Found at i:46232651 original size:237 final size:237
Alignment explanation
Indices: 46232211--46232651 Score: 618
Period size: 237 Copynumber: 1.9 Consensus size: 237
46232201 AGCCACGAAA
* * * *
46232211 GCTTTCTTTTCAGAGATTTGCCACAAAGGCATCATTTTTATTCAGTACTCACTAAAAAGGCTTCC
1 GCTTTCCTTTAAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTCACCAAAAAGGCTTCC
* * *
46232276 CTTTTAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCGAAAAAGGCTTTCCTTTTA
66 CTTTCAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCCAAAAAGGCTTTCCTTTAA
* * *
46232341 GAGATTTGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCTTTCTTTTAAGTGATT
131 GAGATTTGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCTTCCTTTCAAGAGATT
*
46232406 TTCCACAAAATGCATCATTTTTATTTAGTACTCGTCACAAAG
196 TGCCACAAAATGCATCATTTTTATTTAGTACTCGTCACAAAG
* * * * * *
46232448 GCTTTCCTTTAAGAGATTTTCCACAAAGGTATCCTTTTCATTCAGTACTCGCCACAAAGGCTTTC
1 GCTTTCCTTTAAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTCACCAAAAAGGCTTCC
* * * *
46232513 CTTTCA-ATGATTTTCCACAAAGGCATCCTTTTCATTCAGTACTCGCCACAAAGGCTTTCCTTTA
66 CTTTCAGA-GATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCCAAAAAGGCTTTCCTTTA
* * *
46232577 AGAGATTCT-CCACAAAGGCATCCTTTTCATTCAATATTCGCCACAAAGGCTCTCCTTTCAA-AG
130 AGAGATT-TGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCT-TCCTTTCAAGAG
46232640 ATTTGCCACAAA
193 ATTTGCCACAAA
46232652 GACATCCTTT
Statistics
Matches: 177, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
236 1 0.01
237 168 0.95
238 8 0.05
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (237 bp):
GCTTTCCTTTAAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTCACCAAAAAGGCTTCC
CTTTCAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCCAAAAAGGCTTTCCTTTAA
GAGATTTGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCTTCCTTTCAAGAGATT
TGCCACAAAATGCATCATTTTTATTTAGTACTCGTCACAAAG
Found at i:46232663 original size:28 final size:29
Alignment explanation
Indices: 46232468--46232665 Score: 122
Period size: 28 Copynumber: 6.7 Consensus size: 29
46232458 AAGAGATTTT
* * *
46232468 CCACAAAGGTATCCTTTTCATTCAGTACTCG
1 CCACAAAGGCATCCTTTTCA-TAAG-ATTCG
* * **
46232499 CCACAAAGGCTTTCC-TTTCA-ATGATTTT
1 CCACAAAGGC-ATCCTTTTCATAAGATTCG
* *
46232527 CCACAAAGGCATCCTTTTCATTCAGTACTCG
1 CCACAAAGGCATCCTTTTCA-TAAG-ATTCG
* *
46232558 CCACAAAGGCTTTCC-TTT-A-AGAGATTCT
1 CCACAAAGGC-ATCCTTTTCATA-AGATTCG
*
46232586 CCACAAAGGCATCCTTTTCATTCAATATTCG
1 CCACAAAGGCATCCTTTTCA-T-AAGATTCG
* *
46232617 CCACAAAGGC-TCTCCTTTCA-AAGATTTG
1 CCACAAAGGCATC-CTTTTCATAAGATTCG
*
46232645 CCACAAAGACATCCTTTTCAT
1 CCACAAAGGCATCCTTTTCAT
46232666 TCAGTACTTG
Statistics
Matches: 127, Mismatches: 25, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
27 6 0.05
28 54 0.43
29 6 0.05
30 4 0.03
31 50 0.39
32 7 0.06
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (29 bp):
CCACAAAGGCATCCTTTTCATAAGATTCG
Found at i:46232714 original size:51 final size:51
Alignment explanation
Indices: 46232633--46232734 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
46232623 AGGCTCTCCT
* * *
46232633 TTCAAAGATTTGCCACAAAGACATCCTTTTCATTCAGTACTTGCCACAAAG
1 TTCAAAGATTTGCCACAAAGACATCATTTTCATTCAGTACTCGCCAAAAAG
* * * *
46232684 TTCAATGATTTTCTACAAATGA-ATCATTTTCTTTCAGTACTCGCCAAAAAG
1 TTCAAAGATTTGCCACAAA-GACATCATTTTCATTCAGTACTCGCCAAAAAG
46232735 GCTTTCCTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 41 0.95
52 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (51 bp):
TTCAAAGATTTGCCACAAAGACATCATTTTCATTCAGTACTCGCCAAAAAG
Found at i:46232788 original size:29 final size:29
Alignment explanation
Indices: 46232731--46232804 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
46232721 TACTCGCCAA
** * **
46232731 AAAGGCTTTCCTTTTTGTAGGTTTGCCAC
1 AAAGGCTTTCCTTTTCATAAGTTCACCAC
46232760 AAAGGCTTTCCTTTTCATAAGTTCACCAC
1 AAAGGCTTTCCTTTTCATAAGTTCACCAC
* *
46232789 AAAGGTTTTTCTTTTC
1 AAAGGCTTTCCTTTTC
46232805 TGACATGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (29 bp):
AAAGGCTTTCCTTTTCATAAGTTCACCAC
Found at i:46233195 original size:15 final size:15
Alignment explanation
Indices: 46233174--46233228 Score: 101
Period size: 15 Copynumber: 3.7 Consensus size: 15
46233164 TTATTAGAAT
46233174 CATCAGATTTCAAGC
1 CATCAGATTTCAAGC
*
46233189 TATCAGATTTCAAGC
1 CATCAGATTTCAAGC
46233204 CATCAGATTTCAAGC
1 CATCAGATTTCAAGC
46233219 CATCAGATTT
1 CATCAGATTT
46233229 TAGTCTTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.31
Consensus pattern (15 bp):
CATCAGATTTCAAGC
Found at i:46234855 original size:261 final size:262
Alignment explanation
Indices: 46234378--46234901 Score: 861
Period size: 261 Copynumber: 2.0 Consensus size: 262
46234368 GCAGCCTTAT
* * *
46234378 TTTGAAAGCAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATTGAGGGTATATCAACCA
1 TTTGAAAGAAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATCGAGGGCATATCAACCA
46234443 TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
66 TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
*
46234508 GCGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
131 ACGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
* * ** *
46234573 AAACTTTTCTATTCCAATGTGAAGATAATTGCGAGTGAAGATTGCTCTAGATTCGCGCTTCAATA
196 AAACTTTTCTATTCCAATGTGAAGACAATTACGAGCAAAGATTGCTCTAGATTCACGCTTCAATA
46234638 TA
261 TA
* *
46234640 TTTGAAAGAAGTTAAAGATACAATTTGATATCAAGCATTTATTAGTATCGAGGGCATATCAAGCA
1 TTTGAAAGAAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATCGAGGGCATATCAACCA
* *
46234705 T-AAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTGTATAGATTTAGACATAGAAGTTCAG
66 TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
* * * *
46234769 ATGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCTTTTCTTTTCATGTTCGTGTATTTG
131 ACGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
* * *
46234834 AAACTTTTTTATTCGAATGTGAAGACAATTACGAGCAAAGATTGCTCTCGATTCACGCTTCAATA
196 AAACTTTTCTATTCCAATGTGAAGACAATTACGAGCAAAGATTGCTCTAGATTCACGCTTCAATA
46234899 TA
261 TA
46234901 T
1 T
46234902 ATATTCATGA
Statistics
Matches: 242, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
261 181 0.75
262 61 0.25
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (262 bp):
TTTGAAAGAAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATCGAGGGCATATCAACCA
TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
ACGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
AAACTTTTCTATTCCAATGTGAAGACAATTACGAGCAAAGATTGCTCTAGATTCACGCTTCAATA
TA
Found at i:46241152 original size:21 final size:21
Alignment explanation
Indices: 46241127--46241167 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
46241117 GGGAGCAGTT
46241127 TTTCAATCAATTTAAAAATGG
1 TTTCAATCAATTTAAAAATGG
46241148 TTTCAATCAATTTAAAAATG
1 TTTCAATCAATTTAAAAATG
46241168 CTTTGGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTCAATCAATTTAAAAATGG
Found at i:46252460 original size:45 final size:44
Alignment explanation
Indices: 46252318--46252473 Score: 170
Period size: 44 Copynumber: 3.5 Consensus size: 44
46252308 GATCCATTCT
* * * *
46252318 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTATCACTTCAATCTGCTCC
* * * *
46252362 ACTACAACTTCAGGGAGATAGGA-TTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTATC-ACTTCAATCTGCTCC
* * * *
46252406 ACTGTAACTTCAGAGAGATAAGATTTACCATCTTCGATCTGCCCC
1 ACTGCAACTTCAGAGAGATAAGATTTATCA-CTTCAATCTGCTCC
*
46252451 ACTGCAACTTCAGAGGGATAAGA
1 ACTGCAACTTCAGAGAGATAAGA
46252474 CCTGCTTGCT
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.03
44 51 0.56
45 37 0.41
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATTTATCACTTCAATCTGCTCC
Found at i:46252662 original size:131 final size:131
Alignment explanation
Indices: 46252525--46253004 Score: 775
Period size: 131 Copynumber: 3.7 Consensus size: 131
46252515 AGACCTGCCA
* * * *
46252525 TCTTCGATCTGCTCCGCTACT-GCTTAGGGAGACAAGATCTGTAATTTCCATCCTATTCCACTGC
1 TCTTCGATCTGCTCCACTA-TAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGC
* * * *
46252589 TGAC-CAGGGACATTGGACTTGTGGCTTGAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCG
65 TG-CTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCG
46252653 CCG
129 CCG
**
46252656 TCTTCGATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
* * *
46252721 GCTCAGGGAAATAGGAATTGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCACC
66 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
46252786 G
131 G
*
46252787 TCTTCAATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
*
46252852 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGAC
66 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
46252917 G
131 G
* *
46252918 TCTTCGATCTGCTCCACTATAGCTTAGAGAGATAAGATCTGTAGTGTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
46252983 GCTCAGGGAAATAGGACTTGTG
66 GCTCAGGGAAATAGGACTTGTG
46253005 ATTTCACCGA
Statistics
Matches: 325, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
130 2 0.01
131 323 0.99
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (131 bp):
TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
G
Found at i:46252729 original size:44 final size:42
Alignment explanation
Indices: 46252681--46252860 Score: 98
Period size: 44 Copynumber: 4.1 Consensus size: 42
46252671 ACTATTTCTT
46252681 AGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCTGCTC
1 AGGGAGATAAGAT-TGTAGTTT-CAACCTATTCCACTGCTGCTC
* * * * * * * *
46252725 AGGGAAATAGGAATTGTGGCTTAAATCTATTTCC-CTACTCCT-
1 AGGGAGATAAG-ATTGTAGTTTCAACCTA-TTCCACTGCTGCTC
* * * ** * *
46252767 GGGGAAGATAAGATT-CACCGTCTTCAATCTGCTCCACT-ATAGCTT
1 AGGG-AGATAAGATTGTA--GT-TTCAACCTATTCCACTGCT-GCTC
46252812 AGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCTGCTC
1 AGGGAGATAAGAT-TGTAGTTT-CAACCTATTCCACTGCTGCTC
46252856 AGGGA
1 AGGGA
46252861 AATAGGACTT
Statistics
Matches: 97, Mismatches: 26, Indels: 26
0.65 0.17 0.17
Matches are distributed among these distances:
42 6 0.06
43 23 0.24
44 60 0.62
45 7 0.07
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
AGGGAGATAAGATTGTAGTTTCAACCTATTCCACTGCTGCTC
Found at i:46254229 original size:8 final size:7
Alignment explanation
Indices: 46254205--46254270 Score: 84
Period size: 7 Copynumber: 9.4 Consensus size: 7
46254195 CCCCTTAGCC
46254205 TTTTT-A
1 TTTTTCA
46254211 TTTTT-A
1 TTTTTCA
46254217 CTTTTTCA
1 -TTTTTCA
46254225 TTTTTCA
1 TTTTTCA
46254232 TTTTTCA
1 TTTTTCA
46254239 -TTTTCA
1 TTTTTCA
46254245 TTTTTTCA
1 -TTTTTCA
46254253 TTTTTTCA
1 -TTTTTCA
46254261 TTTTTCA
1 TTTTTCA
46254268 TTT
1 TTT
46254271 CTTTTTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.21
7 29 0.52
8 15 0.27
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:46254278 original size:14 final size:13
Alignment explanation
Indices: 46254205--46254279 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 13
46254195 CCCCTTAGCC
*
46254205 TTTTT-ATTTTTAC
1 TTTTTCATTTTT-T
*
46254218 TTTTTCATTTTTCA
1 TTTTTCATTTTT-T
*
46254232 TTTTTCATTTTCAT
1 TTTTTCATTTT-TT
46254246 TTTTTCATTTTTT
1 TTTTTCATTTTTT
46254259 CATTTTTCATTTCTTT
1 --TTTTTCATTT-TTT
46254275 TTTTT
1 TTTTT
46254280 TGACTCAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
13 6 0.12
14 33 0.63
15 10 0.19
16 3 0.06
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCATTTTTT
Found at i:46254279 original size:29 final size:28
Alignment explanation
Indices: 46254205--46254278 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
46254195 CCCCTTAGCC
* *
46254205 TTTTT-ATTTTTACTTTTTCATTTTTCA
1 TTTTTCATTTTCATTTTTTCATTTTTCA
46254232 TTTTTCATTTTCATTTTTTCATTTTTTCA
1 TTTTTCATTTTCATTTTTTCA-TTTTTCA
*
46254261 TTTTTCA-TTTCTTTTTTT
1 TTTTTCATTTTCATTTTTT
46254279 TTGACTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.12
28 23 0.55
29 14 0.33
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTTCATTTTCATTTTTTCATTTTTCA
Found at i:46255511 original size:7 final size:7
Alignment explanation
Indices: 46255501--46255595 Score: 50
Period size: 7 Copynumber: 12.7 Consensus size: 7
46255491 TTCATCTAGA
46255501 TTTTTTC
1 TTTTTTC
46255508 TTTTTTC
1 TTTTTTC
*
46255515 TTCGTTTC
1 TT-TTTTC
*
46255523 TTCTTTC
1 TTTTTTC
46255530 TTTTTCTCTC
1 -TTTT-T-TC
*
46255540 ATTTTTTA
1 -TTTTTTC
*
46255548 TTTTTTA
1 TTTTTTC
46255555 TTTTGATT-
1 TTTT--TTC
46255563 TTTTTTC
1 TTTTTTC
46255570 TTTTTT-
1 TTTTTTC
**
46255576 TTCCTTC
1 TTTTTTC
46255583 TTTTTTTC
1 -TTTTTTC
46255591 TTTTT
1 TTTTT
46255596 ATTGAATCTA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
6 6 0.09
7 35 0.50
8 19 0.27
9 4 0.06
10 6 0.09
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:46255573 original size:20 final size:19
Alignment explanation
Indices: 46255540--46255577 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
46255530 TTTTTCTCTC
46255540 ATTTTTTATTTTTTATTTTG
1 ATTTTTTATTTTTT-TTTTG
46255560 ATTTTTT-TTCTTTTTTTT
1 ATTTTTTATT-TTTTTTTT
46255578 CCTTCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.84
Consensus pattern (19 bp):
ATTTTTTATTTTTTTTTTG
Found at i:46255573 original size:21 final size:21
Alignment explanation
Indices: 46255501--46255598 Score: 62
Period size: 21 Copynumber: 4.7 Consensus size: 21
46255491 TTCATCTAGA
*
46255501 TTTTTTCTTTTT-TCTT-CGTT
1 TTTTTTCTTTTTAT-TTCCATT
* *
46255521 TCTTCTTTCTTTTTCTCT-CATT
1 T-TT-TTTCTTTTTATTTCCATT
* **
46255543 TTTTAT-TTTTTATTTTGATT
1 TTTTTTCTTTTTATTTCCATT
*
46255563 TTTTTTCTTTTT-TTTCCTTCT
1 TTTTTTCTTTTTATTTCCAT-T
46255584 TTTTTTCTTTTTATT
1 TTTTTTCTTTTTATT
46255599 GAATCTAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
19 7 0.11
20 15 0.25
21 22 0.36
22 16 0.26
23 1 0.02
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTTTTATTTCCATT
Found at i:46261878 original size:30 final size:30
Alignment explanation
Indices: 46261731--46261918 Score: 121
Period size: 30 Copynumber: 6.3 Consensus size: 30
46261721 GACATGTCCG
**
46261731 TTTTCATAATTTGATAGCCGAAGTTATCCC
1 TTTTCATAATTTGATAGCCGAAGCCATCCC
** * ** *
46261761 TTAACATAGTTTGATAATCGAAGCAATCCC
1 TTTTCATAATTTGATAGCCGAAGCCATCCC
* * * * *
46261791 TTTTTATAATTTGATGGTCGTCA-CCATCCT
1 TTTTCATAATTTGATAGCCG-AAGCCATCCC
** * *** *
46261821 TTTTCATAATTCAATGGTCTTCA-CCATCCG
1 TTTTCATAATTTGATAG-CCGAAGCCATCCC
*
46261851 TTTTCATAATTTGATGGCCGAAGCCATCCC
1 TTTTCATAATTTGATAGCCGAAGCCATCCC
* *
46261881 TTTTCA-AAGATTGATAGCCAAAGCCATCCC
1 TTTTCATAA-TTTGATAGCCGAAGCCATCCC
46261911 TTTTCATA
1 TTTTCATA
46261919 GTTCAATGGT
Statistics
Matches: 121, Mismatches: 32, Indels: 9
0.75 0.20 0.06
Matches are distributed among these distances:
29 4 0.03
30 115 0.95
31 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (30 bp):
TTTTCATAATTTGATAGCCGAAGCCATCCC
Found at i:46261938 original size:30 final size:30
Alignment explanation
Indices: 46261786--46261945 Score: 128
Period size: 30 Copynumber: 5.3 Consensus size: 30
46261776 AATCGAAGCA
* *
46261786 ATCCCTTTTTATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * *
46261816 ATCCTTTTTCATAATTCAATGGTCTTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * * *
46261846 ATCCGTTTTCATAATTTGATGGCCG-AAGCC
1 ATCCCTTTTCATAATTCGATGGTCGTCA-CC
* * ***
46261876 ATCCCTTTTCAAAGATT-GATAG-CCAAAGCC
1 ATCCCTTTTCATA-ATTCGATGGTCGTCA-CC
* *
46261906 ATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
46261936 ATCCCTTTTC
1 ATCCCTTTTC
46261946 TTGATCGATA
Statistics
Matches: 103, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
29 4 0.04
30 94 0.91
31 5 0.05
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATGGTCGTCACC
Found at i:46271611 original size:25 final size:25
Alignment explanation
Indices: 46271577--46271638 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
46271567 TTTAGGCATT
46271577 CATTTCATGCATTTGCATTACATGA
1 CATTTCATGCATTTGCATTACATGA
46271602 CATTTCATGCATTTGCATTACATGA
1 CATTTCATGCATTTGCATTACATGA
**
46271627 CATCACATGCAT
1 CATTTCATGCAT
46271639 AAATCCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (25 bp):
CATTTCATGCATTTGCATTACATGA
Found at i:46275232 original size:129 final size:129
Alignment explanation
Indices: 46274997--46275478 Score: 786
Period size: 129 Copynumber: 3.7 Consensus size: 129
46274987 ATGAAGATAG
* * *
46274997 CAGATCTTGTCACCCTAAGCAGTAGCGGAGCAGATCGAAGATGGGGAAATCTTATCTTCAAGTGT
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGA-CGGCAAATCTTATCTTCAAGTGT
*
46275062 AAGGAAGCAAATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGAGAAATTA
65 AAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGAGAAATTA
* *
46275127 CAAATCTTGCCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
* * * *
46275192 AGGAAGCAGATTTAAGCCATAAGTCCTATATCCCTAGTCAGCAGCGGAATAGGTTGGGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGAGAAATTA
*
46275256 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
* *
46275321 AGAAAGGAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT-AGGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGA-GAAATTA
* **
46275385 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGTGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
*
46275450 AGGAAGCAGATTTAAGCCACAAATCCTAT
66 AGGAAGCAGATTTAAGCCACAAGTCCTAT
46275479 CTCCTTGAAG
Statistics
Matches: 327, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
129 289 0.88
130 38 0.12
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (129 bp):
CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGAGAAATTA
Found at i:46275587 original size:129 final size:129
Alignment explanation
Indices: 46275454--46275711 Score: 428
Period size: 129 Copynumber: 2.0 Consensus size: 129
46275444 AGTGTAAGGA
* *
46275454 AGCAGATTTAAGCC-ACAAATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGAT
1 AGCAGATTGAAGCCGA-AAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGAT
* *
46275518 CTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGG
65 CTTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGG
* *
46275583 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATT
1 AGCAGATTGAAGCCGAAAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
**
46275648 TTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGTGG
66 TTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGG
46275712 TGCACACTGA
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
129 119 0.99
130 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (129 bp):
AGCAGATTGAAGCCGAAAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
TTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGG
Found at i:46275653 original size:44 final size:44
Alignment explanation
Indices: 46275476--46275711 Score: 191
Period size: 44 Copynumber: 5.5 Consensus size: 44
46275466 CCACAAATCC
* * *
46275476 TATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
* * * * * *
46275520 TATCTCTCTGAAGTTGCAGTAGAGTGGA-T--CGCATTAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
* * * * *
46275561 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-CAATAGATCT
* * *
46275605 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
* * * * *
46275649 TATCTCACTGAAGTTGCAGTAGAGTGGA-T--CGC-ATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAAT-AGATCT
*
46275690 TATCTCCCTGAGGTTGCAGTGG
1 TATCTCCCTGAAGTTGCAGTGG
46275712 TGCACACTGA
Statistics
Matches: 149, Mismatches: 37, Indels: 15
0.74 0.18 0.07
Matches are distributed among these distances:
40 2 0.01
41 55 0.37
42 1 0.01
43 5 0.03
44 83 0.56
45 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
Found at i:46275743 original size:129 final size:129
Alignment explanation
Indices: 46275471--46275748 Score: 396
Period size: 129 Copynumber: 2.2 Consensus size: 129
46275461 TTAAGCCACA
* * *
46275471 AATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCCCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCACTGAAGTTG
* * * *** *
46275536 CAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
66 CAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCACACTGAAGAAAAC
* *
46275600 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTTTATCTCACTGAAGTTG
1 AATCCTATCCCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCACTGAAGTTG
** *
46275665 CAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGTGGTGCACACTG-AGAAAAC
66 CAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCACACTGAAGAAAAC
*
46275728 AAGTCTTATCCCCCTGAAGTT
1 AA-TCCTATCCCCCTGAAGTT
46275749 ACAGTGTGGC
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
128 5 0.04
129 128 0.96
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (129 bp):
AATCCTATCCCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCACTGAAGTTG
CAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCACACTGAAGAAAAC
Found at i:46283850 original size:106 final size:107
Alignment explanation
Indices: 46283222--46283850 Score: 721
Period size: 106 Copynumber: 5.9 Consensus size: 107
46283212 TGTGTTTCTA
* * * * * * *
46283222 GTAGGTCATCGAGCCGTTTTAGAATTTTCGATATTAAATCAGCTAACT-AAAAAAAGCTTGGGTT
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAA-CTTAGGTT
* * *
46283286 GCAATCTTAAATCAACTAAACTTTATAATATCAGTTA-TGAAT
65 GCGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
*
46283328 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATTAGCTAACTCAAAGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
* * **
46283393 CGATATTAAACCAACTAACCTTTATAATATCAATTA-TGAAT
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
** * * *
46283434 GTAGGTCATCGATTTGTTTTAGGAGTTGCAATCTTAAATCAGTTAACTCAATGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
* * * **
46283499 AGATCTTAAATCAGCTAACCTTTATAATATCAACT-GTGAGC
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
* * * * * * * *
46283540 ATAGGTCATTGAACTGTTTTTGGATTTGCGATCTTAAATTAGTTACCTCAAAGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
* * * * * *
46283605 CGATCCTAAATTAGCTAACCCTTATAATATCAG-TTGTGAAC
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
* * * * * * *
46283646 ATGGGTCATCAAGTTGTTTTAGGAGTTACGATATTAAATCAGCTAACTCAAAGAAACTTAGGTTA
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
*** *
46283711 CGATCTTCGGTCAACTAAACTTTATAATATCAGCTAGT-AAT
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
* * *
46283752 GTAGATCATCGAGCTATTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAAGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
*
46283817 CGATCTTAAATCAACTAACTTTTATAATATCAGC
66 CGATCTTAAATCAACTAACCTTTATAATATCAGC
46283851 ACTTTTAAAT
Statistics
Matches: 439, Mismatches: 80, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
105 1 0.00
106 429 0.98
107 9 0.02
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (107 bp):
GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
Found at i:46295294 original size:13 final size:13
Alignment explanation
Indices: 46295276--46295304 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
46295266 TACAATTTTA
46295276 CATTACGGTGATT
1 CATTACGGTGATT
46295289 CATTACGGTGATT
1 CATTACGGTGATT
46295302 CAT
1 CAT
46295305 AAAAGATAAA
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:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (13 bp):
CATTACGGTGATT
Found at i:46304337 original size:25 final size:25
Alignment explanation
Indices: 46304265--46304372 Score: 69
Period size: 25 Copynumber: 4.3 Consensus size: 25
46304255 AAACCAAATG
* **
46304265 AAGCCTTTGTGG-AAAGTTATTTGTG
1 AAGCC-TTGTGGCGAAGTTATTTGAA
* * *
46304290 AAGCCCTTGGGGCGAA-ATCTTTGAA
1 AAG-CCTTGTGGCGAAGTTATTTGAA
*
46304315 AAGCCTATGTGGCG-TGTTATTTGAA
1 AAGCCT-TGTGGCGAAGTTATTTGAA
* * *
46304340 AATCCTTAGTGGCGAAGTTATCTGGA
1 AAGCCTT-GTGGCGAAGTTATTTGAA
46304366 AAGCCTT
1 AAGCCTT
46304373 TGTGTCAAGT
Statistics
Matches: 62, Mismatches: 15, Indels: 11
0.70 0.17 0.12
Matches are distributed among these distances:
24 4 0.06
25 40 0.65
26 18 0.29
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (25 bp):
AAGCCTTGTGGCGAAGTTATTTGAA
Found at i:46304453 original size:71 final size:72
Alignment explanation
Indices: 46304371--46304509 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 72
46304361 CTGGAAAGCC
* * * *
46304371 TTTGTGTCAAGTCATTTGGAAAACC-GTATGGCAAATTCTGCGATGCCTAAGTGGCGAGTTGTTA
1 TTTGTGGCAAGTCATTTGCAAAACCTGTATGGCAAATTCTACAATGCCTAAGTGGCGAGTTGTTA
46304435 CTCCACA
66 CTCCACA
* ** *
46304442 TTTGTGGCAAGTCATTTGCAAAGCCTGTATGGTGAATTCTACAATGCGTAAGTGGCGAGTTGTTA
1 TTTGTGGCAAGTCATTTGCAAAACCTGTATGGCAAATTCTACAATGCCTAAGTGGCGAGTTGTTA
46304507 CTC
66 CTC
46304510 TGCCTTTGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 22 0.37
72 37 0.63
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (72 bp):
TTTGTGGCAAGTCATTTGCAAAACCTGTATGGCAAATTCTACAATGCCTAAGTGGCGAGTTGTTA
CTCCACA
Found at i:46306977 original size:18 final size:19
Alignment explanation
Indices: 46306943--46306978 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
46306933 TTCTAATTAG
*
46306943 TTTTAAATGTTAATTATTC
1 TTTTAAATGTAAATTATTC
46306962 TTTTAAA-GTAAATTATT
1 TTTTAAATGTAAATTATT
46306979 AGCCATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTAAATGTAAATTATTC
Found at i:46308298 original size:39 final size:39
Alignment explanation
Indices: 46308236--46308373 Score: 154
Period size: 39 Copynumber: 3.5 Consensus size: 39
46308226 AACATGTTTT
* *
46308236 TGAGTATTACGATATATGGTTGAATGTTATGTGATTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* * *
46308275 TGAGTATTGTGATATGTGCTTGAACGTTATGT-ACTTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGA-TTATA
* * *
46308314 TGAGTATTGCAATATATGCTTAAATGTTATATGATTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* *
46308353 TGTGTCA-TGTGATATATGCTT
1 TGAGT-ATTGCGATATATGCTT
46308374 AAAAGTGAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.01
39 79 0.96
40 2 0.02
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
Found at i:46309776 original size:23 final size:21
Alignment explanation
Indices: 46309715--46309782 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
46309705 CCTAGAATAA
*
46309715 TTTTGTATTAATTTATTTTTCT
1 TTTTGTATTAAGTTATTTTT-T
* *
46309737 TTTTATATTTAGTGTTATTTTTT
1 TTTTGTA-TTA-AGTTATTTTTT
*
46309760 TCTTTGTATTGAAGTTATATTTT
1 T-TTTGTATT-AAGTTATTTTTT
46309783 CTCGAGTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
22 6 0.17
23 16 0.44
24 14 0.39
ACGTcount: A:0.19, C:0.03, G:0.09, T:0.69
Consensus pattern (21 bp):
TTTTGTATTAAGTTATTTTTT
Found at i:46314306 original size:48 final size:45
Alignment explanation
Indices: 46314211--46314319 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 45
46314201 GTGTAGGTTC
* * * *
46314211 AACCCTAACGGTGACCAGGCACTATTATTCGATTCGTGTAGGCTT
1 AACCCTAACGGTAACCAGGCACTATAATTCGATTCGTGCACGCTT
** *
46314256 AACCCTAACGGGTAACCAGGCACTATAATTAATTATTCGTGCACGTTT
1 AACCCTAAC-GGTAACCAGGCACTATAATT--CGATTCGTGCACGCTT
*
46314304 AACCCAAACAGGTAAC
1 AACCCTAAC-GGTAAC
46314320 TAAACACTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
45 9 0.17
46 18 0.35
48 25 0.48
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (45 bp):
AACCCTAACGGTAACCAGGCACTATAATTCGATTCGTGCACGCTT
Found at i:46321169 original size:14 final size:14
Alignment explanation
Indices: 46321150--46321177 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46321140 TTACACTCAA
46321150 AATTTAAAGTAGGG
1 AATTTAAAGTAGGG
46321164 AATTTAAAGTAGGG
1 AATTTAAAGTAGGG
46321178 GTTTAGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (14 bp):
AATTTAAAGTAGGG
Found at i:46327486 original size:9 final size:9
Alignment explanation
Indices: 46327457--46327615 Score: 97
Period size: 9 Copynumber: 16.9 Consensus size: 9
46327447 ATATTTTTTA
46327457 AAAAATTAT
1 AAAAATTAT
*
46327466 ATAAACTTAT
1 A-AAAATTAT
*
46327476 AAAGATTAT
1 AAAAATTAT
46327485 AAAAATTAT
1 AAAAATTAT
*
46327494 AAAACTTAT
1 AAAAATTAT
* *
46327503 AGATATTAT
1 AAAAATTAT
46327512 AAAAATTTAT
1 AAAAA-TTAT
46327522 AATAAATTAT
1 AA-AAATTAT
*
46327532 AAAAATATTT
1 AAAAAT-TAT
46327542 AAAATATT-T
1 AAAA-ATTAT
* *
46327551 -AAGATTTT
1 AAAAATTAT
*
46327559 AAAATTTTAT
1 AAAA-ATTAT
*
46327569 ATAAATTAT
1 AAAAATTAT
* *
46327578 AAAAAATCAC
1 -AAAAATTAT
*
46327588 ACAAACTTAT
1 A-AAAATTAT
*
46327598 AAATATTAT
1 AAAAATTAT
46327607 AAAATATTA
1 AAAA-ATTA
46327616 CAAGAAGAAA
Statistics
Matches: 113, Mismatches: 26, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
7 3 0.03
8 3 0.03
9 53 0.47
10 49 0.43
11 5 0.04
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (9 bp):
AAAAATTAT
Found at i:46327495 original size:18 final size:17
Alignment explanation
Indices: 46327458--46327611 Score: 85
Period size: 19 Copynumber: 8.3 Consensus size: 17
46327448 TATTTTTTAA
*
46327458 AAAATTATATAAACTTAT
1 AAAATTATA-AAAATTAT
46327476 AAAGATTATAAAAATTAT
1 AAA-ATTATAAAAATTAT
* *
46327494 AAAACTTATAGATATTAT
1 AAAA-TTATAAAAATTAT
46327512 AAAAATTTATAATAAATTAT
1 -AAAA-TTATAA-AAATTAT
*
46327532 AAAAATATTTAAAATATT-T
1 -AAAAT-TATAAAA-ATTAT
* * *
46327551 AAGATTTTAAAATTTTAT
1 AAAATTATAAAA-ATTAT
* *
46327569 ATAAATTATAAAAAATCAC
1 A-AAATTAT-AAAAATTAT
*
46327588 ACAAACTTATAAATATTAT
1 A-AAA-TTATAAAAATTAT
46327607 AAAAT
1 AAAAT
46327612 ATTACAAGAA
Statistics
Matches: 108, Mismatches: 18, Indels: 21
0.73 0.12 0.14
Matches are distributed among these distances:
17 12 0.11
18 33 0.31
19 37 0.34
20 26 0.24
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATTATAAAAATTAT
Found at i:46327547 original size:22 final size:20
Alignment explanation
Indices: 46327507--46327547 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
46327497 ACTTATAGAT
*
46327507 ATTATAAAAATTTATAATAA
1 ATTATAAAAATTTAAAATAA
46327527 ATTATAAAAATATTTAAAATA
1 ATTAT-AAAA-ATTTAAAATA
46327548 TTTAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATAAAAATTTAAAATAA
Found at i:46327818 original size:7 final size:7
Alignment explanation
Indices: 46327806--46327832 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
46327796 TTTATCTTTA
46327806 ATTTATT
1 ATTTATT
46327813 ATTTATT
1 ATTTATT
46327820 ATTTATT
1 ATTTATT
46327827 ATTTAT
1 ATTTAT
46327833 CTTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTATT
Found at i:46329311 original size:19 final size:19
Alignment explanation
Indices: 46329267--46329311 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
46329257 TTATTTCAGA
46329267 ATTAT-AAAATATTAAAAT
1 ATTATAAAAATATTAAAAT
*
46329285 ATTA-AAAAAGTATTATAAT
1 ATTATAAAAA-TATTAAAAT
46329304 -TTATAAAA
1 ATTATAAAA
46329312 GTGTTCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTATAAAAATATTAAAAT
Found at i:46329312 original size:18 final size:19
Alignment explanation
Indices: 46329267--46329313 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
46329257 TTATTTCAGA
46329267 ATTATAAAA-TATTAAAAT
1 ATTATAAAAGTATTAAAAT
* *
46329285 ATTAAAAAAGTATTATAAT
1 ATTATAAAAGTATTAAAAT
46329304 -TTATAAAAGT
1 ATTATAAAAGT
46329314 GTTCAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
ATTATAAAAGTATTAAAAT
Found at i:46330666 original size:22 final size:22
Alignment explanation
Indices: 46330624--46330664 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
46330614 AAAATGAAAA
46330624 TAATTTTTAAAAATATTTTTAT
1 TAATTTTTAAAAATATTTTTAT
*
46330646 TAATTTTT-AATATATTTTT
1 TAATTTTTAAAAATATTTTT
46330665 TAGATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAAAATATTTTTAT
Found at i:46331513 original size:24 final size:24
Alignment explanation
Indices: 46331486--46331537 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
46331476 TTAGTAAGTC
*
46331486 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
46331510 AAATATATTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
46331534 AAAT
1 AAAT
46331538 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:46335466 original size:25 final size:25
Alignment explanation
Indices: 46335410--46335527 Score: 82
Period size: 25 Copynumber: 4.8 Consensus size: 25
46335400 GCTCTCTCTT
* *
46335410 GAGCCATATAATGGGAAGCTCATAT
1 GAGCCATATAACGGGAAGCTCATAA
* * *
46335435 GAACCATGTAACGGGAAGCTTATAA
1 GAGCCATATAACGGGAAGCTCATAA
* ** **
46335460 GAGCCATA-ATCAAGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATAA
* *
46335484 GAGCCA-ATAATGGGTAGCTC-TGAA
1 GAGCCATATAACGGGAAGCTCAT-AA
46335508 GAGCCAT-TAATCGGGAAGCT
1 GAGCCATATAA-CGGGAAGCT
46335528 TTGGATAGCC
Statistics
Matches: 67, Mismatches: 22, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
23 2 0.03
24 32 0.48
25 33 0.49
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATAA
Found at i:46350854 original size:37 final size:38
Alignment explanation
Indices: 46350813--46350934 Score: 153
Period size: 37 Copynumber: 3.3 Consensus size: 38
46350803 TCCATCTGAA
*
46350813 AACACGCCAAATGCTCAT-AAGAACTCATCCACCCGAT
1 AACACGCCAAATGCTCATCAAGAGCTCATCCACCCGAT
* * * * *
46350850 AACACGCCAATTGCTC-TGAAGAGCT-AGTGCAACCGAA
1 AACACGCCAAATGCTCATCAAGAGCTCA-TCCACCCGAT
46350887 AACACGCCAAATGCTCATCAA-AGCTCATCCACCCGAT
1 AACACGCCAAATGCTCATCAAGAGCTCATCCACCCGAT
46350924 AACACGCCAAA
1 AACACGCCAAA
46350935 ACAAGGAGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
36 2 0.03
37 65 0.92
38 4 0.06
ACGTcount: A:0.38, C:0.34, G:0.14, T:0.15
Consensus pattern (38 bp):
AACACGCCAAATGCTCATCAAGAGCTCATCCACCCGAT
Found at i:46355082 original size:9 final size:9
Alignment explanation
Indices: 46355068--46355117 Score: 82
Period size: 9 Copynumber: 5.6 Consensus size: 9
46355058 TTTTGGTTAA
46355068 AATTAACCG
1 AATTAACCG
46355077 AATTAACCG
1 AATTAACCG
*
46355086 AATTACCCG
1 AATTAACCG
46355095 AATTAACCG
1 AATTAACCG
*
46355104 AATTACCCG
1 AATTAACCG
46355113 AATTA
1 AATTA
46355118 TATGTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:46355095 original size:18 final size:18
Alignment explanation
Indices: 46355068--46355117 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
46355058 TTTTGGTTAA
*
46355068 AATTAACCGAATTAACCG
1 AATTACCCGAATTAACCG
46355086 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
46355104 AATTACCCGAATTA
1 AATTACCCGAATTA
46355118 TATGTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:46355168 original size:26 final size:25
Alignment explanation
Indices: 46355125--46355174 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
46355115 TTATATGTTT
*
46355125 TTTTATTTTTAAACTTTATTTTTAG
1 TTTTAGTTTTAAACTTTATTTTTAG
*
46355150 TTTTAGTTTTAGAATTTTATTTTTA
1 TTTTAGTTTTA-AACTTTATTTTTA
46355175 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (25 bp):
TTTTAGTTTTAAACTTTATTTTTAG
Found at i:46355172 original size:13 final size:14
Alignment explanation
Indices: 46355125--46355174 Score: 61
Period size: 12 Copynumber: 3.8 Consensus size: 14
46355115 TTATATGTTT
46355125 TTTTATTTTTA-AA
1 TTTTATTTTTAGAA
*
46355138 CTTTATTTTTAG--
1 TTTTATTTTTAGAA
*
46355150 TTTTAGTTTTAGAA
1 TTTTATTTTTAGAA
46355164 TTTTATTTTTA
1 TTTTATTTTTA
46355175 TTTATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.33
13 10 0.33
14 10 0.33
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTATTTTTAGAA
Found at i:46355225 original size:18 final size:18
Alignment explanation
Indices: 46355202--46355255 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
46355192 AATTTTTATG
46355202 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
46355220 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
46355238 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
46355256 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:46356022 original size:43 final size:44
Alignment explanation
Indices: 46355917--46356025 Score: 150
Period size: 43 Copynumber: 2.5 Consensus size: 44
46355907 AATTGCCGCA
* * *
46355917 AAAGATCATGTTCTTTAGCAGC-ATTTGTAGTAAAAGCGCCGTT
1 AAAGATCATGTTCTATAGCGGCGATTTGTAATAAAAGCGCCGTT
* **
46355960 AAATATCATGTTCTATAGCGGCGA-TTGTAATAAAAGCGTTGTT
1 AAAGATCATGTTCTATAGCGGCGATTTGTAATAAAAGCGCCGTT
46356003 AAAGATCATGTTCTATAGCGGCG
1 AAAGATCATGTTCTATAGCGGCG
46356026 TTTTCCCACA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (44 bp):
AAAGATCATGTTCTATAGCGGCGATTTGTAATAAAAGCGCCGTT
Found at i:46358838 original size:24 final size:24
Alignment explanation
Indices: 46358810--46358861 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
46358800 ATGGGAAAGA
*
46358810 AAAAATTAAGTTAGGGAATTGGGG
1 AAAAACTAAGTTAGGGAATTGGGG
*
46358834 AAAAACTAAGTTAGGGATTTGGGG
1 AAAAACTAAGTTAGGGAATTGGGG
46358858 AAAA
1 AAAA
46358862 TGATTTGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.23
Consensus pattern (24 bp):
AAAAACTAAGTTAGGGAATTGGGG
Found at i:46358994 original size:41 final size:42
Alignment explanation
Indices: 46358934--46359043 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
46358924 AAAAATATTC
* *
46358934 GTGGCGTTTATGGGCAAAACGCCGCTATTG-CTTT-ACCTTTA
1 GTGGCGTTTAT-GGAAAAACGCCGCTATCGTCTTTAACCTTTA
* * *
46358975 GTGGCATTTATGAGAAAAACGCCGCTATCGTTTTTAACCTTTT
1 GTGGCGTTTATG-GAAAAACGCCGCTATCGTCTTTAACCTTTA
* *
46359018 GCGGCGTTTATGCAAAAACGCCGCTA
1 GTGGCGTTTATGGAAAAACGCCGCTA
46359044 ACGTTGCTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 25 0.43
42 16 0.28
43 16 0.28
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (42 bp):
GTGGCGTTTATGGAAAAACGCCGCTATCGTCTTTAACCTTTA
Found at i:46361750 original size:44 final size:44
Alignment explanation
Indices: 46361729--46362045 Score: 256
Period size: 44 Copynumber: 7.4 Consensus size: 44
46361719 ATCTGTAATT
*
46361729 TTCAACCTATTTCACTGCTGCTCAGAGAGATAAGATTCACAATC
1 TTCAACCTATTCCACTGCTGCTCAGAGAGATAAGATTCACAATC
* *
46361773 TTCAACCTATTCCACTGCTGACTAAG-GAGATAGGATT--C-A-C
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* *
46361813 --C-A---ATTCCACTGCTGAC-CAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGA-TTCACAATC
* * *
46361851 TTCAACCTATTCCACTGTTGAC-CAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* * *
46361895 TTCAACCTATTCTACTGCTGACT-AGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* * * * *
46361939 TTCAACCTATTCCACTACTGAC-CAGGGGGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* * * *
46361983 TTCAACCTATTCCATTGCTGAC-CAGGGAGATAGGACTT-ATAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGA-TTCACAATC
46362027 TTCAACCTATTCCACTGCT
1 TTCAACCTATTCCACTGCT
46362046 TTCCAGGGAG
Statistics
Matches: 240, Mismatches: 17, Indels: 32
0.83 0.06 0.11
Matches are distributed among these distances:
33 2 0.01
34 23 0.10
35 2 0.01
36 1 0.00
37 2 0.01
38 2 0.01
40 2 0.01
41 2 0.01
42 1 0.00
43 2 0.01
44 196 0.82
45 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGCTCAGAGAGATAAGATTCACAATC
Found at i:46362052 original size:44 final size:44
Alignment explanation
Indices: 46361815--46362063 Score: 376
Period size: 44 Copynumber: 5.7 Consensus size: 44
46361805 GGATTCACCA
46361815 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
*
46361859 ATTCCACTGTTGACCAGGGAGATAGGA-TTCACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCT
* *
46361903 ATTCTACTGCTGACTAGGGAGATAGGA-TTCACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCT
* * *
46361947 ATTCCACTACTGACCAGGGGGATAGGACTCACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
* *
46361991 ATTCCATTGCTGACCAGGGAGATAGGACTTATAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
**
46362035 ATTCCACTGCTTTCCAGGGAGATAGGACT
1 ATTCCACTGCTGACCAGGGAGATAGGACT
46362064 AGTCTCTTCG
Statistics
Matches: 186, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 2 0.01
44 183 0.98
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
Found at i:46364926 original size:9 final size:9
Alignment explanation
Indices: 46364907--46364939 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
46364897 ATGCAAAGCT
46364907 AATGC-ATG
1 AATGCAATG
46364915 AATGCAATG
1 AATGCAATG
*
46364924 AATGCCATG
1 AATGCAATG
46364933 AATGCAA
1 AATGCAA
46364940 AAGAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (9 bp):
AATGCAATG
Found at i:46366217 original size:23 final size:22
Alignment explanation
Indices: 46366177--46366220 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
46366167 AAATTATAAA
*
46366177 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
46366199 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
46366221 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:46366963 original size:22 final size:22
Alignment explanation
Indices: 46366941--46367020 Score: 112
Period size: 22 Copynumber: 3.7 Consensus size: 22
46366931 AAATTAAATC
* *
46366941 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
46366964 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGCATATCATATCT
46366986 TCTAAGATTGCATATCATA---
1 TCTAAGATTGCATATCATATCT
46367005 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
46367021 CTTGAAGATT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 16 0.29
22 29 0.53
23 10 0.18
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:46368945 original size:31 final size:31
Alignment explanation
Indices: 46368910--46368968 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
46368900 AACAGCCTTA
46368910 TGACTTAAATAAAAACTTTTGAATAATTTAG
1 TGACTTAAATAAAAACTTTTGAATAATTTAG
* *
46368941 TGACTTAAATGAAATCTTTTGAATAATT
1 TGACTTAAATAAAAACTTTTGAATAATT
46368969 CAATGATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAATTTAG
Found at i:46369418 original size:28 final size:25
Alignment explanation
Indices: 46369387--46369456 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 25
46369377 TCATTCAATT
*
46369387 TTAAAAATATAAATAAATATTTCCAAAA
1 TTAAAAAAATAAA-AAATATTT--AAAA
* *
46369415 TTAAAAAGATTAAGAAAATATTTAAAT
1 TTAAAAA-AATAA-AAAATATTTAAAA
46369442 TTAAAAAAATAAAAA
1 TTAAAAAAATAAAAA
46369457 TATGGGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 3 0.08
26 4 0.11
27 10 0.28
28 7 0.19
29 11 0.31
30 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (25 bp):
TTAAAAAAATAAAAAATATTTAAAA
Found at i:46370965 original size:29 final size:28
Alignment explanation
Indices: 46370911--46370968 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
46370901 CCTACAAAAA
*
46370911 TTTTAATTTTTTTAACTTTATATATATT
1 TTTTAATTTTTTTAAATTTATATATATT
*
46370939 TTTTATATTTTTTTAGAATTTCT-TATATT
1 TTTTA-ATTTTTTTA-AATTTATATATATT
46370968 T
1 T
46370969 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 16 0.62
30 5 0.19
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTTAATTTTTTTAAATTTATATATATT
Found at i:46372419 original size:14 final size:15
Alignment explanation
Indices: 46372386--46372421 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
46372376 CACTTGTTTT
*
46372386 TTTTAATTTTATATA
1 TTTTAGTTTTATATA
46372401 TTTTAGTTTTATA-A
1 TTTTAGTTTTATATA
46372415 TTTTAGT
1 TTTTAGT
46372422 CACTTGTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTAGTTTTATATA
Found at i:46373898 original size:10 final size:10
Alignment explanation
Indices: 46373883--46373916 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
46373873 TTCCCCTGTT
46373883 TAAATAAAAA
1 TAAATAAAAA
46373893 TAAATAAAAA
1 TAAATAAAAA
46373903 TAAATAAAAA
1 TAAATAAAAA
46373913 TAAA
1 TAAA
46373917 AGTTGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:46379258 original size:24 final size:25
Alignment explanation
Indices: 46379212--46379259 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
46379202 TAATAAATAT
*
46379212 ATATATTTAAAATTTTTAATTTTAAA
1 ATATATTTAAAATTCTT-ATTTTAAA
*
46379238 ATATTTTTAAAATTCTT-TTTTA
1 ATATATTTAAAATTCTTATTTTA
46379260 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
26 15 0.75
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATATTTAAAATTCTTATTTTAAA
Found at i:46383671 original size:27 final size:26
Alignment explanation
Indices: 46383641--46383729 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 26
46383631 AATTGTAAAA
46383641 ATTATAATTATTTTTAAATGTATAACT
1 ATTATAATTATTTTTAAATGTATAA-T
* *
46383668 ATTA-CA--ATTTTTAAAT-TA-AAA
1 ATTATAATTATTTTTAAATGTATAAT
* *
46383689 ATTCTAATTATTTTTAATTGTATAAGT
1 ATTATAATTATTTTTAAATGTATAA-T
* *
46383716 ATTACAAGTATTTT
1 ATTATAATTATTTT
46383730 ACTTCAGCAC
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 2 0.04
24 19 0.40
25 2 0.04
26 3 0.06
27 15 0.32
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
ATTATAATTATTTTTAAATGTATAAT
Found at i:46406796 original size:2 final size:2
Alignment explanation
Indices: 46406789--46406831 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
46406779 TTTGAATAGA
*
46406789 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC T- TC -C TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
46406829 TC T
1 TC T
46406832 TGAACATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:46409440 original size:12 final size:12
Alignment explanation
Indices: 46409423--46409457 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
46409413 TAGGAGTGAT
46409423 TGTTTGTTTTTC
1 TGTTTGTTTTTC
46409435 TGTTTGTTTTTC
1 TGTTTGTTTTTC
*
46409447 TTTTTGTTTTT
1 TGTTTGTTTTT
46409458 GTTTTAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (12 bp):
TGTTTGTTTTTC
Found at i:46409462 original size:12 final size:12
Alignment explanation
Indices: 46409425--46409462 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
46409415 GGAGTGATTG
*
46409425 TTTGTTTTTCTG
1 TTTGTTTTTCTT
46409437 TTTGTTTTTCTT
1 TTTGTTTTTCTT
*
46409449 TTTGTTTTTGTT
1 TTTGTTTTTCTT
46409461 TT
1 TT
46409463 AAGAAACCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (12 bp):
TTTGTTTTTCTT
Found at i:46409581 original size:28 final size:27
Alignment explanation
Indices: 46409524--46409582 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
46409514 AAAAGCCCTT
46409524 TTTTTTAAATTTACCGAAATAGGCCGA
1 TTTTTTAAATTTACCGAAATAGGCCGA
* *
46409551 TTTTTTAATTATTTACCGGAATGGGCC-A
1 TTTTTTAA--ATTTACCGAAATAGGCCGA
46409579 TTTT
1 TTTT
46409583 CCCCGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 15 0.54
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATAGGCCGA
Found at i:46409999 original size:124 final size:125
Alignment explanation
Indices: 46409777--46410095 Score: 561
Period size: 124 Copynumber: 2.6 Consensus size: 125
46409767 NNNGGACTCC
* * *
46409777 ATTTCAGC-ACAGTTGGTCATGTAAGAAATAATTTTTTTTTGACGTTTTCTGAGCAAATAATATA
1 ATTTC-GCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGACG-TTTCTGAGCAAATAGTGTA
46409841 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCG
64 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCG
46409903 ATTTCGCTACAGTTGGTCATGTAGGAAATAA-TTTTTTTTGACGTTTCTGAGCAAATAGTGTAAA
1 ATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTGTAAA
*
46409967 ATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCG
66 ATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCG
*
46410027 ATTTTGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTGTAAA
1 ATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTGTAAA
46410092 ATCG
66 ATCG
46410096 TGCCCTCGTG
Statistics
Matches: 186, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
124 108 0.58
125 51 0.27
126 27 0.15
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (125 bp):
ATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTGTAAA
ATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCG
Found at i:46413066 original size:26 final size:27
Alignment explanation
Indices: 46413037--46413088 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
46413027 GAAAATATTA
46413037 AAAATTTTAAAATTAT-TTTAAAAAAT
1 AAAATTTTAAAATTATCTTTAAAAAAT
*
46413063 AAAATTTTAAAATTTTCTTTAAAAAA
1 AAAATTTTAAAATTATCTTTAAAAAA
46413089 ATGAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAATTTTAAAATTATCTTTAAAAAAT
Found at i:46413199 original size:52 final size:51
Alignment explanation
Indices: 46413121--46413226 Score: 133
Period size: 52 Copynumber: 2.1 Consensus size: 51
46413111 ATTTAATATG
* * *
46413121 GAGTTTAGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTCGA
1 GAGTTTAGAGATATTTTGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
* * *
46413172 GAGTTTAAGAGA-ATTTTGAAAGGAAATTGAGAGAATTTTTGAAGGACTTTGA
1 GAGTTT-AGAGATATTTTG-AAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
46413224 GAG
1 GAG
46413227 AATTTTTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 11 0.23
52 36 0.77
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (51 bp):
GAGTTTAGAGATATTTTGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
Found at i:46413206 original size:22 final size:22
Alignment explanation
Indices: 46413179--46413247 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 22
46413169 CGAGAGTTTA
46413179 AGAGAA-TTTTGAAAGGAAATTG
1 AGAGAATTTTTG-AAGGAAATTG
**
46413201 AGAGAATTTTTGAAGGACTTTG
1 AGAGAATTTTTGAAGGAAATTG
*
46413223 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
46413245 AGA
1 AGA
46413248 TAGGATTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
22 36 0.88
23 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.26, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:46416220 original size:21 final size:21
Alignment explanation
Indices: 46416194--46416254 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
46416184 AGTGTCAAAT
46416194 TTTTTAAATTAGGGTTATT-GG
1 TTTTTAAATTAGGGTT-TTGGG
**
46416215 TTTTTAGGGTTAGGGTTTTGGG
1 TTTTTA-AATTAGGGTTTTGGG
* *
46416237 TATTTAAAGTAGGGTTTT
1 TTTTTAAATTAGGGTTTT
46416255 TTTAGTTTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.51
Consensus pattern (21 bp):
TTTTTAAATTAGGGTTTTGGG
Found at i:46426562 original size:17 final size:17
Alignment explanation
Indices: 46426540--46426577 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
46426530 AACATTGAAA
46426540 AAAAAAATA-ATTAACTC
1 AAAAAAATATA-TAACTC
46426557 AAAAAAATATATAACTC
1 AAAAAAATATATAACTC
46426574 AAAA
1 AAAA
46426578 CATGCATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAAATATATAACTC
Found at i:46429243 original size:38 final size:38
Alignment explanation
Indices: 46429192--46429268 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
46429182 GCCAAACTAG
*
46429192 CCATCTTCCCAATTGAAATTGTAGACGACATAATAATC
1 CCATCTCCCCAATTGAAATTGTAGACGACATAATAATC
* *
46429230 CCATCTCCCCAATTGGAATTGTGGACGACATAATAATC
1 CCATCTCCCCAATTGAAATTGTAGACGACATAATAATC
46429268 C
1 C
46429269 TTCTCAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (38 bp):
CCATCTCCCCAATTGAAATTGTAGACGACATAATAATC
Found at i:46434446 original size:24 final size:24
Alignment explanation
Indices: 46434399--46434446 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
46434389 TAAGAATTTG
* *
46434399 AAAAATATATTATAAAATGTAATA
1 AAAAATAAATTATAAAATGAAATA
46434423 AAAAATAAATTATATAAAT-AAATA
1 AAAAATAAATTATA-AAATGAAATA
46434447 TAAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAATAAATTATAAAATGAAATA
Found at i:46436868 original size:9 final size:9
Alignment explanation
Indices: 46436854--46436886 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
46436844 GATTTAATTC
46436854 TTTTTTTTG
1 TTTTTTTTG
*
46436863 TTTTTTTTA
1 TTTTTTTTG
46436872 TTTTTTTTG
1 TTTTTTTTG
46436881 TTTTTT
1 TTTTTT
46436887 CATTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:46441301 original size:18 final size:17
Alignment explanation
Indices: 46441275--46441308 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
46441265 GTTACTCTTG
46441275 TAAAATATTAAATTAAAA
1 TAAAATATT-AATTAAAA
*
46441293 TAAATTATTAATTAAA
1 TAAAATATTAATTAAA
46441309 TTCCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATATTAATTAAAA
Found at i:46441611 original size:18 final size:20
Alignment explanation
Indices: 46441588--46441625 Score: 53
Period size: 18 Copynumber: 1.9 Consensus size: 20
46441578 TTACATGTAC
46441588 AAATAA-TTGAAA-AATAAA
1 AAATAACTTGAAACAATAAA
46441606 AAATAACCTTGAAACAATAA
1 AAATAA-CTTGAAACAATAA
46441626 TATTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATAACTTGAAACAATAAA
Found at i:46455655 original size:23 final size:22
Alignment explanation
Indices: 46455582--46455655 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
46455572 AATGCCTAAT
*
46455582 AAATCTGAAATAATAATACATAA
1 AAATCT-AAGTAATAATACATAA
* * *
46455605 TAAATTTAAG-AATAAATATATCAT
1 -AAATCTAAGTAAT-AATACAT-AA
46455629 AAATCTAAGCTAATAATACATAA
1 AAATCTAAG-TAATAATACATAA
46455652 AAAT
1 AAAT
46455656 TTATGATGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.08
23 21 0.54
24 12 0.31
25 3 0.08
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATCTAAGTAATAATACATAA
Found at i:46457600 original size:13 final size:13
Alignment explanation
Indices: 46457582--46457606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46457572 AGCTAGATGA
46457582 TTGGTTATTAAAT
1 TTGGTTATTAAAT
46457595 TTGGTTATTAAA
1 TTGGTTATTAAA
46457607 CAGGACTATT
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTGGTTATTAAAT
Found at i:46460751 original size:13 final size:13
Alignment explanation
Indices: 46460733--46460758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46460723 ATTGAATCAA
46460733 GTAATAAAGTGAT
1 GTAATAAAGTGAT
46460746 GTAATAAAGTGAT
1 GTAATAAAGTGAT
46460759 AAGTAAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
GTAATAAAGTGAT
Found at i:46472515 original size:23 final size:23
Alignment explanation
Indices: 46472485--46472531 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
46472475 TTTTGAGAAG
46472485 TATGTTGAGATATGTTATGCATT
1 TATGTTGAGATATGTTATGCATT
46472508 TATGTTGAGATATGTTATGCATT
1 TATGTTGAGATATGTTATGCATT
46472531 T
1 T
46472532 GAACAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.21, T:0.49
Consensus pattern (23 bp):
TATGTTGAGATATGTTATGCATT
Found at i:46479326 original size:14 final size:14
Alignment explanation
Indices: 46479307--46479333 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46479297 AAACCTCTAG
46479307 ACTTGGTTAATTGA
1 ACTTGGTTAATTGA
46479321 ACTTGGTTAATTG
1 ACTTGGTTAATTG
46479334 TTTGTAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (14 bp):
ACTTGGTTAATTGA
Found at i:46488067 original size:51 final size:51
Alignment explanation
Indices: 46487940--46488086 Score: 190
Period size: 50 Copynumber: 2.9 Consensus size: 51
46487930 AGTGAAAGTG
* *
46487940 ATGGTCACGTGTGTAGTACTATGTGCAGACTACTACGTGTACCGAAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGAT
* * * * *
46487991 A-GGTCGCAAGTGTAGTACTATGTGCAGGCTACTACGTGTATCG-GATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGAT
* *
46488040 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGAA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
46488087 CATCATTGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
49 4 0.05
50 38 0.47
51 38 0.47
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGAT
Found at i:46488079 original size:26 final size:26
Alignment explanation
Indices: 46488000--46488079 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
46487990 TAGGTCGCAA
*
46488000 GTGTAGTACTATGTGCAGGCTACTAC
1 GTGTAGTACTATGTGCAGGCTACTAT
* *
46488026 GTGTA-T-CGGATG-GTAATGG-TCAC-AT
1 GTGTAGTAC-TATGTG-CA-GGCT-ACTAT
46488051 GTGTAGTACTATGTGCAGGCTACTAT
1 GTGTAGTACTATGTGCAGGCTACTAT
46488077 GTG
1 GTG
46488080 AACCGAACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 18
0.63 0.08 0.29
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
GTGTAGTACTATGTGCAGGCTACTAT
Found at i:46488137 original size:45 final size:45
Alignment explanation
Indices: 46488081--46488175 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
46488071 TACTATGTGA
* * *
46488081 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTACTATGTGCTGAATCC
*
46488126 ACCGGACATCATTGATTAATAAGGTGGTTACTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTACTATGTGCTGAATCC
46488171 ACCGA
1 ACCGA
46488176 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTACTATGTGCTGAATCC
Found at i:46495238 original size:26 final size:26
Alignment explanation
Indices: 46495209--46495261 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
46495199 CACACAATCT
*
46495209 TGAAAAGAGTATGCTCATATGAGCTG
1 TGAAAAGAGTATGCTCACATGAGCTG
* * *
46495235 TGAAATGGGTCTGCTCACATGAGCTG
1 TGAAAAGAGTATGCTCACATGAGCTG
46495261 T
1 T
46495262 TGGTCAGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (26 bp):
TGAAAAGAGTATGCTCACATGAGCTG
Found at i:46502089 original size:29 final size:29
Alignment explanation
Indices: 46502027--46502126 Score: 175
Period size: 29 Copynumber: 3.5 Consensus size: 29
46502017 AAAAATAAAA
* *
46502027 ATTTACTAAAATATTAC-ACCTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
46502055 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
46502084 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
46502113 ATTTACCAAAATAT
1 ATTTACCAAAATAT
46502127 ATCAAAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 16 0.23
29 53 0.77
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:46502237 original size:27 final size:27
Alignment explanation
Indices: 46502207--46502273 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
46502197 CGCCAATGGT
46502207 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* **
46502234 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
46502261 ATTGGCGGCACCA
1 ATTGGCGGCACCA
46502274 CTCGTATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:46502438 original size:19 final size:21
Alignment explanation
Indices: 46502400--46502438 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
46502390 AATAATTGAT
*
46502400 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
46502421 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
46502439 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:46502502 original size:3 final size:3
Alignment explanation
Indices: 46502484--46502518 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
46502474 AAAATAAAAG
*
46502484 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46502519 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:46502523 original size:3 final size:3
Alignment explanation
Indices: 46502517--46502560 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
46502507 ATTATTATTA
46502517 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
46502561 AGTATGAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:46502815 original size:12 final size:12
Alignment explanation
Indices: 46502798--46502828 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46502788 ATAATTTTAG
46502798 TGTGTATTATTT
1 TGTGTATTATTT
46502810 TGTGTATTATTT
1 TGTGTATTATTT
*
46502822 TGAGTAT
1 TGTGTAT
46502829 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:46509067 original size:19 final size:19
Alignment explanation
Indices: 46509032--46509069 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
46509022 TTTAAACACA
46509032 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
46509051 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
46509070 ACCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:46509149 original size:4 final size:4
Alignment explanation
Indices: 46509132--46509241 Score: 68
Period size: 4 Copynumber: 26.2 Consensus size: 4
46509122 TCTCCTTTCC
*
46509132 CTTT CTTT CCTT CTTT CTTT CTTT -TTT CTTCT CTTCT CCTTT -TCTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTT-T -CTTT CT-TT
*
46509178 C-TT CTTT CTTT CCTTT -TTT CTCTT C-TC CTTT CCTTTT CTTT CTTT
1 CTTT CTTT CTTT -CTTT CTTT CT-TT CTTT CTTT -C-TTT CTTT CTTT
*
46509223 CCTCTC CTTT CTTT CTTT C
1 -CT-TT CTTT CTTT CTTT C
46509242 CCTCCTTCTG
Statistics
Matches: 86, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
3 12 0.14
4 47 0.55
5 20 0.23
6 7 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:46509179 original size:34 final size:35
Alignment explanation
Indices: 46509088--46509223 Score: 103
Period size: 34 Copynumber: 4.0 Consensus size: 35
46509078 TTCCCTTTTT
*
46509088 TTTCTT-TCTTC-CCTCTTCTTCTTT-TTT-TTTC
1 TTTCTTCTCTTCTCCTTTTCTTCTTTCTTTCTTTC
* *
46509119 --TCTTCTCCTT-TCCCTTTCTTTCCTTCTTTCTTTC
1 TTTCTTCT-CTTCTCCTTTTC-TTCTTTCTTTCTTTC
46509153 TTTTTTCTTCTCTTCTCCTTTTCTTC-TTCTTTCTTTCC
1 ---TTTCTTCTCTTCTCCTTTTCTTCTTTCTTTCTTT-C
* *
46509191 TTTTTTCTCTTCTCC-TTTCCT-TTTCTTTCTTTC
1 TTTCTTCTCTTCTCCTTTTCTTCTTTCTTTCTTTC
46509224 CTCTCCTTTC
Statistics
Matches: 85, Mismatches: 6, Indels: 26
0.73 0.05 0.22
Matches are distributed among these distances:
29 4 0.05
30 1 0.01
31 8 0.09
32 5 0.06
33 4 0.05
34 19 0.22
35 14 0.16
37 10 0.12
38 7 0.08
39 13 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (35 bp):
TTTCTTCTCTTCTCCTTTTCTTCTTTCTTTCTTTC
Found at i:46509185 original size:49 final size:49
Alignment explanation
Indices: 46509081--46509203 Score: 140
Period size: 44 Copynumber: 2.7 Consensus size: 49
46509071 CCTTTTTTTC
* *
46509081 CCTTTT-TT-TTCTTTC-TTCCCTC-TTC-TTCTTTTTTTTTCTCTTCT
1 CCTTTTCTTCTTCTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCT
46509125 CC-TTTC--C--CTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCT
1 CCTTTTCTTCTTCTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCT
*
46509169 CCTTTTCTTCTTCTTTCTTTCCTTTTTTCTCTTCT
1 CCTTTTCTTCTTCTTTCTTTCCTTCTTTCT-TTCT
46509204 CCTTTCCTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
41 5 0.08
42 6 0.09
43 6 0.09
44 22 0.34
45 4 0.06
47 1 0.02
49 17 0.26
50 4 0.06
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (49 bp):
CCTTTTCTTCTTCTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCT
Found at i:46509224 original size:34 final size:36
Alignment explanation
Indices: 46509102--46509225 Score: 134
Period size: 35 Copynumber: 3.5 Consensus size: 36
46509092 TTTCTTCCCT
46509102 CTTCTTCTTT-TTT--TTTCTCTTCTCCTT-TCCCTTTC
1 CTTCTTCTTTCTTTCCTTT-TCTTCT-CTTCT-CCTTTC
* * *
46509137 TTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTCCTTTT
1 CTT-CTTCTTTCTTTC-CTTTTCTTCTCTTCTCCTTTC
46509175 CTTCTTCTTTCTTTCCTTTT-TTCTCTTCTCCTTTC
1 CTTCTTCTTTCTTTCCTTTTCTTCTCTTCTCCTTTC
46509210 CTT-TTCTTTCTTTCCT
1 CTTCTTCTTTCTTTCCT
46509226 CTCCTTTCTT
Statistics
Matches: 78, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
34 13 0.17
35 19 0.24
36 11 0.14
37 15 0.19
38 10 0.13
39 7 0.09
40 3 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (36 bp):
CTTCTTCTTTCTTTCCTTTTCTTCTCTTCTCCTTTC
Done.