Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 180 of 208
Found at i:55032775 original size:18 final size:18
Alignment explanation
Indices: 55032737--55032775 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
55032727 GTATATTCCT
*
55032737 AAAACATAAAAAAAAACA
1 AAAACATAAAAAAAAAAA
*
55032755 AAAACA-AAAAAAAGAAA
1 AAAACATAAAAAAAAAAA
55032772 AAAA
1 AAAA
55032776 TAATTTGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAACATAAAAAAAAAAA
Found at i:55037666 original size:42 final size:39
Alignment explanation
Indices: 55037585--55037667 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
55037575 ATTTTAACGC
* * * *
55037585 AAATATTAACAATGAATGAAAAATAAAAGATAAATAAAT
1 AAATAATAACAATGAATAAAAAATAAAAAATAAAAAAAT
*
55037624 AAATAATATCAATGAATAACAACAATAAAACAATAAAAAAAT
1 AAATAATAACAATGAATAA-AA-AATAAAA-AATAAAAAAAT
55037666 AA
1 AA
55037668 CAAAGCCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 16 0.44
40 2 0.06
41 7 0.19
42 11 0.31
ACGTcount: A:0.69, C:0.06, G:0.05, T:0.20
Consensus pattern (39 bp):
AAATAATAACAATGAATAAAAAATAAAAAATAAAAAAAT
Found at i:55051617 original size:27 final size:27
Alignment explanation
Indices: 55051574--55051658 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 27
55051564 ATAAACATAT
* * *
55051574 ATAGAAAAATATTTTAATTTA-TGAAAA
1 ATAGAAAATTATTTAAAATTACT-AAAA
55051601 ATTAGAAAATTATTTAAAATTACTAAAA
1 A-TAGAAAATTATTTAAAATTACTAAAA
55051629 ATAGAAAAGTTATTATAAAA-TA-TAAAA
1 ATAGAAAA-TTATT-TAAAATTACTAAAA
55051656 ATA
1 ATA
55051659 TATAGAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 16 0.31
28 29 0.57
29 6 0.12
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (27 bp):
ATAGAAAATTATTTAAAATTACTAAAA
Found at i:55051925 original size:19 final size:19
Alignment explanation
Indices: 55051884--55051933 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
55051874 AAAATTTTGG
*
55051884 AAAATATTAAAAAATTAAA
1 AAAATATAAAAAAATTAAA
*
55051903 AAAATATAAAAAAATTATTA
1 AAAATATAAAAAAATTA-AA
*
55051923 AAAGTATAAAA
1 AAAATATAAAA
55051934 GCCTAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATATAAAAAAATTAAA
Found at i:55054599 original size:2 final size:2
Alignment explanation
Indices: 55054594--55054629 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
55054584 TAATCACCGA
55054594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55054630 GAAAAACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55054770 original size:27 final size:26
Alignment explanation
Indices: 55054731--55054787 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
55054721 TTTTTCTAAT
55054731 TTTTTTATAAATTTTAAATATCTTTCTA
1 TTTTTTATAAATTTTAAATAT-TTT-TA
*
55054759 TTTTTTAT-AATTTTGAATATTTTTA
1 TTTTTTATAAATTTTAAATATTTTTA
55054784 TTTT
1 TTTT
55054788 CTTTTCTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 11 0.39
28 8 0.29
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTTTATAAATTTTAAATATTTTTA
Found at i:55063617 original size:44 final size:45
Alignment explanation
Indices: 55063559--55063651 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
55063549 TACAACATCT
*
55063559 ATTCCATTCAACCAAACACA-AGAATT-CT-ATTACAACTTTATTCC
1 ATTCCATTCAACCAAACA-ATA-AATTACTGATTACAACTCTATTCC
*
55063603 ATTCGATTCAACCAAACAATTAAATTACTGATTACAACTCTATTCC
1 ATTCCATTCAACCAAACAA-TAAATTACTGATTACAACTCTATTCC
55063649 ATT
1 ATT
55063652 ACAGCTCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 3 0.07
46 18 0.42
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (45 bp):
ATTCCATTCAACCAAACAATAAATTACTGATTACAACTCTATTCC
Found at i:55063654 original size:16 final size:16
Alignment explanation
Indices: 55063633--55063684 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
55063623 TAAATTACTG
* *
55063633 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCT
*
55063649 ATTACAGCTCTAATCT
1 ATTACAGCTCTATTCT
*
55063665 ATTACAGCCCTATTCT
1 ATTACAGCTCTATTCT
55063681 ATTA
1 ATTA
55063685 GAGTGAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCT
Found at i:55065024 original size:18 final size:18
Alignment explanation
Indices: 55065001--55065037 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55064991 CGCTTAGGAA
55065001 AAAACGCCGCTAAAGAAC
1 AAAACGCCGCTAAAGAAC
55065019 AAAACGCCGCTAAAGAAC
1 AAAACGCCGCTAAAGAAC
55065037 A
1 A
55065038 TGTTCTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.27, G:0.16, T:0.05
Consensus pattern (18 bp):
AAAACGCCGCTAAAGAAC
Found at i:55065056 original size:60 final size:62
Alignment explanation
Indices: 55064958--55065078 Score: 210
Period size: 60 Copynumber: 2.0 Consensus size: 62
55064948 GTTTTCAAAT
* *
55064958 AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGAAC
1 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAGAAACGCCGCTAAAGAAC
55065019 AAAA-CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAGAAACGCCGCTAAAGAA
1 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAGAAACGCCGCTAAAGAA
55065079 AATGTTCTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 37 0.65
61 20 0.35
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (62 bp):
AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAGAAACGCCGCTAAAGAAC
Found at i:55065077 original size:43 final size:43
Alignment explanation
Indices: 55065020--55065143 Score: 173
Period size: 43 Copynumber: 2.9 Consensus size: 43
55065010 CTAAAGAACA
55065020 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTAGAAAAG
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTA-AAAAG
*
55065063 AAACGCCGCTAAAGAAAATGTTCTTTAGCGGCGCTTTAAAAAG
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTAAAAAG
* *
55065106 AAATGCCGCTAAAG-ACAATGCTCTTTTAGCGGCG-TTTA
1 AAACGCCGCTAAAGAAC-ATGTTC-TTTAGCGGCGCTTTA
55065144 TTCTTAAGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
42 1 0.01
43 60 0.81
44 13 0.18
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTAAAAAG
Found at i:55065558 original size:21 final size:21
Alignment explanation
Indices: 55065501--55065552 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
55065491 TTTGGCCTGC
55065501 TCTGCTTCTCTTGCTGCAGCT
1 TCTGCTTCTCTTGCTGCAGCT
55065522 TCTGCTTCTCTTGCTGCAGCT
1 TCTGCTTCTCTTGCTGCAGCT
55065543 TCTGCTTCTC
1 TCTGCTTCTC
55065553 GCGCTGTCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.04, C:0.35, G:0.17, T:0.44
Consensus pattern (21 bp):
TCTGCTTCTCTTGCTGCAGCT
Found at i:55065567 original size:21 final size:21
Alignment explanation
Indices: 55065500--55065570 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
55065490 TTTTGGCCTG
55065500 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCTCTTGCTGCAGC
*
55065521 TTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCTCTTGCTGCAGC
* **
55065542 TTCTGCTTCTCGCGCTGTC-GC
1 CTCTGCTTCTCTTGCTG-CAGC
55065563 CTCTGCTT
1 CTCTGCTT
55065571 TAAGTTGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 44 0.98
22 1 0.02
ACGTcount: A:0.03, C:0.37, G:0.20, T:0.41
Consensus pattern (21 bp):
CTCTGCTTCTCTTGCTGCAGC
Found at i:55066982 original size:67 final size:67
Alignment explanation
Indices: 55066910--55067048 Score: 253
Period size: 67 Copynumber: 2.1 Consensus size: 67
55066900 TTTGTTGAGA
*
55066910 ATTCATTATATAATGAATTTATTAAACATTCAATCAATTA-ACTAACCAAAATTGATAATTCATT
1 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACA-TAACCAAAATTGATAATTCATT
55066974 GAC
65 GAC
55066977 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
1 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
55067042 AC
66 AC
55067044 ATTCA
1 ATTCA
55067049 ATCAATTAAT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (67 bp):
ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
AC
Found at i:55067129 original size:16 final size:16
Alignment explanation
Indices: 55067108--55067143 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
55067098 ATTAATTGAA
*
55067108 ATAAAATTGTAAATCG
1 ATAAAATTGCAAATCG
55067124 ATAAAATTGCAAATCG
1 ATAAAATTGCAAATCG
55067140 ATAA
1 ATAA
55067144 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGCAAATCG
Found at i:55070036 original size:114 final size:112
Alignment explanation
Indices: 55069797--55070038 Score: 287
Period size: 114 Copynumber: 2.1 Consensus size: 112
55069787 NNGTTTTAAT
* * *
55069797 CAAGCGCCACTAATTCTAATACTCCTAAAGACCAAACTCTGCGTTTTGGTTAAGATGATTTGCGG
1 CAAGCGCCACTAATTCTAATACTCCTAAAAACCAAACTCTGCGTTTTGGTTAAGATGATTGGAGG
* ** *
55069862 CGCATCCGACAAACGCCGCTGATGTTATACTTTAGCGGCGTTTTTTA
66 CGCATCCCACAAACGCCGCTGATACTATACTTTAGCGGCATTTTTTA
55069909 TCAAGCGCCACTAATTCTAATACTCCTAAAAACCAAAACTCTGCGTTTTGGTTAAGAT-ATCTGG
1 -CAAGCGCCACTAATTCTAATACTCCTAAAAACC-AAACTCTGCGTTTTGGTTAAGATGAT-TGG
* * *
55069973 AGGCGCTTCCCACCAAACGCTGCT-ATAACTATCCTTTA-CTGGCATTTTCCTTA
63 AGGCGCATCCCA-CAAACGCCGCTGAT-ACTATACTTTAGC-GGCATTTT--TTA
55070026 -AA-CGCCACTAATT
1 CAAGCGCCACTAATT
55070039 ATAGTATACA
Statistics
Matches: 112, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
113 34 0.30
114 48 0.43
115 27 0.24
117 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (112 bp):
CAAGCGCCACTAATTCTAATACTCCTAAAAACCAAACTCTGCGTTTTGGTTAAGATGATTGGAGG
CGCATCCCACAAACGCCGCTGATACTATACTTTAGCGGCATTTTTTA
Found at i:55070175 original size:116 final size:112
Alignment explanation
Indices: 55070028--55070291 Score: 266
Period size: 114 Copynumber: 2.3 Consensus size: 112
55070018 TTTCCTTAAA
** * *
55070028 CGCCACTAATTATAGTATACATCAAGACCAAAACGGAGCGTTTTGATTACGATATC-TTGCGGCG
1 CGCCACTAATTGCAATATACATCAAGACCAAAACGGA-CGTTTTGATTA--ACATCGTTGCGGCG
* ** * * * *
55070092 TTTAATGC-TATGCGCCGCTAATACTATACATTAGCGGTGTTTTATTTATAAG
63 CTT--CCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTT-TTCATAAG
** *
55070144 CGCCACTAATTGCAATATACATCAAGACC-AAACTCTACGTTTTGGTTAACATCGTTTGCGGCGC
1 CGCCACTAATTGCAATATACATCAAGACCAAAAC-GGACGTTTTGATTAACATCG-TTGCGGCGC
*
55070208 TTCCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTTTTCGTAAG
64 TTCCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTTTTCATAAG
* *
55070257 CGCCAC-AAATGCCAATATACATCAAGACCAGAACG
1 CGCCACTAATTG-CAATATACATCAAGACCAAAACG
55070292 CTGCGTGTTG
Statistics
Matches: 124, Mismatches: 18, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
112 4 0.03
113 34 0.27
114 35 0.28
115 24 0.19
116 27 0.22
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (112 bp):
CGCCACTAATTGCAATATACATCAAGACCAAAACGGACGTTTTGATTAACATCGTTGCGGCGCTT
CCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTTTTCATAAG
Found at i:55071937 original size:2 final size:2
Alignment explanation
Indices: 55071930--55071964 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55071920 AAATCATGTC
55071930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55071965 ACAAGTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55076564 original size:26 final size:26
Alignment explanation
Indices: 55076533--55076590 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
55076523 TTTACCCCAA
* *
55076533 TAAAATTTTGACGATTTTATCCCTGG
1 TAAAATTTTAACGATTTTAGCCCTGG
* * *
55076559 TAAAATTTTAATGATTTTGGCCGTGG
1 TAAAATTTTAACGATTTTAGCCCTGG
55076585 TAAAAT
1 TAAAAT
55076591 GTCGAGAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (26 bp):
TAAAATTTTAACGATTTTAGCCCTGG
Found at i:55079321 original size:13 final size:13
Alignment explanation
Indices: 55079303--55079327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55079293 TAAAAATATT
55079303 AAATTAATATTTA
1 AAATTAATATTTA
55079316 AAATTAATATTT
1 AAATTAATATTT
55079328 TAGTGAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTAATATTTA
Found at i:55079933 original size:13 final size:13
Alignment explanation
Indices: 55079904--55079932 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55079894 TATCTCTTTG
55079904 TTTTCAATTGCTT
1 TTTTCAATTGCTT
55079917 TTTTCAATTG-TT
1 TTTTCAATTGCTT
55079929 TTTT
1 TTTT
55079933 TTTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (13 bp):
TTTTCAATTGCTT
Found at i:55080607 original size:2 final size:2
Alignment explanation
Indices: 55080600--55080638 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55080590 AATTAGCTCT
55080600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55080639 TTACTACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55082743 original size:27 final size:27
Alignment explanation
Indices: 55082704--55082824 Score: 143
Period size: 27 Copynumber: 4.5 Consensus size: 27
55082694 TAGGTTGTGG
* * *
55082704 CTATTTCATAGGCACGACTAGTTGAGC
1 CTATCTCACAGGCGCGACTAGTTGAGC
*
55082731 CTATCTCAAAGGCGCGACTAGTTGAGC
1 CTATCTCACAGGCGCGACTAGTTGAGC
* *
55082758 CTATCTGACAGGCGCAACTAGTTGAGC
1 CTATCTCACAGGCGCGACTAGTTGAGC
* * *
55082785 CTATCTGACAGGCGCTACTAGTTGTGC
1 CTATCTCACAGGCGCGACTAGTTGAGC
* *
55082812 CTAACTCAGAGGC
1 CTATCTCACAGGC
55082825 ACGAATGGTA
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (27 bp):
CTATCTCACAGGCGCGACTAGTTGAGC
Found at i:55085250 original size:16 final size:16
Alignment explanation
Indices: 55085216--55085250 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
55085206 AAAATCAAAT
* *
55085216 AAAATTACATTATATA
1 AAAATTACATTAAAAA
55085232 AAAATTACATTAAAAA
1 AAAATTACATTAAAAA
55085248 AAA
1 AAA
55085251 TCACAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTACATTAAAAA
Found at i:55086200 original size:60 final size:60
Alignment explanation
Indices: 55086107--55086225 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
55086097 ATACTAATCT
* * * *
55086107 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
55086167 AAACACAAAAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
55086226 TAAAAAGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.33
Consensus pattern (60 bp):
AAACACAAAAAGTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:55086237 original size:60 final size:60
Alignment explanation
Indices: 55086119--55086237 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
55086109 ACACAACAAT
* * *
55086119 TTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTACAAACACAAAAAG
1 TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAAACAAAAAG
* *
55086179 TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTATAAAAAGAAAAA
1 TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAAACAAAAA
55086238 AATTACATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (60 bp):
TTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAAACAAAAAG
Found at i:55086410 original size:3 final size:3
Alignment explanation
Indices: 55086404--55086453 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
55086394 CTTTCTTTAT
*
55086404 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TT- TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
55086450 TTC T
1 TTC T
55086454 CCTTTCTCTC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:55086436 original size:14 final size:14
Alignment explanation
Indices: 55086404--55086466 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
55086394 CTTTCTTTAT
55086404 TTCTTCTTCTTCTTC
1 TTCTTCTTCTTC-TC
55086419 TTCTTCTTCTTCTC
1 TTCTTCTTCTTCTC
* *
55086433 TTCTTCTTCTTTTT
1 TTCTTCTTCTTCTC
*
55086447 TTCTTCTCCTT-TC
1 TTCTTCTTCTTCTC
55086460 TCTCTTC
1 T-TCTTC
55086467 CGGTGGATGG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
13 2 0.05
14 29 0.67
15 12 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCTTCTTCTTCTC
Found at i:55096573 original size:20 final size:19
Alignment explanation
Indices: 55096540--55096577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
55096530 GTCTCTCTAG
*
55096540 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATTT
55096559 GCATTGCATTACATGCATT
1 GCATT-CATTACATGCATT
55096578 AAAATCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (19 bp):
GCATTCATTACATGCATTT
Found at i:55097798 original size:44 final size:44
Alignment explanation
Indices: 55097735--55097825 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
55097725 CATCTTTGCG
55097735 ATTATTTTTGAGCCAATGTTTTCATTCTTTACGGATAATTCTAT
1 ATTATTTTTGAGCCAATGTTTTCATTCTTTACGGATAATTCTAT
55097779 ATTATTTTTGAGCCAATGTTTTCATTCTTTACGGATAATTCTAT
1 ATTATTTTTGAGCCAATGTTTTCATTCTTTACGGATAATTCTAT
55097823 ATT
1 ATT
55097826 CTTTCATTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (44 bp):
ATTATTTTTGAGCCAATGTTTTCATTCTTTACGGATAATTCTAT
Found at i:55097828 original size:21 final size:21
Alignment explanation
Indices: 55097758--55097829 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
55097748 CAATGTTTTC
55097758 ATTCTTTACGGATAATTCTAT
1 ATTCTTTACGGATAATTCTAT
* ** ** *
55097779 ATTATTTTTGAGCCAATGT-TTT
1 ATTCTTTACG-GATAAT-TCTAT
55097801 CATTCTTTACGGATAATTCTAT
1 -ATTCTTTACGGATAATTCTAT
55097823 ATTCTTT
1 ATTCTTT
55097830 CATTCTTTTA
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
21 15 0.43
22 12 0.34
23 8 0.23
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (21 bp):
ATTCTTTACGGATAATTCTAT
Found at i:55098535 original size:10 final size:10
Alignment explanation
Indices: 55098520--55098548 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
55098510 AGATACGATT
55098520 AAAAAATCAA
1 AAAAAATCAA
55098530 AAAAAAT-AA
1 AAAAAATCAA
55098539 AAAAAATCAA
1 AAAAAATCAA
55098549 GGTCAAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAATCAA
Found at i:55099495 original size:13 final size:13
Alignment explanation
Indices: 55099477--55099522 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
55099467 CTCTGAGTCA
*
55099477 AAAAATGAGAATG
1 AAAAATGAAAATG
55099490 AAAAATGAAAAATG
1 AAAAATG-AAAATG
55099504 -AAAATGAAAATG
1 AAAAATGAAAATG
55099516 AAAAATG
1 AAAAATG
55099523 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 6 0.20
13 19 0.63
14 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (13 bp):
AAAAATGAAAATG
Found at i:55099498 original size:7 final size:7
Alignment explanation
Indices: 55099477--55099522 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
55099467 CTCTGAGTCA
55099477 AAAAATG
1 AAAAATG
*
55099484 -AGAATG
1 AAAAATG
55099490 AAAAATG
1 AAAAATG
55099497 AAAAATG
1 AAAAATG
55099504 -AAAATG
1 AAAAATG
55099510 -AAAATG
1 AAAAATG
55099516 AAAAATG
1 AAAAATG
55099523 GAGAGGCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 17 0.49
7 18 0.51
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:55099500 original size:6 final size:6
Alignment explanation
Indices: 55099478--55099519 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
55099468 TCTGAGTCAA
*
55099478 AAAATG AGAATG AAAAATG AAAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG -AAAATG -AAAATG AAAATG AAAATG AAAA
55099520 ATGGAGAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 21 0.64
7 12 0.36
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:55101103 original size:44 final size:44
Alignment explanation
Indices: 55101040--55101397 Score: 190
Period size: 44 Copynumber: 7.7 Consensus size: 44
55101030 TAAAGCCAGA
*
55101040 AATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
* * **
55101084 AATCTTATCTCCCTGAGATTACAGCAGAGCGGATT-AAAATA--
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
* * * * *
55101125 AAGGGTTTTATCTCTCTGA-AGTTACAGTAGAGTACATCGCATCAGATTGAAGCCAGA
1 AA---TCTTATCTCCCTGAGA-TTACAG-CG-G---A--G---CAGATTGAAGCTAGT
55101182 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
* * ** **
55101226 AATCCTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AGT
* * * * *
55101270 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGAGA-TTAC---AGCG--GA--G---CAGATTGAAGCTAGT
* * *
55101324 AATCTTATCTCCCTGAGATTACCGCGAAGCCGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
* *
55101368 AATCCTATCTCCCTGAGATTACAGTGGAGC
1 AATCTTATCTCCCTGAGATTACAGCGGAGC
55101398 GAAATTAAAA
Statistics
Matches: 235, Mismatches: 45, Indels: 68
0.68 0.13 0.20
Matches are distributed among these distances:
41 2 0.01
43 9 0.04
44 149 0.63
45 2 0.01
46 1 0.00
47 5 0.02
49 5 0.02
51 4 0.02
52 1 0.00
53 3 0.01
54 45 0.19
55 7 0.03
57 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
Found at i:55101151 original size:142 final size:142
Alignment explanation
Indices: 55100883--55101454 Score: 930
Period size: 142 Copynumber: 4.0 Consensus size: 142
55100873 TGTAAGGAAA
* *
55100883 CAGATTTAAGCCACAAATCCTT-TCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCC
1 CAGATTGAAGCCAGAAAT-CTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCC
* * *
55100947 TATCTCCCTGAGATTACAGTGGAGCTAATTAAAATAAAGGGTCTTATCTCTCTGAAGCTACAGTA
65 TATCTCCCTGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
*
55101012 GAGTAGATCACAT
130 GAGTAGATCGCAT
* * * *
55101025 CATATTAAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCTT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
** * * *
55101090 ATCTCCCTGAGATTACAGCAGAGCGGATTAAAATAAAGGGTTTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
55101155 AGTACATCGCAT
131 AGTAGATCGCAT
55101167 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
55101232 ATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
55101297 AGTAGATCGCAT
131 AGTAGATCGCAT
* * *
55101309 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACCGCGAAGCCGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
55101374 ATCTCCCTGAGATTACAGTGGAGCGAAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
66 ATCTCCCTGAGATTACAGTGGAGCG-AATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
55101439 GAGTAGATCGCAT
130 GAGTAGATCGCAT
55101452 CAG
1 CAG
55101455 GTCTTATCTC
Statistics
Matches: 400, Mismatches: 28, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
141 3 0.01
142 343 0.86
143 54 0.14
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:55101248 original size:98 final size:96
Alignment explanation
Indices: 55101069--55101255 Score: 216
Period size: 98 Copynumber: 1.9 Consensus size: 96
55101059 TACAGCGGAG
* * * **
55101069 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCAGAGCGGATTAAAATAAAGGGTTTT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAATAAA--GTCCT
*
55101134 ATCTCTCTGAAGTTACAGTAGAGTACATCGCAT
64 ATCTCCCTGAAGTTACAGTAGAGTACATCGCAT
* **
55101167 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA-TCC
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATT-AAAATA--AAGTCC
*
55101231 TATCTCCCTG-AGATTACAGTGGAGT
63 TATCTCCCTGAAG-TTACAGTAGAGT
55101256 GGATTAAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
97 2 0.03
98 67 0.89
99 4 0.05
101 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (96 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAATAAAGTCCTAT
CTCCCTGAAGTTACAGTAGAGTACATCGCAT
Found at i:55101584 original size:50 final size:50
Alignment explanation
Indices: 55101530--55101705 Score: 185
Period size: 50 Copynumber: 3.5 Consensus size: 50
55101520 ACCGTGGAAT
* *
55101530 AGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGATATTACAGTTAAAG
1 AGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAAG
* * * * * *
55101580 AGATTAAAGCTACAACAGTGAATCTTATTTCCCAGACAGTGCAG-TAGAG
1 AGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAAG
* *** *
55101629 CA-AGTTAAAGCCACAACGGTAAATCTTGTTTTTTCGACATTGCAGTTAAAA
1 -AGA-TTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAAG
* *
55101680 AGATTAAAGCCACAATGGCGAATCTT
1 AGATTAAAGCCACAACGGTGAATCTT
55101706 ACTTTCCAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
49 5 0.05
50 91 0.91
51 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAGTTAAAG
Found at i:55103095 original size:12 final size:12
Alignment explanation
Indices: 55103058--55103095 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
55103048 TTATTAAACT
*
55103058 TTTATATCATTA
1 TTTATATTATTA
*
55103070 TATATATTATTA
1 TTTATATTATTA
55103082 TTTATATTATTA
1 TTTATATTATTA
55103094 TT
1 TT
55103096 AAACTTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:55103112 original size:41 final size:41
Alignment explanation
Indices: 55103036--55103124 Score: 112
Period size: 41 Copynumber: 2.1 Consensus size: 41
55103026 TTTTTATACA
*
55103036 TATTA-TTATATGTTATTAAACTTTTATATCATTATATATAT
1 TATTATTTATATATTATTAAACTTTTATAT-ATTATATATAT
55103077 TATTATTTATATTATTATTAAACTTTTCAT-T-TTATATATAT
1 TATTATTTATA-TATTATTAAACTTTT-ATATATTATATATAT
55103118 TACTTAT
1 TA-TTAT
55103125 CTAGACTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
41 17 0.40
42 9 0.21
43 15 0.35
44 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (41 bp):
TATTATTTATATATTATTAAACTTTTATATATTATATATAT
Found at i:55109723 original size:21 final size:21
Alignment explanation
Indices: 55109699--55109747 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
55109689 TTATAATTAA
*
55109699 TTTATTTTGTTCGCTAACGTG
1 TTTATTTTGTTCGCTAACATG
55109720 TTTATTTTGTTCGCTAACATG
1 TTTATTTTGTTCGCTAACATG
55109741 TTT-TTTT
1 TTTATTTT
55109748 CTAACACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.59
Consensus pattern (21 bp):
TTTATTTTGTTCGCTAACATG
Found at i:55110158 original size:29 final size:28
Alignment explanation
Indices: 55110110--55110177 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
55110100 AAGCTATAAC
*
55110110 CACATATATATTATAAATAATAAAACCCA
1 CACATATATATTATAAATAACAAAA-CCA
** *
55110139 CACATATATATTATGTATAACAGAACCA
1 CACATATATATTATAAATAACAAAACCA
*
55110167 CGCATATATAT
1 CACATATATAT
55110178 GTACTATGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (28 bp):
CACATATATATTATAAATAACAAAACCA
Found at i:55110846 original size:19 final size:20
Alignment explanation
Indices: 55110808--55110847 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
55110798 ATTTTCTTAA
*
55110808 TAATTTAAGAAAAACATAAT
1 TAATTTAAAAAAAACATAAT
55110828 TAATTTAAAAAAAAC-TAAT
1 TAATTTAAAAAAAACATAAT
55110847 T
1 T
55110848 TATCAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
TAATTTAAAAAAAACATAAT
Found at i:55116678 original size:93 final size:92
Alignment explanation
Indices: 55116573--55116763 Score: 239
Period size: 94 Copynumber: 2.0 Consensus size: 92
55116563 TTTAAAAACT
55116573 AAAATATATTTAACATAATGATAAATATAAAAATATATTTT-TT-TCATTATATAA-T-TATTAA
1 AAAATATATTTAACAT-A--AT-AATAT-AAAATATATTTTATTAT-ATTATATAACTATATTAA
*
55116634 TT-TATTTATATAAATAAAGGAGTTATTAATTA
60 TTATATTTATATAAATAAAAGAGTTATTAATTA
* * *
55116666 AAAATATTTTTAACATAATAATATATAATATATTTTATTATATTATATAACTACATATTTATTAT
1 AAAATATATTTAACATAATAATATAAAATATATTTTATTATATTATATAACT--ATATTAATTAT
55116731 ATTTATATAAATAAAAGAGTTATTAATTA
64 ATTTATATAAATAAAAGAGTTATTAATTA
55116760 AAAA
1 AAAA
55116764 GATGAGTTAA
Statistics
Matches: 87, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
88 11 0.13
89 16 0.18
90 4 0.05
92 1 0.01
93 22 0.25
94 33 0.38
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (92 bp):
AAAATATATTTAACATAATAATATAAAATATATTTTATTATATTATATAACTATATTAATTATAT
TTATATAAATAAAAGAGTTATTAATTA
Found at i:55116713 original size:24 final size:25
Alignment explanation
Indices: 55116686--55116740 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
55116676 TAACATAATA
*
55116686 ATATATAATATAT-TTTATTATATT
1 ATATATAATACATATTTATTATATT
*
55116710 ATATA-ACTACATATTTATTATATT
1 ATATATAATACATATTTATTATATT
55116734 -TATATAA
1 ATATATAA
55116741 ATAAAAGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
ATATATAATACATATTTATTATATT
Found at i:55127477 original size:13 final size:13
Alignment explanation
Indices: 55127459--55127485 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55127449 TCGTGAGAAA
55127459 GCGAGCTCGACTT
1 GCGAGCTCGACTT
55127472 GCGAGCTCGACTT
1 GCGAGCTCGACTT
55127485 G
1 G
55127486 TGAACCGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (13 bp):
GCGAGCTCGACTT
Found at i:55133221 original size:31 final size:30
Alignment explanation
Indices: 55133164--55133223 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
55133154 ACATGCACTA
*
55133164 TTTTTTATCAGTTTGGTCATTGTACTTTAC
1 TTTTTTATCAGTTTGGTCATTATACTTTAC
*
55133194 TTTTGTTATCAGTTTGG-CCTCTATACTTTA
1 TTTT-TTATCAGTTTGGTCAT-TATACTTTA
55133224 ATTATGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.55
Consensus pattern (30 bp):
TTTTTTATCAGTTTGGTCATTATACTTTAC
Found at i:55137945 original size:20 final size:20
Alignment explanation
Indices: 55137907--55137960 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
55137897 AAAATTGATC
*
55137907 TTTTGATAAAAATTCT-AAAA
1 TTTT-ATAAAAATACTAAAAA
55137927 TTTTATAAAAATACATAAAAA
1 TTTTATAAAAATAC-TAAAAA
*
55137948 TTATTAAAAAAAT
1 TT-TTATAAAAAT
55137961 GGTGTTGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 5 0.17
21 6 0.21
22 9 0.31
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
TTTTATAAAAATACTAAAAA
Found at i:55140218 original size:58 final size:57
Alignment explanation
Indices: 55140091--55140229 Score: 163
Period size: 57 Copynumber: 2.4 Consensus size: 57
55140081 TGGTACATAG
* * * * * *
55140091 CGTAAGACCATGGATGAAAGACGTCATGACAACATGGTATAAGGTAAAGGTATATGG
1 CGTAAGACCATAGATGAAAGACGCCATGACAACATGGTATAAAGTAAAGGTAAACGA
* * **
55140148 CATAAGACCATAGATGAAAGACGCCATGGCGGCAAT-GTATAAAGTATAAGGTAAACGA
1 CGTAAGACCATAGATGAAAGACGCCATGACAAC-ATGGTATAAAGTA-AAGGTAAACGA
55140206 CGTAAGACCATAGATGAAAGACGC
1 CGTAAGACCATAGATGAAAGACGC
55140230 TTTGACAGCT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 36 0.52
58 33 0.48
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (57 bp):
CGTAAGACCATAGATGAAAGACGCCATGACAACATGGTATAAAGTAAAGGTAAACGA
Found at i:55140455 original size:29 final size:29
Alignment explanation
Indices: 55140397--55140455 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
55140387 AAGTCTGTTT
* * *
55140397 GGACATTAAACACAAGGTAAGTTTGCTGG
1 GGACAGTAAACACAAGGTAAGTCTGATGG
*
55140426 GGACAGTAAACACGAGGTAAGTCTGATGG
1 GGACAGTAAACACAAGGTAAGTCTGATGG
55140455 G
1 G
55140456 ATGCAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (29 bp):
GGACAGTAAACACAAGGTAAGTCTGATGG
Found at i:55144694 original size:9 final size:9
Alignment explanation
Indices: 55144679--55144709 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55144669 TCAGTACATG
55144679 CATTATTAT
1 CATTATTAT
*
55144688 TATTATTAT
1 CATTATTAT
55144697 CATTATTAT
1 CATTATTAT
55144706 CATT
1 CATT
55144710 TTTTCAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (9 bp):
CATTATTAT
Found at i:55161610 original size:20 final size:19
Alignment explanation
Indices: 55161563--55161612 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
55161553 CAAGATAAAC
55161563 ATTAAATT-A-AATTTAAT
1 ATTAAATTAATAATTTAAT
55161580 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
55161600 ATTAAATTAATAA
1 ATTAAATTAATAA
55161613 AATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 3 0.11
20 17 0.61
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:55163191 original size:45 final size:45
Alignment explanation
Indices: 55163108--55163207 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
55163098 TAACTGTAGC
* *
55163108 AGTAACAGTAACAGTATTCAACACATAAAGTGCTGAATCTGTAAT
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAAT
* * * *
55163153 AGTAACGGTAACAGTTTTTAACACACAAAGTG-TCGAATCGGTAAC
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCT-GAATCGGTAAT
*
55163198 AATAACAGTA
1 AGTAACAGTA
55163208 GTCGGCATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAAT
Found at i:55164445 original size:30 final size:29
Alignment explanation
Indices: 55164411--55164467 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
55164401 TTATCAAATA
*
55164411 AATAAA-ATCTTTTAATATAATAATTTAATT
1 AATAAATATATTTTAAT-TAA-AATTTAATT
*
55164441 AATAAATATATTTTACTTAAAATTTAA
1 AATAAATATATTTTAATTAAAATTTAA
55164468 GAAAATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
AATAAATATATTTTAATTAAAATTTAATT
Found at i:55164591 original size:17 final size:16
Alignment explanation
Indices: 55164560--55164603 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
55164550 GATTTATTTA
55164560 ATAATATAATATCATT
1 ATAATATAATATCATT
*
55164576 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
55164593 AATTATATAAT
1 -ATAATATAAT
55164604 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:55166413 original size:27 final size:26
Alignment explanation
Indices: 55166389--55166477 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 26
55166379 GATTACCCTG
55166389 TGTTTACTGTCCCTGTAGACTACCCCA
1 TGTTTACTGTCCC-GTAGACTACCCCA
* *
55166416 TGTTTGCTGTCCCGATGGACTACCCCA
1 TGTTTACTGTCCCG-TAGACTACCCCA
* * **
55166443 TGTTTATTGTCCCAGCAGACTATTCCA
1 TGTTTACTGTCCC-GTAGACTACCCCA
55166470 TGTTTACT
1 TGTTTACT
55166478 ATCTTGACAC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.02
27 49 0.96
28 1 0.02
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (26 bp):
TGTTTACTGTCCCGTAGACTACCCCA
Found at i:55173047 original size:105 final size:105
Alignment explanation
Indices: 55172865--55173072 Score: 373
Period size: 105 Copynumber: 2.0 Consensus size: 105
55172855 ACATTACCCG
55172865 GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACTTGAATTAAACAATTTATTCACCTAAT
1 GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACTTGAATTAAACAATTTATTCACCTAAT
*
55172930 ATCTTGATCCGTAGAAATCCTTAAATTATGCTAATATCCA
66 ATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATCCA
* *
55172970 GGAAAGAATCTGCCTAGACTGCATCTTTCATTATCAA-TCTGAATTAAACAATTTATTCACCTAA
1 GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACT-TGAATTAAACAATTTATTCACCTAA
55173034 TATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATC
65 TATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATC
55173073 TCTCTTCAAG
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 1 0.01
105 98 0.99
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (105 bp):
GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACTTGAATTAAACAATTTATTCACCTAAT
ATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATCCA
Found at i:55175997 original size:37 final size:37
Alignment explanation
Indices: 55175956--55176141 Score: 309
Period size: 37 Copynumber: 5.0 Consensus size: 37
55175946 GCTGAAGCTA
* *
55175956 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55175993 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
55176030 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55176067 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55176104 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
55176141 C
1 C
55176142 TAAAACTACC
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 142 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:55182660 original size:37 final size:37
Alignment explanation
Indices: 55182619--55182804 Score: 309
Period size: 37 Copynumber: 5.0 Consensus size: 37
55182609 GCTGAAGCTA
* *
55182619 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55182656 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
55182693 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55182730 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55182767 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
55182804 C
1 C
55182805 TAAAACTACC
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 142 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:55184474 original size:21 final size:21
Alignment explanation
Indices: 55184450--55184497 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
55184440 GTCTTATATG
*
55184450 CTTAATGAATATTTAATTAAT
1 CTTAATGAATATTTAATTAAA
* ** *
55184471 CTTATTTTATTTTTAATTAAA
1 CTTAATGAATATTTAATTAAA
55184492 CTTAAT
1 CTTAAT
55184498 TAGATTAATG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (21 bp):
CTTAATGAATATTTAATTAAA
Found at i:55189690 original size:25 final size:25
Alignment explanation
Indices: 55189623--55189702 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
55189613 AGCTGTAAAT
*
55189623 GGTAAGCTCATACAAGCTGAATATC
1 GGTAAGCTCATGCAAGCTGAATATC
* *
55189648 AGTAAGCTCATGCGAGCTGAATATC
1 GGTAAGCTCATGCAAGCTGAATATC
*
55189673 GGTAAGCTC-TCTCAAGCTGAGA-ATC
1 GGTAAGCTCAT-GCAAGCTGA-ATATC
55189698 GGTAA
1 GGTAA
55189703 CCCTAATAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.02
25 45 0.96
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCATGCAAGCTGAATATC
Found at i:55196377 original size:17 final size:18
Alignment explanation
Indices: 55196357--55196394 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
55196347 TGGCATGCCA
55196357 ATTGTATTAAAAT-ATTT
1 ATTGTATTAAAATAATTT
*
55196374 ATTGTATTAAATTAATTT
1 ATTGTATTAAAATAATTT
55196392 ATT
1 ATT
55196395 AATAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTGTATTAAAATAATTT
Found at i:55204165 original size:28 final size:29
Alignment explanation
Indices: 55204110--55204165 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
55204100 TGACTGAACT
55204110 GAATTAATTCAATTAACCGGTCGGTTAACC
1 GAATTAATTCAATTAA-CGGTCGGTTAACC
* *
55204140 GAATTAATTCGATTGA-GGTCGGTTAA
1 GAATTAATTCAATTAACGGTCGGTTAA
55204166 TAATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
30 14 0.58
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (29 bp):
GAATTAATTCAATTAACGGTCGGTTAACC
Found at i:55209868 original size:4 final size:4
Alignment explanation
Indices: 55209859--55209897 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
55209849 ATAACTTGAG
*
55209859 TATT TATT TATT TATT TATT T-TT CATTT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TA-TT TATT TATT TAT
55209898 GTACAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 26 0.84
5 3 0.10
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:55211443 original size:17 final size:17
Alignment explanation
Indices: 55211421--55211474 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
55211411 TAGATACCCC
55211421 ATATATCGATGCCCCAT
1 ATATATCGATGCCCCAT
** * *
55211438 ATATATAAAGGTCCCAT
1 ATATATCGATGCCCCAT
*
55211455 A-AAATCGATGCCCCAT
1 ATATATCGATGCCCCAT
55211471 ATAT
1 ATAT
55211475 CAAATATTTC
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (17 bp):
ATATATCGATGCCCCAT
Found at i:55216170 original size:16 final size:17
Alignment explanation
Indices: 55216146--55216184 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
55216136 AATAAACAAT
*
55216146 TAAAATAAATT-GGAAA
1 TAAATTAAATTGGGAAA
55216162 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
55216179 TAAATT
1 TAAATT
55216185 TAGATTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:55216579 original size:201 final size:201
Alignment explanation
Indices: 55216234--55216637 Score: 763
Period size: 201 Copynumber: 2.0 Consensus size: 201
55216224 CTCGGTGGAT
*
55216234 CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTGTAACAG
1 CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
55216299 TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
66 TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
*
55216364 CCTTATCGATTATCTAATTGAGATACACACGTTCTCGATTCAAGATTCCAGCAGTCTTGCGCTCT
131 CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTCAAGATTCCAGCAGTCTTGCGCTCT
55216429 AAAGAA
196 AAAGAA
*
55216435 CCCAGATTTAGAATCAATCCTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
1 CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
*
55216500 TTAAGAACGTCTTAACCGCCCATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
66 TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
*
55216565 CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTTAAGATTCCAGCAGTCTTGCGCTCT
131 CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTCAAGATTCCAGCAGTCTTGCGCTCT
55216630 AAAGAA
196 AAAGAA
55216636 CC
1 CC
55216638 GAACTCGAAT
Statistics
Matches: 198, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 198 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (201 bp):
CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTCAAGATTCCAGCAGTCTTGCGCTCT
AAAGAA
Found at i:55223077 original size:16 final size:17
Alignment explanation
Indices: 55223056--55223093 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
55223046 ATAATTTTTT
*
55223056 AAAAAATAATTT-TACA
1 AAAAAATAATTTGAACA
*
55223072 AAAAAATTATTTGAACA
1 AAAAAATAATTTGAACA
55223089 AAAAA
1 AAAAA
55223094 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAAATAATTTGAACA
Found at i:55225343 original size:21 final size:19
Alignment explanation
Indices: 55225296--55225346 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
55225286 AAAAAAATTA
*
55225296 TTTACTTTTAAAGGATTTT
1 TTTATTTTTAAAGGATTTT
*
55225315 TTTAATTTTTGAAATGATATTT
1 TTT-ATTTTT-AAAGGAT-TTT
55225337 TTTATTTTTA
1 TTTATTTTTA
55225347 TGACACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.11
20 6 0.22
21 12 0.44
22 6 0.22
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTATTTTTAAAGGATTTT
Found at i:55225647 original size:16 final size:16
Alignment explanation
Indices: 55225626--55225656 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55225616 CATGTTAAAG
55225626 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
55225642 CATATATATTTGAAA
1 CATATAAATTTGAAA
55225657 ACTTTTTTGA
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:55225807 original size:10 final size:9
Alignment explanation
Indices: 55225776--55225817 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
55225766 TTTAACTTTC
55225776 TTTATATATT
1 TTTATA-ATT
55225786 CTTTATAATT
1 -TTTATAATT
55225796 TTT-TAAATT
1 TTTAT-AATT
55225805 TTTATAATT
1 TTTATAATT
55225814 TTTA
1 TTTA
55225818 AAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 18 0.62
10 4 0.14
11 6 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATAATT
Found at i:55225810 original size:18 final size:18
Alignment explanation
Indices: 55225787--55225909 Score: 61
Period size: 17 Copynumber: 6.6 Consensus size: 18
55225777 TTATATATTC
55225787 TTTATAATTTTTTAAATT
1 TTTATAATTTTTTAAATT
**
55225805 TTTATAA-TTTTTAAAAA
1 TTTATAATTTTTTAAATT
* * **
55225822 TATATAA-ATTTGGAATT
1 TTTATAATTTTTTAAATT
* *
55225839 TTTATAAATATTTTGAATT
1 TTTAT-AATTTTTTAAATT
* *
55225858 TTAAAAATTATTTTGAAATT
1 TTTATAATT-TTTT-AAATT
* * *
55225878 TTGAAAATTATTTTGAATTTT
1 TTTATAATT-TTTT-AA-ATT
55225899 TTTATAATTTT
1 TTTATAATTTT
55225910 GGTTGAGAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
17 23 0.28
18 12 0.15
19 16 0.20
20 22 0.27
21 9 0.11
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTATAATTTTTTAAATT
Found at i:55225879 original size:20 final size:19
Alignment explanation
Indices: 55225838--55225898 Score: 88
Period size: 20 Copynumber: 3.2 Consensus size: 19
55225828 AATTTGGAAT
*
55225838 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
55225856 TTTTAAAAATTATTTTGAAA
1 TTTTAAAAATTATTTTG-AA
*
55225876 TTTTGAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
55225895 TTTT
1 TTTT
55225899 TTTATAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
18 8 0.21
19 13 0.33
20 18 0.46
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:55225899 original size:20 final size:19
Alignment explanation
Indices: 55225829--55225899 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
55225819 AAATATATAA
*
55225829 ATTTGGAATTTTTATAAA-T
1 ATTTTGAATTTTTA-AAATT
*
55225848 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
*
55225867 ATTTTGAAATTTTGAAAATT
1 ATTTTG-AATTTTTAAAATT
55225887 ATTTTGAATTTTT
1 ATTTTGAATTTTT
55225900 TTATAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.07
19 25 0.54
20 18 0.39
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:55229225 original size:30 final size:31
Alignment explanation
Indices: 55229181--55229240 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
55229171 GGGGGTGGGA
*
55229181 TGGGAGAGAAGTAAAAGTTTTAAGGGAAAAG
1 TGGGAGAGAAGTAAAACTTTTAAGGGAAAAG
* **
55229212 TGGGAG-GGAGTAAAACTTTTGGGGGAAAA
1 TGGGAGAGAAGTAAAACTTTTAAGGGAAAA
55229241 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAGAGAAGTAAAACTTTTAAGGGAAAAG
Found at i:55229465 original size:193 final size:193
Alignment explanation
Indices: 55229076--55229456 Score: 453
Period size: 193 Copynumber: 2.0 Consensus size: 193
55229066 TGGGGGGGAG
* *
55229076 AATTTTGAGGGAAAGTAAATAGGGGGAGTAAAATTTGAGAGGAAAAATATTAAAAAAAAATTGGG
1 AATTTTGAAGGAAAGTAAATAGGGGAAGTAAAATTTGAGAGGAAAAATATTAAAAAAAAATTGGG
* * * *
55229141 GGATGGGGAGGGATGGGTTTGGGGTAGATGGGGGGTGGGATGGGAGAGAAGTAAAAGTTTTAAGG
66 GGATGGGGA-GAATGGATTTGGGATAGATGGGGGGTGGGAGGGGAGAGAAGTAAAAGTTTTAAGG
* ** *
55229206 GAAAAGTGGGAGGGAGTAAAACTTTTGGGGGAAAATAAAAAATTTTGAGGGTTTTTGAGAGTAA
130 GAAAAGTGGGAAGGAGTAAAACTTTTGGGGGAAAATAAAAAAGATTGAGGGTATTTGAGAGTAA
*
55229270 AATTTT-AAGGAAAGGTAAAT-GGGGAAGTAAAATTTTG-GAGGAAAAATATTAAAAGAAAATT-
1 AATTTTGAAGGAAA-GTAAATAGGGGAAGTAAAA-TTTGAGAGGAAAAATATTAAAAAAAAATTG
** * * *
55229331 TTGG-T-GGGA-AATGGATTTGGGATAGATGGGGGGTTGGGAGGGGAGGGGAGTAAAAGTTTT-G
64 GGGGATGGGGAGAATGGATTTGGGATAGATGGGGGG-TGGGAGGGGAGAGAAGTAAAAGTTTTAA
** * *
55229392 GGGGGAAGT-GGAATGAGTAAAAGTTTTGGGGGAAAAGTAAAAAAGATTG-GGG-ATTTGAG-GT
128 GGGAAAAGTGGGAAGGAGTAAAACTTTTGGGGGAAAA-TAAAAAAGATTGAGGGTATTTGAGAGT
55229453 AA
192 AA
55229455 AA
1 AA
55229457 ATGTAAAATA
Statistics
Matches: 163, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
185 6 0.04
186 6 0.04
187 27 0.17
188 38 0.23
189 23 0.14
190 4 0.02
191 1 0.01
192 2 0.01
193 40 0.25
194 16 0.10
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (193 bp):
AATTTTGAAGGAAAGTAAATAGGGGAAGTAAAATTTGAGAGGAAAAATATTAAAAAAAAATTGGG
GGATGGGGAGAATGGATTTGGGATAGATGGGGGGTGGGAGGGGAGAGAAGTAAAAGTTTTAAGGG
AAAAGTGGGAAGGAGTAAAACTTTTGGGGGAAAATAAAAAAGATTGAGGGTATTTGAGAGTAA
Found at i:55229504 original size:19 final size:17
Alignment explanation
Indices: 55229478--55229514 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
55229468 TATAGTTTGA
55229478 TATTTAGTTTATTCAAAT
1 TATTTAG-TTATTCAAAT
55229496 TATTCTAGTTATTCAAAT
1 TATT-TAGTTATTCAAAT
55229514 T
1 T
55229515 TGAAAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (17 bp):
TATTTAGTTATTCAAAT
Found at i:55230303 original size:2 final size:2
Alignment explanation
Indices: 55230296--55230330 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55230286 CTAGGATGCT
55230296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55230331 GAATTTGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55232728 original size:21 final size:21
Alignment explanation
Indices: 55232698--55232742 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
55232688 TACACCAAAA
*
55232698 TAGGCTTTTAACGGCGTTTTT
1 TAGGCCTTTAACGGCGTTTTT
*
55232719 TAGGCCTTTAGCGGCGTTTTT
1 TAGGCCTTTAACGGCGTTTTT
55232740 TAG
1 TAG
55232743 TGCCGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.44
Consensus pattern (21 bp):
TAGGCCTTTAACGGCGTTTTT
Found at i:55232890 original size:43 final size:43
Alignment explanation
Indices: 55232846--55233081 Score: 312
Period size: 43 Copynumber: 5.5 Consensus size: 43
55232836 GCGACACTAT
* *
55232846 AGAACATGACCTTTAGCGGCGC-TTTACCCACAAACGCCGCTAT
1 AGAACATGACCTTTAGCGGCGCTTTTA-TCACAAACGCCGCTAA
* * **** * *
55232889 AGAACATGATCTTTAGCGGTGCTTCGCCCAAAAACGCAGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
* *
55232932 AGATCACGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
* * *
55232975 AGATCACGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
55233018 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
*
55233061 AGATCATGACCTTTAGCGGCG
1 AGAACATGACCTTTAGCGGCG
55233082 TTTATGAAAA
Statistics
Matches: 169, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 168 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
Found at i:55234290 original size:191 final size:192
Alignment explanation
Indices: 55234071--55234492 Score: 487
Period size: 192 Copynumber: 2.2 Consensus size: 192
55234061 AAAGGTCCCA
* * * * *
55234071 AACTTGGTCTATTATGTTCATTAACATCATCA-AAAATCATCAATTACATCCTAATAACAATTTC
1 AACTTAGTCTATTATATTCATTAACATCAACATAAAAACATCAATTACATCCTAATAACAATTCC
* * * * *
55234135 AACTCCAAAGTT-GACTAAAGAAGCTTTGCAGGATATGA-AAACACAAGTGCATTTCCATTCAAG
66 AACCCCAAAGTTCAACTAAA-AAGCATTGCAGGATA-CACAAACACAAATGCATTTCCATTCAAG
** * * * *
55234198 TAAATTGTTGTGTTGTAATCACGAAG-TTCAAATGAAAACCATGACTTGAACCCATAAAAAATTC
129 T-AATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATTC
* *
55234262 AACTTAGTCTATTGTATTCATTAACATCAACATAAAAACATCAATTACTTCCTAATAACAATTCC
1 AACTTAGTCTATTATATTCATTAACATCAACATAAAAACATCAATTACATCCTAATAACAATTCC
* * **
55234327 AACCCCAAATTTCAATTAAAAAGCATTGCAGGATACACAAATGCAAATGCATTTCCATTCAAGTA
66 AACCCCAAAGTTCAACTAAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTCAAGTA
* * * *
55234392 ATAATAGTGTTTTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATTATAGATTAC
131 ATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATT-C
** *
55234455 AAACTTAGTC-A-TATGCTCATTAACATGAACATTAAAAA
1 -AACTTAGTCTATTATATTCATTAACATCAACA-TAAAAA
55234493 AACAATTCTA
Statistics
Matches: 194, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
191 48 0.25
192 124 0.64
193 13 0.07
194 9 0.05
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (192 bp):
AACTTAGTCTATTATATTCATTAACATCAACATAAAAACATCAATTACATCCTAATAACAATTCC
AACCCCAAAGTTCAACTAAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTCAAGTA
ATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATTC
Found at i:55236912 original size:21 final size:21
Alignment explanation
Indices: 55236895--55236935 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55236885 TCACTAACTC
55236895 TTAACCTCTAACCCCTAACCT
1 TTAACCTCTAACCCCTAACCT
*
55236916 TTAACCTCTAACCCTTAACC
1 TTAACCTCTAACCCCTAACC
55236936 CCAAACCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.41, G:0.00, T:0.29
Consensus pattern (21 bp):
TTAACCTCTAACCCCTAACCT
Found at i:55236913 original size:14 final size:14
Alignment explanation
Indices: 55236896--55236968 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
55236886 CACTAACTCT
55236896 TAACCTCTAACCCC
1 TAACCTCTAACCCC
* *
55236910 TAACCTTTAACCTC
1 TAACCTCTAACCCC
55236924 TAACC-CTTAACCCC
1 TAACCTC-TAACCCC
* * *
55236938 AAACCCCTAACCCA
1 TAACCTCTAACCCC
*
55236952 TAA-CTACTAGCCCC
1 TAACCT-CTAACCCC
55236966 TAA
1 TAA
55236969 ACCTTATTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
13 1 0.02
14 44 0.96
15 1 0.02
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (14 bp):
TAACCTCTAACCCC
Found at i:55236942 original size:21 final size:21
Alignment explanation
Indices: 55236897--55236955 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
55236887 ACTAACTCTT
* ***
55236897 AACCTCTAACCCCTAACCTTT
1 AACCTCTAACCCATAACCCCA
*
55236918 AACCTCTAACCCTTAACCCCA
1 AACCTCTAACCCATAACCCCA
*
55236939 AACCCCTAACCCATAAC
1 AACCTCTAACCCATAAC
55236956 TACTAGCCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCTCTAACCCATAACCCCA
Found at i:55237126 original size:81 final size:81
Alignment explanation
Indices: 55236962--55237130 Score: 220
Period size: 80 Copynumber: 2.1 Consensus size: 81
55236952 TAACTACTAG
* *
55236962 CCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACTTAACCCG
1 CCCCTAAACCTTATTTAATATATAAATTAAAAACAATAATTAATCTAAACCCTAAACCTAACCCG
*
55237027 AACCCCTAACCCATAA
66 AACCACTAACCCATAA
*
55237043 CCCCTAAACCTTATTT-A-ATATAGATTAAAACACAATAATTAATCTAAACCCTAAACCCTAA-C
1 CCCCTAAACCTTATTTAATATATAAATTAAAA-ACAATAATTAATCTAAACCCTAAA-CCTAACC
* *
55237105 CTAA-CACTAAATCCATAA
64 CGAACCACT-AACCCATAA
*
55237123 ACCCTAAA
1 CCCCTAAA
55237131 TCCCTAACTC
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
79 15 0.19
80 43 0.55
81 20 0.26
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (81 bp):
CCCCTAAACCTTATTTAATATATAAATTAAAAACAATAATTAATCTAAACCCTAAACCTAACCCG
AACCACTAACCCATAA
Found at i:55237565 original size:41 final size:41
Alignment explanation
Indices: 55237503--55237778 Score: 391
Period size: 41 Copynumber: 6.7 Consensus size: 41
55237493 AAATATTTTT
* *
55237503 GCGGCGCTT-TTATAAAAACGCCGCTAAAAGC-CCGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCT-AAAGCTCTGAGCATTA
*
55237544 GCGGTGCTT-TCTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTCT-TCAAAAACGCCGCTAAAGCTCTGAGCATTA
* * *
55237585 GCGACGCTT-TTATAAAAACGCCGCTAAAAGC-CCGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCT-AAAGCTCTGAGCATTA
55237626 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
*
55237667 GCGGCGCTTCTTCAAAAACGCCACTAAAGCTCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
*
55237708 GCGGCGCTTCATCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
*
55237749 GCGGCGCTTCTTCAAAAGCGCCGCTAAAGC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGC
55237779 CCCGAAAGGT
Statistics
Matches: 214, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
40 11 0.05
41 195 0.91
42 8 0.04
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
Found at i:55243515 original size:67 final size:67
Alignment explanation
Indices: 55243407--55243540 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
55243397 TATATGAGAT
* * *
55243407 TGGGACATTTGATGTATTGAAAATTGAAATGAGACTCTATTAACTGTTTCGAGCTAAGTCGGATA
1 TGGGACATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAACTGTTTCGAGCTAAGTCAGATA
55243472 TA
66 TA
* * *
55243474 TGGGAGATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAATTGTTTCGGGCTAAGTCAGATA
1 TGGGACATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAACTGTTTCGAGCTAAGTCAGATA
55243539 TA
66 TA
55243541 GATGGCATGC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.34
Consensus pattern (67 bp):
TGGGACATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAACTGTTTCGAGCTAAGTCAGATA
TA
Found at i:55243868 original size:20 final size:19
Alignment explanation
Indices: 55243813--55243860 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
55243803 ATGGCAAAGT
* *
55243813 TGAGAAATG-ATTATGAGA
1 TGAGAAATGAAATATGAAA
55243831 TGAGAAATGAAATATGAAA
1 TGAGAAATGAAATATGAAA
55243850 TGATGAAATGA
1 TGA-GAAATGA
55243861 GATGTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 10 0.38
20 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (19 bp):
TGAGAAATGAAATATGAAA
Found at i:55250309 original size:30 final size:31
Alignment explanation
Indices: 55250273--55250335 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
55250263 TGTGGGTAGT
*
55250273 CCACACGAGCTA-TTTTTTGGGCCGTGTGGA
1 CCACACGAGCTAGCTTTTTGGGCCGTGTGGA
*
55250303 CCACACGAGCTAGCTTTTTGGGCCTTGTGGA
1 CCACACGAGCTAGCTTTTTGGGCCGTGTGGA
55250334 CC
1 CC
55250336 TTTTGGGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (31 bp):
CCACACGAGCTAGCTTTTTGGGCCGTGTGGA
Found at i:55259119 original size:21 final size:21
Alignment explanation
Indices: 55259095--55259143 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
55259085 CCAATCAAGT
* *
55259095 TACCATTTCTGATTCACTCCA
1 TACCATTTCTGACTCAATCCA
55259116 TACCATTTCTGACTCAATCCA
1 TACCATTTCTGACTCAATCCA
55259137 TACCATT
1 TACCATT
55259144 CCATATACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.04, T:0.37
Consensus pattern (21 bp):
TACCATTTCTGACTCAATCCA
Found at i:55265510 original size:18 final size:18
Alignment explanation
Indices: 55265473--55265519 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
55265463 TTTAAAATTT
* *
55265473 TGGGCCCATATTCTCATG
1 TGGGCCCACATGCTCATG
*
55265491 TGGGCCCACATGCTCGTG
1 TGGGCCCACATGCTCATG
55265509 T-GGCCCACATG
1 TGGGCCCACATG
55265520 GCCTGGCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.15, C:0.32, G:0.28, T:0.26
Consensus pattern (18 bp):
TGGGCCCACATGCTCATG
Found at i:55266318 original size:6 final size:6
Alignment explanation
Indices: 55266301--55266335 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
55266291 TACCCACTAA
*
55266301 CCACCT CTACCT CCACCT CCACCT CCACCT CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
55266336 ACCTTAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17
Consensus pattern (6 bp):
CCACCT
Found at i:55267798 original size:5 final size:6
Alignment explanation
Indices: 55267775--55267832 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
55267765 AAATATTGTG
* * **
55267775 ATAATT ATAATT ATAATT -TAATTT AAAATT ATTATT -TAAAA ATAATT
1 ATAATT ATAATT ATAATT ATAA-TT ATAATT ATAATT ATAATT ATAATT
55267822 ATAATT -TAATT
1 ATAATT ATAATT
55267833 TTGAAATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
5 10 0.24
6 29 0.71
7 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:55267864 original size:35 final size:34
Alignment explanation
Indices: 55267781--55267865 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 34
55267771 TGTGATAATT
55267781 ATAATTATAATTTAATTTAAAATTATTATTTAAAA
1 ATAATTATAATTTAATTTAAAATTATTA-TTAAAA
*
55267816 ATAATTATAATTTAATTTTGAAATTATTA-TAAAA
1 ATAATTATAATTTAA-TTTAAAATTATTATTAAAA
* *
55267850 ATGATTTATTATTTAA
1 AT-AATTATAATTTAA
55267866 AAAATGGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 7 0.16
35 26 0.58
36 12 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (34 bp):
ATAATTATAATTTAATTTAAAATTATTATTAAAA
Found at i:55278558 original size:18 final size:18
Alignment explanation
Indices: 55278535--55278613 Score: 70
Period size: 18 Copynumber: 4.2 Consensus size: 18
55278525 TTAAAATTAA
55278535 ATAAAAATATTAAAAATT
1 ATAAAAATATTAAAAATT
*
55278553 ATAAAACA-ATTAGAAATTT
1 ATAAAA-ATATTA-AAAATT
* *
55278572 ATAAAAAAATAAAAAATT
1 ATAAAAATATTAAAAATT
* *
55278590 CTAAATATATTATAAAAATT
1 ATAAAAATA-T-TAAAAATT
55278610 ATAA
1 ATAA
55278614 TCAAGTATGT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 22 0.46
19 16 0.33
20 10 0.21
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.32
Consensus pattern (18 bp):
ATAAAAATATTAAAAATT
Found at i:55278588 original size:19 final size:19
Alignment explanation
Indices: 55278535--55278589 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
55278525 TTAAAATTAA
*
55278535 ATAAAAATATTAAAAA-TT
1 ATAAAAAAATTAAAAATTT
* *
55278553 ATAAAACAATTAGAAATTT
1 ATAAAAAAATTAAAAATTT
*
55278572 ATAAAAAAATAAAAAATT
1 ATAAAAAAATTAAAAATT
55278590 CTAAATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAAAATTAAAAATTT
Found at i:55279483 original size:2 final size:2
Alignment explanation
Indices: 55279476--55279506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55279466 TAGTAAGGAC
55279476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55279507 GGACTATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55280686 original size:20 final size:19
Alignment explanation
Indices: 55280640--55280692 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
55280630 ATGCATATTT
55280640 AATTATTTATA-TTTAAGA
1 AATTATTTATATTTTAAGA
* *
55280658 ATATAATTTATTATTTTAATA
1 A-ATTATTTA-TATTTTAAGA
55280679 AATTATTTAATATT
1 AATTATTT-ATATT
55280693 ACAATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.04
19 7 0.25
20 12 0.43
21 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTATTTATATTTTAAGA
Found at i:55280759 original size:12 final size:12
Alignment explanation
Indices: 55280723--55280787 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 12
55280713 AATTAACAAT
55280723 AATAAT-TTTTA
1 AATAATATTTTA
*
55280734 AATAATATTCTA
1 AATAATATTTTA
55280746 AAT-ATATTATTA
1 AATAATATT-TTA
*
55280758 AAAAATA-TTTA
1 AATAATATTTTA
*
55280769 TATTAATATTTT-
1 -AATAATATTTTA
55280781 AATAATA
1 AATAATA
55280788 AATATATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 20 0.47
12 17 0.40
13 6 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
AATAATATTTTA
Found at i:55280782 original size:24 final size:24
Alignment explanation
Indices: 55280723--55280782 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
55280713 AATTAACAAT
*
55280723 AATAAT-TTTTAAATAATATTCTA
1 AATAATATTTTAAAAAATATTCTA
55280746 AAT-ATATTATTAAAAAATATT-TA
1 AATAATATT-TTAAAAAATATTCTA
*
55280769 TATTAATATTTTAA
1 -AATAATATTTTAA
55280783 TAATAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 2 0.06
23 7 0.23
24 17 0.55
25 5 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AATAATATTTTAAAAAATATTCTA
Found at i:55283873 original size:25 final size:26
Alignment explanation
Indices: 55283820--55283869 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
55283810 AAACTTACAT
*
55283820 TTAATTTTATTTTATATTATAATTCA
1 TTAATTTTATTTTATATTATAAATCA
55283846 TTAA-TTTATTTT-TATTCA-AAATCA
1 TTAATTTTATTTTATATT-ATAAATCA
55283870 ATTACCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (26 bp):
TTAATTTTATTTTATATTATAAATCA
Found at i:55287648 original size:2 final size:2
Alignment explanation
Indices: 55287641--55287679 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55287631 GTTTAAAATA
55287641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55287680 CATGAAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55287846 original size:12 final size:13
Alignment explanation
Indices: 55287828--55287869 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
55287818 AGGAAAGATT
55287828 TAATAATAATATA
1 TAATAATAATATA
55287841 -AATAATAACATATA
1 TAATAAT-A-ATATA
55287855 TACATAATAATATA
1 TA-ATAATAATATA
55287869 T
1 T
55287870 TAAAGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.24
13 1 0.04
14 11 0.44
15 2 0.08
16 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:55287861 original size:16 final size:16
Alignment explanation
Indices: 55287836--55287873 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55287826 TTTAATAATA
55287836 ATATAAATAATAACAT
1 ATATAAATAATAACAT
* *
55287852 ATATACATAATAATAT
1 ATATAAATAATAACAT
55287868 AT-TAAA
1 ATATAAA
55287874 GTTGAAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATAATAACAT
Found at i:55288079 original size:18 final size:18
Alignment explanation
Indices: 55288056--55288152 Score: 57
Period size: 18 Copynumber: 5.6 Consensus size: 18
55288046 TGTTAACACT
55288056 TAAAATAATATTATATAA
1 TAAAATAATATTATATAA
**
55288074 TAAAATAAT-GCATATACA
1 TAAAATAATATTATATA-A
55288092 T--AA-AATATTATATAGA
1 TAAAATAATATTATATA-A
*
55288108 T-AAAT-ATATGA-ACTAA
1 TAAAATAATATTATA-TAA
*
55288124 TAATAATAATAATA-ATAA
1 TAA-AATAATATTATATAA
55288142 TAATAATAATA
1 TAA-AATAATA
55288153 ATAATAATGG
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
15 3 0.05
16 12 0.19
17 15 0.24
18 28 0.44
19 5 0.08
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAAATAATATTATATAA
Found at i:55288175 original size:3 final size:3
Alignment explanation
Indices: 55288121--55288160 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
55288111 ATATATGAAC
55288121 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
55288161 GGTAGTAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55292338 original size:23 final size:23
Alignment explanation
Indices: 55292313--55292378 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
55292303 TTTTTTAAAA
55292313 TTTAAAAAATTTAAAAATAATTAT
1 TTTAAAAAATTTAAAAAT-ATTAT
*
55292337 TTTTAAAAA-TTAAAAATATTAT
1 TTTAAAAAATTTAAAAATATTAT
*
55292359 TGTTACAAAATTATAAAAAT
1 T-TTAAAAAATT-TAAAAAT
55292379 TATAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.17
23 14 0.39
24 9 0.25
25 7 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTAAAAAATTTAAAAATATTAT
Found at i:55298798 original size:15 final size:15
Alignment explanation
Indices: 55298778--55298884 Score: 58
Period size: 15 Copynumber: 7.3 Consensus size: 15
55298768 AGGTTGCACA
55298778 TAGGGGTTCACACCT
1 TAGGGGTTCACACCT
*** *
55298793 TAGGGGTTTGTA-CA
1 TAGGGGTTCACACCT
* *
55298807 TATGGGTTCACACTT
1 TAGGGGTTCACACCT
* *
55298822 TAGAGGTTCGCACCT
1 TAGGGGTTCACACCT
** * * *
55298837 TAAAGTTTCTCACAT
1 TAGGGGTTCACACCT
*
55298852 TA-GGGTTCGCACC-
1 TAGGGGTTCACACCT
*
55298865 TAGGGGTTCACACGT
1 TAGGGGTTCACACCT
55298880 TAGGG
1 TAGGG
55298885 TTTGCACCTA
Statistics
Matches: 65, Mismatches: 24, Indels: 6
0.68 0.25 0.06
Matches are distributed among these distances:
13 2 0.03
14 25 0.38
15 38 0.58
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (15 bp):
TAGGGGTTCACACCT
Found at i:55298800 original size:28 final size:28
Alignment explanation
Indices: 55298769--55298911 Score: 92
Period size: 29 Copynumber: 5.0 Consensus size: 28
55298759 ACACATATAA
*
55298769 GGTTGCACATAGGGGTTCACACCTTAGG
1 GGTTGCACATAGGGGTTCACACATTAGG
* * * *
55298797 GGTTTGTACATATGGGTTCACACTTTAGA
1 GG-TTGCACATAGGGGTTCACACATTAGG
* ** * *
55298826 GGTTCGCACCTTAAAGTTTCTCACATTA-G
1 GGTT-GCA-CATAGGGGTTCACACATTAGG
* *
55298855 GGTTCGCACCTAGGGGTTCACACGTTAGG
1 GGTT-GCACATAGGGGTTCACACATTAGG
* * **
55298884 GTTTGCACCTA-GGGTTCGTACATTAGG
1 GGTTGCACATAGGGGTTCACACATTAGG
55298911 G
1 G
55298912 TTCGCATCTA
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
27 14 0.16
28 24 0.27
29 38 0.43
30 13 0.15
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (28 bp):
GGTTGCACATAGGGGTTCACACATTAGG
Found at i:55298873 original size:14 final size:13
Alignment explanation
Indices: 55298852--55298924 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 13
55298842 TTTCTCACAT
55298852 TAGGGTTCGCACC
1 TAGGGTTCGCACC
* *
55298865 TAGGGGTTCACACGT
1 TA-GGGTTCGCAC-C
*
55298880 TAGGGTTTGCACC
1 TAGGGTTCGCACC
* *
55298893 TAGGGTTCGTACAT
1 TAGGGTTCGCAC-C
*
55298907 TAGGGTTCGCATC
1 TAGGGTTCGCACC
55298920 TAGGG
1 TAGGG
55298925 GGTTACACCT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
13 17 0.37
14 27 0.59
15 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.29
Consensus pattern (13 bp):
TAGGGTTCGCACC
Found at i:55301305 original size:18 final size:18
Alignment explanation
Indices: 55301284--55301320 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55301274 TATTGTCTGA
55301284 GGTTCGCA-TACTGTAGGG
1 GGTTCGCACTACT-TAGGG
55301302 GGTTCGCACTACTTAGGG
1 GGTTCGCACTACTTAGGG
55301320 G
1 G
55301321 TCGCAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.27
Consensus pattern (18 bp):
GGTTCGCACTACTTAGGG
Found at i:55302182 original size:43 final size:43
Alignment explanation
Indices: 55302121--55302216 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
55302111 CAGATAAAAA
** *
55302121 GTTTGCAGGCAAACTGCCAGTAAGTTATGTATGAACCACCAGT
1 GTTTGCAGATAAACTGCCAGTAAGTTATGGATGAACCACCAGT
* * * *
55302164 GTTTGCAGATAAATTGCCAGTAAGTTTTGGATGAACCTCTAGT
1 GTTTGCAGATAAACTGCCAGTAAGTTATGGATGAACCACCAGT
55302207 GTTTGCAGAT
1 GTTTGCAGAT
55302217 TATTGAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
GTTTGCAGATAAACTGCCAGTAAGTTATGGATGAACCACCAGT
Found at i:55302385 original size:38 final size:38
Alignment explanation
Indices: 55302303--55302397 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
55302293 GTACAAAAAT
* * *
55302303 AGTAGACATGCTTAACATGTATTTAGTTCAATAGTAGC
1 AGTAGACATGCTTAACATGTATTAAGCTCAACAGTAGC
* * *
55302341 AATAGACATGTTTAACATGTATTAAGCTCAACCA-TCGC
1 AGTAGACATGCTTAACATGTATTAAGCTCAA-CAGTAGC
* *
55302379 AGTAGACATTCTTCACATG
1 AGTAGACATGCTTAACATG
55302398 CCTTTAGTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
38 45 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTAAGCTCAACAGTAGC
Found at i:55302755 original size:38 final size:38
Alignment explanation
Indices: 55302704--55302805 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
55302694 AAAGAAACAG
55302704 TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
1 TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
* * *
55302742 TAGACATGCTTAACATGTATTCAGTTCAATAGTAGCAG
1 TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
* *
55302780 TAAACATGCTTCACATGCT-TTCAATT
1 TAGACATGCTTAACATG-TATTCAATT
55302806 TCAATTGTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 56 0.98
39 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (38 bp):
TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
Found at i:55318096 original size:38 final size:38
Alignment explanation
Indices: 55318011--55318105 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
55318001 GGACATGAAT
*
55318011 AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGT
1 AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGC
* * * *
55318049 AATAGACATGCTTAACATGTATTTAGTTTAATAGTTGC
1 AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGC
* *
55318087 AGTAAACATGCTTCACATG
1 AGTAGACATGCTTAACATG
55318106 CTTTCAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGC
Found at i:55324425 original size:2 final size:2
Alignment explanation
Indices: 55324418--55324464 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
55324408 TATCGACAAC
55324418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55324460 AT AT A
1 AT AT A
55324465 AAATAAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55325634 original size:36 final size:36
Alignment explanation
Indices: 55325587--55325658 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
55325577 TGTACCTTTG
55325587 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
1 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
55325623 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
1 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
55325659 AAAAATATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.19
Consensus pattern (36 bp):
TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
Found at i:55326003 original size:4 final size:4
Alignment explanation
Indices: 55325996--55326149 Score: 71
Period size: 4 Copynumber: 39.0 Consensus size: 4
55325986 GAAGGAGAGG
* *
55325996 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA
* * *
55326045 -AAA GAAT GTAAG GAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GAAA G-AA
1 GAAA GAAA G-AAA GAAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
*
55326091 G-AA G-AA G-AA GAAGA GGAAA GGAAA GGAGAG GAAA -AAA GAAA G-AA
1 GAAA GAAA GAAA GAA-A -GAAA -GAAA -GA-AA GAAA GAAA GAAA GAAA
*
55326135 -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
55326150 AGGAAAGGAG
Statistics
Matches: 123, Mismatches: 11, Indels: 32
0.74 0.07 0.19
Matches are distributed among these distances:
3 31 0.25
4 58 0.47
5 30 0.24
6 4 0.03
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:55326057 original size:28 final size:30
Alignment explanation
Indices: 55326000--55326156 Score: 100
Period size: 28 Copynumber: 5.3 Consensus size: 30
55325990 GAGAGGGAAA
55326000 GAAA-GAAAGAAAGAAAGAAAGAAAGGAAG
1 GAAAGGAAAGAAAGAAAGAAAGAAAGGAAG
* * *
55326029 GAGAGGAAAGAAAG-AA-AAAGAATGTAAG
1 GAAAGGAAAGAAAGAAAGAAAGAAAGGAAG
* *
55326057 GAAAGGAAAG-GAGAAGAGAAA-AAA--AAA
1 GAAAGGAAAGAAAGAA-AGAAAGAAAGGAAG
*
55326084 GAAAGAAGAAG-AAG-AAGAAGAGGAAAGGAAAG
1 GAAAGGA-AAGAAAGAAAGAA-A-GAAAGG-AAG
* *
55326116 GAGAGGAAA-AAAGAAAGAAAAAGAAGGAAAG
1 GAAAGGAAAGAAAGAAAGAAAGA-AAGG-AAG
*
55326147 AAAAGGAAAG
1 GAAAGGAAAG
55326157 GAGAAGAGAA
Statistics
Matches: 98, Mismatches: 15, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
26 4 0.04
27 12 0.12
28 25 0.26
29 11 0.11
30 13 0.13
31 21 0.21
32 12 0.12
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (30 bp):
GAAAGGAAAGAAAGAAAGAAAGAAAGGAAG
Done.