Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 183 of 230
Found at i:54900682 original size:8 final size:8
Alignment explanation
Indices: 54900665--54900709 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
54900655 ATTTGTAATA
*
54900665 AAATACAT
1 AAATAGAT
54900673 AAATAGAT
1 AAATAGAT
54900681 -AATA-AT
1 AAATAGAT
54900687 -AATAGAT
1 AAATAGAT
*
54900694 AAATAAAT
1 AAATAGAT
54900702 AAATAGAT
1 AAATAGAT
54900710 GCCCGATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 6 0.19
7 6 0.19
8 20 0.62
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (8 bp):
AAATAGAT
Found at i:54900695 original size:21 final size:20
Alignment explanation
Indices: 54900660--54900703 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
54900650 GTGCAATTTG
*
54900660 TAATAAAATACATAAATAGA
1 TAATAAAATACATAAATAAA
*
54900680 TAATAATAATAGATAAATAAA
1 TAATAA-AATACATAAATAAA
54900701 TAA
1 TAA
54900704 ATAGATGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
TAATAAAATACATAAATAAA
Found at i:54902481 original size:94 final size:94
Alignment explanation
Indices: 54902273--54902542 Score: 267
Period size: 94 Copynumber: 2.9 Consensus size: 94
54902263 ATGATGTGTT
* * * * * *
54902273 GCTTCAATCTAA-TCCACTGCAATTTCAGGGAGATTAGACTTATAGCTTTAATCTACTCCACTAT
1 GCTTCAATC-AATTCCACTGCAACTTCAGGGA-ATAAGATTTGTAGCTTTAATCTGCTCCACTAC
* * * *
54902337 AACTTTAGGGAGATGAGATTGGTAATTTTTT
64 AACTTTAGGGAGATAAGATTGGTAACTTGTA
* * * * *
54902368 GTTTTAATCTATTCTACTGCAACTTCAGGGAATAAGATTTGTAGCCTTT-ATCTGCTCCACTGCA
1 GCTTCAATCAATTCCACTGCAACTTCAGGGAATAAGATTTGTAG-CTTTAATCTGCTCCACTACA
* *
54902432 ACTTTAGGGAGATAAGATTTGTGACTTGTA
65 ACTTTAGGGAGATAAGATTGGTAACTTGTA
* * * * *
54902462 GCTTCAAT-AAGTTCCACTGCAACTTTAGGAAAATGAGATTTGTAGCTTTAATTTGCTCCAGTAC
1 GCTTCAATCAA-TTCCACTGCAACTTCAGG-GAATAAGATTTGTAGCTTTAATCTGCTCCACTAC
*
54902526 AACTTTAGAGAGATAAG
64 AACTTTAGGGAGATAAG
54902543 GTTTATAGCT
Statistics
Matches: 142, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
93 1 0.01
94 73 0.51
95 68 0.48
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (94 bp):
GCTTCAATCAATTCCACTGCAACTTCAGGGAATAAGATTTGTAGCTTTAATCTGCTCCACTACAA
CTTTAGGGAGATAAGATTGGTAACTTGTA
Found at i:54902617 original size:45 final size:44
Alignment explanation
Indices: 54902383--54903223 Score: 411
Period size: 44 Copynumber: 18.6 Consensus size: 44
54902373 AATCTATTCT
* * *
54902383 ACTGCAACTTCAGGGA-ATAAGATTTGTAGCCTT-TATCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTGTA-TCTTCAATCTGCTCC
* * ** *
54902426 ACTGCAACTTTAGGGAGATAAGATTTGTGACTTGTAGCTTCAATAAGTTCC
1 ACTGCAACTTCAGAGAGATAAGATTTGT-A----T--CTTCAATCTGCTCC
* * * * * *
54902477 ACTGCAACTTTAG-GAAAATGAGATTTGTAGCTTTAATTTGCTCC
1 ACTGCAACTTCAGAG-AGATAAGATTTGTATCTTCAATCTGCTCC
* * * * * * * *
54902521 AGTACAACTTTAGAGAGATAAGGTTTATAGCTTTAATCTGCTCT
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
* * *
54902565 ACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAATCTACTCT
1 ACTGCAACTTCAGAGAGATAAGATTTG-TATCTTCAATCTGCTCC
* * * *
54902610 ACTGCAACTTCAG-GAAGATAATATTTGTAACTTTAATCTACTCC
1 ACTGCAACTTCAGAG-AGATAAGATTTGTATCTTCAATCTGCTCC
* * * * * * * *
54902654 ACTACGACTTCA-AGGAGATAAGATTTGTGTTTTTAGTTTACTCC
1 ACTGCAACTTCAGA-GAGATAAGATTTGTATCTTCAATCTGCTCC
* * * * **
54902698 ACTACAAGTTCAGGGAGATAAGATTAGTATCTTCAATCTAATCC
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
* * ** * *
54902742 ACTGCAACCTT-AG-G-GAGAAGATTTCTGGCTTTAATCTACTCC
1 ACTGCAA-CTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
* *
54902784 ACTACAACTTCAGAGAGATAAGATTCACCACG-ATGACTTCAATC--CATCC
1 ACTGCAACTTCAGAGAGATAAGATT-----TGTAT--CTTCAATCTGC-TCC
* * * * * **
54902833 TACTGCAAATTCA-AGGGTATAGGATTTGTGGTTTGTAGCCTTAATCTATTCC
1 -ACTGCAACTTCAGAGAG-ATAAGATTTGT-ATCT-T---C--AATCTGCTCC
* * * * * *
54902885 ACTACAA-TCTCAGGGAAATAAGATTCGCTATCTTCAATCCGCTCT
1 ACTGCAACT-TCAGAGAGATAAGATTTG-TATCTTCAATCTGCTCC
* * *
54902930 ACTGCATCTTCAG-GAAGATAAGATTTGTTATCTTTAACCTGCTCC
1 ACTGCAACTTCAGAG-AGATAAGATTTG-TATCTTCAATCTGCTCC
* * * * * *
54902975 ACTACAATTTCAGGGAGATAAGGTTTGTAGT-TTTAATCTGCTCT
1 ACTGCAACTTCAGAGAGATAAGATTTGTA-TCTTCAATCTGCTCC
* * *
54903019 ACTGCCACTTCAGAGAGATAATATTCGCTATCTTCAATTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTG-TATCTTCAA-TCTGCTCC
* * * *
54903065 ACTGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATTTGCTCT
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
* *
54903109 ACTGCAACTTTAGAGAGATAAGATTTGCTATTTTCAATCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTG-TATCTTCAATCTGCTCC
* * * * *
54903154 ACTGTAACTTTAGGGAGATAAGATTAGT-TCTTCAATTTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
* *
54903197 ATTGCAATTTCA-AGGAGATAAGATTTG
1 ACTGCAACTTCAGA-GAGATAAGATTTG
54903224 CCATGGTGAC
Statistics
Matches: 610, Mismatches: 137, Indels: 102
0.72 0.16 0.12
Matches are distributed among these distances:
41 3 0.00
42 29 0.05
43 50 0.08
44 241 0.40
45 153 0.25
46 34 0.06
47 2 0.00
48 2 0.00
49 7 0.01
50 31 0.05
51 53 0.09
52 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATTTGTATCTTCAATCTGCTCC
Found at i:54902644 original size:133 final size:131
Alignment explanation
Indices: 54902474--54902808 Score: 363
Period size: 133 Copynumber: 2.5 Consensus size: 131
54902464 TTCAATAAGT
* * * * * *
54902474 TCCACTGCAACTTTAGGAAAATGAGATTTGTAGCTTTAATTTGCTCCAGTACAACTTTAGAGAGA
1 TCCACTGCAAC-TTAGGAAGATAAGATTTGTAGCTTTAATCTACTCCACTACAACTTCAGAGAGA
* * * * *
54902539 TAAGGTTTATAG-CTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAAT
65 TAAGATTTAT-GTCTTTAATCTACTCCACTACAACTTCAGAGAGATAAGATTAG-TATCTTCAAT
*
54902603 CTAC
128 CTAA
* * * *
54902607 TCTACTGCAACTTCAGGAAGATAATATTTGTAACTTTAATCTACTCCACTACGACTTCA-AGGAG
1 TCCACTGCAACTT-AGGAAGATAAGATTTGTAGCTTTAATCTACTCCACTACAACTTCAGA-GAG
* * * * * *
54902671 ATAAGATTTGTGTTTTTAGTTTACTCCACTACAAGTTCAGGGAGATAAGATTAGTATCTTCAATC
64 ATAAGATTTATGTCTTTAATCTACTCCACTACAACTTCAGAGAGATAAGATTAGTATCTTCAATC
54902736 TAA
129 TAA
* * *
54902739 TCCACTGCAACCTTAGG--GAGAAGATTTCTGGCTTTAATCTACTCCACTACAACTTCAGAGAGA
1 TCCACTGCAA-CTTAGGAAGATAAGATTTGTAGCTTTAATCTACTCCACTACAACTTCAGAGAGA
54902802 TAAGATT
65 TAAGATT
54902809 CACCACGATG
Statistics
Matches: 168, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
130 45 0.27
131 1 0.01
132 29 0.17
133 93 0.55
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (131 bp):
TCCACTGCAACTTAGGAAGATAAGATTTGTAGCTTTAATCTACTCCACTACAACTTCAGAGAGAT
AAGATTTATGTCTTTAATCTACTCCACTACAACTTCAGAGAGATAAGATTAGTATCTTCAATCTA
A
Found at i:54903124 original size:90 final size:89
Alignment explanation
Indices: 54902925--54903224 Score: 345
Period size: 90 Copynumber: 3.4 Consensus size: 89
54902915 TCTTCAATCC
* * * * * *
54902925 GCTCTACTGCATCTTCAG-GAAGATAAGATTTGTTATCTTTAACCTGCTCCACTACAATTTCAGG
1 GCTCTACTGCAACTTCAGAG-AGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGG
* * *
54902989 GAGATAAGGTTTGTAGTTTTAATCT
65 GAGATAAGATTTGTAGCTTTAATTT
* * * *
54903014 GCTCTACTGCCACTTCAGAGAGATAATATTCGCTATCTTCAATTCTGCTCCACTGCAACTTCAGA
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAA-TCTGCTCCACTGCAACTTCAGG
54903079 GAGATAAGATTTGTAGCTTTAATTT
65 GAGATAAGATTTGTAGCTTTAATTT
* * * *
54903104 GCTCTACTGCAACTTTAGAGAGATAAGATTTGCTATTTTCAATCTGCTCCACTGTAACTTTAGGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGG
* * *
54903169 AGATAAGATTAGT-TCTTCAATTT
66 AGATAAGATTTGTAGCTTTAATTT
* * *
54903192 GCTCCATTGCAATTTCA-AGGAGATAAGATTTGC
1 GCTCTACTGCAACTTCAGA-GAGATAAGATTTGC
54903225 CATGGTGACC
Statistics
Matches: 180, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.01
88 35 0.19
89 66 0.37
90 78 0.43
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (89 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGG
AGATAAGATTTGTAGCTTTAATTT
Found at i:54910105 original size:40 final size:40
Alignment explanation
Indices: 54910017--54910107 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
54910007 GCATTTTAAC
* *
54910017 AAACGCCGCAATAGATCGAGAATTAGTAGCGATTTTTATG
1 AAACGCCGCAATAGATCAAGAATTAGCAGCGATTTTTATG
* * * * *
54910057 AAAGGCCGCTATAGATCAAGTATTAGCGGCGCTTTTT-TGG
1 AAACGCCGCAATAGATCAAGAATTAGCAGCGATTTTTAT-G
54910097 AAACGCCGCAA
1 AAACGCCGCAA
54910108 ACAAAATGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (40 bp):
AAACGCCGCAATAGATCAAGAATTAGCAGCGATTTTTATG
Found at i:54910206 original size:14 final size:14
Alignment explanation
Indices: 54910190--54910294 Score: 66
Period size: 14 Copynumber: 7.4 Consensus size: 14
54910180 TACACTTTTT
*
54910190 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAA
*
54910204 GGTTTTAGGATTTAA
1 GG-TTTAGGGTTTAA
*
54910219 AGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
* ** *
54910233 GGGTTAGTATGTAA
1 GGTTTAGGGTTTAA
** * *
54910247 GGTTTAATGTCTAT
1 GGTTTAGGGTTTAA
*
54910261 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAA
* *
54910275 GGTTTATGGTATAA
1 GGTTTAGGGTTTAA
*
54910289 TGTTTA
1 GGTTTA
54910295 TTATTTTCGG
Statistics
Matches: 68, Mismatches: 22, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
14 57 0.84
15 11 0.16
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:54910893 original size:39 final size:39
Alignment explanation
Indices: 54910844--54910921 Score: 122
Period size: 41 Copynumber: 2.0 Consensus size: 39
54910834 CATTATATTC
54910844 AATTTTAAAATTGAACAATT-AAATAATGTCATATTAAA
1 AATTTTAAAATTGAACAATTAAAATAATGTCATATTAAA
*
54910882 AATTTTAAAAATTTAACAATTAAAAATAATGTCATATTAA
1 AATTTT-AAAATTGAACAATT-AAAATAATGTCATATTAA
54910922 TGTATCAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 6 0.17
39 13 0.36
41 17 0.47
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (39 bp):
AATTTTAAAATTGAACAATTAAAATAATGTCATATTAAA
Found at i:54911233 original size:126 final size:123
Alignment explanation
Indices: 54910991--54911256 Score: 302
Period size: 126 Copynumber: 2.1 Consensus size: 123
54910981 AAAAACGCCA
* * * * *
54910991 CAACAATGTCTTAAAAATTATACAAAACGGCGCCGTTTGGTTACAGGAATTTGATTTTTAGTGGC
1 CAACAATGTATTAAAAAGTATACAAAACGACGCCGTTTGCTTACAGGAATTTAATTTTTAGTGGC
* * *
54911056 GTTTTCTCCACAATGCTGCAAAAGGTATGGAATAGCGGCGTTTGTTATAAAAACACTG
66 GTTTTCTCCACAATGCCGCAAAAGGTAAGCAATAGCGGCGTTTGTTATAAAAACACTG
* * * * *
54911114 TAACAATGTATTAAAAAGTGTACAAAAACTACGTCGTTTGCTTACAGGATTTTAACTTTTTAGTG
1 CAACAATGTATTAAAAAGTATAC-AAAACGACGCCGTTTGCTTACAGGAATTTAA-TTTTTAGTG
* * * * **
54911179 GTG-TTTCTCTCAGAATCGCCGCAAAAGGTAAGCATTAGCGGCGTTT-TGTCTAAAAATGCTG
64 GCGTTTTCTC-CACAAT-GCCGCAAAAGGTAAGCAATAGCGGCGTTTGT-TATAAAAACACTG
54911240 CAACAATGTATTAAAAA
1 CAACAATGTATTAAAAA
54911257 TTGTTCAGAA
Statistics
Matches: 118, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
123 19 0.16
124 31 0.26
125 17 0.14
126 51 0.43
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (123 bp):
CAACAATGTATTAAAAAGTATACAAAACGACGCCGTTTGCTTACAGGAATTTAATTTTTAGTGGC
GTTTTCTCCACAATGCCGCAAAAGGTAAGCAATAGCGGCGTTTGTTATAAAAACACTG
Found at i:54911382 original size:20 final size:20
Alignment explanation
Indices: 54911359--54911399 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54911349 CGCAGTCAGC
54911359 CCCTAATTCCCCTTCCAAAT
1 CCCTAATTCCCCTTCCAAAT
*
54911379 CCCTAATTCCCCTTCTAAAT
1 CCCTAATTCCCCTTCCAAAT
54911399 C
1 C
54911400 TCTTCCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (20 bp):
CCCTAATTCCCCTTCCAAAT
Found at i:54911691 original size:40 final size:38
Alignment explanation
Indices: 54911635--54911748 Score: 113
Period size: 40 Copynumber: 2.9 Consensus size: 38
54911625 GGCGTTTGGA
* *
54911635 TAAAAAATGCCGCTAAAAATCAAGCATTAGCGGCG-CTT
1 TAAAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGACTT
* * *
54911673 CTAAAAAAACGCCACTAAAGATTGAGCATTAGTGGCGAACTT
1 -T-AAAAAACGCCGCTAAA-AATGAGCATTAGCGGCG-ACTT
**
54911715 TGGAAAACGCCGCTAAAAATGAGCATTAGCGGCG
1 TAAAAAACGCCGCTAAAAATGAGCATTAGCGGCG
54911749 TTTTTCAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
39 16 0.26
40 39 0.64
41 3 0.05
42 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (38 bp):
TAAAAAACGCCGCTAAAAATGAGCATTAGCGGCGACTT
Found at i:54911976 original size:104 final size:105
Alignment explanation
Indices: 54911789--54911983 Score: 250
Period size: 104 Copynumber: 1.9 Consensus size: 105
54911779 CACAACGACG
* * *
54911789 TCGTTTTCTAAGTTTGCGGGGCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGGTTT
1 TCGTTTTCTAAGTTTGAGGGGCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAAAGCTCAGGGCTT
54911854 TAGCGGCGTTTTCCAAAAAGCGCCGCAAAAAACCTAAGCC
66 TAGCGGCGTTTTCCAAAAAGCGCCGCAAAAAACCTAAGCC
* * * * * * *
54911894 TCGTTTTCTGAGTTTTAGGGGTTTTAGTGGC-TTTTTTAGAAAGCGTCGCTAAAGCAT-GGGGCT
1 TCGTTTTCTAAGTTTGAGGGGCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAAAGC-TCAGGGCT
* **
54911957 TTAGTGGCGTTTTTGAAAAAGCGCCGC
65 TTAGCGGCGTTTTCCAAAAAGCGCCGC
54911984 TAATGCTTAG
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
104 48 0.63
105 28 0.37
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (105 bp):
TCGTTTTCTAAGTTTGAGGGGCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAAAGCTCAGGGCTT
TAGCGGCGTTTTCCAAAAAGCGCCGCAAAAAACCTAAGCC
Found at i:54911985 original size:41 final size:41
Alignment explanation
Indices: 54911911--54912066 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
54911901 CTGAGTTTTA
* * *
54911911 GGGGTTTTAGTGGC-TTTTTTAGAAAGCGTCGCTAAAGCAT
1 GGGGTTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAAAGCAT
* * *
54911951 GGGGCTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCTT
1 GGGGTTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAAAGCAT
* * * * * *
54911992 AGGGTTTTAGCGGCGTTTTTGGATAAGCGCCACTAATGC-T
1 GGGGTTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAAAGCAT
* * **
54912032 CGGGGTTTTTAGCGGCGCTTTTCCAAAAGCGCCGC
1 -GGGG-TTTTAGTGGCGTTTTTGAAAAAGCGCCGC
54912067 AAAAATATTT
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 14 0.15
41 57 0.60
42 24 0.25
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (41 bp):
GGGGTTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAAAGCAT
Found at i:54912062 original size:42 final size:41
Alignment explanation
Indices: 54911973--54912064 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
54911963 GCGTTTTTGA
* * * **
54911973 AAAAGCGCCGCTAATGCTTAGGGTTTTAGCGGCGTTTTTGG
1 AAAAGCGCCACTAATGCTCAGGGTTTTAGCGGCGCTTTTCC
* *
54912014 ATAAGCGCCACTAATGCTCGGGGTTTTTAGCGGCGCTTTTCC
1 AAAAGCGCCACTAATGCTCAGGG-TTTTAGCGGCGCTTTTCC
54912056 AAAAGCGCC
1 AAAAGCGCC
54912065 GCAAAAATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 19 0.45
42 23 0.55
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
AAAAGCGCCACTAATGCTCAGGGTTTTAGCGGCGCTTTTCC
Found at i:54912305 original size:7 final size:7
Alignment explanation
Indices: 54912295--54912333 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
54912285 ATTATTATTA
54912295 TTTAGGG
1 TTTAGGG
54912302 TTTAGGG
1 TTTAGGG
*
54912309 TTAAGGG
1 TTTAGGG
* *
54912316 TATATGG
1 TTTAGGG
54912323 TTTAGGG
1 TTTAGGG
54912330 TTTA
1 TTTA
54912334 AAGTTTAGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:54912383 original size:14 final size:15
Alignment explanation
Indices: 54912357--54912405 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 15
54912347 ACTATTTGAA
54912357 GGTTTATAGATTATG
1 GGTTTATAGATTATG
54912372 GGTTTA-AGATTAT-
1 GGTTTATAGATTATG
*
54912385 GGTTTATAGTTTATG
1 GGTTTATAGATTATG
*
54912400 CGTTTA
1 GGTTTA
54912406 AGGTTTAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 11 0.37
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (15 bp):
GGTTTATAGATTATG
Found at i:54912411 original size:7 final size:7
Alignment explanation
Indices: 54912401--54912567 Score: 97
Period size: 7 Copynumber: 23.7 Consensus size: 7
54912391 TAGTTTATGC
54912401 GTTTAAG
1 GTTTAAG
54912408 GTTTAAG
1 GTTTAAG
* *
54912415 GGTTACG
1 GTTTAAG
*
54912422 GTTTATG
1 GTTTAAG
54912429 GTTTAAG
1 GTTTAAG
54912436 GTTTATA-
1 GTTTA-AG
*
54912443 GATTAAG
1 GTTTAAG
*
54912450 GGTTAAG
1 GTTTAAG
54912457 GTTTAAG
1 GTTTAAG
*
54912464 GTTTAGG
1 GTTTAAG
* *
54912471 GGTTAGG
1 GTTTAAG
*
54912478 GGTTAAG
1 GTTTAAG
*
54912485 AG-TTGAG
1 -GTTTAAG
* *
54912492 GGTTATG
1 GTTTAAG
*
54912499 GTTTATG
1 GTTTAAG
*
54912506 GTTTATG
1 GTTTAAG
*
54912513 GTTTATG
1 GTTTAAG
54912520 GTTTAAAG
1 GTTT-AAG
*
54912528 G-TTGAG
1 GTTTAAG
*
54912534 GTTTAAT
1 GTTTAAG
*
54912541 GTTTAGG
1 GTTTAAG
* *
54912548 GGTTAGGG
1 GTTTA-AG
54912556 GTTTAAG
1 GTTTAAG
54912563 GTTTA
1 GTTTA
54912568 TGTTTTATGA
Statistics
Matches: 129, Mismatches: 24, Indels: 14
0.77 0.14 0.08
Matches are distributed among these distances:
6 5 0.04
7 113 0.88
8 11 0.09
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.42
Consensus pattern (7 bp):
GTTTAAG
Found at i:54912432 original size:28 final size:28
Alignment explanation
Indices: 54912393--54912574 Score: 118
Period size: 28 Copynumber: 6.4 Consensus size: 28
54912383 ATGGTTTATA
*
54912393 GTTTATGCGTTTAAGGTTTAAGGGTTACG
1 GTTTATG-GTTTAAGGTTTAAGGGTTAAG
*
54912422 GTTTATGGTTTAAGGTTTATA-GATTAAG
1 GTTTATGGTTTAAGGTTTA-AGGGTTAAG
* * * *
54912450 GGTTAAGGTTTAAGGTTTAGGGGTTAGG
1 GTTTATGGTTTAAGGTTTAAGGGTTAAG
* * * * * * *
54912478 GGTTAAGAG-TTGAGGGTTATGGTTTATG
1 GTTTATG-GTTTAAGGTTTAAGGGTTAAG
* * *
54912506 GTTTATGGTTTATGGTTTAAAGGTTGAG
1 GTTTATGGTTTAAGGTTTAAGGGTTAAG
* * *
54912534 GTTTAAT-GTTTAGGGGTTAGGGGTTTAAG
1 GTTT-ATGGTTTAAGGTTTAAGGG-TTAAG
*
54912563 GTTTATGTTTTA
1 GTTTATGGTTTA
54912575 TGATTCAAGG
Statistics
Matches: 118, Mismatches: 28, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
27 1 0.01
28 94 0.80
29 23 0.19
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.43
Consensus pattern (28 bp):
GTTTATGGTTTAAGGTTTAAGGGTTAAG
Found at i:54912440 original size:35 final size:35
Alignment explanation
Indices: 54912295--54912588 Score: 150
Period size: 35 Copynumber: 8.3 Consensus size: 35
54912285 ATTATTATTA
* * *
54912295 TTTAGGGTTT-AGGGTTAAGGGTATATGGTTTAGGG
1 TTTAAGGTTTAAGGGTTAA-GGTTTATGGTTTATGG
* *** * *
54912330 TTTAAAGTTT-AGGAGTTACTATTTGAAGGTTTATAG
1 TTTAAGGTTTAAGG-GTTAAGGTTT-ATGGTTTATGG
* * * * *
54912366 ATTATGGGTTTAA-GATTATGGTTTATAGTTTATGCG
1 TTTA-AGGTTTAAGGGTTAAGGTTTATGGTTTATG-G
* *
54912402 TTTAAGGTTTAAGGGTTACGGTTTATGGTTTAAGG
1 TTTAAGGTTTAAGGGTTAAGGTTTATGGTTTATGG
* * *
54912437 TTTATA-GATTAAGGGTTAAGGTTTAAGGTTTAGGG
1 TTTA-AGGTTTAAGGGTTAAGGTTTATGGTTTATGG
* * * * * *
54912472 GTTAGGGGTTAAGAGTTGAGGGTTATGGTTTATGG
1 TTTAAGGTTTAAGGGTTAAGGTTTATGGTTTATGG
* * * *
54912507 TTTATGGTTTATGGTTTAAAGGTTGA-GGTTTAAT-G
1 TTTAAGGTTTAAGGGTT-AAGGTTTATGGTTT-ATGG
* * * * *
54912542 TTTAGGGGTTAGGGGTTTAAGGTTTATGTTTTATGA
1 TTTAAGGTTTAAGGG-TTAAGGTTTATGGTTTATGG
*
54912578 TTCAAGGTTTA
1 TTTAAGGTTTA
54912589 GGGGATAGGG
Statistics
Matches: 190, Mismatches: 56, Indels: 25
0.70 0.21 0.09
Matches are distributed among these distances:
35 120 0.63
36 64 0.34
37 5 0.03
38 1 0.01
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.44
Consensus pattern (35 bp):
TTTAAGGTTTAAGGGTTAAGGTTTATGGTTTATGG
Found at i:54915751 original size:57 final size:57
Alignment explanation
Indices: 54915671--54915787 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
54915661 TATGCTCTAA
54915671 TTTATGTTTTATTTTTCATTATTATGATAGTGCATGGCTAATCCTTCTATATGCTTG
1 TTTATGTTTTATTTTTCATTATTATGATAGTGCATGGCTAATCCTTCTATATGCTTG
*
54915728 TTTATGTTTTATTTTTCATTATTATGATGGTGCATGGCTAATCCTTCTATATGCTTG
1 TTTATGTTTTATTTTTCATTATTATGATAGTGCATGGCTAATCCTTCTATATGCTTG
54915785 TTT
1 TTT
54915788 GATATTGCAC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.54
Consensus pattern (57 bp):
TTTATGTTTTATTTTTCATTATTATGATAGTGCATGGCTAATCCTTCTATATGCTTG
Found at i:54917183 original size:71 final size:72
Alignment explanation
Indices: 54917094--54917237 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 72
54917084 ACATAATATA
* * *
54917094 ATATTTGATTAAAATAATTTTTTTTAAAGGTTATGTTTTTAGTGGCG-TTTTTGCGAGAAGCGCC
1 ATATTTGATTAAAATAATTTTTTTTAAAGGTTATATTTTTAGCGGCGTTTTTTGCGACAAGCGCC
54917158 ACTAAAG
66 ACTAAAG
54917165 ATATTTGATTAAAATAATTTTTTTTAAAGGTTATATTTTTAGCGGCGTTTTTTTGCGACAAGCGC
1 ATATTTGATTAAAATAATTTTTTTTAAAGGTTATATTTTTAGCGGCG-TTTTTTGCGACAAGCGC
*
54917230 CATTAAAG
65 CACTAAAG
54917238 GTTTGTTCTT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 45 0.67
73 22 0.33
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (72 bp):
ATATTTGATTAAAATAATTTTTTTTAAAGGTTATATTTTTAGCGGCGTTTTTTGCGACAAGCGCC
ACTAAAG
Found at i:54917302 original size:43 final size:42
Alignment explanation
Indices: 54917244--54917387 Score: 171
Period size: 43 Copynumber: 3.4 Consensus size: 42
54917234 AAAGGTTTGT
* * *
54917244 TCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGA
1 TCTTTAGCGGCGTTTGTG-CAAAAGCGCCGCTAAAGGTCGTGG
** * *
54917287 TCTTTAGTAGCGTTTGTGCCAAAAGCGCTGCTAAGGGTCGTGG
1 TCTTTAGCGGCGTTTGTG-CAAAAGCGCCGCTAAAGGTCGTGG
* *
54917330 TCTATAGCGGCGTTTGTCGCAAAAGTGCCGCTAAAGGTCGTGG
1 TCTTTAGCGGCGTTTGT-GCAAAAGCGCCGCTAAAGGTCGTGG
*
54917373 TCTTTATCGGCGTTT
1 TCTTTAGCGGCGTTT
54917388 TTTTTTCTAA
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 83 0.99
44 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (42 bp):
TCTTTAGCGGCGTTTGTGCAAAAGCGCCGCTAAAGGTCGTGG
Found at i:54917478 original size:22 final size:22
Alignment explanation
Indices: 54917450--54917493 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
54917440 TCTCGGTGCT
* *
54917450 AAAAAGCGCTGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
54917472 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
54917494 TTTTGCTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.25, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:54918237 original size:52 final size:52
Alignment explanation
Indices: 54918127--54918229 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 52
54918117 TTTAGGAATT
* ** *
54918127 TGGTTAATGTTGCTGCAAGTTCTTTTTTGCTGTAAGTTCTAGTTAATGTTGC
1 TGGTTAATGTTACTGCAAGTTCTTTTTTGCTCCAAGTTCTAGCTAATGTTGC
* **
54918179 TGGTTAATGTTATTGCAAGTTCTTTTTTGCTCCATTTTCTA-CTAAGTGTTG
1 TGGTTAATGTTACTGCAAGTTCTTTTTTGCTCCAAGTTCTAGCTAA-TGTTG
54918230 TATGTTAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 3 0.07
52 40 0.93
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (52 bp):
TGGTTAATGTTACTGCAAGTTCTTTTTTGCTCCAAGTTCTAGCTAATGTTGC
Found at i:54919300 original size:21 final size:18
Alignment explanation
Indices: 54919276--54919338 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
54919266 ATGTTTTTAA
54919276 AACTTACAAAATATATATCAT
1 AACTTACAAAAT-T-TA-CAT
*
54919297 AACTTACATAATTTACAT
1 AACTTACAAAATTTACAT
* *
54919315 AACTTACATAACTTACAT
1 AACTTACAAAATTTACAT
54919333 AACTTA
1 AACTTA
54919339 ATAACTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
18 26 0.65
19 2 0.05
20 1 0.03
21 11 0.28
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACAAAATTTACAT
Found at i:54919373 original size:56 final size:56
Alignment explanation
Indices: 54919303--54919491 Score: 254
Period size: 56 Copynumber: 3.3 Consensus size: 56
54919293 TCATAACTTA
* * *
54919303 CATAATTTACATAACTTACATAACTTACATAACTTAATAACTTATATATATCATAC
1 CATAACTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAT
*
54919359 CATAACTTAAATAACTCACATAACTTAC-TCAACTTAATAACTTATATACATCATATCATAT
1 CATAACTTACATAACTCACATAACTTACAT-AACTTAATAAC-T-TAT--AT-ATATCATAT
* * *
54919420 CATAATTTACATAACTCACATAACTTACCTAACTTAATAACTTATGTATATCATAT
1 CATAACTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAT
54919476 CATAACTTACATAACT
1 CATAACTTACATAACT
54919492 TGCATAATAC
Statistics
Matches: 118, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
55 1 0.01
56 60 0.51
57 2 0.02
58 3 0.03
59 3 0.03
60 3 0.03
61 45 0.38
62 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.36
Consensus pattern (56 bp):
CATAACTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAT
Found at i:54919442 original size:61 final size:60
Alignment explanation
Indices: 54919286--54919479 Score: 256
Period size: 61 Copynumber: 3.3 Consensus size: 60
54919276 AACTTACAAA
* * *
54919286 ATATATATCATAACTTACATAATTTACATAACTTACATAACTTACAT-AACTTAATAACTT
1 ATATATATCATATCATACATAATTTACATAACTCACATAACTTAC-TCAACTTAATAACTT
* *
54919346 ATATATATCATA-C---CATAACTTAAATAACTCACATAACTTACTCAACTTAATAACTT
1 ATATATATCATATCATACATAATTTACATAACTCACATAACTTACTCAACTTAATAACTT
*
54919402 ATATACATCATATCATATCATAATTTACATAACTCACATAACTTAC-CTAACTTAATAACTT
1 ATATATATCATATCATA-CATAATTTACATAACTCACATAACTTACTC-AACTTAATAACTT
*
54919463 ATGTATATCATATCATA
1 ATATATATCATATCATA
54919480 ACTTACATAA
Statistics
Matches: 119, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
55 1 0.01
56 49 0.41
57 1 0.01
59 1 0.01
60 13 0.11
61 54 0.45
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.37
Consensus pattern (60 bp):
ATATATATCATATCATACATAATTTACATAACTCACATAACTTACTCAACTTAATAACTT
Found at i:54919462 original size:8 final size:9
Alignment explanation
Indices: 54919294--54919498 Score: 152
Period size: 9 Copynumber: 22.6 Consensus size: 9
54919284 AAATATATAT
54919294 CATAACTTA
1 CATAACTTA
*
54919303 CATAATTTA
1 CATAACTTA
54919312 CATAACTTA
1 CATAACTTA
54919321 CATAACTTA
1 CATAACTTA
54919330 CATAACTTA
1 CATAACTTA
54919339 -ATAACTTA
1 CATAACTTA
* *
54919347 TATATATCATA
1 CATA-A-CTTA
54919358 CCATAACTTA
1 -CATAACTTA
* *
54919368 AATAACTCA
1 CATAACTTA
54919377 CATAACTTA
1 CATAACTTA
54919386 C-TCAACTTA
1 CAT-AACTTA
54919395 -ATAACTTA
1 CATAACTTA
* *
54919403 TAT-ACAT-
1 CATAACTTA
* *
54919410 CATATCATA
1 CATAACTTA
*
54919419 TCATAATTTA
1 -CATAACTTA
*
54919429 CATAACTCA
1 CATAACTTA
54919438 CATAACTTA
1 CATAACTTA
*
54919447 CCTAACTTA
1 CATAACTTA
54919456 -ATAACTTA
1 CATAACTTA
* * *
54919464 TGTATATCATA
1 --CATAACTTA
54919475 TCATAACTTA
1 -CATAACTTA
*
54919485 CATAACTTG
1 CATAACTTA
54919494 CATAA
1 CATAA
54919499 TACATAAATA
Statistics
Matches: 156, Mismatches: 27, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
7 2 0.01
8 28 0.18
9 97 0.62
10 16 0.10
11 10 0.06
12 3 0.02
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:54925432 original size:43 final size:43
Alignment explanation
Indices: 54925310--54925433 Score: 194
Period size: 43 Copynumber: 2.9 Consensus size: 43
54925300 AGATCATTCT
* * * * *
54925310 TATAAAAGTGTCGCTAAAGAACATGACATTTAGCGGCGTTTGC
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGTTAGC
*
54925353 TATAAAAGCGCCACTAAAGAACATGACCTTTAGCGGTGTTAGC
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGTTAGC
54925396 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTG
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTG
54925434 CCTATCTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (43 bp):
TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGTTAGC
Found at i:54925463 original size:42 final size:43
Alignment explanation
Indices: 54925310--54925456 Score: 181
Period size: 43 Copynumber: 3.4 Consensus size: 43
54925300 AGATCATTCT
* * * * * *
54925310 TATAAAAGTGTCGCTAAAGAACATGACATTTAGCGGCGTTTGC
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGCTAGC
* *
54925353 TATAAAAGCGCCACTAAAGAACATGACCTTTAGCGGTGTTAGC
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGCTAGC
*
54925396 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGCCTATC
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTG-CTAGC
*
54925440 T-TTAAA-CGCCGCTAAAG
1 TATAAAAGCGCCGCTAAAG
54925457 GTCATGATCT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
42 11 0.12
43 78 0.84
44 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (43 bp):
TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGTGCTAGC
Found at i:54925802 original size:23 final size:22
Alignment explanation
Indices: 54925774--54925828 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
54925764 ATGCAATTTG
54925774 TAATAAAATACATAAATAGAT-AA
1 TAATAAAATA-AT-AATAGATAAA
54925797 TAAT--AATAATAATAGATAAA
1 TAATAAAATAATAATAGATAAA
54925817 TAAATAAAATAA
1 T-AATAAAATAA
54925829 ATAGATGCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 7 0.25
20 5 0.18
21 7 0.25
23 9 0.32
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
TAATAAAATAATAATAGATAAA
Found at i:54925886 original size:18 final size:19
Alignment explanation
Indices: 54925864--54925914 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
54925854 GAAAAGATTT
54925864 GAATATAAAAAAAGTAAAA
1 GAATATAAAAAAAGTAAAA
*
54925883 -AATACTAAATAAA-TAAAA
1 GAATA-TAAAAAAAGTAAAA
54925901 GAAT-TAAAATAAAG
1 GAATATAAAA-AAAG
54925915 AAAGGACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (19 bp):
GAATATAAAAAAAGTAAAA
Found at i:54940153 original size:17 final size:17
Alignment explanation
Indices: 54940116--54940163 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
54940106 GAATTTAGAA
*
54940116 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
54940132 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
54940149 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
54940164 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:54941442 original size:46 final size:46
Alignment explanation
Indices: 54941372--54941556 Score: 298
Period size: 46 Copynumber: 4.0 Consensus size: 46
54941362 CATGGAAAAG
*
54941372 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
54941418 TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
54941464 TGTGAAAAGTAGGTATGGTGTTTTAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
54941510 TGTAAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
54941556 T
1 T
54941557 ATAGCAATGT
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 128 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:54945583 original size:41 final size:40
Alignment explanation
Indices: 54945507--54945584 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
54945497 CCGAAATGTA
* * *
54945507 TCACCGGCATTAAGCCTGCTAGACGTTAGGTCTGAATTATT
1 TCACCGACATTAAGCCTGCTAGACATTA-GCCTGAATTATT
54945548 TCACCGACATTAAGCCTGCTAGGCACATT-GCCTGAAT
1 TCACCGACATTAAGCCTGCTA-G-ACATTAGCCTGAAT
54945585 AACTGAGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 27 0.84
42 1 0.03
43 4 0.12
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (40 bp):
TCACCGACATTAAGCCTGCTAGACATTAGCCTGAATTATT
Found at i:54946079 original size:21 final size:21
Alignment explanation
Indices: 54946053--54946094 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54946043 TCATAAAATC
54946053 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
54946074 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
54946095 TATATATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:54953587 original size:21 final size:21
Alignment explanation
Indices: 54953561--54953602 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54953551 TCATAAAATC
54953561 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
54953582 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
54953603 TATATATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:54961407 original size:15 final size:17
Alignment explanation
Indices: 54961368--54961409 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
54961358 AGTACCCTTA
*
54961368 AATACATAATCAATTTT
1 AATAAATAATCAATTTT
54961385 AGATAAATAAT-AA-TTT
1 A-ATAAATAATCAATTTT
54961401 AATAAATAA
1 AATAAATAA
54961410 ATTAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 4 0.17
17 3 0.13
18 8 0.35
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (17 bp):
AATAAATAATCAATTTT
Found at i:54966429 original size:17 final size:18
Alignment explanation
Indices: 54966399--54966444 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
54966389 ATTTAAATTG
54966399 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
54966417 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
54966433 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
54966445 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:54968540 original size:22 final size:21
Alignment explanation
Indices: 54968515--54968555 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
54968505 AATATATAAA
* *
54968515 TATAATATTAATATATAAATTG
1 TATAAAATTAAAATA-AAATTG
54968537 TATAAAATTAAAATAAAAT
1 TATAAAATTAAAATAAAAT
54968556 AAAGTAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TATAAAATTAAAATAAAATTG
Found at i:54971277 original size:19 final size:19
Alignment explanation
Indices: 54971253--54971290 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54971243 AAAGTTAATA
*
54971253 ACAAATTTGATTACGGTGG
1 ACAAATTTGACTACGGTGG
54971272 ACAAATTTGACTACGGTGG
1 ACAAATTTGACTACGGTGG
54971291 GTGGCAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (19 bp):
ACAAATTTGACTACGGTGG
Found at i:54975942 original size:19 final size:19
Alignment explanation
Indices: 54975920--54975987 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 19
54975910 GCACACACGA
*
54975920 TTCCATTAATCTCACACAG
1 TTCCACTAATCTCACACAG
*
54975939 TTCCACTAATCTCACATAG
1 TTCCACTAATCTCACACAG
** *
54975958 TTCCACTAATCAGACACAA
1 TTCCACTAATCTCACACAG
54975977 TTCCACTAATC
1 TTCCACTAATC
54975988 AAACATCATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.29
Consensus pattern (19 bp):
TTCCACTAATCTCACACAG
Found at i:54975988 original size:19 final size:19
Alignment explanation
Indices: 54975911--54975988 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
54975901 ACTTTACATG
* *
54975911 CACACACGATTCCATTAAT
1 CACACACAATTCCACTAAT
* *
54975930 CTCACACAGTTCCACTAAT
1 CACACACAATTCCACTAAT
* * *
54975949 CTCACATAGTTCCACTAAT
1 CACACACAATTCCACTAAT
*
54975968 CAGACACAATTCCACTAAT
1 CACACACAATTCCACTAAT
54975987 CA
1 CA
54975989 AACATCATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (19 bp):
CACACACAATTCCACTAAT
Found at i:54977370 original size:38 final size:38
Alignment explanation
Indices: 54977256--54977371 Score: 153
Period size: 37 Copynumber: 3.1 Consensus size: 38
54977246 AAATTTTAAT
* * *
54977256 ACACCGAAACTAAGCTTGCTAGGCACAAAGCCTGAATA
1 ACACCGACACCAAGCCTGCTAGGCACAAAGCCTGAATA
* * *
54977294 ACACTGGCACCAAGCCTGCTAGTCA-AAAGCCTGAATA
1 ACACCGACACCAAGCCTGCTAGGCACAAAGCCTGAATA
* *
54977331 ACGCCGACACCAAGCCTGCTAGGCACAAAGCTTGAATA
1 ACACCGACACCAAGCCTGCTAGGCACAAAGCCTGAATA
54977369 ACA
1 ACA
54977372 ATATAATTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 33 0.51
38 32 0.49
ACGTcount: A:0.37, C:0.29, G:0.19, T:0.15
Consensus pattern (38 bp):
ACACCGACACCAAGCCTGCTAGGCACAAAGCCTGAATA
Found at i:54978994 original size:18 final size:19
Alignment explanation
Indices: 54978971--54979039 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 19
54978961 TTCATGGTGG
54978971 AAGAAAGAAGA-AAATAAA
1 AAGAAAGAAGAGAAATAAA
*
54978989 AAGAAAGAAGAGAGATAAA
1 AAGAAAGAAGAGAAATAAA
**
54979008 AA-AAAGGAAG-G-AAGGAA
1 AAGAAA-GAAGAGAAATAAA
*
54979025 AAGAAAGAAAAGAAA
1 AAGAAAGAAGAGAAA
54979040 AGAAATGTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.20
18 19 0.46
19 14 0.34
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (19 bp):
AAGAAAGAAGAGAAATAAA
Found at i:54982116 original size:19 final size:19
Alignment explanation
Indices: 54982089--54982131 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54982079 CTTCTATCTT
*
54982089 ATATTTAAAAGAT-TAAAAA
1 ATATATAAAA-ATATAAAAA
54982108 ATATATAAAAATATAAAAA
1 ATATATAAAAATATAAAAA
*
54982127 TTATA
1 ATATA
54982132 GAAATAGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATATATAAAAATATAAAAA
Found at i:54982131 original size:17 final size:18
Alignment explanation
Indices: 54982104--54982137 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54982094 TAAAAGATTA
54982104 AAAAATATATAAAAATAT
1 AAAAATATATAAAAATAT
*
54982122 AAAAAT-TATAGAAATA
1 AAAAATATATAAAAATA
54982138 GTTGAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATATAAAAATAT
Found at i:54987183 original size:20 final size:20
Alignment explanation
Indices: 54987158--54987195 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54987148 GGGAACAATT
*
54987158 TTTCAATCGATTTAAAAATG
1 TTTCAATCGAGTTAAAAATG
*
54987178 TTTCAATTGAGTTAAAAA
1 TTTCAATCGAGTTAAAAA
54987196 ATTTTAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTCAATCGAGTTAAAAATG
Found at i:54990918 original size:152 final size:152
Alignment explanation
Indices: 54990642--54990945 Score: 608
Period size: 152 Copynumber: 2.0 Consensus size: 152
54990632 CACGGTTTTT
54990642 ATTATTCTATTTTCAACCTTTACTTTTGACGTTATTTTTTCTATTAATTTCAGGTTTTCAAATTT
1 ATTATTCTATTTTCAACCTTTACTTTTGACGTTATTTTTTCTATTAATTTCAGGTTTTCAAATTT
54990707 TTATCCCCCCGAACGTCTTGGGCACGACAGCTGCCCCGACATAAATCTGGTCAAGCGAGCAACAA
66 TTATCCCCCCGAACGTCTTGGGCACGACAGCTGCCCCGACATAAATCTGGTCAAGCGAGCAACAA
54990772 TTTACAGTAAACCAGTCTCTGA
131 TTTACAGTAAACCAGTCTCTGA
54990794 ATTATTCTATTTTCAACCTTTACTTTTGACGTTATTTTTTCTATTAATTTCAGGTTTTCAAATTT
1 ATTATTCTATTTTCAACCTTTACTTTTGACGTTATTTTTTCTATTAATTTCAGGTTTTCAAATTT
54990859 TTATCCCCCCGAACGTCTTGGGCACGACAGCTGCCCCGACATAAATCTGGTCAAGCGAGCAACAA
66 TTATCCCCCCGAACGTCTTGGGCACGACAGCTGCCCCGACATAAATCTGGTCAAGCGAGCAACAA
54990924 TTTACAGTAAACCAGTCTCTGA
131 TTTACAGTAAACCAGTCTCTGA
54990946 GGGATCGACC
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (152 bp):
ATTATTCTATTTTCAACCTTTACTTTTGACGTTATTTTTTCTATTAATTTCAGGTTTTCAAATTT
TTATCCCCCCGAACGTCTTGGGCACGACAGCTGCCCCGACATAAATCTGGTCAAGCGAGCAACAA
TTTACAGTAAACCAGTCTCTGA
Found at i:54996746 original size:21 final size:19
Alignment explanation
Indices: 54996722--54996767 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
54996712 AAAAAAATTA
*
54996722 ATTTTCCTATTATTATTATTT
1 ATTTTACTATT-TTATT-TTT
54996743 ATTTTTACTATTTTATTTTT
1 A-TTTTACTATTTTATTTTT
54996763 ATTTT
1 ATTTT
54996768 TATTTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 6 0.26
22 9 0.39
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTACTATTTTATTTTT
Found at i:54996768 original size:21 final size:22
Alignment explanation
Indices: 54996723--54996769 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
54996713 AAAAAATTAA
*
54996723 TTTTCCTATTATTATTATTTAT
1 TTTTACTATTATTATTATTTAT
54996745 TTTTACTATT-TTATT-TTTAT
1 TTTTACTATTATTATTATTTAT
54996765 TTTTA
1 TTTTA
54996770 TTTTTGCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 5 0.21
22 9 0.38
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTACTATTATTATTATTTAT
Found at i:54996772 original size:6 final size:6
Alignment explanation
Indices: 54996729--54996774 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
54996719 TTAATTTTCC
*
54996729 TATTAT TATTATT TATTTT TACTATTT TATTTT TATTTT TATTTT T
1 TATTTT TATT-TT TATTTT TA-T-TTT TATTTT TATTTT TATTTT T
54996775 GCAGGAAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 24 0.67
7 7 0.19
8 5 0.14
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:54997739 original size:22 final size:22
Alignment explanation
Indices: 54997714--54997760 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
54997704 GGGGAATTGA
54997714 TTAAATACTAAAGTTACATATT
1 TTAAATACTAAAGTTACATATT
54997736 TTAAATACTAAAGTTACATATT
1 TTAAATACTAAAGTTACATATT
54997758 TTA
1 TTA
54997761 TGTAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (22 bp):
TTAAATACTAAAGTTACATATT
Found at i:54997993 original size:17 final size:17
Alignment explanation
Indices: 54997959--54997992 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54997949 AGTGGGAGAA
54997959 TATTTTGGGATTTATTT
1 TATTTTGGGATTTATTT
54997976 TATTTTGGGATTT-TTT
1 TATTTTGGGATTTATTT
54997992 T
1 T
54997993 TCCTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.68
Consensus pattern (17 bp):
TATTTTGGGATTTATTT
Found at i:55004886 original size:25 final size:25
Alignment explanation
Indices: 55004815--55005040 Score: 106
Period size: 25 Copynumber: 8.8 Consensus size: 25
55004805 CAGCTCTTTC
* *
55004815 GAGCCATATAA-CAGGAAGCT-CATGT
1 GAGCCAT-TAATCGGGAAGCTCCA-GA
*
55004840 GAGCCATGTAA-CAGGAAGCTCCAGA
1 GAGCCAT-TAATCGGGAAGCTCCAGA
*
55004865 GAGCCATTAATCGGGAAGCTCCTGAAA
1 GAGCCATTAATCGGGAAGCTCC--AGA
* * * *
55004892 GAGCCTTTAATCGGGAAGGTTCAAA
1 GAGCCATTAATCGGGAAGCTCCAGA
* * * * *
55004917 CGAACCAAT-ATCGGGAAGGTTCAAGT
1 -GAGCCATTAATCGGGAA-GCTCCAGA
* * *
55004943 GAGCCAAT-ATCAGGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCCAGA
55004967 GAGCCAATTAATCGGGAAGCT-CATGAAA
1 GAGCC-ATTAATCGGGAAGCTCCA-G--A
* * * *
55004995 AAGCCTTTAATTGGGAAGCTCCAAA
1 GAGCCATTAATCGGGAAGCTCCAGA
*
55005020 GAGCCA-TATATCGGGACGCTC
1 GAGCCATTA-ATCGGGAAGCTC
55005041 ATTAGAGTTG
Statistics
Matches: 156, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
24 14 0.09
25 80 0.51
26 21 0.13
27 34 0.22
28 7 0.04
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCCAGA
Found at i:55005011 original size:103 final size:102
Alignment explanation
Indices: 55004851--55005035 Score: 282
Period size: 103 Copynumber: 1.8 Consensus size: 102
55004841 AGCCATGTAA
* * * *
55004851 CAGGAAGCTCCAGAGAGCCATTAATCGGGAAGCTCCTGAAAGAGCCTTTAATCGGGAAGGTTCAA
1 CAGGAAGCTCCAGAGAGCCATTAATCGGGAAGCTCATGAAAAAGCCTTTAATCGGGAAGCTCCAA
55004916 ACGAACCA-ATATCGGGAAGGTTCAAGTGAGCCAATAT
66 A-GAACCATATATCGGGAAGGTTCAAGTGAGCCAATAT
* *
55004953 CAGGAAGCTCCGGAGAGCCAATTAATCGGGAAGCTCATGAAAAAGCCTTTAATTGGGAAGCTCCA
1 CAGGAAGCTCCAGAGAGCC-ATTAATCGGGAAGCTCATGAAAAAGCCTTTAATCGGGAAGCTCCA
*
55005018 AAGAGCCATATATCGGGA
65 AAGAACCATATATCGGGA
55005036 CGCTCATTAG
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
102 23 0.31
103 51 0.69
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (102 bp):
CAGGAAGCTCCAGAGAGCCATTAATCGGGAAGCTCATGAAAAAGCCTTTAATCGGGAAGCTCCAA
AGAACCATATATCGGGAAGGTTCAAGTGAGCCAATAT
Found at i:55016374 original size:25 final size:25
Alignment explanation
Indices: 55016321--55016374 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
55016311 AAGCTCTTTC
*
55016321 GAGCCATATAACGAGAAGCTCATGT
1 GAGCCATATAACGAGAAGCTCATGA
* *
55016346 GAGCCATGTAACGGGAAGCTCCA-GA
1 GAGCCATATAACGAGAAGCT-CATGA
55016371 GAGC
1 GAGC
55016375 TGTTAATCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.33, C:0.22, G:0.30, T:0.15
Consensus pattern (25 bp):
GAGCCATATAACGAGAAGCTCATGA
Found at i:55016436 original size:25 final size:25
Alignment explanation
Indices: 55016407--55016461 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
55016397 AGAGCCTTTA
55016407 ATCGGGAAGGTTCAAACGAACCAAT
1 ATCGGGAAGGTTCAAACGAACCAAT
* *
55016432 ATCGGGAAGGTTCAAGCGAGCCAAT
1 ATCGGGAAGGTTCAAACGAACCAAT
55016457 ATCGG
1 ATCGG
55016462 AAAACTCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (25 bp):
ATCGGGAAGGTTCAAACGAACCAAT
Found at i:55024964 original size:23 final size:23
Alignment explanation
Indices: 55024934--55024986 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
55024924 TTATCTGCAA
55024934 GGTAAAGTAAGGAGTGTGAGCTT
1 GGTAAAGTAAGGAGTGTGAGCTT
55024957 GGTAAAGTAAGGAGTGTGAGCTT
1 GGTAAAGTAAGGAGTGTGAGCTT
55024980 GGTAAAG
1 GGTAAAG
55024987 CTCAATGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.25
Consensus pattern (23 bp):
GGTAAAGTAAGGAGTGTGAGCTT
Found at i:55033352 original size:25 final size:25
Alignment explanation
Indices: 55033324--55033404 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
55033314 ATGCTCAGAT
*
55033324 GAGCTATGAATCGGTATGCTCTCAC
1 GAGCTATGAATCGGTAAGCTCTCAC
* * * *
55033349 GAGCTGTAAATTGGTAGGCTCAT-AC
1 GAGCTATGAATCGGTAAGCTC-TCAC
*
55033374 GAGCTGTGAATCGGTAAGCTCTCAC
1 GAGCTATGAATCGGTAAGCTCTCAC
55033399 GAGCTA
1 GAGCTA
55033405 AAATTAGTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 1 0.02
25 44 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (25 bp):
GAGCTATGAATCGGTAAGCTCTCAC
Found at i:55033378 original size:50 final size:49
Alignment explanation
Indices: 55033324--55033430 Score: 142
Period size: 50 Copynumber: 2.2 Consensus size: 49
55033314 ATGCTCAGAT
* * * * *
55033324 GAGCTATGAATCGGTATGCTCTCACGAGCTGTAAATTGGTAGGCTCATAC
1 GAGCTATGAATCGGTAAGCTCTCACGAGCT-AAAATTAGTAAGCCCATAC
*
55033374 GAGCTGTGAATCGGTAAGCTCTCACGAGCTAAAATTAGTAAGCCCATAC
1 GAGCTATGAATCGGTAAGCTCTCACGAGCTAAAATTAGTAAGCCCATAC
*
55033423 AAGCTATG
1 GAGCTATG
55033431 GTGTGTCCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 21 0.43
50 28 0.57
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (49 bp):
GAGCTATGAATCGGTAAGCTCTCACGAGCTAAAATTAGTAAGCCCATAC
Found at i:55036599 original size:8 final size:8
Alignment explanation
Indices: 55036588--55036621 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
55036578 AATTTTATAT
55036588 TTTTGAAA
1 TTTTGAAA
55036596 TTTTGAAA
1 TTTTGAAA
55036604 TTTT-ATAA
1 TTTTGA-AA
55036612 TTTTGAAA
1 TTTTGAAA
55036620 TT
1 TT
55036622 ATTTATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 1 0.04
8 22 0.92
9 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (8 bp):
TTTTGAAA
Found at i:55048969 original size:49 final size:50
Alignment explanation
Indices: 55048901--55049005 Score: 169
Period size: 50 Copynumber: 2.1 Consensus size: 50
55048891 TCTTATAGAG
* * *
55048901 AACATATGGAAAGTGTT-AAACACGTTATATTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
55048950 AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
55049000 AA-ATAT
1 AACATAT
55049006 CATGTTTCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
49 20 0.38
50 32 0.62
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (50 bp):
AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
Found at i:55051024 original size:17 final size:16
Alignment explanation
Indices: 55051004--55051046 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
55050994 TTGGGTTGAG
55051004 AAAATAATTTAATTAGAA
1 AAAATAATTTAA-TA-AA
*
55051022 AAATTAATTTAATAAA
1 AAAATAATTTAATAAA
55051038 AAAATAATT
1 AAAATAATT
55051047 AACTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.43
17 2 0.09
18 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATAATTTAATAAA
Found at i:55051031 original size:18 final size:15
Alignment explanation
Indices: 55051004--55051046 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
55050994 TTGGGTTGAG
55051004 AAAATAATTTAATTAGA
1 AAAATAATTTAA-TA-A
55051021 AAAATTAATTTAATAAA
1 AAAA-TAATTTAAT-AA
55051038 AAAATAATT
1 AAAATAATT
55051047 AACTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATAATTTAATAA
Found at i:55052632 original size:9 final size:9
Alignment explanation
Indices: 55052618--55052648 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55052608 GTTAAACGAA
55052618 TCGAGTTAT
1 TCGAGTTAT
*
55052627 TCGAGTTAA
1 TCGAGTTAT
55052636 TCGAGTTAT
1 TCGAGTTAT
55052645 TCGA
1 TCGA
55052649 ATCAACTCGA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:55052720 original size:9 final size:9
Alignment explanation
Indices: 55052703--55052739 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55052693 TGATTTTTTG
55052703 AATTCGAAT
1 AATTCGAAT
*
55052712 AACTCGAAT
1 AATTCGAAT
55052721 AATTCGAAT
1 AATTCGAAT
55052730 AATTCGAAT
1 AATTCGAAT
55052739 A
1 A
55052740 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55069737 original size:25 final size:25
Alignment explanation
Indices: 55069709--55069764 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
55069699 CATCGGATTT
55069709 CTTCAGAGTAAAAGAAATGGG-AGAA
1 CTTCAGAGTAAAAGAAATGGGAAG-A
*
55069734 CTTCAGTGTAAAAGAAATGGGAAGA
1 CTTCAGAGTAAAAGAAATGGGAAGA
55069759 CTTCAG
1 CTTCAG
55069765 CGTTCGGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.20
Consensus pattern (25 bp):
CTTCAGAGTAAAAGAAATGGGAAGA
Found at i:55072550 original size:11 final size:11
Alignment explanation
Indices: 55072536--55072610 Score: 65
Period size: 11 Copynumber: 7.4 Consensus size: 11
55072526 AATTTAAAAA
55072536 AAAAGTATTTT
1 AAAAGTATTTT
*
55072547 AAAAATATTTT
1 AAAAGTATTTT
55072558 AAAA-TATTTT
1 AAAAGTATTTT
55072568 -AAAG----TT
1 AAAAGTATTTT
*
55072574 AAAA-AATTTT
1 AAAAGTATTTT
55072584 AAAAAGTATTTT
1 -AAAAGTATTTT
*
55072596 AAAAATATTTT
1 AAAAGTATTTT
55072607 AAAA
1 AAAA
55072611 TTAAAAATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
9 3 0.06
10 8 0.15
11 32 0.60
12 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:55072563 original size:10 final size:10
Alignment explanation
Indices: 55072536--55072611 Score: 61
Period size: 10 Copynumber: 7.5 Consensus size: 10
55072526 AATTTAAAAA
55072536 AAAAGTATTTT
1 AAAA-TATTTT
55072547 AAAAATATTTT
1 -AAAATATTTT
55072558 AAAATATTTT
1 AAAATATTTT
*
55072568 --AA-A-GTT
1 AAAATATTTT
*
55072574 AAAAAATTTT
1 AAAATATTTT
55072584 AAAAAGTATTTT
1 -AAAA-TATTTT
55072596 AAAAATATTTT
1 -AAAATATTTT
55072607 AAAAT
1 AAAAT
55072612 TAAAAATTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
6 2 0.04
7 1 0.02
8 4 0.07
9 1 0.02
10 17 0.31
11 16 0.29
12 14 0.25
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (10 bp):
AAAATATTTT
Found at i:55072577 original size:16 final size:16
Alignment explanation
Indices: 55072556--55072586 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55072546 TAAAAATATT
*
55072556 TTAAAATATTTTAAAG
1 TTAAAAAATTTTAAAG
55072572 TTAAAAAATTTTAAA
1 TTAAAAAATTTTAAA
55072587 AAGTATTTTA
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTAAAAAATTTTAAAG
Found at i:55072593 original size:28 final size:27
Alignment explanation
Indices: 55072545--55072598 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
55072535 AAAAAGTATT
55072545 TTAAAAATATTTTAAAATATTTTAAAG
1 TTAAAAATATTTTAAAATATTTTAAAG
55072572 TTAAAAA-ATTTTAAAAAGTATTTTAAA
1 TTAAAAATATTTT-AAAA-TATTTTAAA
55072599 AATATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.20
27 11 0.44
28 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
TTAAAAATATTTTAAAATATTTTAAAG
Found at i:55072619 original size:38 final size:38
Alignment explanation
Indices: 55072542--55072617 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 38
55072532 AAAAAAAAGT
*
55072542 ATTTTAAAAATATTTT-AAAATATTTTAAAGTTAAAAA
1 ATTTTAAAAATATTTTAAAAATATTTTAAAATTAAAAA
55072579 ATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
1 ATTTTAAAAA-TATTTTAAAAATATTTTAAAATTAAAAA
55072618 TTAAAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 10 0.28
38 6 0.17
39 20 0.56
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (38 bp):
ATTTTAAAAATATTTTAAAAATATTTTAAAATTAAAAA
Found at i:55072633 original size:38 final size:39
Alignment explanation
Indices: 55072542--55072637 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 39
55072532 AAAAAAAAGT
* *
55072542 ATTTTAAAAA-TATTTT-AAAATATTTTAAAGTTAAAAA
1 ATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
*
55072579 ATTTTAAAAAGTATTTTAAAAATATTTTAAAATT-AAAA
1 ATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
*
55072617 A-TTAAAAAATTAATTTTAAAA
1 ATTTAAAAAAGT-ATTTTAAAA
55072638 TTAAAAAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
37 18 0.34
38 20 0.38
39 15 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (39 bp):
ATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
Found at i:55072635 original size:27 final size:29
Alignment explanation
Indices: 55072602--55072655 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
55072592 TTTTAAAAAT
55072602 ATTTTAAAATT-AAAAA-TTAAAAAATTA
1 ATTTTAAAATTAAAAAATTTAAAAAATTA
55072629 ATTTTAAAATTAAAAAATTTAAAAAAT
1 ATTTTAAAATTAAAAAATTTAAAAAAT
55072656 AAATATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 11 0.44
28 5 0.20
29 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
ATTTTAAAATTAAAAAATTTAAAAAATTA
Found at i:55074960 original size:23 final size:23
Alignment explanation
Indices: 55074922--55074965 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
55074912 ATTTTATCAA
*
55074922 ATTTTTGAAACATTTTCATTGAT
1 ATTTTTGAAACATTTTAATTGAT
* *
55074945 ATTTTTGAAGCTTTTTAATTG
1 ATTTTTGAAACATTTTAATTG
55074966 TAATTGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (23 bp):
ATTTTTGAAACATTTTAATTGAT
Found at i:55079077 original size:297 final size:297
Alignment explanation
Indices: 55078543--55079143 Score: 861
Period size: 297 Copynumber: 2.0 Consensus size: 297
55078533 AGTTAGTTTT
* * * * *
55078543 TGTTTTAATAAGTGAATTAGTGTGTTTTAAGCTATTTTTTATACCCGAATTGGCCAAATGCGCCA
1 TGTTTTAATAAGTGAACTAGTGTGTTTTAAGCTATTTTTGAAACCCAAATTGGCCAAATACGCCA
* ** *
55078608 TAGGGAACCTAATGGTTGATTAAGTGTTGTAATGAGTCAATGGATTACAATAACATAATTGGTTA
66 AAGGGAACCTAATGGTTGATTAAGTACTGTAAGGAGTCAATGGATTACAATAACATAATTGGTTA
* * * ** * *
55078673 ATAAAGCAATTCATGGATTACATTAATATACTTGTATAATTGACCTCATATAGTTTTTGAATGTA
131 ATAAAGCAATTCATGAATTACATTAATACACTTGTATAATTGAACAAACATAGTTTTTGAATGCA
55078738 AAGAAAAATAGAAGAAAATATTGGCTCATGATCTGTCGTAATTTGATACATCAAATTAGGCTCTC
196 AAGAAAAATAGAAGAAAATATTGGCTCATGATCTGTCGTAATTTGATACATCAAATTAGGCTCTC
55078803 CATTACACTTGATGAGCTTATTCTCAAGAAATTTAAA
261 CATTACACTTGATGAGCTTATTCTCAAGAAATTTAAA
* * *
55078840 TGTTTTAATAAGTGAACTAGTGTGTTTTATGCTATTTTTGAAACCTAAATTGGCCAAATACGGCA
1 TGTTTTAATAAGTGAACTAGTGTGTTTTAAGCTATTTTTGAAACCCAAATTGGCCAAATACGCCA
* * * *
55078905 AAGGGAACTTAA-GAGTTGATTAAGTACTGTAGGGAGTCAATGGATTACATTAATATAATTGGTT
66 AAGGGAACCTAATG-GTTGATTAAGTACTGTAAGGAGTCAATGGATTACAATAACATAATTGGTT
* *
55078969 AATAACA-CAATTCATGAATTACA-TAATACACTTTGTATAATTGAACAAACGTGGTTTTTGAAT
130 AATAA-AGCAATTCATGAATTACATTAATACAC-TTGTATAATTGAACAAACATAGTTTTTGAAT
*
55079032 GCAAAGCAAAATAGAA-AGAAATATTGGCTCATGATCT-TCCGTAATTTGATACATCAAATTAGG
193 GCAAAGAAAAATAGAAGA-AAATATTGGCTCATGATCTGT-CGTAATTTGATACATCAAATTAGG
* * *
55079095 CTCTCCATTACACTTTATGAGCTTATTCTCGAGCAATTTAAA
256 CTCTCCATTACACTTGATGAGCTTATTCTCAAGAAATTTAAA
55079137 TGTTTTA
1 TGTTTTA
55079144 TTATATTTTT
Statistics
Matches: 270, Mismatches: 29, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
296 10 0.04
297 259 0.96
298 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (297 bp):
TGTTTTAATAAGTGAACTAGTGTGTTTTAAGCTATTTTTGAAACCCAAATTGGCCAAATACGCCA
AAGGGAACCTAATGGTTGATTAAGTACTGTAAGGAGTCAATGGATTACAATAACATAATTGGTTA
ATAAAGCAATTCATGAATTACATTAATACACTTGTATAATTGAACAAACATAGTTTTTGAATGCA
AAGAAAAATAGAAGAAAATATTGGCTCATGATCTGTCGTAATTTGATACATCAAATTAGGCTCTC
CATTACACTTGATGAGCTTATTCTCAAGAAATTTAAA
Found at i:55081336 original size:20 final size:19
Alignment explanation
Indices: 55081311--55081360 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
55081301 GACCATTAGT
55081311 TTAATTAATTTAAGGTTTAA
1 TTAATTAATTT-AGGTTTAA
* * *
55081331 TTAATTAAATTATGTTTGA
1 TTAATTAATTTAGGTTTAA
55081350 TTAACTTAATT
1 TTAA-TTAATT
55081361 ATATATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (19 bp):
TTAATTAATTTAGGTTTAA
Found at i:55081352 original size:19 final size:19
Alignment explanation
Indices: 55081311--55081362 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
55081301 GACCATTAGT
* *
55081311 TTAATTAATTTAAGGTTTAA
1 TTAATTAAATT-ATGTTTAA
*
55081331 TTAATTAAATTATGTTTGA
1 TTAATTAAATTATGTTTAA
55081350 TTAACTT-AATTAT
1 TTAA-TTAAATTAT
55081363 ATATAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (19 bp):
TTAATTAAATTATGTTTAA
Found at i:55101107 original size:31 final size:31
Alignment explanation
Indices: 55101044--55101108 Score: 112
Period size: 32 Copynumber: 2.1 Consensus size: 31
55101034 ACTTACACAT
55101044 AACATTTACGCATAATAAAACTCAAACAAAA
1 AACATTTACGCATAATAAAACTCAAACAAAA
*
55101075 AACATTATACGCATAATAAACCTCAAACAAAA
1 AACATT-TACGCATAATAAAACTCAAACAAAA
55101107 AA
1 AA
55101109 TATGAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.58, C:0.20, G:0.03, T:0.18
Consensus pattern (31 bp):
AACATTTACGCATAATAAAACTCAAACAAAA
Found at i:55103025 original size:18 final size:17
Alignment explanation
Indices: 55103002--55103035 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55102992 TTCTCATAAC
55103002 TTATAACTATAAAAAATA
1 TTATAACTA-AAAAAATA
*
55103020 TTATAATTAAAAAAAT
1 TTATAACTAAAAAAAT
55103036 GCTAATGTTT
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:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TTATAACTAAAAAAATA
Found at i:55106361 original size:21 final size:19
Alignment explanation
Indices: 55106313--55106363 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
55106303 GCCCTAGGTA
55106313 ATATGCAAA-C-ATTGTAT
1 ATATGCAAACCTATTGTAT
* *
55106330 ACATGTAAACCTATTTGTAGT
1 ATATGCAAACCTA-TTGTA-T
55106351 ATATGCAAACCTA
1 ATATGCAAACCTA
55106364 AATGTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.27
18 1 0.04
19 1 0.04
20 5 0.19
21 12 0.46
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (19 bp):
ATATGCAAACCTATTGTAT
Found at i:55106686 original size:34 final size:34
Alignment explanation
Indices: 55106604--55106692 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
55106594 AACACTATAC
* * * *
55106604 TATGATATGCGAACCCTAGGAATATGCGACCTTG
1 TATGTTATGCGAACCCTAGGTATACGCGACCTTA
* **
55106638 TATGATT-TGTGAACCCTAGGTATACGCGAGTTTA
1 TATG-TTATGCGAACCCTAGGTATACGCGACCTTA
*
55106672 TATGTTATGCGAACCGTAGGT
1 TATGTTATGCGAACCCTAGGT
55106693 TAATGCGAGC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
33 2 0.05
34 41 0.93
35 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (34 bp):
TATGTTATGCGAACCCTAGGTATACGCGACCTTA
Found at i:55108643 original size:16 final size:16
Alignment explanation
Indices: 55108609--55108646 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55108599 TGTTAATAAA
*
55108609 TTTTA-TTTCTTTTAG
1 TTTTATTTTATTTTAG
*
55108624 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAG
55108640 TTTTATT
1 TTTTATT
55108647 ATTTTTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTTTAG
Found at i:55115081 original size:23 final size:23
Alignment explanation
Indices: 55115054--55115098 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
55115044 CGAAAATATT
55115054 AAATATATATA-TTTTTATTTTTA
1 AAATATA-ATAGTTTTTATTTTTA
55115077 AAATATAATAGTTTTTTATTTT
1 AAATATAATAG-TTTTTATTTT
55115099 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 7 0.35
24 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:55115209 original size:9 final size:9
Alignment explanation
Indices: 55115195--55115222 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
55115185 TTTTGTTACA
55115195 ACAATTAAT
1 ACAATTAAT
55115204 ACAATTAAT
1 ACAATTAAT
55115213 ACAATTAAT
1 ACAATTAAT
55115222 A
1 A
55115223 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:55115244 original size:68 final size:68
Alignment explanation
Indices: 55115165--55115365 Score: 298
Period size: 59 Copynumber: 3.1 Consensus size: 68
55115155 TCAAGTTTGT
* *
55115165 TTTACTAATCAAATGTTAAATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
55115230 AAA
66 AAA
55115233 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
55115289 AAA
66 AAA
55115292 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
55115355 AAT
66 AAA
55115358 TTTACTAA
1 TTTACTAA
55115366 CAATTAATTT
Statistics
Matches: 121, Mismatches: 3, Indels: 20
0.84 0.02 0.14
Matches are distributed among these distances:
59 56 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 31 0.26
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:55115375 original size:16 final size:16
Alignment explanation
Indices: 55115354--55115395 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
55115344 AATAATTTGA
*
55115354 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
55115370 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
55115386 TAGTTTTAAT
1 TAATTTTAAT
55115396 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:55115379 original size:22 final size:23
Alignment explanation
Indices: 55115369--55115424 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
55115359 TTACTAACAA
* * *
55115369 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
55115391 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
55115414 TTAATTTTAAT
1 TTAATTTTAAT
55115425 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:55120926 original size:23 final size:23
Alignment explanation
Indices: 55120900--55120996 Score: 158
Period size: 23 Copynumber: 4.2 Consensus size: 23
55120890 TGTTATTGAT
55120900 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
**
55120923 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACATAA
*
55120946 TAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
55120969 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
55120992 CAGTG
1 CAGTG
55120997 TTGCACTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:55120953 original size:46 final size:46
Alignment explanation
Indices: 55120901--55120989 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
55120891 GTTATTGATC
55120901 AGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCGGCTACATTTT
1 AGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCGGCTACATTTT
55120947 AGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCGGCTACAT
55120990 ATCAGTGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
AGTGGTAGCTTCGGCTACATAACAGTGGTAGCTTCGGCTACATTTT
Found at i:55124571 original size:22 final size:24
Alignment explanation
Indices: 55124521--55124571 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
55124511 TTGCAATGCT
55124521 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
55124546 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
55124567 TTTAT
1 TTTAT
55124572 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:55124733 original size:20 final size:20
Alignment explanation
Indices: 55124708--55124747 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55124698 AATATTTTCC
*
55124708 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55124728 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55124748 TCATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55125278 original size:16 final size:14
Alignment explanation
Indices: 55125243--55125281 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
55125233 TGACTTGAAT
*
55125243 AATTCGAATAACTC
1 AATTCGATTAACTC
55125257 AATTCGATTAACTC
1 AATTCGATTAACTC
55125271 GAAATTCGATT
1 --AATTCGATT
55125282 TTTTTCGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (14 bp):
AATTCGATTAACTC
Found at i:55131419 original size:16 final size:16
Alignment explanation
Indices: 55131398--55131450 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
55131388 TTGGTTCGCT
**
55131398 GTAATGGAATTCAGGC
1 GTAATGGAATAAAGGC
* *
55131414 GTAATGAAATAAAGAC
1 GTAATGGAATAAAGGC
*
55131430 GTAATGGAATAGAGGC
1 GTAATGGAATAAAGGC
55131446 GTAAT
1 GTAAT
55131451 AGCAATTCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.28, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAAAGGC
Found at i:55131536 original size:39 final size:39
Alignment explanation
Indices: 55131477--55131575 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
55131467 GATTGAATAT
*
55131477 AATGGAATAGAGGCATAATAGTATTCTTGTGTTTGGTTG
1 AATGGAATAGAGGCATAATAGTATTCTTGTATTTGGTTG
* *
55131516 AATGAAATAGAGGCGTAATAGTATTCTTGTATTTGGTTG
1 AATGGAATAGAGGCATAATAGTATTCTTGTATTTGGTTG
55131555 AATGGAATAGAGGCATAATAG
1 AATGGAATAGAGGCATAATAG
55131576 CATAAGAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (39 bp):
AATGGAATAGAGGCATAATAGTATTCTTGTATTTGGTTG
Found at i:55131737 original size:29 final size:28
Alignment explanation
Indices: 55131704--55131794 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
55131694 AATAATAATT
55131704 TAAAATAATTATTATTAAATATAATTTAA
1 TAAAATAATTATTATTAAATATAATTT-A
* * *
55131733 TAAAA-AATATATAATTTAATAAAATTCT-
1 TAAAATAAT-TATTATTAAATATAATT-TA
* * *
55131761 TAATATAATTATTCTTATAT-TAATTTA
1 TAAAATAATTATTATTAAATATAATTTA
55131788 CTAAAAT
1 -TAAAAT
55131795 CATAATATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 19 0.40
29 22 0.47
30 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TAAAATAATTATTATTAAATATAATTTA
Found at i:55131749 original size:56 final size:57
Alignment explanation
Indices: 55131671--55131799 Score: 147
Period size: 56 Copynumber: 2.3 Consensus size: 57
55131661 AATAAGATTA
55131671 TTAATATAAATAATAAACAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAACAATTTAATAA-AATTCTTAAAATAATTATTATTAAAT-TAAT
* * * * *
55131729 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATTAAT
1 TTAATAAAATAATAAACAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
* *
55131785 TTACTAAAATCATAA
1 TTAATAAAATAATAA
55131800 TATATAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
55 2 0.03
56 28 0.47
57 24 0.40
58 6 0.10
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (57 bp):
TTAATAAAATAATAAACAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAAT
Found at i:55131765 original size:24 final size:23
Alignment explanation
Indices: 55131658--55131767 Score: 67
Period size: 19 Copynumber: 4.9 Consensus size: 23
55131648 GTTATTAAAT
*
55131658 TTTAATAAGATTATTAATATA-AA
1 TTTAATAAAATT-TTAATATATAA
*
55131681 --TAATAAACAATTTAATA-ATAA
1 TTTAATAAA-ATTTTAATATATAA
*
55131702 TTTAA-AATAATTATTATTAAATATAA
1 TTTAATAA-AATT-TTA--ATATATAA
55131728 TTTAATAAAA----AATATATAA
1 TTTAATAAAATTTTAATATATAA
55131747 TTTAATAAAATTCTTAATATA
1 TTTAATAAAATT-TTAATATA
55131768 ATTATTCTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 29
0.66 0.05 0.29
Matches are distributed among these distances:
19 17 0.25
20 1 0.01
21 15 0.22
22 6 0.09
23 7 0.10
24 6 0.09
25 2 0.03
26 11 0.16
27 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (23 bp):
TTTAATAAAATTTTAATATATAA
Found at i:55132206 original size:77 final size:77
Alignment explanation
Indices: 55132092--55132253 Score: 306
Period size: 77 Copynumber: 2.1 Consensus size: 77
55132082 ATTTTTTGTC
55132092 CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
55132157 ATATTGACATAA
66 ATATTGACATAA
*
55132169 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
*
55132234 TTATTGACATAA
66 ATATTGACATAA
55132246 CACTTTAA
1 CACTTTAA
55132254 GATTGTCTCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 83 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (77 bp):
CACTTTAATAATTAAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
ATATTGACATAA
Found at i:55134161 original size:31 final size:31
Alignment explanation
Indices: 55134123--55134184 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
55134113 AGTTCTTTCA
55134123 AACAACACCCTTAGCAACAAAAATTAAGTTT
1 AACAACACCCTTAGCAACAAAAATTAAGTTT
55134154 AACAACACCCTTAGCAACAAAAATTAAGTTT
1 AACAACACCCTTAGCAACAAAAATTAAGTTT
55134185 TCTTTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (31 bp):
AACAACACCCTTAGCAACAAAAATTAAGTTT
Found at i:55137669 original size:85 final size:85
Alignment explanation
Indices: 55137521--55137705 Score: 289
Period size: 85 Copynumber: 2.2 Consensus size: 85
55137511 AACACTCCAC
* * *
55137521 ATACTTGTGTTATTGCAGGTATGTCACAGGATCATCCCAAATTGGATTCTAACCTTATCTCTAAT
1 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
* *
55137586 ATTGTCTTACGTATGATGAA
66 ATTGTCTTACATATGATAAA
* * *
55137606 ATACTTATGTTGTTGCAGGTATGCCACAGGATCATCCTAAATTGAATTCTAACCTTATTTCTAAT
1 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
*
55137671 ATTGTCTTACATATGGTAAA
66 ATTGTCTTACATATGATAAA
55137691 ATACTTGTGTTGTTG
1 ATACTTGTGTTGTTG
55137706 TAAAGAAAGG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (85 bp):
ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
ATTGTCTTACATATGATAAA
Found at i:55142247 original size:16 final size:16
Alignment explanation
Indices: 55142226--55142294 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
55142216 TTGGTTCGCT
55142226 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
55142242 GTAATGTAATAGAGGC
1 GTAATGGAATAGAGGC
* *
55142258 GTAATGGATTAGAAGC
1 GTAATGGAATAGAGGC
*
55142274 GTAATGGATTAGAGGC
1 GTAATGGAATAGAGGC
55142290 GTAAT
1 GTAAT
55142295 AGCAATTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:55142332 original size:45 final size:44
Alignment explanation
Indices: 55142274--55142363 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
55142264 GATTAGAAGC
* *
55142274 GTAATGGATTAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGCAATAG-AATTC-ATGTGTTTGGTTGAAT
* * *
55142319 GTAATGGAATAGAGGTGCAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGCAATAGAATTCATGTGTTTGGTTGAAT
55142363 G
1 G
55142364 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.03
44 18 0.46
45 20 0.51
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.37
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGCAATAGAATTCATGTGTTTGGTTGAAT
Found at i:55142547 original size:18 final size:17
Alignment explanation
Indices: 55142526--55142560 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55142516 TTATTATTAA
*
55142526 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55142544 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55142561 TCTTAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55142686 original size:17 final size:17
Alignment explanation
Indices: 55142646--55142679 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55142636 TTATTATTAA
55142646 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55142663 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55142680 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55142715 original size:119 final size:119
Alignment explanation
Indices: 55142506--55142979 Score: 763
Period size: 119 Copynumber: 4.0 Consensus size: 119
55142496 TTAACCATAT
* *
55142506 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAGT
1 TTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATAATTTAATAAAATTCTTAATATT
* * * * * * *
55142571 CAATATTCTTATCTGAATTTACTAAAATAATAACATATGATACTATAAAATATAT
65 AAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
55142626 TTTAACATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTCTTAATATTA
1 TTTAACATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTCTTAATATTA
* **
55142691 AATATTATTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
55142745 TTTAACATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTCTTAATATTA
1 TTTAACATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTCTTAATATTA
* *
55142810 AATACTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATAA
66 AATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
* * *
55142864 TTTAAAATAATTATTATTAATTATAATTTAAT-AAA-ATATAATTTAATAAAATTATTAATATTA
1 TTTAACATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTCTTAATATTA
*
55142927 AATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
66 AATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATA
55142980 GATTAATAAT
Statistics
Matches: 335, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
117 79 0.24
118 3 0.01
119 223 0.67
120 30 0.09
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (119 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAATATATAATTTAATAAAATTCTTAATATTA
AATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
Found at i:55142769 original size:41 final size:41
Alignment explanation
Indices: 55142605--55142920 Score: 139
Period size: 41 Copynumber: 7.9 Consensus size: 41
55142595 AAATAATAAC
* *
55142605 ATATGATACTATAAAATATATTTTAACATAATTATTATTAA
1 ATATAATACTATAAAATATAATTTAACATAATTATTATTAA
* * * * *
55142646 ATATAAT-TTAATAAAATATATAATTTAATAAAATTCTTAAT-A
1 ATATAATACT-AT-AAA-ATATAATTTAACATAATTATTATTAA
* ** * * *
55142688 TTA-AATA-T-TATTATATGAATTT-TC-TAA-AATCA-TAA
1 ATATAATACTATAAAATAT-AATTTAACATAATTATTATTAA
55142723 TATATAATACTATAAAATATAATTTAACATAATTATTATTAA
1 -ATATAATACTATAAAATATAATTTAACATAATTATTATTAA
* * * * *
55142765 ATATAAT-TTAATAAAATATATAATTTAATAAAATTCTTAAT-A
1 ATATAATACT-AT-AAA-ATATAATTTAACATAATTATTATTAA
* * * * *
55142807 TTA-AATACTCT--TATATGAATTT-A-ATAA-AATCA-TAA
1 ATATAATACTATAAAATAT-AATTTAACATAATTATTATTAA
* *
55142842 TATATAATACTATATAATATAATTTAAAATAATTATTATTAA
1 -ATATAATACTATAAAATATAATTTAACATAATTATTATTAA
* * * *
55142884 TTATAAT-TTAATAAAATATAATTTAATAAAATTATTA
1 ATATAATACT-ATAAAATATAATTTAACATAATTATTA
55142921 ATATTAAATA
Statistics
Matches: 201, Mismatches: 45, Indels: 58
0.66 0.15 0.19
Matches are distributed among these distances:
34 2 0.01
35 6 0.03
36 9 0.04
37 20 0.10
38 22 0.11
39 13 0.06
40 10 0.05
41 61 0.30
42 19 0.09
43 39 0.19
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (41 bp):
ATATAATACTATAAAATATAATTTAACATAATTATTATTAA
Found at i:55142781 original size:15 final size:15
Alignment explanation
Indices: 55142734--55142915 Score: 77
Period size: 15 Copynumber: 11.5 Consensus size: 15
55142724 ATATAATACT
55142734 ATAAAATATAATTTA
1 ATAAAATATAATTTA
* *
55142749 ACATAAT-T-A-TT-
1 ATAAAATATAATTTA
*
55142760 ATTAAATATAATTTA
1 ATAAAATATAATTTA
55142775 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
*
55142792 ATAAAATTCTTAATATTAA
1 ATAAAA-T-ATAAT-TT-A
**
55142811 ATACTCTTATATGAATTTA
1 ATA---AAATAT-AATTTA
55142830 ATAAAATCATAATATATA
1 ATAAAAT-ATAAT-T-TA
** *
55142848 ATACTATATAATATA
1 ATAAAATATAATTTA
* *
55142863 ATTTAAA-ATAATTATT
1 A-TAAAATATAATT-TA
* *
55142879 ATTAATTATAATTTA
1 ATAAAATATAATTTA
55142894 ATAAAATATAATTTA
1 ATAAAATATAATTTA
55142909 ATAAAAT
1 ATAAAAT
55142916 TATTAATATT
Statistics
Matches: 123, Mismatches: 24, Indels: 40
0.66 0.13 0.21
Matches are distributed among these distances:
11 4 0.03
12 3 0.02
13 2 0.02
14 3 0.02
15 41 0.33
16 21 0.17
17 24 0.20
18 9 0.07
19 8 0.07
20 3 0.02
21 4 0.03
22 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:55142807 original size:22 final size:18
Alignment explanation
Indices: 55142764--55142798 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
55142754 ATTATTATTA
55142764 AATATAATTTAATAAAAT
1 AATATAATTTAATAAAAT
55142782 -ATATAATTTAATAAAAT
1 AATATAATTTAATAAAAT
55142799 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAATTTAATAAAAT
Found at i:55142909 original size:26 final size:26
Alignment explanation
Indices: 55142859--55142927 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 26
55142849 TACTATATAA
*
55142859 TATAATTTAAAATAATTATTATTAAT
1 TATAATTTAAAATAATTAATATTAAT
55142885 TATAATTT--AATAA--AATA-TAAT
1 TATAATTTAAAATAATTAATATTAAT
*
55142906 T-TAA-T-AAAATTATTAATATTAA
1 TATAATTTAAAATAATTAATATTAA
55142928 ATATTCTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 1 0.03
20 7 0.19
21 5 0.14
22 7 0.19
23 3 0.08
24 5 0.14
26 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TATAATTTAAAATAATTAATATTAAT
Found at i:55157498 original size:16 final size:18
Alignment explanation
Indices: 55157459--55157504 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
55157449 TTTCTTTTTC
*
55157459 TTTTATGTTTATGTTTAT
1 TTTTATTTTTATGTTTAT
*
55157477 TGTTATTTTTA-G-TTAT
1 TTTTATTTTTATGTTTAT
55157493 TTTTATTTTTAT
1 TTTTATTTTTAT
55157505 TTTCTTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 14 0.58
17 1 0.04
18 9 0.38
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTATGTTTAT
Found at i:55157506 original size:6 final size:6
Alignment explanation
Indices: 55157436--55157507 Score: 51
Period size: 6 Copynumber: 12.5 Consensus size: 6
55157426 AGTTTCTCTG
* * * * * * *
55157436 TTTTCT TTTTAG TTTTCT TTTT-C TTTTAT GTTTAT GTTTAT TGTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
55157483 TTTTA- -GTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
55157508 CTTAGAATTA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
4 3 0.06
5 4 0.08
6 44 0.86
ACGTcount: A:0.12, C:0.04, G:0.07, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:55157556 original size:26 final size:26
Alignment explanation
Indices: 55157489--55157556 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
55157479 TTATTTTTAG
*
55157489 TTATTTTTATTTTTATTTTCTTAGAA
1 TTATTTTTATTTTTATCTTCTTAGAA
* * *
55157515 TTA-TTTCATTTCTTATCTT-TTGGAC
1 TTATTTTTATTT-TTATCTTCTTAGAA
55157540 TATATTTTTATTTTTAT
1 T-TATTTTTATTTTTAT
55157557 GGTTGTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 12 0.35
26 15 0.44
27 7 0.21
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (26 bp):
TTATTTTTATTTTTATCTTCTTAGAA
Found at i:55165618 original size:119 final size:120
Alignment explanation
Indices: 55165442--55165664 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
55165432 TACTCGTTCA
* *
55165442 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
*
55165507 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * *
55165562 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* * * *
55165624 ATATGGTCACTTAGCATAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
55165665 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 67 0.74
120 19 0.21
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:55165664 original size:40 final size:40
Alignment explanation
Indices: 55165421--55165664 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
55165411 CGGAATTTAA
** *
55165421 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
55165461 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55165501 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55165541 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55165580 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
55165620 CCGGATATGGTCACTTAGCATAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
55165660 CCGGA
1 CCGGA
55165665 CATCATTCAA
Statistics
Matches: 178, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.18
40 133 0.75
41 11 0.06
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55170687 original size:22 final size:21
Alignment explanation
Indices: 55170661--55170723 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 21
55170651 TGTGAATTTA
55170661 ATTTTTATATTTTAATTTGTTT
1 ATTTTTATATTTTAATTT-TTT
*
55170683 A-TTTTA-ATTTTTATATTTTT
1 ATTTTTATATTTTAAT-TTTTT
55170703 ATGTTTTATATTTTGAATTTT
1 AT-TTTTATATTTT-AATTTT
55170724 GAATTTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 11 0.32
21 7 0.21
22 6 0.18
23 8 0.24
24 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
ATTTTTATATTTTAATTTTTT
Found at i:55170700 original size:8 final size:8
Alignment explanation
Indices: 55170657--55170716 Score: 53
Period size: 7 Copynumber: 8.2 Consensus size: 8
55170647 AAGCTGTGAA
55170657 TTTA-ATT
1 TTTATATT
55170664 TTTATA-T
1 TTTATATT
55170671 TTTA-ATT
1 TTTATATT
55170678 TGTT-TA-T
1 T-TTATATT
55170685 TTTA-ATT
1 TTTATATT
55170692 TTTATATT
1 TTTATATT
*
55170700 TTTAT-GT
1 TTTATATT
55170707 TTTATATT
1 TTTATATT
55170715 TT
1 TT
55170717 GAATTTTGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
6 4 0.09
7 24 0.56
8 15 0.35
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (8 bp):
TTTATATT
Found at i:55170709 original size:15 final size:14
Alignment explanation
Indices: 55170657--55170723 Score: 91
Period size: 14 Copynumber: 4.6 Consensus size: 14
55170647 AAGCTGTGAA
55170657 TTTAATTTTTATAT
1 TTTAATTTTTATAT
55170671 TTTAATTTGTT-TAT
1 TTTAATTT-TTATAT
55170685 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
55170699 TTTTATGTTTTATAT
1 TTTAAT-TTTTATAT
55170714 TTTGAATTTT
1 TTT-AATTTT
55170724 GAATTTTGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.04
14 27 0.57
15 16 0.34
16 2 0.04
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (14 bp):
TTTAATTTTTATAT
Done.