Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 133 of 135
Found at i:41070742 original size:20 final size:20
Alignment explanation
Indices: 41070701--41070742 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
41070691 TACATTCAAA
* *
41070701 AAAAATATTTATTATTTTAT
1 AAAAATATTAATTATTTAAT
41070721 AAAAATAATTAATT-TTTAAT
1 AAAAAT-ATTAATTATTTAAT
41070741 AA
1 AA
41070743 TTTCATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAATATTAATTATTTAAT
Found at i:41081674 original size:2 final size:2
Alignment explanation
Indices: 41081667--41081694 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41081657 TGTTTTTCAG
41081667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41081695 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41081699 original size:2 final size:2
Alignment explanation
Indices: 41081694--41081724 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41081684 ATATATATAT
41081694 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41081725 ACTTGTAAAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41083682 original size:3 final size:3
Alignment explanation
Indices: 41083674--41083703 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41083664 ACCATTTGAG
41083674 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41083704 TAGACTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41085352 original size:49 final size:46
Alignment explanation
Indices: 41085271--41085377 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 46
41085261 TAATATAATG
* * *
41085271 ATTTTACCTTTTAACTTAATAAGTAAATATTTATTAAAACGACATA
1 ATTTTACCTTTTAACTTAAAAAGTAAACATTTATCAAAACGACATA
*
41085317 ATTTTGCCTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACGACATA
1 ATTTTACCTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACGACATA
* *
41085366 GTTTTACTTTTT
1 ATTTTACCTTTT
41085378 TTTTCGGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 14 0.27
47 3 0.06
48 3 0.06
49 31 0.61
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (46 bp):
ATTTTACCTTTTAACTTAAAAAGTAAACATTTATCAAAACGACATA
Found at i:41089334 original size:199 final size:198
Alignment explanation
Indices: 41088993--41089389 Score: 731
Period size: 199 Copynumber: 2.0 Consensus size: 198
41088983 ATAAACAAAT
41088993 AAATAAAACATGTTCTAGTTTGAGATGTATATTCTAACACAAACTACATGCTATACGTATGAAGA
1 AAATAAAACATGTTCTAGTTTGAGATGTATATTCTAACACAAACTACATGCTATACGTATGAAGA
* * *
41089058 TATGTTACATGTATGAGCATGAAAATGAAAAAAATGTAGTAATATATATATTCAAACACTTGTTA
66 TATGTTACATGCATCAGCATGAAAATGAAAAAAATGAAGTAATATATATATTCAAACACTTGTTA
*
41089123 GAAATTCAGCTCATATAGTAGCTGGCAAAATTTACACAAATGAATCACAAAGGTTTGACATCTTT
131 GAAATACAGCTCATATAGTAGCTGGCAAAATTTACACAAATGAATCACAAAGG-TTGACATCTTT
41089188 CTAC
195 CTAC
*
41089192 AAATAAAATATGTTCTAGTTTGAGATGTATATTCTAACACAAACTACATGCTATACGTATGAAGA
1 AAATAAAACATGTTCTAGTTTGAGATGTATATTCTAACACAAACTACATGCTATACGTATGAAGA
41089257 TATGTTACATGCATCAGCATGAAAATGAAAAAAATGAAGTAATATATATATTCAAACACTTGTTA
66 TATGTTACATGCATCAGCATGAAAATGAAAAAAATGAAGTAATATATATATTCAAACACTTGTTA
*
41089322 GAAATACAGCTCATATAGTAGCTGGTAAAATTTACACAAATGAATCACAAAGGTTGACATCTTTC
131 GAAATACAGCTCATATAGTAGCTGGCAAAATTTACACAAATGAATCACAAAGGTTGACATCTTTC
41089387 TAC
196 TAC
41089390 CACCAAATTC
Statistics
Matches: 192, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
198 15 0.08
199 177 0.92
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (198 bp):
AAATAAAACATGTTCTAGTTTGAGATGTATATTCTAACACAAACTACATGCTATACGTATGAAGA
TATGTTACATGCATCAGCATGAAAATGAAAAAAATGAAGTAATATATATATTCAAACACTTGTTA
GAAATACAGCTCATATAGTAGCTGGCAAAATTTACACAAATGAATCACAAAGGTTGACATCTTTC
TAC
Found at i:41091387 original size:17 final size:16
Alignment explanation
Indices: 41091367--41091407 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
41091357 TATATTATTT
41091367 TATTTTATTTTATTTAA
1 TATTTTATTTTA-TTAA
*
41091384 TATTTAATTTTATTAA
1 TATTTTATTTTATTAA
*
41091400 AATTTTAT
1 TATTTTAT
41091408 ATATAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTTATTTTATTAA
Found at i:41091422 original size:23 final size:23
Alignment explanation
Indices: 41091378--41091428 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
41091368 ATTTTATTTT
* * *
41091378 ATTTAATATTTAATTTTATTAAA
1 ATTTTATATATAATTATATTAAA
* *
41091401 ATTTTATATATAATTATCTTAAT
1 ATTTTATATATAATTATATTAAA
41091424 ATTTT
1 ATTTT
41091429 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTTATATATAATTATATTAAA
Found at i:41091714 original size:23 final size:23
Alignment explanation
Indices: 41091688--41091738 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
41091678 ATTTAATCTT
*
41091688 TTTTAACTTTGACCCATTCAAAA
1 TTTTAACTTTGACCCATCCAAAA
* *
41091711 TTTTAACTTTGGCCCCTCCAAAA
1 TTTTAACTTTGACCCATCCAAAA
41091734 TTTTA
1 TTTTA
41091739 TAATTTTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (23 bp):
TTTTAACTTTGACCCATCCAAAA
Found at i:41093936 original size:140 final size:140
Alignment explanation
Indices: 41093683--41093954 Score: 436
Period size: 140 Copynumber: 1.9 Consensus size: 140
41093673 TGTGTTTTAG
* * * *
41093683 AATGATCGATAGAGGCATGAAGTTTTTTGCTTGGTTTGTGCTTTGTTGTACCTTCTCAGGGCTGC
1 AATGATCAATAGAGGAATGAAGTTTTTTGCTCGGTTTGTGCTTCGTTGTACCTTCTCAGGGCTGC
* * * *
41093748 TATAAGTAGTTTTGTTCTTGTGTGTTTATGTTGAAGTTATTTGTTGTAACTATATAGTTCATTTA
66 TATAAGGAGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAACTATATAGTTCATTTA
41093813 TTAGTGATTA
131 TTAGTGATTA
* *
41093823 AATGATCAATAGAGGAATGAAGTTTTTTGCTCGGTTTGTGCTTCGTTTTACCTTGTCAGGGCTGC
1 AATGATCAATAGAGGAATGAAGTTTTTTGCTCGGTTTGTGCTTCGTTGTACCTTCTCAGGGCTGC
* *
41093888 TATAAGGGGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAATTATATAGTTCATTTA
66 TATAAGGAGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAACTATATAGTTCATTTA
41093953 TT
131 TT
41093955 GTTTTAAGCA
Statistics
Matches: 120, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
140 120 1.00
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (140 bp):
AATGATCAATAGAGGAATGAAGTTTTTTGCTCGGTTTGTGCTTCGTTGTACCTTCTCAGGGCTGC
TATAAGGAGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAACTATATAGTTCATTTA
TTAGTGATTA
Found at i:41094162 original size:197 final size:195
Alignment explanation
Indices: 41093823--41094239 Score: 591
Period size: 197 Copynumber: 2.1 Consensus size: 195
41093813 TTAGTGATTA
* * * *
41093823 AATGATCAATAGAGGAATGAAGTTTTTTGCTCGGTTTGTGCTTCGTTTTACCTTGTCAGGGCTGC
1 AATGATCAGTAGAGGAATGAAGTTTTTTGCTCGGTGTGTGCTTCATTTCACCTTGTCAGGGCTGC
* * *
41093888 TATAAGGGGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAATTATATAGTTCATTTA
66 TATAAGGAGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAACTATACAGTTCATTTA
* * * * * * *
41093953 TTGTTTTAAGCATATCAACCATGTGGTAATCCCGGTTAATAACAACATCGATTATTAGAGTTTAG
131 TCGGTCTAAGCATATCAACCATATGGTAATCCCGGTCAATAACAACATCAATTATTACAGTTTAG
41094018 AATATGATCAGTAGAGGAATGAAGTTTTTTGCTCGGTGTGTGCTTCATTTCACCTTGTCAGGGCT
1 -A-ATGATCAGTAGAGGAATGAAGTTTTTTGCTCGGTGTGTGCTTCATTTCACCTTGTCAGGGCT
* * **
41094083 GCTATAAGGAGTTTTGTTCTTGTGTGTTTATGTTGAAGTTATTTGCTGTAACTATACAGTTTGTT
64 GCTATAAGGAGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAACTATACAGTTCATT
* * * ** *
41094148 TGTCGGTCTAAGCATATCAACCATATGGTAATTCTGGTCAATAATGACATCAATTATTACTGTTT
129 TATCGGTCTAAGCATATCAACCATATGGTAATCCCGGTCAATAACAACATCAATTATTACAGTTT
41094213 AG
194 AG
*
41094215 AATGACCAGTAGAGGAATGAAGTTT
1 AATGATCAGTAGAGGAATGAAGTTT
41094240 CTTTCTTGGT
Statistics
Matches: 195, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
195 23 0.12
196 2 0.01
197 170 0.87
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (195 bp):
AATGATCAGTAGAGGAATGAAGTTTTTTGCTCGGTGTGTGCTTCATTTCACCTTGTCAGGGCTGC
TATAAGGAGTTCTGTTCTTGTGTGTTTATGTTGAAGTTATATGCTGTAACTATACAGTTCATTTA
TCGGTCTAAGCATATCAACCATATGGTAATCCCGGTCAATAACAACATCAATTATTACAGTTTAG
Found at i:41105774 original size:28 final size:29
Alignment explanation
Indices: 41105731--41105787 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
41105721 AAATGTTAAT
*
41105731 TTTTAAAAATAATTATCGAATTAGATCGA
1 TTTTAAAAATAATTATAGAATTAGATCGA
*
41105760 TTTTAAAAA-AATTATAGGATTAGATCGA
1 TTTTAAAAATAATTATAGAATTAGATCGA
41105788 AAACGCTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (29 bp):
TTTTAAAAATAATTATAGAATTAGATCGA
Found at i:41114283 original size:17 final size:18
Alignment explanation
Indices: 41114253--41114288 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41114243 TACATAACCA
41114253 TTTTATATGCTTATAAAT
1 TTTTATATGCTTATAAAT
*
41114271 TTTTATTTG-TTATAAAT
1 TTTTATATGCTTATAAAT
41114288 T
1 T
41114289 ACATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTTATATGCTTATAAAT
Found at i:41120886 original size:30 final size:32
Alignment explanation
Indices: 41120852--41120915 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
41120842 TTACAAAATT
* *
41120852 AAAACACGAT-AAT-ATATAAGTTTAATTTTA
1 AAAACACGATGAATGATATAAGATTAAATTTA
* *
41120882 AAAACATGATGAATGATATTAGATTAAATTTA
1 AAAACACGATGAATGATATAAGATTAAATTTA
41120914 AA
1 AA
41120916 TAAATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.32
31 3 0.11
32 16 0.57
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (32 bp):
AAAACACGATGAATGATATAAGATTAAATTTA
Found at i:41121078 original size:2 final size:2
Alignment explanation
Indices: 41121071--41121111 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41121061 TAGAAACTTA
41121071 AT 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 AT A
41121112 AGAAAAATGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41126513 original size:14 final size:14
Alignment explanation
Indices: 41126496--41126528 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
41126486 TATTGTTACA
41126496 TGATAATTAGATAG
1 TGATAATTAGATAG
41126510 TGATAATTAGATAG
1 TGATAATTAGATAG
41126524 TGATA
1 TGATA
41126529 GTGGCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
TGATAATTAGATAG
Found at i:41127403 original size:50 final size:50
Alignment explanation
Indices: 41127328--41127429 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
41127318 ACACTGTAAT
41127328 AAAATTGTAATGGAATAGAATAAGGTCCCAAATATTACATAATTTGGATG
1 AAAATTGTAATGGAATAGAATAAGGTCCCAAATATTACATAATTTGGATG
41127378 AAAATTGTAATGGAATAGAATAAGGTCCCAAATATTACATAATTTGGATG
1 AAAATTGTAATGGAATAGAATAAGGTCCCAAATATTACATAATTTGGATG
41127428 AA
1 AA
41127430 TAGAAAAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (50 bp):
AAAATTGTAATGGAATAGAATAAGGTCCCAAATATTACATAATTTGGATG
Found at i:41127449 original size:50 final size:50
Alignment explanation
Indices: 41127336--41127449 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 50
41127326 ATAAAATTGT
* ****
41127336 AATGGAATAGAATAAGGTCCCAAATATTACATAATTTGGATGAAAATTGT
1 AATGCAATAGAATAAGGTCCCAAATATTACATAATTTGGATGAAAAGAAA
* *
41127386 AATGGAATAGAATAAGGTCCCAAATATTACATAATTTGGATGAATAGAAA
1 AATGCAATAGAATAAGGTCCCAAATATTACATAATTTGGATGAAAAGAAA
41127436 AATGACAAT-GAATA
1 AATG-CAATAGAATA
41127450 GGTTAGATCG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 54 0.95
51 3 0.05
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (50 bp):
AATGCAATAGAATAAGGTCCCAAATATTACATAATTTGGATGAAAAGAAA
Found at i:41143295 original size:75 final size:75
Alignment explanation
Indices: 41143203--41143544 Score: 585
Period size: 75 Copynumber: 4.6 Consensus size: 75
41143193 ATGGGAATTG
*
41143203 GGGTTCTGACCTAACTGGCTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
1 GGGTTCTGACCTGACTGGCTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
*
41143268 ACTGGAACCA
66 TCTGGAACCA
* * *
41143278 GGGTTCTGATCTGACTGGCTCTCTTATATTCTGGCCCATATTTTGAGGTGGTTGTCGTGGTGGAT
1 GGGTTCTGACCTGACTGGCTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
*
41143343 TTTGGAACCA
66 TCTGGAACCA
41143353 GGGTTCTGACCTGACTGGCTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
1 GGGTTCTGACCTGACTGGCTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
*
41143418 TTTGGAACCA
66 TCTGGAACCA
* *
41143428 GGGTTCTGACCTGACTGGCTCTCTTTTATTATGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
1 GGGTTCTGACCTGACTGGCTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
41143493 TCTGGAACCA
66 TCTGGAACCA
* *
41143503 GGGTTCTGACCTGACTGACTCTCTTGTACTCTGGCCCATATT
1 GGGTTCTGACCTGACTGGCTCTCTTGTATTCTGGCCCATATT
41143545 AGGTTGTTCA
Statistics
Matches: 251, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 251 1.00
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.36
Consensus pattern (75 bp):
GGGTTCTGACCTGACTGGCTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
TCTGGAACCA
Found at i:41153857 original size:14 final size:15
Alignment explanation
Indices: 41153838--41153871 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41153828 AAAAATCGTG
*
41153838 ATAAAAA-TAAGTAA
1 ATAAAAATTAAATAA
41153852 ATAAAAATTAAATAA
1 ATAAAAATTAAATAA
41153867 ATAAA
1 ATAAA
41153872 GACCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
ATAAAAATTAAATAA
Found at i:41154315 original size:28 final size:28
Alignment explanation
Indices: 41154283--41154375 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
41154273 TTTTTTTTCA
41154283 ATCACTCAATTATGAATTTTTTAAATTG
1 ATCACTCAATTATGAATTTTTTAAATTG
* * *
41154311 ATCACTTAATTATGAAATTTTT-CA---
1 ATCACTCAATTATGAATTTTTTAAATTG
* *
41154335 ATCACTCAAATATAAATATTTTTAAATTG
1 ATCACTCAATTATGAAT-TTTTTAAATTG
*
41154364 ATCACTTAATTA
1 ATCACTCAATTA
41154376 ATCGAAATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
24 13 0.26
25 5 0.10
26 1 0.02
27 1 0.02
28 20 0.40
29 10 0.20
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (28 bp):
ATCACTCAATTATGAATTTTTTAAATTG
Found at i:41154363 original size:53 final size:54
Alignment explanation
Indices: 41154276--41154384 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 54
41154266 TATGTGATTT
* *
41154276 TTTTTCAATCACTCAATTATGAATTTTTTAAATTGATCACTTAATT-AT-GAAA
1 TTTTTCAATCACTCAAATATAAATTTTTTAAATTGATCACTTAATTAATCGAAA
41154328 TTTTTCAATCACTCAAATATAAATATTTTTAAATTGATCACTTAATTAATCGAAA
1 TTTTTCAATCACTCAAATATAAAT-TTTTTAAATTGATCACTTAATTAATCGAAA
41154383 TT
1 TT
41154385 ATTATTTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
52 22 0.42
53 22 0.42
54 2 0.04
55 6 0.12
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.45
Consensus pattern (54 bp):
TTTTTCAATCACTCAAATATAAATTTTTTAAATTGATCACTTAATTAATCGAAA
Found at i:41154573 original size:23 final size:23
Alignment explanation
Indices: 41154540--41154584 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41154530 GGATCAAATT
* *
41154540 AAAAAATTTATAGTTGAATGATA
1 AAAAAAATTATAATTGAATGATA
*
41154563 AAAAAAATTATAATTGGATGAT
1 AAAAAAATTATAATTGAATGAT
41154585 GAATTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (23 bp):
AAAAAAATTATAATTGAATGATA
Found at i:41154819 original size:17 final size:18
Alignment explanation
Indices: 41154786--41154820 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41154776 TAAAAAGAAA
41154786 ATATTTTATATAAAATAT
1 ATATTTTATATAAAATAT
*
41154804 ATATTTTTTA-AAAATAT
1 ATATTTTATATAAAATAT
41154821 TCAACCATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTTATATAAAATAT
Found at i:41160951 original size:31 final size:31
Alignment explanation
Indices: 41160890--41160968 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
41160880 CTTTTTTTGG
*
41160890 TCTAATTTAGTA-CTCAAACTTGACAA-TTTT
1 TCTAATTTGGTACCT-AAACTTGACAATTTTT
**
41160920 TCTTAATTTGGTACCTAAACTTGACTCTTTTT
1 TC-TAATTTGGTACCTAAACTTGACAATTTTT
*
41160952 TCTAATTTGGTCCCTAA
1 TCTAATTTGGTACCTAA
41160969 TATTTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 2 0.05
31 32 0.76
32 8 0.19
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (31 bp):
TCTAATTTGGTACCTAAACTTGACAATTTTT
Found at i:41161179 original size:31 final size:31
Alignment explanation
Indices: 41161141--41161212 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
41161131 AAAAGCTTAG
41161141 GTACCAAATTAGGAAAAAATGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAATGTCAAGTTCAA
*
41161172 GTACCAAATTAGGAAAAATTGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAATGTCAAGTTCAA
*
41161203 GTATCAAATT
1 GTACCAAATT
41161213 GGGTCAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAGGAAAAAATGTCAAGTTCAA
Found at i:41174967 original size:20 final size:20
Alignment explanation
Indices: 41174930--41174967 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41174920 TTAATTTTTA
*
41174930 TTTATCTTTAAATTTTATCT
1 TTTATCTTTAAATGTTATCT
41174950 TTTAT-TTTATAATGTTAT
1 TTTATCTTTA-AATGTTAT
41174968 TAGTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTATCTTTAAATGTTATCT
Found at i:41188654 original size:3 final size:3
Alignment explanation
Indices: 41188646--41188677 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41188636 TAGATAGTTA
41188646 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41188678 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41192727 original size:18 final size:18
Alignment explanation
Indices: 41192704--41192746 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41192694 CGTCGTTGCT
*
41192704 ATCATCGCCATCATTGTC
1 ATCATCGCCATCATTATC
* *
41192722 ATCATCACCTTCATTATC
1 ATCATCGCCATCATTATC
41192740 ATCATCG
1 ATCATCG
41192747 GACCAGGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.33, G:0.07, T:0.35
Consensus pattern (18 bp):
ATCATCGCCATCATTATC
Found at i:41192871 original size:3 final size:3
Alignment explanation
Indices: 41192863--41192898 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
41192853 CTGTAAAAAG
* *
41192863 ATC ATC ATC ATC GTC GTC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
41192899 TTCTTCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.06, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:41193028 original size:183 final size:180
Alignment explanation
Indices: 41192769--41193139 Score: 607
Period size: 183 Copynumber: 2.0 Consensus size: 180
41192759 TTCGAGTTGA
41192769 GTTTTCGATTTCGAGGCAGAATTGACAACTCTGCAACTGGCGCATCATTGTCCTCATCGGCGTCA
1 GTTTTCGATTTCGAGGCAGAATTGACAACTCTGCAACTGGCGCATCATTGTCCTCATCGGCGTCA
41192834 TCACCATCATCATCAATAGCTGTAAAAAGATCATCATCATCGTCGTCATCATCATCATCATCATC
66 TCACCATCATCATCAATAGCTGTAAAAAGATCATCATCATCGTCGTCATCATCATCATCATCA--
* * * *
41192899 TTCTTCTTCTTCACCGTTCGACCAATCTAAGGAGAACAAACGACGGGAAGCTT
129 -TCATCTTCTTCACCGTTCAACCAATCTAAGGAGAACAAACGACAGGAAGCTC
* *
41192952 GTTTTCGATTTCGGGGCAGAATTGACAACTCTGCAACTGGCGCATCATTGTCCTCATCGTCGTCA
1 GTTTTCGATTTCGAGGCAGAATTGACAACTCTGCAACTGGCGCATCATTGTCCTCATCGGCGTCA
* * * * *
41193017 TCACCATCATCATCAATAGCTTTAAAAAGATCATCGTCGTCGTCGTCGTCGTCATCATCATCATC
66 TCACCATCATCATCAATAGCTGTAAAAAGATCATCATCATCGTCGTCATCATCATCATCATCATC
*
41193082 ATCTTCTTCACCGTTTAACCAATCTAAGGAGAACAAACGACAGGAAGCTC
131 ATCTTCTTCACCGTTCAACCAATCTAAGGAGAACAAACGACAGGAAGCTC
41193132 GTTTTCGA
1 GTTTTCGA
41193140 ACCTTTTGCA
Statistics
Matches: 176, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
180 55 0.31
183 121 0.69
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (180 bp):
GTTTTCGATTTCGAGGCAGAATTGACAACTCTGCAACTGGCGCATCATTGTCCTCATCGGCGTCA
TCACCATCATCATCAATAGCTGTAAAAAGATCATCATCATCGTCGTCATCATCATCATCATCATC
ATCTTCTTCACCGTTCAACCAATCTAAGGAGAACAAACGACAGGAAGCTC
Found at i:41199658 original size:23 final size:23
Alignment explanation
Indices: 41199632--41199678 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41199622 AAAATTTTAA
*
41199632 TAAATA-AAAATATATGAAATTAT
1 TAAATATAAAATAT-TAAAATTAT
*
41199655 TAAATATTAAATATTAAAATTAT
1 TAAATATAAAATATTAAAATTAT
41199678 T
1 T
41199679 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAATATAAAATATTAAAATTAT
Found at i:41199698 original size:15 final size:14
Alignment explanation
Indices: 41199651--41199699 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
41199641 ATATATGAAA
41199651 TTATTAAATATTAA-
1 TTATTAAA-ATTAAT
* *
41199665 ATATTAAAATTATT
1 TTATTAAAATTAAT
41199679 TTATTAAAATTAGAT
1 TTATTAAAATTA-AT
41199694 TTATTA
1 TTATTA
41199700 TAACGTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 4 0.14
14 18 0.62
15 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTATTAAAATTAAT
Found at i:41201527 original size:23 final size:22
Alignment explanation
Indices: 41201483--41201535 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
41201473 AGCACTATAT
*
41201483 GTACTCTCTGATTAGCATTTCG
1 GTACTCTCTGATTAGCACTTCG
* *
41201505 TGTGCTCTCTGATTAGTACTTCG
1 -GTACTCTCTGATTAGCACTTCG
41201528 GTACTCTC
1 GTACTCTC
41201536 CGTTTGTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (22 bp):
GTACTCTCTGATTAGCACTTCG
Found at i:41207940 original size:13 final size:13
Alignment explanation
Indices: 41207922--41207948 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41207912 TTTCATCCTC
41207922 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
41207935 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
41207948 T
1 T
41207949 CCCTCGTTCC
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:41214144 original size:2 final size:2
Alignment explanation
Indices: 41214137--41214171 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41214127 TATCGAATAT
41214137 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41214172 TCTTTTCTAA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:41225127 original size:68 final size:66
Alignment explanation
Indices: 41225022--41225201 Score: 266
Period size: 68 Copynumber: 2.8 Consensus size: 66
41225012 GCACCAACCA
41225022 ATACATACATACATACATGCATGGCAATACCATATGAAAATGGTGTAATAAACG-CAGCATGTAC
1 ATACAT-CATACAT-CATGCATGGCAATACCATATGAAAATGGTGTAATAAACGTC-GCATGTAC
41225086 ATAC
63 ATAC
41225090 ATACATGCATACATCCATGCATGGCAATACCATATGAAAATGGTGTAATAAACGTCGCATGTACA
1 ATACAT-CATACAT-CATGCATGGCAATACCATATGAAAATGGTGTAATAAACGTCGCATGTACA
41225155 TAC
64 TAC
41225158 AT--A-CAT--A-CATGCATGGCAATACCATATGAAAATGGTGTAATAAA
1 ATACATCATACATCATGCATGGCAATACCATATGAAAATGGTGTAATAAA
41225202 GGCATAATGT
Statistics
Matches: 109, Mismatches: 2, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
60 37 0.34
62 1 0.01
64 3 0.03
66 1 0.01
68 66 0.61
69 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (66 bp):
ATACATCATACATCATGCATGGCAATACCATATGAAAATGGTGTAATAAACGTCGCATGTACATA
C
Found at i:41229412 original size:22 final size:22
Alignment explanation
Indices: 41229340--41229414 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
41229330 CAGGTGCCTG
*
41229340 AAAAATTTTTCATTTAAATTTTTT
1 AAAAA-TTTTAATTT-AATTTTTT
* * ** *
41229364 TAAAATTTTAAATTAA-TAATA
1 AAAAATTTTAATTTAATTTTTT
41229385 ATAAAATTTTAATTTAATTTTTT
1 A-AAAATTTTAATTTAATTTTTT
41229408 AAAAATT
1 AAAAATT
41229415 ATATTTTTAC
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
21 2 0.05
22 22 0.58
23 10 0.26
24 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
AAAAATTTTAATTTAATTTTTT
Found at i:41230922 original size:69 final size:69
Alignment explanation
Indices: 41230842--41230981 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
41230832 TCAATCCCTA
*
41230842 TAATATAGCGACCTCGCAAATACTTTAACCCATTAACTTGCCAATGTTCTATGACTATCCTCTTT
1 TAATATAGCGACCTCCCAAATACTTTAACCCATTAACTTGCCAATGTTCTATGACTATCCTCTTT
41230907 AGAT
66 AGAT
* *
41230911 TAATATAGCGACCTCCCAAATATTTTAACCCATTAACTTGCCAATGTTCTATGACTATCCTTTTT
1 TAATATAGCGACCTCCCAAATACTTTAACCCATTAACTTGCCAATGTTCTATGACTATCCTCTTT
41230976 AGAT
66 AGAT
41230980 TA
1 TA
41230982 TTCTCATCAT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (69 bp):
TAATATAGCGACCTCCCAAATACTTTAACCCATTAACTTGCCAATGTTCTATGACTATCCTCTTT
AGAT
Found at i:41231293 original size:13 final size:13
Alignment explanation
Indices: 41231275--41231309 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
41231265 GCTTTGGACT
41231275 GCATCAAGGTACA
1 GCATCAAGGTACA
41231288 GCATCAAGGTACA
1 GCATCAAGGTACA
41231301 GCATCAAGG
1 GCATCAAGG
41231310 CATGAAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (13 bp):
GCATCAAGGTACA
Found at i:41238072 original size:31 final size:31
Alignment explanation
Indices: 41238036--41238099 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
41238026 ACGATCAATA
* * *
41238036 ACTTAAATAAAAACTTTGGGATAGTTCAGTG
1 ACTTAAATAAAAACTTTCGAATAATTCAGTG
*
41238067 ACTTAAATGAAAACTTTCGAATAATTCAGTG
1 ACTTAAATAAAAACTTTCGAATAATTCAGTG
41238098 AC
1 AC
41238100 CAAATTGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCGAATAATTCAGTG
Found at i:41246665 original size:30 final size:29
Alignment explanation
Indices: 41246627--41246887 Score: 346
Period size: 30 Copynumber: 8.7 Consensus size: 29
41246617 AAGATTCGGG
*
41246627 GGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGTCAAAAT-GTAATTTTGGAAAAGTTTT
41246655 GGGCTCAAAATGTAATTTTGGAAAAGTTTT
1 GGG-TCAAAATGTAATTTTGGAAAAGTTTT
* *
41246685 AGGGTTAAAATATAATTTTGGAAAAGTTTT
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41246715 AGGGTCAAAACGTAATTTTGGAAAAGTTTT
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTT
** *
41246745 AGGGTCAAAACATAATTTTGGAAAAGGTTTA
1 -GGGTCAAAATGTAATTTTGGAAAA-GTTTT
41246776 GGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41246805 GGGGTCAAAACGTAATTTTGGAAAAGTTTT
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTT
41246835 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTT
41246865 GGGGTCAAAATGTAATTTCTGGA
1 -GGGTCAAAATGTAATTT-TGGA
41246888 TAATTTAGGG
Statistics
Matches: 213, Mismatches: 13, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
28 3 0.01
29 14 0.07
30 185 0.87
31 11 0.05
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:41246761 original size:90 final size:89
Alignment explanation
Indices: 41246637--41246887 Score: 387
Period size: 90 Copynumber: 2.8 Consensus size: 89
41246627 GGGTAAAATG
* * *
41246637 GTAATTTTTG-AAAGTTTTGGGCTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATATAAT
1 GTAATTTTGGAAAAGTTTTGGG-TCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAAT
41246701 TTTGGAAAAGTTTTAGGGTCAAAAC
65 TTTGGAAAAGTTTTAGGGTCAAAAC
** *
41246726 GTAATTTTGGAAAAGTTTTAGGGTCAAAACATAATTTTGGAAAAGGTTTAGGGTCAAAATGTAAT
1 GTAATTTTGGAAAAGTTTT-GGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAAT
*
41246791 TTTGGAAAAGTTTTGGGGTCAAAAC
65 TTTGGAAAAGTTTTAGGGTCAAAAC
*
41246816 GTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAAT
1 GTAATTTTGGAAAAGTTTT-GGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAAT
41246881 TTCTGGA
65 TT-TGGA
41246888 TAATTTAGGG
Statistics
Matches: 147, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
89 9 0.06
90 131 0.89
91 7 0.05
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (89 bp):
GTAATTTTGGAAAAGTTTTGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATT
TTGGAAAAGTTTTAGGGTCAAAAC
Found at i:41248618 original size:18 final size:15
Alignment explanation
Indices: 41248560--41248615 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
41248550 GCAGGTTCAA
*
41248560 TGGTGGTGGCAGGGC
1 TGGTGGTGGCAGAGC
41248575 ATGGTGGAT-G--GAGC
1 -TGGTGG-TGGCAGAGC
41248589 TGGTGGTGGCAGAGC
1 TGGTGGTGGCAGAGC
41248604 TGGTGGTGGCAG
1 TGGTGGTGGCAG
41248616 CAGCATAGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.03
13 7 0.20
14 3 0.09
15 16 0.46
16 7 0.20
17 1 0.03
ACGTcount: A:0.12, C:0.11, G:0.55, T:0.21
Consensus pattern (15 bp):
TGGTGGTGGCAGAGC
Found at i:41248815 original size:6 final size:6
Alignment explanation
Indices: 41248781--41248888 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
41248771 TATTTGGACT
* **
41248781 TTTAAA -TTATAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA
1 TTTAAA TTTA-AA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * *
41248831 TTCAAA -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41248879 --TAAA TTTAAA
1 TTTAAA TTTAAA
41248889 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.05
5 11 0.13
6 49 0.59
7 12 0.14
8 7 0.08
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:41248852 original size:25 final size:25
Alignment explanation
Indices: 41248824--41248873 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
41248814 TTTTATTTAA
* *
41248824 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
41248849 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
41248874 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:41248852 original size:31 final size:31
Alignment explanation
Indices: 41248817--41248880 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
41248807 TTTTAATTTT
*
41248817 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
41248848 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
41248879 TA
1 TA
41248881 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:41248867 original size:42 final size:43
Alignment explanation
Indices: 41248795--41248888 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
41248785 AATTATAATG
* * ** *
41248795 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
41248837 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
41248879 -TAAATTTAAA
1 TTAAATTTAAA
41248889 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.22
42 31 0.69
43 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:41248890 original size:17 final size:16
Alignment explanation
Indices: 41248818--41248888 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
41248808 TTTAATTTTT
41248818 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
41248836 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
41248849 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
41248866 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
41248882 ATTTAAA
1 ATTTAAA
41248889 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:41249355 original size:68 final size:68
Alignment explanation
Indices: 41249249--41249975 Score: 1152
Period size: 68 Copynumber: 10.6 Consensus size: 68
41249239 TCAATTTCGG
* * * *
41249249 AGACTTGTTATCCAACTCTTCTTCAATTTCAAGAGG-ATGACATTGCTCTTATTTCAATTTCAGA
1 AGACGTGTTATCC-ACTCTACTTCAATTTCAAG-GGAATGACGTTGCTCTTACTTCAATTTCAGA
* *
41249313 GGTAA
64 GATGA
** * * *
41249318 AGATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGC-TCTTACTTCAATTTCAGAG
*
41249383 AGGA
65 ATGA
41249387 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
41249452 TGA
66 TGA
41249455 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
41249520 TGA
66 TGA
* *
41249523 AGTCGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
*
41249588 TAA
66 TGA
** * * *
41249591 AGATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGC-TCTTACTTCAATTTCAGAG
41249656 ATGA
65 ATGA
41249660 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
41249725 TGA
66 TGA
41249728 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
41249793 TGA
66 TGA
* *
41249796 AGTCGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
*
41249861 TAA
66 TGA
** *
41249864 AGATATGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTTAGAGA
1 AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
41249929 TGA
66 TGA
*
41249932 AGACCTGTTATCCACTCTACTTCAATTTCAAGAGG-ATGACGTTG
1 AGACGTGTTATCCACTCTACTTCAATTTCAAG-GGAATGACGTTG
41249976 AGACCTGCAG
Statistics
Matches: 611, Mismatches: 43, Indels: 9
0.92 0.06 0.01
Matches are distributed among these distances:
67 2 0.00
68 476 0.78
69 133 0.22
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (68 bp):
AGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGA
TGA
Found at i:41249756 original size:273 final size:273
Alignment explanation
Indices: 41249254--41249975 Score: 1315
Period size: 273 Copynumber: 2.6 Consensus size: 273
41249244 TTCGGAGACT
* * *
41249254 TGTTATCCAACTCTTCTTCAATTTCAAGAGG-ATGACATTGCTCTTATTTCAATTTCAGAGGTAA
1 TGTTATCC-ACTCTACTTCAATTTCAAG-GGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAA
41249318 AGATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAG
64 AGATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAG
*
41249383 AGGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCA
129 ATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCA
41249448 GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATT
194 GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATT
41249513 TCAGAGATGAAGTCG
259 TCAGAGATGAAGTCG
41249528 TGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAG
1 TGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAG
41249593 ATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAGAT
66 ATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAGAT
41249658 GAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGA
131 GAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGA
41249723 GATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTC
196 GATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTC
41249788 AGAGATGAAGTCG
261 AGAGATGAAGTCG
41249801 TGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAG
1 TGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAG
* * * *
41249866 ATATGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGC-TCTTACTTCAATTTTAGAGAT
66 ATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAGAT
*
41249930 GAAGACCTGTTATCCACTCTACTTCAATTTCAAGAGG-ATGACGTTG
131 GAAGACGTGTTATCCACTCTACTTCAATTTCAAG-GGAATGACGTTG
41249976 AGACCTGCAG
Statistics
Matches: 437, Mismatches: 9, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
272 64 0.15
273 365 0.84
274 8 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (273 bp):
TGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGGTAAAG
ATATGTTATCCACTCTACTTCAATTTCGAGGGGATGACGCTGCTTCTTACTTCAATTTCAGAGAT
GAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGA
GATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTC
AGAGATGAAGTCG
Found at i:41261974 original size:30 final size:29
Alignment explanation
Indices: 41261935--41262316 Score: 516
Period size: 30 Copynumber: 12.8 Consensus size: 29
41261925 AAAGATTCAG
41261935 GGGGT-AAAATGGTAATTTTTGG-AAGTTTT
1 GGGGTCAAAAT-GTAA-TTTTGGAAAGTTTT
*
41261964 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
*
41261994 GGGGTCAAAATGTAATTTTGGAAAAGTTTC
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
41262024 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
* *
41262054 AGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
*
41262084 GGGGTCAAAACGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
* ** *
41262114 AGGGTCAAAACATAATTTTGGAAAAGGTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
41262144 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
*
41262174 GGGGTCAAAACGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
*
41262204 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
*
41262234 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
41262264 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTT
41262294 GGGGTCAAAATGTAATTTCTGGA
1 GGGGTCAAAATGTAATTT-TGGA
41262317 TAATTTAGGG
Statistics
Matches: 329, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
28 6 0.02
29 8 0.02
30 312 0.95
31 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGGAAAGTTTT
Found at i:41262033 original size:60 final size:60
Alignment explanation
Indices: 41261935--41262316 Score: 608
Period size: 60 Copynumber: 6.4 Consensus size: 60
41261925 AAAGATTCAG
*
41261935 GGGGT-AAAATGGTAATTTTTGG--AAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAAT-GTAA-TTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41261994 GGGGTCAAAATGTAATTTTGGAAAAGTTTCGGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
* * *
41262054 AGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAACGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
* ** *
41262114 AGGGTCAAAACATAATTTTGGAAAAGGTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
41262174 GGGGTCAAAACGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41262234 GGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
41262294 GGGGTCAAAATGTAATTTCTGGA
1 GGGGTCAAAATGTAATTT-TGGA
41262317 TAATTTAGGG
Statistics
Matches: 302, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
58 6 0.02
59 9 0.03
60 283 0.94
61 4 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (60 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:41262064 original size:90 final size:90
Alignment explanation
Indices: 41261935--41262316 Score: 608
Period size: 90 Copynumber: 4.2 Consensus size: 90
41261925 AAAGATTCAG
41261935 GGGGT-AAAATGGTAATTTTTGG--AAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGG
1 GGGGTCAAAAT-GTAA-TTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGG
* *
41261997 GTCAAAATGTAATTTTGGAAAAGTTTC
64 GTCAAAACGTAATTTTGGAAAAGTTTT
*
41262024 GGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGT
41262089 CAAAACGTAATTTTGGAAAAGTTTT
66 CAAAACGTAATTTTGGAAAAGTTTT
* ** * *
41262114 AGGGTCAAAACATAATTTTGGAAAAGGTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGT
41262179 CAAAACGTAATTTTGGAAAAGTTTT
66 CAAAACGTAATTTTGGAAAAGTTTT
* * *
41262204 GGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGT
*
41262269 CAAAATGTAATTTTGGAAAAGTTTT
66 CAAAACGTAATTTTGGAAAAGTTTT
41262294 GGGGTCAAAATGTAATTTCTGGA
1 GGGGTCAAAATGTAATTT-TGGA
41262317 TAATTTAGGG
Statistics
Matches: 272, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
88 6 0.02
89 9 0.03
90 253 0.93
91 4 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (90 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGT
CAAAACGTAATTTTGGAAAAGTTTT
Found at i:41262224 original size:19 final size:19
Alignment explanation
Indices: 41262200--41262254 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
41262190 TTTGGAAAAG
41262200 TTTTGGGGTTAAAATGTAA
1 TTTTGGGGTTAAAATGTAA
41262219 TTTT--GG--AAAA-G---
1 TTTTGGGGTTAAAATGTAA
41262230 TTTTGGGGTTAAAATGTAA
1 TTTTGGGGTTAAAATGTAA
41262249 TTTTGG
1 TTTTGG
41262255 AAAAGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (19 bp):
TTTTGGGGTTAAAATGTAA
Found at i:41264047 original size:18 final size:15
Alignment explanation
Indices: 41263989--41264044 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
41263979 ACAGGTTCAA
*
41263989 TGGTGGTGGCAGGGC
1 TGGTGGTGGCAGAGC
41264004 ATGGTGGAT-G--GAGC
1 -TGGTGG-TGGCAGAGC
41264018 TGGTGGTGGCAGAGC
1 TGGTGGTGGCAGAGC
41264033 TGGTGGTGGCAG
1 TGGTGGTGGCAG
41264045 CAGCATAGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.03
13 7 0.20
14 3 0.09
15 16 0.46
16 7 0.20
17 1 0.03
ACGTcount: A:0.12, C:0.11, G:0.55, T:0.21
Consensus pattern (15 bp):
TGGTGGTGGCAGAGC
Found at i:41264244 original size:6 final size:6
Alignment explanation
Indices: 41264210--41264317 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
41264200 TATTTGGACT
* **
41264210 TTTAAA -TTATAA TGTTAAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA
1 TTTAAA TTTA-AA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * *
41264260 TTCAAA -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41264308 --TAAA TTTAAA
1 TTTAAA TTTAAA
41264318 ATCAATTTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.05
5 11 0.13
6 49 0.59
7 12 0.14
8 7 0.08
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:41264281 original size:25 final size:25
Alignment explanation
Indices: 41264253--41264302 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
41264243 TTTTATTTAA
* *
41264253 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
41264278 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
41264303 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:41264281 original size:31 final size:31
Alignment explanation
Indices: 41264246--41264309 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
41264236 TTTTAATTTT
*
41264246 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
41264277 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
41264308 TA
1 TA
41264310 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:41264296 original size:42 final size:43
Alignment explanation
Indices: 41264224--41264317 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 43
41264214 AATTATAATG
* * ** *
41264224 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
41264266 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
41264308 -TAAATTTAAA
1 TTAAATTTAAA
41264318 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.22
42 31 0.69
43 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:41264319 original size:17 final size:16
Alignment explanation
Indices: 41264247--41264317 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
41264237 TTTAATTTTT
41264247 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
41264265 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
41264278 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
41264295 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
41264311 ATTTAAA
1 ATTTAAA
41264318 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:41265075 original size:41 final size:41
Alignment explanation
Indices: 41265018--41265113 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
41265008 TTGTTCGTAG
* *
41265018 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGAGTGAAT
1 AGAATTCTTGTTAAGGTAGAGATTGTTAGAATTGAGTGAAT
* *
41265059 AGAATTCTTGTTAAGGTAGATATTGTTAGAATTGAGTGACT
1 AGAATTCTTGTTAAGGTAGAGATTGTTAGAATTGAGTGAAT
*
41265100 ATAATTCTTGTTAA
1 AGAATTCTTGTTAA
41265114 AATAAAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTAGAGATTGTTAGAATTGAGTGAAT
Found at i:41268201 original size:24 final size:24
Alignment explanation
Indices: 41268168--41268230 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
41268158 AGAAATAATC
* *
41268168 TTTCAGTTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
41268192 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
41268216 TTTAAATCAAACTCT
1 TTTCAATTAAACTCT
41268231 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:41270176 original size:24 final size:24
Alignment explanation
Indices: 41270143--41270189 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41270133 AGAAATAATC
*
41270143 TTTCAGTTAAACTCTATTTATTTA
1 TTTCAATTAAACTCTATTTATTTA
*
41270167 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTATTTATTT
41270190 GTTTAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTA
Found at i:41270202 original size:24 final size:24
Alignment explanation
Indices: 41270151--41270205 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
41270141 TCTTTCAGTT
*
41270151 AAACTCTATTTATTTATTTCAATT
1 AAACTCTATTTATTTATTTCAATC
* *
41270175 AAACTCTGTTTATTTGTTT-AAGTC
1 AAACTCTATTTATTTATTTCAA-TC
41270199 AAACTCT
1 AAACTCT
41270206 TATTAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTATTTCAATC
Found at i:41271038 original size:14 final size:14
Alignment explanation
Indices: 41270991--41271038 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
41270981 GTACAAGTTC
41270991 TTTTTCTTATTTAA
1 TTTTTCTTATTTAA
**
41271005 GTTTCTTCTATAGATAA
1 -TTT-TTCT-TATTTAA
41271022 TTTTTCTTATTTAA
1 TTTTTCTTATTTAA
41271036 TTT
1 TTT
41271039 ATTGGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 7 0.26
17 5 0.19
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTTTCTTATTTAA
Found at i:41280291 original size:32 final size:32
Alignment explanation
Indices: 41280250--41280314 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
41280240 TAGAAATAAA
* *
41280250 TGAATTTTTAGTAGAAAGATCAGTTTTTTTTT
1 TGAATTTTTAGTAGAAAGATCAATTTATTTTT
*
41280282 TGAATTTTTAGTAGCAAGATCAATTTATTTTT
1 TGAATTTTTAGTAGAAAGATCAATTTATTTTT
41280314 T
1 T
41280315 AATCTAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (32 bp):
TGAATTTTTAGTAGAAAGATCAATTTATTTTT
Found at i:41281427 original size:223 final size:221
Alignment explanation
Indices: 41280853--41281602 Score: 1401
Period size: 222 Copynumber: 3.4 Consensus size: 221
41280843 AAAGGATTGA
*
41280853 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTAGAAAAGGGACACA
1 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTGGAAAAGGGACACA
41280918 AATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCTGTAGCTTGAGAAAGGATTGTATGAAAC
66 AATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCTGTAGCTTGAGAAAGGATTGTATGAAAC
*
41280983 AGGGATATTATTCCTTTCCAATAGTTTTATGACACATCAATAATTTCATCATAAATTTCAGGATT
131 AGGGATATTATCCCTTTCCAATAGTTTTATGACACATCAATAATTTCATCATAAATTTCAGGATT
41281048 TTAATTGTAATTTGATTTTTTTCAGG
196 TTAATTGTAATTTGATTTTTTTCAGG
*
41281074 ATGAAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAGCTATTGGAAAAGGGACAC
1 ATG-AAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTGGAAAAGGGACAC
41281139 AAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCTGTAGCTTGAGAAAGGATTGTATGAAA
65 AAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCTGTAGCTTGAGAAAGGATTGTATGAAA
*
41281204 CAAGGATATTATCCCTTTCCAATAGTTTTATGACACATCAATAATTTCATCATAAATTTCAGGAT
130 CAGGGATATTATCCCTTTCCAATAGTTTTATGACACATCAATAATTTCATCATAAATTTCAGGAT
41281269 TTTAATTGTAATTTGATTTTTTTTGCAGG
195 TTTAATTGTAATTTGA-TTTTTTT-CAGG
*
41281298 ATGGAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTGGAAAAGGGACACA
1 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTGGAAAAGGGACACA
41281363 AATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCTGTAGCTTGAGAAAGGATTGTATGAAAC
66 AATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCTGTAGCTTGAGAAAGGATTGTATGAAAC
* *
41281428 AGGGATATTATCCATTTCTAATAGTTTTATGACACATCAATAATTTCATCATAAATTTCAGGATT
131 AGGGATATTATCCCTTTCCAATAGTTTTATGACACATCAATAATTTCATCATAAATTTCAGGATT
*
41281493 TTAATTGTAATTTAATTTTTTTCAGG
196 TTAATTGTAATTTGATTTTTTTCAGG
41281519 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTGGAAAAGGGACACA
1 ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTGGAAAAGGGACACA
41281584 AATGACGTGGTGTCACTGT
66 AATGACGTGGTGTCACTGT
41281603 AGGGAAAAGG
Statistics
Matches: 515, Mismatches: 11, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
221 90 0.17
222 210 0.41
223 208 0.40
224 7 0.01
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (221 bp):
ATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCATAAAACTATTGGAAAAGGGACACA
AATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCTGTAGCTTGAGAAAGGATTGTATGAAAC
AGGGATATTATCCCTTTCCAATAGTTTTATGACACATCAATAATTTCATCATAAATTTCAGGATT
TTAATTGTAATTTGATTTTTTTCAGG
Found at i:41283430 original size:60 final size:59
Alignment explanation
Indices: 41283331--41283465 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 59
41283321 GTAGTCATCC
* * *
41283331 AACTATTACTAAATTTTTCTTTGGTCACTTAATTATGAAATATTACAAAATGGTCACCT
1 AACTATTACTAAATTTTTATTTGGTCACATAACTATGAAATATTACAAAATGGTCACCT
* * * *
41283390 AACTATTAGTAAATTTATTATTTGGTCAGATAACTATGAAATATTACAAAATGGTAACCA
1 AACTATTACTAAATTT-TTATTTGGTCACATAACTATGAAATATTACAAAATGGTCACCT
*
41283450 AATTATT-C-AAATTTTT
1 AACTATTACTAAATTTTT
41283466 CTTTTTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 2 0.03
58 6 0.09
59 15 0.23
60 43 0.65
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (59 bp):
AACTATTACTAAATTTTTATTTGGTCACATAACTATGAAATATTACAAAATGGTCACCT
Found at i:41296497 original size:17 final size:19
Alignment explanation
Indices: 41296456--41296498 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41296446 ACATCATTAA
*
41296456 AAATAATATAATATATAAT
1 AAATAATAAAATATATAAT
*
41296475 ATATAATAAAAT-TAT-AT
1 AAATAATAAAATATATAAT
41296492 AAATAAT
1 AAATAAT
41296499 TTAATATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 3 0.14
19 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAATAAAATATATAAT
Found at i:41301742 original size:85 final size:86
Alignment explanation
Indices: 41301633--41301807 Score: 244
Period size: 85 Copynumber: 2.0 Consensus size: 86
41301623 AAAAAAATTT
* * * *
41301633 CGCTAAAGAACATGGTCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGATCTTTAG
1 CGCTAAAGAAAATGATCTTTAGCGGCACTTTTACCACAAACGCCGCTAAAGAACATGATCTTTAG
* **
41301698 TGGCGCTTTTCTCGTAAACGC
66 TGGCGCTTATCTCACAAACGC
* * * *
41301719 CGCTAAA-AAAATGATCTTTAGCGGTACTTTTCCCACAAACGCCGCTGAAGAACGTGATCTTTAG
1 CGCTAAAGAAAATGATCTTTAGCGGCACTTTTACCACAAACGCCGCTAAAGAACATGATCTTTAG
41301783 TGGCGCTTATCTCACAAACGC
66 TGGCGCTTATCTCACAAACGC
41301804 CGCT
1 CGCT
41301808 TTTCTCACAA
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 71 0.91
86 7 0.09
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (86 bp):
CGCTAAAGAAAATGATCTTTAGCGGCACTTTTACCACAAACGCCGCTAAAGAACATGATCTTTAG
TGGCGCTTATCTCACAAACGC
Found at i:41301749 original size:42 final size:43
Alignment explanation
Indices: 41301633--41301807 Score: 226
Period size: 43 Copynumber: 4.1 Consensus size: 43
41301623 AAAAAAATTT
* *
41301633 CGCTAAAGAACATGGTCTTTAGCGGCGCTTTTATCACAAACGC
1 CGCTAAAGAACATGATCTTTAGCGGCGCTTTTCTCACAAACGC
* **
41301676 CGCTAAAGAACATGATCTTTAGTGGCGCTTTTCTCGTAAACGC
1 CGCTAAAGAACATGATCTTTAGCGGCGCTTTTCTCACAAACGC
* ** *
41301719 CGCTAAA-AAAATGATCTTTAGCGGTACTTTTCCCACAAACGC
1 CGCTAAAGAACATGATCTTTAGCGGCGCTTTTCTCACAAACGC
* * * *
41301761 CGCTGAAGAACGTGATCTTTAGTGGCGCTTATCTCACAAACGC
1 CGCTAAAGAACATGATCTTTAGCGGCGCTTTTCTCACAAACGC
41301804 CGCT
1 CGCT
41301808 TTTCTCACAA
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 34 0.31
43 77 0.69
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (43 bp):
CGCTAAAGAACATGATCTTTAGCGGCGCTTTTCTCACAAACGC
Found at i:41301813 original size:18 final size:18
Alignment explanation
Indices: 41301786--41301822 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
41301776 TCTTTAGTGG
41301786 CGCTTATCTCACAAACGC
1 CGCTTATCTCACAAACGC
*
41301804 CGCTTTTCTCACAAACGC
1 CGCTTATCTCACAAACGC
41301822 C
1 C
41301823 TCTAAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.11, T:0.24
Consensus pattern (18 bp):
CGCTTATCTCACAAACGC
Found at i:41301840 original size:61 final size:61
Alignment explanation
Indices: 41301745--41301862 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 61
41301735 TTTAGCGGTA
* *
41301745 CTTTTCCCACAAACGCCGCTGAAGAACGTGATCTTTAGTGGCGCTTATCTCACAAACGCCG
1 CTTTTCCCACAAACGCCGCTAAAGAACGTGATCTTTAGCGGCGCTTATCTCACAAACGCCG
* * *
41301806 CTTTTCTCACAAACGCCTCTAAAGAACGTGATCTTTAGCGGCGCTTTTCTCACAAAC
1 CTTTTCCCACAAACGCCGCTAAAGAACGTGATCTTTAGCGGCGCTTATCTCACAAAC
41301863 ACCGATAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (61 bp):
CTTTTCCCACAAACGCCGCTAAAGAACGTGATCTTTAGCGGCGCTTATCTCACAAACGCCG
Found at i:41301872 original size:43 final size:43
Alignment explanation
Indices: 41301804--41301933 Score: 188
Period size: 43 Copynumber: 3.0 Consensus size: 43
41301794 TCACAAACGC
* *
41301804 CGCTTTTCTCACAAACGCCTCTAAAGAACGTGATCTTTAGCGG
1 CGCTTTTCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGG
* * * *
41301847 CGCTTTTCTCACAAACACCGATAAAGAACATGTTCTTTAGTGG
1 CGCTTTTCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGG
* *
41301890 CGCTTTTCTCACAAACGCTGCTAAAGAAAATGATCTTTAGCGG
1 CGCTTTTCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGG
41301933 C
1 C
41301934 CGCTAAAATT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (43 bp):
CGCTTTTCTCACAAACGCCGCTAAAGAACATGATCTTTAGCGG
Found at i:41301884 original size:104 final size:103
Alignment explanation
Indices: 41301701--41301907 Score: 279
Period size: 104 Copynumber: 2.0 Consensus size: 103
41301691 TCTTTAGTGG
** * * * *
41301701 CGCTTTTCTCGTAAACGCCGCTAAAAAAATGATCTTTAGCGGTACTTTTCCCACAAACGCCGCTG
1 CGCTTTTCTCACAAACGCCGCTAAAAAAATGATCTTTAGCGGCACTTTTCCCACAAACACCGATA
*
41301766 AAGAACGTGATCTTTAGTGGCGCTTATCTCACAAACGC
66 AAGAACATGATCTTTAGTGGCGCTTATCTCACAAACGC
* ** * *
41301804 CGCTTTTCTCACAAACGCCTCTAAAGAACGTGATCTTTAGCGGCGCTTTTCTCACAAACACCGAT
1 CGCTTTTCTCACAAACGCCGCTAAA-AAAATGATCTTTAGCGGCACTTTTCCCACAAACACCGAT
* *
41301869 AAAGAACATGTTCTTTAGTGGCGCTTTTCTCACAAACGC
65 AAAGAACATGATCTTTAGTGGCGCTTATCTCACAAACGC
41301908 TGCTAAAGAA
Statistics
Matches: 89, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
103 22 0.25
104 67 0.75
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (103 bp):
CGCTTTTCTCACAAACGCCGCTAAAAAAATGATCTTTAGCGGCACTTTTCCCACAAACACCGATA
AAGAACATGATCTTTAGTGGCGCTTATCTCACAAACGC
Found at i:41302411 original size:13 final size:13
Alignment explanation
Indices: 41302393--41302424 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41302383 CCCAGCCAAT
41302393 TCCAAAACCTGAA
1 TCCAAAACCTGAA
41302406 TCCAAAACCTGAA
1 TCCAAAACCTGAA
41302419 TCCAAA
1 TCCAAA
41302425 CCCAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.31, G:0.06, T:0.16
Consensus pattern (13 bp):
TCCAAAACCTGAA
Found at i:41305575 original size:42 final size:42
Alignment explanation
Indices: 41305508--41305592 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
41305498 CAATTGTACT
*
41305508 CTATCACTATTCCAAATCCGATTCAAGCACGCGGATGTTACA
1 CTATCACTATTCCAAATCCGATTCAAGAACGCGGATGTTACA
* * * *
41305550 CTATTACTATTCCAACTCC-AGTTCAATAATGCGGATGTTACA
1 CTATCACTATTCCAAATCCGA-TTCAAGAACGCGGATGTTACA
41305592 C
1 C
41305593 AATATTCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (42 bp):
CTATCACTATTCCAAATCCGATTCAAGAACGCGGATGTTACA
Found at i:41307429 original size:41 final size:41
Alignment explanation
Indices: 41307384--41307499 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
41307374 TTAGCGGTAT
* * *
41307384 TTTCTTATAAACGCCGTTAATGCTTTGACCTTTAGTAGCGC
1 TTTCTCATAAACGCCGTTAATGCTCTGACCTTTAGCAGCGC
* * * * * *
41307425 TTTCTCATAAACACTGCTAATGCTCTAATCTTTAGCGGCGC
1 TTTCTCATAAACGCCGTTAATGCTCTGACCTTTAGCAGCGC
* * *
41307466 TTTCTCACAAATGCCGTTAATACTCTGACCTTTA
1 TTTCTCATAAACGCCGTTAATGCTCTGACCTTTA
41307500 ACGGTGTTTA
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (41 bp):
TTTCTCATAAACGCCGTTAATGCTCTGACCTTTAGCAGCGC
Found at i:41307460 original size:82 final size:82
Alignment explanation
Indices: 41307329--41307499 Score: 191
Period size: 82 Copynumber: 2.1 Consensus size: 82
41307319 CTATTACTTA
* * * * * *
41307329 ACCTTTAGTAGCGCTTACTCATAAACGCCGCTAAAGGTTAGAGCATTAGCGGTATTTTCTTATAA
1 ACCTTTAGTAGCGCTTACTCATAAACACCGCTAAAGCTTAGAGCATTAGCGGCACTTTCTCACAA
* *
41307394 ACGCCGTTAATGCTTTG
66 ACGCCGTTAATACTCTG
* * * * * *
41307411 ACCTTTAGTAGCGCTTTCTCATAAACACTGCTAATGCTCTA-ATCTTTAGCGGCGCTTTCTCACA
1 ACCTTTAGTAGCGCTTACTCATAAACACCGCTAAAGCT-TAGAGCATTAGCGGCACTTTCTCACA
*
41307475 AATGCCGTTAATACTCTG
65 AACGCCGTTAATACTCTG
41307493 ACCTTTA
1 ACCTTTA
41307500 ACGGTGTTTA
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
82 71 0.97
83 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (82 bp):
ACCTTTAGTAGCGCTTACTCATAAACACCGCTAAAGCTTAGAGCATTAGCGGCACTTTCTCACAA
ACGCCGTTAATACTCTG
Found at i:41307914 original size:21 final size:21
Alignment explanation
Indices: 41307888--41307929 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41307878 CAAAACGAGC
**
41307888 TTTTTTGCCTTTAAATTTTGA
1 TTTTTTGAATTTAAATTTTGA
*
41307909 TTTTTTGAATTTGAATTTTGA
1 TTTTTTGAATTTAAATTTTGA
41307930 AACATTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.62
Consensus pattern (21 bp):
TTTTTTGAATTTAAATTTTGA
Found at i:41308873 original size:16 final size:17
Alignment explanation
Indices: 41308840--41308878 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
41308830 GACTGAGTCA
41308840 ATTAACTATTAAATATTG
1 ATTAACTATT-AATATTG
41308858 ATTAACTATT-ATATTG
1 ATTAACTATTAATATTG
41308874 ATTAA
1 ATTAA
41308879 TATACATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (17 bp):
ATTAACTATTAATATTG
Found at i:41309036 original size:41 final size:41
Alignment explanation
Indices: 41309000--41309140 Score: 176
Period size: 41 Copynumber: 3.5 Consensus size: 41
41308990 GGCGCTTATT
* *
41309000 TTGCTCTGACCTTTAGCGGCGCTTGCCCAGAAGCGCTGCTA
1 TTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCTGCTA
* * * * * *
41309041 TTGCTCGGACCTTTAGCTGCGCTGGCCCATAAACTCCGCTA
1 TTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCTGCTA
* *
41309082 TTGCTCTGTCCTTTAGCAGCGCTTGCCCATAAGCGCCGCTA
1 TTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCTGCTA
*
41309123 TTGCTCT-ACCTTTTGCAG
1 TTGCTCTGACCTTTAGCAG
41309141 GGTTTATGTA
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 9 0.11
41 76 0.89
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.30
Consensus pattern (41 bp):
TTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCTGCTA
Found at i:41312617 original size:13 final size:13
Alignment explanation
Indices: 41312599--41312629 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
41312589 ATTCAACCCA
41312599 TCTAATTGATAGG
1 TCTAATTGATAGG
41312612 TCTAATTGATAGG
1 TCTAATTGATAGG
41312625 TCTAA
1 TCTAA
41312630 ATGAATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (13 bp):
TCTAATTGATAGG
Found at i:41314117 original size:17 final size:17
Alignment explanation
Indices: 41314082--41314160 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
41314072 GATCTTTAGG
*
41314082 TTTAAATTCATTATTAAA
1 TTTAAATTTATT-TTAAA
41314100 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
41314117 TTTAAAAATATTTAAATAAA
1 TTTAAATTTATTT---TAAA
* *
41314137 TTTAAAATTTAATTAAAA
1 TTT-AAATTTATTTTAAA
41314155 TTTAAA
1 TTTAAA
41314161 GTCCAAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
17 19 0.38
18 17 0.34
20 7 0.14
21 7 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:41315875 original size:162 final size:162
Alignment explanation
Indices: 41315688--41316187 Score: 793
Period size: 162 Copynumber: 3.1 Consensus size: 162
41315678 GGTTTTCAAT
*
41315688 TTAGTTCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
* *
41315753 TCTAGTCCTTGTCATTTTTAATTTGTTTTCATTTAATCCTTAAATCAACTTTTATTTAATTACAC
66 TCTAGTCCTTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAAATTTTATTTAATTACAC
*
41315818 AATTGGCCCAATAATTTTTCAAGGTTTATAAA
131 AATTGGCCCAATAATTTTTCAAGATTTATAAA
* * * * *
41315850 TTAGTCCTTTGACTGTTTAACTGCACCAGAGGCTGCTATGTGTCACTTTTTGGCTTATTTATCTG
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
* * * **
41315915 TCTGGTCCCTGTCATTTCTAATTTGTTTTAATTCGATCCTTAAATCAAATTTTATTTAATTACAC
66 TCTAGTCCTTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAAATTTTATTTAATTACAC
41315980 AATTGGCCCAATAATTTTTCAAGATTTATAAA
131 AATTGGCCCAATAATTTTTCAAGATTTATAAA
* * *
41316012 TTAGTCCTTTGACTGTTTGGCTACACCAGAGGTTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
* * *
41316077 TCTAGTCCTTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAATTTTTATTTAATTATAA
66 TCTAGTCCTTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAAATTTTATTTAATTACAC
* * *
41316142 AACTGGCCCGAGAATTTTTCAAGATTTATAAA
131 AATTGGCCCAATAATTTTTCAAGATTTATAAA
41316174 TTAGTCCTTTGACT
1 TTAGTCCTTTGACT
41316188 TCTGGGTACC
Statistics
Matches: 305, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
162 305 1.00
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
TCTAGTCCTTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAAATTTTATTTAATTACAC
AATTGGCCCAATAATTTTTCAAGATTTATAAA
Found at i:41316319 original size:58 final size:58
Alignment explanation
Indices: 41316238--41316376 Score: 260
Period size: 58 Copynumber: 2.4 Consensus size: 58
41316228 GTTTTATTCT
41316238 CGAACTTTCCAAAATTCCATTTTGACCCTAATTTTACCAAAAATTACCATTTTACCCC
1 CGAACTTTCCAAAATTCCATTTTGACCCTAATTTTACCAAAAATTACCATTTTACCCC
*
41316296 CGAACTTTCCAAAATTCCATTTTGACCCTAATTTTACCAAAAATTACCATTTTACCCT
1 CGAACTTTCCAAAATTCCATTTTGACCCTAATTTTACCAAAAATTACCATTTTACCCC
*
41316354 CGAACTTTCTAAAATTCCATTTT
1 CGAACTTTCCAAAATTCCATTTT
41316377 TAGCCCCGGT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 79 1.00
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (58 bp):
CGAACTTTCCAAAATTCCATTTTGACCCTAATTTTACCAAAAATTACCATTTTACCCC
Found at i:41316367 original size:29 final size:29
Alignment explanation
Indices: 41316236--41316376 Score: 132
Period size: 29 Copynumber: 4.9 Consensus size: 29
41316226 TGGTTTTATT
*
41316236 CTCGAACTTTCCAAAATTCCATTTTGACC
1 CTCGAACTTTCAAAAATTCCATTTTGACC
*
41316265 CT--AATTTTACCAAAAATTACCATTTT-ACC
1 CTCGAACTTT--CAAAAATT-CCATTTTGACC
* *
41316294 CCCGAACTTTCCAAAATTCCATTTTGACC
1 CTCGAACTTTCAAAAATTCCATTTTGACC
*
41316323 CT--AATTTTACCAAAAATTACCATTTT-ACC
1 CTCGAACTTT--CAAAAATT-CCATTTTGACC
*
41316352 CTCGAACTTTCTAAAATTCCATTTT
1 CTCGAACTTTCAAAAATTCCATTTT
41316377 TAGCCCCGGT
Statistics
Matches: 91, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
27 10 0.11
28 14 0.15
29 43 0.47
30 14 0.15
31 10 0.11
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (29 bp):
CTCGAACTTTCAAAAATTCCATTTTGACC
Found at i:41316480 original size:96 final size:96
Alignment explanation
Indices: 41316302--41316481 Score: 231
Period size: 97 Copynumber: 1.9 Consensus size: 96
41316292 CCCCCGAACT
* * * * *
41316302 TTCCAAAATTCCATTTTGACCCTAATTTTACCAAAAATTACCATTTTACCCTCGAACTTTCTAAA
1 TTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCTCGAACTGTCCAAA
*
41316367 ATTCCATTTTTAGCCCCGGTTTCACCAAAGC
66 ATTCCATTTTTACCCCCGGTTTCACCAAAGC
** *
41316398 TTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTACCC-CTGCAC-GTCCA
1 TTCCAAAATTCCA-TTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCTC-GAACTGTCCA
41316461 AAATTACCA-TTTTACCCCCGG
64 AAATT-CCATTTTTACCCCCGG
41316482 GTATCCAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
96 33 0.46
97 39 0.54
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (96 bp):
TTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCTCGAACTGTCCAAA
ATTCCATTTTTACCCCCGGTTTCACCAAAGC
Found at i:41323578 original size:1 final size:1
Alignment explanation
Indices: 41323572--41323606 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
41323562 CTTTTAATTG
*
41323572 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
41323607 AATAGTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:41327473 original size:20 final size:20
Alignment explanation
Indices: 41327448--41327491 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
41327438 TATTAATGAG
41327448 TAAAAAAATAATTTTAAATT
1 TAAAAAAATAATTTTAAATT
41327468 TAAAAAAATAATTTTAAATT
1 TAAAAAAATAATTTTAAATT
41327488 TAAA
1 TAAA
41327492 TTAATTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAAAATAATTTTAAATT
Found at i:41327637 original size:22 final size:21
Alignment explanation
Indices: 41327611--41327662 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
41327601 AATTTAACAA
41327611 TTTAATAACTTAAATAAATT-TT
1 TTTAATAA-TTAAAT-AATTATT
*
41327633 TTTAAATAATTTAATAATTATT
1 TTT-AATAATTAAATAATTATT
41327655 TTATAATA
1 TT-TAATA
41327663 TTATAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAATAATTAAATAATTATT
Found at i:41327640 original size:23 final size:22
Alignment explanation
Indices: 41327613--41327662 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
41327603 TTTAACAATT
*
41327613 TAATAACTTAAATAAATTTTTTTA
1 TAATAA-TTAAAT-AATTATTTTA
*
41327637 -AATAATTTAATAATTATTTTA
1 TAATAATTAAATAATTATTTTA
41327658 TAATA
1 TAATA
41327663 TTATAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATAATTAAATAATTATTTTA
Found at i:41328207 original size:19 final size:20
Alignment explanation
Indices: 41328185--41328228 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41328175 TTAAAAAATA
41328185 TATAAAT-TTTGGAATTTTT
1 TATAAATATTTGGAATTTTT
*
41328204 TATAAATATTTTGAATTTTT
1 TATAAATATTTGGAATTTTT
41328224 T-TAAA
1 TATAAA
41328229 AAAAATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
TATAAATATTTGGAATTTTT
Found at i:41328245 original size:21 final size:20
Alignment explanation
Indices: 41328188--41328247 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
41328178 AAAAATATAT
* *
41328188 AAATTTTGGAATTTTTTATAA
1 AAATTTT-GAATTTTTAAAAA
*
41328209 ATATTTTGAATTTTTTTAAAAA
1 AAATTTTGAA--TTTTTAAAAA
41328231 AAATTTTGTAATTTTTA
1 AAATTTTG-AATTTTTA
41328248 TTGAAAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.09
21 12 0.38
22 15 0.47
23 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
AAATTTTGAATTTTTAAAAA
Found at i:41332567 original size:21 final size:21
Alignment explanation
Indices: 41332543--41332586 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41332533 ATACAACTGT
41332543 TTTAAT-ATTTAATTATAAATA
1 TTTAATGA-TTAATTATAAATA
* *
41332564 TTTAATGATTATTTTTAAATA
1 TTTAATGATTAATTATAAATA
41332585 TT
1 TT
41332587 AAAAATATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAATGATTAATTATAAATA
Found at i:41332649 original size:24 final size:23
Alignment explanation
Indices: 41332609--41332666 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
41332599 TATACATTCT
*
41332609 AATTAGAT-TTTATAAATAATTAA
1 AATTA-ATATTTAAAAATAATTAA
* **
41332632 TATTAATTATTTAAAAATCTTTAA
1 AATTAA-TATTTAAAAATAATTAA
41332656 AATTAATATTT
1 AATTAATATTT
41332667 CATATAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 10 0.36
24 17 0.61
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAAAAATAATTAA
Found at i:41335000 original size:6 final size:6
Alignment explanation
Indices: 41334991--41335017 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41334981 ACCTCCACCG
41334991 CCGCAA CCGCAA CCGCAA CCGCAA CCG
1 CCGCAA CCGCAA CCGCAA CCGCAA CCG
41335018 GCGTCGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.52, G:0.19, T:0.00
Consensus pattern (6 bp):
CCGCAA
Found at i:41341271 original size:28 final size:28
Alignment explanation
Indices: 41341227--41341288 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
41341217 TCTAACCTTT
*
41341227 ATTAATTATAAAGGTTCATTTTAATATA
1 ATTAATTATAAAAGTTCATTTTAATATA
41341255 ATTAATTATAAAAGTTCATTTTAATATA
1 ATTAATTATAAAAGTTCATTTTAATATA
41341283 ATTAAT
1 ATTAAT
41341289 ATTAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (28 bp):
ATTAATTATAAAAGTTCATTTTAATATA
Found at i:41341369 original size:21 final size:21
Alignment explanation
Indices: 41341343--41341383 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41341333 ATAAAATTGC
*
41341343 TTTGAATTTATTAATATAATA
1 TTTGAATTCATTAATATAATA
*
41341364 TTTGAATTCATTGATATAAT
1 TTTGAATTCATTAATATAAT
41341384 TATATTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTGAATTCATTAATATAATA
Found at i:41344788 original size:6 final size:6
Alignment explanation
Indices: 41344777--41344837 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
41344767 TTTTATAATA
* * * *
41344777 TTAAAT TTAAAT TTAAA- TTAAAA TTGAAT TTAAA- ATAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
41344823 TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAA
41344838 TTTCAAAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 13 0.30
6 31 0.70
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:41344798 original size:17 final size:17
Alignment explanation
Indices: 41344778--41344846 Score: 86
Period size: 17 Copynumber: 4.1 Consensus size: 17
41344768 TTTATAATAT
*
41344778 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAA
* *
41344795 TAAAATTGAATTTAAAA
1 TAAATTTAAATTTAAAA
*
41344812 TAAATTTAAAATTAAAA
1 TAAATTTAAATTTAAAA
41344829 TAAATTT-AATTTCAAAA
1 TAAATTTAAATTT-AAAA
41344846 T
1 T
41344847 GGTTTGGATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 4 0.09
17 40 0.91
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:41348947 original size:31 final size:30
Alignment explanation
Indices: 41348909--41348971 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
41348899 GTTATTAAAC
* *
41348909 TTGACAATTG-TTCTCATATTGAGACCTGAAT
1 TTGACAATTGATTCT-ACATGGAGACCT-AAT
41348940 TTGACAATTGATTCTACATGGAGACCTAAT
1 TTGACAATTGATTCTACATGGAGACCTAAT
41348970 TT
1 TT
41348972 TTAGGGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.17
31 20 0.69
32 4 0.14
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (30 bp):
TTGACAATTGATTCTACATGGAGACCTAAT
Found at i:41350529 original size:31 final size:30
Alignment explanation
Indices: 41350481--41350554 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
41350471 GGTTAACAAC
**
41350481 AATTTTGAGGGGCTTAA-T-AAGAATTTCTAA
1 AATTTTGAGGGATTTAATTCAA-AATTTC-AA
41350511 AGATTTTGAGGGATTTAATTCAAAATTTCAA
1 A-ATTTTGAGGGATTTAATTCAAAATTTCAA
*
41350542 AATTTTGGGGGAT
1 AATTTTGAGGGAT
41350555 AATGATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 12 0.32
31 17 0.45
32 7 0.18
33 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (30 bp):
AATTTTGAGGGATTTAATTCAAAATTTCAA
Found at i:41362062 original size:17 final size:18
Alignment explanation
Indices: 41362040--41362075 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41362030 TTTGTTTAGT
41362040 AATA-TTTTTATCTCAAA
1 AATATTTTTTATCTCAAA
*
41362057 AATATTTTTTATTTCAAA
1 AATATTTTTTATCTCAAA
41362075 A
1 A
41362076 GTACTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTTTTTATCTCAAA
Found at i:41362083 original size:18 final size:18
Alignment explanation
Indices: 41362040--41362083 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
41362030 TTTGTTTAGT
41362040 AATA-TTTTTATCTCAAA
1 AATACTTTTTATCTCAAA
* *
41362057 AATATTTTTTATTTCAAA
1 AATACTTTTTATCTCAAA
*
41362075 AGTACTTTT
1 AATACTTTT
41362084 GAGAAGCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (18 bp):
AATACTTTTTATCTCAAA
Found at i:41362220 original size:20 final size:21
Alignment explanation
Indices: 41362197--41362248 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41362187 TTAATTCAGT
*
41362197 AAATAAAT-TAAAAATTCGAA
1 AAATAAATATAAAAATTCAAA
41362217 AAAT-AATCATAAAAATTCAAA
1 AAATAAAT-ATAAAAATTCAAA
*
41362238 AAATAATTATA
1 AAATAAATATA
41362249 GGAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.11
20 4 0.15
21 18 0.67
22 2 0.07
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAAATATAAAAATTCAAA
Found at i:41362231 original size:21 final size:21
Alignment explanation
Indices: 41362205--41362244 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41362195 GTAAATAAAT
*
41362205 TAAAAATTCGAAAAATAATCA
1 TAAAAATTCAAAAAATAATCA
41362226 TAAAAATTCAAAAAATAAT
1 TAAAAATTCAAAAAATAAT
41362245 TATAGGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAAAATTCAAAAAATAATCA
Found at i:41367192 original size:3 final size:3
Alignment explanation
Indices: 41367184--41367212 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41367174 TTAGGTGATC
41367184 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41367213 TCAATGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:41371910 original size:264 final size:264
Alignment explanation
Indices: 41371435--41371952 Score: 842
Period size: 264 Copynumber: 2.0 Consensus size: 264
41371425 AAATTGTCAT
* * *
41371435 ATTTCAAATTTTGTGCTTGTTTCAAGCCCAAATAGACCATTATAGTTTCTTTTAACATATGAAAA
1 ATTTCAAATATTGTGCTTGTTTCAAGCCCAAATAGACCATCATAGTTACTTTTAACATATGAAAA
** * *
41371500 GATAGATCAATGATCATCCTTCAACATATGATATTAATACTATATGTCCAGAAAGACCACTGAAG
66 GATAGATCAAAAATCATCCTTCAACATATGACATTAATACTATATGTCCAGAAAGACCACTGAAA
41371565 CCTTGTAAACCAATGCCTGGTCCTTATGGATACTGGTTTTCTAACATTATGCCTGTCTCCACAAT
131 CCTTGTAAACCAATGCCTGGTCCTTATGGATACTGGTTTTCTAACATTATGCCTGTCTCCACAAT
* *
41371630 TGCAACTTACTGATATGTTTTGTTTTTCTGCCAAAACATATATAATACATAAGTGGAACTTAGTG
196 TGCAACATACTGATATGTTTTGTTTTTCTACCAAAACATATATAATACATAAGTGGAACTTAGTG
41371695 TATC
261 TATC
*
41371699 ATTTCAAATATTGTGCTTGTTTCAAGTCCAAATAGACCATCATAGTTACTTTTAACATATGAAAA
1 ATTTCAAATATTGTGCTTGTTTCAAGCCCAAATAGACCATCATAGTTACTTTTAACATATGAAAA
* *
41371764 GATAGATCAAAAATCATCCTTCAACATATGACATTAATACTATATGTCTA-CAA-ACCACTGAAA
66 GATAGATCAAAAATCATCCTTCAACATATGACATTAATACTATATGTCCAGAAAGACCACTGAAA
* * ** *
41371827 CCTTTTAAACCAATGCCTGGTCTTTATGGATTACTGGTTTTCTAACATTAATGTTTGTCTCCATA
131 CCTTGTAAACCAATGCCTGGTCCTTATGGA-TACTGGTTTTCTAACATT-ATGCCTGTCTCCACA
*
41371892 ATTGCAACATAGTGATATGTTTTGTTTTTCTACCAAAACATATATAATACATAAGTGGAAC
194 ATTGCAACATACTGATATGTTTTGTTTTTCTACCAAAACATATATAATACATAAGTGGAAC
41371953 AGAAATTTTA
Statistics
Matches: 234, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
262 37 0.16
263 20 0.09
264 177 0.76
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (264 bp):
ATTTCAAATATTGTGCTTGTTTCAAGCCCAAATAGACCATCATAGTTACTTTTAACATATGAAAA
GATAGATCAAAAATCATCCTTCAACATATGACATTAATACTATATGTCCAGAAAGACCACTGAAA
CCTTGTAAACCAATGCCTGGTCCTTATGGATACTGGTTTTCTAACATTATGCCTGTCTCCACAAT
TGCAACATACTGATATGTTTTGTTTTTCTACCAAAACATATATAATACATAAGTGGAACTTAGTG
TATC
Found at i:41376801 original size:16 final size:16
Alignment explanation
Indices: 41376782--41376829 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
41376772 TTTATTTGCC
41376782 TCATATTACATTTTAG
1 TCATATTACATTTTAG
41376798 TCAT-TT--ATGTTT-G
1 TCATATTACAT-TTTAG
*
41376811 TAATATTACATTTTAG
1 TCATATTACATTTTAG
41376827 TCA
1 TCA
41376830 CTTACGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
13 6 0.24
14 5 0.20
15 5 0.20
16 9 0.36
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (16 bp):
TCATATTACATTTTAG
Found at i:41379871 original size:2 final size:2
Alignment explanation
Indices: 41379866--41379891 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41379856 GAAAAAAAGA
41379866 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
41379892 GAACCAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41380779 original size:187 final size:189
Alignment explanation
Indices: 41380453--41380828 Score: 551
Period size: 187 Copynumber: 2.0 Consensus size: 189
41380443 CTCCTGAACC
* * * * *
41380453 ATGGAACTGGAATGTGTATTTGTTTCCTCTTTGGTGTTGTGGTGTGGTAATCCGATACTTGATTT
1 ATGGAACTGAAATGTGTATTTGCTTCCTCTCTGGTATTGT-GAGTGGTAATCCGATACTTGATTT
* *
41380518 TATTCCCTGTGAGGTTAGCTATTGAACTTCTCGAAAGTAACATTGAATTGTTTGATGCATGATGG
65 TATTACCTGTGAGGTTAGCCATTGAACTTCTCGAAAGTAACATTGAATTGTTTGATGCATGATGG
* *
41380583 TTAATGTTTGAATGGAAGTTTACTTTATGTTCGTTTTTGAGGTTAGTTAGGTAGTGTATT
130 TTAATGTTTGAATGAAAGTTTACTTTATGTTCGTTTTCGAGGTTAGTTAGGTAGTGTATT
* * *
41380643 ATGGAACTGAAATGTGTATTTGCTTCCTCTCTGGTATTGT-AG-GGTAATCTGTTCCTTGATTTT
1 ATGGAACTGAAATGTGTATTTGCTTCCTCTCTGGTATTGTGAGTGGTAATCCGATACTTGATTTT
* * *
41380706 ATTACCTGTGAGGTTAGCCATTGAACTTTTC-ATAAGTAACATTGCATTGTTTGATGCATGTTGG
66 ATTACCTGTGAGGTTAGCCATTGAACTTCTCGA-AAGTAACATTGAATTGTTTGATGCATGATGG
* * *
41380770 TTCATGTTTGAGTGAAAGTTTACTTTATGTTTGTTTTCGAGGTTAGTTAGGTAGTGTAT
130 TTAATGTTTGAATGAAAGTTTACTTTATGTTCGTTTTCGAGGTTAGTTAGGTAGTGTAT
41380829 CATAGTTCTG
Statistics
Matches: 167, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
186 1 0.01
187 129 0.77
188 1 0.01
190 36 0.22
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (189 bp):
ATGGAACTGAAATGTGTATTTGCTTCCTCTCTGGTATTGTGAGTGGTAATCCGATACTTGATTTT
ATTACCTGTGAGGTTAGCCATTGAACTTCTCGAAAGTAACATTGAATTGTTTGATGCATGATGGT
TAATGTTTGAATGAAAGTTTACTTTATGTTCGTTTTCGAGGTTAGTTAGGTAGTGTATT
Found at i:41380978 original size:158 final size:158
Alignment explanation
Indices: 41380697--41380990 Score: 416
Period size: 158 Copynumber: 1.9 Consensus size: 158
41380687 TAATCTGTTC
* * *
41380697 CTTGATTTTATTACCTGTGAGGTTAGCCATTGAACTTTTCATAAGTAACATTGCATTGTTTGATG
1 CTTGATTTTATTACCTGTGAGGTCAGCCATTGAACTTCTCAAAAGTAACATTGCATTGTTTGATG
* * ** * *
41380762 CATGTTGGTTCATGTTTGAGTGAAAGTTTACTTTATGTTTGTTTTCGAGGTTAGTTAGGTAGTGT
66 CATGATGGTTCATGTTTGAATGAAAGTTTACTTTATGTTCATTTTAGAGGTTACTTAGGTAGTGT
41380827 ATCATAGTTCTGGTGTGGTAATCCTGTA
131 ATCATAGTTCTGGTGTGGTAATCCTGTA
*
41380855 CTTGATTTTATT-CTCTGTGAGGGTCAGCCATTGAACTTCTCAAAAGTAACGTTGCATT-TCTT-
1 CTTGATTTTATTAC-CTGTGA-GGTCAGCCATTGAACTTCTCAAAAGTAACATTGCATTGT-TTG
* *
41380917 AGTGCGTGATGTTTCATGTTTGAATG-AAGTTTACTTTATGTTCATTTTAGAGGTTACTTAGGTA
63 A-TGCATGATGGTTCATGTTTGAATGAAAGTTTACTTTATGTTCATTTTAGAGGTTACTTAGGTA
41380981 GTGTATCATA
127 GTGTATCATA
41380991 TGTTGAAATA
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
157 1 0.01
158 64 0.53
159 55 0.46
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (158 bp):
CTTGATTTTATTACCTGTGAGGTCAGCCATTGAACTTCTCAAAAGTAACATTGCATTGTTTGATG
CATGATGGTTCATGTTTGAATGAAAGTTTACTTTATGTTCATTTTAGAGGTTACTTAGGTAGTGT
ATCATAGTTCTGGTGTGGTAATCCTGTA
Found at i:41393244 original size:24 final size:24
Alignment explanation
Indices: 41393205--41393253 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41393195 ATTTTAATAT
*
41393205 ATTTTGTGTTGATTTGATTGAGGA
1 ATTTTGTGTGGATTTGATTGAGGA
* * *
41393229 ATTTTGTGTGGTTTTGTTTGTGGA
1 ATTTTGTGTGGATTTGATTGAGGA
41393253 A
1 A
41393254 ATTATTAGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (24 bp):
ATTTTGTGTGGATTTGATTGAGGA
Found at i:41397698 original size:13 final size:13
Alignment explanation
Indices: 41397682--41397743 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
41397672 TAAATCAAAA
*
41397682 TTTTCAAAAGTAT
1 TTTTCAAAAGTAC
41397695 TTTTCAAAA-TCAC
1 TTTTCAAAAGT-AC
* *
41397708 TTTTCCAAAGTAT
1 TTTTCAAAAGTAC
* **
41397721 TTTTTAAAAACAC
1 TTTTCAAAAGTAC
41397734 TTTTCAAAAG
1 TTTTCAAAAG
41397744 CAATGCTAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
12 1 0.03
13 35 0.95
14 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.42
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:41397711 original size:26 final size:26
Alignment explanation
Indices: 41397682--41397743 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
41397672 TAAATCAAAA
*
41397682 TTTTCAAAAGTATTTTTCAAAATCAC
1 TTTTCAAAAGTATTTTTCAAAAACAC
* *
41397708 TTTTCCAAAGTATTTTTTAAAAACAC
1 TTTTCAAAAGTATTTTTCAAAAACAC
41397734 TTTTCAAAAG
1 TTTTCAAAAG
41397744 CAATGCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.42
Consensus pattern (26 bp):
TTTTCAAAAGTATTTTTCAAAAACAC
Found at i:41401924 original size:20 final size:20
Alignment explanation
Indices: 41401889--41401929 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41401879 TACTTTGTGC
* *
41401889 TATTTTTTTTATTTTTATAT
1 TATTTTTTTGAATTTTATAT
*
41401909 TATTTTTTTGAATTTTTTAT
1 TATTTTTTTGAATTTTATAT
41401929 T
1 T
41401930 TTTGAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (20 bp):
TATTTTTTTGAATTTTATAT
Found at i:41404759 original size:16 final size:16
Alignment explanation
Indices: 41404734--41404768 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
41404724 TGTGTTTTTT
*
41404734 ATTGATATAATCTTCA
1 ATTGAAATAATCTTCA
41404750 ATTGAAATAATCTTCA
1 ATTGAAATAATCTTCA
41404766 ATT
1 ATT
41404769 CTGACTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTGAAATAATCTTCA
Found at i:41410937 original size:14 final size:15
Alignment explanation
Indices: 41410926--41410966 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
41410916 TAAGTTTAGA
41410926 TTTTTAATTTTAAAT
1 TTTTTAATTTTAAAT
41410941 TTTTTAA--TT-AAT
1 TTTTTAATTTTAAAT
*
41410953 TTTTTATTTTTAAA
1 TTTTTAATTTTAAA
41410967 ATAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTAATTTTAAAT
Done.