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 147 of 230
Found at i:43381701 original size:22 final size:22
Alignment explanation
Indices: 43381675--43381744 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
43381665 AGATGAGTTG
43381675 TATTAATGACCAGCAACTCATT
1 TATTAATGACCAGCAACTCATT
* *
43381697 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACCAGCA-ACTCA-TT
43381716 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGCAACTCATT
43381739 TATTAA
1 TATTAA
43381745 ACTAAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.25
22 15 0.42
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGCAACTCATT
Found at i:43381707 original size:42 final size:42
Alignment explanation
Indices: 43381646--43381751 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
43381636 TCATTAAATA
43381646 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
43381689 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
43381731 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
43381752 GGCTTAAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 54 0.86
43 9 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:43382995 original size:12 final size:12
Alignment explanation
Indices: 43382955--43383010 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
43382945 ATTTCTTTTG
43382955 TTTCAATTTCTT
1 TTTCAATTTCTT
* *
43382967 TCCCTTTAATCTCTT
1 T---TTCAATTTCTT
43382982 TTTCAATTTCTT
1 TTTCAATTTCTT
*
43382994 TTTCAACTTCTT
1 TTTCAATTTCTT
43383006 TTTCA
1 TTTCA
43383011 CTCTCAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 26 0.72
15 10 0.28
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:43383074 original size:12 final size:12
Alignment explanation
Indices: 43383057--43383089 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
43383047 TTTTCTTTTT
43383057 GCTTTTT-AAAG
1 GCTTTTTCAAAG
43383068 GCTTTTTCAAAG
1 GCTTTTTCAAAG
43383080 GCTTTTTCAA
1 GCTTTTTCAA
43383090 GTTCTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (12 bp):
GCTTTTTCAAAG
Found at i:43383193 original size:21 final size:20
Alignment explanation
Indices: 43383160--43383203 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
43383150 TTTCGTTTGT
43383160 TTTTCTTCTTTTGCTTTT-TC
1 TTTTCTTCTTTTG-TTTTCTC
*
43383180 TTTTCTTTTCTTTGTTTTCTC
1 TTTTCTTCT-TTTGTTTTCTC
43383201 TTT
1 TTT
43383204 ACAAGAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTCTTCTTTTGTTTTCTC
Found at i:43385102 original size:20 final size:20
Alignment explanation
Indices: 43385079--43385135 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
43385069 GGGTTAAGAT
*
43385079 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
43385099 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
43385119 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
43385136 AAACGGAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:43388810 original size:13 final size:12
Alignment explanation
Indices: 43388768--43388810 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
43388758 GAACTCTTTT
*
43388768 TCTTTTTCATTC
1 TCTTTTTCAATC
43388780 TCTTTTTCAATC
1 TCTTTTTCAATC
*
43388792 TGTTTTTCAATC
1 TCTTTTTCAATC
*
43388804 TCATTTT
1 TCTTTTT
43388811 GTTTCCTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.14, C:0.21, G:0.02, T:0.63
Consensus pattern (12 bp):
TCTTTTTCAATC
Found at i:43388924 original size:15 final size:15
Alignment explanation
Indices: 43388904--43388960 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 15
43388894 TTTTCTTGCC
43388904 TCTCTTTTCTTTT-G
1 TCTCTTTTCTTTTCG
43388918 ATCTCTTTTTTCTTTTCG
1 -TCTC--TTTTCTTTTCG
43388936 TCT-TTTTCTTTTC-
1 TCTCTTTTCTTTTCG
*
43388949 TC-ATTTTCTTTT
1 TCTCTTTTCTTTT
43388961 TACAAGAGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.29
14 10 0.26
15 4 0.11
17 12 0.32
18 1 0.03
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.72
Consensus pattern (15 bp):
TCTCTTTTCTTTTCG
Found at i:43388943 original size:14 final size:13
Alignment explanation
Indices: 43388919--43388960 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
43388909 TTTCTTTTGA
43388919 TCTCTTTTTTCTTT
1 TCTC-TTTTTCTTT
43388933 TCGTCTTTTTCTTT
1 TC-TCTTTTTCTTT
*
43388947 TCTCATTTTCTTT
1 TCTCTTTTTCTTT
43388960 T
1 T
43388961 TACAAGAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 13 0.50
15 2 0.08
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (13 bp):
TCTCTTTTTCTTT
Found at i:43388961 original size:14 final size:14
Alignment explanation
Indices: 43388925--43388960 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
43388915 TTGATCTCTT
*
43388925 TTTTCTTTTCGTCT
1 TTTTCTTTTCGTCA
43388939 TTTTCTTTTC-TCA
1 TTTTCTTTTCGTCA
43388952 TTTTCTTTT
1 TTTTCTTTT
43388961 TACAAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTCGTCA
Found at i:43392192 original size:47 final size:47
Alignment explanation
Indices: 43392071--43392412 Score: 540
Period size: 47 Copynumber: 7.2 Consensus size: 47
43392061 AATTCTAAAT
43392071 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
43392118 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
43392166 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
43392213 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
43392261 TATGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
43392310 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*** * * * * * * *
43392357 TGTGACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
43392404 TGTGATAAG
1 TGTGATAAG
43392413 TCCCGAAGGG
Statistics
Matches: 274, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
47 136 0.50
48 92 0.34
49 46 0.17
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:43392217 original size:95 final size:94
Alignment explanation
Indices: 43392071--43392412 Score: 540
Period size: 95 Copynumber: 3.6 Consensus size: 94
43392061 AATTCTAAAT
43392071 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAAGGCCTAATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAAGGCCTAATG
43392136 GCCGATGTGATGAATGTGAAAGTGTATATA
65 GCCGATGTGATGAATGTGAAAGTGTATATA
*
43392166 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAGGGCCTAATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAAGGCCTAATG
43392231 GCCGATGTGATGAATGTGAAAGTGTATATA
65 GCCGATGTGATGAATGTGAAAGTGTATATA
*
43392261 TATGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT
43392326 GGCCGATGTGATGAATGTGAAAGTGTATATA
64 GGCCGATGTGATGAATGTGAAAGTGTATATA
*** * * * * * * *
43392357 TGTGACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
43392413 TCCCGAAGGG
Statistics
Matches: 231, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
94 13 0.06
95 134 0.58
96 74 0.32
97 10 0.04
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATA
Found at i:43396204 original size:20 final size:21
Alignment explanation
Indices: 43396158--43396204 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
43396148 GTAAGCTCGG
43396158 TTGAGCTCAAACGAGCTGAAA
1 TTGAGCTCAAACGAGCTGAAA
** *
43396179 -CAAGCTCAAATGAGCT-AAA
1 TTGAGCTCAAACGAGCTGAAA
43396198 TTGAGCT
1 TTGAGCT
43396205 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (21 bp):
TTGAGCTCAAACGAGCTGAAA
Found at i:43400362 original size:12 final size:12
Alignment explanation
Indices: 43400342--43400376 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
43400332 CTATTAAATT
43400342 TTAATTAATAAG
1 TTAATTAATAAG
* *
43400354 TTCATTAATTAG
1 TTAATTAATAAG
43400366 TTAATTAATAA
1 TTAATTAATAA
43400377 ACCACATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (12 bp):
TTAATTAATAAG
Found at i:43404613 original size:30 final size:30
Alignment explanation
Indices: 43404579--43404676 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
43404569 AGCTCACTCC
43404579 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
43404609 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
43404639 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
43404669 TAGCTCAT
1 TAGCTCAT
43404677 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:43408182 original size:11 final size:10
Alignment explanation
Indices: 43408146--43408191 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
43408136 AGCTCCCTTG
43408146 AGCTCGTTTT
1 AGCTCGTTTT
* *
43408156 AACTCGTTTG
1 AGCTCGTTTT
43408166 AGCTCGTATTT
1 AGCTCGT-TTT
*
43408177 AGCTCGTTTC
1 AGCTCGTTTT
43408187 AGCTC
1 AGCTC
43408192 ATTCCTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:43408182 original size:21 final size:20
Alignment explanation
Indices: 43408143--43408191 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
43408133 ATCAGCTCCC
43408143 TTGAGCTCGTTTTAACTCGT
1 TTGAGCTCGTTTTAACTCGT
*
43408163 TTGAGCTCGTATTTAGCTCGT
1 TTGAGCTCGT-TTTAACTCGT
*
43408184 TTCAGCTC
1 TTGAGCTC
43408192 ATTCCTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGAGCTCGTTTTAACTCGT
Found at i:43408512 original size:30 final size:30
Alignment explanation
Indices: 43408453--43408549 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
43408443 AGCTCACTCC
* *
43408453 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAAC-TTCAGCTTACGAGCTAAACCT
* * *
43408483 TAGCTCAACTTCAGCTTAGGAGTTTAACCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
* * * *
43408513 CAGCACAACTTTAGCTTACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
43408543 TAGCTCA
1 TAGCTCA
43408550 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 50 0.96
31 2 0.04
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTTACGAGCTAAACCT
Found at i:43411220 original size:11 final size:12
Alignment explanation
Indices: 43411188--43411218 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43411178 TTGAGAGAAC
43411188 TTGAAAAAGCCT
1 TTGAAAAAGCCT
43411200 TTGAAAAAGCCT
1 TTGAAAAAGCCT
43411212 TTGAAAA
1 TTGAAAA
43411219 GCAAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:43411242 original size:18 final size:18
Alignment explanation
Indices: 43411221--43411255 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43411211 TTTGAAAAGC
43411221 AAAATGAAAATGAAAAAT
1 AAAATGAAAATGAAAAAT
* *
43411239 AAAATGAGATTGAAAAA
1 AAAATGAAAATGAAAAA
43411256 GAGAACGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (18 bp):
AAAATGAAAATGAAAAAT
Found at i:43411296 original size:30 final size:31
Alignment explanation
Indices: 43411243--43411302 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
43411233 AAAAATAAAA
*
43411243 TGAGATTGAAAAAGAGAACG-AAAAGAAATC
1 TGAGAGTGAAAAAGAGAACGAAAAAGAAATC
*
43411273 TGAGAGTGAAAAAGA-AGATGAAAAAGAAAT
1 TGAGAGTGAAAAAGAGA-ACGAAAAAGAAAT
43411303 TGAAACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 16 0.62
31 9 0.35
ACGTcount: A:0.58, C:0.03, G:0.25, T:0.13
Consensus pattern (31 bp):
TGAGAGTGAAAAAGAGAACGAAAAAGAAATC
Found at i:43413544 original size:30 final size:31
Alignment explanation
Indices: 43413508--43413604 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
43413498 AACTCACTCC
*
43413508 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
43413538 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
43413568 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
43413598 TAGCTCA
1 TAGCTCA
43413605 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:43415201 original size:13 final size:13
Alignment explanation
Indices: 43415183--43415211 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43415173 AATAGTTGTG
43415183 TGTTATTTAATTA
1 TGTTATTTAATTA
43415196 TGTTATTTAATTA
1 TGTTATTTAATTA
43415209 TGT
1 TGT
43415212 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:43417519 original size:4 final size:4
Alignment explanation
Indices: 43417510--43417537 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
43417500 TTAAACTAAG
43417510 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
43417538 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:43418963 original size:18 final size:18
Alignment explanation
Indices: 43418942--43418980 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43418932 TTTCTTCAAC
* *
43418942 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
43418960 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
43418978 TTC
1 TTC
43418981 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:43425491 original size:12 final size:13
Alignment explanation
Indices: 43425432--43425489 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
43425422 TTGTAGATTC
*
43425432 AAAAAAAATCG-A
1 AAAAAAAATTGAA
*
43425444 AAAAAAAATCGAA
1 AAAAAAAATTGAA
43425457 AAAAAAAATTGAA
1 AAAAAAAATTGAA
43425470 AAAAAAAATTGAA
1 AAAAAAAATTGAA
43425483 AAGAAAA
1 AA-AAAA
43425490 TTTGCATACG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
12 11 0.26
13 28 0.65
14 4 0.09
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.10
Consensus pattern (13 bp):
AAAAAAAATTGAA
Found at i:43436707 original size:30 final size:30
Alignment explanation
Indices: 43436673--43436732 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
43436663 ATTTAATACT
43436673 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* *
43436703 AACTTTTGCAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
43436733 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:43443885 original size:22 final size:22
Alignment explanation
Indices: 43443834--43443899 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
43443824 GGTATTTGGG
* *
43443834 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
43443855 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
43443877 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
43443900 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:43447411 original size:17 final size:18
Alignment explanation
Indices: 43447389--43447422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43447379 ACAACACTCC
*
43447389 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
43447406 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
43447423 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:43447530 original size:15 final size:16
Alignment explanation
Indices: 43447505--43447536 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
43447495 TATCTCACAC
43447505 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
43447521 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
43447536 T
1 T
43447537 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:43448510 original size:13 final size:12
Alignment explanation
Indices: 43448494--43448566 Score: 58
Period size: 13 Copynumber: 5.7 Consensus size: 12
43448484 TTTTGCTCGA
43448494 TTTTTTTTTCACT
1 TTTTTTTTTCA-T
*
43448507 TTTTTTTTTGAAT
1 TTTTTTTTT-CAT
43448520 TTTTTTTTAATCA-
1 TTTTTTTT--TCAT
*
43448533 ATTTTTTTTCGAAT
1 TTTTTTTTTC--AT
*
43448547 TTTTTTTTTGAT
1 TTTTTTTTTCAT
43448559 TTTTTTTT
1 TTTTTTTT
43448567 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
11 2 0.04
12 10 0.20
13 26 0.53
14 10 0.20
15 1 0.02
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCAT
Found at i:43448522 original size:12 final size:12
Alignment explanation
Indices: 43448493--43448567 Score: 64
Period size: 14 Copynumber: 5.9 Consensus size: 12
43448483 TTTTTGCTCG
*
43448493 ATTTTTTTTTCA
1 ATTTTTTTTTGA
*
43448505 CTTTTTTTTTTGA
1 -ATTTTTTTTTGA
43448518 ATTTTTTTTT-A
1 ATTTTTTTTTGA
43448529 ATCAATTTTTTTTCGA
1 AT---TTTTTTTT-GA
43448545 ATTTTTTTTTTG-
1 A-TTTTTTTTTGA
43448557 ATTTTTTTTTG
1 ATTTTTTTTTG
43448568 TTACTCCAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
11 13 0.25
12 10 0.19
13 11 0.21
14 16 0.30
16 2 0.04
17 1 0.02
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:43448522 original size:40 final size:39
Alignment explanation
Indices: 43448478--43448567 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 39
43448468 TTTGGTCACC
* * *
43448478 ATTTTTTTTTGCTCGATTTTTTTTTC-ACTTTTTTTTTTG
1 ATTTTTTTTTGATC-AATTTTTTTTCGAATTTTTTTTTTG
*
43448517 AATTTTTTTTTAATCAATTTTTTTTCGAATTTTTTTTTTG
1 -ATTTTTTTTTGATCAATTTTTTTTCGAATTTTTTTTTTG
43448557 ATTTTTTTTTG
1 ATTTTTTTTTG
43448568 TTACTCCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
39 20 0.45
40 24 0.55
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (39 bp):
ATTTTTTTTTGATCAATTTTTTTTCGAATTTTTTTTTTG
Found at i:43448524 original size:27 final size:26
Alignment explanation
Indices: 43448494--43448555 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
43448484 TTTTGCTCGA
* *
43448494 TTTTTTTTTCACTTTTTTTTTTGAATT
1 TTTTTTTTTCA-ATTTTTTTTCGAATT
*
43448521 TTTTTTTAATCAATTTTTTTTCGAATT
1 TTTTTTT-TTCAATTTTTTTTCGAATT
43448548 TTTTTTTT
1 TTTTTTTT
43448556 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTCAATTTTTTTTCGAATT
Found at i:43452759 original size:30 final size:30
Alignment explanation
Indices: 43452725--43452784 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
43452715 ATTTAATACG
43452725 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
43452755 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
43452785 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:43457411 original size:14 final size:14
Alignment explanation
Indices: 43457394--43457428 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
43457384 TAATTCAGTG
43457394 AAAAAAATTCGTAC
1 AAAAAAATTCGTAC
* *
43457408 AAAAAATTTCGTAT
1 AAAAAAATTCGTAC
43457422 AAAAAAA
1 AAAAAAA
43457429 AAGAACATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.23
Consensus pattern (14 bp):
AAAAAAATTCGTAC
Found at i:43458870 original size:14 final size:14
Alignment explanation
Indices: 43458853--43458883 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43458843 TGGATAGTTG
43458853 AAGAAAGGCTAAGA
1 AAGAAAGGCTAAGA
*
43458867 AAGAAAGGTTAAGA
1 AAGAAAGGCTAAGA
43458881 AAG
1 AAG
43458884 GTTCAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.29, T:0.10
Consensus pattern (14 bp):
AAGAAAGGCTAAGA
Found at i:43460136 original size:30 final size:30
Alignment explanation
Indices: 43460041--43460137 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
43460031 AGCTCACTCC
* * *
43460041 TAGCTC-ACTTTCAACTCGCGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
43460071 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
43460101 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
43460131 TAGCTCA
1 TAGCTCA
43460138 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:43461870 original size:13 final size:13
Alignment explanation
Indices: 43461852--43461897 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
43461842 TATACAAGTC
43461852 AAAAAAAATTC--
1 AAAAAAAATTCAA
43461863 AAAAAAAATTCAA
1 AAAAAAAATTCAA
43461876 AAAAAAAA-TCGAA
1 AAAAAAAATTC-AA
43461889 AAGAAAAAA
1 AA-AAAAAA
43461898 AAATCTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.35
12 2 0.06
13 12 0.39
14 6 0.19
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:43461890 original size:11 final size:11
Alignment explanation
Indices: 43461850--43461881 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
43461840 GTTATACAAG
43461850 TCAAAAAAAAT
1 TCAAAAAAAAT
43461861 TCAAAAAAAAT
1 TCAAAAAAAAT
43461872 TCAAAAAAAA
1 TCAAAAAAAA
43461882 AATCGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:43461895 original size:18 final size:18
Alignment explanation
Indices: 43461874--43461913 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
43461864 AAAAAAATTC
43461874 AAAAAAAAAATC-GAAAA
1 AAAAAAAAAATCTGAAAA
*
43461891 GAAAAAAAAATCTGAAAA
1 AAAAAAAAAATCTGAAAA
43461909 AAAAA
1 AAAAA
43461914 GTGTTTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAATCTGAAAA
Found at i:43462611 original size:30 final size:30
Alignment explanation
Indices: 43462577--43462673 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
43462567 AGCTCACTCC
*
43462577 TAGCTC-ACTTTCGACTTACGAGCTAAACCT
1 TAGCTCAACTTTAG-CTTACGAGCTAAACCT
* * * *
43462607 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTTACGAGCTAAACCT
* * *
43462637 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTTACGAGCTAAACCT
43462667 TAGCTCA
1 TAGCTCA
43462674 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 47 0.89
31 6 0.11
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTTACGAGCTAAACCT
Found at i:43479406 original size:22 final size:23
Alignment explanation
Indices: 43479381--43479440 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
43479371 TGGACTGAAT
43479381 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
43479403 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
43479425 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
43479441 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:43479408 original size:4 final size:4
Alignment explanation
Indices: 43479390--43479423 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
43479380 TATAAAAATT
43479390 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
43479424 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:43480844 original size:18 final size:18
Alignment explanation
Indices: 43480823--43480861 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43480813 TTTCTTCAAC
*
43480823 TTCTATTTCAAATTTCTT
1 TTCTATTTCAAATTCCTT
* *
43480841 TTCTGTTTCACATTCCTT
1 TTCTATTTCAAATTCCTT
43480859 TTC
1 TTC
43480862 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (18 bp):
TTCTATTTCAAATTCCTT
Found at i:43483214 original size:22 final size:23
Alignment explanation
Indices: 43483189--43483248 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
43483179 TGGACTGAAT
43483189 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
43483211 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
43483233 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
43483249 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:43483216 original size:4 final size:4
Alignment explanation
Indices: 43483198--43483231 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
43483188 TATAAAAATT
43483198 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
43483232 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:43484793 original size:20 final size:19
Alignment explanation
Indices: 43484770--43484834 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
43484760 AAGCTCAAAC
43484770 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
43484790 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
43484810 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
43484830 GAGCT
1 GAGCT
43484835 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:43488215 original size:17 final size:18
Alignment explanation
Indices: 43488179--43488219 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43488169 TTTAACTTGA
* *
43488179 TTTTTTTTTGGTCACCTT
1 TTTTTTTTTGCTCACATT
43488197 TTTTTTTTTGCTCA-ATT
1 TTTTTTTTTGCTCACATT
43488214 TTTTTT
1 TTTTTT
43488220 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTTTTTTGCTCACATT
Found at i:43488241 original size:14 final size:14
Alignment explanation
Indices: 43488224--43488276 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
43488214 TTTTTTCACT
43488224 TTTTTTTTTGAATA
1 TTTTTTTTTGAATA
*
43488238 TTTTTTTTTCAATCAA
1 TTTTTTTTTGAAT--A
43488254 TTTTTTTTTTCGAAT-
1 -TTTTTTTTT-GAATA
43488269 TTTTTTTT
1 TTTTTTTT
43488277 GATTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 20 0.61
16 1 0.03
17 9 0.27
18 3 0.09
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTGAATA
Found at i:43488281 original size:11 final size:13
Alignment explanation
Indices: 43488255--43488286 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
43488245 TTCAATCAAT
43488255 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
43488268 TTTTTTTTT-G-A
1 TTTTTTTTTCGAA
43488279 TTTTTTTT
1 TTTTTTTT
43488287 GTTACTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:43489924 original size:20 final size:19
Alignment explanation
Indices: 43489901--43489965 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
43489891 AAGCTCAAAC
43489901 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
43489921 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
43489941 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
43489961 GAGCT
1 GAGCT
43489966 GTGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:43495679 original size:22 final size:23
Alignment explanation
Indices: 43495654--43495713 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
43495644 TGGACTGAAT
43495654 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
43495676 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
43495698 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
43495714 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:43495681 original size:4 final size:4
Alignment explanation
Indices: 43495663--43495696 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
43495653 TATAAAAATT
43495663 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
43495697 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:43496837 original size:30 final size:30
Alignment explanation
Indices: 43496752--43496848 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
43496742 TAAACTAAAA
* *
43496752 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
43496782 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
*
43496812 TGAGTTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
43496841 ATGAGCTA
1 -TGAGCTA
43496849 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:43498709 original size:14 final size:14
Alignment explanation
Indices: 43498687--43498734 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
43498677 ACCTAAACCG
* *
43498687 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
43498701 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
43498715 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
43498729 ACCATT
1 ACCATT
43498735 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:43500690 original size:30 final size:30
Alignment explanation
Indices: 43500619--43500701 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
43500609 CTTTTGTTTC
*
43500619 AATTTCCTTTTCA-TCTTCTTTTTCACTCTCA
1 AATTT-CTTTTCATTC-TCTTTTTCAATCTCA
*
43500650 AATTTCTTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTCATTCTCTTTTTCAATCTCA
* *
43500679 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTC-TTTTCATTCTCTTTTT
43500702 TCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 33 0.73
31 7 0.16
ACGTcount: A:0.13, C:0.23, G:0.01, T:0.63
Consensus pattern (30 bp):
AATTTCTTTTCATTCTCTTTTTCAATCTCA
Found at i:43500701 original size:18 final size:18
Alignment explanation
Indices: 43500652--43500707 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
43500642 CACTCTCAAA
* *
43500652 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
43500669 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
43500687 TTTCATTTTCTTTTTTCTT
1 TTTCATTTTC-ATTTTCTT
43500706 TT
1 TT
43500708 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:43500708 original size:12 final size:12
Alignment explanation
Indices: 43500677--43500701 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43500667 TTTTTCAATC
43500677 TCATTTTCTTTT
1 TCATTTTCTTTT
43500689 TCATTTTCTTTT
1 TCATTTTCTTTT
43500701 T
1 T
43500702 TCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:43500719 original size:12 final size:12
Alignment explanation
Indices: 43500704--43500734 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43500694 TTCTTTTTTC
43500704 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43500716 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43500728 TTTTCAA
1 TTTTCAA
43500735 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:43500792 original size:5 final size:5
Alignment explanation
Indices: 43500782--43500838 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
43500772 CTCTTGCCTC
*
43500782 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
43500829 TCTTT TCTTT
1 TCTTT TCTTT
43500839 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:43500822 original size:15 final size:14
Alignment explanation
Indices: 43500782--43500838 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
43500772 CTCTTGCCTC
*
43500782 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
43500797 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
43500812 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
43500829 TCTTTTCTTT
1 TCTTTTCTTT
43500839 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:43500839 original size:21 final size:21
Alignment explanation
Indices: 43500782--43500849 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
43500772 CTCTTGCCTC
* *
43500782 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
43500803 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
43500824 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
43500844 CTCTTT
1 -TCTTT
43500850 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:43501722 original size:15 final size:15
Alignment explanation
Indices: 43501702--43501749 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
43501692 TCAAAGATGG
43501702 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
43501717 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
43501731 GTTTATGGATATAAA
1 GTTTATGGATATGAA
43501746 GTTT
1 GTTT
43501750 TTTTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:43501736 original size:14 final size:14
Alignment explanation
Indices: 43501696--43501739 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
43501686 AAGGATTCAA
43501696 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
43501710 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
43501725 AGATGGGTTTATGG
1 AGATGGGTTTATGG
43501739 A
1 A
43501740 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:43505048 original size:14 final size:14
Alignment explanation
Indices: 43505026--43505070 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
43505016 TTAAAGAAGC
43505026 AACTCATTAAATTA
1 AACTCATTAAATTA
*
43505040 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
43505053 AACTCATTTAATTA
1 AACTCATTAAATTA
43505067 AACT
1 AACT
43505071 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:43505114 original size:42 final size:42
Alignment explanation
Indices: 43505053--43505200 Score: 269
Period size: 42 Copynumber: 3.5 Consensus size: 42
43505043 TCATTAAATA
43505053 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
*
43505096 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGT
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
*
43505138 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGG
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
43505180 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
43505201 GGCTTAAATG
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
42 94 0.91
43 9 0.09
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:43508302 original size:42 final size:42
Alignment explanation
Indices: 43508243--43508348 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
43508233 CATTTAAGCC
43508243 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
43508285 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
43508327 TCTTCA-TTTAATTAAATGAGTT
1 TCTT-AGTTTAA-TAAATGAGTT
43508349 TATTTAATGA
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
42 51 0.82
43 11 0.18
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:43508363 original size:13 final size:14
Alignment explanation
Indices: 43508332--43508372 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
43508322 ACTCATCTTC
*
43508332 ATTTAATTAAATGA
1 ATTTAATTTAATGA
*
43508346 GTTT-ATTTAATGA
1 ATTTAATTTAATGA
43508359 ATTTAATTTAATGA
1 ATTTAATTTAATGA
43508373 GTTGCTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (14 bp):
ATTTAATTTAATGA
Found at i:43509966 original size:30 final size:30
Alignment explanation
Indices: 43509932--43510028 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
43509922 TAAACTAAAA
*
43509932 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
43509962 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
43509992 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
43510021 ATGAGCTA
1 -TGAGCTA
43510029 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:43512223 original size:12 final size:12
Alignment explanation
Indices: 43512208--43512238 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43512198 TTCTTTTTGC
43512208 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43512220 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43512232 TTTTCAA
1 TTTTCAA
43512239 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:43512224 original size:42 final size:42
Alignment explanation
Indices: 43512137--43512226 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 42
43512127 GTTTCTTTTG
**
43512137 TTTCAATTCCTTTTTCATCTTCTTTTTCACTTTCAAATTTCT
1 TTTCAATTCCTTTTTCATCTTCTTTTTCACTTTCAAAGCTCT
* * *
43512179 TTTCATTTCCTTTTTCATTTTCTTTTTGC-TTTTCAAAGGCT-T
1 TTTCAATTCCTTTTTCATCTTCTTTTT-CACTTTCAAA-GCTCT
43512221 TTTCAA
1 TTTCAA
43512227 AGGCTTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.16, C:0.21, G:0.03, T:0.60
Consensus pattern (42 bp):
TTTCAATTCCTTTTTCATCTTCTTTTTCACTTTCAAAGCTCT
Found at i:43512315 original size:6 final size:6
Alignment explanation
Indices: 43512299--43512348 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
43512289 TTTCTTTTTA
*
43512299 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
43512348 T
1 T
43512349 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:43512331 original size:37 final size:37
Alignment explanation
Indices: 43512288--43512358 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
43512278 CTTGCCTCTC
43512288 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
43512325 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
43512359 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:43512359 original size:16 final size:16
Alignment explanation
Indices: 43512284--43512344 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
43512274 GCCTCTTGCC
*
43512284 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
43512300 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
43512316 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
43512332 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
43512345 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:43513302 original size:10 final size:11
Alignment explanation
Indices: 43513278--43513317 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
43513268 TTTAACTCGA
43513278 TTTTTTTGTCAC
1 TTTTTTT-TCAC
43513290 TTTTTTTTC-C
1 TTTTTTTTCAC
*
43513300 TTTTTTTTCAA
1 TTTTTTTTCAC
43513311 TTTTTTT
1 TTTTTTT
43513318 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.38
11 9 0.35
12 7 0.27
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCAC
Found at i:43513325 original size:11 final size:11
Alignment explanation
Indices: 43513277--43513328 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
43513267 TTTTAACTCG
43513277 ATTTTTTTGTCA
1 ATTTTTTT-TCA
*
43513289 CTTTTTTTTC-
1 ATTTTTTTTCA
*
43513299 CTTTTTTTTCA
1 ATTTTTTTTCA
*
43513310 A-TTTTTTTGA
1 ATTTTTTTTCA
43513320 ATTTTTTTT
1 ATTTTTTTT
43513329 TCTGAATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 19 0.54
11 9 0.26
12 7 0.20
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.75
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:43515160 original size:29 final size:29
Alignment explanation
Indices: 43515127--43515186 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
43515117 ATAACCAAAC
* *
43515127 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
43515156 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
43515185 CT
1 CT
43515187 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:43515179 original size:15 final size:15
Alignment explanation
Indices: 43515133--43515180 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
43515123 AAACCTACAA
*
43515133 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
43515148 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
43515162 AAACTTCATATCCAT
1 AAACTTCATATCCAT
43515177 AAAC
1 AAAC
43515181 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:43517875 original size:30 final size:30
Alignment explanation
Indices: 43517841--43517923 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
43517831 TAAACTAAAA
43517841 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
43517871 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
43517901 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCGTGAG
43517924 TTGAAAGCGA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:43521030 original size:9 final size:10
Alignment explanation
Indices: 43521023--43521079 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
43521013 AAGAGAAAAT
43521023 AAAGAAAAGA
1 AAAGAAAAGA
43521033 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
43521045 AAAGAAGA-A
1 AAAGAAAAGA
43521054 AAAGAAAATGA
1 AAAGAAAA-GA
43521065 AATA-AAAAGA
1 AA-AGAAAAGA
43521075 AAAGA
1 AAAGA
43521080 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:43521047 original size:6 final size:5
Alignment explanation
Indices: 43521023--43521079 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
43521013 AAGAGAAAAT
*
43521023 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
43521070 AAAGA AAAGA
1 AAAGA AAAGA
43521080 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:43521054 original size:15 final size:14
Alignment explanation
Indices: 43521023--43521079 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
43521013 AAGAGAAAAT
43521023 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
43521039 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
43521054 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
43521070 AAAGAAAAGA
1 AAAGAAAAGA
43521080 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:43521158 original size:11 final size:12
Alignment explanation
Indices: 43521127--43521157 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43521117 TTGAGAGAAC
43521127 TTGAAAAAGCCT
1 TTGAAAAAGCCT
43521139 TTGAAAAAGCCT
1 TTGAAAAAGCCT
43521151 TTGAAAA
1 TTGAAAA
43521158 GAAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:43523356 original size:30 final size:30
Alignment explanation
Indices: 43523262--43523357 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
43523252 AGCTCACTCC
* * *
43523262 TAGCTC-ACTTTAACTCACGAGCTAAACCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
* * * **
43523291 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAG-CT
*
43523321 CAGCTCAACTTTAGCTCAAGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
43523351 TAGCTCA
1 TAGCTCA
43523358 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
29 8 0.16
30 39 0.78
31 3 0.06
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
Found at i:43523382 original size:38 final size:38
Alignment explanation
Indices: 43523340--43523412 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
43523330 TTTAGCTCAA
43523340 GAGCTAAAGCTT-AGCTCATTTTAGTTTAAACTCGGCGT
1 GAGCTAAAG-TTGAGCTCATTTTAGTTTAAACTCGGCGT
43523378 GAGCTAAAGTTGAGCTCATTTTAGTTTAAACTCGG
1 GAGCTAAAGTTGAGCTCATTTTAGTTTAAACTCGG
43523413 TTTTGTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 2 0.06
38 32 0.94
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (38 bp):
GAGCTAAAGTTGAGCTCATTTTAGTTTAAACTCGGCGT
Found at i:43525397 original size:30 final size:30
Alignment explanation
Indices: 43525363--43525459 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
43525353 AGCTCACTCC
43525363 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * * *
43525393 TAGCTTAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
43525423 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
43525453 TAGCTCA
1 TAGCTCA
43525460 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:43527328 original size:10 final size:10
Alignment explanation
Indices: 43527313--43527350 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
43527303 GCTCGTTTCC
*
43527313 AGCTCACTCG
1 AGCTCAATCG
43527323 AGCTCAAGTC-
1 AGCTCAA-TCG
43527333 AGCTCAATCG
1 AGCTCAATCG
43527343 AGCTCAAT
1 AGCTCAAT
43527351 TTAGCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:43527356 original size:20 final size:20
Alignment explanation
Indices: 43527312--43527349 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43527302 AGCTCGTTTC
*
43527312 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
43527332 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
43527350 TTTAGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:43533780 original size:48 final size:47
Alignment explanation
Indices: 43533725--43533830 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
43533715 TTGTCTTTTC
*
43533725 TTTCTTTTTCAATTT--TCTCTTTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCATCTC-TTTT--TCACATCCTTT-TTCAATCTCAA
*
43533773 TTTCTTTTTCGATTTCATTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCA-TCTCTTTTTCACATCCTTTTTCAATCTCAA
43533821 TTTCTTTTTC
1 TTTCTTTTTC
43533831 CATGACACTC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
48 40 0.77
49 4 0.08
50 4 0.08
51 4 0.08
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (47 bp):
TTTCTTTTTCAATTTCATCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:43533829 original size:18 final size:17
Alignment explanation
Indices: 43533762--43533890 Score: 61
Period size: 18 Copynumber: 7.4 Consensus size: 17
43533752 CACACTTTTG
43533762 TTCAATCTCAATTTCTTT
1 TTCAATCTC-ATTTCTTT
* *
43533780 TTCGATTTCATTCTCTTT
1 TTCAATCTCATT-TCTTT
*
43533798 TTC-A---CA-TCCTTT
1 TTCAATCTCATTTCTTT
43533810 TTCAATCTCAATTTCTTT
1 TTCAATCTC-ATTTCTTT
* *
43533828 TTCCATGACACTCGTTTCTTT
1 TT-CA--A-TCTCATTTCTTT
* * *
43533849 TACACTCTCGTTTCTTT
1 TTCAATCTCATTTCTTT
*
43533866 CTTCAATCTCACTCTCTTT
1 -TTCAATCTCA-TTTCTTT
43533885 TTCAAT
1 TTCAAT
43533891 TTCTTGTTCC
Statistics
Matches: 85, Mismatches: 13, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.08
13 2 0.02
14 2 0.02
16 1 0.01
17 16 0.19
18 35 0.41
19 8 0.09
20 2 0.02
21 9 0.11
22 3 0.04
ACGTcount: A:0.17, C:0.27, G:0.03, T:0.53
Consensus pattern (17 bp):
TTCAATCTCATTTCTTT
Found at i:43534869 original size:10 final size:9
Alignment explanation
Indices: 43534856--43534891 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
43534846 TTTTCACTTT
43534856 TTTTTTGTTC
1 TTTTTT-TTC
43534866 TTTTTTTTAC
1 TTTTTTTT-C
43534876 TTTTTTTTC
1 TTTTTTTTC
43534885 TTTTTTT
1 TTTTTTT
43534892 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:43536372 original size:20 final size:20
Alignment explanation
Indices: 43536349--43536395 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43536339 GGGTTAAGAT
*
43536349 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
43536369 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
43536389 TGAGCTG
1 TGAGCTG
43536396 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:43539055 original size:14 final size:14
Alignment explanation
Indices: 43539008--43539055 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
43538998 GTACGAATGG
*
43539008 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
43539022 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
43539036 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
43539050 ATTGGT
1 AATGGT
43539056 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:43542033 original size:30 final size:30
Alignment explanation
Indices: 43541962--43542044 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
43541952 CTTTTGTTTT
* *
43541962 AATTTCTTTTTCATCTTCTTTTTCACTCACA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCACA
*
43541993 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCACA
* *
43542022 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
43542045 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.11
30 31 0.70
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCACA
Found at i:43542062 original size:12 final size:12
Alignment explanation
Indices: 43542047--43542077 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43542037 TTCTTTTTGC
43542047 TTTTCAAAGGCT
1 TTTTCAAAGGCT
*
43542059 TTTTCGAAGGCT
1 TTTTCAAAGGCT
43542071 TTTTCAA
1 TTTTCAA
43542078 GTTCTCTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:43542135 original size:5 final size:5
Alignment explanation
Indices: 43542125--43542181 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
43542115 CTCTTGCCTC
*
43542125 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
43542172 TCTTT TCTTT
1 TCTTT TCTTT
43542182 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:43542165 original size:15 final size:14
Alignment explanation
Indices: 43542125--43542181 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
43542115 CTCTTGCCTC
*
43542125 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
43542140 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
43542155 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
43542172 TCTTTTCTTT
1 TCTTTTCTTT
43542182 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:43542182 original size:21 final size:21
Alignment explanation
Indices: 43542125--43542192 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
43542115 CTCTTGCCTC
* *
43542125 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
43542146 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
43542167 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
43542187 CTCTTT
1 -TCTTT
43542193 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:43542650 original size:30 final size:30
Alignment explanation
Indices: 43542614--43542711 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
43542604 AGCTCACTCC
43542614 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
43542644 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* *
43542674 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCC-
1 TAGCTCATA-TTCAGCTCACGAGCTAAA-CCT
43542704 TAGCTCAT
1 TAGCTCAT
43542712 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:43544773 original size:13 final size:13
Alignment explanation
Indices: 43544741--43544787 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
43544731 TTTCAGATTT
43544741 TTTTTCTTTTCAAA
1 TTTTT-TTTTCAAA
** *
43544755 AATTTTTTT-GAA
1 TTTTTTTTTCAAA
43544767 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
43544780 TTTTTTTT
1 TTTTTTTT
43544788 GACTTGTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
12 9 0.35
13 14 0.54
14 3 0.12
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:43544776 original size:25 final size:25
Alignment explanation
Indices: 43544741--43544789 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
43544731 TTTCAGATTT
43544741 TTTTTCTTTTCAAAAATTTTTTTGAA
1 TTTTTCTTTTC-AAAATTTTTTTGAA
*
43544767 TTTTT-TTTTCAAATTTTTTTTGA
1 TTTTTCTTTTCAAAATTTTTTTGA
43544790 CTTGTATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 5 0.23
26 5 0.23
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTTCTTTTCAAAATTTTTTTGAA
Found at i:43546384 original size:20 final size:20
Alignment explanation
Indices: 43546338--43546384 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43546328 AGCTCGTTTC
*
43546338 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
43546358 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
43546378 CAGCTCA
1 CAGCTCA
43546385 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:43549017 original size:18 final size:17
Alignment explanation
Indices: 43548934--43549062 Score: 61
Period size: 18 Copynumber: 7.4 Consensus size: 17
43548924 GGAACAAGAA
*
43548934 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGA-AATGAG
*
43548952 ATTGAAGAAAGAAACGAG
1 ATTGAA-AAAGAAATGAG
* * *
43548970 AGTGTAAAAGAAACGAGTG
1 ATTGAAAAAGAAATGA--G
*
43548989 TCATGGAAAAAGAAATTGAG
1 --ATTGAAAAAGAAA-TGAG
*
43549009 ATTGAAAAAG-GAT--G
1 ATTGAAAAAGAAATGAG
*
43549023 --TGAAAAAGAGAATGAA
1 ATTGAAAAAGA-AATGAG
*
43549039 ATCGAAAAAGAAATTGAG
1 ATTGAAAAAGAAA-TGAG
43549057 ATTGAA
1 ATTGAA
43549063 CAAAAGTGTG
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
12 8 0.10
14 3 0.04
16 1 0.01
17 13 0.16
18 39 0.47
19 6 0.07
20 1 0.01
21 10 0.12
22 2 0.02
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.17
Consensus pattern (17 bp):
ATTGAAAAAGAAATGAG
Found at i:43549094 original size:48 final size:47
Alignment explanation
Indices: 43548994--43549099 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 47
43548984 GAGTGTCATG
*
43548994 GAAAAAGAAATTGAGATTGAAAAAGGATGTGAAAAAGAGAATGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAGGATGGGAAAAAGAGAA-GAAATC
*
43549042 GAAAAAGAAATTGAGATTGAACAAAAGTG-TGAGGAAAAAGAG-A-AAATT
1 GAAAAAGAAATTGAGATTG-A-AAAAG-GATG-GGAAAAAGAGAAGAAATC
43549090 GAAAAAGAAA
1 GAAAAAGAAA
43549100 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
48 33 0.63
49 1 0.02
50 8 0.15
51 10 0.19
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAGGATGGGAAAAAGAGAAGAAATC
Found at i:43555600 original size:20 final size:20
Alignment explanation
Indices: 43555554--43555600 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43555544 TAGTCGTTTC
*
43555554 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
43555574 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
43555594 CAGCTCA
1 CAGCTCA
43555601 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:43560431 original size:15 final size:14
Alignment explanation
Indices: 43560413--43560441 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43560403 AAAAAGAAGG
43560413 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
43560427 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
43560441 A
1 A
43560442 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:43561186 original size:15 final size:15
Alignment explanation
Indices: 43561154--43561187 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43561144 GTTCAACGAA
*
43561154 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
43561169 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
43561184 GAGG
1 GAGG
43561188 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:43566850 original size:15 final size:16
Alignment explanation
Indices: 43566811--43566851 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
43566801 AACAACACTC
43566811 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
43566827 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
43566841 CTTTCTTTTTC
1 CTTTCTTTTTC
43566852 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:43566995 original size:17 final size:15
Alignment explanation
Indices: 43566958--43566996 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
43566948 TATGTCCCAC
43566958 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
43566974 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
43566991 TCATTT
1 TCATTT
43566997 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:43569026 original size:14 final size:14
Alignment explanation
Indices: 43569007--43569069 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
43568997 TTGGAGTAAC
43569007 AAAAAAAA-TCAAA
1 AAAAAAAATTCAAA
43569020 AAAAAAAATTCGAAA
1 AAAAAAAATTC-AAA
* *
43569035 AAAAAATTGATTCAGA
1 AAAAAA--AATTCAAA
43569051 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
43569065 AAAAA
1 AAAAA
43569070 TCGAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.19
14 13 0.31
15 9 0.21
16 8 0.19
17 4 0.10
ACGTcount: A:0.75, C:0.06, G:0.05, T:0.14
Consensus pattern (14 bp):
AAAAAAAATTCAAA
Found at i:43569047 original size:17 final size:18
Alignment explanation
Indices: 43569027--43569060 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43569017 AAAAAAAAAA
43569027 ATTC-GAAAAAAAAATTG
1 ATTCAGAAAAAAAAATTG
43569044 ATTCAGAAAAAAAAATT
1 ATTCAGAAAAAAAAATT
43569061 CAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.24
Consensus pattern (18 bp):
ATTCAGAAAAAAAAATTG
Found at i:43569078 original size:13 final size:13
Alignment explanation
Indices: 43569007--43569079 Score: 53
Period size: 13 Copynumber: 5.4 Consensus size: 13
43568997 TTGGAGTAAC
*
43569007 AAAAAAAATCAAA
1 AAAAAAAATCGAA
43569020 AAAAAAAATTCGAA
1 AAAAAAAA-TCGAA
43569034 AAAAAAATTGATTCAGAA
1 AAAAAAA---A-TC-GAA
*
43569052 AAAAAAATTC---
1 AAAAAAAATCGAA
43569062 AAAAAAAATCGAA
1 AAAAAAAATCGAA
43569075 AAAAA
1 AAAAA
43569080 GGAAAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
10 9 0.18
13 13 0.27
14 13 0.27
17 4 0.08
18 10 0.20
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:43569117 original size:31 final size:29
Alignment explanation
Indices: 43569017--43569117 Score: 85
Period size: 31 Copynumber: 3.3 Consensus size: 29
43569007 AAAAAAAATC
* *
43569017 AAAAAAAAAAATTCGAAAAAAAAATTGATTC
1 AAAAAAAAAAATT-G-AAAAAAAATCGATTA
* * **
43569048 AGAAAAAAAAATTCAAAAAAAATCGAAAA
1 AAAAAAAAAAATTGAAAAAAAATCGATTA
*
43569077 AAAGGAAAAAAAAGTGACAAAAAAATCGAGTTA
1 AAA--AAAAAAAATTGA-AAAAAAATCGA-TTA
43569110 AAAAAAAA
1 AAAAAAAA
43569118 GAAAAAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
29 13 0.24
31 27 0.49
32 11 0.20
33 4 0.07
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (29 bp):
AAAAAAAAAAATTGAAAAAAAATCGATTA
Found at i:43569123 original size:11 final size:10
Alignment explanation
Indices: 43569109--43569149 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
43569099 AAATCGAGTT
43569109 AAAAAAAAAG
1 AAAAAAAAAG
43569119 AAAAAAAAAG
1 AAAAAAAAAG
*
43569129 TAAAAGAAAAG
1 -AAAAAAAAAG
43569140 AACAAAAAAA
1 AA-AAAAAAA
43569150 AGTGAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 12 0.44
11 15 0.56
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:43569138 original size:24 final size:24
Alignment explanation
Indices: 43569111--43569158 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43569101 ATCGAGTTAA
43569111 AAAAAAAGAAAAAAAAAGT-AAAAG
1 AAAAAAA-AAAAAAAAAGTGAAAAG
* *
43569135 AAAAGAACAAAAAAAAGTGAAAAG
1 AAAAAAAAAAAAAAAAGTGAAAAG
43569159 TATTGTGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAGTGAAAAG
Found at i:43570080 original size:15 final size:16
Alignment explanation
Indices: 43570060--43570091 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
43570050 AGAAAATGAA
43570060 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
43570075 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
43570091 A
1 A
43570092 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:43570206 original size:17 final size:18
Alignment explanation
Indices: 43570174--43570207 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43570164 AAAAGAGAGT
*
43570174 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
43570192 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
43570208 GGAGTGTTGT
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:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:43573427 original size:29 final size:30
Alignment explanation
Indices: 43573383--43573453 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
43573373 ATTCAATCAC
43573383 TCTT-TTTTTTTCAATT-TCG-ATTTTTTTT
1 TCTTCTTTTTTTCAATTCT-GAATTTTTTTT
*
43573411 CTTTTCTTTTTTT-AATTCTGAATTTTTTTT
1 -TCTTCTTTTTTTCAATTCTGAATTTTTTTT
43573441 TCTTCTTTTTTTC
1 TCTTCTTTTTTTC
43573454 TTCAATACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.75
Consensus pattern (30 bp):
TCTTCTTTTTTTCAATTCTGAATTTTTTTT
Found at i:43573512 original size:12 final size:12
Alignment explanation
Indices: 43573495--43573539 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
43573485 TGAATACAAC
43573495 TTTTTTTTTGAA
1 TTTTTTTTTGAA
**
43573507 TTTTTTTTCAAA
1 TTTTTTTTTGAA
43573519 TTTTTTTTTTGAA
1 -TTTTTTTTTGAA
43573532 TTTTTTTT
1 TTTTTTTT
43573540 ACAATACCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Done.