Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 88 of 131
Found at i:29400540 original size:25 final size:25
Alignment explanation
Indices: 29400476--29400551 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
29400466 AATGCACCCT
* *
29400476 TTTAACAGAGATAGTCACAAAGGCATTCA
1 TTTAACGGAGATAGCCACAAAGG----CA
* *
29400505 TTTAACTGAGATAGCTACAAAGGCA
1 TTTAACGGAGATAGCCACAAAGGCA
29400530 TTTAACGGAGATAGCCACAAAG
1 TTTAACGGAGATAGCCACAAAG
29400552 CTATTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 22 0.52
29 20 0.48
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (25 bp):
TTTAACGGAGATAGCCACAAAGGCA
Found at i:29400558 original size:54 final size:54
Alignment explanation
Indices: 29400434--29400581 Score: 163
Period size: 54 Copynumber: 2.7 Consensus size: 54
29400424 AGCGATGGCT
* * * * *
29400434 ACAAAGGCATCCTTTTAACAAAGATAGCCACAAATGCACCCTTTTAACAGAGATAGTC
1 ACAAAGGCATTCATTTAACAGAGATAGCCACAAAGGCA----TTTAACAGAGATAGCC
* * *
29400492 ACAAAGGCATTCATTTAACTGAGATAGCTACAAAGGCATTTAACGGAGATAGCC
1 ACAAAGGCATTCATTTAACAGAGATAGCCACAAAGGCATTTAACAGAGATAGCC
*
29400546 ACAAA-GCTATTCATTTAACAGGGATAGCCACAAAGG
1 ACAAAGGC-ATTCATTTAACAGAGATAGCCACAAAGG
29400582 TTGATAACAG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.03
54 44 0.56
58 32 0.41
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (54 bp):
ACAAAGGCATTCATTTAACAGAGATAGCCACAAAGGCATTTAACAGAGATAGCC
Found at i:29400639 original size:29 final size:28
Alignment explanation
Indices: 29400599--29400693 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 28
29400589 CAGATAGTAA
* *
29400599 CCACAAAAGCTTTCTTATAATAGAGATCT
1 CCACAAAGGCTTTCTT-TAATAGAGATCG
* *
29400628 CCATAAAGGCTTCCATTTAATAGAGATCG
1 CCACAAAGGCTTTC-TTTAATAGAGATCG
* *
29400657 CCACAATGGCTTTCTTT--CAGAGA-CAG
1 CCACAAAGGCTTTCTTTAATAGAGATC-G
29400683 CCACAAAGGCT
1 CCACAAAGGCT
29400694 CACTTATACG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.02
26 16 0.29
28 3 0.05
29 33 0.60
30 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (28 bp):
CCACAAAGGCTTTCTTTAATAGAGATCG
Found at i:29413856 original size:18 final size:17
Alignment explanation
Indices: 29413835--29413868 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29413825 TTTCAAGATT
*
29413835 TTTTTAATTTTTGTATTC
1 TTTTCAATTTTT-TATTC
29413853 TTTTCAATTTTTTATT
1 TTTTCAATTTTTTATT
29413869 TTAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCAATTTTTTATTC
Found at i:29418221 original size:19 final size:19
Alignment explanation
Indices: 29418199--29418262 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
29418189 TTTGTTTATG
29418199 TTAGAAATATTTGTATTCT
1 TTAGAAATATTTGTATTCT
* * *
29418218 TTAGAATTTTTTGTATTGCA
1 TTAGAAATATTTGTATT-CT
* *
29418238 TTAGAAATATTGGTATCCT
1 TTAGAAATATTTGTATTCT
29418257 TTAGAA
1 TTAGAA
29418263 TTTTTGGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 22 0.61
20 14 0.39
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.48
Consensus pattern (19 bp):
TTAGAAATATTTGTATTCT
Found at i:29418269 original size:19 final size:19
Alignment explanation
Indices: 29418211--29418273 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
29418201 AGAAATATTT
* *
29418211 GTATTCTTTAGAATTTTTT
1 GTATCCTTTAGAATTTTTG
* * * *
29418230 GTATTGCATTAGAAATATTG
1 GTA-TCCTTTAGAATTTTTG
29418250 GTATCCTTTAGAATTTTTG
1 GTATCCTTTAGAATTTTTG
29418269 GTATC
1 GTATC
29418274 ACTATAATTC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (19 bp):
GTATCCTTTAGAATTTTTG
Found at i:29422588 original size:47 final size:48
Alignment explanation
Indices: 29422535--29422630 Score: 185
Period size: 47 Copynumber: 2.0 Consensus size: 48
29422525 TTGACAAGCT
29422535 TAGTGCTTGGTTTTATGTATTGGCATTATGCCATTATT-ACTTATGAA
1 TAGTGCTTGGTTTTATGTATTGGCATTATGCCATTATTCACTTATGAA
29422582 TAGTGCTTGGTTTTATGTATTGGCATTATGCCATTATTCACTTATGAA
1 TAGTGCTTGGTTTTATGTATTGGCATTATGCCATTATTCACTTATGAA
29422630 T
1 T
29422631 GAAATCAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 38 0.79
48 10 0.21
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (48 bp):
TAGTGCTTGGTTTTATGTATTGGCATTATGCCATTATTCACTTATGAA
Found at i:29425969 original size:14 final size:14
Alignment explanation
Indices: 29425950--29425997 Score: 96
Period size: 14 Copynumber: 3.4 Consensus size: 14
29425940 TGTATCATTC
29425950 GAATTCGATATAGT
1 GAATTCGATATAGT
29425964 GAATTCGATATAGT
1 GAATTCGATATAGT
29425978 GAATTCGATATAGT
1 GAATTCGATATAGT
29425992 GAATTC
1 GAATTC
29425998 TCTTTTCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (14 bp):
GAATTCGATATAGT
Found at i:29432804 original size:13 final size:13
Alignment explanation
Indices: 29432767--29432807 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
29432757 TTTTGCTTTA
29432767 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
29432780 CT--TTGTGCCTCTG
1 CTGCTT-TG-CTCTG
29432793 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
29432806 CT
1 CT
29432808 TTGCTTTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 16 0.67
14 2 0.08
15 2 0.08
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (13 bp):
CTGCTTTGCTCTG
Found at i:29436833 original size:11 final size:11
Alignment explanation
Indices: 29436807--29436847 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
29436797 AAAAATTAGC
*
29436807 AGAAGAGAAGGA
1 AGAAGA-AAGGG
29436819 AGAAGAAAGGG
1 AGAAGAAAGGG
29436830 AGAAGAAA-GG
1 AGAAGAAAGGG
29436840 AGAAGAAA
1 AGAAGAAA
29436848 AAAAAGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 10 0.36
11 12 0.43
12 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (11 bp):
AGAAGAAAGGG
Found at i:29436952 original size:17 final size:16
Alignment explanation
Indices: 29436921--29436955 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
29436911 TATTGTGTAG
29436921 TTTGTTTATTGTTAAT
1 TTTGTTTATTGTTAAT
*
29436937 TTTGTGTTATTTTTAAT
1 TTTGT-TTATTGTTAAT
29436954 TT
1 TT
29436956 ATTTTAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.71
Consensus pattern (16 bp):
TTTGTTTATTGTTAAT
Found at i:29439365 original size:19 final size:19
Alignment explanation
Indices: 29439338--29439376 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29439328 CGTGCAATGA
29439338 GCTACAGGGATGGATAGCC
1 GCTACAGGGATGGATAGCC
*
29439357 GCTATAGGGATGGATAGCC
1 GCTACAGGGATGGATAGCC
29439376 G
1 G
29439377 TTATGCGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (19 bp):
GCTACAGGGATGGATAGCC
Found at i:29440726 original size:14 final size:15
Alignment explanation
Indices: 29440702--29440730 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29440692 TTTTTCTGTG
29440702 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
29440717 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
29440731 AGTTTCGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:29440968 original size:28 final size:28
Alignment explanation
Indices: 29440922--29440978 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
29440912 TATAGTTTTT
29440922 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
29440950 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
29440978 A
1 A
29440979 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:29441933 original size:43 final size:42
Alignment explanation
Indices: 29441880--29441995 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 42
29441870 TATGTGTTTT
29441880 CGTGTAAGACCACGTCTGGGACGTCGGCATCGATATCTGATTA
1 CGTGTAAGACCACGTCTGGGACGT-GGCATCGATATCTGATTA
* * *
29441923 CGTGCAAGACC-CTGTCTGGGACAATGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTGGCATCGATATCTGATTA
* *
29441966 CATATAAGACCACGTCTGGGACGATGGCAT
1 CGTGTAAGACCACGTCTGGGACG-TGGCAT
29441996 TGTACGAGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
42 1 0.02
43 59 0.95
44 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTGGCATCGATATCTGATTA
Found at i:29444394 original size:32 final size:32
Alignment explanation
Indices: 29444356--29444424 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
29444346 TTTATACAAA
29444356 CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
1 CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
* * * *
29444388 TCTTAAATGTGGCTAATTGCCTTGTAAGTCCT
1 CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
29444420 CCTTA
1 CCTTA
29444425 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (32 bp):
CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
Found at i:29444524 original size:29 final size:29
Alignment explanation
Indices: 29444469--29444524 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
29444459 TATATTGTGT
**
29444469 TTAAACAAGCCTTTAACCTATTTTTTTAG
1 TTAAACAAGCCTTTAACCTATGGTTTTAG
* * *
29444498 TTAAATAAGCTTTTAACTTATGGTTTT
1 TTAAACAAGCCTTTAACCTATGGTTTT
29444525 TACTCATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (29 bp):
TTAAACAAGCCTTTAACCTATGGTTTTAG
Found at i:29445937 original size:11 final size:11
Alignment explanation
Indices: 29445921--29445945 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29445911 TTGAGTAACA
29445921 AAAAACATAGT
1 AAAAACATAGT
29445932 AAAAACATAGT
1 AAAAACATAGT
29445943 AAA
1 AAA
29445946 TACGTGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAACATAGT
Found at i:29446030 original size:17 final size:17
Alignment explanation
Indices: 29445976--29446033 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
29445966 CAGTAAAAAA
29445976 TACAATAATAATATAAT
1 TACAATAATAATATAAT
* * * *
29445993 TAAAATTAT-GT-TAGTT
1 TACAATAATAATATA-AT
29446009 TACAATAATAATATAAT
1 TACAATAATAATATAAT
29446026 TACAATAA
1 TACAATAA
29446034 ACATAAATTA
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
15 2 0.07
16 9 0.30
17 17 0.57
18 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
TACAATAATAATATAAT
Found at i:29446420 original size:101 final size:103
Alignment explanation
Indices: 29446293--29446674 Score: 450
Period size: 101 Copynumber: 3.6 Consensus size: 103
29446283 TAAAAAACAC
* *
29446293 AAAAAATTACATTTATAAAAAGTCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAA
1 AAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAA
**
29446358 TCATAAATCCCTAACAAAATAACTTTAAAATAA-TT-A
66 TCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
*
29446394 AAAAAATTGA-ATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAGCCTA
1 AAAAAATT-ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTA
* *
29446458 ATTATAAAATTACTAACAAAATAACTTTCAAATAATTTAAAAAAAA
65 ATCAT-AAATTACTAACAAAATAACTTTAAAATAATTT------AA
* * *
29446504 ACATAAAATTTTACATTCATAAAAAATCACAATAAATATTAAACTAAACTAAAAACAAACGATTT
1 A-A-AAAA--TTACATTCATAAAAAATCACAAT--A-A--ACACTAAACTAAACACAAACAATTT
* *
29446569 ATAACTTAATCATAAATTACTAACAAAATGACTTTAAAATAATTTTAA
57 ATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAA-TTTAA
*
29446617 AAAAAATTACATTCATAAAAATTCAC-A-AAACACTAAACTAAACACAAACAATTTATAA
1 AAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAA
29446675 AACAAAATAA
Statistics
Matches: 241, Mismatches: 19, Indels: 41
0.80 0.06 0.14
Matches are distributed among these distances:
101 63 0.26
102 53 0.22
103 2 0.01
104 1 0.00
105 1 0.00
108 1 0.00
109 19 0.08
110 2 0.01
111 5 0.02
112 5 0.02
113 4 0.02
114 21 0.09
116 1 0.00
117 1 0.00
118 27 0.11
119 35 0.15
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.27
Consensus pattern (103 bp):
AAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAA
TCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
Found at i:29446616 original size:119 final size:114
Alignment explanation
Indices: 29446404--29446674 Score: 305
Period size: 119 Copynumber: 2.4 Consensus size: 114
29446394 AAAAAATTGA
* * * *
29446404 ATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAGCCTAATTATAAAATT
1 ATTCATAAAAAATCACAATAAAAACTAAACTAAAAACAAACAATTTATAACCTAATCATAAAATT
*
29446469 ACTAACAAAATAACTTTCAAATAATTTAAAAAAAAACATAAAATTTTAC
66 ACTAACAAAATAACTTTAAAATAATTTAAAAAAAAACATAAAATTTTAC
* *
29446518 ATTCATAAAAAATCACAATAAATATTAAACTAAACTAAAAACAAACGATTTATAACTTAATCAT-
1 ATTCATAAAAAATCACAAT--A-A--AAACTAAACTAAAAACAAACAATTTATAACCTAATCATA
* *
29446582 AAATTACTAACAAAATGACTTTAAAATAATTT-----TAAA-A-AAAA--TTAC
61 AAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAAACATAAAATTTTAC
* * *
29446627 ATTCATAAAAATTCAC-A-AAACACTAAACTAAACACAAACAATTTATAA
1 ATTCATAAAAAATCACAATAAAAACTAAACTAAAAACAAACAATTTATAA
29446675 AACAAAATAA
Statistics
Matches: 139, Mismatches: 13, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
102 26 0.19
104 1 0.01
105 1 0.01
108 1 0.01
109 19 0.14
111 4 0.03
112 1 0.01
113 3 0.02
114 19 0.14
116 1 0.01
117 1 0.01
118 30 0.22
119 32 0.23
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.27
Consensus pattern (114 bp):
ATTCATAAAAAATCACAATAAAAACTAAACTAAAAACAAACAATTTATAACCTAATCATAAAATT
ACTAACAAAATAACTTTAAAATAATTTAAAAAAAAACATAAAATTTTAC
Found at i:29446776 original size:17 final size:17
Alignment explanation
Indices: 29446754--29446791 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
29446744 AAATACAAAA
*
29446754 AAATAACTAATCTCTTT
1 AAATAACTAATCCCTTT
29446771 AAATAACTAATCCCTTT
1 AAATAACTAATCCCTTT
29446788 AAAT
1 AAAT
29446792 TAAAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATAACTAATCCCTTT
Found at i:29446860 original size:20 final size:22
Alignment explanation
Indices: 29446837--29446887 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
29446827 TTTTTTTTTA
*
29446837 TTTCTTTCTTCTTCTT-T-TCC
1 TTTCTTTCTTCTCCTTCTCTCC
*
29446857 TTTCTTTTTTCTCCTTCCTCTCC
1 TTTCTTTCTTCTCCTT-CTCTCC
29446880 TTTCTTTC
1 TTTCTTTC
29446888 CCTCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 14 0.56
22 1 0.04
23 10 0.40
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCTTTCTTCTCCTTCTCTCC
Found at i:29447578 original size:20 final size:21
Alignment explanation
Indices: 29447541--29447579 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29447531 TTTTAAACAT
* *
29447541 AAATAATTAAAATGTAACTTA
1 AAATAAATAAAATATAACTTA
29447562 AAATAAATAAAA-ATAACT
1 AAATAAATAAAATATAACT
29447580 ATTTTAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATAAATAAAATATAACTTA
Found at i:29451439 original size:25 final size:24
Alignment explanation
Indices: 29451411--29451504 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 24
29451401 AAGCTCTTTC
*
29451411 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCA-GA
* ** *
29451436 GAGCCATGTAATGGGAAGCTCCAAA
1 GAGCCATATAACAGGAAGCT-CAGA
* *
29451461 GAGCCAT-TAACAGGAAGTTCAAGC
1 GAGCCATATAACAGGAAGCTC-AGA
* *
29451485 GAGCCA-ATATCGGGAAGCTC
1 GAGCCATATAACAGGAAGCTC
29451505 CGGAAAGACA
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
23 1 0.02
24 26 0.49
25 24 0.45
26 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (24 bp):
GAGCCATATAACAGGAAGCTCAGA
Found at i:29451488 original size:24 final size:25
Alignment explanation
Indices: 29451410--29451490 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
29451400 GAAGCTCTTT
* *
29451410 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGTTCAAG
* * ** *
29451435 TGAGCCATGTAATGGGAAGCTCCAA-
1 CGAGCCATATAACAGGAAG-TTCAAG
*
29451460 AGAGCCAT-TAACAGGAAGTTCAAG
1 CGAGCCATATAACAGGAAGTTCAAG
29451484 CGAGCCA
1 CGAGCCA
29451491 ATATCGGGAA
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
23 4 0.10
24 14 0.33
25 22 0.52
26 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGTTCAAG
Found at i:29451518 original size:48 final size:49
Alignment explanation
Indices: 29451414--29451557 Score: 120
Period size: 48 Copynumber: 2.9 Consensus size: 49
29451404 CTCTTTCGAG
* **
29451414 CCATATAACAGGAAGCTCATGTGAGCCATG-TAAT-GGGAAGCTCC-AAAGA
1 CCAT-TAACAGGAAGTTCATAAGAGCCA-GAT-ATCGGGAAGCTCCGAAAGA
*
29451463 GCCATTAACAGGAAGTTCA-AGCGAGCCA-ATATCGGGAAGCTCCGGAAAGA
1 -CCATTAACAGGAAGTTCATA-AGAGCCAGATATCGGGAAGCTCC-GAAAGA
** * *
29451513 -CATTAATGGGAAGTTCATAAGAGCCAGTTATTGGGAAGCTCCGAA
1 CCATTAACAGGAAGTTCATAAGAGCCAGATATCGGGAAGCTCCGAA
29451558 GAGCCATATA
Statistics
Matches: 79, Mismatches: 8, Indels: 16
0.77 0.08 0.16
Matches are distributed among these distances:
47 2 0.03
48 35 0.44
49 33 0.42
50 9 0.11
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (49 bp):
CCATTAACAGGAAGTTCATAAGAGCCAGATATCGGGAAGCTCCGAAAGA
Found at i:29451549 original size:25 final size:25
Alignment explanation
Indices: 29451519--29451586 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
29451509 AAGACATTAA
*
29451519 TGGGAAGTTCATAAGAGCCAGT-TAT
1 TGGGAAGCTCATAAGAGCCA-TATAT
**
29451544 TGGGAAGCTCCGAAGAGCCATATAT
1 TGGGAAGCTCATAAGAGCCATATAT
* *
29451569 CGGGACGCTCATAAGAGC
1 TGGGAAGCTCATAAGAGC
29451587 TGCGATGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (25 bp):
TGGGAAGCTCATAAGAGCCATATAT
Found at i:29451653 original size:24 final size:24
Alignment explanation
Indices: 29451626--29451732 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 24
29451616 ACAACCAATA
*
29451626 GGGATGCTC-CGAAGAGCTATTAAC
1 GGGATGCTCACG-AGAGCTAATAAC
* * * * *
29451650 GGGAAGCTCGCAAGAACCATATAAC
1 GGGATGCTCACGAGAGCTA-ATAAC
* * * *
29451675 GGGAAGCTCATGAGAGCCAAATATC
1 GGGATGCTCACGAGAG-CTAATAAC
*
29451700 GGGATGCTCATGAGAGCTAATAAC
1 GGGATGCTCACGAGAGCTAATAAC
29451724 GGGATGCTC
1 GGGATGCTC
29451733 TTTCGAGCTG
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
24 28 0.42
25 36 0.55
26 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.18
Consensus pattern (24 bp):
GGGATGCTCACGAGAGCTAATAAC
Found at i:29451741 original size:24 final size:24
Alignment explanation
Indices: 29451670--29451732 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 24
29451660 CAAGAACCAT
* *
29451670 ATAACGGGAAGCTCATGAGAGCCAA
1 ATAACGGGATGCTCATGAGAG-CTA
*
29451695 ATATCGGGATGCTCATGAGAGCTA
1 ATAACGGGATGCTCATGAGAGCTA
29451719 ATAACGGGATGCTC
1 ATAACGGGATGCTC
29451733 TTTCGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (24 bp):
ATAACGGGATGCTCATGAGAGCTA
Found at i:29453672 original size:28 final size:30
Alignment explanation
Indices: 29453641--29453716 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
29453631 TCCAGAGATT
*
29453641 GCCACAAAGGCTTTCCTTTCA-GAGT-CTC
1 GCCACAAAGGCTTTCCTTTCATAAGTACTC
* *
29453669 GCCACAAAGG-TGTCTTTTCATTAAGTACTC
1 GCCACAAAGGCTTTCCTTTCA-TAAGTACTC
*
29453699 GTCACAAAGGCTTTCCTT
1 GCCACAAAGGCTTTCCTT
29453717 CTTTTGGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 8 0.21
28 10 0.26
29 3 0.08
30 12 0.32
31 5 0.13
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.32
Consensus pattern (30 bp):
GCCACAAAGGCTTTCCTTTCATAAGTACTC
Found at i:29464186 original size:25 final size:24
Alignment explanation
Indices: 29464158--29464251 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 24
29464148 AAGCTCTTTC
*
29464158 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCA-GA
* ** *
29464183 GAGCCATGTAATGGGAAGCTCCAAA
1 GAGCCATATAACAGGAAGCT-CAGA
* *
29464208 GAGCCAT-TAACAGGAAGTTCAAGC
1 GAGCCATATAACAGGAAGCTC-AGA
* *
29464232 GAGCCA-ATATCGGGAAGCTC
1 GAGCCATATAACAGGAAGCTC
29464252 CGGAAAGACA
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
23 1 0.02
24 26 0.49
25 24 0.45
26 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (24 bp):
GAGCCATATAACAGGAAGCTCAGA
Found at i:29464235 original size:24 final size:25
Alignment explanation
Indices: 29464157--29464237 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
29464147 GAAGCTCTTT
* *
29464157 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGTTCAAG
* * ** *
29464182 TGAGCCATGTAATGGGAAGCTCCAA-
1 CGAGCCATATAACAGGAAG-TTCAAG
*
29464207 AGAGCCAT-TAACAGGAAGTTCAAG
1 CGAGCCATATAACAGGAAGTTCAAG
29464231 CGAGCCA
1 CGAGCCA
29464238 ATATCGGGAA
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
23 4 0.10
24 14 0.33
25 22 0.52
26 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGTTCAAG
Found at i:29464265 original size:48 final size:49
Alignment explanation
Indices: 29464161--29464304 Score: 120
Period size: 48 Copynumber: 2.9 Consensus size: 49
29464151 CTCTTTCGAG
* **
29464161 CCATATAACAGGAAGCTCATGTGAGCCATG-TAAT-GGGAAGCTCC-AAAGA
1 CCAT-TAACAGGAAGTTCATAAGAGCCA-GAT-ATCGGGAAGCTCCGAAAGA
*
29464210 GCCATTAACAGGAAGTTCA-AGCGAGCCA-ATATCGGGAAGCTCCGGAAAGA
1 -CCATTAACAGGAAGTTCATA-AGAGCCAGATATCGGGAAGCTCC-GAAAGA
** * *
29464260 -CATTAATGGGAAGTTCATAAGAGCCAGTTATTGGGAAGCTCCGAA
1 CCATTAACAGGAAGTTCATAAGAGCCAGATATCGGGAAGCTCCGAA
29464305 GAGCCATATA
Statistics
Matches: 79, Mismatches: 8, Indels: 16
0.77 0.08 0.16
Matches are distributed among these distances:
47 2 0.03
48 35 0.44
49 33 0.42
50 9 0.11
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (49 bp):
CCATTAACAGGAAGTTCATAAGAGCCAGATATCGGGAAGCTCCGAAAGA
Found at i:29464296 original size:25 final size:25
Alignment explanation
Indices: 29464266--29464333 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
29464256 AAGACATTAA
*
29464266 TGGGAAGTTCATAAGAGCCAGT-TAT
1 TGGGAAGCTCATAAGAGCCA-TATAT
**
29464291 TGGGAAGCTCCGAAGAGCCATATAT
1 TGGGAAGCTCATAAGAGCCATATAT
* *
29464316 CGGGACGCTCATAAGAGC
1 TGGGAAGCTCATAAGAGC
29464334 TGCGATGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (25 bp):
TGGGAAGCTCATAAGAGCCATATAT
Found at i:29464400 original size:24 final size:24
Alignment explanation
Indices: 29464373--29464479 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 24
29464363 ACAACCAATA
*
29464373 GGGATGCTC-CGAAGAGCTATTAAC
1 GGGATGCTCACG-AGAGCTAATAAC
* * * * *
29464397 GGGAAGCTCGCAAGAACCATATAAC
1 GGGATGCTCACGAGAGCTA-ATAAC
* * * *
29464422 GGGAAGCTCATGAGAGCCAAATATC
1 GGGATGCTCACGAGAG-CTAATAAC
*
29464447 GGGATGCTCATGAGAGCTAATAAC
1 GGGATGCTCACGAGAGCTAATAAC
29464471 GGGATGCTC
1 GGGATGCTC
29464480 TTTCGAGCTG
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
24 28 0.42
25 36 0.55
26 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.18
Consensus pattern (24 bp):
GGGATGCTCACGAGAGCTAATAAC
Found at i:29464488 original size:24 final size:24
Alignment explanation
Indices: 29464417--29464479 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 24
29464407 CAAGAACCAT
* *
29464417 ATAACGGGAAGCTCATGAGAGCCAA
1 ATAACGGGATGCTCATGAGAG-CTA
*
29464442 ATATCGGGATGCTCATGAGAGCTA
1 ATAACGGGATGCTCATGAGAGCTA
29464466 ATAACGGGATGCTC
1 ATAACGGGATGCTC
29464480 TTTCGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (24 bp):
ATAACGGGATGCTCATGAGAGCTA
Found at i:29466419 original size:28 final size:30
Alignment explanation
Indices: 29466388--29466463 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
29466378 TCCAGAGATT
*
29466388 GCCACAAAGGCTTTCCTTTCA-GAGT-CTC
1 GCCACAAAGGCTTTCCTTTCATAAGTACTC
* *
29466416 GCCACAAAGG-TGTCTTTTCATTAAGTACTC
1 GCCACAAAGGCTTTCCTTTCA-TAAGTACTC
*
29466446 GTCACAAAGGCTTTCCTT
1 GCCACAAAGGCTTTCCTT
29466464 CTTTTGGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 8 0.21
28 10 0.26
29 3 0.08
30 12 0.32
31 5 0.13
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.32
Consensus pattern (30 bp):
GCCACAAAGGCTTTCCTTTCATAAGTACTC
Found at i:29474651 original size:46 final size:46
Alignment explanation
Indices: 29474580--29474692 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
29474570 CAACACTAAT
*
29474580 ATGTAGCCGAAGCTACCACTATTATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
29474626 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
*
29474672 ACGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTG
29474693 ATCAATAACA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
Found at i:29474692 original size:23 final size:23
Alignment explanation
Indices: 29474580--29474693 Score: 176
Period size: 23 Copynumber: 5.0 Consensus size: 23
29474570 CAACACTAAT
*
29474580 ATGTAGCCGAAGCTACCACT-ATT
1 ATGTAGCCGAAGCTACCACTGA-A
29474603 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
**
29474626 ATGTAGCCGAAGCTACCACTGTT
1 ATGTAGCCGAAGCTACCACTGAA
29474649 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
*
29474672 ACGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
29474694 TCAATAACAC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
23 83 0.99
24 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:29479683 original size:141 final size:143
Alignment explanation
Indices: 29479506--29479796 Score: 478
Period size: 141 Copynumber: 2.0 Consensus size: 143
29479496 GTAGGTAGGC
*
29479506 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTGGACGACAAG
1 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTAGACGACAAG
* * * *
29479571 ATCATGCAATTTTGGGCAT-GGGGTTAACTATTTGACCCCGTAAAGAAGGTGATAAAAGATGGAC
66 ACCATGCAATTTTAGGCATAGGGGTTAACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAC
29479635 ATATCTGCTAAG-
131 ATATCTGCTAAGT
* *
29479647 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCTATGTAGACGGCAAG
1 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTAGACGACAAG
* *
29479712 ACCATGCAATTTTAGGCATAGGGGTTGACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAG
66 ACCATGCAATTTTAGGCATAGGGGTTAACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAC
*
29479777 ATGTCTGCTAAGT
131 ATATCTGCTAAGT
29479790 TATTGGA
1 TATTGGA
29479797 CTAAAAAAAC
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 79 0.57
142 52 0.38
143 7 0.05
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (143 bp):
TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTAGACGACAAG
ACCATGCAATTTTAGGCATAGGGGTTAACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAC
ATATCTGCTAAGT
Found at i:29485210 original size:17 final size:17
Alignment explanation
Indices: 29485190--29485240 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
29485180 TATTGTTTAA
29485190 TAAATTAATCTTATTTT
1 TAAATTAATCTTATTTT
*
29485207 TAAAAATAAT-TTATTTTT
1 T-AAATTAATCTTA-TTTT
*
29485225 TAACTTAATCTTATTT
1 TAAATTAATCTTATTT
29485241 ATGTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAATTAATCTTATTTT
Found at i:29485224 original size:18 final size:20
Alignment explanation
Indices: 29485169--29485227 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
29485159 ATTAAGCACC
*
29485169 AAATGTAATTATATTGTTTAAT
1 AAAT-TAATT-TATTTTTTAAT
29485191 AAATTAATCTTA-TTTTTAA-
1 AAATTAAT-TTATTTTTTAAT
29485210 AAA-TAATTTATTTTTTAA
1 AAATTAATTTATTTTTTAA
29485228 CTTAATCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 3 0.09
18 11 0.32
19 3 0.09
20 6 0.18
21 6 0.18
22 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATTAATTTATTTTTTAAT
Found at i:29485238 original size:18 final size:18
Alignment explanation
Indices: 29485191--29485240 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
29485181 ATTGTTTAAT
29485191 AAATTAATCTTATTTTTA
1 AAATTAATCTTATTTTTA
* *
29485209 AAAATAAT-TTATTTTTT
1 AAATTAATCTTATTTTTA
*
29485226 AACTTAATCTTATTT
1 AAATTAATCTTATTT
29485241 ATGTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTAATCTTATTTTTA
Found at i:29490510 original size:24 final size:24
Alignment explanation
Indices: 29490478--29490527 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
29490468 TAGAGTCCTT
* *
29490478 TACGTCCCACAAATGGCTCTCATA
1 TACGTCCCACAAAGGGCACTCATA
*
29490502 TACGTCCCATAAAGGGCACTCATA
1 TACGTCCCACAAAGGGCACTCATA
29490526 TA
1 TA
29490528 ATGGTGCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (24 bp):
TACGTCCCACAAAGGGCACTCATA
Found at i:29491203 original size:31 final size:31
Alignment explanation
Indices: 29491168--29491230 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
29491158 CTAAAGCCCG
29491168 CTTAAATTTGTAAGCTTTTCAAACTAATCTC
1 CTTAAATTTGTAAGCTTTTCAAACTAATCTC
*
29491199 CTTAAATTTGTAAGCTTTTCAAATTAATCTC
1 CTTAAATTTGTAAGCTTTTCAAACTAATCTC
29491230 C
1 C
29491231 AAAATTACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (31 bp):
CTTAAATTTGTAAGCTTTTCAAACTAATCTC
Found at i:29492482 original size:25 final size:24
Alignment explanation
Indices: 29492446--29492492 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
29492436 TTTCTATCAT
29492446 ATTACTAAATTTATAATTAAAAATA
1 ATTACTAAATTTA-AATTAAAAATA
*
29492471 ATTA-TAATATTTAATTTAAAAA
1 ATTACTAA-ATTTAAATTAAAAA
29492493 ATTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTACTAAATTTAAATTAAAAATA
Found at i:29513549 original size:44 final size:43
Alignment explanation
Indices: 29513490--29513601 Score: 161
Period size: 44 Copynumber: 2.6 Consensus size: 43
29513480 GAATAGGGCG
*
29513490 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACC-AT
* **
29513534 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCAT
*
29513577 AGATCTTATCTCTCTGAAGTTGCAG
1 A-ATCTTATCTCCCTGAAGTTGCAG
29513602 GGAACATATC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 3 0.05
44 58 0.95
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCAT
Found at i:29515371 original size:26 final size:24
Alignment explanation
Indices: 29515336--29515384 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
29515326 GCATGTCATT
29515336 TTTATTATTATTTATATTAATTTCG
1 TTTATTATTATTTATATT-ATTTCG
*
29515361 TTTATTTATTATTTATGTTATTTC
1 TTTA-TTATTATTTATATTATTTC
29515385 TATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTATTATTATTTATATTATTTCG
Found at i:29522295 original size:42 final size:42
Alignment explanation
Indices: 29522234--29522455 Score: 293
Period size: 42 Copynumber: 5.3 Consensus size: 42
29522224 TTCTATAAAT
* * * * *
29522234 GCCGCTATAGGTCATGACCTTTAGCAGCGCTTTTCCAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAAC
* *
29522276 ACCGCTATAGATCAGGACCTTTAGCGGCGCTTCCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAAC
29522318 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAAC
* * *
29522360 GCCGCTATAGCTCAAGATCTTTAGCGGCGCTTTCCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTT-CCCACAAAC
* * *
29522403 GTCGCTATAGAACA-AACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTCCCACAAAC
*
29522445 GTCGCTATAGA
1 GCCGCTATAGA
29522456 GCATGTTTTA
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
42 138 0.86
43 23 0.14
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (42 bp):
GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAAC
Found at i:29522550 original size:35 final size:35
Alignment explanation
Indices: 29522511--29522577 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
29522501 CTACGAAAAT
*
29522511 TTTAACTTTA-AAACTAAATATAAAAAATTAATGAA
1 TTTAAATTTAGAAACTAAA-ATAAAAAATTAATGAA
** *
29522546 TTTAAATTTAGAATTTAAAATAATAAATTAAT
1 TTTAAATTTAGAAACTAAAATAAAAAATTAAT
29522578 AATACAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.78
36 6 0.22
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (35 bp):
TTTAAATTTAGAAACTAAAATAAAAAATTAATGAA
Found at i:29527901 original size:14 final size:14
Alignment explanation
Indices: 29527882--29528079 Score: 134
Period size: 14 Copynumber: 13.9 Consensus size: 14
29527872 CTAGTTAATC
29527882 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
29527896 TAAA-CCTAAACCC
1 TAAACCCTAAACCA
29527909 TAAAACCCTAAAACCA
1 T-AAACCCT-AAACCA
*
29527925 TAAACCCTTAA-CA
1 TAAACCCTAAACCA
* *
29527938 AATAACCTCTAAACCT
1 TA-AACC-CTAAACCA
* *
29527954 TAAACCC-CAACCTT
1 TAAACCCTAAACC-A
*
29527968 TAAACCATAAACCA
1 TAAACCCTAAACCA
* *
29527982 TAAACCATAACCCA
1 TAAACCCTAAACCA
*
29527996 TAAACCCATAATCCA
1 TAAACCC-TAAACCA
* ***
29528011 TAAACCTTCAAATGG
1 TAAACCCT-AAACCA
*
29528026 T-AACACCTAAACCT
1 TAAAC-CCTAAACCA
*
29528040 TAAACTCTAAACCA
1 TAAACCCTAAACCA
*
29528054 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
29528068 AAAACCCTAAAC
1 TAAACCCTAAAC
29528080 TGTAGTGATA
Statistics
Matches: 143, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
13 16 0.11
14 77 0.54
15 42 0.29
16 8 0.06
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:29527916 original size:8 final size:7
Alignment explanation
Indices: 29527881--29528079 Score: 75
Period size: 7 Copynumber: 27.9 Consensus size: 7
29527871 ACTAGTTAAT
29527881 CTAAACC
1 CTAAACC
29527888 CTAAACC
1 CTAAACC
*
29527895 ATAAA-C
1 CTAAACC
29527901 CTAAACC
1 CTAAACC
29527908 CTAAAACC
1 CT-AAACC
29527916 CTAAAACC
1 CT-AAACC
*
29527924 ATAAACC
1 CTAAACC
*
29527931 CTTAA-C
1 CTAAACC
**
29527937 AAATAACC
1 CTA-AACC
29527945 TCTAAACC
1 -CTAAACC
*
29527953 TTAAACC
1 CTAAACC
*
29527960 C-CAACC
1 CTAAACC
*
29527966 TTTAAACC
1 -CTAAACC
*
29527974 ATAAACC
1 CTAAACC
*
29527981 ATAAACC
1 CTAAACC
*
29527988 AT-AACC
1 CTAAACC
29527994 CATAAACC
1 C-TAAACC
*
29528002 CATAATCC
1 C-TAAACC
*
29528010 ATAAACC
1 CTAAACC
* **
29528017 TTCAAATG
1 CT-AAACC
*
29528025 GT-AACAC
1 CTAAAC-C
29528032 CTAAACC
1 CTAAACC
* *
29528039 TTAAACT
1 CTAAACC
29528046 CTAAACC
1 CTAAACC
* *
29528053 ATATACC
1 CTAAACC
29528060 CTAAACC
1 CTAAACC
**
29528067 AAAAACC
1 CTAAACC
29528074 CTAAAC
1 CTAAAC
29528080 TGTAGTGATA
Statistics
Matches: 141, Mismatches: 39, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
6 16 0.11
7 83 0.59
8 41 0.29
9 1 0.01
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:29528004 original size:22 final size:21
Alignment explanation
Indices: 29527972--29528013 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
29527962 AACCTTTAAA
29527972 CCATAAACCATAAACCATAAC
1 CCATAAACCATAAACCATAAC
*
29527993 CCATAAACCCATAATCCATAA
1 CCATAAA-CCATAAACCATAA
29528014 ACCTTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
CCATAAACCATAAACCATAAC
Found at i:29528159 original size:66 final size:66
Alignment explanation
Indices: 29528082--29528281 Score: 382
Period size: 66 Copynumber: 3.0 Consensus size: 66
29528072 CCCTAAACTG
29528082 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
29528147 T
66 T
29528148 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
29528213 T
66 T
* *
29528214 TAGTAATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTTCGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
29528279 T
66 T
29528280 TA
1 TA
29528282 ATATATAAAT
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 132 1.00
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (66 bp):
TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
T
Found at i:29528210 original size:33 final size:33
Alignment explanation
Indices: 29528107--29528211 Score: 83
Period size: 33 Copynumber: 3.2 Consensus size: 33
29528097 CAATATTTTA
29528107 AAATTAATACTATCTCTTTTACGATTATATAAG
1 AAATTAATACTATCTCTTTTACGATTATATAAG
* * * * * * *
29528140 AAATTATTTAGTGATAAT-TAATT-C-AATATTTTA-
1 AAATTA-ATACT-AT-CTCT-TTTACGATTATATAAG
29528173 AAATTAATACTATCTCTTTTACGATTATATAAG
1 AAATTAATACTATCTCTTTTACGATTATATAAG
29528206 AAATTA
1 AAATTA
29528212 TTTAGTAATA
Statistics
Matches: 50, Mismatches: 14, Indels: 16
0.62 0.17 0.20
Matches are distributed among these distances:
30 3 0.06
31 4 0.08
32 9 0.18
33 18 0.36
34 9 0.18
35 4 0.08
36 3 0.06
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.44
Consensus pattern (33 bp):
AAATTAATACTATCTCTTTTACGATTATATAAG
Found at i:29528545 original size:42 final size:41
Alignment explanation
Indices: 29528401--29528556 Score: 206
Period size: 41 Copynumber: 3.8 Consensus size: 41
29528391 CCTCAGCATT
* * *
29528401 ATTAGCGGTGCTTTCCCAAAAACGCCGCTAAAGCCCTAGGC
1 ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAAGGCCTGGGC
* * *
29528442 ATTAGCGGCGCTTTCAC-AAAAATGCCGCTAAAGGCCTGGAC
1 ATTAGCGGTGCTTTC-CTAAAAACGCCGCTAAAGGCCTGGGC
*
29528483 ATTAGCGGTGCTTTCATAAAAACGCCGCTAAAGGCCTGGGGC
1 ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAAGGCCT-GGGC
* *
29528525 ATTAGCGGTACTTTCCTAAAAATGCCGCTAAA
1 ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAA
29528557 TCCCCGAAAG
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
41 67 0.67
42 33 0.33
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (41 bp):
ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAAGGCCTGGGC
Found at i:29528710 original size:12 final size:12
Alignment explanation
Indices: 29528695--29528720 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29528685 GTTTTTATCC
29528695 AAACGCCGCTAA
1 AAACGCCGCTAA
29528707 AAACGCCGCTAA
1 AAACGCCGCTAA
29528719 AA
1 AA
29528721 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:29529005 original size:49 final size:50
Alignment explanation
Indices: 29528885--29529024 Score: 210
Period size: 49 Copynumber: 2.8 Consensus size: 50
29528875 TGTACAGCCA
* * **
29528885 ATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCC
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCC
* * *
29528935 ATGCCATGTGCCAGACATGGTCTTACGTGGGACCTCTCATCTCGGTG-CC
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCC
29528984 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
29529025 ATCTCAATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 40 0.50
50 40 0.50
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCC
Found at i:29534929 original size:50 final size:50
Alignment explanation
Indices: 29534862--29535005 Score: 200
Period size: 50 Copynumber: 2.9 Consensus size: 50
29534852 TCTTGTACAA
* * **
29534862 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *
29534912 CCTATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGGTG
*
29534962 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
29535006 ATCTCAATGA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
49 1 0.01
50 79 0.98
51 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:29537264 original size:19 final size:18
Alignment explanation
Indices: 29537216--29537257 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29537206 CGATAGAATT
29537216 TTTGTCATAAAATAATTAA
1 TTTGT-ATAAAATAATTAA
*
29537235 TTTTTATAAAATAATTAA
1 TTTGTATAAAATAATTAA
*
29537253 ATTGT
1 TTTGT
29537258 GTTAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (18 bp):
TTTGTATAAAATAATTAA
Found at i:29538207 original size:201 final size:201
Alignment explanation
Indices: 29537862--29538264 Score: 806
Period size: 201 Copynumber: 2.0 Consensus size: 201
29537852 GCTGCCTATT
29537862 GAAATCATCCCTTACACTCTCATTCTCTCTTCTCCTCTCTCACTTTCTCTCAACTTTTCCTTCCC
1 GAAATCATCCCTTACACTCTCATTCTCTCTTCTCCTCTCTCACTTTCTCTCAACTTTTCCTTCCC
29537927 ATTTTCCCTTTTGCTCAAGTGCTAATTTCTTCTCTTGGGAAAGAGGTCCTCATCAGCCATTTTTG
66 ATTTTCCCTTTTGCTCAAGTGCTAATTTCTTCTCTTGGGAAAGAGGTCCTCATCAGCCATTTTTG
29537992 AGTAGCAATTAAAGTGTTCATAATCTACCTTGATAGCCAAGGACAACAGAGAATGAAGAACAAAG
131 AGTAGCAATTAAAGTGTTCATAATCTACCTTGATAGCCAAGGACAACAGAGAATGAAGAACAAAG
29538057 AACTCA
196 AACTCA
29538063 GAAATCATCCCTTACACTCTCATTCTCTCTTCTCCTCTCTCACTTTCTCTCAACTTTTCCTTCCC
1 GAAATCATCCCTTACACTCTCATTCTCTCTTCTCCTCTCTCACTTTCTCTCAACTTTTCCTTCCC
29538128 ATTTTCCCTTTTGCTCAAGTGCTAATTTCTTCTCTTGGGAAAGAGGTCCTCATCAGCCATTTTTG
66 ATTTTCCCTTTTGCTCAAGTGCTAATTTCTTCTCTTGGGAAAGAGGTCCTCATCAGCCATTTTTG
29538193 AGTAGCAATTAAAGTGTTCATAATCTACCTTGATAGCCAAGGACAACAGAGAATGAAGAACAAAG
131 AGTAGCAATTAAAGTGTTCATAATCTACCTTGATAGCCAAGGACAACAGAGAATGAAGAACAAAG
29538258 AACTCA
196 AACTCA
29538264 G
1 G
29538265 TCAAGCCGCA
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 202 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.34
Consensus pattern (201 bp):
GAAATCATCCCTTACACTCTCATTCTCTCTTCTCCTCTCTCACTTTCTCTCAACTTTTCCTTCCC
ATTTTCCCTTTTGCTCAAGTGCTAATTTCTTCTCTTGGGAAAGAGGTCCTCATCAGCCATTTTTG
AGTAGCAATTAAAGTGTTCATAATCTACCTTGATAGCCAAGGACAACAGAGAATGAAGAACAAAG
AACTCA
Found at i:29539001 original size:14 final size:14
Alignment explanation
Indices: 29538982--29539008 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29538972 AAATGTTTTT
29538982 ACTTAGTTTTTAAC
1 ACTTAGTTTTTAAC
29538996 ACTTAGTTTTTAA
1 ACTTAGTTTTTAA
29539009 TCATCTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (14 bp):
ACTTAGTTTTTAAC
Found at i:29543776 original size:22 final size:21
Alignment explanation
Indices: 29543751--29543794 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
29543741 TGATAAACTT
29543751 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
29543773 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
29543794 T
1 T
29543795 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:29545334 original size:19 final size:18
Alignment explanation
Indices: 29545288--29545335 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
29545278 GATAGAATTT
*
29545288 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
29545307 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
29545325 TTGTATTAAAA
1 TTGTA-TAAAA
29545336 ATTTTAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:29555227 original size:24 final size:24
Alignment explanation
Indices: 29555152--29555229 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
29555142 ATTGAGCGCC
*
29555152 AGAATAGGGACTGAGAGAGGGGTA
1 AGAATAGAGACTGAGAGAGGGGTA
* *
29555176 AGAATA-AGA-TG-GATTTGAAGCGCT-
1 AGAATAGAGACTGAGA---G-AGGGGTA
29555200 AGAATAGAGACTGAGAGAGGGGTA
1 AGAATAGAGACTGAGAGAGGGGTA
29555224 AGAATA
1 AGAATA
29555230 AGAATAAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 6 0.15
24 20 0.49
25 7 0.17
26 2 0.05
27 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.37, T:0.17
Consensus pattern (24 bp):
AGAATAGAGACTGAGAGAGGGGTA
Found at i:29562545 original size:43 final size:43
Alignment explanation
Indices: 29562455--29562650 Score: 171
Period size: 43 Copynumber: 4.6 Consensus size: 43
29562445 CCATTCCAAT
** * * ** *
29562455 TATACTGGCACGTA-AGTGCATCATTGGATGAAACCGAAGCTAC
1 TATACTGGCACACACAGTGCATCAATGGAT-AAACCAAAGAAAA
*
29562498 TATACTGGCACACACAGTGCATCAATGGATAAATCAAAGAAAA
1 TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
* * * * * * *
29562541 TATACAGGAAAACACAGTGCATCAACGTAAAAACCGAAGAAAA
1 TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
* * * *
29562584 TAAACTGGCATACACAGTGCATCATTGGATACACCAAAGAAAA
1 TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
* *
29562627 TATA-TCGGTACACACAATGCATCA
1 TATACT-GGCACACACAGTGCATCA
29562651 TCAGATAAAA
Statistics
Matches: 121, Mismatches: 30, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
42 1 0.01
43 106 0.88
44 14 0.12
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (43 bp):
TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
Found at i:29581712 original size:8 final size:8
Alignment explanation
Indices: 29581695--29581729 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
29581685 TTCAAATAGT
29581695 AAATAATA
1 AAATAATA
*
29581703 AAATATTA
1 AAATAATA
*
29581711 AAAAAATA
1 AAATAATA
29581719 AAATAATA
1 AAATAATA
29581727 AAA
1 AAA
29581730 AATTTTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAATAATA
Found at i:29588585 original size:16 final size:16
Alignment explanation
Indices: 29588566--29588600 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29588556 TAGTAATTTT
29588566 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
29588582 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
29588598 AAT
1 AAT
29588601 TACAAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:29591803 original size:21 final size:21
Alignment explanation
Indices: 29591773--29591829 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
29591763 ATCACAAAGA
* *
29591773 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
29591793 AAAAAGAGAAGTAACTTGGAT
1 AAAAAGAGAAGTAACTTAGAC
*
29591814 AAAAAGAGAACTAACT
1 AAAAAGAGAAGTAACT
29591830 CGAACAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.54, C:0.07, G:0.23, T:0.16
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:29593983 original size:42 final size:42
Alignment explanation
Indices: 29593936--29594193 Score: 185
Period size: 43 Copynumber: 6.2 Consensus size: 42
29593926 GAAGCTTTGC
* *
29593936 ACCCAGCGCTGGTCGGTAAAATCGACAAATATGTATATGTGT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
*
29593978 ACCCAGCACTGGTCGGTAAAATCGAAAAATATTATATATGTGT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATA-TATATATGTGT
* * * * * *
29594021 GCCCAGCACTAGTCGGTAAAACCAACAAATATATATGTATATAT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATATATA--TATGTGT
* * * * ** * *
29594065 ATGTCAAGCACTAGTTGGTGGAACCGAAAAATATATATATGTG-
1 A--CCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
* *
29594108 -CCCAACACTGGTCTGTAAAA-CTG-CAAATATATATATG-G-
1 ACCCAGCACTGGTCGGTAAAATC-GACAAATATATATATGTGT
* * *
29594146 --CTAGCACTGGTCGGTAAAACCGGC-AA-ATATATATGTGT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
*
29594184 GCCCAGCACT
1 ACCCAGCACT
29594194 TCAAGATGCA
Statistics
Matches: 171, Mismatches: 33, Indels: 26
0.74 0.14 0.11
Matches are distributed among these distances:
36 9 0.05
37 20 0.12
38 3 0.02
39 14 0.08
40 20 0.12
42 33 0.19
43 36 0.21
44 9 0.05
46 27 0.16
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (42 bp):
ACCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
Found at i:29594154 original size:37 final size:40
Alignment explanation
Indices: 29594093--29594193 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 40
29594083 TGGAACCGAA
* *
29594093 AAATATATATATGTGCCCAACACTGGTCTGTAAAA-CTGC
1 AAATATATATATGTGCCCAACACTGGTCGGTAAAACCGGC
* *
29594132 AAATATATATATG-G-CTAGCACTGGTCGGTAAAACCGGC
1 AAATATATATATGTGCCCAACACTGGTCGGTAAAACCGGC
* *
29594170 AAATATATATGTGTGCCCAGCACT
1 AAATATATATATGTGCCCAACACT
29594194 TCAAGATGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
37 16 0.30
38 16 0.30
39 14 0.26
40 7 0.13
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (40 bp):
AAATATATATATGTGCCCAACACTGGTCGGTAAAACCGGC
Found at i:29599416 original size:26 final size:25
Alignment explanation
Indices: 29599364--29599425 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
29599354 AAACTCTTCT
*
29599364 AAAAGAAAACTCAAGAGAAATTCTTG
1 AAAA-AAAACTCAAGAGAAATTATTG
*
29599390 AAAAAAAACTCAAAGAGAATTTATTG
1 AAAAAAAACTC-AAGAGAAATTATTG
29599416 ACTAAAAAAA
1 A--AAAAAAA
29599426 TAAGTTGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 7 0.23
26 17 0.55
28 7 0.23
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (25 bp):
AAAAAAAACTCAAGAGAAATTATTG
Found at i:29601490 original size:25 final size:25
Alignment explanation
Indices: 29601462--29601510 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29601452 CATGCAGTAG
* *
29601462 CAGTCTGGTCCTGAGCCCTATACAA
1 CAGTCTGGGCCTGAGCCCAATACAA
* *
29601487 CAGTGTGGGCCTTAGCCCAATACA
1 CAGTCTGGGCCTGAGCCCAATACA
29601511 GTAATAGTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (25 bp):
CAGTCTGGGCCTGAGCCCAATACAA
Found at i:29601682 original size:26 final size:26
Alignment explanation
Indices: 29601660--29601721 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
29601650 TGCAGCAAGA
29601660 CTACCAGTAATAGTAATGTAGCAAAG
1 CTACCAGTAATAGTAATGTAGCAAAG
* * *
29601686 CTGCCAGTAACAGTATATGTGGCAAAG
1 CTACCAGTAATAGTA-ATGTAGCAAAG
*
29601713 CCACCAGTA
1 CTACCAGTA
29601722 CAGTATACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (26 bp):
CTACCAGTAATAGTAATGTAGCAAAG
Found at i:29601724 original size:26 final size:27
Alignment explanation
Indices: 29601662--29601728 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
29601652 CAGCAAGACT
* *
29601662 ACCAGTAATAGTA-ATGTAGCAAAGCT
1 ACCAGTAACAGTATATGTAGCAAAGCC
* *
29601688 GCCAGTAACAGTATATGTGGCAAAGCC
1 ACCAGTAACAGTATATGTAGCAAAGCC
29601715 ACCAGT-ACAGTATA
1 ACCAGTAACAGTATA
29601729 CTTACCCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 19 0.54
27 16 0.46
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (27 bp):
ACCAGTAACAGTATATGTAGCAAAGCC
Found at i:29601893 original size:27 final size:26
Alignment explanation
Indices: 29601875--29602126 Score: 283
Period size: 27 Copynumber: 9.3 Consensus size: 26
29601865 GGGTATAACA
29601875 GTCATTTTACCCTTC-AGGGGTATTTC
1 GTCATTTTACCCTTCGA-GGGTATTTC
*
29601901 GGTCATTTTACCCTGCGAGGGTATTTC
1 -GTCATTTTACCCTTCGAGGGTATTTC
* *
29601928 AGTTATTTTACCCTTCGAGGGTTTTTC
1 -GTCATTTTACCCTTCGAGGGTATTTC
** *
29601955 GATCATTCCACCCTGCGAGGGTATTTC
1 G-TCATTTTACCCTTCGAGGGTATTTC
* *
29601982 GATCATTTTACCCTTTGAGGGTATTTTG
1 G-TCATTTTACCCTTCGAGGGTA-TTTC
*
29602010 GTCATTTTACCCTTCGGGGGTATTTC
1 GTCATTTTACCCTTCGAGGGTATTTC
29602036 GATCATTTTACCCTTCGAGGGTATTTC
1 G-TCATTTTACCCTTCGAGGGTATTTC
* *
29602063 GGTTACTTTACCCTTC-AGGGGTATTTC
1 -GTCATTTTACCCTTCGA-GGGTATTTC
*
29602090 AGTCATTTTACCCTTCGAGGATATTTC
1 -GTCATTTTACCCTTCGAGGGTATTTC
29602117 AGTCATTTTA
1 -GTCATTTTA
29602127 GGCCCATTAC
Statistics
Matches: 193, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.03
27 180 0.93
28 7 0.04
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (26 bp):
GTCATTTTACCCTTCGAGGGTATTTC
Found at i:29601955 original size:54 final size:54
Alignment explanation
Indices: 29601873--29602126 Score: 318
Period size: 54 Copynumber: 4.7 Consensus size: 54
29601863 AGGGGTATAA
29601873 CAGTCATTTTACCCTTC-AGGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
1 CAGTCATTTTACCCTTCGA-GGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
* * * **
29601927 CAGTTATTTTACCCTTCGAGGGTTTTTCGATCATTCCACCCTGCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
* * * *
29601981 C-GATCATTTTACCCTTTGAGGGTATTTTGGTCATTTTACCCTTCGGGGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
* * *
29602035 C-GATCATTTTACCCTTCGAGGGTATTTCGGTTACTTTACCCTTC-AGGGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGA-GGGTATTT
* *
29602089 CAGTCATTTTACCCTTCGAGGATATTTCAGTCATTTTA
1 CAGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA
29602127 GGCCCATTAC
Statistics
Matches: 173, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 170 0.98
55 2 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (54 bp):
CAGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
Found at i:29602123 original size:81 final size:81
Alignment explanation
Indices: 29601876--29602126 Score: 328
Period size: 81 Copynumber: 3.1 Consensus size: 81
29601866 GGTATAACAG
* *
29601876 TCATTTTACCCTTC-AGGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTTCAGTTATTTTACC
1 TCATTTTACCCTTCGA-GGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACC
*
29601940 CTTCGAGGGTTTTTCGA
65 CTTCGAGGGTATTTCGA
** * * * **
29601957 TCATTCCACCCTGCGAGGGTATTTCGATCATTTTACCCTTTGAGGGTATTTTGGTCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCC
*
29602022 TTCGGGGGTATTTCGA
66 TTCGAGGGTATTTCGA
* *
29602038 TCATTTTACCCTTCGAGGGTATTTCGGTTACTTTACCCTTC-AGGGGTATTTCAGTCATTTTACC
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGA-GGGTATTTCAGTCATTTTACC
*
29602102 CTTCGAGGATATTTC-A
65 CTTCGAGGGTATTTCGA
29602118 GTCATTTTA
1 -TCATTTTA
29602127 GGCCCATTAC
Statistics
Matches: 145, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.01
81 142 0.98
82 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCC
TTCGAGGGTATTTCGA
Found at i:29607700 original size:12 final size:12
Alignment explanation
Indices: 29607683--29607707 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29607673 CTTGTAAACC
29607683 TTTCAAAACACT
1 TTTCAAAACACT
29607695 TTTCAAAACACT
1 TTTCAAAACACT
29607707 T
1 T
29607708 ACGGATAAGG
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTCAAAACACT
Found at i:29609413 original size:9 final size:9
Alignment explanation
Indices: 29609399--29609466 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
29609389 GTAGTGATTC
29609399 AATTCGGTT
1 AATTCGGTT
29609408 AATTCGGTT
1 AATTCGGTT
* *
29609417 AATTCAGAT
1 AATTCGGTT
*
29609426 AATTCGGGT
1 AATTCGGTT
*
29609435 AATTCAGTT
1 AATTCGGTT
*
29609444 AATTCGGGT
1 AATTCGGTT
29609453 AATTCGGTT
1 AATTCGGTT
29609462 AATTC
1 AATTC
29609467 AATTAATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29609431 original size:27 final size:27
Alignment explanation
Indices: 29609399--29609474 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
29609389 GTAGTGATTC
*
29609399 AATTCGGTTAATTCGGTTAATTCAGAT
1 AATTCGGTTAATTCAGTTAATTCAGAT
* * *
29609426 AATTCGGGTAATTCAGTTAATTCGGGT
1 AATTCGGTTAATTCAGTTAATTCAGAT
*
29609453 AATTCGGTTAATTCAATTAATT
1 AATTCGGTTAATTCAGTTAATT
29609475 TGATTAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (27 bp):
AATTCGGTTAATTCAGTTAATTCAGAT
Found at i:29609482 original size:27 final size:27
Alignment explanation
Indices: 29609393--29609483 Score: 94
Period size: 27 Copynumber: 3.3 Consensus size: 27
29609383 AATTATGTAG
*
29609393 TGATTCAATTCGGTTAATTCGGTTAATT
1 TGATT-AATTCGGTTAATTCAGTTAATT
* *
29609421 CAGA-TAATTCGGGTAATTCAGTTAATT
1 -TGATTAATTCGGTTAATTCAGTTAATT
* ** *
29609448 CGGGTAATTCGGTTAATTCAATTAATT
1 TGATTAATTCGGTTAATTCAGTTAATT
29609475 TGATTAATT
1 TGATTAATT
29609484 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
26 1 0.02
27 47 0.92
28 1 0.02
29 2 0.04
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (27 bp):
TGATTAATTCGGTTAATTCAGTTAATT
Found at i:29625050 original size:14 final size:14
Alignment explanation
Indices: 29625031--29625061 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29625021 TTGCAAGGAG
29625031 AATGCAATTTATTC
1 AATGCAATTTATTC
29625045 AATGCAATTTATTC
1 AATGCAATTTATTC
29625059 AAT
1 AAT
29625062 CTGTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (14 bp):
AATGCAATTTATTC
Found at i:29636314 original size:42 final size:43
Alignment explanation
Indices: 29636206--29636363 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
29636196 AGCTCGTACA
** * * *
29636206 ATGCCAACATCCCAGATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACATCCCAGACATGGTCTTACACGAAATCATATATCG
*
29636249 ATGCC-ACTATCCCAGACAAGGTCTTACACGAAATCATATA-CG
1 ATGCCAAC-ATCCCAGACATGGTCTTACACGAAATCATATATCG
* * *
29636291 AAGCCAATATCCCAGACATGGTCTTACACGTAAATC-TCAAATCG
1 ATGCCAACATCCCAGACATGGTCTTACACG-AAATCAT-ATATCG
* *
29636335 ATGCCAACATCCTAGACGTGGTCTTACAC
1 ATGCCAACATCCCAGACATGGTCTTACAC
29636364 AAGATCACAT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
42 30 0.31
43 39 0.41
44 27 0.28
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (43 bp):
ATGCCAACATCCCAGACATGGTCTTACACGAAATCATATATCG
Found at i:29638147 original size:24 final size:24
Alignment explanation
Indices: 29638115--29638165 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
29638105 TTATGGGGAG
29638115 AAGTGTCATATGTTTTCTGATCAT
1 AAGTGTCATATGTTTTCTGATCAT
29638139 AAGTGTCATATGTTTTCTGATCAT
1 AAGTGTCATATGTTTTCTGATCAT
29638163 AAG
1 AAG
29638166 AGTTTGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (24 bp):
AAGTGTCATATGTTTTCTGATCAT
Found at i:29646645 original size:22 final size:21
Alignment explanation
Indices: 29646591--29646645 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
29646581 GCAAATCTGT
29646591 CTAAAA-TAATA-AAAATTAA
1 CTAAAATTAATATAAAATTAA
*
29646610 -TGAAAATTTGATATAAAATTAA
1 CT-AAAA-TTAATATAAAATTAA
29646632 CTAAAATTCAATAT
1 CTAAAATT-AATAT
29646646 GTTCATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
21 6 0.21
22 16 0.57
23 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (21 bp):
CTAAAATTAATATAAAATTAA
Found at i:29649270 original size:22 final size:21
Alignment explanation
Indices: 29649216--29649270 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
29649206 GCAAATCTGT
29649216 CTAAAA-TAATA-AAAATTAA
1 CTAAAATTAATATAAAATTAA
*
29649235 -TGAAAATTTGATATAAAATTAA
1 CT-AAAA-TTAATATAAAATTAA
29649257 CTAAAATTCAATAT
1 CTAAAATT-AATAT
29649271 GTTCATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
21 6 0.21
22 16 0.57
23 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (21 bp):
CTAAAATTAATATAAAATTAA
Found at i:29650121 original size:67 final size:67
Alignment explanation
Indices: 29649997--29650127 Score: 181
Period size: 67 Copynumber: 2.0 Consensus size: 67
29649987 CAAACTTGTT
* * * *
29649997 TCAAAGAATATTCTAAATAGTACTGAGTCTAGTGTTTAGGACAATTTAAAGATAATTACGAGAAT
1 TCAAAGAAAATTCTAAATAGTACTAAGTCTAGTGTTTAGGACAATTTAAAGACAATTAAGAGAAT
29650062 CA
66 CA
* * * * *
29650064 TCAATGAAAATTCTGAATAGTATTAAGTCTAGTGTTTGGGACAATTTAATGACAATTAAGAGAA
1 TCAAAGAAAATTCTAAATAGTACTAAGTCTAGTGTTTAGGACAATTTAAAGACAATTAAGAGAA
29650128 AAGTGATGGC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (67 bp):
TCAAAGAAAATTCTAAATAGTACTAAGTCTAGTGTTTAGGACAATTTAAAGACAATTAAGAGAAT
CA
Found at i:29652141 original size:24 final size:23
Alignment explanation
Indices: 29652109--29652158 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
29652099 AGTGTAAAAT
*
29652109 ATTAATAATTTAAT-AAATTGAAA
1 ATTAATAATTAAATAAAATT-AAA
29652132 ATTAATTAATTAAATAAAATTAAA
1 ATTAA-TAATTAAATAAAATTAAA
29652156 ATT
1 ATT
29652159 TAGGAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 14 0.58
25 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTAATAATTAAATAAAATTAAA
Found at i:29658508 original size:32 final size:32
Alignment explanation
Indices: 29658472--29658536 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
29658462 GCCTAGGGAC
*
29658472 TGATTTGCAAAACTGTTAAAGGATTAGGGTTT
1 TGATTTGCAAAACTATTAAAGGATTAGGGTTT
29658504 TGATTTGCAAAACTATTAAAGGATTAGGGTTT
1 TGATTTGCAAAACTATTAAAGGATTAGGGTTT
29658536 T
1 T
29658537 TCATAAACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (32 bp):
TGATTTGCAAAACTATTAAAGGATTAGGGTTT
Found at i:29659129 original size:41 final size:41
Alignment explanation
Indices: 29659083--29659271 Score: 236
Period size: 41 Copynumber: 4.6 Consensus size: 41
29659073 TAGTTAATTA
** *
29659083 ACCCCTGAATTGCACATATGTATCCCTATTTGTACTT-TAG
1 ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* * *
29659123 TACCCCTGAATTACACATATGTGCCCCTATTTGGACTTCGAT
1 -ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* *
29659165 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGAG
1 ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* * * *
29659206 ACCCCTAAATTACACATATATGCCCCTATTTGTTCTTCGAG
1 ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* *
29659247 ACCCTTGAATTGCACATACGTGCCC
1 ACCCCTGAATTGCACATATGTGCCC
29659272 TTGTTTACAC
Statistics
Matches: 125, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
41 124 0.99
42 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (41 bp):
ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
Found at i:29659192 original size:21 final size:21
Alignment explanation
Indices: 29659125--29659192 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
29659115 TACTTTAGTA
* *
29659125 CCCCTGAATTACACATATGTG
1 CCCCTGAATTGCACATACGTG
* * * *
29659146 CCCCT-ATTTGGAC-TTCGATA
1 CCCCTGAATTGCACATACG-TG
29659166 CCCCTGAATTGCACATACGTG
1 CCCCTGAATTGCACATACGTG
29659187 CCCCTG
1 CCCCTG
29659193 TTTGTACTTC
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 11 0.32
21 18 0.53
22 3 0.09
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (21 bp):
CCCCTGAATTGCACATACGTG
Found at i:29659220 original size:82 final size:82
Alignment explanation
Indices: 29659083--29659277 Score: 266
Period size: 82 Copynumber: 2.4 Consensus size: 82
29659073 TAGTTAATTA
* ** * * * *
29659083 ACCCCTGAATTGCACATATGTATCCCTATTTGTACTTTAGTACCCCTGAATTACACATATGTGCC
1 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTGAGTACCCCTAAATTACACATATATGCC
*
29659148 CCTATTTGGACTTCGAT
66 CCTATTTGGACTTCGAG
29659165 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGAG-ACCCCTAAATTACACATATATGC
1 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTT-GAGTACCCCTAAATTACACATATATGC
**
29659229 CCCTATTTGTTCTTCGAG
65 CCCTATTTGGACTTCGAG
* *
29659247 ACCCTTGAATTGCACATACGTGCCCTTGTTT
1 ACCCCTGAATTGCACATACGTGCCCCTGTTT
29659278 ACACTCCAGT
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
82 98 0.98
83 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (82 bp):
ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTGAGTACCCCTAAATTACACATATATGCC
CCTATTTGGACTTCGAG
Found at i:29660605 original size:74 final size:74
Alignment explanation
Indices: 29660482--29660626 Score: 263
Period size: 74 Copynumber: 2.0 Consensus size: 74
29660472 AAGTTTTGAG
*
29660482 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGGAT
1 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGAAT
29660547 TGATTATTA
66 TGATTATTA
* *
29660556 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATTATGTGGTTATGTGAATAATTGTGAAT
1 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGAAT
29660621 TGATTA
66 TGATTA
29660627 CTGTGATGCG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (74 bp):
TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGAAT
TGATTATTA
Found at i:29663129 original size:17 final size:17
Alignment explanation
Indices: 29663109--29663148 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29663099 TATACCAAAA
29663109 AAATAAAACAAATAAAT
1 AAATAAAACAAATAAAT
* **
29663126 AAATAAAATAAATTCAT
1 AAATAAAACAAATAAAT
29663143 AAATAA
1 AAATAA
29663149 TGAGAGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAACAAATAAAT
Found at i:29663261 original size:9 final size:8
Alignment explanation
Indices: 29663230--29663301 Score: 58
Period size: 9 Copynumber: 8.4 Consensus size: 8
29663220 ACAATTTGGC
29663230 ATAAAAT-
1 ATAAAATA
29663237 ATATAAATAA
1 ATA-AAAT-A
29663247 ATAAAATA
1 ATAAAATA
29663255 ATGAAAACT-
1 AT-AAAA-TA
29663264 ATAAAATA
1 ATAAAATA
29663272 ATAATAATA
1 ATAA-AATA
*
29663281 ATAATAGTA
1 ATAA-AATA
29663290 ATAATAATA
1 ATAA-AATA
29663299 ATA
1 ATA
29663302 GTAACGAAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
7 4 0.07
8 15 0.27
9 33 0.59
10 4 0.07
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (8 bp):
ATAAAATA
Found at i:29663276 original size:3 final size:3
Alignment explanation
Indices: 29663264--29663301 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
29663254 AATGAAAACT
*
29663264 ATA A-A ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29663302 GTAACGAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29665212 original size:217 final size:214
Alignment explanation
Indices: 29664917--29665583 Score: 759
Period size: 217 Copynumber: 3.1 Consensus size: 214
29664907 TCTGTTTGCA
* * *
29664917 CCACTGCAACTTCAGGGGTATAAGATCTGCTTGCTTAGTCTGCTCCGCTACAAGTTCAGGGAGAT
1 CCACTGCAACTTCAGGGGGATAAGAT-TGCTTGCTTAGTCTGCTCCGCTGCAACTTCAGGGAGAT
*
29664982 AAGACTAGATGCGATCTGCTCTCTTCAACTTCAGAGAGATAAGATCTGTCATTTTAATACGCTCC
65 AAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGT-ATTTTAATACGCTCC
* * *
29665047 GCTACAACTTCAGGGAGATAGGATTATTGAATTTAATCTACTCCACTGCAACTTCAGGGAGATAA
129 ACTGCAACTTCAGGGAGATAGGATTATTGAATTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
*
29665112 GATTCGTCATCTTCAATCTGC-
194 GATT-GTCATCTTCAATCCGCT
* * * *
29665133 CCTACTGCAACTTTAGGGGGATAAGAGTTGGTTGCTTAGTCTGCTCCGCTGCAACTTTACGGAGA
1 CC-ACTGCAACTTCAGGGGGATAAGA-TTGCTTGCTTAGTCTGCTCCGCTGCAACTTCAGGGAGA
**
29665198 TAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTTATTTTAATTTGCTC
64 TAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTG-TATTTTAATACGCTC
* ** * *
29665263 CACTGCAACTTCAAGGAGATAGGATTATTGGTTTTAATTTGCTCCACTGTAACTTCAGGGAGATA
128 CACTGCAACTTCAGGGAGATAGGATTATTGAATTTAATCTGCTCCACTGCAACTTCAGGGAGATA
*
29665328 AGATTATCTATCTTCAATCCGCT
193 AGATTGTC-ATCTTCAATCCGCT
* * * *
29665351 CCACTGCAACTTCAGGGAGATAGGATTTGCTAT-CTTCAGTCCGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGGGGATAAGA-TTGCT-TGCTT-AGTCTGCTCCGCTGCAACTTCAGGGAG
* * * * * * * * * * * * *
29665415 ATAGGATTTGTATCTTCAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTTGTATCTTCAATC
63 ATAAGACTAG-A--TGCGATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTAT-TTTAATA
* * * *
29665480 CGCTCCACTGCAACTTTAGGGAGATAGGA-T-TTGTATCTTCAATCCGCTCCACTGCAACTTTAG
123 CGCTCCACTGCAACTTCAGGGAGATAGGATTATTGAAT-TT-AATCTGCTCCACTGCAACTTCAG
*
29665543 GGAGATAGGATTTGT-ATCTTCAATCCGCT
186 GGAGATAAGA-TTGTCATCTTCAATCCGCT
29665572 CCACTGCAACTT
1 CCACTGCAACTT
29665584 TAAGAAGATA
Statistics
Matches: 383, Mismatches: 53, Indels: 25
0.83 0.11 0.05
Matches are distributed among these distances:
216 4 0.01
217 214 0.56
218 35 0.09
219 1 0.00
220 4 0.01
221 40 0.10
222 82 0.21
223 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (214 bp):
CCACTGCAACTTCAGGGGGATAAGATTGCTTGCTTAGTCTGCTCCGCTGCAACTTCAGGGAGATA
AGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTATTTTAATACGCTCCAC
TGCAACTTCAGGGAGATAGGATTATTGAATTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
TTGTCATCTTCAATCCGCT
Found at i:29665599 original size:44 final size:44
Alignment explanation
Indices: 29665007--29665601 Score: 543
Period size: 44 Copynumber: 13.5 Consensus size: 44
29664997 CTGCTCTCTT
* * * * * * *
29665007 CAACTTCAGAGAGATAAGATCTGTCAT-TTTAATACGCTCCGCTA
1 CAACTTCAGGGAGATAGGATTTGT-ATCTTCAATCCGCTCCACTG
* **
29665051 CAACTTCAGGGAGATAGGATTATTGAAT-TT-AATCTACTCCACTG
1 CAACTTCAGGGAGATAGGA-T-TTGTATCTTCAATCCGCTCCACTG
* * *
29665095 CAACTTCAGGGAGATAAGATTCGTCATCTTCAATCTGC-CCTACTG
1 CAACTTCAGGGAGATAGGATTTGT-ATCTTCAATCCGCTCC-ACTG
* * * * * * *
29665140 CAACTTTAGGGGGATAAGAGTTGGT-TGCTT-AGTCTGCTCCGCTG
1 CAACTTCAGGGAGATAGGA-TTTGTAT-CTTCAATCCGCTCCACTG
* * * * * * * * *
29665184 CAACTTTACGGAGATAAGACTAG-A--TGCGATCTGCT-CTCTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
* * * * **
29665224 CAACTTCAGAGAGATAAGATCTGTTAT-TTTAATTTGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTG-TATCTTCAATCCGCTCCACTG
* **
29665268 CAACTTCAAGGAGATAGGATTATTGGT-T-TT-AATTTGCTCCACTG
1 CAACTTCAGGGAGATAGGA-T-TT-GTATCTTCAATCCGCTCCACTG
* * *
29665312 TAACTTCAGGGAGATAAGATTATCTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATT-TGTATCTTCAATCCGCTCCACTG
*
29665357 CAACTTCAGGGAGATAGGATTTGCTATCTTCAGTCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTG-TATCTTCAATCCGCTCCACTG
29665402 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
*
29665446 CAACTTTAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
*
29665490 CAACTTTAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
*
29665534 CAACTTTAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
* * *
29665578 CAACTTTAAGAAGATAGGATTTGT
1 CAACTTCAGGGAGATAGGATTTGT
29665602 GGTTTCACCG
Statistics
Matches: 473, Mismatches: 55, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
40 22 0.05
41 6 0.01
42 5 0.01
43 15 0.03
44 301 0.64
45 115 0.24
46 8 0.02
47 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
Found at i:29666511 original size:26 final size:26
Alignment explanation
Indices: 29666482--29666532 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
29666472 CAAGTATCTT
29666482 GAAAAGAACAAAGTATTCCAAGAACG
1 GAAAAGAACAAAGTATTCCAAGAACG
* *
29666508 GAAAATAATAAAGTATTCCAAGAAC
1 GAAAAGAACAAAGTATTCCAAGAAC
29666533 AACAAGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (26 bp):
GAAAAGAACAAAGTATTCCAAGAACG
Found at i:29667832 original size:23 final size:23
Alignment explanation
Indices: 29667802--29667846 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29667792 AATTCTGGGC
*
29667802 TTTGGTTTTTTATATTT-TTTGTA
1 TTTGGTTTATTAT-TTTCTTTGTA
29667825 TTTGGTTTATTATTTTCTTTGT
1 TTTGGTTTATTATTTTCTTTGT
29667847 GTATGCGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.11, C:0.02, G:0.13, T:0.73
Consensus pattern (23 bp):
TTTGGTTTATTATTTTCTTTGTA
Found at i:29668980 original size:16 final size:16
Alignment explanation
Indices: 29668929--29668971 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
29668919 TATCTTAAAA
29668929 TATGAATATGTGTTTAT
1 TATG-ATATGTGTTTAT
*
29668946 TGTGATATGTGTTTA-
1 TATGATATGTGTTTAT
29668961 TATGATATGTG
1 TATGATATGTG
29668972 ACTATTATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 11 0.46
17 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (16 bp):
TATGATATGTGTTTAT
Found at i:29683234 original size:21 final size:20
Alignment explanation
Indices: 29683210--29683251 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
29683200 TGAAATGCAA
29683210 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
29683231 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
29683251 T
1 T
29683252 GACCATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:29695564 original size:24 final size:24
Alignment explanation
Indices: 29695532--29695588 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
29695522 ATGGTGAAGT
*
29695532 CACTCAATAACGTTGTGGCCAAGC
1 CACTCAATAACATTGTGGCCAAGC
* *
29695556 CACTCAATAGCATTGTGGTCAAGC
1 CACTCAATAACATTGTGGCCAAGC
29695580 CACTCAATA
1 CACTCAATA
29695589 TCGCAGACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (24 bp):
CACTCAATAACATTGTGGCCAAGC
Found at i:29695627 original size:87 final size:87
Alignment explanation
Indices: 29695481--29695651 Score: 288
Period size: 87 Copynumber: 2.0 Consensus size: 87
29695471 ACACTCCACG
* * *
29695481 TTGTGGCCAAGCCACTCAATATCGTAGACAAGCTGCACATTATGGTGAAGTCACTCAATAACGTT
1 TTGTGGCCAAGCCACTCAATATCGCAGACAAGCTGCACATTATGGTCAAGCCACTCAATAACGTT
*
29695546 GTGGCCAAGCCACTCAATAGCA
66 GTGACCAAGCCACTCAATAGCA
* *
29695568 TTGTGGTCAAGCCACTCAATATCGCAGACAAGCTGCACGTTATGGTCAAGCCACTCAATAACGTT
1 TTGTGGCCAAGCCACTCAATATCGCAGACAAGCTGCACATTATGGTCAAGCCACTCAATAACGTT
29695633 GTGACCAAGCCACTCAATA
66 GTGACCAAGCCACTCAATA
29695652 TTGCAGTAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (87 bp):
TTGTGGCCAAGCCACTCAATATCGCAGACAAGCTGCACATTATGGTCAAGCCACTCAATAACGTT
GTGACCAAGCCACTCAATAGCA
Found at i:29696697 original size:11 final size:11
Alignment explanation
Indices: 29696683--29696729 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
29696673 GGTCCGGCAA
29696683 TGGTGAAGTGG
1 TGGTGAAGTGG
*
29696694 TGGTGCAGTGG
1 TGGTGAAGTGG
*
29696705 TGGTGAGGTGG
1 TGGTGAAGTGG
29696716 TGGTGAAGTGG
1 TGGTGAAGTGG
29696727 TGG
1 TGG
29696730 AGAATGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.13, C:0.02, G:0.57, T:0.28
Consensus pattern (11 bp):
TGGTGAAGTGG
Found at i:29707132 original size:15 final size:16
Alignment explanation
Indices: 29707104--29707133 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29707094 CACGTTCTCT
29707104 AAAGAACATGAAAAAG
1 AAAGAACATGAAAAAG
29707120 AAAGAAC-TGAAAAA
1 AAAGAACATGAAAAA
29707134 TAAACCTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.07
Consensus pattern (16 bp):
AAAGAACATGAAAAAG
Found at i:29707802 original size:27 final size:27
Alignment explanation
Indices: 29707772--29708092 Score: 376
Period size: 27 Copynumber: 11.9 Consensus size: 27
29707762 GTTATAACCA
* *
29707772 AAATACCTCCATAGGATAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
29707799 AAATACACCCATAGGGTAGAATAACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
29707826 AAATACCTCCAT-GAGGT-AGATGATCG
1 AAATACCCCCATAG-GGTAAAATGACCG
*
29707852 AAATACCCCCATAGGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
**
29707879 AAATACCCCCATAGGGTAAAATGATTG
1 AAATACCCCCATAGGGTAAAATGACCG
* ** *
29707906 AAATACCCTCATAGAATAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* ***
29707933 AAATATCCCCATAGGGTAAAATGAATA
1 AAATACCCCCATAGGGTAAAATGACCG
*
29707960 AAATACCCCCATAGGATAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
29707987 AAATACCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
29708014 AAATACCCCCATAAGGTAGAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
29708041 ACATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
*
29708068 ACATACCCCCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
29708093 TGTTATACCC
Statistics
Matches: 248, Mismatches: 43, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
26 20 0.08
27 228 0.92
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:29722745 original size:23 final size:24
Alignment explanation
Indices: 29722719--29722787 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 24
29722709 TATCGAGTTA
*
29722719 AAACGGTAAGCTCCGT-AGAGCTG
1 AAACGGTAAGCTCCATAAGAGCTG
*
29722742 AAACAGTAAGCT-CATAAGAGCTG
1 AAACGGTAAGCTCCATAAGAGCTG
*
29722765 AAACGGTAAGCT-CATACGAGCTG
1 AAACGGTAAGCTCCATAAGAGCTG
29722788 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 2 0.05
23 39 0.95
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.17
Consensus pattern (24 bp):
AAACGGTAAGCTCCATAAGAGCTG
Found at i:29727604 original size:27 final size:26
Alignment explanation
Indices: 29727565--29727762 Score: 130
Period size: 27 Copynumber: 7.3 Consensus size: 26
29727555 TCCTCATGGT
*
29727565 CTTCCACAAAAGATAGTCCTGGCAGA
1 CTTCCACAAAAGATAGTCCTGACAGA
* *
29727591 CTTTCCACATAAGATAGTCTTGATCA-A
1 C-TTCCACAAAAGATAGTCCTGA-CAGA
* * *
29727618 CCTTCCGCATTTCAA-ATAGTCCTAACAGA
1 -CTTCCACA---AAAGATAGTCCTGACAGA
* *
29727647 CTTCCACAAAAGATAGTCTTGACGGA
1 CTTCCACAAAAGATAGTCCTGACAGA
* *
29727673 CTTCCACAAAAGATAGCCCTAACAGA
1 CTTCCACAAAAGATAGTCCTGACAGA
* * **
29727699 CCTTTCACATAAGATAGTCCTGATGGA
1 -CTTCCACAAAAGATAGTCCTGACAGA
** * *
29727726 CTTCCCACATTTCAGATAGTCCTTACGGA
1 CTT-CCACA--AAAGATAGTCCTGACAGA
29727755 CTTCCACA
1 CTTCCACA
29727763 TATTCGGTAT
Statistics
Matches: 134, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
25 2 0.01
26 37 0.28
27 49 0.37
28 17 0.13
29 27 0.20
30 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (26 bp):
CTTCCACAAAAGATAGTCCTGACAGA
Found at i:29727738 original size:108 final size:108
Alignment explanation
Indices: 29727565--29727762 Score: 274
Period size: 108 Copynumber: 1.8 Consensus size: 108
29727555 TCCTCATGGT
* ** * *
29727565 CTTCCACAAAAGATAGTCCTGGCAGACTTTCCACATAAGATAGTCTTGATCAACCTTCCGCATTT
1 CTTCCACAAAAGATAGCCCTAACAGACTTTCCACATAAGATAGTCCTGATCAACCTTCCACATTT
29727630 CAAATAGTCCTAACAGACTTCCACAAAAGATAGTCTTGACGGA
66 CAAATAGTCCTAACAGACTTCCACAAAAGATAGTCTTGACGGA
**
29727673 CTTCCACAAAAGATAGCCCTAACAGACCTTT-CACATAAGATAGTCCTGATGGA-CTTCCCACAT
1 CTTCCACAAAAGATAGCCCTAACAGA-CTTTCCACATAAGATAGTCCTGATCAACCTT-CCACAT
* * *
29727736 TTCAGATAGTCCTTACGGACTTCCACA
64 TTCAAATAGTCCTAACAGACTTCCACA
29727763 TATTCGGTAT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.04
108 71 0.91
109 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (108 bp):
CTTCCACAAAAGATAGCCCTAACAGACTTTCCACATAAGATAGTCCTGATCAACCTTCCACATTT
CAAATAGTCCTAACAGACTTCCACAAAAGATAGTCTTGACGGA
Found at i:29731228 original size:30 final size:32
Alignment explanation
Indices: 29731177--29731245 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 32
29731167 ACGAACGTCC
* **
29731177 TTCTTTGCTCTCTACTCTCTGCCCTCTGCTGG
1 TTCTTTGCCCTCTACTCTCTGCCCTCTGCCAG
29731209 TTCTTTGCCCTC-A-TCTCTGCCCTCTGCCAG
1 TTCTTTGCCCTCTACTCTCTGCCCTCTGCCAG
29731239 TTCTTTG
1 TTCTTTG
29731246 TCCTGCCCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 22 0.65
31 1 0.03
32 11 0.32
ACGTcount: A:0.04, C:0.38, G:0.14, T:0.43
Consensus pattern (32 bp):
TTCTTTGCCCTCTACTCTCTGCCCTCTGCCAG
Found at i:29731255 original size:23 final size:26
Alignment explanation
Indices: 29731223--29731285 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 26
29731213 TTGCCCTCAT
29731223 CTCTGCCCTCTGCCAGTTCTTTG-T-
1 CTCTGCCCTCTGCCAGTTCTTTGTTC
*
29731247 C-CTGCCCTCTGCCGGTTCTTTGTTC
1 CTCTGCCCTCTGCCAGTTCTTTGTTC
29731272 CTCTGCCCTCTGCC
1 CTCTGCCCTCTGCC
29731286 GGCGAGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 20 0.57
24 2 0.06
25 1 0.03
26 12 0.34
ACGTcount: A:0.02, C:0.43, G:0.17, T:0.38
Consensus pattern (26 bp):
CTCTGCCCTCTGCCAGTTCTTTGTTC
Found at i:29731257 original size:30 final size:30
Alignment explanation
Indices: 29731177--29731259 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
29731167 ACGAACGTCC
* **
29731177 TTCTTTGCTCTCTACTCTCTGCCCTCTGCTGG
1 TTCTTTGCCCTC-AC-CTCTGCCCTCTGCCAG
*
29731209 TTCTTTGCCCTCATCTCTGCCCTCTGCCAG
1 TTCTTTGCCCTCACCTCTGCCCTCTGCCAG
*
29731239 TTCTTTGTCCTGC-CCTCTGCC
1 TTCTTTGCCCT-CACCTCTGCC
29731260 GGTTCTTTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
30 31 0.70
31 2 0.05
32 11 0.25
ACGTcount: A:0.04, C:0.41, G:0.14, T:0.41
Consensus pattern (30 bp):
TTCTTTGCCCTCACCTCTGCCCTCTGCCAG
Found at i:29731387 original size:8 final size:8
Alignment explanation
Indices: 29731374--29731411 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
29731364 GGATAGGAGA
29731374 TAAACCAT
1 TAAACCAT
29731382 TAAACCAT
1 TAAACCAT
29731390 TAAACCAT
1 TAAACCAT
29731398 TAAACCAT
1 TAAACCAT
29731406 TAAACC
1 TAAACC
29731412 CAAGTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (8 bp):
TAAACCAT
Found at i:29744126 original size:18 final size:18
Alignment explanation
Indices: 29744098--29744140 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
29744088 CCCAATCTTC
* *
29744098 TCCCTTTTCCCCTTCTCCT
1 TCCC-TTTCCCCTACCCCT
29744117 TCCCTTTCCCCTACCCCT
1 TCCCTTTCCCCTACCCCT
29744135 TCCCTT
1 TCCCTT
29744141 CCCGTTTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.02, C:0.56, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCCTTTCCCCTACCCCT
Found at i:29745606 original size:30 final size:30
Alignment explanation
Indices: 29745570--29745627 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
29745560 GCATTTGTAC
29745570 AAGACCATAAGTACCAATTTGCTATGACAT
1 AAGACCATAAGTACCAATTTGCTATGACAT
*
29745600 AAGACCATAAGTACTAATTTGCTATGAC
1 AAGACCATAAGTACCAATTTGCTATGAC
29745628 TGGCATGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (30 bp):
AAGACCATAAGTACCAATTTGCTATGACAT
Found at i:29746706 original size:14 final size:14
Alignment explanation
Indices: 29746683--29746722 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29746673 ACAAAAAAGT
*
29746683 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
29746697 AAATCATTTTACGG
1 AAAACATTTTACAG
29746711 AAAACATTTTAC
1 AAAACATTTTAC
29746723 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:29774784 original size:20 final size:20
Alignment explanation
Indices: 29774746--29774799 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
29774736 TACTCTTTTT
**
29774746 TTATAAAAAAAATCATAAAAA
1 TTAT-AAAAAAATTTTAAAAA
*
29774767 TTATAAAATAATTTTAAAAA
1 TTATAAAAAAATTTTAAAAA
29774787 TTATAAAAAAATT
1 TTATAAAAAAATT
29774800 AAATATTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TTATAAAAAAATTTTAAAAA
Done.