Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015087.1 Kokia drynarioides strain JFW-HI SEQ_130131, whole genome shotgun sequence
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: 183326
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 403 characters in sequence are not A, C, G, or T
Found at i:1115 original size:18 final size:17
Alignment explanation
Indices: 1092--1125 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1082 GTTATTAATT
1092 ACATAATATATAAAAATA
1 ACATAATATA-AAAAATA
1110 ACATAATATAAAAAAT
1 ACATAATATAAAAAAT
1126 TATAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ACATAATATAAAAAATA
Found at i:3114 original size:48 final size:48
Alignment explanation
Indices: 3043--3144 Score: 177
Period size: 48 Copynumber: 2.1 Consensus size: 48
3033 CGTTGGCATA
*
3043 GCGATCGTCATGTAAATTAAAGTCTTTTATTAGCATATGGAAATTGTT
1 GCGATTGTCATGTAAATTAAAGTCTTTTATTAGCATATGGAAATTGTT
*
3091 GCGATTGTTATGTAAATTAAAGTCTTTTATTAGCATATGGAAATTGTT
1 GCGATTGTCATGTAAATTAAAGTCTTTTATTAGCATATGGAAATTGTT
*
3139 GGGATT
1 GCGATT
3145 TCGTTTCAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (48 bp):
GCGATTGTCATGTAAATTAAAGTCTTTTATTAGCATATGGAAATTGTT
Found at i:5434 original size:24 final size:21
Alignment explanation
Indices: 5396--5440 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
5386 TAATATTAGT
5396 TTTCTTAAAAATATTAAATAAA
1 TTTCTTAAAAATATT-AATAAA
5418 TTTCTTAAAAAATTATTAATAAA
1 TTTCTT-AAAAA-TATTAATAAA
5441 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 11 0.52
24 4 0.19
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTCTTAAAAATATTAATAAA
Found at i:10995 original size:20 final size:20
Alignment explanation
Indices: 10972--11014 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
10962 CTATTAATTA
10972 ATTTACTCAATATTTAATCC
1 ATTTACTCAATATTTAATCC
10992 ATTTACTCAATATTTAATCC
1 ATTTACTCAATATTTAATCC
11012 ATT
1 ATT
11015 ACCTTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTACTCAATATTTAATCC
Found at i:35557 original size:3 final size:3
Alignment explanation
Indices: 35549--35577 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35539 GTGCAAAACA
35549 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
35578 GTAACAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:37825 original size:17 final size:17
Alignment explanation
Indices: 37800--37832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37790 ATTATATTAC
*
37800 TAGTGATTTAATTTTAG
1 TAGTCATTTAATTTTAG
37817 TAGTCATTTAATTTTA
1 TAGTCATTTAATTTTA
37833 ATTTGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (17 bp):
TAGTCATTTAATTTTAG
Found at i:52002 original size:21 final size:21
Alignment explanation
Indices: 51976--52026 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
51966 TTCTGGAGAG
51976 TCCAAGATTTAATGTTTATGA
1 TCCAAGATTTAATGTTTATGA
51997 TCCAAGATTTAATGTTTATGA
1 TCCAAGATTTAATGTTTATGA
*
52018 TCCAGGATT
1 TCCAAGATT
52027 CATAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (21 bp):
TCCAAGATTTAATGTTTATGA
Found at i:52345 original size:2 final size:2
Alignment explanation
Indices: 52338--52395 Score: 64
Period size: 2 Copynumber: 29.0 Consensus size: 2
52328 AAAATATCAC
* * * *
52338 AT AT AT AT AC ACT -T AT AT AT AT AT AC AT AC AT AT AT CT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52380 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
52396 GGATCCTCGA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:52395 original size:16 final size:16
Alignment explanation
Indices: 52338--52394 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
52328 AAAATATCAC
52338 ATATATATACACT-TAT
1 ATATATATACA-TATAT
*
52354 ATATATATACATACAT
1 ATATATATACATATAT
* *
52370 ATATCTATATATATAT
1 ATATATATACATATAT
52386 ATATATATA
1 ATATATATA
52395 TGGATCCTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 34 0.97
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATATACATATAT
Found at i:58099 original size:26 final size:26
Alignment explanation
Indices: 58048--58099 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
58038 CTCTGTAATT
* *
58048 ATTCGAATAATAAAATAATTTGAATA
1 ATTCGAATAATAAAATAATGTAAATA
**
58074 ATTCGAATAATAAAATGGTGTAAATA
1 ATTCGAATAATAAAATAATGTAAATA
58100 TATTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (26 bp):
ATTCGAATAATAAAATAATGTAAATA
Found at i:58196 original size:27 final size:30
Alignment explanation
Indices: 58157--58216 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
58147 AAAAAAAAAG
58157 AAATTTAAAATATTTAT-AAAAAAATTC-A
1 AAATTTAAAATATTTATAAAAAAAATTCTA
* *
58185 AAATTT-ATATATTTTTAAAAAAAATTCTA
1 AAATTTAAAATATTTATAAAAAAAATTCTA
58214 AAA
1 AAA
58217 ATATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 16 0.57
29 4 0.14
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATTTAAAATATTTATAAAAAAAATTCTA
Found at i:58221 original size:28 final size:29
Alignment explanation
Indices: 58169--58223 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
58159 ATTTAAAATA
*
58169 TTTATAAAAAAATTCAAAATTTATATATT
1 TTTATAAAAAAATTCAAAATATATATATT
58198 TTTA-AAAAAAATTCTAAAA-ATATATA
1 TTTATAAAAAAATTC-AAAATATATATA
58224 AAAAAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTATAAAAAAATTCAAAATATATATATT
Found at i:58299 original size:19 final size:19
Alignment explanation
Indices: 58272--58311 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
58262 TGGACTTAAT
*
58272 TAATGATTCAAATTTATCA
1 TAATAATTCAAATTTATCA
58291 TAATAATTCAAATTTATCA
1 TAATAATTCAAATTTATCA
58310 TA
1 TA
58312 CTCAATTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (19 bp):
TAATAATTCAAATTTATCA
Found at i:71569 original size:14 final size:14
Alignment explanation
Indices: 71550--71596 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
71540 TGGGGAAGTG
*
71550 TTAAATGCTAATAT
1 TTAAATGATAATAT
71564 TTAAAT-ATAAATAT
1 TTAAATGAT-AATAT
*
71578 TT-AATGATTATAT
1 TTAAATGATAATAT
71591 TTAAAT
1 TTAAAT
71597 ATTTAAGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (14 bp):
TTAAATGATAATAT
Found at i:71656 original size:24 final size:24
Alignment explanation
Indices: 71624--71681 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
71614 TATAATCTAT
* *
71624 TTAAAATTTTA-AAATAATTAATA
1 TTAATATTTTAGAAATAATTAAAA
*
71647 TTAAT-TATTTAGAAATATTTAAAA
1 TTAATAT-TTTAGAAATAATTAAAA
71671 TTAATATTTTA
1 TTAATATTTTA
71682 TATAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 19 0.66
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTAATATTTTAGAAATAATTAAAA
Found at i:71909 original size:26 final size:26
Alignment explanation
Indices: 71867--71932 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
71857 TCAAAAGCAT
*
71867 TTTTCAAAAGCAC-TTTCCACCACAC
1 TTTTCAAAAACACTTTTCCACCACAC
71892 TTTTCAAAAACACTTTTCCACCACAC
1 TTTTCAAAAACACTTTTCCACCACAC
71918 TTTTCAAAAACACTT
1 TTTTCAAAAACACTT
71933 CTCAAAAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 12 0.31
26 27 0.69
ACGTcount: A:0.35, C:0.32, G:0.02, T:0.32
Consensus pattern (26 bp):
TTTTCAAAAACACTTTTCCACCACAC
Found at i:71930 original size:13 final size:13
Alignment explanation
Indices: 71857--71942 Score: 75
Period size: 13 Copynumber: 6.7 Consensus size: 13
71847 TCAAATTTTA
* *
71857 TCAAAAGCATTTT
1 TCAAAAACACTTT
*
71870 TCAAAAGCAC-TT
1 TCAAAAACACTTT
* **
71882 TCCACCACACTTT
1 TCAAAAACACTTT
71895 TCAAAAACACTTT
1 TCAAAAACACTTT
* **
71908 TCCACCACACTTT
1 TCAAAAACACTTT
*
71921 TCAAAAACACTTC
1 TCAAAAACACTTT
71934 TCAAAAACA
1 TCAAAAACA
71943 ATACTAAACT
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
12 8 0.14
13 49 0.86
ACGTcount: A:0.40, C:0.30, G:0.02, T:0.28
Consensus pattern (13 bp):
TCAAAAACACTTT
Found at i:79241 original size:25 final size:25
Alignment explanation
Indices: 79207--79260 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
79197 TCTAGAAGCT
79207 TTCTCTGTTAAATTTCTTTCTCCAA
1 TTCTCTGTTAAATTTCTTTCTCCAA
79232 TTCTCTGTTAAATTTCTTTCTCCAA
1 TTCTCTGTTAAATTTCTTTCTCCAA
79257 TTCT
1 TTCT
79261 ACATTTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.54
Consensus pattern (25 bp):
TTCTCTGTTAAATTTCTTTCTCCAA
Found at i:84113 original size:11 final size:11
Alignment explanation
Indices: 84089--84200 Score: 73
Period size: 11 Copynumber: 10.2 Consensus size: 11
84079 AAAAAATTTA
84089 TTGTTA-TATT
1 TTGTTATTATT
*
84099 TTGTTATTGTT
1 TTGTTATTATT
*
84110 TTGTTGTTATT
1 TTGTTATTATT
* *
84121 TTGTTATCATA
1 TTGTTATTATT
*
84132 TTATTATTATT
1 TTGTTATTATT
*
84143 TTTTTATTATT
1 TTGTTATTATT
* * * *
84154 TGGATATTGTA
1 TTGTTATTATT
**
84165 TAATTATTATT
1 TTGTTATTATT
* * *
84176 TTATTGTTAATA
1 TTGTTATT-ATT
84188 TTGTTATTATT
1 TTGTTATTATT
84199 TT
1 TT
84201 AGAGGTATTT
Statistics
Matches: 74, Mismatches: 26, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
10 6 0.08
11 60 0.81
12 8 0.11
ACGTcount: A:0.22, C:0.01, G:0.10, T:0.67
Consensus pattern (11 bp):
TTGTTATTATT
Found at i:84962 original size:21 final size:21
Alignment explanation
Indices: 84911--84966 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
84901 TAAAATAAAA
*
84911 TAAATTCAAATCATATATATT
1 TAAATTCAAATAATATATATT
*
84932 TCAATT--AATAATATATA-T
1 TAAATTCAAATAATATATATT
84950 TAATATTCAAATAATAT
1 TAA-ATTCAAATAATAT
84967 TTATCACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.10
19 13 0.45
21 13 0.45
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTCAAATAATATATATT
Found at i:84988 original size:22 final size:21
Alignment explanation
Indices: 84958--85011 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
84948 ATTAATATTC
* *
84958 AAATAATATTTATCACAAAGAT
1 AAATGATATTTATCACAAA-AG
*
84980 AAATGATA-TTATCATAAAAG
1 AAATGATATTTATCACAAAAG
*
85000 AAATGTTATTTA
1 AAATGATATTTA
85012 ATTTTTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.30
21 12 0.44
22 7 0.26
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (21 bp):
AAATGATATTTATCACAAAAG
Found at i:85153 original size:29 final size:27
Alignment explanation
Indices: 85120--85185 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
85110 AATAAATTTA
*
85120 ATTTATTTAATTATACATTATCTATAACT
1 ATTTA-TTAATTATA-AATATCTATAACT
*
85149 ATTTATT-ATT-TAAATATTTATAACT
1 ATTTATTAATTATAAATATCTATAACT
85174 ATTTATTAATTA
1 ATTTATTAATTA
85186 AATATTCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 18 0.55
26 5 0.15
27 3 0.09
28 2 0.06
29 5 0.15
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTTATTAATTATAAATATCTATAACT
Found at i:85170 original size:25 final size:25
Alignment explanation
Indices: 85142--85191 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
85132 ATACATTATC
*
85142 TATAACTATTTATTATTTAAATATT
1 TATAACTATTTATTAATTAAATATT
85167 TATAACTATTTATTAATTAAATATT
1 TATAACTATTTATTAATTAAATATT
85192 CTAAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TATAACTATTTATTAATTAAATATT
Found at i:86037 original size:16 final size:16
Alignment explanation
Indices: 86013--86043 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86003 ACTTATTATA
*
86013 AATAGATTTCATAAAT
1 AATAAATTTCATAAAT
86029 AATAAATTTCATAAA
1 AATAAATTTCATAAA
86044 CATTTTTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
AATAAATTTCATAAAT
Found at i:89268 original size:16 final size:16
Alignment explanation
Indices: 89247--89281 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
89237 TCTCATTGAT
89247 AAACATAGAAAAAAAC
1 AAACATAGAAAAAAAC
*
89263 AAACATAGAAACAAAC
1 AAACATAGAAAAAAAC
89279 AAA
1 AAA
89282 TTATGTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.74, C:0.14, G:0.06, T:0.06
Consensus pattern (16 bp):
AAACATAGAAAAAAAC
Found at i:91224 original size:43 final size:43
Alignment explanation
Indices: 91005--91224 Score: 225
Period size: 43 Copynumber: 5.2 Consensus size: 43
90995 TTATTTGGAA
*
91005 AAACGCCGTTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
* *
91048 AAACACTGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
* * * *
91091 AAATGTCGTTAAAAAACATGGTCTTTAGCGGCGCTTTT-TCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCT-CAC
* *** ** *
91134 AAACGCTGCTGTCGCTAA-A-GAAC-AT-GCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAG--AACATGGTCTTTAGCGGCGCTTTTCTCAC
* * *
91175 AAACGCCGCTAATGAACATGGTCTTTAGCGGCTCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
91218 AAACGCC
1 AAACGCC
91225 ACTATACCAG
Statistics
Matches: 140, Mismatches: 29, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 26 0.19
42 4 0.03
43 104 0.74
44 1 0.01
45 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
Found at i:92893 original size:19 final size:19
Alignment explanation
Indices: 92838--92900 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
92828 TCATTTGTTA
*
92838 ATTTTTTATAATTTTTTATG
1 ATTTTTTATTA-TTTTTATG
*
92858 -TTTTATGTA-TATATTTATG
1 ATTTT-T-TATTATTTTTATG
*
92877 ATTTTTTATTATTTTTATA
1 ATTTTTTATTATTTTTATG
92896 ATTTT
1 ATTTT
92901 CTCTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.06
19 25 0.71
20 6 0.17
21 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
ATTTTTTATTATTTTTATG
Found at i:94502 original size:30 final size:30
Alignment explanation
Indices: 94466--94527 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
94456 GGAAAAAAGG
94466 TATGTGAATCACGAATAAGCCAACCAATGA
1 TATGTGAATCACGAATAAGCCAACCAATGA
94496 TATGTGAATCACGAATAAGCCAACCAATGA
1 TATGTGAATCACGAATAAGCCAACCAATGA
94526 TA
1 TA
94528 AAGGCAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (30 bp):
TATGTGAATCACGAATAAGCCAACCAATGA
Found at i:95768 original size:22 final size:23
Alignment explanation
Indices: 95732--95774 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
95722 CATCAAAAAA
95732 TTAAAAATTGATCA-TTAAATTT
1 TTAAAAATTGATCATTTAAATTT
**
95754 TTAAAAATTTTTCATTTAAAT
1 TTAAAAATTGATCATTTAAAT
95775 CATTTATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAAAATTGATCATTTAAATTT
Found at i:97041 original size:41 final size:41
Alignment explanation
Indices: 96987--97243 Score: 300
Period size: 41 Copynumber: 6.3 Consensus size: 41
96977 GCGCTATTAC
* * * *
96987 TGCTCTGACCTTTAGTGACGCTTTCCCTTAAGCACCGCTAT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTAT
* * * * *
97028 TGCTTTGATCTTTAGCGACGCTTGCCCATAAGCGTCGCTAT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTAT
* * *
97069 TGCTCTGACCTTTAGCGGTGCTTTCCCATAAGCGCTGCAAT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTAT
* * * *
97110 TACACTTACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTGT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTAT
* * * *
97151 TGCTCTGATCTTTAGCGGCGCTTTCCTATAAGCGTCGCTGT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTAT
* * *
97192 TGCTCTGACCTTTAGCAGCGCTTTTCCATAAGCGCAGCTAT
1 TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTAT
97233 TGCTCT-ACCTT
1 TGCTCTGACCTT
97244 CTGCGGCATT
Statistics
Matches: 181, Mismatches: 35, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
40 5 0.03
41 176 0.97
ACGTcount: A:0.16, C:0.30, G:0.20, T:0.33
Consensus pattern (41 bp):
TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTAT
Found at i:97173 original size:123 final size:123
Alignment explanation
Indices: 96994--97226 Score: 349
Period size: 123 Copynumber: 1.9 Consensus size: 123
96984 TACTGCTCTG
* * *
96994 ACCTTTAGTGACGCTTTCCCTTAAGCACCGCTATTGCTTTGATCTTTAGCGACGCTTGCCCATAA
1 ACCTTTAGCGACGCTTTCCCATAAGCACCGCTATTGCTCTGATCTTTAGCGACGCTTGCCCATAA
* *
97059 GCGTCGCTATTGCTCTGACCTTTAGCGGTGCTTTCCCATAAGCGCTGCAATTACACTT
66 GCGTCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGCGCTGCAATTACACTT
* * * * * *
97117 ACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTGTTGCTCTGATCTTTAGCGGCGCTTTCCTATAA
1 ACCTTTAGCGACGCTTTCCCATAAGCACCGCTATTGCTCTGATCTTTAGCGACGCTTGCCCATAA
* *
97182 GCGTCGCTGTTGCTCTGACCTTTAGCAGCGCTTTTCCATAAGCGC
66 GCGTCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGCGC
97227 AGCTATTGCT
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.33
Consensus pattern (123 bp):
ACCTTTAGCGACGCTTTCCCATAAGCACCGCTATTGCTCTGATCTTTAGCGACGCTTGCCCATAA
GCGTCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGCGCTGCAATTACACTT
Found at i:98630 original size:25 final size:25
Alignment explanation
Indices: 98592--98686 Score: 147
Period size: 25 Copynumber: 3.8 Consensus size: 25
98582 CGAAGTACTT
* *
98592 AACAGAAGCGCATAAGTCCT-GAGGA
1 AACAGAAGCACATAAGTGCTGGA-GA
98617 AACAGAAGCACATAAGTGCTGGAGA
1 AACAGAAGCACATAAGTGCTGGAGA
98642 AACAGAAGCACATAAGTGCTGGAGA
1 AACAGAAGCACATAAGTGCTGGAGA
*
98667 AACAAAAGCACATAAGTGCT
1 AACAGAAGCACATAAGTGCT
98687 AGGAAATAGT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
25 64 0.97
26 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (25 bp):
AACAGAAGCACATAAGTGCTGGAGA
Found at i:98758 original size:22 final size:22
Alignment explanation
Indices: 98699--98767 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
98689 GAAATAGTAG
* *
98699 GCACACACAGTGCTAAACAGAA
1 GCACACACAGTGTTGAACAGAA
* *
98721 GCACACACAGTATTGAATAGAA
1 GCACACACAGTGTTGAACAGAA
*
98743 GCACACATAGTGTTGAACAGTAA
1 GCACACACAGTGTTGAACAG-AA
98766 GC
1 GC
98768 GTGCTAGCGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (22 bp):
GCACACACAGTGTTGAACAGAA
Found at i:100744 original size:25 final size:25
Alignment explanation
Indices: 100708--100758 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
100698 CTTCATCTTC
*
100708 TCTAATAAAAACTTTTCTACAAATT
1 TCTAATAAAAACTTTACTACAAATT
*
100733 TCTAA-AATAAACTTTACTTCAAATT
1 TCTAATAA-AAACTTTACTACAAATT
100758 T
1 T
100759 TTTTCCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (25 bp):
TCTAATAAAAACTTTACTACAAATT
Found at i:101027 original size:22 final size:20
Alignment explanation
Indices: 101001--101046 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
100991 TTTATTTTTG
*
101001 AATTTTAACTATATTTAATCTT
1 AATTTTAAATAT-TTTAAT-TT
*
101023 AATTTTAAATATTTTTATTT
1 AATTTTAAATATTTTAATTT
101043 AATT
1 AATT
101047 AAAAACGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 11 0.50
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTTTAAATATTTTAATTT
Found at i:105948 original size:34 final size:35
Alignment explanation
Indices: 105910--105980 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 35
105900 CCATACTCCC
*
105910 TTTAAATTTATTTTAAA-TTAAATTTGTTTAAAAT
1 TTTAAATTTATTTTAAATTTAAATTTATTTAAAAT
*
105944 TTTAAATTTATTTTAAATTTAAATTTATTTTAAAT
1 TTTAAATTTATTTTAAATTTAAATTTATTTAAAAT
105979 TT
1 TT
105981 AATTTAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 17 0.50
35 17 0.50
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAAAT
Found at i:105966 original size:17 final size:17
Alignment explanation
Indices: 105910--105986 Score: 113
Period size: 16 Copynumber: 4.6 Consensus size: 17
105900 CCATACTCCC
105910 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
105927 -TTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
105943 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
105961 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
105978 TTT-AATTTA
1 TTTAAATTTA
105987 AGTTTAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
16 20 0.37
17 20 0.37
18 14 0.26
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:105992 original size:17 final size:16
Alignment explanation
Indices: 105914--105994 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 16
105904 ACTCCCTTTA
* *
105914 AATTTATTTTAAATTA
1 AATTTAGTTTAAATTT
105930 AATTT-GTTTAAAATTTT
1 AATTTAGTTT-AAA-TTT
*
105947 AAATTTATTTTAAATTT
1 -AATTTAGTTTAAATTT
*
105964 AAATTTATTTTAAATTT
1 -AATTTAGTTTAAATTT
105981 AATTTAAGTTTAAA
1 AATTT-AGTTTAAA
105995 ATTATTTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.05
16 13 0.23
17 29 0.52
18 8 0.14
19 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
AATTTAGTTTAAATTT
Found at i:105993 original size:11 final size:11
Alignment explanation
Indices: 105959--105993 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
105949 ATTTATTTTA
105959 AATTTAAATTT
1 AATTTAAATTT
*
105970 ATTTTAAATTT
1 AATTTAAATTT
*
105981 AATTTAAGTTT
1 AATTTAAATTT
105992 AA
1 AA
105994 AATTATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:107941 original size:30 final size:29
Alignment explanation
Indices: 107898--108334 Score: 299
Period size: 30 Copynumber: 14.7 Consensus size: 29
107888 AGGTCCCCGA
107898 AACTTCCAAAAATCCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
107927 AAC-TCCTAAAAAATCCCATTTTAAACCTCG
1 AACTTCC--AAAAATCCCATTTTTACCCTCG
* * *
107957 AAACTTCAAAAAATCCCATTTTTAACCCCCAA
1 -AACTTCCAAAAATCCCATTTTT-ACCCTC-G
* * *
107989 AACTTCTAAAAATCCTATTTTGGA-CCTCG
1 AACTTCCAAAAATCCCATTTT-TACCCTCG
*
108018 AACCTTCCAAAAATTACCA-TTTTACCCTCG
1 AA-CTTCCAAAAA-TCCCATTTTTACCCTCG
* *
108048 AACTTCCAAAAATCCCAATTTTGACCCT-A
1 AACTTCCAAAAATCCC-ATTTTTACCCTCG
* * *
108077 AACCTTCCAAAATTACCA-TTTTACCCCCCG
1 AA-CTTCCAAAAATCCCATTTTTA-CCCTCG
108107 AACTTCCAAAAATCCCATTTTTTA-CCTCG
1 AACTTCCAAAAATCCCA-TTTTTACCCTCG
* * *
108136 AACCTTTCAAAAATTACCA-TTTTACCCCCG
1 AA-CTTCCAAAAA-TCCCATTTTTACCCTCG
108166 AACTTCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
* * * *
108195 AACCTTTCGAAAATTACCA-TTTTACCC-CTA
1 AA-C-TTCCAAAAATCCCATTTTTACCCTC-G
* *
108225 AACTTCCAAAATTCCCATTTTTGACCC-AG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
* *
108254 AACCTTTCAAAAATTACCA-TTTTAGCCC-CG
1 AA-CTTCCAAAAA-TCCCATTTTTA-CCCTCG
* *
108284 AACTTCCAAAAATCCCAATTTTGACTC-CG
1 AACTTCCAAAAATCCC-ATTTTTACCCTCG
* *
108313 AACCTTCCAAAACTACCATTTT
1 AA-CTTCCAAAAATCCCATTTT
108335 GCCCCCGTGC
Statistics
Matches: 323, Mismatches: 51, Indels: 68
0.73 0.12 0.15
Matches are distributed among these distances:
28 29 0.09
29 97 0.30
30 141 0.44
31 54 0.17
32 2 0.01
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCTCG
Found at i:108081 original size:59 final size:59
Alignment explanation
Indices: 107900--108341 Score: 447
Period size: 59 Copynumber: 7.5 Consensus size: 59
107890 GTCCCCGAAA
* * * * *
107900 CTTCCAAAAA-TCCCATTTTTACCCTCGAAC-TCCTAAAAAATCCC-ATTTTAAACCTCGAAA
1 CTTCCAAAAATTACCA-TTTTACCCCCGAACTTCC--AAAAATCCCAATTTTGACCCT-GAAC
* * * * *
107960 CTT-CAAAAAATCCCATTTTTAACCCCCAAAACTTCTAAAAAT-CCTATTTTGGA-CCTCGAAC
1 CTTCCAAAAATTACCA-TTTT-ACCCCC-GAACTTCCAAAAATCCCAATTTT-GACCCT-GAAC
* *
108021 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCTAAAC
1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCTGAAC
* *
108080 CTTCC-AAAATTACCATTTTACCCCCCGAACTTCCAAAAATCCCATTTTTTA-CCTCGAAC
1 CTTCCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAATCCCAATTTTGACCCT-GAAC
* *
108139 CTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAAC
1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCT-GAAC
* * ** * * *
108198 CTTTCGAAAATTACCATTTTACCCCTAAACTTCCAAAATTCCCATTTTTGACCCAGAAC
1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCTGAAC
* *
108257 CTTTCAAAAATTACCATTTTAGCCCCGAACTTCCAAAAATCCCAATTTTGACTCC-GAAC
1 CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGAC-CCTGAAC
* *
108316 CTTCC-AAAACTACCATTTTGCCCCCG
1 CTTCCAAAAATTACCATTTTACCCCCG
108342 TGCATCCGAA
Statistics
Matches: 335, Mismatches: 33, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
58 36 0.11
59 204 0.61
60 49 0.15
61 30 0.09
62 14 0.04
63 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (59 bp):
CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCTGAAC
Found at i:108147 original size:118 final size:118
Alignment explanation
Indices: 107916--108340 Score: 506
Period size: 118 Copynumber: 3.6 Consensus size: 118
107906 AAAATCCCAT
* * * * *
107916 TTTTACCCTCGAAC-TCCTAAAAAATCCC-ATTTTAAACCTCGAAA-CTTCAAAAAATCCCATTT
1 TTTTACCCTCGAACTTCC--AAAAATCCCAATTTT-GACC-CTAAACCTTCCAAAATTACCA-TT
* * * *
107978 TTAACCCCCAAAACTTCTAAAAATCCTATTTTGGACCTCGAACCTTCCAAAAATTACCA
61 TT-ACCCCCAAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTTCAAAAATTACCA
108037 TTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCTAAACCTTCCAAAATTACCATTTTACC
1 TTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCTAAACCTTCCAAAATTACCATTTTACC
** *
108102 CCCCGAACTTCCAAAAATCCCATTTTTTACCTCGAACCTTTCAAAAATTACCA
66 CCCAAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTTCAAAAATTACCA
* * * *
108155 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAACCTTTCGAAAATTACCATTTTA
1 TTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCT-AAACC-TTCCAAAATTACCATTTTA
* *
108219 -CCCCTAAACTTCCAAAATTCCCATTTTTGACC-CAGAACCTTTCAAAAATTACCA
64 CCCCCAAAACTTCCAAAAATCCCATTTTTGACCTC-GAACCTTTCAAAAATTACCA
* * *
108273 TTTTAGCCC-CGAACTTCCAAAAATCCCAATTTTGACTCC-GAACCTTCCAAAACTACCATTTTG
1 TTTTA-CCCTCGAACTTCCAAAAATCCCAATTTTGAC-CCTAAACCTTCCAAAATTACCATTTTA
108336 CCCCC
64 CCCCC
108341 GTGCATCCGA
Statistics
Matches: 270, Mismatches: 24, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
117 20 0.07
118 173 0.64
119 29 0.11
120 26 0.10
121 19 0.07
122 3 0.01
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (118 bp):
TTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCTAAACCTTCCAAAATTACCATTTTACC
CCCAAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTTCAAAAATTACCA
Found at i:108335 original size:29 final size:28
Alignment explanation
Indices: 108016--108339 Score: 251
Period size: 29 Copynumber: 11.0 Consensus size: 28
108006 TTTTGGACCT
108016 CGAACCTTCCAAAAATTACCATTTTACCC
1 CGAACCTTCC-AAAATTACCATTTTACCC
* *
108045 TCGAA-CTTCCAAAAATCCCAATTTTGACCC
1 -CGAACCTTCCAAAATTACC-ATTTT-ACCC
**
108075 TAAACCTTCCAAAATTACCATTTTACCCCC
1 CGAACCTTCCAAAATTACCATTTTA--CCC
* * *
108105 CGAA-CTTCCAAAAATCCCATTTTTTACCT
1 CGAACCTTCCAAAATTACCA--TTTTACCC
*
108134 CGAACCTTTCAAAAATTACCATTTTACCCC
1 CGAACC-TTCCAAAATTACCATTTTA-CCC
* * *
108164 CGAA-CTTCCAAAAATCCCATTTTTGACCT
1 CGAACCTTCCAAAATTACCA-TTTT-ACCC
*
108193 CGAACCTTTCGAAAATTACCATTTTACCC
1 CGAACC-TTCCAAAATTACCATTTTACCC
* * *
108222 CTAAACTTCCAAAATTCCCATTTTTGACCC
1 CGAACCTTCCAAAATTACCA-TTTT-ACCC
* *
108252 AGAACCTTTCAAAAATTACCATTTTAGCCC
1 CGAACC-TTCCAAAATTACCATTTTA-CCC
* * *
108282 CGAA-CTTCCAAAAATCCCAATTTTGACTC
1 CGAACCTTCCAAAATTACC-ATTTT-ACCC
* *
108311 CGAACCTTCCAAAACTACCATTTTGCCC
1 CGAACCTTCCAAAATTACCATTTTACCC
108339 C
1 C
108340 CGTGCATCCG
Statistics
Matches: 232, Mismatches: 41, Indels: 44
0.73 0.13 0.14
Matches are distributed among these distances:
28 44 0.19
29 81 0.35
30 68 0.29
31 39 0.17
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (28 bp):
CGAACCTTCCAAAATTACCATTTTACCC
Found at i:116015 original size:17 final size:17
Alignment explanation
Indices: 115993--116031 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
115983 GGTGGAGAAT
* *
115993 TTGTTCGTTGAGAGTTC
1 TTGTTCGTAGAGAATTC
116010 TTGTTCGTAGAGAATTC
1 TTGTTCGTAGAGAATTC
116027 TTGTT
1 TTGTT
116032 AAGGTGGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
TTGTTCGTAGAGAATTC
Found at i:121561 original size:22 final size:20
Alignment explanation
Indices: 121524--121569 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
121514 ATCAAAAATA
*
121524 AAAAATAAAGACTAATAAAG
1 AAAAATAAAGAATAATAAAG
*
121544 AAAAATAAATGCAATAATAAAT
1 AAAAATAAA-G-AATAATAAAG
121566 AAAA
1 AAAA
121570 CCATTAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 12 0.55
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAAATAAAGAATAATAAAG
Found at i:132193 original size:9 final size:9
Alignment explanation
Indices: 132181--132307 Score: 51
Period size: 9 Copynumber: 13.4 Consensus size: 9
132171 TAAAATATAA
132181 AAAAATTAT
1 AAAAATTAT
132190 AAAAACTTAT
1 AAAAA-TTAT
*
132200 AATAAA-TAA
1 AA-AAATTAT
132209 ATAAAATTATT
1 A-AAAATTA-T
132220 AAAAATTAT
1 AAAAATTAT
* * *
132229 ATAATTTAA
1 AAAAATTAT
*
132238 AAAATATGTTT
1 AAAA-AT-TAT
* * *
132249 AGAATTTTT
1 AAAAATTAT
*
132258 AAAAATAAT
1 AAAAATTAT
**
132267 -AATGTTAT
1 AAAAATTAT
*
132275 AAAAAACTAT
1 -AAAAATTAT
132285 AAAAATTATT
1 AAAAATTA-T
*
132295 AAAAATTTT
1 AAAAATTAT
132304 AAAA
1 AAAA
132308 TATTGTGATT
Statistics
Matches: 85, Mismatches: 23, Indels: 20
0.66 0.18 0.16
Matches are distributed among these distances:
8 5 0.06
9 41 0.48
10 31 0.36
11 8 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:132199 original size:10 final size:10
Alignment explanation
Indices: 132180--132229 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
132170 TTAAAATATA
132180 AAAAAATTAT
1 AAAAAATTAT
*
132190 AAAAACTTAT
1 AAAAAATTAT
*
132200 AATAAA-TA-
1 AAAAAATTAT
132208 AATAAAATTAT
1 AA-AAAATTAT
*
132219 TAAAAATTAT
1 AAAAAATTAT
132229 A
1 A
132230 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
8 2 0.06
9 5 0.16
10 23 0.74
11 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:132238 original size:29 final size:28
Alignment explanation
Indices: 132177--132242 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
132167 TTTTTAAAAT
132177 ATAAAAAAATTATAAAAACTTATAATAA
1 ATAAAAAAATTATAAAAACTTATAATAA
132205 ATAAATAAAATTATTAAAAA-TTAT-ATAA
1 ATAAA-AAAATTA-TAAAAACTTATAATAA
* *
132233 TTTAAAAAAT
1 ATAAAAAAAT
132243 ATGTTTAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 5 0.15
28 12 0.35
29 11 0.32
30 6 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAAAAAATTATAAAAACTTATAATAA
Found at i:145861 original size:30 final size:31
Alignment explanation
Indices: 145825--145889 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
145815 TATGTTTAAT
*
145825 AAAACAGTCACTCAA-CT-TTGAAAATGTGAC
1 AAAACAGTCACTAAAGCTATTGAAAA-GTGAC
*
145855 AAAACAGTCACTAAAGTTATTGAAAAGTGAC
1 AAAACAGTCACTAAAGCTATTGAAAAGTGAC
145886 AAAA
1 AAAA
145890 TAATCCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 14 0.45
31 10 0.32
32 7 0.23
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (31 bp):
AAAACAGTCACTAAAGCTATTGAAAAGTGAC
Found at i:146034 original size:27 final size:27
Alignment explanation
Indices: 145979--146034 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
145969 TTCTTCCTTT
*
145979 TTCATCCACTACCACTTATTCCTCGTC
1 TTCATCCACTACCACTTATTCCTCATC
* * *
146006 TTCATCCACTACCATTTTTTTCTCATC
1 TTCATCCACTACCACTTATTCCTCATC
146033 TT
1 TT
146035 TTTCTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.36, G:0.02, T:0.45
Consensus pattern (27 bp):
TTCATCCACTACCACTTATTCCTCATC
Found at i:146866 original size:27 final size:26
Alignment explanation
Indices: 146819--146873 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
146809 TTAAAGAAAA
146819 AAGATGAGAAAAAGTGATAGTGGATG
1 AAGATGAGAAAAAGTGATAGTGGATG
* *
146845 AAGATGAGGAATAAGTGGTAGTGGATG
1 AAGATGA-GAAAAAGTGATAGTGGATG
146872 AA
1 AA
146874 AAAGGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (26 bp):
AAGATGAGAAAAAGTGATAGTGGATG
Found at i:146995 original size:31 final size:30
Alignment explanation
Indices: 146957--147023 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
146947 AAGAGGATTA
*
146957 TTTTGTCAC-TTTTCGATAACTTTAGTGACTG
1 TTTTGTCACATTTT-GA-AACTTGAGTGACTG
* *
146988 TTTTGTCACATTTTTAAAGTTGAGTGACTG
1 TTTTGTCACATTTTGAAACTTGAGTGACTG
147018 TTTTGT
1 TTTTGT
147024 TAAACGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 18 0.56
31 10 0.31
32 4 0.12
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (30 bp):
TTTTGTCACATTTTGAAACTTGAGTGACTG
Found at i:154861 original size:101 final size:101
Alignment explanation
Indices: 154686--154886 Score: 368
Period size: 101 Copynumber: 2.0 Consensus size: 101
154676 TGTGGTATCG
154686 AGAAGTCGCAAAAGAGAATATAGGGGTTGGGATTAAAGAAGTCATTATAATGCTTGAACATGATT
1 AGAAGTCGCAAAAGAGAATATAGGGGTTGGGATTAAAGAAGTCATTATAATGCTTGAACATGATT
154751 GATCTCATTGTTTTTATTGGTTGTAGT-AGCTCTCCA
66 GATCTCATTGTTTTTATTGGTTGTAGTCA-CTCTCCA
*
154787 AGAAGTCGCAAAAGAGAATATAGGGGTTGGGATTATAGAAGTCATTATAATGCTTGAACATGATT
1 AGAAGTCGCAAAAGAGAATATAGGGGTTGGGATTAAAGAAGTCATTATAATGCTTGAACATGATT
*
154852 GATCTCATTGTTTTTGTTGGTTGTAGTCACTCTCC
66 GATCTCATTGTTTTTATTGGTTGTAGTCACTCTCC
154887 GGGTTTTTAA
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
101 96 0.99
102 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (101 bp):
AGAAGTCGCAAAAGAGAATATAGGGGTTGGGATTAAAGAAGTCATTATAATGCTTGAACATGATT
GATCTCATTGTTTTTATTGGTTGTAGTCACTCTCCA
Found at i:155652 original size:8 final size:8
Alignment explanation
Indices: 155641--155665 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
155631 TCGTTTTAAA
155641 AAAAAAAG
1 AAAAAAAG
155649 AAAAAAAG
1 AAAAAAAG
155657 AAAAAAAG
1 AAAAAAAG
155665 A
1 A
155666 GATACCTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:155955 original size:29 final size:29
Alignment explanation
Indices: 155922--155977 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
155912 TTTTTTAAAA
*
155922 AAAATTCT-TAAAAAATTTCATAAAATTCT
1 AAAATTCTCTAAAAAATAT-ATAAAATTCT
*
155951 AAAATTTTCTAAAAAATATATAAAATT
1 AAAATTCTCTAAAAAATATATAAAATT
155978 TCAAGCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATTCTCTAAAAAATATATAAAATTCT
Found at i:161062 original size:131 final size:131
Alignment explanation
Indices: 160828--161090 Score: 517
Period size: 131 Copynumber: 2.0 Consensus size: 131
160818 TTTCTGTATT
160828 ACAATCTAACCATGTACCACTTAGTATTAGTTAAATATTAGATAATCAATGAGTCAATATTTGCT
1 ACAATCTAACCATGTACCACTTAGTATTAGTTAAATATTAGATAATCAATGAGTCAATATTTGCT
*
160893 TCCTTTTTGCTTTGCGTGCAAAAACCGTTGAGGACATTATATAAAGAATATTAATGTAATTAATG
66 TCCTTTTTGCTTTGCGTGCAAAAACCGTTGAAGACATTATATAAAGAATATTAATGTAATTAATG
160958 C
131 C
160959 ACAATCTAACCATGTACCACTTAGTATTAGTTAAATATTAGATAATCAATGAGTCAATATTTGCT
1 ACAATCTAACCATGTACCACTTAGTATTAGTTAAATATTAGATAATCAATGAGTCAATATTTGCT
161024 TCCTTTTTGCTTTGCGTGCAAAAACCGTTGAAGACATTATATAAAGAATATTAATGTAATTAATG
66 TCCTTTTTGCTTTGCGTGCAAAAACCGTTGAAGACATTATATAAAGAATATTAATGTAATTAATG
161089 C
131 C
161090 A
1 A
161091 TTATTCTATT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 131 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (131 bp):
ACAATCTAACCATGTACCACTTAGTATTAGTTAAATATTAGATAATCAATGAGTCAATATTTGCT
TCCTTTTTGCTTTGCGTGCAAAAACCGTTGAAGACATTATATAAAGAATATTAATGTAATTAATG
C
Found at i:162273 original size:43 final size:43
Alignment explanation
Indices: 162234--162346 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
162224 TATTTATTTT
*
162234 CACCATTTGAGCAGTTTATCTACAATGTTGAGTGGTTTATCCA
1 CACCATTTGAGCAGTTTATCTACAACGTTGAGTGGTTTATCCA
* * * * *
162277 CATCGTTTGAGTAGTTTATCTGCACCGTTGAGTGGTTTATCCA
1 CACCATTTGAGCAGTTTATCTACAACGTTGAGTGGTTTATCCA
*
162320 CACCGTATT-AGCAGCTTTTATCTACAA
1 CACCAT-TTGAGCAG--TTTATCTACAA
162347 AAAATGACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
43 46 0.81
44 2 0.04
45 9 0.16
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (43 bp):
CACCATTTGAGCAGTTTATCTACAACGTTGAGTGGTTTATCCA
Found at i:162293 original size:22 final size:21
Alignment explanation
Indices: 162240--162321 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
162230 TTTTCACCAT
* *
162240 TTGAGCAGTTTATCTACAAT-G
1 TTGAGTAGTTTATCCAC-ATCG
*
162261 TTGAGTGGTTTATCCACATCG
1 TTGAGTAGTTTATCCACATCG
** *
162282 TTTGAGTAGTTTATCTGCACCG
1 -TTGAGTAGTTTATCCACATCG
*
162304 TTGAGTGGTTTATCCACA
1 TTGAGTAGTTTATCCACA
162322 CCGTATTAGC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 2 0.04
21 30 0.61
22 17 0.35
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (21 bp):
TTGAGTAGTTTATCCACATCG
Found at i:162323 original size:21 final size:21
Alignment explanation
Indices: 162260--162325 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
162250 TATCTACAAT
*
162260 GTTGAGTGGTTTATCCACATC
1 GTTGAGTGGTTTATCCACACC
* **
162281 GTTTGAGTAGTTTATCTGCACC
1 G-TTGAGTGGTTTATCCACACC
162303 GTTGAGTGGTTTATCCACACC
1 GTTGAGTGGTTTATCCACACC
162324 GT
1 GT
162326 ATTAGCAGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (21 bp):
GTTGAGTGGTTTATCCACACC
Found at i:164945 original size:23 final size:25
Alignment explanation
Indices: 164914--164959 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
164904 TGCCCATATT
*
164914 ATTTTTTTTATTTT-TTT-AATAAA
1 ATTTATTTTATTTTATTTGAATAAA
164937 ATTTATTTTATTTTATTTGAATA
1 ATTTATTTTATTTTATTTGAATA
164960 TTTAATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 3 0.15
25 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTATTTTATTTTATTTGAATAAA
Found at i:180300 original size:96 final size:96
Alignment explanation
Indices: 180128--180319 Score: 248
Period size: 96 Copynumber: 2.0 Consensus size: 96
180118 TTTTTGGGAA
* **
180128 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGACGCAATATTTCA
1 AAGGATATTCGATCATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAATATTTCA
*
180193 GAATCGAAGAT-AAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTGCCTCGATT
* * *
180224 AAGGGTATTCGATCATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAA-ATTTTC
1 AAGGATATTCGATCATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAATA-TTTC
*
180288 -GAAATTCG-AGATAAAAGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAAGAACATTGCCTCGATT
180320 TTAAAGTCTT
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 2 0.02
96 76 0.90
97 6 0.07
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATCATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAATATTTCA
GAATCGAAGATAAAAGAACATTGCCTCGATT
Found at i:180742 original size:30 final size:29
Alignment explanation
Indices: 180699--180844 Score: 204
Period size: 29 Copynumber: 5.0 Consensus size: 29
180689 TTTGGACACC
180699 CGAGGGT-AAAATGGTAATTTTTGGAAGTT
1 CGAGGGTAAAAATGG-AATTTTTGGAAGTT
** *
180728 TTAGGTTAAAAATGGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTT
* *
180757 CGAGGCTAAAAATGGAGTTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTT
*
180786 CGAGGGTAAAAATGAGATTTTTTGGAAGTT
1 CGAGGGTAAAAATG-GAATTTTTGGAAGTT
*
180816 CGAGGGTAAAAATAGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGGAATTTTTGGAAGTT
180845 TCAAGGTGCA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
29 70 0.67
30 34 0.33
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
CGAGGGTAAAAATGGAATTTTTGGAAGTT
Found at i:180815 original size:59 final size:58
Alignment explanation
Indices: 180706--180844 Score: 197
Period size: 59 Copynumber: 2.4 Consensus size: 58
180696 ACCCGAGGGT
** *
180706 AAAATGGTAATTTTTGGAAGTTTTAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGCTA
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCGAGGCTA
* * *
180765 AAAATGGAGTTTTTGGAAGTTCGAGGGTAAAAATGAGATTTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATG-GAATTTTTGGAAGTTCGAGGCTA
*
180824 AAAATAGAATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
180845 TCAAGGTGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 24 0.34
59 47 0.66
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCGAGGCTA
Found at i:181241 original size:29 final size:28
Alignment explanation
Indices: 181209--181271 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
181199 AAAATGAGAC
*
181209 TTTTCGGATACCCGAGGGAAAAATGGTAA
1 TTTT-GGATACCCGAGGGAAAAATGGAAA
* * **
181238 TTTTGGATTCTCGAGGGTGAAATGGAAA
1 TTTTGGATACCCGAGGGAAAAATGGAAA
181266 TTTTGG
1 TTTTGG
181272 GAAAATTTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGAGGGAAAAATGGAAA
Found at i:181384 original size:29 final size:29
Alignment explanation
Indices: 181221--181385 Score: 87
Period size: 28 Copynumber: 5.8 Consensus size: 29
181211 TTCGGATACC
*
181221 CGAGGGAAAAATGGTAA-TTTTGGA-TTCT
1 CGAGGGTAAAATGGTAATTTTTGGACTT-T
* * * *
181249 CGAGGGTGAAATGGAAATTTTGGGAAAATTT
1 CGAGGGTAAAATGGTAATTTTTGG--ACTTT
* * *
181280 -G-GGGTTAAAAT-GAAATTTTTAGACATT
1 CGAGGG-TAAAATGGTAATTTTTGGACTTT
* * *
181307 CG-GGGTAACAGGGTAA-TTTTGAGAGTTT
1 CGAGGGTAAAATGGTAATTTTTG-GACTTT
* *
181335 CGA-AGTCGAAAATGG-AGTTTTTGGACTTT
1 CGAGGGT--AAAATGGTAATTTTTGGACTTT
181364 CGAGGGTAAAATGGTAATTTTT
1 CGAGGGTAAAATGGTAATTTTT
181386 AGAAGTTTTA
Statistics
Matches: 101, Mismatches: 22, Indels: 27
0.67 0.15 0.18
Matches are distributed among these distances:
27 11 0.11
28 36 0.36
29 32 0.32
30 18 0.18
31 2 0.02
32 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (29 bp):
CGAGGGTAAAATGGTAATTTTTGGACTTT
Found at i:181415 original size:30 final size:30
Alignment explanation
Indices: 181371--181688 Score: 289
Period size: 30 Copynumber: 10.7 Consensus size: 30
181361 TTTCGAGGGT
181371 AAAATGGTAATTTTTAGAAGTTTTAGGGTCA
1 AAAATGG-AATTTTTAGAAGTTTTAGGGTCA
* *
181402 AAAATGGAATTTTTATAAGTTTTGGGGTCA
1 AAAATGGAATTTTTAGAAGTTTTAGGGTCA
* *
181432 AAAAT-GAGATTTTTGGAAGCTTTGAGGGT-A
1 AAAATGGA-ATTTTTAGAAG-TTTTAGGGTCA
181462 AAAATGGAATTTTTAAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTT-AGAAGTTTTAGGGTCA
* * * *
181493 AAAATGGGATTTTTGGAAGTTTGA-GGTTA
1 AAAATGGAATTTTTAGAAGTTTTAGGGTCA
* *
181522 AAAATGAAATTTTTAGAAGTTTT-GGTGTTA
1 AAAATGGAATTTTTAGAAGTTTTAGG-GTCA
* * **
181552 AAAATGGGATTCTT-GAAAGTTTGGGGGT-A
1 AAAATGGAATTTTTAG-AAGTTTTAGGGTCA
* *
181581 AAAATAG-ATTTTTAGAAGTTTT-GGGTTA
1 AAAATGGAATTTTTAGAAGTTTTAGGGTCA
* * **
181609 AAAATGGGATTTTTGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTAGAAGTTTTAGGGTCA
*
181638 AAAATGGAATTTTTAGAAG-TTTCGGTGTCA
1 AAAATGGAATTTTTAGAAGTTTTAGG-GTCA
*
181668 AAAAT-GAGATTTTTGGAAGTT
1 AAAATGGA-ATTTTTAGAAGTT
181689 CGAGGATAAA
Statistics
Matches: 239, Mismatches: 31, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
27 4 0.02
28 22 0.09
29 70 0.29
30 106 0.44
31 37 0.15
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTAGAAGTTTTAGGGTCA
Found at i:181572 original size:59 final size:58
Alignment explanation
Indices: 181371--181707 Score: 406
Period size: 59 Copynumber: 5.7 Consensus size: 58
181361 TTTCGAGGGT
* * * * *
181371 AAAATGGTAATTTTTAGAAGTTTTAGGGTCAAAAATGGAATTTTTATAAGTTTTGGGGTCA
1 AAAATGG-GATTTTTGGAAGTTTGAGGGT-AAAAATGAAATTTTTAGAAGTTTT-GGGTCA
* *
181432 AAAATGAGATTTTTGGAAGCTTTGAGGGTAAAAATGGAATTTTTAAGAAGTTTTAGGGTCA
1 AAAATGGGATTTTTGGAAG-TTTGAGGGTAAAAATGAAATTTTT-AGAAGTTTT-GGGTCA
* *
181493 AAAATGGGATTTTTGGAAGTTTGAGGTTAAAAATGAAATTTTTAGAAGTTTTGGTGTTA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTAGAAGTTTTGG-GTCA
* * * * *
181552 AAAATGGGATTCTTGAAAGTTTGGGGGTAAAAAT-AGATTTTTAGAAGTTTTGGGTTA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTAGAAGTTTTGGGTCA
* * *
181609 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTTCGGTGTCA
1 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTAGAAGTTTTGG-GTCA
* * * *
181668 AAAATGAGATTTTTGGAAGTTCGAGGATAAAAACGAAATT
1 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATT
181708 CTTGGATAGT
Statistics
Matches: 244, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
57 36 0.15
58 36 0.15
59 79 0.32
60 47 0.19
61 46 0.19
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTAGAAGTTTTGGGTCA
Found at i:181699 original size:29 final size:29
Alignment explanation
Indices: 181343--181723 Score: 257
Period size: 30 Copynumber: 12.9 Consensus size: 29
181333 TTCGAAGTCG
*
181343 AAAATG-GAGTTTTTGG-ACTTTCGAGGGT-
1 AAAATGAGA-TTTTTGGAAGTTT-GAGGGTA
* *
181371 AAAATG-GTAATTTTTAGAAGTTTTAGGGTCA
1 AAAATGAG--ATTTTTGGAAGTTTGAGGGT-A
**
181402 AAAATG-GAATTTTTATAAGTTTTG-GGGTCA
1 AAAATGAG-ATTTTTGGAAG-TTTGAGGGT-A
181432 AAAATGAGATTTTTGGAAGCTTTGAGGGTA
1 AAAATGAGATTTTTGGAAG-TTTGAGGGTA
* *
181462 AAAATG-GAATTTTTAAGAAGTTTTAGGGTCA
1 AAAATGAG-ATTTTT-GGAAGTTTGAGGGT-A
* *
181493 AAAATGGGATTTTTGGAAGTTTGAGGTTA
1 AAAATGAGATTTTTGGAAGTTTGAGGGTA
* * *
181522 AAAATGAAATTTTTAGAAGTTTTG-GTGTTA
1 AAAATGAGATTTTTGGAAG-TTTGAG-GGTA
* * * *
181552 AAAATGGGATTCTTGAAAGTTTGGGGGTA
1 AAAATGAGATTTTTGGAAGTTTGAGGGTA
* *
181581 AAAAT-AGATTTTTAGAAGTTTTG-GGTTA
1 AAAATGAGATTTTTGGAAG-TTTGAGGGTA
* *
181609 AAAATGGGATTTTTGGAAGTTTGGGGGTA
1 AAAATGAGATTTTTGGAAGTTTGAGGGTA
* *
181638 AAAATG-GAATTTTTAGAAGTTTCG-GTGTCA
1 AAAATGAG-ATTTTTGGAAGTTT-GAGGGT-A
* *
181668 AAAATGAGATTTTTGGAAGTTCGAGGATA
1 AAAATGAGATTTTTGGAAGTTTGAGGGTA
* * *
181697 AAAACGAAATTCTTGGATAGTTT-AGGG
1 AAAATGAGATTTTTGGA-AGTTTGAGGG
181724 ACCTTCAGGG
Statistics
Matches: 288, Mismatches: 41, Indels: 47
0.77 0.11 0.12
Matches are distributed among these distances:
28 30 0.10
29 102 0.35
30 122 0.42
31 33 0.11
32 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGAGATTTTTGGAAGTTTGAGGGTA
Found at i:182872 original size:3 final size:3
Alignment explanation
Indices: 182866--182902 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
182856 AATATCACAG
*
182866 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
182903 ATGCTATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Done.