Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012565.1 Kokia drynarioides strain JFW-HI SEQ_127574, 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: 341411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:212 original size:28 final size:25
Alignment explanation
Indices: 161--212 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
151 AGGCATGTTC
* *
161 GTTTTTATTTTTTAATTTTATTATA
1 GTTTTCATTTTTTAACTTTATTATA
186 GTTTTCATTATTTTCAACTTTAGTTAT
1 GTTTTCATT-TTTT-AACTTTA-TTAT
213 TGATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 8 0.36
26 4 0.18
27 6 0.27
28 4 0.18
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (25 bp):
GTTTTCATTTTTTAACTTTATTATA
Found at i:609 original size:9 final size:9
Alignment explanation
Indices: 595--623 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
585 AATAGCACAT
595 ATTTTTATA
1 ATTTTTATA
604 ATTTTTATA
1 ATTTTTATA
613 ATTTTTATA
1 ATTTTTATA
622 AT
1 AT
624 ATCAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4861 original size:52 final size:52
Alignment explanation
Indices: 4762--5205 Score: 678
Period size: 52 Copynumber: 8.6 Consensus size: 52
4752 TTCCCATTTA
* * * * *
4762 ATACTCACGATGACACCA-AGCCATCGGACTTTA-AATTCGTAAGAGGATCCAT
1 ATACTCACGATGACA-CAGAGTCATCGGACCTCATAATCCGTAA-AGGATTCAT
* * *
4814 ATTCTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
4866 ATACTCACGATGACACAAAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
4918 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
4970 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
5022 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * *
5074 ATATTCATGATGACACAGAGTCATCAGACCTCATAATTCAT-AAGGATTCAT
1 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
5125 ATACTCGCGATGACACAAAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
5177 ATACTCACGATGACACATAGTCATCGGAC
1 ATACTCACGATGACACAGAGTCATCGGAC
5206 TTTTTTGCAT
Statistics
Matches: 360, Mismatches: 29, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
51 45 0.12
52 308 0.86
53 7 0.02
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (52 bp):
ATACTCACGATGACACAGAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:11056 original size:81 final size:81
Alignment explanation
Indices: 10957--11116 Score: 311
Period size: 81 Copynumber: 2.0 Consensus size: 81
10947 TGATCAGAGG
*
10957 TAACGAGTACCAGGTCAAAGTGCTAATCGAGCTGATACGAGACATCCAACACTTGTCTATCGGCT
1 TAACGAGTACCAGGTCAAAGTGCTAATCGAACTGATACGAGACATCCAACACTTGTCTATCGGCT
11022 AGATGTAGAGAGGAGA
66 AGATGTAGAGAGGAGA
11038 TAACGAGTACCAGGTCAAAGTGCTAATCGAACTGATACGAGACATCCAACACTTGTCTATCGGCT
1 TAACGAGTACCAGGTCAAAGTGCTAATCGAACTGATACGAGACATCCAACACTTGTCTATCGGCT
11103 AGATGTAGAGAGGA
66 AGATGTAGAGAGGA
11117 CCAAGATGCA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (81 bp):
TAACGAGTACCAGGTCAAAGTGCTAATCGAACTGATACGAGACATCCAACACTTGTCTATCGGCT
AGATGTAGAGAGGAGA
Found at i:16111 original size:21 final size:21
Alignment explanation
Indices: 16087--16128 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16077 GAGGTTGAGA
16087 TAGTGGAATATCATGGAATTT
1 TAGTGGAATATCATGGAATTT
*
16108 TAGTGGAATATCATGGCATTT
1 TAGTGGAATATCATGGAATTT
16129 AGGTTTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (21 bp):
TAGTGGAATATCATGGAATTT
Found at i:18032 original size:21 final size:21
Alignment explanation
Indices: 17991--18065 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
17981 TGAGTTTTTA
* *
17991 GTATCGATAGAAGTA-AGACTT
1 GTATCGGTAGAAG-AGACACTT
18012 GTATCGGTAGAAGAGACACTT
1 GTATCGGTAGAAGAGACACTT
* ** * *
18033 GTATAGGTAGAACTGTCACTA
1 GTATCGGTAGAAGAGACACTT
18054 GTATCGGTAGAA
1 GTATCGGTAGAA
18066 ATCTACACTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (21 bp):
GTATCGGTAGAAGAGACACTT
Found at i:20138 original size:13 final size:13
Alignment explanation
Indices: 20122--20155 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20112 ATAAACAATA
20122 AAATAATAATCCT
1 AAATAATAATCCT
*
20135 AAATATTAATCCT
1 AAATAATAATCCT
*
20148 AAAAAATA
1 AAATAATA
20156 GAGTTTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATCCT
Found at i:28306 original size:15 final size:16
Alignment explanation
Indices: 28286--28318 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
28276 CATTTTTAAA
28286 TTTACTTTTA-TTGTT
1 TTTACTTTTACTTGTT
28301 TTTACTTTTACTTGTT
1 TTTACTTTTACTTGTT
28317 TT
1 TT
28319 CTTTAAGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (16 bp):
TTTACTTTTACTTGTT
Found at i:29327 original size:93 final size:93
Alignment explanation
Indices: 29208--29393 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 93
29198 CAAAGTATGA
* * *
29208 TTCCAATTTGTTAACAGTCGCTTACTACCTTGAACCCATAGCACAACTACGGCACTAGATCGCAT
1 TTCCAATTTGTTAACAGTCGCCTACTACCTTGAACCCATAGCACAACTACGACACTAGATCACAT
*
29273 GTGCCTCCTGCACTCTATCCTTAAGGGT
66 GTACCTCCTGCACTCTATCCTTAAGGGT
* * *
29301 TTCCACTTTGTTAACAGTCGCCTACTACCTTTAACCTATAGCACAACTACGACACTAGATCACAT
1 TTCCAATTTGTTAACAGTCGCCTACTACCTTGAACCCATAGCACAACTACGACACTAGATCACAT
* *
29366 GTACCTCTTTCACTCTATCCTTAAGGGT
66 GTACCTCCTGCACTCTATCCTTAAGGGT
29394 CACCACATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (93 bp):
TTCCAATTTGTTAACAGTCGCCTACTACCTTGAACCCATAGCACAACTACGACACTAGATCACAT
GTACCTCCTGCACTCTATCCTTAAGGGT
Found at i:31314 original size:10 final size:10
Alignment explanation
Indices: 31299--31339 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
31289 AAACAATCAC
31299 AAAAAGAAAG
1 AAAAAGAAAG
31309 AAAAAGAAAG
1 AAAAAGAAAG
*
31319 AAGAAGAAAAG
1 AAAAAG-AAAG
31330 AGAAAAGAAA
1 A-AAAAGAAA
31340 AAGAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 15 0.56
11 8 0.30
12 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:32719 original size:39 final size:39
Alignment explanation
Indices: 32665--32744 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
32655 TTATTATTGG
32665 TATGATTTCATTGGAACCTTATTGTAGTGACAATTCATC
1 TATGATTTCATTGGAACCTTATTGTAGTGACAATTCATC
32704 TATGATTTCATTGGAACCTTATTGTAGTGACAATTCATC
1 TATGATTTCATTGGAACCTTATTGTAGTGACAATTCATC
32743 TA
1 TA
32745 CACTATACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (39 bp):
TATGATTTCATTGGAACCTTATTGTAGTGACAATTCATC
Found at i:35070 original size:21 final size:21
Alignment explanation
Indices: 35041--35116 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
35031 AGAGTTTTTA
* *
35041 GTATTGGTAGAAGTA-AGACTT
1 GTATCGGTAGAAG-AGACACTT
*
35062 GTTTCGGTAGAAGAGACACTT
1 GTATCGGTAGAAGAGACACTT
** *
35083 GTATCGGTAGAACTGTCACTT
1 GTATCGGTAGAAGAGACACTT
*
35104 GTATCGATAGAAG
1 GTATCGGTAGAAG
35117 TCTACACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGAGACACTT
Found at i:46410 original size:8 final size:8
Alignment explanation
Indices: 46397--46422 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
46387 TATCACATAA
46397 TTTATTAC
1 TTTATTAC
46405 TTTATTAC
1 TTTATTAC
46413 TTTATTAC
1 TTTATTAC
46421 TT
1 TT
46423 GTCACGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATTAC
Found at i:56786 original size:15 final size:15
Alignment explanation
Indices: 56766--56796 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56756 AGAACTACTT
56766 ATCTTCTGACCTCAC
1 ATCTTCTGACCTCAC
56781 ATCTTCTGACCTCAC
1 ATCTTCTGACCTCAC
56796 A
1 A
56797 GTTCAGACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.39, G:0.06, T:0.32
Consensus pattern (15 bp):
ATCTTCTGACCTCAC
Found at i:62812 original size:6 final size:6
Alignment explanation
Indices: 62769--62823 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
62759 TCAAAATTTC
* * * *
62769 TTTC-T TTTCTC TCTCTT TCTCTT TTTCTT ATTAC-T TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT -TTTCTT TTTCTT TTTCTT
62816 TTTCTT TT
1 TTTCTT TT
62824 CAAATGACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
5 7 0.17
6 31 0.76
7 3 0.07
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:65000 original size:28 final size:28
Alignment explanation
Indices: 64955--65009 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
64945 TGTGTGGTCA
* *
64955 TCCACCTTCTCTTGGATCCCTAGCAACG
1 TCCACCTTCTCCTAGATCCCTAGCAACG
*
64983 TCCACCTTCTCCTAGATCCTTAGCAAC
1 TCCACCTTCTCCTAGATCCCTAGCAAC
65010 ACGTTTACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.40, G:0.11, T:0.29
Consensus pattern (28 bp):
TCCACCTTCTCCTAGATCCCTAGCAACG
Found at i:73127 original size:8 final size:9
Alignment explanation
Indices: 73107--73134 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
73097 AAGAGTTATA
73107 TTTTAGACT
1 TTTTAGACT
73116 TTTTAGACT
1 TTTTAGACT
73125 TTTTAGACT
1 TTTTAGACT
73134 T
1 T
73135 AGTGAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (9 bp):
TTTTAGACT
Found at i:77601 original size:48 final size:48
Alignment explanation
Indices: 77525--77621 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
77515 AGACATGCAT
*
77525 GGAACAAAATCGTAAGTTGCCTCGTTACGGATTTGTCCTAGGGCTCTA
1 GGAACAAAATCGTAAGTTGCCTCATTACGGATTTGTCCTAGGGCTCTA
* *
77573 GGAACAAAATTGTAAGTTGCCTCATTACGGATTTTTCCTAGGGCTCTA
1 GGAACAAAATCGTAAGTTGCCTCATTACGGATTTGTCCTAGGGCTCTA
77621 G
1 G
77622 ATGTTTAGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (48 bp):
GGAACAAAATCGTAAGTTGCCTCATTACGGATTTGTCCTAGGGCTCTA
Found at i:93767 original size:20 final size:19
Alignment explanation
Indices: 93735--93782 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
93725 TTTTTCTTTT
93735 TTTTTCTTC-CTTTTATTC
1 TTTTTCTTCACTTTTATTC
* *
93753 TTTTTCTTCATCTTTTCTTT
1 TTTTTCTTCA-CTTTTATTC
93773 TTTTTCTTCA
1 TTTTTCTTCA
93783 GCCTTAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
20 17 0.65
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTCTTCACTTTTATTC
Found at i:105454 original size:78 final size:78
Alignment explanation
Indices: 105360--105517 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
105350 AAGGCCTAAG
105360 GGTTTACAGAACTTTACGAGCTTTTTTTTCATACATACTAACCAATCACAATTTATACATATACA
1 GGTTTACAGAACTTTACGAGCTTTTTTTTCATACATACTAACCAATCACAATTTATACATATACA
105425 AACTTGCAACTCA
66 AACTTGCAACTCA
105438 GGTTTACAGAACTTTACGAGCTTTTTTTTCATACATACTAACCAATCACAATTTATACATATACA
1 GGTTTACAGAACTTTACGAGCTTTTTTTTCATACATACTAACCAATCACAATTTATACATATACA
105503 AACTTGCAACTCA
66 AACTTGCAACTCA
105516 GG
1 GG
105518 ATACTAACTC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (78 bp):
GGTTTACAGAACTTTACGAGCTTTTTTTTCATACATACTAACCAATCACAATTTATACATATACA
AACTTGCAACTCA
Found at i:106126 original size:21 final size:21
Alignment explanation
Indices: 106108--106171 Score: 112
Period size: 21 Copynumber: 3.0 Consensus size: 21
106098 AAAATGACGG
106108 TTCTACC-AGTACAACTGACAC
1 TTCTACCGA-TACAACTGACAC
106129 TTCTACCGATACAACTGACAC
1 TTCTACCGATACAACTGACAC
106150 TTCTACCGATACAACTGACAC
1 TTCTACCGATACAACTGACAC
106171 T
1 T
106172 AGAGAGCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (21 bp):
TTCTACCGATACAACTGACAC
Found at i:106476 original size:92 final size:92
Alignment explanation
Indices: 106319--106503 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
106309 TCATGAGAAG
*
106319 TAAGCATAACAACATCATAGTACATGCTATATAACCAAGTGATGTAAATATTACCGAGCAAGCTC
1 TAAGCATAACAACATCATAGTACATGCTATATAACCAAGTGATGTAAATATTACCGAGAAAGCTC
106384 CCATAATTGTGTGACTTCTTGAGGTGA
66 CCATAATTGTGTGACTTCTTGAGGTGA
106411 TAAGCATAACAACATCATAGTACATGCTATATAACCAAGTGATGTAAATATTACCGAGAAAGCTC
1 TAAGCATAACAACATCATAGTACATGCTATATAACCAAGTGATGTAAATATTACCGAGAAAGCTC
106476 CCATAATTGTGTGACTTCTTGAGGTGA
66 CCATAATTGTGTGACTTCTTGAGGTGA
106503 T
1 T
106504 CCAATCTTCT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (92 bp):
TAAGCATAACAACATCATAGTACATGCTATATAACCAAGTGATGTAAATATTACCGAGAAAGCTC
CCATAATTGTGTGACTTCTTGAGGTGA
Found at i:115346 original size:21 final size:23
Alignment explanation
Indices: 115316--115358 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
115306 ATTCACATGT
115316 TTTCTTACTCATTCTT-CTTTTG
1 TTTCTTACTCATTCTTCCTTTTG
*
115338 TTTC-TACTCATTTTTCCTTTT
1 TTTCTTACTCATTCTTCCTTTT
115359 TTTTTTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTCTTACTCATTCTTCCTTTTG
Found at i:115384 original size:25 final size:25
Alignment explanation
Indices: 115333--115385 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
115323 CTCATTCTTC
115333 TTTTGTTTCTACTCATTTTTCCTTT
1 TTTTGTTTCTACTCATTTTTCCTTT
* * *
115358 TTTTTTTTCT-CTTATTTTT-CTTA
1 TTTTGTTTCTACTCATTTTTCCTTT
115381 TTTTG
1 TTTTG
115386 CTAGACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 7 0.29
24 8 0.33
25 9 0.38
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTGTTTCTACTCATTTTTCCTTT
Found at i:121295 original size:14 final size:15
Alignment explanation
Indices: 121271--121301 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
121261 TAGTGTTTTG
121271 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
121286 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
121300 AA
1 AA
121302 TAAAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:133438 original size:18 final size:18
Alignment explanation
Indices: 133415--133476 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
133405 CACATTCCCT
*
133415 TTGTCATTGCATTTTTAA
1 TTGTCATTGCATTTTCAA
* * *
133433 TTGTCACTGCATGTGC-A
1 TTGTCATTGCATTTTCAA
*
133450 TTGTCATTGCATTTTCAT
1 TTGTCATTGCATTTTCAA
133468 TTGTCATTG
1 TTGTCATTG
133477 TAAATTAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (18 bp):
TTGTCATTGCATTTTCAA
Found at i:134350 original size:13 final size:13
Alignment explanation
Indices: 134334--134376 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
134324 TTTATTTATT
134334 GCATACATTTTTA
1 GCATACATTTTTA
134347 GCATACATTTTTA
1 GCATACATTTTTA
134360 GCATACATTTTTA
1 GCATACATTTTTA
134373 GCAT
1 GCAT
134377 TTTTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (13 bp):
GCATACATTTTTA
Found at i:142426 original size:24 final size:24
Alignment explanation
Indices: 142401--142447 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
142391 AACTATTCAT
142401 TTTATCTTA-ATTTTC-TCTGACAA
1 TTTATCTTATATTTTCAT-TGACAA
*
142424 TTTATTTTATATTTTCATTGACAA
1 TTTATCTTATATTTTCATTGACAA
142448 ATTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTATCTTATATTTTCATTGACAA
Found at i:142477 original size:28 final size:28
Alignment explanation
Indices: 142446--142503 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
142436 TTTCATTGAC
142446 AAATTAACTCTTTTAGCTGTGCAGTTCT
1 AAATTAACTCTTTTAGCTGTGCAGTTCT
142474 AAATTAACTCTTTTAGCTGTGCAGTTCT
1 AAATTAACTCTTTTAGCTGTGCAGTTCT
142502 AA
1 AA
142504 CTCAATTACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (28 bp):
AAATTAACTCTTTTAGCTGTGCAGTTCT
Found at i:154187 original size:29 final size:29
Alignment explanation
Indices: 154135--154215 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
154125 TGTAAACAAT
* * *
154135 TATAGTTGAGCCTTGTAAAAACTACAATGC
1 TATAGTTAAG-CTTATAAAAACTACAAGGC
* *
154165 TATAGTTAAGCTTATAAAAACTACAGGGT
1 TATAGTTAAGCTTATAAAAACTACAAGGC
* *
154194 TCTAGTTAAGC-CATAAAAACTA
1 TATAGTTAAGCTTATAAAAACTA
154216 GGGGGAAGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 10 0.23
29 25 0.57
30 9 0.20
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (29 bp):
TATAGTTAAGCTTATAAAAACTACAAGGC
Found at i:155859 original size:25 final size:24
Alignment explanation
Indices: 155796--155859 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
155786 AACAGAGCCT
*
155796 TTGTGGCAAGTTATCTGTAAATCCC
1 TTGTGGC-AGTTATCTGAAAATCCC
* *
155821 TTGGGGCGAATTATCTGAAAAT-CC
1 TTGTGGC-AGTTATCTGAAAATCCC
155845 TATGTGGCATGTTAT
1 T-TGTGGCA-GTTAT
155860 TTGGGAAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (24 bp):
TTGTGGCAGTTATCTGAAAATCCC
Found at i:161566 original size:25 final size:26
Alignment explanation
Indices: 161508--161563 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
161498 GCGTATTATT
*
161508 TAGGAAGCCTTAGTGACAAAGTTATC
1 TAGGAAGCCTTAGTGACAAAGTCATC
* *
161534 TAGGAAGCCTTTGTGTC-AAGTCATC
1 TAGGAAGCCTTAGTGACAAAGTCATC
161559 T-GGAA
1 TAGGAA
161564 AGCTTGAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 4 0.15
25 8 0.30
26 15 0.56
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (26 bp):
TAGGAAGCCTTAGTGACAAAGTCATC
Found at i:164135 original size:21 final size:21
Alignment explanation
Indices: 164111--164158 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
164101 TATGTCACTT
*
164111 TTTTATTGAT-AACTTATTTTA
1 TTTTATTGATAAAC-TATGTTA
*
164132 TTTTA-TGGTAAACTATGTTA
1 TTTTATTGATAAACTATGTTA
164152 TTTTATT
1 TTTTATT
164159 TTACATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
TTTTATTGATAAACTATGTTA
Found at i:165068 original size:11 final size:11
Alignment explanation
Indices: 165054--165078 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
165044 AAAAAATGTA
165054 TATATTGTTTT
1 TATATTGTTTT
165065 TATATTGTTTT
1 TATATTGTTTT
165076 TAT
1 TAT
165079 TTTGCCTATG
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (11 bp):
TATATTGTTTT
Found at i:176503 original size:14 final size:14
Alignment explanation
Indices: 176471--176500 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
176461 AATTTGATTC
176471 TTTATATCTTTTAA
1 TTTATATCTTTTAA
176485 TTTATATC-TTTAA
1 TTTATATCTTTTAA
176498 TTT
1 TTT
176501 TATTGCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATATCTTTTAA
Found at i:176560 original size:22 final size:25
Alignment explanation
Indices: 176528--176585 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
176518 AGTCCTTTTA
176528 TTTATTCATTT-CAACCCT-TT-ATT
1 TTTATT-ATTTCCAACCCTGTTAATT
* *
176551 TTTTTTATTTCCAACCTTGTTAATT
1 TTTATTATTTCCAACCCTGTTAATT
176576 TTTATTATTT
1 TTTATTATTT
176586 AGATTTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.14
23 11 0.38
24 2 0.07
25 12 0.41
ACGTcount: A:0.21, C:0.16, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTATTATTTCCAACCCTGTTAATT
Found at i:180469 original size:40 final size:41
Alignment explanation
Indices: 180324--180475 Score: 166
Period size: 42 Copynumber: 3.6 Consensus size: 41
180314 TGAATCACTT
* *
180324 TATGTTTAAAGGAAGACTTATGTCTCGGAATGAGCATGAGAG
1 TATGTTTAAAGGAAGACTTATGACTCGGTA-GAGCATGAGAG
* * *
180366 TATATTTAAAGGAAGACTCATGACACGGGATA-AGCATGAGAG
1 TATGTTTAAAGGAAGACTTATGACTC-GG-TAGAGCATGAGAG
* *
180408 TATGTTTAAAAAGGAAAACTTATGACTCGGTAGAGCATAAGA-
1 TATGTTT--AAAGGAAGACTTATGACTCGGTAGAGCATGAGAG
180450 T-TGTTTGAAAGGAAGACTTATGACTC
1 TATGTTT-AAAGGAAGACTTATGACTC
180476 TGTTACTAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
40 18 0.19
41 5 0.05
42 41 0.44
43 12 0.13
44 17 0.18
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (41 bp):
TATGTTTAAAGGAAGACTTATGACTCGGTAGAGCATGAGAG
Found at i:181637 original size:21 final size:21
Alignment explanation
Indices: 181611--181654 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
181601 GGGCCAAAAG
*
181611 TTAGTTTGAAAGATTAAGACT
1 TTAGTTTAAAAGATTAAGACT
181632 TTAGTTTAAAAGATTAAGACT
1 TTAGTTTAAAAGATTAAGACT
181653 TT
1 TT
181655 GAGCATTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (21 bp):
TTAGTTTAAAAGATTAAGACT
Found at i:182996 original size:26 final size:26
Alignment explanation
Indices: 182962--183177 Score: 220
Period size: 26 Copynumber: 8.3 Consensus size: 26
182952 CTAGCTCGAT
182962 AGAGCTAAATTTTGTTTGGGCTCGTA
1 AGAGCTAAATTTTGTTTGGGCTCGTA
* * * *
182988 TGAGATAAATTTTATTTGGGCTCATA
1 AGAGCTAAATTTTGTTTGGGCTCGTA
* *
183014 AGAGCTAAATTCTGTCTGGGCTCGTA
1 AGAGCTAAATTTTGTTTGGGCTCGTA
*
183040 AGAGCTAAATTTTGTTTGAGCTCGTA
1 AGAGCTAAATTTTGTTTGGGCTCGTA
* * * *
183066 AGAGCTAAATTCTGTCTAGTCTCGTA
1 AGAGCTAAATTTTGTTTGGGCTCGTA
* * * *
183092 AGAG-TTAATTTCTATTTGGACTCCTA
1 AGAGCTAAATTT-TGTTTGGGCTCGTA
* * *
183118 AGAGCTAAACTCTGTTTGGGCTAGTA
1 AGAGCTAAATTTTGTTTGGGCTCGTA
* *
183144 AGAGCTAAACTCTT-TATGGGCTCGTA
1 AGAGCTAAA-TTTTGTTTGGGCTCGTA
183170 AGAGCTAA
1 AGAGCTAA
183178 CCTCTAGAAT
Statistics
Matches: 150, Mismatches: 37, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
25 5 0.03
26 140 0.93
27 5 0.03
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (26 bp):
AGAGCTAAATTTTGTTTGGGCTCGTA
Found at i:183019 original size:52 final size:52
Alignment explanation
Indices: 182962--183177 Score: 249
Period size: 52 Copynumber: 4.2 Consensus size: 52
182952 CTAGCTCGAT
* * * * *
182962 AGAGCTAAATTTTGTTTGGGCTCGTATGAGATAAATTTTATTTGGGCTCATA
1 AGAGCTAAATTCTGTCTGGGCTCGTAAGAGCTAAATTTTATTTGGGCTCGTA
* *
183014 AGAGCTAAATTCTGTCTGGGCTCGTAAGAGCTAAATTTTGTTTGAGCTCGTA
1 AGAGCTAAATTCTGTCTGGGCTCGTAAGAGCTAAATTTTATTTGGGCTCGTA
* * * * *
183066 AGAGCTAAATTCTGTCTAGTCTCGTAAGAG-TTAATTTCTATTTGGACTCCTA
1 AGAGCTAAATTCTGTCTGGGCTCGTAAGAGCTAAATTT-TATTTGGGCTCGTA
* * *
183118 AGAGCTAAACTCTGTTTGGGCTAGTAAGAGCTAAACTCTTTA--TGGGCTCGTA
1 AGAGCTAAATTCTGTCTGGGCTCGTAAGAGCTAAA-T-TTTATTTGGGCTCGTA
183170 AGAGCTAA
1 AGAGCTAA
183178 CCTCTAGAAT
Statistics
Matches: 138, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
51 6 0.04
52 124 0.90
53 3 0.02
54 3 0.02
55 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
AGAGCTAAATTCTGTCTGGGCTCGTAAGAGCTAAATTTTATTTGGGCTCGTA
Found at i:183191 original size:26 final size:26
Alignment explanation
Indices: 183116--183189 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
183106 TTTGGACTCC
**
183116 TAAGAGCTAAACTCTGTTTGGGCTAG
1 TAAGAGCTAAACTCTGAATGGGCTAG
** *
183142 TAAGAGCTAAACTCTTTATGGGCTCG
1 TAAGAGCTAAACTCTGAATGGGCTAG
*
183168 TAAGAGCTAACCTCTAGAATGG
1 TAAGAGCTAAACTCT-GAATGG
183190 CTTAAAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (26 bp):
TAAGAGCTAAACTCTGAATGGGCTAG
Found at i:211233 original size:27 final size:26
Alignment explanation
Indices: 211196--211323 Score: 159
Period size: 26 Copynumber: 4.9 Consensus size: 26
211186 GATAGAGCGT
* *
211196 AATTCTGTCTAGGCTCGTATGAGCTTA
1 AATTTTGTCTAGGCTCGTAAGAGC-TA
211223 AATTTTGTCTAGGCTCGTAAGAGCTA
1 AATTTTGTCTAGGCTCGTAAGAGCTA
211249 AATTTTGTCT-GGTCTCGTAAGAGCTA
1 AATTTTGTCTAGG-CTCGTAAGAGCTA
* *
211275 ATTTTTGTCTAGGCTTGTAAGAGCTA
1 AATTTTGTCTAGGCTCGTAAGAGCTA
* * * *
211301 AACTCTATCTAGACTCGTAAGAG
1 AATTTTGTCTAGGCTCGTAAGAG
211324 TTAACCTTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
25 2 0.02
26 63 0.71
27 24 0.27
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (26 bp):
AATTTTGTCTAGGCTCGTAAGAGCTA
Found at i:213725 original size:28 final size:27
Alignment explanation
Indices: 213637--213808 Score: 98
Period size: 29 Copynumber: 6.1 Consensus size: 27
213627 AACATGTGGC
* *
213637 AAAAAATGATAAAAGATAAA-AAACA-A
1 AAAAAATTATAAAA-ATAAATAAATATA
* * * *
213663 TAAAAATTATAAAAATTATTAAATTTTA
1 AAAAAATTATAAAAATAAATAAA-TATA
*
213691 TTAAAAATTATAAAAATAAATAAATATA
1 -AAAAAATTATAAAAATAAATAAATATA
* *
213719 GCAAAAATTAT-AAAATATATACGAATATA
1 -AAAAAATTATAAAAATAAATA--AATATA
* **
213748 AAAAAATTATAAAATTTTATAAAATCATA
1 AAAAAATTATAAAAATAAAT-AAAT-ATA
* * *
213777 AGAAAATTATAGAAATGTAAAAAAATATA
1 AAAAAATTATA-AAA-ATAAATAAATATA
213806 AAA
1 AAA
213809 TTTGTAAAAG
Statistics
Matches: 114, Mismatches: 21, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
25 3 0.03
26 15 0.13
27 9 0.08
28 25 0.22
29 52 0.46
30 8 0.07
31 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAAATTATAAAAATAAATAAATATA
Found at i:213768 original size:29 final size:29
Alignment explanation
Indices: 213693--213808 Score: 91
Period size: 28 Copynumber: 4.1 Consensus size: 29
213683 AAATTTTATT
* * *
213693 AAAAATTATAAAAATAAAT-AAAT-ATAGC
1 AAAAATTATAAAATTATATAAAATCATA-A
*
213721 AAAAATTATAAAA-TATATACGAAT-ATAA
1 AAAAATTATAAAATTATATA-AAATCATAA
*
213749 AAAAATTATAAAATTTTATAAAATCATAA
1 AAAAATTATAAAATTATATAAAATCATAA
* *
213778 GAAAATTATAGAAATGTA-AAAAAAT-ATAA
1 AAAAATTATA-AAAT-TATATAAAATCATAA
213807 AA
1 AA
213809 TTTGTAAAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.05
28 29 0.40
29 29 0.40
30 10 0.14
31 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (29 bp):
AAAAATTATAAAATTATATAAAATCATAA
Found at i:214150 original size:16 final size:16
Alignment explanation
Indices: 214130--214193 Score: 85
Period size: 16 Copynumber: 3.9 Consensus size: 16
214120 TTTGGTACTT
214130 TTTTTTACTG-TTTTA
1 TTTTTTACTGTTTTTA
214145 TTTTTTACTGTTTTTA
1 TTTTTTACTGTTTTTA
*
214161 TTTTTTACTTTTTTGTGCA
1 TTTTTTACTGTTTT-T--A
214180 TTTTTTACTGTTTT
1 TTTTTTACTGTTTT
214194 GATTACTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.23
16 18 0.42
17 1 0.02
19 14 0.33
ACGTcount: A:0.11, C:0.08, G:0.08, T:0.73
Consensus pattern (16 bp):
TTTTTTACTGTTTTTA
Found at i:214261 original size:21 final size:20
Alignment explanation
Indices: 214236--214292 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
214226 TTTGGTGCTA
214236 TTTTTATTGTTATTTTTATTG
1 TTTTT-TTGTTATTTTTATTG
* *
214257 CTTTTTTTGTTTTTTTTTTTG
1 -TTTTTTTGTTATTTTTATTG
214278 TTATTTTTGTTATTT
1 TT-TTTTTGTTATTT
214293 GGATGTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.06
21 24 0.77
22 5 0.16
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.81
Consensus pattern (20 bp):
TTTTTTTGTTATTTTTATTG
Found at i:214834 original size:11 final size:10
Alignment explanation
Indices: 214820--214887 Score: 75
Period size: 10 Copynumber: 6.8 Consensus size: 10
214810 TTTTTACGCA
214820 TTTTATAATTT
1 TTTTATAA-TT
214831 TTTTATAATT
1 TTTTATAATT
**
214841 TTTTATAAAA
1 TTTTATAATT
* *
214851 ATTTACAATT
1 TTTTATAATT
214861 TTTTATAATT
1 TTTTATAATT
*
214871 TTTTATGA-T
1 TTTTATAATT
214880 TTTTATAA
1 TTTTATAA
214888 AAAAAAATTC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
9 8 0.17
10 31 0.66
11 8 0.17
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:214917 original size:10 final size:10
Alignment explanation
Indices: 214902--214965 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
214892 AAATTCTAAG
214902 TTTTATTAAA
1 TTTTATTAAA
*
214912 TTTTA-T-AT
1 TTTTATTAAA
214920 TTTTATTAAA
1 TTTTATTAAA
* * *
214930 ATTTAATAAT
1 TTTTATTAAA
214940 TTTTA-TAAA
1 TTTTATTAAA
* *
214949 TTTTATTTAT
1 TTTTATTAAA
214959 TTTTATT
1 TTTTATT
214966 TTTAATAGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
8 6 0.14
9 10 0.24
10 26 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTATTAAA
Found at i:214933 original size:19 final size:18
Alignment explanation
Indices: 214902--214965 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
214892 AAATTCTAAG
214902 TTTTATTAAATTTTATAT
1 TTTTATTAAATTTTATAT
*
214920 TTTTATTAAAATTTAATAAT
1 TTTTATT-AAATTTTAT-AT
214940 TTTTA-TAAATTTTATTTAT
1 TTTTATTAAATTTTA--TAT
214959 TTTTATT
1 TTTTATT
214966 TTTAATAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 14 0.36
19 16 0.41
20 9 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATTAAATTTTATAT
Found at i:215250 original size:89 final size:84
Alignment explanation
Indices: 215090--215272 Score: 242
Period size: 89 Copynumber: 2.1 Consensus size: 84
215080 GACTTTTCTA
* * * *
215090 ATGCA-TTTGACAGTTCAAGTACCCAATTGAGTAAAAAAAAAAGGCTTAATTATTTTTTTTGAAA
1 ATGCATTTTGAAAGTTCAAGCACCCAATTAAGTAAAAAAAAAAGGCTTAATTACTTTTTTTGAAA
**
215154 AAAATTAAGGGTTTTTTTT
66 AAAATTAAGAATTTTTTTT
* *
215173 ATGCATTTTGAAAGTTCAAGCACCCAATTAAGTACAAAAAAAGGCAGGGGCTTAATTGCTTTTTT
1 ATGCATTTTGAAAGTTCAAGCACCCAATTAAGTA-AAAAAAA---A-AGGCTTAATTACTTTTTT
215238 TGAAAAAAATTAAGAATTTTTTTT
61 TGAAAAAAATTAAGAATTTTTTTT
215262 ATGCATTTTGA
1 ATGCATTTTGA
215273 TAACTCAAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
83 5 0.06
84 25 0.29
85 7 0.08
88 1 0.01
89 48 0.56
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (84 bp):
ATGCATTTTGAAAGTTCAAGCACCCAATTAAGTAAAAAAAAAAGGCTTAATTACTTTTTTTGAAA
AAAATTAAGAATTTTTTTT
Found at i:215326 original size:90 final size:89
Alignment explanation
Indices: 215134--215328 Score: 218
Period size: 89 Copynumber: 2.2 Consensus size: 89
215124 AAAAAAAAGG
** * *
215134 CTTAATTATTTTTTTTGAAAAAAATTAAGGGTTTTTTTTATGCATTTTGAAAGTTCAAGCACCCA
1 CTTAATTATTTTTTTTGAAAAAAATTAAGAATTTTTTTTATGCATTTTGAAAGCTCAAACACCCA
**
215199 ATTAAGTACAAAAAAAGGCAGGGG
66 ATTAAGTACAAAAAAAGGCAGGAA
** * *
215223 CTTAATTGCTTTTTTTGAAAAAAATTAAGAATTTTTTTTATGCATTTTGATAA-CTCAAATACTC
1 CTTAATTATTTTTTTTGAAAAAAATTAAGAATTTTTTTTATGCATTTTGA-AAGCTCAAACACCC
215287 AATTGAA-TGA-AATAGAAAA-GCAGGAA
65 AATT-AAGT-ACAA-A-AAAAGGCAGGAA
*
215313 CTTAATTTTTTTTTTT
1 CTTAATTATTTTTTTT
215329 TTTTAAGTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
89 60 0.67
90 25 0.28
91 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (89 bp):
CTTAATTATTTTTTTTGAAAAAAATTAAGAATTTTTTTTATGCATTTTGAAAGCTCAAACACCCA
ATTAAGTACAAAAAAAGGCAGGAA
Found at i:218996 original size:143 final size:143
Alignment explanation
Indices: 218743--219010 Score: 346
Period size: 143 Copynumber: 1.9 Consensus size: 143
218733 CACAGCTTTA
* * *
218743 TCTTGCCCCATTGCAACTTTAAGGAGATAAGATTTGCATTTATAGTTTCATTCCAACCCACTGCA
1 TCTTGCCCCAATGCAACTTCAAGGAGATAAGATTTGCATTTATAGTTTCATTCCAACCCAATGCA
* * *
218808 AATTCAAGGAGATTGGAATTGCTATTTTATCTGCTTTACTATAACTTC-AAGAAGATAGGATTCG
66 AATTCAAGGAGATTGGAATTACTATTTTATCTGCTTCACGATAACTTCAAAG-AGATAGGATTCG
218872 ATGTCACAATTTCG
130 ATGTCACAATTTCG
* * *
218886 TCTTGCCGCAATGCAACTTCATGGAGATAAGGTTTGC-TGTTATAGTTTCATTCCAACCCAATGC
1 TCTTGCCCCAATGCAACTTCAAGGAGATAAGATTTGCAT-TTATAGTTTCATTCCAACCCAATGC
* * * * *
218950 AACTTC-AGGAGGATTGGAATTATTGTTTTGT-TCGCTTCACGGTAACTTCAAAGAGATAGGA
65 AAATTCAAGGA-GATTGGAATTACTATTTTATCT-GCTTCACGATAACTTCAAAGAGATAGGA
219011 CTTGCTTATG
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
142 6 0.06
143 98 0.92
144 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (143 bp):
TCTTGCCCCAATGCAACTTCAAGGAGATAAGATTTGCATTTATAGTTTCATTCCAACCCAATGCA
AATTCAAGGAGATTGGAATTACTATTTTATCTGCTTCACGATAACTTCAAAGAGATAGGATTCGA
TGTCACAATTTCG
Found at i:219089 original size:50 final size:50
Alignment explanation
Indices: 219035--219194 Score: 144
Period size: 50 Copynumber: 3.2 Consensus size: 50
219025 TTCAATCTGA
* * *
219035 TCCATTGTAACTTCAGGGATATAGGATTTGATGTCGTAACTTCATCTTGC
1 TCCATTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTCATCTTGC
* * * * * * * **
219085 TCCATTGCATCTTCAAGGAGATAAAATTTGCTTTTGTAGCTTCAATCTAAC
1 TCCATTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTC-ATCTTGC
* * *
219136 -CCACTACAACTTCAAGGG-TATAAGATTTGATGTCGTAGCTTCATTTTGC
1 TCCATTGCAACTTC-AGGGATATAAGATTTGATGTCGTAGCTTCATCTTGC
*
219185 TCCACTGCAA
1 TCCATTGCAA
219195 TTGTAGGGGG
Statistics
Matches: 82, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
49 4 0.05
50 70 0.85
51 8 0.10
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (50 bp):
TCCATTGCAACTTCAGGGATATAAGATTTGATGTCGTAGCTTCATCTTGC
Found at i:219116 original size:100 final size:101
Alignment explanation
Indices: 219012--219373 Score: 335
Period size: 100 Copynumber: 3.6 Consensus size: 101
219002 GAGATAGGAC
* * * * ** *
219012 TTGCTTATGTAGTTTCAATCTGATCCATTGTAACTTCAGGGATATAGGATTTGATGTCGTAACTT
1 TTGCTTACGTAGCTTCAATCTGACCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGCTT
*
219077 CATCTTGCTCCATTGC-ATCTTCAAGGAGATAAA-AT
66 CATCTTGCTCCACTGCAAT-TTCAAGGAGATAAAGAT
** * *
219112 TTGCTTTTGTAGCTTCAATCTAACCCACTACAACTTCAAGGG-TATAAGATTTGATGTCGTAGCT
1 TTGCTTACGTAGCTTCAATCTGACCCACTACAACTTC-AGGGATATAGGATTTGATGTCGTAGCT
* * *
219176 TCATTTTGCTCCACTGCAATTGT-AGGGGGATAAAGAT
65 TCATCTTGCTCCACTGCAATT-TCAAGGAGATAAAGAT
* * * * *
219213 TTACTT-CGATAGCTTCAATCCT-ACCCACTACAACTTCAGGGGTATAGGATTTGGTTTTGTAGC
1 TTGCTTACG-TAGCTTCAAT-CTGACCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGC
* * * * * *
219276 CTAATCTTGCTCTACTACAATTTCAAAGAAATAAAGAT
64 TTCATCTTGCTCCACTGCAATTTCAAGGAGATAAAGAT
* ** * *
219314 TTGC-TACCGTAGTTTCAATCTGATTC-CTGCAACTTCAAGGATATAGGATTTGATGTCGTA
1 TTGCTTA-CGTAGCTTCAATCTGACCCACTACAACTTCAGGGATATAGGATTTGATGTCGTA
219374 CTGATCCCTT
Statistics
Matches: 213, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
100 112 0.53
101 97 0.46
102 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (101 bp):
TTGCTTACGTAGCTTCAATCTGACCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGCTT
CATCTTGCTCCACTGCAATTTCAAGGAGATAAAGAT
Found at i:219254 original size:51 final size:49
Alignment explanation
Indices: 219043--219265 Score: 130
Period size: 50 Copynumber: 4.4 Consensus size: 49
219033 GATCCATTGT
** * * * * *
219043 AACTTCAGGGATATAGGATTTGATGTCGTAACTTC-ATCTTGCTCCATTGC
1 AACTTCAGGGGGATAAGATTTGATGTCGTAGCTTCAATC-TAC-CCACTAC
* * * * * * *
219093 ATCTTCAAGGAGATAAAATTTGCTTTTGTAGCTTCAATCTAACCCACTAC
1 AACTTCAGGGGGATAAGATTTGATGTCGTAGCTTCAATCT-ACCCACTAC
* * * * * *
219143 AACTTCAAGGGTATAAGATTTGATGTCGTAGCTTCATTTTGCTCCACTGC
1 AACTTCAGGGGGATAAGATTTGATGTCGTAGCTTCAATCTAC-CCACTAC
*
219193 AA-TTGTAGGGGGATAAAGATTT-ACT-TCGATAGCTTCAATCCTACCCACTAC
1 AACTT-CAGGGGGAT-AAGATTTGA-TGTCG-TAGCTTCAAT-CTACCCACTAC
* *
219244 AACTTCAGGGGTATAGGATTTG
1 AACTTCAGGGGGATAAGATTTG
219266 GTTTTGTAGC
Statistics
Matches: 130, Mismatches: 33, Indels: 19
0.71 0.18 0.10
Matches are distributed among these distances:
49 3 0.02
50 87 0.67
51 36 0.28
52 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (49 bp):
AACTTCAGGGGGATAAGATTTGATGTCGTAGCTTCAATCTACCCACTAC
Found at i:219258 original size:101 final size:100
Alignment explanation
Indices: 219043--219373 Score: 287
Period size: 101 Copynumber: 3.3 Consensus size: 100
219033 GATCCATTGT
* *
219043 AACTTCAGGGATATAGGATTTGATGTCGTAACTTCATCTTGCTCCATTGCATCTTCAAGGAGATA
1 AACTTCAGGGGTATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTGCATCTTCAAGGAGATA
* *
219108 AAATTTGCTTTTGTAGCTTCAATCTAACCCACTAC
66 AAATTTACTTTCGTAGCTTCAATCTAACCCACTAC
* * * * * *
219143 AACTTCAAGGGTATAAGATTTGATGTCGTAGCTTCATTTTGCTCCACTGCAAT-TGT-AGGGGGA
1 AACTTCAGGGGTATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTGC-ATCT-TCAAGGAGA
219206 TAAAGATTTAC-TTCGATAGCTTCAATCCT-ACCCACTAC
64 TAAA-ATTTACTTTCG-TAGCTTCAAT-CTAACCCACTAC
* * * * * * * * * *
219244 AACTTCAGGGGTATAGGATTTGGTTTTGTAGCCTAATCTTGCTCTACTACAAT-TTCAAAGAAAT
1 AACTTCAGGGGTATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTGC-ATCTTCAAGGAGAT
* ** * * ** *
219308 AAAGATTTGCTACCGTAGTTTCAATCTGATTC-CTGC
65 AAA-ATTTACTTTCGTAGCTTCAATCTAACCCACTAC
* *
219344 AACTTCAAGGATATAGGATTTGATGTCGTA
1 AACTTCAGGGGTATAGGATTTGATGTCGTA
219374 CTGATCCCTT
Statistics
Matches: 187, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
100 88 0.47
101 95 0.51
102 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (100 bp):
AACTTCAGGGGTATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTGCATCTTCAAGGAGATA
AAATTTACTTTCGTAGCTTCAATCTAACCCACTAC
Found at i:220238 original size:4 final size:4
Alignment explanation
Indices: 220229--220255 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
220219 TTTATTTTAT
220229 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
220256 TGGTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:221516 original size:12 final size:11
Alignment explanation
Indices: 221495--221524 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
221485 CAGCATAAAC
221495 TTTTTTTTTCT
1 TTTTTTTTTCT
221506 TTTTCTTTTTCT
1 TTTT-TTTTTCT
221518 TTTTTTT
1 TTTTTTT
221525 ATTTCAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:221564 original size:44 final size:45
Alignment explanation
Indices: 221516--221614 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 45
221506 TTTTCTTTTT
* * * *
221516 CTTTTTTTTATTTCAAGATGCCTTTTGCGGGTTTTCGTCTCGA-C
1 CTTTTTTTTATTTCAAAATGCCCTTTGCGAGTTTTCATCTCGACC
*
221560 CTTTTTTTTATTTTAAAATGCCCTTTGCGAGTTTTCATCTCGACC
1 CTTTTTTTTATTTCAAAATGCCCTTTGCGAGTTTTCATCTCGACC
221605 CTTTTTTTTA
1 CTTTTTTTTA
221615 ACCTCATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 38 0.78
45 11 0.22
ACGTcount: A:0.14, C:0.20, G:0.13, T:0.53
Consensus pattern (45 bp):
CTTTTTTTTATTTCAAAATGCCCTTTGCGAGTTTTCATCTCGACC
Found at i:228458 original size:6 final size:6
Alignment explanation
Indices: 228447--228495 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
228437 GTTGTGATCA
* * * *
228447 AAAGTG AAAGTG AAAGTC AAAGTG AAAGTG AAATTG GAATTG AAAGTG
1 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG
228495 A
1 A
228496 TATGAATTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.29, T:0.20
Consensus pattern (6 bp):
AAAGTG
Found at i:233765 original size:18 final size:20
Alignment explanation
Indices: 233738--233788 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
233728 CAGCTCTTCA
233738 TTATTTAAATTTATTA-A-T
1 TTATTTAAATTTATTATATT
* *
233756 TTATTAAAATATATTATATT
1 TTATTTAAATTTATTATATT
233776 TTATTTAAATTTA
1 TTATTTAAATTTA
233789 AATTAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 14 0.52
19 1 0.04
20 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTAAATTTATTATATT
Found at i:236807 original size:9 final size:9
Alignment explanation
Indices: 236760--236809 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
236750 TAATTTTTTT
236760 AAAAAATAA
1 AAAAAATAA
*
236769 TAAAAATAA
1 AAAAAATAA
*
236778 TTCAAAAATAA
1 --AAAAAATAA
*
236789 AAGAAATAA
1 AAAAAATAA
236798 AAAAAATAA
1 AAAAAATAA
236807 AAA
1 AAA
236810 GGTTAGTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 26 0.76
11 8 0.24
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (9 bp):
AAAAAATAA
Found at i:236906 original size:46 final size:46
Alignment explanation
Indices: 236839--236930 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
236829 AATTGAGGGA
236839 AACAACCAAGCTGTCATTCCATCTTAATAGTTTAACAATTTAATTT
1 AACAACCAAGCTGTCATTCCATCTTAATAGTTTAACAATTTAATTT
236885 AACAACCAAGCTGTCATTCCATCTTAATAGTTTAACAATTTAATTT
1 AACAACCAAGCTGTCATTCCATCTTAATAGTTTAACAATTTAATTT
236931 TCTATAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (46 bp):
AACAACCAAGCTGTCATTCCATCTTAATAGTTTAACAATTTAATTT
Found at i:238223 original size:27 final size:27
Alignment explanation
Indices: 238192--238248 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
238182 TGGTTGGTCA
238192 AGAGTAGTTTTCTATTGGTCCGGGTTT
1 AGAGTAGTTTTCTATTGGTCCGGGTTT
*
238219 AGAGTAGTTTTCTATTGGTTCGGGTTT
1 AGAGTAGTTTTCTATTGGTCCGGGTTT
238246 AGA
1 AGA
238249 AAAATCTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.09, G:0.30, T:0.44
Consensus pattern (27 bp):
AGAGTAGTTTTCTATTGGTCCGGGTTT
Found at i:246341 original size:25 final size:25
Alignment explanation
Indices: 246313--246361 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
246303 AAGAGTAGTC
* * *
246313 ATGAACTTCAAATATAAATAATAAA
1 ATGAACATCAAAAATAAAAAATAAA
*
246338 ATGAACATGAAAAATAAAAAATAA
1 ATGAACATCAAAAATAAAAAATAA
246362 TGAAACGAAT
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:0.65, C:0.06, G:0.06, T:0.22
Consensus pattern (25 bp):
ATGAACATCAAAAATAAAAAATAAA
Found at i:246375 original size:28 final size:28
Alignment explanation
Indices: 246328--246384 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
246318 CTTCAAATAT
*
246328 AAATAATAAAATGAACATGAAAAATAAA
1 AAATAATAAAACGAACATGAAAAATAAA
* *
246356 AAATAATGAAACGAATATGAAAAATAAA
1 AAATAATAAAACGAACATGAAAAATAAA
246384 A
1 A
246385 TGTTTGGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.18
Consensus pattern (28 bp):
AAATAATAAAACGAACATGAAAAATAAA
Found at i:248819 original size:37 final size:37
Alignment explanation
Indices: 248766--248901 Score: 146
Period size: 37 Copynumber: 3.6 Consensus size: 37
248756 GGATCATCGA
* *
248766 CACAAAGGCTTGCTAGGCACAAAGCCCGAATACACCGG
1 CACAAA-GCCTGCTAGGCACATAGCCCGAATACACCGG
* * * * * *
248804 CACAAAGCCTGCTAGGTACATAGTCCAAACACATCGA
1 CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGG
* **
248841 CACGAAGCCTGCTAGGCACATAGCCCGAATACACTAG
1 CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGG
* *
248878 CACAAAGCTTGCTAGGTACATAGC
1 CACAAAGCCTGCTAGGCACATAGC
248902 TTGAATTCTT
Statistics
Matches: 78, Mismatches: 20, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
37 72 0.92
38 6 0.08
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.15
Consensus pattern (37 bp):
CACAAAGCCTGCTAGGCACATAGCCCGAATACACCGG
Found at i:248882 original size:74 final size:75
Alignment explanation
Indices: 248760--248900 Score: 221
Period size: 74 Copynumber: 1.9 Consensus size: 75
248750 CTTCTTGGAT
* *
248760 CATCGACACAAAGGCTTGCTAGGCACAAAGCCCGAATACACCGGCACAAAGCCTGCTAGGTACAT
1 CATCGACACAAAGGCCTGCTAGGCACAAAGCCCGAATACACCAGCACAAAGCCTGCTAGGTACAT
248825 AGTCCAAACA
66 AGTCCAAACA
* * * *
248835 CATCGACACGAA-GCCTGCTAGGCACATAGCCCGAATACACTAGCACAAAGCTTGCTAGGTACAT
1 CATCGACACAAAGGCCTGCTAGGCACAAAGCCCGAATACACCAGCACAAAGCCTGCTAGGTACAT
248899 AG
66 AG
248901 CTTGAATTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 49 0.82
75 11 0.18
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.15
Consensus pattern (75 bp):
CATCGACACAAAGGCCTGCTAGGCACAAAGCCCGAATACACCAGCACAAAGCCTGCTAGGTACAT
AGTCCAAACA
Found at i:256449 original size:17 final size:19
Alignment explanation
Indices: 256413--256450 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
256403 GCACATGTAA
*
256413 TTCCAATTCATATAATCAT
1 TTCCAATTCAAATAATCAT
256432 TTCC-ATTCAAAT-ATCAT
1 TTCCAATTCAAATAATCAT
256449 TT
1 TT
256451 ATCAAGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (19 bp):
TTCCAATTCAAATAATCAT
Found at i:272298 original size:16 final size:15
Alignment explanation
Indices: 272250--272315 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
272240 GTATTGAAGC
* *
272250 AGAAGAAGAAGAAGA
1 AGAAGAAAAAAAAGA
* *
272265 AGAAAGAAAGAAATGA
1 AG-AAGAAAAAAAAGA
272281 AGAAG-AAAAAAAG-
1 AGAAGAAAAAAAAGA
272294 AGAAGGAAAAAAAAGA
1 AGAA-GAAAAAAAAGA
272310 AGAAGA
1 AGAAGA
272316 CGTTGCCCCG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 4 0.10
14 7 0.17
15 15 0.37
16 15 0.37
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AGAAGAAAAAAAAGA
Found at i:272303 original size:13 final size:13
Alignment explanation
Indices: 272280--272313 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
272270 GAAAGAAATG
272280 AAGAAGAAAAAAA
1 AAGAAGAAAAAAA
* *
272293 GAGAAGGAAAAAA
1 AAGAAGAAAAAAA
272306 AAGAAGAA
1 AAGAAGAA
272314 GACGTTGCCC
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAAA
Found at i:275398 original size:19 final size:20
Alignment explanation
Indices: 275371--275410 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
275361 ATTCAAATTA
* *
275371 TCATCTATAC-ACTTATTTT
1 TCATATATACAACATATTTT
275390 TCATATATACAACATATTTT
1 TCATATATACAACATATTTT
275410 T
1 T
275411 ATCCAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (20 bp):
TCATATATACAACATATTTT
Found at i:277463 original size:32 final size:30
Alignment explanation
Indices: 277401--277463 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
277391 ATGCATGACT
*
277401 ACTAGATACATCTATAAATACATTCATTAA
1 ACTAGATACATATATAAATACATTCATTAA
* *
277431 ACTAGATACATATACTCTAATACATTCGTTAA
1 ACTAGATACATATA-T-AAATACATTCATTAA
277463 A
1 A
277464 TATAAGTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 13 0.46
31 1 0.04
32 14 0.50
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.33
Consensus pattern (30 bp):
ACTAGATACATATATAAATACATTCATTAA
Found at i:281831 original size:33 final size:32
Alignment explanation
Indices: 281793--281856 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
281783 GCATGACTAT
* * *
281793 TAGATACATCTTCTCTAAATGCATTCATTAAAC
1 TAGATACATATACT-TAAATACATTCATTAAAC
*
281826 TAGATACATATACTTTAATACATTCATTAAA
1 TAGATACATATACTTAAATACATTCATTAAA
281857 TATAAGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.38
Consensus pattern (32 bp):
TAGATACATATACTTAAATACATTCATTAAAC
Found at i:286964 original size:30 final size:31
Alignment explanation
Indices: 286913--286975 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
286903 AATTTATATC
286913 TTTATAATTTTAAAAAAATTAAA-TCAAATT
1 TTTATAATTTTAAAAAAATTAAAGTCAAATT
* * * *
286943 TTTATAATTTTAGAGAGATTAAAGTGAAATT
1 TTTATAATTTTAAAAAAATTAAAGTCAAATT
286974 TT
1 TT
286976 ACTTTTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTATAATTTTAAAAAAATTAAAGTCAAATT
Found at i:287423 original size:16 final size:16
Alignment explanation
Indices: 287402--287434 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
287392 TATTAATATA
287402 AATTATTT-TGAGTTTG
1 AATTATTTCTGA-TTTG
287418 AATTATTTCTGATTTG
1 AATTATTTCTGATTTG
287434 A
1 A
287435 GCTATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (16 bp):
AATTATTTCTGATTTG
Found at i:294330 original size:11 final size:11
Alignment explanation
Indices: 294314--294338 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
294304 TCTAAAGTAC
294314 TTTTCTTTTCT
1 TTTTCTTTTCT
294325 TTTTCTTTTCT
1 TTTTCTTTTCT
294336 TTT
1 TTT
294339 GNNGGGGGGG
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:295133 original size:21 final size:22
Alignment explanation
Indices: 295086--295133 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
295076 TTTAAGGATT
* *
295086 AATTTTTTAAAATTATGAGAGTT
1 AATTTTTTAAAATTAT-AGACTA
295109 AATTTTTTAAAATTAT-GACTA
1 AATTTTTTAAAATTATAGACTA
295130 AATT
1 AATT
295134 GATATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
23 16 0.70
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (22 bp):
AATTTTTTAAAATTATAGACTA
Found at i:298311 original size:20 final size:20
Alignment explanation
Indices: 298274--298312 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
298264 CAAGTCACAG
**
298274 TCTCATACCAATTTCACATA
1 TCTCATACCAATACCACATA
*
298294 TCTCATATCAATACCACAT
1 TCTCATACCAATACCACAT
298313 TTTATAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (20 bp):
TCTCATACCAATACCACATA
Found at i:300595 original size:26 final size:26
Alignment explanation
Indices: 300541--300696 Score: 154
Period size: 26 Copynumber: 6.0 Consensus size: 26
300531 TTGTAAAACG
* *
300541 TAGCTTCTT-TGAGTCCAGAACAGAGTT
1 TAGC-TCTTATGAGCCCAG-ACAGAATT
*
300568 TAGCTCTTATGAGCCCAGATAGAATT
1 TAGCTCTTATGAGCCCAGACAGAATT
* * * *
300594 TAGTTCATACGAGCCCAAACAGAATT
1 TAGCTCTTATGAGCCCAGACAGAATT
* * *
300620 TAACTCATATGAGCCCAGACAGAGTT
1 TAGCTCTTATGAGCCCAGACAGAATT
*
300646 TAGCTCTTATGAGCCTAGACA-AAGTT
1 TAGCTCTTATGAGCCCAGACAGAA-TT
* *
300672 TAGCTCTTACGAGCCCAAACAGAAT
1 TAGCTCTTATGAGCCCAGACAGAAT
300697 AAAACTCATT
Statistics
Matches: 106, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.01
26 91 0.86
27 14 0.13
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (26 bp):
TAGCTCTTATGAGCCCAGACAGAATT
Found at i:300655 original size:78 final size:78
Alignment explanation
Indices: 300550--300739 Score: 240
Period size: 78 Copynumber: 2.4 Consensus size: 78
300540 GTAGCTTCTT
* *
300550 TGAGTCCAGAACAGAGTTTAGCTCTTATGAGCCCAGATAGAA-TTTAGTTCATACGAGCCCAAAC
1 TGAG-CCAGAACAGAGTTTAGCTCTTATGAGCCCAGACA-AAGTTTAGCTCATACGAGCCCAAAC
**
300614 AGAATTTAACTCATA
64 AGAATAAAACTCATA
* *
300629 TGAGCCCAG-ACAGAGTTTAGCTCTTATGAGCCTAGACAAAGTTTAGCTCTTACGAGCCCAAACA
1 TGAG-CCAGAACAGAGTTTAGCTCTTATGAGCCCAGACAAAGTTTAGCTCATACGAGCCCAAACA
*
300693 GAATAAAACTCATT
65 GAATAAAACTCATA
* * *
300707 TGAGCCAGAAATAGAGTATCGCTCTTATGAGCC
1 TGAGCCAG-AACAGAGTTTAGCTCTTATGAGCC
300740 AGAAATAGTG
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
77 6 0.06
78 63 0.65
79 28 0.29
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (78 bp):
TGAGCCAGAACAGAGTTTAGCTCTTATGAGCCCAGACAAAGTTTAGCTCATACGAGCCCAAACAG
AATAAAACTCATA
Found at i:307615 original size:17 final size:19
Alignment explanation
Indices: 307595--307629 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
307585 TTAAAATAGT
307595 AACAAAA-TTA-ATAATAA
1 AACAAAAGTTATATAATAA
307612 AACAAAAGTTATATAATA
1 AACAAAAGTTATATAATA
307630 CTCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (19 bp):
AACAAAAGTTATATAATAA
Found at i:309402 original size:15 final size:16
Alignment explanation
Indices: 309384--309413 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
309374 TTATTAAATA
309384 TTAAATT-AAATTAAC
1 TTAAATTAAAATTAAC
309399 TTAAATTAAAATTAA
1 TTAAATTAAAATTAA
309414 TATATTCTAA
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:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATTAAAATTAAC
Found at i:309552 original size:36 final size:36
Alignment explanation
Indices: 309498--309571 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
309488 GAATTTGAGT
* *
309498 AAAATTTTAAGTTCATA-TTTAAGATTGGGCTTGGGC
1 AAAATTTTAAATTCATATTTTAA-ATCGGGCTTGGGC
309534 AAAATTTTAAAATT-ATATTTTAAATCGGGCTTGGGC
1 AAAATTTT-AAATTCATATTTTAAATCGGGCTTGGGC
309570 AA
1 AA
309572 GTATTTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 25 0.74
37 9 0.26
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (36 bp):
AAAATTTTAAATTCATATTTTAAATCGGGCTTGGGC
Found at i:309801 original size:3 final size:3
Alignment explanation
Indices: 309793--309818 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
309783 TAATACTAAA
309793 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
309819 GATTTTGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:322359 original size:5 final size:5
Alignment explanation
Indices: 322349--322374 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
322339 ATGGTGAACT
322349 ACACC ACACC ACACC ACACC ACACC A
1 ACACC ACACC ACACC ACACC ACACC A
322375 ATAGAACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (5 bp):
ACACC
Found at i:332827 original size:170 final size:170
Alignment explanation
Indices: 332542--332852 Score: 568
Period size: 170 Copynumber: 1.8 Consensus size: 170
332532 CTTTAATTGT
*
332542 TGGTTTTTAAGGATTTTACTTCAATCAACTAGTCACTACTCCAGTTGGATCTTTCGATCTTCCGA
1 TGGTTTTTAAGGATTTTACTTCAATCAACTAGTCACTACCCCAGTTGGATCTTTCGATCTTCCGA
* *
332607 CAGCATAACAAGTCGATAGAGACTACTTATCGCTAGATGTCTGGTGGTACTAAAAAGAATATATG
66 CAGCATAACAAGTCGATAGAGACTACTTATCGCTAGATGTCTGATGGTACTAAAAAGAACATATG
332672 TTTTCTCCCCATTTATTATATAATTTCTTCCCATTAATCA
131 TTTTCTCCCCATTTATTATATAATTTCTTCCCATTAATCA
* *
332712 TGGTTTTTAAGGATTTTATTTCAATCAACTAGTCATTACCCCAGTTGGATCTTTCGATCTTCCGA
1 TGGTTTTTAAGGATTTTACTTCAATCAACTAGTCACTACCCCAGTTGGATCTTTCGATCTTCCGA
*
332777 CAGCATAACAAGTTGATAGAGACTACTTATCGCTAGATGTCTGATGGTACTAAAAAGAACATATG
66 CAGCATAACAAGTCGATAGAGACTACTTATCGCTAGATGTCTGATGGTACTAAAAAGAACATATG
332842 TTTTCTCCCCA
131 TTTTCTCCCCA
332853 CTTTTTCTAC
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 135 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (170 bp):
TGGTTTTTAAGGATTTTACTTCAATCAACTAGTCACTACCCCAGTTGGATCTTTCGATCTTCCGA
CAGCATAACAAGTCGATAGAGACTACTTATCGCTAGATGTCTGATGGTACTAAAAAGAACATATG
TTTTCTCCCCATTTATTATATAATTTCTTCCCATTAATCA
Found at i:341092 original size:17 final size:17
Alignment explanation
Indices: 341063--341109 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
341053 CTGTAGTATA
*
341063 ATTGTCCCTGCATTTTT
1 ATTGTCACTGCATTTTT
*
341080 ATTTTCACTGCATTTTT
1 ATTGTCACTGCATTTTT
*
341097 ATTGTCGCTGCAT
1 ATTGTCACTGCAT
341110 CTACATTGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.15, C:0.21, G:0.13, T:0.51
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Done.