Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019059.1 Corchorus olitorius cultivar O-4 contig19092, 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: 90418
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1262 original size:21 final size:23
Alignment explanation
Indices: 1238--1287 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
1228 CAAGCAAAGG
1238 CAACTCAGTTAC-AAAGA-AAAA
1 CAACTCAGTTACGAAAGAGAAAA
1259 CAA--CAGTTACTGAAAGAGAAAA
1 CAACTCAGTTAC-GAAAGAGAAAA
*
1281 CAGCTCA
1 CAACTCA
1288 CCATTCTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
19 7 0.30
21 8 0.35
22 6 0.26
24 2 0.09
ACGTcount: A:0.52, C:0.20, G:0.14, T:0.14
Consensus pattern (23 bp):
CAACTCAGTTACGAAAGAGAAAA
Found at i:1267 original size:19 final size:21
Alignment explanation
Indices: 1243--1282 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1233 AAAGGCAACT
1243 CAGTTAC-AAAGA-AAAACAA
1 CAGTTACGAAAGAGAAAACAA
1262 CAGTTACTGAAAGAGAAAACA
1 CAGTTAC-GAAAGAGAAAACA
1283 GCTCACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.12
Consensus pattern (21 bp):
CAGTTACGAAAGAGAAAACAA
Found at i:3833 original size:14 final size:14
Alignment explanation
Indices: 3814--3854 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3804 TTTTTATAAT
* *
3814 TAAAAAAATTTCAA
1 TAAAAATATTTAAA
*
3828 TAAAAATATTAAAA
1 TAAAAATATTTAAA
3842 TAAAAATATTTAA
1 TAAAAATATTTAA
3855 TTTTATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAATATTTAAA
Found at i:12563 original size:27 final size:27
Alignment explanation
Indices: 12508--12565 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12498 TTTGCTACTC
* * ** *
12508 AACTTTTCCTACTCCTTTACATTACCA
1 AACTGTTCCTACTCCTTAACAACAACA
12535 AACTGTTCCTACTCCTTAACAACAACA
1 AACTGTTCCTACTCCTTAACAACAACA
12562 AACT
1 AACT
12566 ACATCAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.33
Consensus pattern (27 bp):
AACTGTTCCTACTCCTTAACAACAACA
Found at i:15515 original size:59 final size:59
Alignment explanation
Indices: 15351--15516 Score: 278
Period size: 59 Copynumber: 2.8 Consensus size: 59
15341 CATGTTTCTC
**
15351 TTAAAGGCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTCAGATTTTTCCTT
1 TTAAAGGCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGGGATTTTTCCTT
*
15410 TTAAAGGCCATTCCCAAAGTCTTAATTCATTTGGGGTTAGGCACTTGGGATTTTTCCTT
1 TTAAAGGCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGGGATTTTTCCTT
* * *
15469 TTAAAGCCCATTTCCAAAGTCTTAATTCATTTGGTCTTAGGCACTTGG
1 TTAAAGGCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGG
15517 TTTCTTTTTC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 100 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (59 bp):
TTAAAGGCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGGGATTTTTCCTT
Found at i:17948 original size:2 final size:2
Alignment explanation
Indices: 17943--17975 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17933 TGTGTGTGTG
17943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17976 CAAATAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20926 original size:26 final size:26
Alignment explanation
Indices: 20865--21113 Score: 230
Period size: 26 Copynumber: 9.1 Consensus size: 26
20855 GAGAGAAAAT
* **
20865 TTAAAGAGTAAAAGGAAATTTGATGG
1 TTAAAGAGTAAAAGGAAATTTGGTAA
* *
20891 TCAAAAAGTAAAAGGAAATTTGGTAA
1 TTAAAGAGTAAAAGGAAATTTGGTAA
* *
20917 TTAAAGAGTAAAATGAAATTGGGTAA
1 TTAAAGAGTAAAAGGAAATTTGGTAA
**
20943 TTAAAGAGTAATTGGGAAATTTGGTTAA
1 TTAAAGAGTAA-AAGGAAATTTGG-TAA
*
20971 TTAAAGAGTAAAAGGAAATTTGGTCA
1 TTAAAGAGTAAAAGGAAATTTGGTAA
20997 TTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAA
1 TTAAAGAGTAAAAGG--A------AATTTGGTAA
* *
21031 TTAAAGAGTAAAATGAAATTGGGTAA
1 TTAAAGAGTAAAAGGAAATTTGGTAA
**
21057 TTAAAAGAGTAATTGGTAAATTTGGGTAA
1 TT-AAAGAGTAAAAGG-AAATTT-GGTAA
*
21086 CTAAAGAGTAAAAGGAAA-TTGGTTAA
1 TTAAAGAGTAAAAGGAAATTTGG-TAA
21112 TT
1 TT
21114 TGGTTAATTA
Statistics
Matches: 182, Mismatches: 27, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
25 2 0.01
26 88 0.48
27 31 0.17
28 31 0.17
29 6 0.03
32 1 0.01
34 23 0.13
ACGTcount: A:0.46, C:0.01, G:0.23, T:0.29
Consensus pattern (26 bp):
TTAAAGAGTAAAAGGAAATTTGGTAA
Found at i:20981 original size:54 final size:53
Alignment explanation
Indices: 20904--21113 Score: 249
Period size: 54 Copynumber: 3.8 Consensus size: 53
20894 AAAAGTAAAA
*
20904 GGAAATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAATTAAAGAGTAATTG
1 GGAAATTTGGTAATTAAAGAGTAAAAGGAAATTGGGTAATTAAAGAGTAATTG
* *
20957 GGAAATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCATTAAAGAGTAAAAGGAAATTG
1 GGAAATTTGG-TAATTAAAGAGTAAAAGGAAATTGGGTAATTAAAGAGT-------AATTG
** *
21018 GTTAATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAATTAAAAGAGTAATTG
1 GGAAATTTGGTAATTAAAGAGTAAAAGGAAATTGGGTAATT-AAAGAGTAATTG
* * *
21072 GTAAATTTGGGTAACTAAAGAGTAAAAGGAAATTGGTTAATT
1 GGAAATTT-GGTAATTAAAGAGTAAAAGGAAATTGGGTAATT
21114 TGGTTAATTA
Statistics
Matches: 135, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
53 10 0.07
54 47 0.35
55 30 0.22
60 28 0.21
61 20 0.15
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.30
Consensus pattern (53 bp):
GGAAATTTGGTAATTAAAGAGTAAAAGGAAATTGGGTAATTAAAGAGTAATTG
Found at i:21034 original size:34 final size:34
Alignment explanation
Indices: 20987--21058 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
20977 AGTAAAAGGA
* *
20987 AATTTGGTCATTAAAGAGTAAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGGT
*
21021 AATTTGGTAATTAAAGAGTAAAATGAAATTGGGT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGGT
21055 AATT
1 AATT
21059 AAAAGAGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.33
Consensus pattern (34 bp):
AATTTGGTAATTAAAGAGTAAAAGGAAATTGGGT
Found at i:21104 original size:55 final size:53
Alignment explanation
Indices: 21005--21113 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 53
20995 CATTAAAGAG
* * *
21005 TAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAAT
1 TAAAAGGAAATTGGTAAATTTGGTAACTAAAGAGTAAAAGGAAATTGGGTAAT
* *
21058 TAAAAGAGTAATTGGTAAATTTGGGTAACTAAAGAGTAAAAGGAAATTGGTTAAT
1 TAAAAG-GAAATTGGTAAATTT-GGTAACTAAAGAGTAAAAGGAAATTGGGTAAT
21113 T
1 T
21114 TGGTTAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 6 0.12
54 13 0.27
55 30 0.61
ACGTcount: A:0.45, C:0.01, G:0.23, T:0.31
Consensus pattern (53 bp):
TAAAAGGAAATTGGTAAATTTGGTAACTAAAGAGTAAAAGGAAATTGGGTAAT
Found at i:21107 original size:35 final size:35
Alignment explanation
Indices: 21058--21140 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
21048 ATTGGGTAAT
*
21058 TAAAAGAGTAATTGGTAAATTTGGGTAACTAAAGAG
1 TAAAAG-GAAATTGGTAAATTTGGGTAACTAAAGAG
* * *
21094 TAAAAGGAAATTGGTTAATTTGGTTAATTAAAGAG
1 TAAAAGGAAATTGGTAAATTTGGGTAACTAAAGAG
21129 TAAAAGGAAATT
1 TAAAAGGAAATT
21141 TGGTCATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 37 0.86
36 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.23, T:0.30
Consensus pattern (35 bp):
TAAAAGGAAATTGGTAAATTTGGGTAACTAAAGAG
Found at i:21110 original size:89 final size:86
Alignment explanation
Indices: 20933--21197 Score: 298
Period size: 89 Copynumber: 3.0 Consensus size: 86
20923 AGTAAAATGA
* * * *
20933 AATTGGGTAATTAAAGAGT-AATTGGGAAATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCA
1 AATTTGGTAATTAAAGAGTAAAAT--GAAA-TTGGGTAATTAAAGAGTAAAAGGAAATTTGGTAA
*
20997 TTAAAGAGTAAAAGGAAATTGGTT
63 CTAAAGAGTAAAAGGAAATTGGTT
**
21021 AATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAATTAAAAGAGTAATTGGTAAATTTGGGTAA
1 AATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAATT-AAAGAGTAAAAGG-AAATTT-GGTAA
21086 CTAAAGAGTAAAAGGAAATTGGTT
63 CTAAAGAGTAAAAGGAAATTGGTT
* * * *
21110 AATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCATTAAAGAGTGAAAGGAAAGGGAATTTGG
1 AATTTGG-TAATTAAAGAGTAAAATGAAATTGGGTAATTAAAGAGT---A--AAAGGAAATTTGG
* *
21175 TAATTAAAGAGTAAAATGAAATT
60 TAACTAAAGAGTAAAAGGAAATT
21198 AGACAATTAA
Statistics
Matches: 152, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
86 9 0.06
87 15 0.10
88 24 0.16
89 44 0.29
90 28 0.18
92 24 0.16
93 5 0.03
94 3 0.02
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.30
Consensus pattern (86 bp):
AATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAATTAAAGAGTAAAAGGAAATTTGGTAACTA
AAGAGTAAAAGGAAATTGGTT
Found at i:21153 original size:26 final size:26
Alignment explanation
Indices: 21110--21242 Score: 131
Period size: 26 Copynumber: 4.9 Consensus size: 26
21100 GAAATTGGTT
21110 AATTTGGTTAATTAAAGAGTAAAAGGA
1 AATTTGG-TAATTAAAGAGTAAAAGGA
* *
21137 AATTTGGTCATTAAAGAGTGAAAGGAAAGGG
1 AATTTGGTAATTAAAGAGT---A--AAAGGA
*
21168 AATTTGGTAATTAAAGAGTAAAATGA
1 AATTTGGTAATTAAAGAGTAAAAGGA
* ** * * *
21194 AATTAGACAATTAATGAGTAAGAGAA
1 AATTTGGTAATTAAAGAGTAAAAGGA
21220 AATTTGGTAATTAAAGAGTAAAA
1 AATTTGGTAATTAAAGAGTAAAA
21243 TTTAGTAATG
Statistics
Matches: 84, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
26 52 0.62
27 7 0.08
28 1 0.01
29 1 0.01
31 23 0.27
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.27
Consensus pattern (26 bp):
AATTTGGTAATTAAAGAGTAAAAGGA
Found at i:21172 original size:31 final size:31
Alignment explanation
Indices: 21131--21195 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
21121 TTAAAGAGTA
* *
21131 AAAGGAAATTTGGTCATTAAAGAGTGAAAGG
1 AAAGGAAATTTGGTAATTAAAGAGTAAAAGG
* *
21162 AAAGGGAATTTGGTAATTAAAGAGTAAAATG
1 AAAGGAAATTTGGTAATTAAAGAGTAAAAGG
21193 AAA
1 AAA
21196 TTAGACAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (31 bp):
AAAGGAAATTTGGTAATTAAAGAGTAAAAGG
Found at i:21207 original size:57 final size:55
Alignment explanation
Indices: 21087--21243 Score: 153
Period size: 57 Copynumber: 2.8 Consensus size: 55
21077 TTTGGGTAAC
* * *
21087 TAAAGAGTAAAAGGAAATTGGTTAATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCAT
1 TAAAGAGT-AAAGGAAA--GG--AATTTGG-TAATTAAAGAGTAAAATGAAATTTAGACAT
21148 TAAAGAGTGAAAGGAAAGGGAATTTGGTAATTAAAGAGTAAAATGAAA-TTAGACAAT
1 TAAAGAGT-AAAGGAAA-GGAATTTGGTAATTAAAGAGTAAAATGAAATTTAGAC-AT
*
21205 TAATGAGT-AA-GAGAA--AATTTGGTAATTAAAGAGTAAAAT
1 TAAAGAGTAAAGGA-AAGGAATTTGGTAATTAAAGAGTAAAAT
21244 TTAGTAATGA
Statistics
Matches: 88, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
52 24 0.27
54 2 0.02
55 4 0.05
56 4 0.05
57 29 0.33
58 7 0.08
60 2 0.02
61 16 0.18
ACGTcount: A:0.48, C:0.01, G:0.23, T:0.27
Consensus pattern (55 bp):
TAAAGAGTAAAGGAAAGGAATTTGGTAATTAAAGAGTAAAATGAAATTTAGACAT
Found at i:21243 original size:21 final size:20
Alignment explanation
Indices: 21213--21251 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21203 ATTAATGAGT
*
21213 AAGAGAAAATTTGGTAATTA
1 AAGAGAAAATTTAGTAATTA
21233 AAGAGTAAAATTTAGTAAT
1 AAGAG-AAAATTTAGTAAT
21252 GAAATTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (20 bp):
AAGAGAAAATTTAGTAATTA
Found at i:21462 original size:21 final size:21
Alignment explanation
Indices: 21417--21461 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
21407 AAAATGAGGT
*
21417 AAAATGAAATTTTGCTAATTA
1 AAAATGAAATTTCGCTAATTA
*
21438 AAAATGAAA-TTCGGTAATTA
1 AAAATGAAATTTCGCTAATTA
21458 AAAA
1 AAAA
21462 AAAGGGGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (21 bp):
AAAATGAAATTTCGCTAATTA
Found at i:25468 original size:21 final size:21
Alignment explanation
Indices: 25428--25468 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25418 AGAGATCGCT
* *
25428 CGCCGAGACGAAGAGGCGAAG
1 CGCCGAGAAGAAGAGACGAAG
*
25449 CGCCGAGAAGAAGCGACGAA
1 CGCCGAGAAGAAGAGACGAA
25469 TGCTCAGATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.39, T:0.00
Consensus pattern (21 bp):
CGCCGAGAAGAAGAGACGAAG
Found at i:33824 original size:58 final size:59
Alignment explanation
Indices: 33693--33857 Score: 296
Period size: 58 Copynumber: 2.8 Consensus size: 59
33683 CCTGTTTCTC
*
33693 TTAAAGCCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGAGATTTTTCCTT
1 TTAAAGCCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGGGATTTTTCCTT
*
33752 TTAAAGCCCATTCCCAAAGTCTTAATTCATTTGGGCTTA-ACACTTGGGATTTTTCCTT
1 TTAAAGCCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGGGATTTTTCCTT
*
33810 TTAAAGCTCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGG
1 TTAAAGCCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGG
33858 TTTCTTTTTC
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
58 55 0.54
59 46 0.46
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (59 bp):
TTAAAGCCCATTCCCAAAGTCTTAATTCATTTGGGCTTAGGCACTTGGGATTTTTCCTT
Found at i:36281 original size:2 final size:2
Alignment explanation
Indices: 36274--36310 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
36264 ACTTTGTTTG
36274 TA TA TA TA TA TA -A TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36311 CAAATAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:37280 original size:26 final size:26
Alignment explanation
Indices: 37217--37676 Score: 221
Period size: 26 Copynumber: 16.6 Consensus size: 26
37207 GAGAGAGAAA
*
37217 AATTAAAGAGTAAAAGGAAATTTGAT
1 AATTAAAGAGTAAAAGGAAATTTGGT
** * * *
37243 GGTCAAAAAGTAAAGGGAAATTTGGT
1 AATTAAAGAGTAAAAGGAAATTTGGT
* *
37269 AATTAAAGAGTAAAATGAAATTGGGT
1 AATTAAAGAGTAAAAGGAAATTTGGT
**
37295 AATTAAAGAGTAATTGGGAAATTTGGTT
1 AATTAAAGAGTAA-AAGGAAATTTGG-T
37323 AATTAAAGAGTAAAAGGAAATTTGGT
1 AATTAAAGAGTAAAAGGAAATTTGGT
*
37349 CATTAAAGAGTAAAAGGAAATTGGTTAATTTGGT
1 AATTAAAGAGTAAAAGG--A------AATTTGGT
* *
37383 AATTAAAGAGTAAAATGAAATTGGGT
1 AATTAAAGAGTAAAAGGAAATTTGGT
**
37409 AATTAAAGAGTAATTGGTAAATTTGGGT
1 AATTAAAGAGTAAAAGG-AAATTT-GGT
*
37437 AACTAAAGAG--AAAGGAAA-TTGGTT
1 AATTAAAGAGTAAAAGGAAATTTGG-T
** * * * *
37461 AATT-TGGTTAATTAAAGAGTAAA--AGGA
1 AATTAAAG---AGTAAA-AGGAAATTTGGT
* *
37488 AATTTGGTCATTAAAGAGTGAAAGGAAATTGGTTAATTTGGT
1 AA--T--T-A--AAG-AGTAAAAGG--A------AATTTGGT
* **
37530 AATTAAAGAGTAAAATGAAATCGGGT
1 AATTAAAGAGTAAAAGGAAATTTGGT
* **
37556 AATTAAAAAGTAATTGGTAAATTTGGTT
1 AATTAAAGAGTAAAAGG-AAATTTGG-T
*
37584 AATTAAAGAGTAAAAGGGAATTTGGT
1 AATTAAAGAGTAAAAGGAAATTTGGT
* * **
37610 AATTAAAGAGTAAAATGAAATTAGAC
1 AATTAAAGAGTAAAAGGAAATTTGGT
* * *
37636 AATTAATGAGTAAGAGAAAATTTGGT
1 AATTAAAGAGTAAAAGGAAATTTGGT
37662 AATTAAAGAGTAAAA
1 AATTAAAGAGTAAAA
37677 TTTAGTAATG
Statistics
Matches: 320, Mismatches: 75, Indels: 78
0.68 0.16 0.16
Matches are distributed among these distances:
23 3 0.01
24 6 0.02
25 3 0.01
26 167 0.52
27 38 0.12
28 46 0.14
29 6 0.02
31 1 0.00
32 4 0.01
33 4 0.01
34 31 0.10
35 2 0.01
37 1 0.00
38 1 0.00
40 3 0.01
42 4 0.01
ACGTcount: A:0.47, C:0.01, G:0.23, T:0.29
Consensus pattern (26 bp):
AATTAAAGAGTAAAAGGAAATTTGGT
Found at i:37388 original size:34 final size:34
Alignment explanation
Indices: 37341--37559 Score: 123
Period size: 34 Copynumber: 6.1 Consensus size: 34
37331 AGTAAAAGGA
*
37341 AATTTGGTCATTAAAGAGTAAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
*
37375 AATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAATT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATT-GG---TT
*
37413 AAAGAGTAATTGGTAAATTTGGGTAACTAAAG-AGAAAGGAAATTGGTT
1 --A-A-T--TTGGT-AA--T---TAA--AGAGTA-AAAGGAAATTGGTT
37461 AATTTGGTTAATTAAAGAGTAAAAGG--A------
1 AATTTGG-TAATTAAAGAGTAAAAGGAAATTGGTT
* *
37488 AATTTGGTCATTAAAGAGTGAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
* * *
37522 AATTTGGTAATTAAAGAGTAAAATGAAATCGGGT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
37556 AATT
1 AATT
37560 AAAAAGTAAT
Statistics
Matches: 144, Mismatches: 12, Indels: 58
0.67 0.06 0.27
Matches are distributed among these distances:
26 16 0.11
27 7 0.05
28 1 0.01
33 1 0.01
34 61 0.42
35 10 0.07
36 1 0.01
37 3 0.02
38 2 0.01
40 2 0.01
41 1 0.01
42 7 0.05
43 1 0.01
44 6 0.04
45 3 0.02
46 1 0.01
47 1 0.01
48 2 0.01
50 3 0.02
51 3 0.02
52 12 0.08
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (34 bp):
AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
Found at i:37443 original size:28 final size:29
Alignment explanation
Indices: 37260--37623 Score: 236
Period size: 26 Copynumber: 12.8 Consensus size: 29
37250 AAGTAAAGGG
*
37260 AAATTT-GGTAATTAAAGAGTAAAAT-G-
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
*
37286 AAA-TTGGGTAATTAAAGAGT-AATTGGG
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
* *
37313 AAATTTGGTTAATTAAAGAGTAAA-AGG-
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
*
37340 AAATTT-GGTCATTAAAGAGTAAAAGGAAATTGGT
1 AAATTTGGGTAATTAAAGAGT------AAATTGGT
* *
37374 TAATTT-GGTAATTAAAGAGTAAAAT-G-
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
37400 AAA-TTGGGTAATTAAAGAGT-AATTGGT
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
* *
37427 AAATTTGGGTAACTAAAGAGAAAGGAAATTGGT
1 AAATTTGGGTAA-TTAA-AG--AGTAAATTGGT
* * *
37460 TAATTTGGTTAATTAAAGAGTAAA-AGG-
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
*
37487 AAATTT-GGTCATTAAAGAGTGAAAGGAAATTGGT
1 AAATTTGGGTAATTAAAGAGT------AAATTGGT
* *
37521 TAATTT-GGTAATTAAAGAGTAAAAT-G-
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
* *
37547 AAA-TCGGGTAATTAAAAAGT-AATTGGT
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
* *
37574 AAATTTGGTTAATTAAAGAGTAAA-AGG-
1 AAATTTGGGTAATTAAAGAGTAAATTGGT
*
37601 GAATTT-GGTAATTAAAGAGTAAA
1 AAATTTGGGTAATTAAAGAGTAAA
37624 ATGAAATTAG
Statistics
Matches: 268, Mismatches: 35, Indels: 70
0.72 0.09 0.19
Matches are distributed among these distances:
25 14 0.05
26 91 0.34
27 27 0.10
28 52 0.19
29 12 0.04
30 2 0.01
31 2 0.01
32 11 0.04
33 21 0.08
34 36 0.13
ACGTcount: A:0.45, C:0.01, G:0.23, T:0.30
Consensus pattern (29 bp):
AAATTTGGGTAATTAAAGAGTAAATTGGT
Found at i:37457 original size:33 final size:34
Alignment explanation
Indices: 37420--37491 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
37410 ATTAAAGAGT
37420 AATTGGTAAATTTGGGTAACTAAAGAG-AAAGGA
1 AATTGGTAAATTTGGGTAACTAAAGAGAAAAGGA
* * *
37453 AATTGGTTAATTTGGTTAATTAAAGAGTAAAAGGA
1 AATTGGTAAATTTGGGTAACTAAAGAG-AAAAGGA
37488 AATT
1 AATT
37492 TGGTCATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 24 0.71
35 10 0.29
ACGTcount: A:0.44, C:0.01, G:0.24, T:0.31
Consensus pattern (34 bp):
AATTGGTAAATTTGGGTAACTAAAGAGAAAAGGA
Found at i:37475 original size:61 final size:59
Alignment explanation
Indices: 37401--37619 Score: 227
Period size: 61 Copynumber: 3.7 Consensus size: 59
37391 AGTAAAATGA
* **
37401 AATTGGGTAATTAAAGAGTAATTGGTAAATTTGGGTAACTAAAGA-GAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGG-AAATTT-GGTAACTAAAGAGGAAAGGAAATTGGTT
* *
37461 AATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCATTAAAGAGTGAAAGGAAATTGGTT
1 AATTTGG-TAATTAAAGAGTAAAAGGAAATTTGGTAACTAAAGAG-GAAAGGAAATTGGTT
* ** * * *
37522 AATTTGGTAATTAAAGAGTAAAATGAAATCGGGTAA-T-TA-A--AAA-GTAATTGGTA
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTTGGTAACTAAAGAGGAAAGGAAATTGGTT
* *
37575 AATTTGGTTAATTAAAGAGTAAAAGGGAATTTGGTAATTAAAGAG
1 AATTTGG-TAATTAAAGAGTAAAAGGAAATTTGGTAACTAAAGAG
37620 TAAAATGAAA
Statistics
Matches: 134, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
53 15 0.11
54 28 0.21
55 1 0.01
56 1 0.01
57 2 0.01
58 1 0.01
59 11 0.08
60 37 0.28
61 38 0.28
ACGTcount: A:0.44, C:0.01, G:0.24, T:0.31
Consensus pattern (59 bp):
AATTTGGTAATTAAAGAGTAAAAGGAAATTTGGTAACTAAAGAGGAAAGGAAATTGGTT
Found at i:37495 original size:147 final size:141
Alignment explanation
Indices: 37289--37631 Score: 508
Period size: 147 Copynumber: 2.4 Consensus size: 141
37279 TAAAATGAAA
* * **
37289 TTGGGTAATTAAAGAGTAATTGGGAAATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCATTA
1 TTGGGTAACTAAAGAGAAAAAGGG-AATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCATTA
* *
37354 AAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATGAAATTGGGTAATTAAAGAG
65 AAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATGAAATCGGGTAATTAAAAAG
37419 TAATTGGTAAAT
130 TAATTGGTAAAT
*
37431 TTGGGTAACTAAAGAGAAAGGAAATTGGTTAATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGT
1 TTGGGTAACTAAAGAG-AA--AAA--GG-GAATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGT
*
37496 CATTAAAGAGTGAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATGAAATCGGGTAATTA
60 CATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATGAAATCGGGTAATTA
37561 AAAAGTAATTGGTAAAT
125 AAAAGTAATTGGTAAAT
* * * *
37578 TTGGTTAATTAAAGAGTAAAAGGGAATTTGG-TAATTAAAGAGTAAAATGAAATT
1 TTGGGTAACTAAAGAGAAAAAGGGAATTTGGTTAATTAAAGAGTAAAAGGAAATT
37632 AGACAATTAA
Statistics
Matches: 182, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
140 22 0.12
141 7 0.04
142 17 0.09
143 1 0.01
144 3 0.02
145 1 0.01
146 1 0.01
147 130 0.71
ACGTcount: A:0.44, C:0.01, G:0.24, T:0.31
Consensus pattern (141 bp):
TTGGGTAACTAAAGAGAAAAAGGGAATTTGGTTAATTAAAGAGTAAAAGGAAATTTGGTCATTAA
AGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATGAAATCGGGTAATTAAAAAGT
AATTGGTAAAT
Found at i:37677 original size:21 final size:20
Alignment explanation
Indices: 37647--37685 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
37637 ATTAATGAGT
*
37647 AAGAGAAAATTTGGTAATTA
1 AAGAGAAAATTTAGTAATTA
37667 AAGAGTAAAATTTAGTAAT
1 AAGAG-AAAATTTAGTAAT
37686 GAAATTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (20 bp):
AAGAGAAAATTTAGTAATTA
Found at i:37896 original size:21 final size:21
Alignment explanation
Indices: 37851--37895 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
37841 AAAATGAGGT
*
37851 AAAATGAAATTTTGCTAATTA
1 AAAATGAAATTTCGCTAATTA
*
37872 AAAATGAAA-TTCGGTAATTA
1 AAAATGAAATTTCGCTAATTA
37892 AAAA
1 AAAA
37896 AAAAGGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (21 bp):
AAAATGAAATTTCGCTAATTA
Found at i:45226 original size:21 final size:21
Alignment explanation
Indices: 45202--45246 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
45192 GTGACACCAC
*
45202 CCACCTGGGTCCTCAAGGAAA
1 CCACATGGGTCCTCAAGGAAA
** *
45223 CCACATGGGTGTTCAAGGCAA
1 CCACATGGGTCCTCAAGGAAA
45244 CCA
1 CCA
45247 TGTGGGCGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (21 bp):
CCACATGGGTCCTCAAGGAAA
Found at i:50041 original size:23 final size:26
Alignment explanation
Indices: 49990--50052 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 26
49980 CAAGTGTGAC
49990 AGAGATTGTATGTGTGGAGAGGTACG
1 AGAGATTGTATGTGTGGAGAGGTACG
* *
50016 AGAGATTGTGTGTGT-GAG-GTTA-G
1 AGAGATTGTATGTGTGGAGAGGTACG
*
50039 AGAGATTGTTTGTG
1 AGAGATTGTATGTG
50053 AATGAGAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.41
24 3 0.09
25 3 0.09
26 14 0.41
ACGTcount: A:0.24, C:0.02, G:0.41, T:0.33
Consensus pattern (26 bp):
AGAGATTGTATGTGTGGAGAGGTACG
Found at i:52188 original size:37 final size:34
Alignment explanation
Indices: 52131--52204 Score: 85
Period size: 37 Copynumber: 2.1 Consensus size: 34
52121 TAAAATTAAC
52131 TAAGAAAGCAATCAAGAAAATTAAAGAAAACAATTGA
1 TAAGAAAGCAATCAAGAAAA-T-AA-AAAACAATTGA
* * * *
52168 TAAGAAAGCAGTGAATAAAATAAAAAATAATTGA
1 TAAGAAAGCAATCAAGAAAATAAAAAACAATTGA
52202 TAA
1 TAA
52205 AAACCTCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 13 0.39
35 2 0.06
36 1 0.03
37 17 0.52
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (34 bp):
TAAGAAAGCAATCAAGAAAATAAAAAACAATTGA
Found at i:53460 original size:19 final size:18
Alignment explanation
Indices: 53427--53462 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53417 TTGAAATAAT
53427 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
53445 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
53463 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:53470 original size:11 final size:10
Alignment explanation
Indices: 53427--53473 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
53417 TTGAAATAAT
53427 TCTTCAATGA
1 TCTTCAATGA
53437 TCTTCAA--A
1 TCTTCAATGA
*
53445 TCTTCAAATTA
1 TCTTC-AATGA
53456 TCTTCAATGA
1 TCTTCAATGA
53466 GTCTTCAA
1 -TCTTCAA
53474 ACACGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:76437 original size:14 final size:15
Alignment explanation
Indices: 76418--76447 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
76408 AACTAGGAAA
76418 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
76432 AATAAATAAACAAGG
1 AATAAATAAACAAGG
76447 A
1 A
76448 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:78172 original size:20 final size:20
Alignment explanation
Indices: 78127--78173 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
78117 AATAACAAAG
78127 AATTATTTTAATAAATTTTA
1 AATTATTTTAATAAATTTTA
** *
78147 TTTTATTTT-ATAATTTTTTA
1 AATTATTTTAATAA-ATTTTA
78167 AATTATT
1 AATTATT
78174 GTAGAGAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTATTTTAATAAATTTTA
Done.