Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012117.1 Corchorus olitorius cultivar O-4 contig12150, 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: 29218
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2014 original size:56 final size:56
Alignment explanation
Indices: 1928--2042 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
1918 CCTATTCTTT
1928 TTTCATAAATAAAAAAAATATATATATAAAAAAAAGAGAGAGAAGAAGAAGTTGTA
1 TTTCATAAATAAAAAAAATATATATATAAAAAAAAGAGAGAGAAGAAGAAGTTGTA
1984 TTTCATAAATAAAAAAAATATATATATAAAAAAAAGAGAGAGAAGAAGAAGTTGTA
1 TTTCATAAATAAAAAAAATATATATATAAAAAAAAGAGAGAGAAGAAGAAGTTGTA
2040 TTT
1 TTT
2043 TGGATTAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (56 bp):
TTTCATAAATAAAAAAAATATATATATAAAAAAAAGAGAGAGAAGAAGAAGTTGTA
Found at i:5932 original size:24 final size:24
Alignment explanation
Indices: 5857--5934 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
5847 GGTAATCAAA
*
5857 GTAAAAAGAAAAAAATGAAATTTG
1 GTAAAAAGAAAAAAGTGAAATTTG
* *
5881 GTGATTAAAACAAAAAGAGT--AATATG
1 GT-A--AAAAGAAAAA-AGTGAAATTTG
*
5907 GTAAAAAGGAAAAAGTGAAATTTG
1 GTAAAAAGAAAAAAGTGAAATTTG
5931 GTAA
1 GTAA
5935 GTAAAATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
22 3 0.07
23 8 0.19
24 11 0.26
25 2 0.05
26 7 0.17
27 9 0.21
28 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.21, T:0.22
Consensus pattern (24 bp):
GTAAAAAGAAAAAAGTGAAATTTG
Found at i:5965 original size:19 final size:19
Alignment explanation
Indices: 5918--5965 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5908 TAAAAAGGAA
* *
5918 AAAGTGAAATTTGGTAAGT
1 AAAGTGAAATTGGGTAACT
*
5937 AAAATGAAATTGGGTAACT
1 AAAGTGAAATTGGGTAACT
*
5956 AAAGTTAAAT
1 AAAGTGAAAT
5966 GGTATTTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.21, T:0.29
Consensus pattern (19 bp):
AAAGTGAAATTGGGTAACT
Found at i:5965 original size:24 final size:24
Alignment explanation
Indices: 5933--5988 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5923 GAAATTTGGT
*
5933 AAGTAAAATGAAATTGGGTAACTA
1 AAGTTAAATGAAATTGGGTAACTA
** * *
5957 AAGTTAAATGGTATTTGGTAATTA
1 AAGTTAAATGAAATTGGGTAACTA
5981 AAGTTAAA
1 AAGTTAAA
5989 AGAGTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (24 bp):
AAGTTAAATGAAATTGGGTAACTA
Found at i:5997 original size:32 final size:32
Alignment explanation
Indices: 5961--6532 Score: 140
Period size: 33 Copynumber: 17.9 Consensus size: 32
5951 TAACTAAAGT
*
5961 TAAATGGTATTTGGTAATTAAAGTTAAAAGAG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
* *
5993 TAAATTGGTATTTGGTAATCAAAGTAAAAAGAA
1 TAAA-TGGTATTTGGTAATTAAAGTAAAAAGAG
* ** **
6026 AAAATGAAATTTGGTAATTAAAACAAAAAGAG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
* *
6058 T-AA---TA--TGGTAA--AAAGGAAAAAGTG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
** ** * *
6082 -AAATTTGGTAAGT-AAAATGAAATTGGGTAACTAA-AG
1 TAAA--TGGTATTTGGTAATTAAA----GTAA-AAAGAG
*
6118 TTAAATGGTATTTGGTAATTAAAGTTAAAAGAG
1 -TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
* *
6151 TAAATTGGTATTTGGTAATCAAAGTAAAAAGAA
1 TAAA-TGGTATTTGGTAATTAAAGTAAAAAGAG
* ** **
6184 AAAATGAAATTT-GTAATTAAAACAAAAAGAG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
* *
6215 T-AA---TA--TGGTAA--AAAGGAAAAAGTG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
** ** * *
6239 -AAATTTGGTAAGT-AAAATGAAATTTGGTAACTAAAG-T
1 TAAA--TGGTATTTGGTAATTAAA----GTAA--AAAGAG
* *
6276 TAAATGGTATTTGGTAATTAAAATAGAAAGAG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
* *
6308 TAAATTGGTATTTGGTAATCAAAGTAAAAAGAA
1 TAAA-TGGTATTTGGTAATTAAAGTAAAAAGAG
* ** * ** *
6341 AAAATGAAATTTGGCAATTAAAACAAGAAGAG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
* ****
6373 TAATATAGTAAAAAG-AGATTAAAGT-AAAAGAG
1 TAA-ATGGTATTTGGTA-ATTAAAGTAAAAAGAG
** * ** *
6405 TAAAATGGTAAAAT-GAAATT-CGGTAACTAAAG-T
1 T-AAATGGT-ATTTGGTAATTAAAGTAA--AAAGAG
* * *
6438 TAAATGGTATTCGGTAATTAAAATAAAAGGAG
1 TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
* *
6470 TAAATTGGTATTTGGTAAATATAGTAAAAAGAG
1 TAAA-TGGTATTTGGTAATTAAAGTAAAAAGAG
* *
6503 TAAAATTTGTATTTGATAATTAAAG-AAAAA
1 T-AAA-TGGTATTTGGTAATTAAAGTAAAAA
6533 TTGGTAAAGA
Statistics
Matches: 384, Mismatches: 101, Indels: 109
0.65 0.17 0.18
Matches are distributed among these distances:
24 24 0.06
25 1 0.00
26 10 0.03
27 1 0.00
28 1 0.00
29 4 0.01
30 6 0.02
31 29 0.08
32 103 0.27
33 139 0.36
34 23 0.06
36 19 0.05
37 14 0.04
38 10 0.03
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.28
Consensus pattern (32 bp):
TAAATGGTATTTGGTAATTAAAGTAAAAAGAG
Found at i:6053 original size:26 final size:25
Alignment explanation
Indices: 6019--6103 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 25
6009 AATCAAAGTA
6019 AAAAGAAAAAATGAAATTTGGTAATT
1 AAAAGAAAAAATGAAATTTGGTAA-T
* * *
6045 AAAACAAAAAGA-GTAATATGGTAA-
1 AAAAGAAAAA-ATGAAATTTGGTAAT
* *
6069 AAAGGAAAAAGTGAAATTTGGTAAGT
1 AAAAGAAAAAATGAAATTTGGTAA-T
6095 AAAATGAAA
1 AAAA-GAAA
6104 TTGGGTAACT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
24 18 0.40
26 22 0.49
27 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.19, T:0.21
Consensus pattern (25 bp):
AAAAGAAAAAATGAAATTTGGTAAT
Found at i:6090 original size:24 final size:23
Alignment explanation
Indices: 6016--6092 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
6006 GGTAATCAAA
*
6016 GTAAAAAGAAAAAATGAAATTTG
1 GTAAAAAGAAAAAGTGAAATTTG
* * * *
6039 GTAATTAAAACAAAAAGAGTAATATG
1 GT-A--AAAAGAAAAAGTGAAATTTG
6065 GTAAAAAGGAAAAAGTGAAATTTG
1 GTAAAAA-GAAAAAGTGAAATTTG
6089 GTAA
1 GTAA
6093 GTAAAATGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
23 6 0.15
24 17 0.41
25 1 0.02
26 17 0.41
ACGTcount: A:0.57, C:0.01, G:0.19, T:0.22
Consensus pattern (23 bp):
GTAAAAAGAAAAAGTGAAATTTG
Found at i:6123 original size:19 final size:19
Alignment explanation
Indices: 6076--6123 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
6066 TAAAAAGGAA
* *
6076 AAAGTGAAATTTGGTAAGT
1 AAAGTGAAATTGGGTAACT
*
6095 AAAATGAAATTGGGTAACT
1 AAAGTGAAATTGGGTAACT
*
6114 AAAGTTAAAT
1 AAAGTGAAAT
6124 GGTATTTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.21, T:0.29
Consensus pattern (19 bp):
AAAGTGAAATTGGGTAACT
Found at i:6123 original size:24 final size:24
Alignment explanation
Indices: 6091--6146 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
6081 GAAATTTGGT
*
6091 AAGTAAAATGAAATTGGGTAACTA
1 AAGTTAAATGAAATTGGGTAACTA
** * *
6115 AAGTTAAATGGTATTTGGTAATTA
1 AAGTTAAATGAAATTGGGTAACTA
6139 AAGTTAAA
1 AAGTTAAA
6147 AGAGTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (24 bp):
AAGTTAAATGAAATTGGGTAACTA
Found at i:6247 original size:24 final size:23
Alignment explanation
Indices: 6174--6249 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 23
6164 GGTAATCAAA
*
6174 GTAAAAAGAAAAAATGAAATTT-
1 GTAAAAAGAAAAAGTGAAATTTG
* * * *
6196 GTAATTAAAACAAAAAGAGTAATATG
1 GT-A--AAAAGAAAAAGTGAAATTTG
6222 GTAAAAAGGAAAAAGTGAAATTTG
1 GTAAAAA-GAAAAAGTGAAATTTG
6246 GTAA
1 GTAA
6250 GTAAAATGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
22 2 0.05
23 5 0.12
24 16 0.40
25 15 0.38
26 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.18, T:0.22
Consensus pattern (23 bp):
GTAAAAAGAAAAAGTGAAATTTG
Found at i:6280 original size:19 final size:19
Alignment explanation
Indices: 6233--6280 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
6223 TAAAAAGGAA
*
6233 AAAGTGAAATTTGGTAAGT
1 AAAGTGAAATTTGGTAACT
*
6252 AAAATGAAATTTGGTAACT
1 AAAGTGAAATTTGGTAACT
*
6271 AAAGTTAAAT
1 AAAGTGAAAT
6281 GGTATTTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.19, T:0.31
Consensus pattern (19 bp):
AAAGTGAAATTTGGTAACT
Found at i:6280 original size:24 final size:24
Alignment explanation
Indices: 6248--6297 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
6238 GAAATTTGGT
6248 AAGTAAAATGAAATTTGGTAACTA
1 AAGTAAAATGAAATTTGGTAACTA
* ** *
6272 AAGTTAAATGGTATTTGGTAATTA
1 AAGTAAAATGAAATTTGGTAACTA
6296 AA
1 AA
6298 ATAGAAAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (24 bp):
AAGTAAAATGAAATTTGGTAACTA
Found at i:6308 original size:315 final size:317
Alignment explanation
Indices: 5828--6501 Score: 1094
Period size: 315 Copynumber: 2.1 Consensus size: 317
5818 AGCAATCAGT
*
5828 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAAATGAAATTTGGTGATTAAAACA
1 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAG-AAAAAATGAAATTTGGTAATTAAAACA
5893 AAAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAA
65 AAAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAA
*
5958 AGTTAAATGGTATTTGGTAATTAAAGTTAAAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAA
130 AGTTAAATGGTATTTGGTAATTAAAGATAAAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAA
* *
6023 GAAAAAATGAAATTTGGTAATTAAAACAAAAAGAGTAATATGGTAAAAAG-GA-AAAAGTGAAAT
195 GAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATATAGTAAAAAGAGATAAAAGT-AAA-
* * * *
6086 TTG-GT-AA-GTAAAATGAAATTGGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTTA
258 -AGAGTAAAGGTAAAATGAAATTCGGTAACTAAAGTTAAATGGTATTCGGTAATTAAA-ATA
6145 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTT-GTAATTAAAACAA
1 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGTAATTAAAACAA
*
6209 AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTTGGTAACTAAA
66 AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAAA
6274 GTTAAATGGTATTTGGTAATTAAA-ATAGAAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAA
131 GTTAAATGGTATTTGGTAATTAAAGATA-AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAA
* *
6338 GAAAAAATGAAATTTGGCAATTAAAACAAGAAGAGTAATATAGTAAAAAGAGATTAAAGTAAAAG
195 GAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATATAGTAAAAAGAGATAAAAGTAAAAG
6403 AGTAAAATGGTAAAATGAAATTCGGTAACTAAAGTTAAATGGTATTCGGTAATTAAAATA
260 AGT-AAA-GGTAAAATGAAATTCGGTAACTAAAGTTAAATGGTATTCGGTAATTAAAATA
*
6463 AAAGGAGTAAATTGGTATTTGGTAAAT-ATAGTAAAAAGA
1 AAA-GAGTAAATTGGTATTTGGT-AATCAAAGTAAAAAGA
6502 GTAAAATTTG
Statistics
Matches: 335, Mismatches: 12, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
314 3 0.01
315 185 0.55
316 19 0.06
317 44 0.13
318 5 0.01
319 76 0.23
320 3 0.01
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.27
Consensus pattern (317 bp):
AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGTAATTAAAACAA
AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAAA
GTTAAATGGTATTTGGTAATTAAAGATAAAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAG
AAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATATAGTAAAAAGAGATAAAAGTAAAAGA
GTAAAGGTAAAATGAAATTCGGTAACTAAAGTTAAATGGTATTCGGTAATTAAAATA
Found at i:6311 original size:157 final size:158
Alignment explanation
Indices: 5828--6501 Score: 1092
Period size: 158 Copynumber: 4.2 Consensus size: 158
5818 AGCAATCAGT
*
5828 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAAATGAAATTTGGTGATTAAAACA
1 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAG-AAAAAATGAAATTTGGTAATTAAAACA
5893 AAAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAA
65 AAAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAA
*
5958 AGTTAAATGGTATTTGGTAATTAAAGTTA
130 AGTTAAATGGTATTTGGTAATTAAAGATA
5987 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGTAATTAAAACAA
1 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGTAATTAAAACAA
6052 AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAAA
66 AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAAA
*
6117 GTTAAATGGTATTTGGTAATTAAAGTTA
131 GTTAAATGGTATTTGGTAATTAAAGATA
6145 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTT-GTAATTAAAACAA
1 AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGTAATTAAAACAA
*
6209 AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTTGGTAACTAAA
66 AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAAA
6274 GTTAAATGGTATTTGGTAATTAAA-ATA
131 GTTAAATGGTATTTGGTAATTAAAGATA
*
6301 GAAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGCAATTAAAACA
1 -AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGTAATTAAAACA
* * * * *
6366 AGAAGAGTAATATAGTAAAAAGAGATTAAAGT-AAA--AGAGTAAAATGGTAAAATGAAATTCGG
65 AAAAGAGTAATATGGTAAAAAG-GA-AAAAGTGAAATTTG-GT--AA--GTAAAATGAAATTGGG
*
6428 TAACTAAAGTTAAATGGTATTCGGTAATTAAA-ATA
123 TAACTAAAGTTAAATGGTATTTGGTAATTAAAGATA
*
6463 AAAGGAGTAAATTGGTATTTGGTAAAT-ATAGTAAAAAGA
1 AAA-GAGTAAATTGGTATTTGGT-AATCAAAGTAAAAAGA
6502 GTAAAATTTG
Statistics
Matches: 493, Mismatches: 11, Indels: 19
0.94 0.02 0.04
Matches are distributed among these distances:
156 2 0.00
157 153 0.31
158 204 0.41
159 42 0.09
160 7 0.01
161 3 0.01
162 79 0.16
163 3 0.01
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.27
Consensus pattern (158 bp):
AAAGAGTAAATTGGTATTTGGTAATCAAAGTAAAAAGAAAAAATGAAATTTGGTAATTAAAACAA
AAAGAGTAATATGGTAAAAAGGAAAAAGTGAAATTTGGTAAGTAAAATGAAATTGGGTAACTAAA
GTTAAATGGTATTTGGTAATTAAAGATA
Found at i:13590 original size:2 final size:2
Alignment explanation
Indices: 13583--13615 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13573 TCCATTTTCT
13583 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13616 TTTATTCAAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:15818 original size:27 final size:28
Alignment explanation
Indices: 15768--15831 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
15758 GGGCTCATAC
* *
15768 TCCAGCAGAGGCCGATGAACAGTAATCT
1 TCCAACAGAGGCCGATGAACAGTAAACT
*
15796 TCCAACAGAGGTC-ATGAACAGTAAACT
1 TCCAACAGAGGCCGATGAACAGTAAACT
15823 TCCAACAGA
1 TCCAACAGA
15832 CTTCTGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (28 bp):
TCCAACAGAGGCCGATGAACAGTAAACT
Found at i:16519 original size:19 final size:18
Alignment explanation
Indices: 16497--16616 Score: 86
Period size: 19 Copynumber: 6.6 Consensus size: 18
16487 GGCTTTAAAT
*
16497 GAATAATGGGCTTTTAGTG
1 GAATAATGGGCTTTTAG-A
**
16516 GAATAATGCCCTTTTAGA
1 GAATAATGGGCTTTTAGA
16534 GAA-AAGTGGGCTTTGTAGA
1 GAATAA-TGGGCTTT-TAGA
* *
16553 GAATAATGGG-TATTAGT
1 GAATAATGGGCTTTTAGA
* **
16570 GAAATAGTGCCCTTTTAGA
1 G-AATAATGGGCTTTTAGA
16589 GAA-AAGTGGG-TTTGTAGA
1 GAATAA-TGGGCTTT-TAGA
16607 GAATAATGGG
1 GAATAATGGG
16617 TATAAATAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
17 10 0.13
18 32 0.41
19 34 0.44
20 2 0.03
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.31
Consensus pattern (18 bp):
GAATAATGGGCTTTTAGA
Found at i:16569 original size:55 final size:54
Alignment explanation
Indices: 16497--16619 Score: 201
Period size: 55 Copynumber: 2.2 Consensus size: 54
16487 GGCTTTAAAT
* *
16497 GAATAATGGGCTTTTAGTGGAATAATGCCCTTTTAGAGAAAAGTGGGCTTTGTAGA
1 GAATAATGGG-TATTAGTGAAATAATGCCCTTTTAGAGAAAAGTGGG-TTTGTAGA
*
16553 GAATAATGGGTATTAGTGAAATAGTGCCCTTTTAGAGAAAAGTGGGTTTGTAGA
1 GAATAATGGGTATTAGTGAAATAATGCCCTTTTAGAGAAAAGTGGGTTTGTAGA
16607 GAATAATGGGTAT
1 GAATAATGGGTAT
16620 AAATAATGGG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
54 21 0.33
55 33 0.52
56 10 0.16
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.32
Consensus pattern (54 bp):
GAATAATGGGTATTAGTGAAATAATGCCCTTTTAGAGAAAAGTGGGTTTGTAGA
Found at i:16616 original size:18 final size:18
Alignment explanation
Indices: 16530--16617 Score: 60
Period size: 18 Copynumber: 4.8 Consensus size: 18
16520 AATGCCCTTT
16530 TAGAGAA-AAGTGGGCTTTG
1 TAGAGAATAA-TGGG-TTTG
16549 TAGAGAATAATGGGTATTAG
1 TAGAGAATAATGGGT-TT-G
* **
16569 T-GA-AATAGTGCCCTTT-
1 TAGAGAATAATG-GGTTTG
16585 TAGAGAA-AAGTGGGTTTG
1 TAGAGAATAA-TGGGTTTG
16603 TAGAGAATAATGGGT
1 TAGAGAATAATGGGT
16618 ATAAATAATG
Statistics
Matches: 54, Mismatches: 6, Indels: 19
0.68 0.08 0.24
Matches are distributed among these distances:
16 1 0.02
17 6 0.11
18 25 0.46
19 18 0.33
20 4 0.07
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.30
Consensus pattern (18 bp):
TAGAGAATAATGGGTTTG
Found at i:27888 original size:6 final size:6
Alignment explanation
Indices: 27877--27941 Score: 98
Period size: 6 Copynumber: 10.8 Consensus size: 6
27867 GGCACCACAA
27877 TATATC TATATC TATATC TATATC TATA-- TACTATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TA-TATC TATATC TATATC
27924 TATATC TATATAC TATAT
1 TATATC TATAT-C TATAT
27942 AAGTCTAAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
6 43 0.78
7 8 0.15
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:27915 original size:23 final size:22
Alignment explanation
Indices: 27885--27932 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 22
27875 AATATATCTA
27885 TATCTATATCTATATCTATATAC
1 TATCTATATCTATATCTATAT-C
27908 TATCTATATCTATATCTATATC
1 TATCTATATCTATATCTATATC
27930 TAT
1 TAT
27933 ATACTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (22 bp):
TATCTATATCTATATCTATATC
Found at i:27915 original size:29 final size:29
Alignment explanation
Indices: 27879--27939 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
27869 CACCACAATA
27879 TATCTATATCTATATCTATATCTATATAC
1 TATCTATATCTATATCTATATCTATATAC
27908 TATCTATATCTATATCTATATCTATATAC
1 TATCTATATCTATATCTATATCTATATAC
27937 TAT
1 TAT
27940 ATAAGTCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.49
Consensus pattern (29 bp):
TATCTATATCTATATCTATATCTATATAC
Done.