Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012965.1 Corchorus capsularis cultivar CVL-1 contig12986, 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: 11237
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:29 original size:22 final size:22
Alignment explanation
Indices: 1--98 Score: 110
Period size: 22 Copynumber: 4.4 Consensus size: 22
1 TCAGT-AAGAGCAAAAATGGTAA
1 TCAGTAAAGAG-AAAAATGGTAA
*
23 TCAGTAAAGAGTAAAAAATAGTAA
1 TCAGTAAAGAG--AAAAATGGTAA
* *
47 TCAGTAAAAAGTAAGAA-GGTAA
1 TCAGTAAAGAG-AAAAATGGTAA
*
69 TCAGTAAAGAGTAAAATGGTAA
1 TCAGTAAAGAGAAAAATGGTAA
91 TCAGTAAA
1 TCAGTAAA
99 ATGGTAATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.05
22 32 0.50
23 9 0.14
24 20 0.31
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.20
Consensus pattern (22 bp):
TCAGTAAAGAGAAAAATGGTAA
Found at i:90 original size:15 final size:15
Alignment explanation
Indices: 72--105 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
62 AAGGTAATCA
*
72 GTAAAGAGTAAAATG
1 GTAAACAGTAAAATG
*
87 GTAATCAGTAAAATG
1 GTAAACAGTAAAATG
102 GTAA
1 GTAA
106 TTAGTAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.24
Consensus pattern (15 bp):
GTAAACAGTAAAATG
Found at i:106 original size:15 final size:15
Alignment explanation
Indices: 78--112 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
68 ATCAGTAAAG
78 AGTAAAATGGTAATC
1 AGTAAAATGGTAATC
*
93 AGTAAAATGGTAATT
1 AGTAAAATGGTAATC
108 AGTAA
1 AGTAA
113 GAGCAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.29
Consensus pattern (15 bp):
AGTAAAATGGTAATC
Found at i:237 original size:13 final size:13
Alignment explanation
Indices: 219--265 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
209 GGTAATCAAT
219 AAAAGAGAATAAG
1 AAAAGAGAATAAG
*
232 AAAAGAGTAATTAG
1 AAAAGAG-AATAAG
*
246 TAAAA-AGAGTAAG
1 -AAAAGAGAATAAG
259 AAAAGAG
1 AAAAGAG
266 TAAAAATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 13 0.46
14 7 0.25
15 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (13 bp):
AAAAGAGAATAAG
Found at i:278 original size:29 final size:29
Alignment explanation
Indices: 217--280 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
207 GTGGTAATCA
**
217 ATAAAAGAGAATAAGAAAAGAGTAATTAG
1 ATAAAAGAGAATAAGAAAAGAGTAAAAAG
*
246 -TAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAATAAGAAAAGAGTAAAAA-G
274 ATAAAAG
1 ATAAAAG
281 TAGCAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 6 0.21
29 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (29 bp):
ATAAAAGAGAATAAGAAAAGAGTAAAAAG
Found at i:5212 original size:13 final size:13
Alignment explanation
Indices: 5174--5256 Score: 50
Period size: 13 Copynumber: 6.1 Consensus size: 13
5164 CAAAATGGTT
5174 ATGG-TTTTCAAA
1 ATGGTTTTTCAAA
5186 A-GGTTTTGAT-AAA
1 ATGGTTTT--TCAAA
5199 ATGGTTTTTCAAA
1 ATGGTTTTTCAAA
5212 ATGGTCATGGTTTTCAAA
1 ATGG---T--TTTTCAAA
5230 A-GGTTTTGAT-AAA
1 ATGGTTTT--TCAAA
5243 ATGGTTTTTCAAA
1 ATGGTTTTTCAAA
5256 A
1 A
5257 AGAGTCATGG
Statistics
Matches: 57, Mismatches: 0, Indels: 27
0.68 0.00 0.32
Matches are distributed among these distances:
11 2 0.04
12 9 0.16
13 19 0.33
14 15 0.26
16 1 0.02
17 2 0.04
18 9 0.16
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (13 bp):
ATGGTTTTTCAAA
Found at i:5279 original size:45 final size:45
Alignment explanation
Indices: 5174--5353 Score: 236
Period size: 44 Copynumber: 3.8 Consensus size: 45
5164 CAAAATGGTT
*
5174 ATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTCAAAATG-GTC
1 ATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTCAAAAAGAGTC
5218 ATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTCAAAAAGAGTC
1 ATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTCAAAAAGAGTC
* *
5263 ATGGTTTTTAAAAGGTTTTGATAAAATAGTTTTTCCAAAAAAAAAAAAGAGTC
1 ATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTT-C-------AAAAAGAGTC
* *
5316 ATGGTTTTCAAAGGGTTTTGATAAAATGGTTTTCCAAA
1 ATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTCAAA
5354 GTTGTGTTTT
Statistics
Matches: 120, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
44 40 0.33
45 38 0.32
46 1 0.01
52 1 0.01
53 40 0.33
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.38
Consensus pattern (45 bp):
ATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTCAAAAAGAGTC
Found at i:5350 original size:52 final size:53
Alignment explanation
Indices: 5253--5353 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
5243 ATGGTTTTTC
* *
5253 AAAAAGAGTCATGGTTTTTAAAAGGTTTTGATAAAATAGTTTTTCCAAAAAAA
1 AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATAGGTTTTCCAAAAAAA
*
5306 AAAAAGAGTCATGGTTTTCAAAGGGTTTTGATAAAAT-GGTTTTCCAAA
1 AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATAGGTTTTCCAAA
5354 GTTGTGTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 10 0.22
53 35 0.78
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.34
Consensus pattern (53 bp):
AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATAGGTTTTCCAAAAAAA
Found at i:5766 original size:18 final size:18
Alignment explanation
Indices: 5716--5760 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5706 GACGAAGAAA
*
5716 AAAGTGAAAATTGAAAGTG
1 AAAG-GAAAAATGAAAGTG
*
5735 AAAGGAAAAATGAACGTG
1 AAAGGAAAAATGAAAGTG
5753 AAAGGAAA
1 AAAGGAAA
5761 GGTGAAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.13
Consensus pattern (18 bp):
AAAGGAAAAATGAAAGTG
Found at i:6073 original size:11 final size:11
Alignment explanation
Indices: 6057--6115 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
6047 AAGTGCATGT
*
6057 AAAAAATGAAA
1 AAAAAAAGAAA
6068 AAAAAAAGAAA
1 AAAAAAAGAAA
6079 GAAGAAAAAGAAA
1 -AA-AAAAAGAAA
*
6092 AGAAAAAGAAA
1 AAAAAAAGAAA
*
6103 AAGAAAAGGAAA
1 AA-AAAAAGAAA
6115 A
1 A
6116 GAGAATGAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 20 0.49
12 12 0.29
13 9 0.22
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:6074 original size:6 final size:6
Alignment explanation
Indices: 6058--6120 Score: 76
Period size: 6 Copynumber: 10.3 Consensus size: 6
6048 AGTGCATGTA
6058 AAAAATG AAAAA- AAAAAG AAAGAAG AAAAAG -AAAAG AAAAAG AAAAAG
1 AAAAA-G AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
*
6106 AAAAGG AAAAGAG AA
1 AAAAAG AAAA-AG AA
6121 TGAAGAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
5 10 0.20
6 26 0.52
7 14 0.28
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:6100 original size:17 final size:17
Alignment explanation
Indices: 6058--6131 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 17
6048 AGTGCATGTA
*
6058 AAAAATGAAAAAAAAAAG
1 AAAAA-GAAAAAGAAAAG
6076 AAAGAAGAAAAAGAAAAG
1 AAA-AAGAAAAAGAAAAG
6094 AAAAAGAAAAAGAAAAGG
1 AAAAAGAAAAAGAAAA-G
*
6112 AAAAGAGAATGAAGAAAAG
1 AAAA-AGAA-AAAGAAAAG
6131 A
1 A
6132 GGCTCTAGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.26
18 22 0.44
19 8 0.16
20 7 0.14
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:6116 original size:11 final size:11
Alignment explanation
Indices: 6058--6131 Score: 67
Period size: 12 Copynumber: 6.1 Consensus size: 11
6048 AGTGCATGTA
*
6058 AAAAATGAAAAA
1 AAAAA-GAAAAG
6070 AAAAAGAAAGAAG
1 AAAAAG-AA-AAG
6083 AAAAAGAAAAG
1 AAAAAGAAAAG
6094 AAAAAGAAAAAG
1 AAAAAG-AAAAG
*
6106 AAAAGGAAAAG
1 AAAAAGAAAAG
6117 AGAATGAAGAAAAG
1 A-AA--AAGAAAAG
6131 A
1 A
6132 GGCTCTAGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
11 16 0.30
12 21 0.40
13 8 0.15
14 8 0.15
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:6470 original size:41 final size:41
Alignment explanation
Indices: 6402--6483 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
6392 AAGTTTTATA
* * *
6402 ATAATATTGCATTTCATTGGTAGGTCCAATATCAAAATTCG
1 ATAAGATTGCATTCCATTGGTAGGTCCAAGATCAAAATTCG
*
6443 ATAAGATTGCATTCCATTTGT-GAGTCCAAGATCAAAATTCG
1 ATAAGATTGCATTCCATTGGTAG-GTCCAAGATCAAAATTCG
6484 CTTTTTAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (41 bp):
ATAAGATTGCATTCCATTGGTAGGTCCAAGATCAAAATTCG
Found at i:7104 original size:69 final size:69
Alignment explanation
Indices: 7026--7541 Score: 672
Period size: 68 Copynumber: 7.6 Consensus size: 69
7016 CGAATGCTTT
*
7026 GGCTTTTCCACAAGGCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
7091 CAGG
66 CAGG
* * *
7095 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCA-ATCAAGCCTTGGTTCTATCCAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
*
7159 CAGC
66 CAGG
*
7163 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-
*
7228 TCAGG
65 GCAGG
*
7233 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTGCATCCAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
7298 CAGG
66 CAGG
* * * *
7302 GGCTTTTCCACAAGCCAAACTCGTTTCCACACAAGTCA-ATCAAGCCTTGGTTCTATCCAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
*
7366 CAAG
66 CAGG
* * * * * *
7370 GGC--TTCCACCAGCCAAACTCGTTTCCACATGAGTCAATT-TAGCCTTGGTTCCATCCAAGCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
*
7432 CAAG
66 CAGG
* ** * *
7436 GGCTTTTCCACTAGCCAAACTCGTTTCCATATAAGTTAGTT-TAGCCTTGGTTCCATCC-A--AG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
7497 CAGG
66 CAGG
* * ** * *
7501 AGCTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTCAGT
7542 CTTCCAAGAC
Statistics
Matches: 399, Mismatches: 42, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
65 30 0.08
66 63 0.16
67 2 0.01
68 140 0.35
69 99 0.25
70 65 0.16
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
CAGG
Found at i:10980 original size:30 final size:30
Alignment explanation
Indices: 10926--11048 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 30
10916 GGCAAATCAG
10926 TAATTAAGTAAAAAGAGTAATCAGTAAATTGA
1 TAATTAAGT-AAAA-AGTAATCAGTAAATTGA
* *
10958 TAATTAAG-AAAACAGCAATCAGTAAA-TCA
1 TAATTAAGTAAAA-AGTAATCAGTAAATTGA
10987 GTAATTAAGTAAAAAGATATTAATCAGTAAATTGA
1 -TAATTAAGTAAAAAG----TAATCAGTAAATTGA
*
11022 TAATTAAGGT-AATAGTAATCAGTAAAT
1 TAATTAA-GTAAAAAGTAATCAGTAAAT
11049 CAGTAGTAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
29 2 0.03
30 38 0.49
31 4 0.05
32 8 0.10
34 21 0.27
35 4 0.05
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.28
Consensus pattern (30 bp):
TAATTAAGTAAAAAGTAATCAGTAAATTGA
Found at i:11029 original size:64 final size:63
Alignment explanation
Indices: 10919--11162 Score: 307
Period size: 64 Copynumber: 3.8 Consensus size: 63
10909 CATCAAGGGC
*
10919 AAATCAGTAATTAAGTAAAAAGAG--TAATCAGTAAATTGATAATTAAGAAAACAGCAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAAAA-AGTAATCAGT
* * *
10981 AAATCAGTAATTAAGTAAAAAGATATTAATCAGTAAATTGATAATTAAGGTAATAGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAA-GAAAAAGTAATCAGT
* *
11045 AAATCAGT-AGTAAGTAAAAAAGAGATTAATCAAGTATA-TGATAATTAAGGAGTAAAAGTAATA
1 AAATCAGTAATTAAGT-AAAAAGAGATTAATC-AGTAAATTGATAATTAA-GA--AAAAG---TA
11108 ATCAGT
58 ATCAGT
11114 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAAGTTGATAATTAA
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAA-TTGATAATTAA
11163 AGAGTCAAGG
Statistics
Matches: 158, Mismatches: 11, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
62 23 0.15
63 6 0.04
64 65 0.41
65 8 0.05
66 4 0.03
68 5 0.03
69 31 0.20
70 16 0.10
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.27
Consensus pattern (63 bp):
AAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAAAAAGTAATCAGT
Done.