Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018088.1 Corchorus olitorius cultivar O-4 contig18121, 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: 28208
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:5133 original size:32 final size:32
Alignment explanation
Indices: 5097--5162 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
5087 TAATAAAAAA
*
5097 AGATAAATAGATATAGAG-ATATAGAGATAAAT
1 AGATAAATAGATACAGAGAATA-AGAGATAAAT
*
5129 AGATAAATAGATACAGAGAATAATAGATAAAT
1 AGATAAATAGATACAGAGAATAAGAGATAAAT
5161 AG
1 AG
5163 GTTGCTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.18, T:0.23
Consensus pattern (32 bp):
AGATAAATAGATACAGAGAATAAGAGATAAAT
Found at i:5214 original size:27 final size:26
Alignment explanation
Indices: 5177--5322 Score: 98
Period size: 27 Copynumber: 5.9 Consensus size: 26
5167 CTAAAAAAAG
*
5177 ATAAT-AA-TAATACATAAATAGATA
1 ATAATAAATTAATAAATAAATAGATA
5201 ATAACTAAATTAATAAAT--A-A-A-A
1 ATAA-TAAATTAATAAATAAATAGATA
* *
5223 A-GATAAA-TAGTAAATAAATAGATA
1 ATAATAAATTAATAAATAAATAGATA
5247 ATAATTAAATTAATAAATAAATAGATAA
1 ATAA-TAAATTAATAAATAAATAGAT-A
* * * *
5275 ATAGTAAATAAATAGAT-AATAGTTA
1 ATAATAAATTAATAAATAAATAGATA
* *
5300 AAAATAAA-TAAAAAGATAAATAG
1 ATAATAAATTAATAA-ATAAATAG
5323 TAAATAAATA
Statistics
Matches: 94, Mismatches: 14, Indels: 26
0.70 0.10 0.19
Matches are distributed among these distances:
19 7 0.07
20 4 0.04
21 2 0.02
22 3 0.03
23 2 0.02
24 10 0.11
25 12 0.13
26 17 0.18
27 33 0.35
28 4 0.04
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (26 bp):
ATAATAAATTAATAAATAAATAGATA
Found at i:5221 original size:4 final size:4
Alignment explanation
Indices: 5185--5386 Score: 97
Period size: 4 Copynumber: 52.8 Consensus size: 4
5175 AGATAATAAT
* * * *
5185 AATA CATA AATA GAT- AATA ACTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
5231 AGTA AATA AATA GAT- AATA ATTA AATT AATA AATA AATA GATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * *
5277 AGTA AATA AATA GATA ATAGTT AA-A AATA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA A-ATA AATA AATA
* ** * * *
5325 AATA AATA GAT- AATA GTTA AAAA AAT- AATA AAT- AATA AAT- AGTG
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
5369 AATA AAT- AATA AAAA AAT
1 AATA AATA AATA AATA AAT
5387 CTTTTTGGTC
Statistics
Matches: 142, Mismatches: 39, Indels: 34
0.66 0.18 0.16
Matches are distributed among these distances:
3 29 0.20
4 105 0.74
5 6 0.04
6 2 0.01
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:5236 original size:19 final size:19
Alignment explanation
Indices: 5214--5365 Score: 92
Period size: 19 Copynumber: 8.3 Consensus size: 19
5204 ACTAAATTAA
5214 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
5233 TAAATAAATAGAT-AATAAT
1 TAAATAAAAAGATAAAT-AG
*
5252 TAAATTAATAA-ATAAATAG
1 TAAA-TAAAAAGATAAATAG
**
5271 ATAAATAGTAA-ATAAATAG
1 -TAAATAAAAAGATAAATAG
* * *
5290 ---AT-AATAGTTAAA-AA
1 TAAATAAAAAGATAAATAG
5304 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
*
5323 TAAATAAATAGAT-AATAG
1 TAAATAAAAAGATAAATAG
*
5341 TTAAA-AAAATA-ATAAATAA
1 -TAAATAAAA-AGATAAATAG
5360 TAAATA
1 TAAATA
5366 GTGAATAAAT
Statistics
Matches: 102, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
14 2 0.02
15 6 0.06
17 2 0.02
18 25 0.25
19 56 0.55
20 11 0.11
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:5256 original size:46 final size:46
Alignment explanation
Indices: 5171--5380 Score: 277
Period size: 46 Copynumber: 4.6 Consensus size: 46
5161 AGGTTGCTAA
* * *
5171 AAAAAGATAATAATAATACATAAATAGATAATAACTAAATTAATAAAT
1 AAAAAGAT-A-AATAGTAAATAAATAGATAATAATTAAATTAATAAAT
5219 AAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
* *
5265 AAATAGATAAATAGTAAATAAATAGATAATAGTTAAA--AATAAAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
* **
5309 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAAAAAT-AAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
* *
5354 AAATA-ATAAATAGTGAATAAATA-ATAA
1 AAAAAGATAAATAGTAAATAAATAGATAA
5381 AAAAATCTTT
Statistics
Matches: 152, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
43 4 0.03
44 60 0.39
45 7 0.05
46 72 0.47
47 1 0.01
48 8 0.05
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (46 bp):
AAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
Found at i:5284 original size:7 final size:8
Alignment explanation
Indices: 5097--5366 Score: 89
Period size: 8 Copynumber: 34.2 Consensus size: 8
5087 TAATAAAAAA
5097 AGATAAAT
1 AGATAAAT
* *
5105 AGATATAG
1 AGATAAAT
* *
5113 AGATATAG
1 AGATAAAT
5121 AGATAAAT
1 AGATAAAT
5129 AGATAAAT
1 AGATAAAT
* *
5137 AGATACAG
1 AGATAAAT
5145 AGA-ATAAT
1 AGATA-AAT
5153 AGATAAAT
1 AGATAAAT
* ***
5161 AGGTTGCT
1 AGATAAAT
*
5169 A-A-AAAA
1 AGATAAAT
5175 AGAT-AAT
1 AGATAAAT
5182 A-AT-AAT
1 AGATAAAT
*
5188 ACATAAAT
1 AGATAAAT
5196 AGATAATAACT
1 AGAT-A-AA-T
* *
5207 AAATTAAT
1 AGATAAAT
* *
5215 AAATAAAA
1 AGATAAAT
5223 AGATAAAT
1 AGATAAAT
5231 AG-TAAAT
1 AGATAAAT
* *
5238 AAATAGAT
1 AGATAAAT
*
5246 A-ATAATT
1 AGATAAAT
* *
5253 AAATTAAT
1 AGATAAAT
*
5261 AAATAAAT
1 AGATAAAT
5269 AGATAAAT
1 AGATAAAT
5277 AGTAAATAAAT
1 AG---ATAAAT
5288 AGAT-AAT
1 AGATAAAT
*
5295 AGTTAAAAAT
1 AG--ATAAAT
* *
5305 AAATAAAA
1 AGATAAAT
5313 AGATAAAT
1 AGATAAAT
5321 AG-TAAAT
1 AGATAAAT
* *
5328 AAATAGAT
1 AGATAAAT
**
5336 A-ATAGTT
1 AGATAAAT
* *
5343 AAAAAAAT
1 AGATAAAT
5351 A-ATAAAT
1 AGATAAAT
5358 A-ATAAAT
1 AGATAAAT
5365 AG
1 AG
5367 TGAATAAATA
Statistics
Matches: 196, Mismatches: 46, Indels: 40
0.70 0.16 0.14
Matches are distributed among these distances:
6 7 0.04
7 48 0.24
8 118 0.60
9 5 0.03
10 6 0.03
11 12 0.06
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.26
Consensus pattern (8 bp):
AGATAAAT
Found at i:5372 original size:18 final size:17
Alignment explanation
Indices: 5235--5381 Score: 74
Period size: 19 Copynumber: 8.4 Consensus size: 17
5225 ATAAATAGTA
*
5235 AATAAATAGATAATAATT
1 AATAAATAG-TAATAAAT
*
5253 AAATTAATA--AATAAAT
1 -AATAAATAGTAATAAAT
5269 AGATAAATAGTAAATAAAT
1 A-ATAAATAGT-AATAAAT
5288 AGAT-AATAGTTAA-AAAT
1 A-ATAAATAG-TAATAAAT
* *
5305 AAATAAAAAGATAA-ATAGT
1 -AATAAATAG-TAATA-AAT
**
5324 AAATAAATAGATAATAGTT
1 -AATAAATAG-TAATAAAT
*
5343 AA-AAA-AATAATAAAT
1 AATAAATAGTAATAAAT
5358 AATAAATAGTGAATAAAT
1 AATAAATAGT-AATAAAT
5376 AATAAA
1 AATAAA
5382 AAAATCTTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
15 9 0.09
16 16 0.16
17 11 0.11
18 31 0.30
19 35 0.34
20 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
AATAAATAGTAATAAAT
Found at i:5747 original size:21 final size:21
Alignment explanation
Indices: 5723--5764 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5713 TAACTAATCC
5723 TAAATAAAAACTAATTAAAAT
1 TAAATAAAAACTAATTAAAAT
* **
5744 TAAATTAACTCTAATTAAAAT
1 TAAATAAAAACTAATTAAAAT
5765 AGAAATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATAAAAACTAATTAAAAT
Found at i:9042 original size:19 final size:18
Alignment explanation
Indices: 9018--9063 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
9008 ATTTTTTTCC
*
9018 TTATATTTTACTTTATTT
1 TTATATTTTAATTTATTT
9036 ATTATATTCTTAATTTATTT
1 -TTATATT-TTAATTTATTT
9056 TTAT-TTTT
1 TTATATTTT
9064 TTCAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 2 0.08
18 2 0.08
19 11 0.44
20 10 0.40
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATATTTTAATTTATTT
Found at i:10982 original size:25 final size:23
Alignment explanation
Indices: 10950--11013 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
10940 ATCTTAGATA
10950 TAATATATATTATTAAATAAATAA-
1 TAATATATATT-TTAAAT-AATAAG
10974 TAA-ATATATTTTAAATAATAAG
1 TAATATATATTTTAAATAATAAG
10996 TAAATAATATATATTTAA
1 T-AAT-ATATAT-TTTAA
11014 TTACTAAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 5 0.14
22 7 0.20
23 9 0.26
24 3 0.09
25 6 0.17
26 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATATATATTTTAAATAATAAG
Found at i:10993 original size:21 final size:23
Alignment explanation
Indices: 10949--11010 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 23
10939 TATCTTAGAT
10949 ATAATATATATTATTAAATAAATA
1 ATAA-ATATATTATTAAATAAATA
10973 ATAAATATATT-TTAAAT-AATA
1 ATAAATATATTATTAAATAAATA
10994 AGTAAATAATATATATT
1 A-TAAAT-ATAT-TATT
11011 TAATTACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.15
22 11 0.32
23 11 0.32
24 5 0.15
25 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAATATATTATTAAATAAATA
Found at i:14920 original size:12 final size:12
Alignment explanation
Indices: 14899--14928 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
14889 CGTGTTTAAA
*
14899 TAAAAAAATAAT
1 TAAAATAATAAT
14911 TAAAATAATAAT
1 TAAAATAATAAT
14923 TAAAAT
1 TAAAAT
14929 TAATTATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TAAAATAATAAT
Found at i:17207 original size:2 final size:2
Alignment explanation
Indices: 17200--17226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17190 AGCCCCTTAC
17200 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 T
17227 GACTTAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20436 original size:36 final size:36
Alignment explanation
Indices: 20388--20460 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
20378 TTTAAAAGTA
20388 GATTCTAAAACCCAAAAGAAGCAATTATTTTATTTG
1 GATTCTAAAACCCAAAAGAAGCAATTATTTTATTTG
*
20424 GATTCTAGAACCCAAAAGAAGCAATTATTTTATTTG
1 GATTCTAAAACCCAAAAGAAGCAATTATTTTATTTG
20460 G
1 G
20461 TGTAAACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (36 bp):
GATTCTAAAACCCAAAAGAAGCAATTATTTTATTTG
Found at i:25332 original size:36 final size:35
Alignment explanation
Indices: 25285--25353 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
25275 GAGATTTTGG
* *
25285 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAAATAC-AAAAATGTAATA
25321 AGAAATATGATAACCAAAAATACAAAAATGTAA
1 AGAAATATGATAACCAAAAATACAAAAATGTAA
25354 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 10 0.32
36 21 0.68
ACGTcount: A:0.62, C:0.07, G:0.09, T:0.22
Consensus pattern (35 bp):
AGAAATATGATAACCAAAAATACAAAAATGTAATA
Found at i:26110 original size:181 final size:181
Alignment explanation
Indices: 25806--26151 Score: 611
Period size: 181 Copynumber: 1.9 Consensus size: 181
25796 TACTAATGTT
*
25806 ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTTTAGTAGATTACT
1 ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTACT
*
25871 CAAGTAATTAAATTGGTAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
66 CAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
25936 AGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAAAA
131 AGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAAAA
* * *
25987 ATTAAGAATGTAAGGATTGGTAAATACAATTTTAATAACTTTTTTAGCTTTTATAGTAGATTACT
1 ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTACT
* * *
26052 TAAGTAATTAAATTGGCAACTTTCATTATTGATCATACAAAGTTACTAAAATTAATAAGGATGTA
66 CAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
*
26117 AGATTATTTGAATCTAGATAGTACTATAATGTTTT
131 AGATTACTTGAATCTAGATAGTACTATAATGTTTT
26152 CATAACTTTT
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 156 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (181 bp):
ATTAAGAATGTAAGGATTGGTAAATACAATTTAAAAAACTTTTATAGCTTTTATAGTAGATTACT
CAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGTA
AGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAAAA
Found at i:27893 original size:95 final size:95
Alignment explanation
Indices: 27773--27951 Score: 315
Period size: 95 Copynumber: 1.9 Consensus size: 95
27763 AAATTGATAA
*
27773 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAGTAGCC
1 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
27838 CTGTAG-TTCTTTTAGTAATTCTTTATTCT
66 CTGTAGTTTCTTTTAGTAATTCTTTATTCT
*
27867 TCTTCTTGCATTCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGC
1 TCTTCTTGCA-TCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGC
*
27932 CCTGTAGTTTTTTTTAGTAA
65 CCTGTAGTTTCTTTTAGTAA
27952 ATTTAAATAG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 10 0.12
95 59 0.74
96 11 0.14
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (95 bp):
TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
CTGTAGTTTCTTTTAGTAATTCTTTATTCT
Done.