Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014381.1 Corchorus olitorius cultivar O-4 contig14414, 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: 46990
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:344 original size:22 final size:22
Alignment explanation
Indices: 300--351 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
290 GCTTACAAGA
* *
300 TTACT-AAAATTTTAATAAAGG
1 TTACTAAAAATTGTAACAAAGG
*
321 TTACTAAAAATTGTAACAAGGG
1 TTACTAAAAATTGTAACAAAGG
343 TTACTAAAA
1 TTACTAAAA
352 CCTTTAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (22 bp):
TTACTAAAAATTGTAACAAAGG
Found at i:787 original size:11 final size:11
Alignment explanation
Indices: 771--811 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
761 TTGACAGCGC
771 AACAAAAACAA
1 AACAAAAACAA
782 AACAAAAACAA
1 AACAAAAACAA
793 AA-AACAAA-AA
1 AACAA-AAACAA
*
803 AACGAAAAC
1 AACAAAAAC
812 GATGCCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:1220 original size:86 final size:84
Alignment explanation
Indices: 1123--1299 Score: 309
Period size: 86 Copynumber: 2.1 Consensus size: 84
1113 TAAGATCACT
*
1123 AAAAATCTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGATTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTT-AAAA-ATTTTAAGTTTAAT
1188 GAAAAATTTATAAGCTTACCA
64 GAAAAATTTATAAGCTTACCA
*
1209 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAACTTTTAAGTTTAATGA
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAATTTTAAGTTTAATGA
1274 AAAATTTATAAGCTTACCA
66 AAAATTTATAAGCTTACCA
1293 AGAAAAT
1 A-AAAAT
1300 TTACAAGGTT
Statistics
Matches: 88, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
84 35 0.40
85 9 0.10
86 44 0.50
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (84 bp):
AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAATTTTAAGTTTAATGA
AAAATTTATAAGCTTACCA
Found at i:1382 original size:21 final size:20
Alignment explanation
Indices: 1335--1374 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1325 CAATTACAAT
*
1335 AAAAGTTAAATAGTTTACTA
1 AAAAGTTAAATAGATTACTA
1355 AAAAGTTAAATAAGATTACT
1 AAAAGTTAAAT-AGATTACT
1375 TGAAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAAGTTAAATAGATTACTA
Found at i:1782 original size:27 final size:27
Alignment explanation
Indices: 1742--1794 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
1732 TAAGGTGACT
1742 AAAAAACTTTATAAGG-CCAAAAAAGG
1 AAAAAACTTTATAAGGTCCAAAAAAGG
*
1768 AAAAAAGTTTAATAAGGTCCAAAAAAG
1 AAAAAACTTT-ATAAGGTCCAAAAAAG
1795 CTCAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.38
27 6 0.25
28 9 0.38
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.17
Consensus pattern (27 bp):
AAAAAACTTTATAAGGTCCAAAAAAGG
Found at i:4210 original size:22 final size:22
Alignment explanation
Indices: 4185--4254 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
4175 TATTTTTATG
*
4185 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAATTACCCTATA
** * *
4207 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATTACCCTATA
4229 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATTACCCTATA
4250 AAATT
1 AAATT
4255 GGACTTATTG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 9 0.22
22 31 0.77
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAATTACCCTATA
Found at i:6560 original size:26 final size:28
Alignment explanation
Indices: 6509--6569 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
6499 TGTGATAGGA
6509 AGAAGGAAGAATTATCCATCAACCATCT
1 AGAAGGAAGAATTATCCATCAACCATCT
* **
6537 AGGAGGAAG-ATT-TCCATCTCCCATCT
1 AGAAGGAAGAATTATCCATCAACCATCT
6563 AGAAGGA
1 AGAAGGA
6570 TGATGCCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 18 0.62
27 3 0.10
28 8 0.28
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (28 bp):
AGAAGGAAGAATTATCCATCAACCATCT
Found at i:9248 original size:21 final size:21
Alignment explanation
Indices: 9224--9299 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
9214 TATTTTTATG
*
9224 AAATTTTGATAATTACCTATT
1 AAATTTTGATAATTACCTATA
** *
9245 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATTACC-TATA
9267 AAATTTTGATAATTACCTATA
1 AAATTTTGATAATTACCTATA
*
9288 AAATTGTGATAA
1 AAATTTTGATAA
9300 ACTCCATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 29 0.62
22 18 0.38
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAATTACCTATA
Found at i:9273 original size:22 final size:21
Alignment explanation
Indices: 9220--9343 Score: 95
Period size: 22 Copynumber: 5.8 Consensus size: 21
9210 TGAATATTTT
**
9220 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACCACC
*
9241 TATTAAATTTTGATAACCACC
1 TATGAAATTTTGATAACCACC
**
9262 ATATGAAATTTTGATAATTACC
1 -TATGAAATTTTGATAACCACC
* * * *
9284 TATAAAATTGTGATAAACTCC
1 TATGAAATTTTGATAACCACC
* * *
9305 ATAAGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACC-ACC
* *
9328 TATAAAATTTTAATAA
1 TATGAAATTTTGATAA
9344 ATTTTCCTAT
Statistics
Matches: 78, Mismatches: 22, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
21 34 0.44
22 43 0.55
23 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:9281 original size:43 final size:43
Alignment explanation
Indices: 9220--9336 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
9210 TGAATATTTT
* * *
9220 TATGAAATTTTGATAATTACCTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAATTACCTATAAAATTGTGATAAACACCA
*
9263 TATGAAATTTTGATAATTACCTATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAATTACCTATAAAATTGTGATAAACACCA
* * * *
9306 TAAGAAACTTTGATAACCTAACTATAAAATT
1 TATGAAATTTTGATAA-TTACCTATAAAATT
9337 TTAATAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
43 53 0.82
44 12 0.18
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.37
Consensus pattern (43 bp):
TATGAAATTTTGATAATTACCTATAAAATTGTGATAAACACCA
Found at i:9372 original size:20 final size:21
Alignment explanation
Indices: 9220--9389 Score: 71
Period size: 22 Copynumber: 7.9 Consensus size: 21
9210 TGAATATTTT
*
9220 TATGAAATTTTGATAAT-TACC
1 TATG-AATTTTGATAATCTTCC
* **
9241 TATTAAATTTTGATAA-CCACC
1 TA-TGAATTTTGATAATCTTCC
*
9262 ATATGAAATTTTGATAAT-TACC
1 -TATG-AATTTTGATAATCTTCC
* * *
9284 TATAAAATTGTGATAAAC-TCC
1 TAT-GAATTTTGATAATCTTCC
* * * **
9305 ATAAGAAACTTTGATAACCTAAC
1 -TATG-AATTTTGATAATCTTCC
* * *
9328 TATAAAATTTTAATAAATTTTCC
1 TAT-GAATTTTGAT-AATCTTCC
9351 TATGAATTTTG-TAATCTTCC
1 TATGAATTTTGATAATCTTCC
*
9371 TATGATTTTTGATAATCTT
1 TATGAATTTTGATAATCTT
9390 TGTGTGAGAT
Statistics
Matches: 109, Mismatches: 27, Indels: 26
0.67 0.17 0.16
Matches are distributed among these distances:
20 17 0.16
21 40 0.37
22 44 0.40
23 8 0.07
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (21 bp):
TATGAATTTTGATAATCTTCC
Found at i:9388 original size:21 final size:20
Alignment explanation
Indices: 9347--9389 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
9337 TTAATAAATT
9347 TTCCTATGAATTTTGTAATC
1 TTCCTATGAATTTTGTAATC
*
9367 TTCCTATGATTTTTGATAATC
1 TTCCTATGAATTTTG-TAATC
9388 TT
1 TT
9390 TGTGTGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.53
Consensus pattern (20 bp):
TTCCTATGAATTTTGTAATC
Found at i:25429 original size:50 final size:50
Alignment explanation
Indices: 25328--25430 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 50
25318 TTTCCTGCAC
* * * *
25328 TTTTTCTCAATTTTTACAACAAAATTGAATCTTTAATTTTCCTTGCACCT
1 TTTTTCTCAATCTTTACAAAAAAATTGAATATTTAATTTTCATTGCACCT
* * *
25378 TTTTTCTCAATCTTTA-AGAAAAAATTGAATATTTACTTTTTATTGCTCCT
1 TTTTTCTCAATCTTTACA-AAAAAATTGAATATTTAATTTTCATTGCACCT
25428 TTT
1 TTT
25431 ATCAATTTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.02
50 44 0.98
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (50 bp):
TTTTTCTCAATCTTTACAAAAAAATTGAATATTTAATTTTCATTGCACCT
Found at i:26293 original size:15 final size:15
Alignment explanation
Indices: 26271--26322 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
26261 TGCTAGCGTG
26271 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
*
26286 ATTGGTGCAAACAAC
1 AATGGTGCAAACAAC
* *
26301 AATGGTGCGAATAAC
1 AATGGTGCAAACAAC
26316 AATGGTG
1 AATGGTG
26323 TGAACAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:26334 original size:15 final size:15
Alignment explanation
Indices: 26271--26335 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
26261 TGCTAGCGTG
*
26271 AATGGTGCAAACAAC
1 AATGGTGCGAACAAC
* *
26286 ATTGGTGCAAACAAC
1 AATGGTGCGAACAAC
*
26301 AATGGTGCGAATAAC
1 AATGGTGCGAACAAC
* *
26316 AATGGTGTGAACAAT
1 AATGGTGCGAACAAC
26331 AATGG
1 AATGG
26336 AAATGGTGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.20
Consensus pattern (15 bp):
AATGGTGCGAACAAC
Found at i:41130 original size:4 final size:4
Alignment explanation
Indices: 41121--41151 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41111 TTTTCTTTTT
41121 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
41152 TTTCAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:43042 original size:21 final size:21
Alignment explanation
Indices: 43016--43064 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
43006 GGGATCGAGA
*
43016 TGGGCGCTGA-GCCTTGTCGCC
1 TGGGCGCTGAGGCATT-TCGCC
43037 TGGGCGCTGAGGCATTTCGCC
1 TGGGCGCTGAGGCATTTCGCC
43058 TGGGCGC
1 TGGGCGC
43065 CCAGCGGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.06, C:0.31, G:0.41, T:0.22
Consensus pattern (21 bp):
TGGGCGCTGAGGCATTTCGCC
Done.