Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016407.1 Corchorus capsularis cultivar CVL-1 contig16428, 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: 25506
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:3705 original size:10 final size:10
Alignment explanation
Indices: 3690--3717 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3680 AGTTTGAAGT
3690 TTTCAGAGGA
1 TTTCAGAGGA
3700 TTTCAGAGGA
1 TTTCAGAGGA
3710 TTTCAGAG
1 TTTCAGAG
3718 AATGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (10 bp):
TTTCAGAGGA
Found at i:11077 original size:52 final size:51
Alignment explanation
Indices: 11019--11172 Score: 163
Period size: 52 Copynumber: 3.0 Consensus size: 51
11009 TATAAAAGGG
* *
11019 AGTCAAATTTTCAATTGCTTAATTAAAATAGCCTAAGGTAGCTAAATCTTAT
1 AGTCAAATTTTCAA-TGCATAATTAAAATAGCCTAAGGTAGCTAAATCCTAT
*
11071 AGTCAAAATTTT-AATGGCCTAATTAAAATAGCCT-AGGATAGCTAAATCCTAT
1 AGTC-AAATTTTCAAT-GCATAATTAAAATAGCCTAAGG-TAGCTAAATCCTAT
* * * * * *
11123 A-TTATATATACAA-ACATAATTAAAATAGCCTAAGATAGCTAAATCCTAT
1 AGTCAAATTTTCAATGCATAATTAAAATAGCCTAAGGTAGCTAAATCCTAT
11172 A
1 A
11173 TTATGTATAC
Statistics
Matches: 88, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
49 31 0.35
50 6 0.07
51 7 0.08
52 37 0.42
53 7 0.08
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (51 bp):
AGTCAAATTTTCAATGCATAATTAAAATAGCCTAAGGTAGCTAAATCCTAT
Found at i:11160 original size:49 final size:49
Alignment explanation
Indices: 11090--11190 Score: 175
Period size: 49 Copynumber: 2.1 Consensus size: 49
11080 TTTAATGGCC
*
11090 TAATTAAAATAGCCTAGGATAGCTAAATCCTATATTATATATACAAACA
1 TAATTAAAATAGCCTAAGATAGCTAAATCCTATATTATATATACAAACA
* *
11139 TAATTAAAATAGCCTAAGATAGCTAAATCCTATATTATGTATACATACA
1 TAATTAAAATAGCCTAAGATAGCTAAATCCTATATTATATATACAAACA
11188 TAA
1 TAA
11191 ATCCTATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (49 bp):
TAATTAAAATAGCCTAAGATAGCTAAATCCTATATTATATATACAAACA
Found at i:11950 original size:51 final size:51
Alignment explanation
Indices: 11874--11999 Score: 252
Period size: 51 Copynumber: 2.5 Consensus size: 51
11864 GTGCCAAATT
11874 TACGGGTTGTATCGGATGATACGATGTTAATTTCGATAAGATACGCATAGA
1 TACGGGTTGTATCGGATGATACGATGTTAATTTCGATAAGATACGCATAGA
11925 TACGGGTTGTATCGGATGATACGATGTTAATTTCGATAAGATACGCATAGA
1 TACGGGTTGTATCGGATGATACGATGTTAATTTCGATAAGATACGCATAGA
11976 TACGGGTTGTATCGGATGATACGA
1 TACGGGTTGTATCGGATGATACGA
12000 ATAATAACAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (51 bp):
TACGGGTTGTATCGGATGATACGATGTTAATTTCGATAAGATACGCATAGA
Found at i:13558 original size:1 final size:1
Alignment explanation
Indices: 13552--13580 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
13542 AGAATTTACC
13552 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13581 CCCGCTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15189 original size:18 final size:18
Alignment explanation
Indices: 15166--15212 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
15156 GAAACCGAAA
15166 TGACCCGACCTCAAATCC
1 TGACCCGACCTCAAATCC
*
15184 TGACCCGACCTCAAATCT
1 TGACCCGACCTCAAATCC
15202 TGACCCGACCT
1 TGACCCGACCT
15213 GAATCAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.26, C:0.43, G:0.13, T:0.19
Consensus pattern (18 bp):
TGACCCGACCTCAAATCC
Found at i:15776 original size:234 final size:233
Alignment explanation
Indices: 15367--15833 Score: 889
Period size: 234 Copynumber: 2.0 Consensus size: 233
15357 AAAATAATTA
*
15367 TATAATATTGAATTTAATTAAATGAAAATAGAGTTTTAGTAAAATAAAATTGTATATTAAAAATT
1 TATAATATTGAATTTAATTAAATGAAAATAGAGTTTTAGTAAAATAAAACTGTATATTAAAAATT
15432 TTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTATAAAGATATT
66 TTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTATAAAGATATT
15497 AGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGAATAGAACTAACAATAGTTTAAGCAAGA
131 AGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGAATAGAACT-ACAATAGTTTAAGCAAGA
*
15562 ATATTTAAGAAATATATTCAAAAAAATAAGGGTATAATG
195 ACATTTAAGAAATATATTCAAAAAAATAAGGGTATAATG
15601 TATAATATTGAATTTAATTAAATGAAAATAGAGTTTTAGTAAAATAAAACTGTATATTAAAAATT
1 TATAATATTGAATTTAATTAAATGAAAATAGAGTTTTAGTAAAATAAAACTGTATATTAAAAATT
15666 TTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTATAAAGATATT
66 TTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTATAAAGATATT
**
15731 AGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGAATAGAACTACAATAGTTTAAGCAAGGG
131 AGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGAATAGAACTACAATAGTTTAAGCAAGAA
15796 CATTTAAGAAATATATTCAAAAAAATAAGGGTATAATG
196 CATTTAAGAAATATATTCAAAAAAATAAGGGTATAATG
15834 GTCGATTCAA
Statistics
Matches: 229, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
233 54 0.24
234 175 0.76
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (233 bp):
TATAATATTGAATTTAATTAAATGAAAATAGAGTTTTAGTAAAATAAAACTGTATATTAAAAATT
TTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAATAAAGAAATTATAAAGATATT
AGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGAATAGAACTACAATAGTTTAAGCAAGAA
CATTTAAGAAATATATTCAAAAAAATAAGGGTATAATG
Found at i:19193 original size:2 final size:2
Alignment explanation
Indices: 19186--19259 Score: 93
Period size: 2 Copynumber: 39.0 Consensus size: 2
19176 CGGACCCGAA
*
19186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
19227 GT AT AT AT -T AT GT AT AT AT AT AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19260 GCTTTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
1 4 0.06
2 58 0.94
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19255 original size:21 final size:23
Alignment explanation
Indices: 19186--19259 Score: 84
Period size: 25 Copynumber: 3.3 Consensus size: 23
19176 CGGACCCGAA
*
19186 ATATA-TATATATATATATATAT
1 ATATATTATATATATATGTATAT
19208 ATATATTATGTATATATATGTATAT
1 ATATATTA--TATATATATGTATAT
19233 AT-TATGTATATATATAT-TA-AT
1 ATATAT-TATATATATATGTATAT
19254 ATATAT
1 ATATAT
19260 GCTTTTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
21 4 0.09
22 10 0.22
23 11 0.24
24 3 0.07
25 18 0.39
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATATTATATATATATGTATAT
Found at i:19648 original size:214 final size:210
Alignment explanation
Indices: 19401--19828 Score: 660
Period size: 214 Copynumber: 2.0 Consensus size: 210
19391 TAAATATATA
* *
19401 CTACATATTATTTAAATAAACATATGGAAATTACTAAAAGATCCCTA-CCTCGGATTAATGAGAA
1 CTACATATTATTTAAATAAACATATGAAAATTACTAAAAGATCCCTACCCT-AGATTAATGAGAA
*
19465 GCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGACCGATTAGTTAAATGCCCTAACTTTTGA
65 GCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGACCGATTACTTAAATGCCCTAACTTTTGA
* *
19530 TTCCATAGGTGATTAAATAACTAGACTTAATTTTTGGTCATTTCTCAAATTACTTTAATAGAGTA
130 TTCCACAGGTGATTAAATAACTAGAC----TTTTTGGTCATTTCTCAAATGACTTTAATAGAGTA
*
19595 GTGGGATTACTAAAAGATCC
191 GTGGAATTACTAAAAGATCC
* *
19615 CTACATATTATTTGAATAAACATATGAAAATTACTAAAAGATCCCTACCCTAGATTAATGAGGAG
1 CTACATATTATTTAAATAAACATATGAAAATTACTAAAAGATCCCTACCCTAGATTAATGAGAAG
* * * ** *
19680 TGAGAGAATTATTTTTTTTCGTCTTTTCCTGCTTGACCGATTACTTAAATGCCTTAACTTTTGAT
66 CGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGACCGATTACTTAAATGCCCTAACTTTTGAT
* *
19745 TCTACAGGTGATTAAATAACTAGACTTTTTGGTCATTTCTCAAATGATTTTAATAGAGTAGTGGA
131 TCCACAGGTGATTAAATAACTAGACTTTTTGGTCATTTCTCAAATGACTTTAATAGAGTAGTGGA
19810 ATTACTAAAAGATCC
196 ATTACTAAAAGATCC
19825 CTAC
1 CTAC
19829 CCCGAATAAA
Statistics
Matches: 197, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
210 56 0.28
214 138 0.70
215 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (210 bp):
CTACATATTATTTAAATAAACATATGAAAATTACTAAAAGATCCCTACCCTAGATTAATGAGAAG
CGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGACCGATTACTTAAATGCCCTAACTTTTGAT
TCCACAGGTGATTAAATAACTAGACTTTTTGGTCATTTCTCAAATGACTTTAATAGAGTAGTGGA
ATTACTAAAAGATCC
Found at i:19973 original size:211 final size:209
Alignment explanation
Indices: 19415--19952 Score: 590
Period size: 214 Copynumber: 2.5 Consensus size: 209
19405 ATATTATTTA
* *
19415 AATAAACATATGGAAATTACTAAAAGATCCCT-ACCTCGGATTAATGAGAAGC-GAGAGAACTAA
1 AATAAACATATGAAAATTACTAAAAGATCCCTAACCTAGGATTAATGAG-AGCTGAGAGAACTAA
* * * *
19478 TTTTTTTCGTCTTTTCCCACTTGACCGATTAGTTAAATGCCCTAACTTTTGATTCCATAGGTGAT
65 TTTTTTTCGTCTTTTCCTACTTGACCGATTACTTAAATG-CCTAACTTTTGATT-TACAGGTGAT
* *
19543 TAAATAACTAGACTTAATTTTTGGTCATTTCTCAAATTACTTTAATAGAGTAGTGGGATTACTAA
128 TAAATAACTAGAC----TTTTTGGTCATTTCTCAAATGACTTTAATAGAGTAGTGGAATTACTAA
* * **
19608 AAGATCCCTACATATTATTTG
189 AAGATCCCTACAGAATAAATG
* * *
19629 AATAAACATATGAAAATTACTAAAAGATCCCTACCCTA-GATTAATGAGGAG-TGAGAGAATTAT
1 AATAAACATATGAAAATTACTAAAAGATCCCTAACCTAGGATTAATGA-GAGCTGAGAGAACTAA
*
19692 TTTTTTTCGTCTTTTCCTGCTTGACCGATTACTTAAATGCCTTAACTTTTGATTCTACAGGTGAT
65 TTTTTTTCGTCTTTTCCTACTTGACCGATTACTTAAATGCC-TAACTTTTGATT-TACAGGTGAT
*
19757 TAAATAACTAGACTTTTTGGTCATTTCTCAAATGATTTTAATAGAGTAGTGGAATTACTAAAAGA
128 TAAATAACTAGACTTTTTGGTCATTTCTCAAATGACTTTAATAGAGTAGTGGAATTACTAAAAGA
*
19822 TCCCTACCCCGAATAAAT-
193 TCCCTA--CAGAATAAATG
* ** * * *
19840 AAT-GAGTTAGGTG-GAATTACTAAAAGATCCCTAACC-AGGATTAATGATGAGCTG-GATAAGT
1 AATAAACATA--TGAAAATTACTAAAAGATCCCTAACCTAGGATTAATGA-GAGCTGAGAGAACT
* * **** *
19901 AATCTTTTTCGTCTTTACCTACTTGGTAAATTATTTAAATGTCCTAACTTTT
63 AATTTTTTTCGTCTTTTCCTACTTGACCGATTACTTAAATG-CCTAACTTTT
19953 TATCGTTGAA
Statistics
Matches: 278, Mismatches: 35, Indels: 25
0.82 0.10 0.07
Matches are distributed among these distances:
210 59 0.21
211 81 0.29
212 11 0.04
213 2 0.01
214 121 0.44
215 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (209 bp):
AATAAACATATGAAAATTACTAAAAGATCCCTAACCTAGGATTAATGAGAGCTGAGAGAACTAAT
TTTTTTCGTCTTTTCCTACTTGACCGATTACTTAAATGCCTAACTTTTGATTTACAGGTGATTAA
ATAACTAGACTTTTTGGTCATTTCTCAAATGACTTTAATAGAGTAGTGGAATTACTAAAAGATCC
CTACAGAATAAATG
Found at i:20669 original size:23 final size:23
Alignment explanation
Indices: 20639--20684 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20629 TATTCCATTT
20639 CTGTTAAATACAACAACAAAGGA
1 CTGTTAAATACAACAACAAAGGA
*
20662 CTGTTAAATGCAACAACAAAGGA
1 CTGTTAAATACAACAACAAAGGA
20685 GAAAATTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.17
Consensus pattern (23 bp):
CTGTTAAATACAACAACAAAGGA
Found at i:24003 original size:11 final size:11
Alignment explanation
Indices: 23987--24011 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23977 TATGAATTAA
23987 TAATAAGGTTG
1 TAATAAGGTTG
23998 TAATAAGGTTG
1 TAATAAGGTTG
24009 TAA
1 TAA
24012 ATAATGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (11 bp):
TAATAAGGTTG
Found at i:24273 original size:31 final size:31
Alignment explanation
Indices: 24238--24299 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
24228 AAAGTCATTA
*
24238 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAATTATTCATGAATCAAGAG
24269 ATGAATATTGTAATTATTCATGAATCAAGAG
1 ATGAATATTGTAATTATTCATGAATCAAGAG
24300 TTCTCTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (31 bp):
ATGAATATTGTAATTATTCATGAATCAAGAG
Done.