Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007610.1 Corchorus capsularis cultivar CVL-1 contig07631, 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: 31219
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7674 original size:2 final size:2
Alignment explanation
Indices: 7669--7700 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7659 TATTTTCTTA
7669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7701 TAAACCCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11308 original size:28 final size:28
Alignment explanation
Indices: 11277--11335 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11267 TTAAAACCAA
* * *
11277 TCAAGTCTCTTCCTTCATTTCA-GCTGTC
1 TCAAGTATCTTCCATCAGTTCAGGC-GTC
11305 TCAAGTATCTTCCATCAGTTCAGGCGTC
1 TCAAGTATCTTCCATCAGTTCAGGCGTC
11333 TCA
1 TCA
11336 TTTCTCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.37
Consensus pattern (28 bp):
TCAAGTATCTTCCATCAGTTCAGGCGTC
Found at i:12671 original size:2 final size:2
Alignment explanation
Indices: 12666--12699 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12656 TTACACACAA
12666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12700 CAATTAGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17705 original size:47 final size:46
Alignment explanation
Indices: 17548--17710 Score: 123
Period size: 47 Copynumber: 3.5 Consensus size: 46
17538 AGTAAGACCC
* * * * *
17548 AAGGTAGCAAAAATTGGCC-AGATGGAAAAGACCATCATCAAAATCG
1 AAGGTGGCCAAAATTGGCCAAAAT-GAAAAGGCTATCATCAAAATCG
* * * * * * * *
17594 ACGGTGGCCAAAATTGTCCAAAATGACCAAGGGTAACCAAT-AAGACCC
1 AAGGTGGCCAAAATTGGCCAAAATGA-AAAGGCT-ATC-ATCAAAATCG
* *
17642 AAGGTGGCAAAAATTGGCCAAAATCGAAAAGGCTATCATCAATATCG
1 AAGGTGGCCAAAATTGGCCAAAAT-GAAAAGGCTATCATCAAAATCG
*
17689 ATGGTGGCCAAAATTGGCCAAA
1 AAGGTGGCCAAAATTGGCCAAA
17711 TTATAGTAAC
Statistics
Matches: 87, Mismatches: 24, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
46 19 0.22
47 32 0.37
48 32 0.37
49 4 0.05
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (46 bp):
AAGGTGGCCAAAATTGGCCAAAATGAAAAGGCTATCATCAAAATCG
Found at i:27074 original size:353 final size:353
Alignment explanation
Indices: 26428--27124 Score: 1349
Period size: 353 Copynumber: 2.0 Consensus size: 353
26418 GCTTTATAAT
26428 TATTGTTTGCTTTATAATTTTCCATAGATTTAGATCTAGATTTACTTTTCTTTACTTTGCTTTGT
1 TATTGTTTGCTTTATAATTTTCCATAGATTTAGATCTAGATTTACTTTTCTTTACTTTGCTTTGT
26493 TTTTAGTTTAATTGTTTTCTTTATAATTAATTTTCTTAATCCCCTGTTTTCTAAGTGATTTTTGG
66 TTTTAGTTTAATTGTTTTCTTTATAATTAATTTTCTTAATCCCCTGTTTTCTAAGTGATTTTTGG
*
26558 AAAAGATATATTCTTTGGAAAAGACCTTCACAATTATAATCCTTCTCTGAGGGATTCGACCCCTA
131 AAAAGATATATTCTTTGGAAAAGACCTTCACAATTATAACCCTTCTCTGAGGGATTCGACCCCTA
*
26623 CTTGCCATAGCTTGTTTAGTTAGTTTTTGTGGGGATTATTTTTATGATTGTTAAACGACCGATCA
196 CTTGCCATAGCTAGTTTAGTTAGTTTTTGTGGGGATTATTTTTATGATTGTTAAACGACCGATCA
26688 CTCTCCTTCAAGGTTTCGACCTCACCGGATTTGTTGATGGCACTCATGCCGCACCACCCAAAGAA
261 CTCTCCTTCAAGGTTTCGACCTCACCGGATTTGTTGATGGCACTCATGCCGCACCACCCAAAGAA
26753 GTGACCAAAGATGGTCGAACGATTTCCA
326 GTGACCAAAGATGGTCGAACGATTTCCA
26781 TATTGTTTGCTTTATAATTTTCCATAGATTTAGATCTAGATTTACTTTTCTTTACTTTGCTTTGT
1 TATTGTTTGCTTTATAATTTTCCATAGATTTAGATCTAGATTTACTTTTCTTTACTTTGCTTTGT
*
26846 TTTTAGTTTAATTGTTTTCTTTATAATTAATTTTTTTAATCCCCTGTTTTCTAAGTGATTTTTGG
66 TTTTAGTTTAATTGTTTTCTTTATAATTAATTTTCTTAATCCCCTGTTTTCTAAGTGATTTTTGG
*
26911 AAAAGATATATTCTTTGGAAAAGACCTTCACAATTATAACCCTTCTCTGTGGGATTCGACCCCTA
131 AAAAGATATATTCTTTGGAAAAGACCTTCACAATTATAACCCTTCTCTGAGGGATTCGACCCCTA
*
26976 CTTGCCCTAGCTAGTTTAGTTAGTTTTTGTGGGGATTATTTTTATGATTGTTAAACGACCGATCA
196 CTTGCCATAGCTAGTTTAGTTAGTTTTTGTGGGGATTATTTTTATGATTGTTAAACGACCGATCA
27041 CTCTCCTTCAAGGTTTCGACCTCACCGGATTTGTTGATGGCACTCATGCCGCACCACCCAAAGAA
261 CTCTCCTTCAAGGTTTCGACCTCACCGGATTTGTTGATGGCACTCATGCCGCACCACCCAAAGAA
27106 GTGACCAAAGATGGTCGAA
326 GTGACCAAAGATGGTCGAA
27125 TTAATTCTTC
Statistics
Matches: 339, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
353 339 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (353 bp):
TATTGTTTGCTTTATAATTTTCCATAGATTTAGATCTAGATTTACTTTTCTTTACTTTGCTTTGT
TTTTAGTTTAATTGTTTTCTTTATAATTAATTTTCTTAATCCCCTGTTTTCTAAGTGATTTTTGG
AAAAGATATATTCTTTGGAAAAGACCTTCACAATTATAACCCTTCTCTGAGGGATTCGACCCCTA
CTTGCCATAGCTAGTTTAGTTAGTTTTTGTGGGGATTATTTTTATGATTGTTAAACGACCGATCA
CTCTCCTTCAAGGTTTCGACCTCACCGGATTTGTTGATGGCACTCATGCCGCACCACCCAAAGAA
GTGACCAAAGATGGTCGAACGATTTCCA
Found at i:29236 original size:18 final size:18
Alignment explanation
Indices: 29210--29298 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
29200 TGTACAGGCA
*
29210 GATGCTCCACTGCCGTAG
1 GATGTTCCACTGCCGTAG
29228 GATGTTCCACTGCCGTAG
1 GATGTTCCACTGCCGTAG
* *
29246 GATGTTCCACTGCTGCAG
1 GATGTTCCACTGCCGTAG
* **
29264 GATGTTCCATTGCCACAG
1 GATGTTCCACTGCCGTAG
*
29282 GATGTTCCGCTGCCGTA
1 GATGTTCCACTGCCGTA
29299 AGAACCTTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (18 bp):
GATGTTCCACTGCCGTAG
Done.