Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007208.1 Corchorus capsularis cultivar CVL-1 contig07229, 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: 28123
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2949 original size:17 final size:17
Alignment explanation
Indices: 2929--2961 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2919 TATCTTTTTC
2929 TTTTTCGTTATTCTTTA
1 TTTTTCGTTATTCTTTA
*
2946 TTTTTCGTTTTTCTTT
1 TTTTTCGTTATTCTTT
2962 CTAGTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTCGTTATTCTTTA
Found at i:13024 original size:27 final size:28
Alignment explanation
Indices: 12991--13058 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
12981 ATCCTAGGGA
*
12991 ACTAACTTTGAATGGGA-AACTGTTTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
13018 ACTAACTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
13045 ACTAACTTGGAATG
1 ACTAACTTTGAATG
13059 AGAGTCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 3 0.08
27 34 0.92
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTGTCTTG
Found at i:17506 original size:27 final size:28
Alignment explanation
Indices: 17473--17540 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
17463 GTCCTAGGGA
* *
17473 ACTAACTTTGAATGGGA-AACTTTTTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
17500 ACTAACTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
17527 ACTAACTTGGAATG
1 ACTAACTTTGAATG
17541 AGAGTCTGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTGTCTTG
Found at i:24886 original size:95 final size:95
Alignment explanation
Indices: 24730--24911 Score: 337
Period size: 95 Copynumber: 1.9 Consensus size: 95
24720 AATGTAAAGC
24730 AGTTATTCTGGTCAATTCATATGCCAAAAGAAGGGAAAAAACAAAAGTTCTAATACCAAGCTTCC
1 AGTTATTCTGGTCAATTCATATGCCAAAAGAAGGGAAAAAACAAAAGTTCTAATACCAAGCTTCC
24795 AAGACCAAAGAATCTTTATTAAAGTAAAAT
66 AAGACCAAAGAATCTTTATTAAAGTAAAAT
* *
24825 AGTTATTTTGGTCAATTCATATGCCAAAAGAAGGGGAAAAACAAAAGTTCTAATACCAAGCTTCC
1 AGTTATTCTGGTCAATTCATATGCCAAAAGAAGGGAAAAAACAAAAGTTCTAATACCAAGCTTCC
*
24890 ATGACCAAAGAATCTTTATTAA
66 AAGACCAAAGAATCTTTATTAA
24912 GGCTGTGTTT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.26
Consensus pattern (95 bp):
AGTTATTCTGGTCAATTCATATGCCAAAAGAAGGGAAAAAACAAAAGTTCTAATACCAAGCTTCC
AAGACCAAAGAATCTTTATTAAAGTAAAAT
Found at i:25388 original size:26 final size:23
Alignment explanation
Indices: 25338--25391 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 23
25328 GTAGTCAATA
25338 AATATTTAATTAATTATAAATTT
1 AATATTTAATTAATTATAAATTT
*
25361 AATATTGTTATTAATTATATATATTT
1 AATATT-TAATTAATTATA-A-ATTT
25387 AATAT
1 AATAT
25392 AAATTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 11 0.41
25 1 0.04
26 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATTTAATTAATTATAAATTT
Found at i:25397 original size:24 final size:24
Alignment explanation
Indices: 25345--25406 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
25335 ATAAATATTT
*
25345 AATTAATTATAAATTTAATATTGT
1 AATTAATTATAAATTTAATATTGA
*
25369 TATTAATTATATATATTTAATA-T-A
1 AATTAATTATA-A-ATTTAATATTGA
*
25393 AATTAAAT-TAAATT
1 AATTAATTATAAATT
25407 ATAAAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 2 0.06
24 16 0.50
25 2 0.06
26 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AATTAATTATAAATTTAATATTGA
Found at i:25547 original size:21 final size:21
Alignment explanation
Indices: 25522--25571 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
25512 TCGCTAATTA
25522 TAATCTCATCTATACAGTACG
1 TAATCTCATCTATACAGTACG
* * **
25543 TAATCTAATCTGTACAGTATT
1 TAATCTCATCTATACAGTACG
25564 TAATCTCA
1 TAATCTCA
25572 CAACTCCAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (21 bp):
TAATCTCATCTATACAGTACG
Found at i:26094 original size:216 final size:216
Alignment explanation
Indices: 25718--26154 Score: 734
Period size: 216 Copynumber: 2.0 Consensus size: 216
25708 ATTGGCAATC
** * *
25718 ATTCGTTTCATGCAGTGGTGTAGTTAGGACATCTGTTTAGTGGGGTCAAAAAATTAACACTTCTT
1 ATTCGTTTCATGCAGTGGTGTAG-T-CCACATCTGGTTAGTGCGGTCAAAAAATTAACACTTCTT
* *
25783 TGTGATTTTTGCTACACTTTTTCAGTTTGATTTAATATTTAAAATTATATATTCTTTAATTTTGT
64 TGTGATTTTTGCTACAATTTTTCAGTTTGATTTAATATTTAAAATTATATATTCTTTAATTTCGT
*
25848 AAATTCAAAATATATTTAATTTTCTTCTTAAATTAGCACTTTTTTTCTTTTATATTAATTTTCTA
129 AAATTCAAAATATATTTAATTTCCTTCTTAAATTAGCACTTTTTTTCTTTTATATTAATTTTCTA
* *
25913 AATTTTTATATTAAACTCATGAA
194 AAATTTTATATTAAAATCATGAA
*
25936 ATTCGTTTCATGCAGTGGTGTAG-CCACATTTGGTTAGTGCGGTCAAAAAATTTAACACTTCTTT
1 ATTCGTTTCATGCAGTGGTGTAGTCCACATCTGGTTAGTGCGGTCAAAAAA-TTAACACTTCTTT
26000 GTGATTTTTGCTACAATTTTTCAGTTTGATTTAATATTTTAAAATTATATATTCTTTAATTTCGT
65 GTGATTTTTGCTACAATTTTTCAGTTTGATTTAATA-TTTAAAATTATATATTCTTTAATTTCGT
26065 AAATTC-AAATATATTTAATTTCCTTCTTAAATTAGCACTTTTTTTCTTTTATATTAATTTTCTA
129 AAATTCAAAATATATTTAATTTCCTTCTTAAATTAGCACTTTTTTTCTTTTATATTAATTTTCTA
26129 AAATTTTATATTAAAATCATGAA
194 AAATTTTATATTAAAATCATGAA
26152 ATT
1 ATT
26155 ATAAAAAAGT
Statistics
Matches: 207, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
215 22 0.11
216 129 0.62
217 33 0.16
218 23 0.11
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (216 bp):
ATTCGTTTCATGCAGTGGTGTAGTCCACATCTGGTTAGTGCGGTCAAAAAATTAACACTTCTTTG
TGATTTTTGCTACAATTTTTCAGTTTGATTTAATATTTAAAATTATATATTCTTTAATTTCGTAA
ATTCAAAATATATTTAATTTCCTTCTTAAATTAGCACTTTTTTTCTTTTATATTAATTTTCTAAA
ATTTTATATTAAAATCATGAA
Found at i:27048 original size:15 final size:15
Alignment explanation
Indices: 27028--27064 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
27018 ATCTGAAATA
27028 CTTCAGATATTGATT
1 CTTCAGATATTGATT
*
27043 CTTCAGATCTTGATT
1 CTTCAGATATTGATT
27058 CTTCAGA
1 CTTCAGA
27065 GTTTTCTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (15 bp):
CTTCAGATATTGATT
Found at i:27076 original size:15 final size:16
Alignment explanation
Indices: 27058--27089 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
27048 GATCTTGATT
27058 CTTCAGAG-TTTTCTG
1 CTTCAGAGCTTTTCTG
27073 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
27089 C
1 C
27090 CTTCTGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Done.