Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007016.1 Corchorus capsularis cultivar CVL-1 contig07037, 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: 27834
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:1173 original size:20 final size:21
Alignment explanation
Indices: 1148--1200 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1138 ACTAGCGCTG
*
1148 GGCG-CCCATGTGCTTTGCTT
1 GGCGACCCATGTGCTTTGCCT
* *
1168 GGCGCCCCATGTGGTTTGCCT
1 GGCGACCCATGTGCTTTGCCT
*
1189 CGCGACCCATGT
1 GGCGACCCATGT
1201 ACTCCTATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.08, C:0.34, G:0.30, T:0.28
Consensus pattern (21 bp):
GGCGACCCATGTGCTTTGCCT
Found at i:1633 original size:38 final size:38
Alignment explanation
Indices: 1582--3200 Score: 1327
Period size: 38 Copynumber: 42.2 Consensus size: 38
1572 AACACAAAGA
* ** *
1582 AGTTATCAAAGTTGACTACAAATAGGTCATCTTTCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * *
1620 AGTTATCGAAGTTGACTAGAAATAGGTCATCCTTCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * *
1658 AGTTATCGAAATTGGCTGGAAACAAGTCATCTTTTAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * *
1696 AGTTATCAAAATTGACAGGAAACAGGTCATC-TTCAAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTC-AGC
* *
1734 AGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* *
1772 AGCTATCGAAATTGACTGGAAACAGGTCATC-TTCAAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTC-AGC
* * * * * *
1810 AATTATGGAAGTTGGCAGGAAACATGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * ** * * *
1848 ACTTACCGAAATTGACCAGAAATAAGTCATTTTTCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * * *
1886 AATTATC-AAGTCGACTGGAAACATGTCTTCTTT-TGT
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * *
1922 TGTTATCAAAATTGATTGGAAACAGGTCATCTTTCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * *
1960 AGTTATTGGAGTTATCGAAATCGACTAGAAACAGGTCATCTTTCAGA
1 ---------AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * * *
2007 AGTTATCAAAATCGACTGGAAACAAGTCATTTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * *
2045 AGTTATCAAAGTTGTCTGGAAACAGGTCATCTTCCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * **
2083 AGTTATCGAAGTTGACTGAAAACAAGTCATCTTTCAAA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * **
2121 AGATATC-AAGATCGATTGGAAACAGGTCATTTTTCATT
1 AGTTATCGAAG-TTGACTGGAAACAGGTCATCTTTCAGC
* * * * * *
2159 GGTCATCAAAGTTGACTAGAAACAGATCATCATTCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * *
2197 AGTTATCGAAGATGGCTGGAAACAGGTCATCTTTCAGT
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
*
2235 AGTTATCGAAGTTGACTGGAAACAAGTCATCTTTCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * ** *
2273 AGTTATCAAAATCGAATGGAAACAAATCATTTTTCA-C
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * *
2310 AGGTCATCAAAGTTGACTGGAAACGATTGGAAATAGGTCATTTTTCA-C
1 A-GTTATCGAAGTTGACTGGAAAC----------AGGTCATCTTTCAGC
* * * *
2358 AACTCATCAAAGTTGACTGGAAACAAGTCATCTTTCAGC
1 -AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * * *
2397 AATTATTGAAGTTGGCTGGAAACAAGTCATCTTACAGT
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* *
2435 AGTTATCGAAGTTGACTGGAAACAAGT-AGTCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCA-TCTTTCAGC
* * *
2473 AGTTATCGAAGTTGGCTGGAAACAGGTCATTTTTCCGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* *
2511 AGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* ** * *
2549 AGTTTTAAAAATTGACTGGAAATAGGTCATC-TTCAAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTC-AGC
* * *
2587 AGTTATCGAAGTTGGCTGGAAATAGGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * *
2625 AGTTTTCAAAATTGACTGGAAATAGGTCATCTTTAAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* *
2663 AGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * * *
2701 AGTTATCGAAATCGACTGAAAACATGACATTTTTCAGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
*** * * *
2739 AGTTATC-AAGGCCAATTGGAAACAGGTCATCTTT-GGT
1 AGTTATCGAA-GTTGACTGGAAACAGGTCATCTTTCAGC
* * * * * *
2776 TGTTATCAAAATTGACTGGAAACATGTCATCTTTTAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* *
2814 AGTTATCAAAGTTGACTAGG-AACAGGTCATCTTTCGGC
1 AGTTATCGAAGTTGACT-GGAAACAGGTCATCTTTCAGC
** *
2852 AGTTATCGAAGTTGGTTGGAAACAGGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * *
2890 AGTTATCGAAATCGACTGGAAACAGGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * *
2928 AGTTATCGAAATCGACTGGAAACAGGTTATCTTTTAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* *
2966 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCGGC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* *
3004 AGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * * * *
3042 AGTTATCGAAATCGATTGGAAACAGATCATCTTCCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * ** * * * * *
3080 AGTTATCAAAATCAACTAGAGACATGTCATTTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * *
3118 AGTTATCAAAGTTGTCTGGAAACAGGTCATCTTTCAAC
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
* * * *
3156 AATTATGGAAGTTGACTGGAAACAGGTCATTTTTCAGA
1 AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
3194 AGTTATC
1 AGTTATC
3201 AAATGCGATT
Statistics
Matches: 1270, Mismatches: 272, Indels: 78
0.78 0.17 0.05
Matches are distributed among these distances:
36 6 0.00
37 82 0.06
38 1100 0.87
39 16 0.01
47 32 0.03
48 33 0.03
49 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (38 bp):
AGTTATCGAAGTTGACTGGAAACAGGTCATCTTTCAGC
Found at i:4903 original size:14 final size:14
Alignment explanation
Indices: 4863--4903 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4853 CATCATCTAA
* *
4863 AAAAACAAAAAAGG
1 AAAAAGAAAAAAAG
*
4877 AAAAAGAGAAAAAG
1 AAAAAGAAAAAAAG
4891 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
4904 AATTGGTGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:7754 original size:25 final size:25
Alignment explanation
Indices: 7722--7781 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
7712 AAGCATGCTA
*
7722 CTAGGAAGCTCGCTGACGCCCGCTG
1 CTAGGAAGCTCGCTGACACCCGCTG
*
7747 CT-GAGAAGCTCGCTGACACTCGCTG
1 CTAG-GAAGCTCGCTGACACCCGCTG
7772 CTAGGAAGCT
1 CTAGGAAGCT
7782 GGCAGAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.03
25 29 0.94
26 1 0.03
ACGTcount: A:0.20, C:0.32, G:0.30, T:0.18
Consensus pattern (25 bp):
CTAGGAAGCTCGCTGACACCCGCTG
Found at i:8290 original size:22 final size:22
Alignment explanation
Indices: 8265--8331 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
8255 TGATCGAGAG
8265 TAAAGAAAATAATTAAGAAAAC
1 TAAAGAAAATAATTAAGAAAAC
* * *
8287 TAAAGCAATTAA-TAACAAATAC
1 TAAAGAAAATAATTAAGAAA-AC
* * *
8309 CAAAGAAAAAAATTTATGAAAAC
1 TAAAGAAAATAA-TTAAGAAAAC
8332 AAATCTCCCA
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
21 6 0.18
22 20 0.61
23 2 0.06
24 5 0.15
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.19
Consensus pattern (22 bp):
TAAAGAAAATAATTAAGAAAAC
Found at i:20817 original size:19 final size:18
Alignment explanation
Indices: 20793--20828 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20783 TGAAGATTTC
20793 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
20812 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
20829 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.