Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008113.1 Corchorus capsularis cultivar CVL-1 contig08134, 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: 18277
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1428 original size:42 final size:42
Alignment explanation
Indices: 1374--1464 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
1364 CCGGCCAAGA
*
1374 CTGCCCGGCCCTGCCAAGCCACAGCCGCGCCACTTGCACCGC
1 CTGCCCGACCCTGCCAAGCCACAGCCGCGCCACTTGCACCGC
1416 CTGCCCGACCCTGCCAAGCCACAGCCGCGCCACTTGCACCGC
1 CTGCCCGACCCTGCCAAGCCACAGCCGCGCCACTTGCACCGC
1458 CTGCCCG
1 CTGCCCG
1465 GCCATGCTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.14, C:0.53, G:0.23, T:0.10
Consensus pattern (42 bp):
CTGCCCGACCCTGCCAAGCCACAGCCGCGCCACTTGCACCGC
Found at i:4861 original size:13 final size:13
Alignment explanation
Indices: 4843--4877 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4833 ATAATTATTG
4843 TTTGCTTTATTAA
1 TTTGCTTTATTAA
4856 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
4869 TCTGCTTTA
1 TTTGCTTTA
4878 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:7080 original size:49 final size:49
Alignment explanation
Indices: 6949--7287 Score: 342
Period size: 49 Copynumber: 6.9 Consensus size: 49
6939 AAAGTGAACT
* * ** * * *
6949 TGCCTTTCGTCCGGAAAGGGCATTTTAAGAAAAAGCGAGTAAGACTAA-
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATAAG
* * * ** *
6997 CGCCTTCCATCCGGGAAGGGCGTTTTAGAAAAAAAGCAAGTAAAAATTAG
1 TGCCTTCCGTCCGGGAAGGGCATTTT-GGGAAAAAGCAAGTAAAAATAAG
* * *
7047 TGCCTTCCGTCCGGGAAGGGCACTTTGGGAAAAAGTAAGCAAAAATAAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATAAG
* * *
7096 CGTCTTCCGTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAA-AGCAAGTAAAAATAAG
* * * *
7145 TGCCTTCCGTCCGGGAAGGACATTTTGGGAAATAGCAGGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATAAG
* * ** *
7194 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAGATAGCGGGTGAAAAA-GAG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGT-AAAAATAAG
* * * *
7243 TGCCTTCCATCTGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAA
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAA
7288 CCGAAAAATT
Statistics
Matches: 244, Mismatches: 42, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
48 32 0.13
49 180 0.74
50 32 0.13
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (49 bp):
TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAAGTAAAAATAAG
Found at i:8707 original size:17 final size:17
Alignment explanation
Indices: 8685--8737 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
8675 ACTCCCTGAT
8685 GAACTATGAACCCTAAA
1 GAACTATGAACCCTAAA
* *
8702 GGACTA-GAA-GCTAAA
1 GAACTATGAACCCTAAA
8717 -AACTTATGAACCCTAAA
1 GAAC-TATGAACCCTAAA
8734 GAAC
1 GAAC
8738 CCCTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 2 0.07
15 7 0.25
16 6 0.21
17 10 0.36
18 3 0.11
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (17 bp):
GAACTATGAACCCTAAA
Found at i:11634 original size:19 final size:18
Alignment explanation
Indices: 11602--11639 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
11592 TTGAAATAAT
*
11602 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
11620 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
11639 T
1 T
11640 AATCTTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:11646 original size:22 final size:21
Alignment explanation
Indices: 11590--11646 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
11580 AATTCTTGCT
* *
11590 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
11612 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
11631 TCTTCAAATAATCTTC
1 TCTTCAAATAATCTTC
11647 GAACACGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.17
19 11 0.38
20 1 0.03
21 1 0.03
22 11 0.38
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:14587 original size:15 final size:15
Alignment explanation
Indices: 14567--14607 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
14557 TCCAAGTTGT
*
14567 TCATCTTCTTGTGGC
1 TCATCTTCTGGTGGC
14582 TCATCTTCTGGTGGC
1 TCATCTTCTGGTGGC
14597 TCATCTTCTGG
1 TCATCTTCTGG
14608 CTTAGCAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.27, G:0.22, T:0.44
Consensus pattern (15 bp):
TCATCTTCTGGTGGC
Found at i:16071 original size:6 final size:6
Alignment explanation
Indices: 16055--16085 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
16045 CAAAGCAAAA
16055 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
16086 TGGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:17459 original size:11 final size:11
Alignment explanation
Indices: 17442--17473 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
17432 ATTGTCTTCA
17442 AATCTTCAAAT
1 AATCTTCAAAT
*
17453 TATCTTCAAAT
1 AATCTTCAAAT
17464 AATCTTCAAA
1 AATCTTCAAA
17474 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:17470 original size:22 final size:22
Alignment explanation
Indices: 17419--17473 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 22
17409 TTGCTCCTTG
*
17419 AAATAATTCTTC-AATTGTCTTC
1 AAATAA-TCTTCAAATTATCTTC
17441 --A-AATCTTCAAATTATCTTC
1 AAATAATCTTCAAATTATCTTC
17460 AAATAATCTTCAAA
1 AAATAATCTTCAAA
17474 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 1 0.04
21 1 0.04
22 10 0.36
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATAATCTTCAAATTATCTTC
Done.