Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011305.1 Corchorus capsularis cultivar CVL-1 contig11326, 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: 18531
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:567 original size:6 final size:6
Alignment explanation
Indices: 556--604 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
546 ACTTGAATTC
* *
556 ATCTAT ATCTAT CTATAT ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
603 AT
1 AT
605 TAAAAAGTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (6 bp):
ATCTAT
Found at i:2422 original size:56 final size:53
Alignment explanation
Indices: 2328--2431 Score: 181
Period size: 56 Copynumber: 1.9 Consensus size: 53
2318 GTCAAATATT
2328 TACAAATACAAATGTAACATACATAAATTTATTTCTATGTATTTAAGTACAAA
1 TACAAATACAAATGTAACATACATAAATTTATTTCTATGTATTTAAGTACAAA
2381 TACAAATACAAATGTAACATTTTACATAAATTTATTTCTATGTATTTAAGT
1 TACAAATACAAATGTAACA---TACATAAATTTATTTCTATGTATTTAAGT
2432 GTTTAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
53 19 0.40
56 29 0.60
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (53 bp):
TACAAATACAAATGTAACATACATAAATTTATTTCTATGTATTTAAGTACAAA
Found at i:2864 original size:2 final size:2
Alignment explanation
Indices: 2847--2903 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
2837 TAAAAACTAG
* * *
2847 TA TA TC TA TA -A TA TA TA TA TA TA TA TA TA TA TC TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2888 TA TA TC TA TA CTA TA T
1 TA TA TA TA TA -TA TA T
2904 TAAAAAGTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2965 original size:62 final size:62
Alignment explanation
Indices: 2890--3203 Score: 338
Period size: 62 Copynumber: 5.0 Consensus size: 62
2880 TATATATCTA
*
2890 TATCTATACTATATTAAAAAGTACGTTCCGGTGTAAAACTTTTGAATCGCCTATTATACCCT
1 TATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTGAATCGCCTATTATACCCT
2952 TATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTGAATCGCCTATTATACCCT
1 TATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTGAATCGCCTATTATACCCT
* * * * ** * * * * * *
3014 TATTTGTCAAATGTATTTCTAAATTGCCATTGTTTAGGTCTATAA--TAT-ATAT---CTA-TAT
1 TA--TCT-ATA-CTATAT-TAAAAAG-TA-CGTTCAGGTGTAAAACTTTTGA-ATCGCCTATTAT
*
3072 A-TCT
58 ACCCT
3076 ATATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTGAATCGCCTATTATACCCT
1 -TATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTGAATCGCCTATTATACCCT
* * *
3139 TACCTATACTATATTAAAGAGTACGTTCAGGTGTAAAACTTTTGAATCTCCTATTATACCCT
1 TATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTGAATCGCCTATTATACCCT
3201 TAT
1 TAT
3204 TTGTCAAATG
Statistics
Matches: 204, Mismatches: 31, Indels: 34
0.76 0.12 0.13
Matches are distributed among these distances:
56 11 0.05
57 1 0.00
58 9 0.04
59 5 0.02
60 2 0.01
61 5 0.02
62 130 0.64
63 8 0.04
64 5 0.02
65 2 0.01
66 5 0.02
67 9 0.04
68 1 0.00
69 11 0.05
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (62 bp):
TATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTGAATCGCCTATTATACCCT
Found at i:3093 original size:187 final size:188
Alignment explanation
Indices: 2866--3239 Score: 705
Period size: 187 Copynumber: 2.0 Consensus size: 188
2856 AATATATATA
*
2866 TATATATATATATCTATATATCTATATCTATACTATATTAAAAAGTACGTTCCGGTGTAAAACTT
1 TATATATATATATCTATATATCTATATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTT
*
2931 TTGAATCGCCTATTATACCCTTATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTG
66 TTGAATCGCCTATTATACCCTTACCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTG
2996 AATCGCCTATTATACCCTTATTTGTCAAATGTATTTCTAAATTGCCATTGTTTAGGTC
131 AATCGCCTATTATACCCTTATTTGTCAAATGTATTTCTAAATTGCCATTGTTTAGGTC
3054 TATA-ATATATATCTATATATCTATATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTT
1 TATATATATATATCTATATATCTATATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTT
*
3118 TTGAATCGCCTATTATACCCTTACCTATACTATATTAAAGAGTACGTTCAGGTGTAAAACTTTTG
66 TTGAATCGCCTATTATACCCTTACCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTG
*
3183 AATCTCCTATTATACCCTTATTTGTCAAATGTATTTCTAAATTGCCATTGTTTAGGT
131 AATCGCCTATTATACCCTTATTTGTCAAATGTATTTCTAAATTGCCATTGTTTAGGT
3240 TTTTATAGTC
Statistics
Matches: 182, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
187 178 0.98
188 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (188 bp):
TATATATATATATCTATATATCTATATCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTT
TTGAATCGCCTATTATACCCTTACCTATACTATATTAAAAAGTACGTTCAGGTGTAAAACTTTTG
AATCGCCTATTATACCCTTATTTGTCAAATGTATTTCTAAATTGCCATTGTTTAGGTC
Found at i:4070 original size:70 final size:70
Alignment explanation
Indices: 3915--4059 Score: 209
Period size: 70 Copynumber: 2.1 Consensus size: 70
3905 TAATTAAAAT
** * * * * * *
3915 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATAATAAAAAAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
3980 AGTTG
66 AGTTG
*
3985 AGTAAAATAATAAAAAAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAATAAAAAAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
4050 AGTTG
66 AGTTG
4055 AGTAA
1 AGTAA
4060 GACTATAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.37
Consensus pattern (70 bp):
AGTAAAATAATAAAAAAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:7416 original size:2 final size:2
Alignment explanation
Indices: 7409--7448 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
7399 AAATTAGTTC
7409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7449 ATGATATCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7449 original size:12 final size:12
Alignment explanation
Indices: 7414--7455 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
7404 AGTTCTATAT
7414 ATATATATATATA
1 ATATATATA-ATA
7427 TATATATATAATA
1 -ATATATATAATA
*
7440 ATATATATAATG
1 ATATATATAATA
7452 ATAT
1 ATAT
7456 CACATCTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 15 0.56
13 3 0.11
14 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
ATATATATAATA
Found at i:7496 original size:2 final size:2
Alignment explanation
Indices: 7489--7514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7479 CTACCAACTT
7489 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
7515 GTAATTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14024 original size:30 final size:30
Alignment explanation
Indices: 13965--14024 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
13955 CAAGTTGAGA
*
13965 GAGGAAGATTGGGAATTATAAACTGTGTTT
1 GAGGAAGATTGGGAATTATAAACTATGTTT
*
13995 GAGGAAGCTTGGGAATTA-AAATCTATGTTT
1 GAGGAAGATTGGGAATTATAAA-CTATGTTT
14025 TTCAAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (30 bp):
GAGGAAGATTGGGAATTATAAACTATGTTT
Done.