Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014600.1 Corchorus capsularis cultivar CVL-1 contig14621, 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: 5624
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:925 original size:6 final size:6
Alignment explanation
Indices: 914--950 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
904 ATAATTGCTA
914 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
951 CTAGTATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:2158 original size:25 final size:25
Alignment explanation
Indices: 2130--2177 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2120 CAATCGACCT
* *
2130 AGGGCGGTCTTTCTTCATTTTATCC
1 AGGGCGATCTTTCTTCAGTTTATCC
2155 AGGGCGATCTTTCTTCAGTTTAT
1 AGGGCGATCTTTCTTCAGTTTAT
2178 GTCAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (25 bp):
AGGGCGATCTTTCTTCAGTTTATCC
Found at i:2253 original size:70 final size:70
Alignment explanation
Indices: 2171--2802 Score: 711
Period size: 70 Copynumber: 9.0 Consensus size: 70
2161 ATCTTTCTTC
* * * * *
2171 AGTTTATGTCAGAATAATTGATTCAGTCGA-CCAGGGCGGTCTTTCCTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
2235 ATTCGA
66 A-TCCA
* *
2241 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2306 ATCCA
66 ATCCA
* *
2311 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2376 ATTCCA
66 A-TCCA
* * *
2382 TGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTATTT-CAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2446 ATCCA
66 ATCCA
* * * * *
2451 AGTTTATGTCAGAATGATCAATTCAGTTGACCTAGGGTGGTTTTTCTTCAGTT-TATGTCGGAA-
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGT-T-TC-CAAG
* *
2514 -TGATCGA
63 TTTATCCA
* * * * *** ** * * *
2521 GGGTGGTCTTTCTTTA-G-TTTATTTCGGTTGACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAG
1 -AGT-TTATGTCAGAATGATCGA-TTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAG
*
2584 TTTATTCGA
63 TTTA-TCCA
* * *
2593 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGTTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2658 ATCCA
66 ATCCA
* * * * *
2663 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTTTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2728 ATCCA
66 ATCCA
* * * * * *
2733 ACTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGAGGTTTTTCATCAGTTGTTTCCAAGTTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
2798 ATCCA
66 ATCCA
2803 GGGTGGTCTT
Statistics
Matches: 473, Mismatches: 74, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
68 1 0.00
69 54 0.11
70 239 0.51
71 165 0.35
72 14 0.03
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:2556 original size:211 final size:210
Alignment explanation
Indices: 2171--2796 Score: 719
Period size: 211 Copynumber: 3.0 Consensus size: 210
2161 ATCTTTCTTC
* * *
2171 AGTTTATGTCAGAATAATTGATTCAGTCGA-CCAGGGCGGTCTTTCCTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTT-ATTTCAAGTTT
* * * *
2235 ATTCGAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAG-TTATTTC
65 A-TCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTTTTTCTTCAGTTTATGTC
* * *
2299 CAAGTTTATCCAAGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTT
129 CAAG-TGATCCAAGTGTCTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTT
2364 GTTTCCAAGTTTATTCCA
193 GTTTCCAAGTTTATTCCA
* *
2382 TGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTATTTCAAGTTTA
1 AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCAAGTTTA
* * * *
2447 TCCAAGTTTATGTCAGAATGATCAATTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTTATGTCGG
66 TCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTTTTTCTTCAGTTTATGTC-C
* * * *** ** *
2512 AA-TGATCGAGGGTGGTCTTTCTTTA-G-TTTATTTCGGTTGACCCAGGGTGGTCTTTCTTCAGT
130 AAGTGATCCA-AGT-GTCTGTCAGAATGATCGA-TTCGGTCGACCCAGGGTGGTCTTTCTTCAGT
* *
2574 TGTTTTCAAGTTTATTCGA
192 TGTTTCCAAGTTTATTCCA
* *
2593 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGTTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTT-CAAGTTT
* * *
2658 ATCCAAGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTT-TTCAG--TAGTTT
65 ATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGT-TTTTCTTCAGTTTA-TGT
* * * * * * * * * *
2720 CCACGTTTATCCAACTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGAGGTTTTTCATCAGT
128 CCAAG-TGATCCAAGTGTCTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGT
2785 TGTTTCCAAGTT
192 TGTTTCCAAGTT
2797 GATCCAGGGT
Statistics
Matches: 344, Mismatches: 58, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
210 64 0.19
211 189 0.55
212 87 0.25
213 4 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (210 bp):
AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCAAGTTTA
TCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTTTTTCTTCAGTTTATGTCCA
AGTGATCCAAGTGTCTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTTGTT
TCCAAGTTTATTCCA
Found at i:2566 original size:35 final size:35
Alignment explanation
Indices: 2476--2574 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 35
2466 GATCAATTCA
* *
2476 GTTGACCTAGGGTGGTTTTTCTTCAGTTTATGTCG
1 GTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
* * * * *
2511 GAATGATCGAGGGTGGTCTTTCTTTAGTTTATTTCG
1 G-TTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
2547 GTTGACCCAGGGTGGTCTTTCTTCAGTT
1 GTTGACCCAGGGTGGTCTTTCTTCAGTT
2575 GTTTTCAAGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 24 0.45
36 29 0.55
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.43
Consensus pattern (35 bp):
GTTGACCCAGGGTGGTCTTTCTTCAGTTTATGTCG
Found at i:2808 original size:282 final size:281
Alignment explanation
Indices: 2269--2812 Score: 783
Period size: 282 Copynumber: 1.9 Consensus size: 281
2259 CGATTCAGTC
*
2269 GACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTTATCCAAGTTTGTGTCAGAATGATCGATT
1 GACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTTATCCAAGTTTATGTCAGAATGATCGATT
* * * *
2334 CGGTCGACCCAGGGTGGTCTTTCTTCAGTTGTTTCCAAGTTTATTCCATGTTTATGTCAGAATGA
66 CAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTTATTCCAAGTTTATGTCAGAATGA
* *
2399 TTGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTATTTCAAGTTTATCCAAGTTTATGTCAGA
131 TCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTATTTCAAGTTTATCCAACTTTATGTCAGA
** * * * * *
2464 ATGATCAATTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTC
196 ATGATCAATTCAGTCAACCCAGGGAGGTTTTTCATCAGTTTATGTCGCAATGATCCAGGGTGGTC
2529 TTTCTTTAGTTTATTTCGGTT
261 TTTCTTTAGTTTATTTCGGTT
* * * *
2550 GACCCAGGGTGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCGAAGTTTATGTCAGAATGATCGAT
1 GACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTTA-TCCAAGTTTATGTCAGAATGATCGAT
* *
2615 TCAGTCGACCCAGGGCGTTCTTTCTTCAGTTATTTCCAAGTTTA-TCCAAGTTTGTGTCAGAATG
65 TCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTTATTCCAAGTTTATGTCAGAATG
* * *
2679 ATCGATTCGGTCGACCCAGGGTGGTCTTTTTTCAG-TAGTTTCCACGTTTATCCAACTTTATGTC
130 ATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTA-TTT-CAAGTTTATCCAACTTTATGTC
*
2743 AGAATGATCGATTCAGTCAACCCAGGGAGGTTTTTCATCAGTTGT-T-TC-CAAGTTGATCCAGG
193 AGAATGATCAATTCAGTCAACCCAGGGAGGTTTTTCATCAGTT-TATGTCGCAA--TGATCCAGG
2805 GTGGTCTT
255 GTGGTCTT
2813 CATTAAAGAT
Statistics
Matches: 233, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
280 4 0.02
281 90 0.39
282 138 0.59
283 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (281 bp):
GACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTTATCCAAGTTTATGTCAGAATGATCGATT
CAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTTATTCCAAGTTTATGTCAGAATGA
TCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTATTTCAAGTTTATCCAACTTTATGTCAGA
ATGATCAATTCAGTCAACCCAGGGAGGTTTTTCATCAGTTTATGTCGCAATGATCCAGGGTGGTC
TTTCTTTAGTTTATTTCGGTT
Done.