Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014930.1 Corchorus olitorius cultivar O-4 contig14963, 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: 39785
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:18647 original size:2 final size:2
Alignment explanation
Indices: 18640--18672 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18630 ATAATTTGCC
18640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18673 GACCTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27804 original size:4 final size:4
Alignment explanation
Indices: 27795--27819 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27785 AACAGAAAAG
27795 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
27820 ATATTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:28701 original size:6 final size:6
Alignment explanation
Indices: 28692--28721 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28682 TTTATATTTA
28692 TTTTTC TTTTTC TTTTTC TTTTT- TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
28722 GACTTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:30160 original size:13 final size:13
Alignment explanation
Indices: 30142--30167 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30132 CAAAGAGCTG
30142 CAAAGCTAAGCCA
1 CAAAGCTAAGCCA
30155 CAAAGCTAAGCCA
1 CAAAGCTAAGCCA
30168 TTATGCCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (13 bp):
CAAAGCTAAGCCA
Found at i:30515 original size:6 final size:6
Alignment explanation
Indices: 30504--30530 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30494 AGTTCTTGAC
30504 TTGAAA TTGAAA TTGAAA TTGAAA TTG
1 TTGAAA TTGAAA TTGAAA TTGAAA TTG
30531 TCTATTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (6 bp):
TTGAAA
Found at i:37234 original size:19 final size:19
Alignment explanation
Indices: 37210--37246 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
37200 CTGTTTAGCA
*
37210 ACTGTAGAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
37229 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
37247 TTAGAACAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:38318 original size:2 final size:2
Alignment explanation
Indices: 38311--38356 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
38301 CTTTACTGAT
*
38311 TA TA TA TA TA T- TT TA 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 TA TA TA TA TA TA TA TA
38352 TA TA T
1 TA TA T
38357 TGCCATTAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:39571 original size:333 final size:334
Alignment explanation
Indices: 38641--39785 Score: 1876
Period size: 334 Copynumber: 3.4 Consensus size: 334
38631 CTTGTATAAT
* * *
38641 CTCAAATTTCGACCACAATACTCATAAAAAATATATAATTCAATGCCAGAAAGATTGAAGG-GCT
1 CTCAATTTTCGGCCACAATACTCATAAAAAATATAAAATTCAATGCCAGAAAGATTGAAGGAG-T
*
38705 TTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCACAATTAATTTC-ACATTAAATTAAAACC
65 TTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCACAATTAATTTCTA-ATTAAATTGAAACC
* *
38769 AGTTTCCGATGCTCGAACAAACAAATCCTTATGTCCTATGTGACTGAAATTTGGTTACTCGAATA
129 AGTTTCCGATGCTCGAAAAAACAAATCCTTATGTCCTATGTGACTGAGATTTGGTTACTCGAATA
38834 TAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGT
194 TAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGT
38899 TTTTAGAGAAAAACTGTGATGGTTACTACACGATATCGCTAAAATTTTGCAAAAAAACTGACCCG
259 TTTTAGAGAAAAACTGTGATGGTTACTACACGATATCGCTAAAATTTTGCAAAAAAACTGACCCG
*
38964 AAAAATTTTTG
324 AAATATTTTTG
*
38975 CTCAATTTTCGGCCACAATACTCATAAAAAATATAAAATTCAATGCCAGAAAGATTGAAGGATTT
1 CTCAATTTTCGGCCACAATACTCATAAAAAATATAAAATTCAATGCCAGAAAGATTGAAGGAGTT
39040 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAG
66 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAG
39105 TTTCCGATGCTCGAAAAAACAAATCCTTATGTCCTATGTGACTGAGATTTGGTTACTCGAATATA
131 TTTCCGATGCTCGAAAAAACAAATCCTTATGTCCTATGTGACTGAGATTTGGTTACTCGAATATA
* *
39170 GATATTTCAAGGAGTCTTGGCGCCAAAAATCATTCAAATCTGAGCCGGGGACCCGGAACGCGTTT
196 GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTT
39235 TTAGAGAAAAACTGTGATGGTTACTACACGATATCGCTAAAATTTTGCAAAAAAACTGACCCGAA
261 TTAGAGAAAAACTGTGATGGTTACTACACGATATCGCTAAAATTTTGCAAAAAAACTGACCCGAA
39300 ATATTTTTGG
326 ATATTTTT-G
* *
39310 CTTAATTTTTGGCCACAATACTCATAAAAAATATAAAATTCAATGCCA-AAAGATTGAAGG-GAT
1 CTCAATTTTCGGCCACAATACTCATAAAAAATATAAAATTCAATGCCAGAAAGATTGAAGGAG-T
* *
39373 TTTCACGTTTCTAATATCGTTTTTCCTATTTTTTT-AGAATTAATTTCTAATTAAATTGAAACCA
65 TTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCACAATTAATTTCTAATTAAATTGAAACCA
*
39437 GTTTCCGATGCTCGAAAAAACAAATCCTTATGTACTATGTGACTGAGATTTGGTTACTCGAATAT
130 GTTTCCGATGCTCGAAAAAACAAATCCTTATGTCCTATGTGACTGAGATTTGGTTACTCGAATAT
* * *
39502 AGATATTTCAAGGATTCTTGGTGCCAAAAATCATGCAAAACTGAGCCGGGGACTCGGAACGCGTT
195 AGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTT
* *
39567 TTTAGAGAAAATCTGTGAT--TT-CTACACGATATCGCT-AAATTTTGAAAAAAAAACTGACCCG
260 TTTAGAGAAAAACTGTGATGGTTACTACACGATATCGCTAAAATTTTG-CAAAAAAACTGACCCG
* *
39628 AAATTTTTTTT
324 AAATATTTTTG
* * * * * *
39639 ATCAATTTTCAGCCACGATACTCATAAAAAATATATAATTCAGTGCCAGAATGATTGAAGGAGTT
1 CTCAATTTTCGGCCACAATACTCATAAAAAATATAAAATTCAATGCCAGAAAGATTGAAGGAGTT
* ** * * *
39704 TTCACGCTTCTAATATCGTTTTTCATATTTTAATCTCAATTAATTTTTAATTAAATTGAAACAAG
66 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAG
39769 TTTCCGATGCTCGAAAA
131 TTTCCGATGCTCGAAAA
Statistics
Matches: 762, Mismatches: 41, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
329 49 0.06
330 82 0.11
331 46 0.06
333 170 0.22
334 367 0.48
335 48 0.06
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (334 bp):
CTCAATTTTCGGCCACAATACTCATAAAAAATATAAAATTCAATGCCAGAAAGATTGAAGGAGTT
TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCACAATTAATTTCTAATTAAATTGAAACCAG
TTTCCGATGCTCGAAAAAACAAATCCTTATGTCCTATGTGACTGAGATTTGGTTACTCGAATATA
GATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTT
TTAGAGAAAAACTGTGATGGTTACTACACGATATCGCTAAAATTTTGCAAAAAAACTGACCCGAA
ATATTTTTG
Done.