Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015718.1 Corchorus olitorius cultivar O-4 contig15751, 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: 31697
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:567 original size:18 final size:18
Alignment explanation
Indices: 544--594 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
534 CTCCCAATAT
* *
544 TTCGGGTCGGGTCATCAA
1 TTCGGGCCGGATCATCAA
562 TTCGGGCCGGATCATCAA
1 TTCGGGCCGGATCATCAA
580 TTCGGGCCGGATCAT
1 TTCGGGCCGGATCAT
595 TTAATTTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.25
Consensus pattern (18 bp):
TTCGGGCCGGATCATCAA
Found at i:7433 original size:63 final size:63
Alignment explanation
Indices: 7365--7555 Score: 170
Period size: 68 Copynumber: 3.0 Consensus size: 63
7355 TATTAACCAG
* * * *
7365 AAAAGTCGGTCTAAAAAGAAAAAAGAGTGGGTCTTTAATGTAGCTCGACTTCCTATTATTTG-
1 AAAAGTAGGTCTAAAAAGAAAAAAGAGTGGGTCTTTCATGTAACTCGACTTCCTATTAATTGT
* * * *
7427 AGAAAGTAAGTTTAAAAAGAGAAAAAAGAAGAGTGGGTATTTCATGTAACTCGACTTCGTATTAA
1 A-AAAGTAGGTCT-AAAA-AG--AAAA-AAGAGTGGGTCTTTCATGTAACTCGACTTCCTATTAA
7492 TTGT
60 TTGT
* * * * * * *
7496 AAAAGTGGGTCTAATAAA-AAAAAAGATTGTGTCTTTCATGTATCTCTATTTCGTATTAAT
1 AAAAGTAGGTCTAA-AAAGAAAAAAGAGTGGGTCTTTCATGTAACTCGACTTCCTATTAAT
7556 ATTAATTGGG
Statistics
Matches: 104, Mismatches: 17, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
62 1 0.01
63 40 0.38
64 8 0.08
65 2 0.02
67 7 0.07
68 45 0.43
69 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (63 bp):
AAAAGTAGGTCTAAAAAGAAAAAAGAGTGGGTCTTTCATGTAACTCGACTTCCTATTAATTGT
Found at i:11675 original size:2 final size:2
Alignment explanation
Indices: 11668--11694 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11658 ATCTAATTAT
11668 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 T
11695 TCAATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17402 original size:65 final size:65
Alignment explanation
Indices: 17242--17392 Score: 248
Period size: 65 Copynumber: 2.3 Consensus size: 65
17232 GCTCAACTTC
* *
17242 GTATTAATTGGGAAAGTAGGTCTACAAAAGATGACATGTCTTTCATGTAACTTGACTTCGTATTA
1 GTATTAATTGGGAAAGTGGGTCTACAAAAGATGACATGTCTTTCATGTAACTCGACTTCGTATTA
* * *
17307 GTATTAATTGGGAAAATGGGTCTACAAAAGATGACGTGTCTTTCATGTAGCTCGACTTCGTATTA
1 GTATTAATTGGGAAAGTGGGTCTACAAAAGATGACATGTCTTTCATGTAACTCGACTTCGTATTA
*
17372 GTATTAATTGTGAAAGTGGGT
1 GTATTAATTGGGAAAGTGGGT
17393 AAAAAAAAGA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 79 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (65 bp):
GTATTAATTGGGAAAGTGGGTCTACAAAAGATGACATGTCTTTCATGTAACTCGACTTCGTATTA
Found at i:23494 original size:42 final size:42
Alignment explanation
Indices: 23432--23518 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
23422 TCAAGTTCTA
23432 CAAAAACAAATCGACCAGGCACCGGGTAACTCTTTGATGAGG
1 CAAAAACAAATCGACCAGGCACCGGGTAACTCTTTGATGAGG
*
23474 CAAAAACAAATCGACTAGGCACCGGGTAACTCTTTGATGAGG
1 CAAAAACAAATCGACCAGGCACCGGGTAACTCTTTGATGAGG
23516 CAA
1 CAA
23519 GAGAGTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (42 bp):
CAAAAACAAATCGACCAGGCACCGGGTAACTCTTTGATGAGG
Found at i:23754 original size:212 final size:211
Alignment explanation
Indices: 23474--23869 Score: 648
Period size: 212 Copynumber: 1.9 Consensus size: 211
23464 TTTGATGAGG
* * * *
23474 CAAAAACAAATCGACTAGGCACCGGGTAACTCTTTGATGAGGCAAGAGAGTAAAATTGAAGATTT
1 CAAAAACAAATCAACCAGGCACCAGGTAACTCTTTGATGAGGCAAGAAAGTAAAATTGAAGATTT
*
23539 TGGGTTCAAAGAAAAAACAAAAAGATCAGAAAAACACACACCACAATTTTCTGGGGAAACCCTGG
66 TGGGTTCAAAGAAAAAACAAAAAGATCAGAAAAACACACACCAAAATTTTCT-GGGAAACCCTGG
* * * *
23604 GAAAGTTTATAGTAAATCAATCGCGTGAGAAAGAAAGTTTACAGACAGAAAAAAGTCACTTTTCA
130 GAAAGTTAACAGTAAATCAATCGCATGAGAAAGAAAGTTTACAGACAAAAAAAAGTCACTTTTCA
23669 ATTGTTCATCAAATTCA
195 ATTGTTCATCAAATTCA
* * *
23686 CAAAAACAAATCAACCAGGCACCATGTAACTCTTTGATGAGGCATGAAAGTAAAATTGAAGGTTT
1 CAAAAACAAATCAACCAGGCACCAGGTAACTCTTTGATGAGGCAAGAAAGTAAAATTGAAGATTT
* *
23751 TGGGTTCAAAGAAAAAACAGAAAGATCAGAAAAACACACACCAAAATTTTCTGGGAAATCCTGGG
66 TGGGTTCAAAGAAAAAACAAAAAGATCAGAAAAACACACACCAAAATTTTCTGGGAAACCCTGGG
*
23816 AAAGTTAACAGTAAATCAATCGCATGAGAAAGAAAGTTTATAGACAAAAAAAAG
131 AAAGTTAACAGTAAATCAATCGCATGAGAAAGAAAGTTTACAGACAAAAAAAAG
23870 GAATGTGGGC
Statistics
Matches: 169, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
211 61 0.36
212 108 0.64
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (211 bp):
CAAAAACAAATCAACCAGGCACCAGGTAACTCTTTGATGAGGCAAGAAAGTAAAATTGAAGATTT
TGGGTTCAAAGAAAAAACAAAAAGATCAGAAAAACACACACCAAAATTTTCTGGGAAACCCTGGG
AAAGTTAACAGTAAATCAATCGCATGAGAAAGAAAGTTTACAGACAAAAAAAAGTCACTTTTCAA
TTGTTCATCAAATTCA
Found at i:24384 original size:14 final size:14
Alignment explanation
Indices: 24365--24393 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24355 GTATCAAGTA
24365 TTGATACTCATAAT
1 TTGATACTCATAAT
24379 TTGATACTCATAAT
1 TTGATACTCATAAT
24393 T
1 T
24394 AAAACTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (14 bp):
TTGATACTCATAAT
Found at i:29504 original size:27 final size:27
Alignment explanation
Indices: 29452--29504 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
29442 TTAACATTGG
** *
29452 CAATTTAGCATCGTTTTTTTGGTTAAA
1 CAATTTAGCATAATTTTTTTGCTTAAA
29479 CAATTTAGCATAATTTTGTTT-CTTAA
1 CAATTTAGCATAATTTT-TTTGCTTAA
29505 TACTGGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (27 bp):
CAATTTAGCATAATTTTTTTGCTTAAA
Found at i:31320 original size:31 final size:31
Alignment explanation
Indices: 31242--31485 Score: 290
Period size: 31 Copynumber: 7.8 Consensus size: 31
31232 TCCGACGTGA
* *
31242 CATGCCATGTGTACCAAAAAGCGACATATGG
1 CATGCCACGTGTACCAAAAAGCGACATGTGG
* * *
31273 CAATGCCACGTTTACCAAAAAGTGACACGTGG
1 C-ATGCCACGTGTACCAAAAAGCGACATGTGG
* * *
31305 CATGCCACATGTACCAAAAAGTGACACGTGG
1 CATGCCACGTGTACCAAAAAGCGACATGTGG
* *
31336 CATGCCACATGTACCAAAAAGTGACATGTGG
1 CATGCCACGTGTACCAAAAAGCGACATGTGG
** *
31367 CATGTTACGTGTACCAAAAAGCAACATGTGG
1 CATGCCACGTGTACCAAAAAGCGACATGTGG
* *
31398 CACGCCATGTGTACCAAAAAGCGACATGTGG
1 CATGCCACGTGTACCAAAAAGCGACATGTGG
* *
31429 CACGCCACGTGTACCAAAAAGCGACATGTGT
1 CATGCCACGTGTACCAAAAAGCGACATGTGG
** * *
31460 CACACCATGTGTACCAAAAAGTGACA
1 CATGCCACGTGTACCAAAAAGCGACA
31486 CATGGCTTGC
Statistics
Matches: 189, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
31 163 0.86
32 26 0.14
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (31 bp):
CATGCCACGTGTACCAAAAAGCGACATGTGG
Done.