Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017842.1 Corchorus olitorius cultivar O-4 contig17875, 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: 63822
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:40802 original size:166 final size:171
Alignment explanation
Indices: 40521--40855 Score: 529
Period size: 166 Copynumber: 2.0 Consensus size: 171
40511 CTATTCTAGA
*
40521 AGTAAGTCTCTTTGGAAACTCTTCTTGATTTTGTGTTTGATTTTGGTTTTCAGAGACAGAAAACC
1 AGTAAGTCTCTTTGGAAACTCTTCTTGACTTTGTG-TTGA-TTTGGTTTTCAGAGACAGAAAACC
*
40586 AAAAAAAATAAAAGATTTTGGATTGAGGGAATGAAAAATCTTACCTTTTTCCTTTTATCTTTGTT
64 AAAAAAAATAAAAGATTTTGCATTGAGGGAATGAAAAATCTTACCTTTTTCCTTTTATCTTTGTT
* *
40651 CATTGTCTTGTTCTTTTTTAGTTTTCCTTCAATGGGTCGTAGC
129 CATTCTCTAGTTCTTTTTTAGTTTTCCTTCAATGGGTCGTAGC
40694 AGTAAGTCTCTTTGGAAACTC-TCTTTG-CTTT-TG-TG-TTT-GTTTTCAGAGACAGAAAACCA
1 AGTAAGTCTCTTTGGAAACTCTTC-TTGACTTTGTGTTGATTTGGTTTTCAGAGACAGAAAACCA
* * * *
40753 AAAAAGATAAAAGATTTTGCCTTGAGGGAATGAAAAATGTTACCTTTTTCTTTTTATCTTTGTTC
65 AAAAAAATAAAAGATTTTGCATTGAGGGAATGAAAAATCTTACCTTTTTCCTTTTATCTTTGTTC
40818 ATTCTCTAGTTCTTTTTTAGTTTTCCTTCAATGGGTCG
130 ATTCTCTAGTTCTTTTTTAGTTTTCCTTCAATGGGTCG
40856 GTAGGGAAAA
Statistics
Matches: 153, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
166 117 0.76
167 3 0.02
169 2 0.01
171 2 0.01
172 5 0.03
173 24 0.16
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (171 bp):
AGTAAGTCTCTTTGGAAACTCTTCTTGACTTTGTGTTGATTTGGTTTTCAGAGACAGAAAACCAA
AAAAAATAAAAGATTTTGCATTGAGGGAATGAAAAATCTTACCTTTTTCCTTTTATCTTTGTTCA
TTCTCTAGTTCTTTTTTAGTTTTCCTTCAATGGGTCGTAGC
Found at i:42082 original size:162 final size:162
Alignment explanation
Indices: 41812--42138 Score: 593
Period size: 162 Copynumber: 2.0 Consensus size: 162
41802 GACACCCATT
* *
41812 GAATCTAATTCATCATCTGGAGGTGCTTCTGGAAAAGAAAACTCCGGCTCAAGGCTTGTAGCAGA
1 GAATCTAAGTCATCATCTGGAGGTGCTTCTGGAAAAGAAAACTCCGGCTCAAAGCTTGTAGCAGA
* *
41877 AAATCATGGAAGAAAGGATGCTCCTCCCTTGGTAGATATTAATGGAGCTGCTGGTGTCACTGTTG
66 AAATCATGGAAGAAAGGATGCTCCTCCCTTGGTAGACATTAATGGAGCTGCTGGTGCCACTGTTG
41942 ACACAAGCTTGGGTAGACAAATTACAATGGAG
131 ACACAAGCTTGGGTAGACAAATTACAATGGAG
*
41974 GAATCTAAGTCATCATCT-GAGGGTGCTTCTGGAAAAGAAAACTCCGGCTCAAAGCTTGTAGCCG
1 GAATCTAAGTCATCATCTGGA-GGTGCTTCTGGAAAAGAAAACTCCGGCTCAAAGCTTGTAGCAG
42038 AAAATCATGGAAGAAAGGATGCTCCTCCCTTGGTAGACATTAATGGAGCTGCTGGTGCCACTGTT
65 AAAATCATGGAAGAAAGGATGCTCCTCCCTTGGTAGACATTAATGGAGCTGCTGGTGCCACTGTT
42103 GACACAAGCTTGGGTAGACAAATTACAATGGAG
130 GACACAAGCTTGGGTAGACAAATTACAATGGAG
42136 GAA
1 GAA
42139 GCTAGAGTAG
Statistics
Matches: 159, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
161 2 0.01
162 157 0.99
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (162 bp):
GAATCTAAGTCATCATCTGGAGGTGCTTCTGGAAAAGAAAACTCCGGCTCAAAGCTTGTAGCAGA
AAATCATGGAAGAAAGGATGCTCCTCCCTTGGTAGACATTAATGGAGCTGCTGGTGCCACTGTTG
ACACAAGCTTGGGTAGACAAATTACAATGGAG
Found at i:48103 original size:27 final size:27
Alignment explanation
Indices: 48043--48104 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
48033 CAGCAATGGG
48043 GAGGAGGGTCACCAGGTCACAAACCAA
1 GAGGAGGGTCACCAGGTCACAAACCAA
* * *
48070 TATGAGGGTCACCAGGTCGCAAACCAA
1 GAGGAGGGTCACCAGGTCACAAACCAA
48097 GAGGAGGG
1 GAGGAGGG
48105 CTTCCCTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.23, G:0.34, T:0.10
Consensus pattern (27 bp):
GAGGAGGGTCACCAGGTCACAAACCAA
Found at i:54617 original size:24 final size:24
Alignment explanation
Indices: 54590--54656 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
54580 TGCCCGTCTG
54590 TAGCCTTGCCCTTCTGCTCGTGAA
1 TAGCCTTGCCCTTCTGCTCGTGAA
*
54614 TAGCCTTGCCCTTCTGCTCGTGAG
1 TAGCCTTGCCCTTCTGCTCGTGAA
54638 TAGCCTTGCCCTTCTGCTC
1 TAGCCTTGCCCTTCTGCTC
54657 CACTCACCTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.09, C:0.36, G:0.21, T:0.34
Consensus pattern (24 bp):
TAGCCTTGCCCTTCTGCTCGTGAA
Found at i:60408 original size:32 final size:32
Alignment explanation
Indices: 60370--60540 Score: 209
Period size: 32 Copynumber: 5.3 Consensus size: 32
60360 TGGTAGAGGA
*
60370 CAAAATTTCAA-GTCATTAAATGCAAATGAAGC
1 CAAAATTGCAATG-CATTAAATGCAAATGAAGC
*
60402 CAAAATTGCAATGCATTAAATGCAAATGAAGT
1 CAAAATTGCAATGCATTAAATGCAAATGAAGC
*
60434 CAAAATTGCAATGCATTAAATGCAAATGAAGT
1 CAAAATTGCAATGCATTAAATGCAAATGAAGC
** *
60466 CAAAATTGCAATGCATTAAATGCAAAACAAGA
1 CAAAATTGCAATGCATTAAATGCAAATGAAGC
* ** * **
60498 CAAAATTACAACCCATTAATTGCAAAAAAAGC
1 CAAAATTGCAATGCATTAAATGCAAATGAAGC
*
60530 CAAATTTGCAA
1 CAAAATTGCAA
60541 ACAAAGTAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
32 124 0.99
33 1 0.01
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (32 bp):
CAAAATTGCAATGCATTAAATGCAAATGAAGC
Found at i:60446 original size:17 final size:17
Alignment explanation
Indices: 60394--60478 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 17
60384 ATTAAATGCA
*
60394 AATGAAGCCAAAATTGC
1 AATGAAGTCAAAATTGC
* *
60411 AATGCA-T-TAAA-TGC
1 AATGAAGTCAAAATTGC
60425 AAATGAAGTCAAAATTGC
1 -AATGAAGTCAAAATTGC
* *
60443 AATGCA-T-TAAA-TGC
1 AATGAAGTCAAAATTGC
60457 AAATGAAGTCAAAATTGC
1 -AATGAAGTCAAAATTGC
60475 AATG
1 AATG
60479 CATTAAATGC
Statistics
Matches: 51, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
14 6 0.12
15 16 0.31
16 3 0.06
17 20 0.39
18 6 0.12
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (17 bp):
AATGAAGTCAAAATTGC
Found at i:61034 original size:20 final size:20
Alignment explanation
Indices: 60980--61034 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
60970 AATTTGGCCC
60980 TAAACTTAGTGAAATAAAAA
1 TAAACTTAGTGAAATAAAAA
* * *
61000 TAAAATT-TTAAAAATAAAAA
1 TAAACTTAGT-GAAATAAAAA
61020 TAAACTTAGTGAAAT
1 TAAACTTAGTGAAAT
61035 TAGTTTTGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (20 bp):
TAAACTTAGTGAAATAAAAA
Found at i:62328 original size:31 final size:29
Alignment explanation
Indices: 62270--62336 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 29
62260 ATGCAATTTG
*
62270 GGATACAACGTTACAAAACAAGCAATTAA
1 GGATATAACGTTACAAAACAAGCAATTAA
*
62299 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTAC-AAAA-CAAGCAATTAA
62330 GGATATA
1 GGATATA
62337 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 17 0.50
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (29 bp):
GGATATAACGTTACAAAACAAGCAATTAA
Found at i:62591 original size:31 final size:31
Alignment explanation
Indices: 62466--62606 Score: 128
Period size: 31 Copynumber: 4.6 Consensus size: 31
62456 CCCTAACTGA
62466 TTATATCCTTAATTGCTTGAAATC-GAAAACG
1 TTATATCCTTAATTGCTTG-AATCAGAAAACG
* * *
62497 TCATATCCCTAATTGCTTGAAAT-AAAAAACG
1 TTATATCCTTAATTGCTTG-AATCAGAAAACG
* ** *
62528 TTATATCCTTAATTGCTTG-TTTTG-TAACG
1 TTATATCCTTAATTGCTTGAATCAGAAAACG
***
62557 TTATATCCTTAATTGCTTGCGGCAGAAAACG
1 TTATATCCTTAATTGCTTGAATCAGAAAACG
* *
62588 TTATATCCTAAATTACTTG
1 TTATATCCTTAATTGCTTG
62607 CTTATCCTCT
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
29 24 0.27
30 1 0.01
31 65 0.72
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAATCAGAAAACG
Found at i:62658 original size:16 final size:17
Alignment explanation
Indices: 62637--62669 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62627 TATTCCGAAG
62637 AAAATAATTT-TTTAAA
1 AAAATAATTTATTTAAA
*
62653 AAAATACTTTATTTAAA
1 AAAATAATTTATTTAAA
62670 TCACTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATAATTTATTTAAA
Found at i:63704 original size:31 final size:29
Alignment explanation
Indices: 63610--63714 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
63600 TTTGCTGCCA
* *** **
63610 CAAGCAATTAAGGATATAACGATACAAAA
1 CAAGCAATTAAGGATATAACGTTTTGATT
*
63639 CAAGCAATTAAGGATATAACGTTTTTATT
1 CAAGCAATTAAGGATATAACGTTTTGATT
*
63668 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTT-GA-TT
63699 CAAGCAATTAAGGATA
1 CAAGCAATTAAGGATA
63715 AATCAGTTAG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
29 47 0.71
30 1 0.02
31 18 0.27
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (29 bp):
CAAGCAATTAAGGATATAACGTTTTGATT
Done.