Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018054.1 Corchorus olitorius cultivar O-4 contig18087, 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: 48029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:85 original size:21 final size:22
Alignment explanation
Indices: 44--87 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
34 TTTTTTTATA
44 TATGACGCAGAAACAAAATTTT
1 TATGACGCAGAAACAAAATTTT
66 TATGACGCA-AAA-ATAAATTTT
1 TATGACGCAGAAACA-AAATTTT
87 T
1 T
88 TTTTCGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.05
21 11 0.52
22 9 0.43
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (22 bp):
TATGACGCAGAAACAAAATTTT
Found at i:88 original size:22 final size:22
Alignment explanation
Indices: 44--88 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34 TTTTTTTATA
*
44 TATGACGCAGAAACAAAATTTT
1 TATGACGCAAAAACAAAATTTT
* *
66 TATGACGCAAAAATAAATTTTT
1 TATGACGCAAAAACAAAATTTT
88 T
1 T
89 TTTCGATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (22 bp):
TATGACGCAAAAACAAAATTTT
Found at i:487 original size:16 final size:15
Alignment explanation
Indices: 449--490 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
439 ACAGAGATTG
*
449 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
464 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
479 ACTAGAAAACAA
1 AC-AGAAAACAA
491 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:12811 original size:25 final size:24
Alignment explanation
Indices: 12765--12811 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
12755 TTTGGTTTGG
* * *
12765 TTAGGGAGAAGGGAATGTAATTTT
1 TTAGGGAGAAAGGAAAGAAATTTT
12789 TTAGGGAAGAAAGGAAAGAAATT
1 TTAGGG-AGAAAGGAAAGAAATT
12812 ATATATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.26
Consensus pattern (24 bp):
TTAGGGAGAAAGGAAAGAAATTTT
Found at i:13187 original size:13 final size:13
Alignment explanation
Indices: 13171--13212 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
13161 GAAGGGAAAG
13171 AAATTATACAAAA
1 AAATTATACAAAA
13184 AAATT-TCACCAAAA
1 AAATTAT-A-CAAAA
*
13198 AAATTATATAAAA
1 AAATTATACAAAA
13211 AA
1 AA
13213 CACTAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.48
14 11 0.44
15 1 0.04
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATTATACAAAA
Found at i:16738 original size:30 final size:30
Alignment explanation
Indices: 16702--16765 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
16692 GATTCATTTG
* * * *
16702 GGAACTTAATAAGTATTTTAATCTTGTTTA
1 GGAACTTAATAAGAACTTTAAACATGTTTA
16732 GGAACTTAATAAGAACTTTAAACATGTTTA
1 GGAACTTAATAAGAACTTTAAACATGTTTA
16762 GGAA
1 GGAA
16766 ATATTTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (30 bp):
GGAACTTAATAAGAACTTTAAACATGTTTA
Found at i:19133 original size:21 final size:22
Alignment explanation
Indices: 19084--19134 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
19074 CTAATCCCGG
* **
19084 TAGGAATAGTAAAACCTTTCTGG
1 TAGGAA-AGTAAAACCTTACTCC
19107 TAGGAAAGTAAAACC-TACTCC
1 TAGGAAAGTAAAACCTTACTCC
19128 TAGGAAA
1 TAGGAAA
19135 AACTATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 9 0.36
23 6 0.24
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (22 bp):
TAGGAAAGTAAAACCTTACTCC
Found at i:22027 original size:30 final size:31
Alignment explanation
Indices: 21993--22069 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 31
21983 TAATGACAAA
21993 ATCAGAATTC-TCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
22023 ATCAGAA-TCTTCTCCTTCACAAACAAAGAG
1 ATCAGAATTCTTCTCCTTCACAAACAAAGAG
*
22053 ATCGGAA-TCTTCCTCCT
1 ATCAGAATTCTT-CTCCT
22070 CGTCATACTC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 2 0.05
30 37 0.84
31 5 0.11
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (31 bp):
ATCAGAATTCTTCTCCTTCACAAACAAAGAG
Found at i:23340 original size:2 final size:2
Alignment explanation
Indices: 23333--23357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23323 ATATGTTTAC
23333 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 T
23358 TAGTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24274 original size:31 final size:32
Alignment explanation
Indices: 24195--24274 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
24185 ATTTGCTCTG
*
24195 TCAGGGGG-TGAATTGTCCTGAATTTAAGAAGT
1 TCAGGGGGCT-AATTGTCCTGAATTTAAGAAAT
* * *
24227 TCATGGGGCTAATTGTCTTGAATTT-GGAAAT
1 TCAGGGGGCTAATTGTCCTGAATTTAAGAAAT
24258 TCAGGGGGC-AAGTTGTC
1 TCAGGGGGCTAA-TTGTC
24275 GCGATTTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.05
31 17 0.41
32 21 0.51
33 1 0.02
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (32 bp):
TCAGGGGGCTAATTGTCCTGAATTTAAGAAAT
Found at i:26760 original size:79 final size:79
Alignment explanation
Indices: 26625--26782 Score: 226
Period size: 79 Copynumber: 2.0 Consensus size: 79
26615 CTTTTCTAAG
** * * * *
26625 TATGTATGTTTGGCTAGAGATACTTCTCTAGGCTTTACTGTTTGCATCTTGTTGTTTTCTCATGA
1 TATGTATGTTCAGCTAGAGATACTTCTCTAGCCTTTACTATTTGCATCCTGCTGTTTTCTCATGA
*
26690 TTCTCCGGAAGTAA
66 TTCTCCAGAAGTAA
* * *
26704 TATGTATGTTCAGCTAGGGATACTTCTCTATCCTTTTCTATTTGCATCCTGCTGTTTTCTCATGA
1 TATGTATGTTCAGCTAGAGATACTTCTCTAGCCTTTACTATTTGCATCCTGCTGTTTTCTCATGA
26769 TTCTCCAGAAGTAA
66 TTCTCCAGAAGTAA
26783 AGTCTCGTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.44
Consensus pattern (79 bp):
TATGTATGTTCAGCTAGAGATACTTCTCTAGCCTTTACTATTTGCATCCTGCTGTTTTCTCATGA
TTCTCCAGAAGTAA
Found at i:38348 original size:15 final size:15
Alignment explanation
Indices: 38328--38358 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38318 CATATTTCGT
38328 CGTATATATCATCCC
1 CGTATATATCATCCC
38343 CGTATATATCATCCC
1 CGTATATATCATCCC
38358 C
1 C
38359 AACATCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.32
Consensus pattern (15 bp):
CGTATATATCATCCC
Found at i:41216 original size:27 final size:27
Alignment explanation
Indices: 41185--41236 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
41175 GTAACCATCA
**
41185 CTAATGGTTTTGTTTTTTGGCCATTCG
1 CTAATGGTTTAATTTTTTGGCCATTCG
41212 CTAATGGTTTAATTTTTTGGCCATT
1 CTAATGGTTTAATTTTTTGGCCATT
41237 TACTTTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.13, G:0.19, T:0.52
Consensus pattern (27 bp):
CTAATGGTTTAATTTTTTGGCCATTCG
Found at i:41733 original size:28 final size:28
Alignment explanation
Indices: 41652--41735 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 28
41642 CTAAACTGCC
*
41652 ATTATACAATTAATACTTTTATTTTCTTA
1 ATTATACAATTAAT-CTTTAATTTTCTTA
* * * *
41681 TAATATTC-ATTAATC---AA-TATATTA
1 -ATTATACAATTAATCTTTAATTTTCTTA
41705 ATTATACAATTAATCTTTAATTTTCTTA
1 ATTATACAATTAATCTTTAATTTTCTTA
41733 ATT
1 ATT
41736 TGGATTTGAT
Statistics
Matches: 40, Mismatches: 9, Indels: 12
0.66 0.15 0.20
Matches are distributed among these distances:
23 5 0.12
24 12 0.30
25 1 0.03
27 2 0.05
28 9 0.22
29 6 0.15
30 5 0.12
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTATACAATTAATCTTTAATTTTCTTA
Found at i:41808 original size:76 final size:76
Alignment explanation
Indices: 41721--41873 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
41711 CAATTAATCT
* * * *
41721 TTAATTTTCTTAATTTGGATTTGATTAAATTTATGGAAATATTAATCTATATATACCTCAGATGG
1 TTAATTCTCTTAATTTGGATTTGATTAAATTTATGAAAATATAAATCTATATATACCTCAAATGG
41786 CATTTCGGTTG
66 CATTTCGGTTG
*
41797 TTAATTCTCTTAATTTGGATTTGATTAAATTTATGAAAATATAAATCTATATATACCTCAAATTG
1 TTAATTCTCTTAATTTGGATTTGATTAAATTTATGAAAATATAAATCTATATATACCTCAAATGG
41862 CATTTCGGTTG
66 CATTTCGGTTG
41873 T
1 T
41874 GTTCCTAGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (76 bp):
TTAATTCTCTTAATTTGGATTTGATTAAATTTATGAAAATATAAATCTATATATACCTCAAATGG
CATTTCGGTTG
Found at i:44243 original size:20 final size:21
Alignment explanation
Indices: 44220--44300 Score: 62
Period size: 20 Copynumber: 3.9 Consensus size: 21
44210 GAAAACTAGT
44220 AAAAAAAGCATAAAAGTTA-A
1 AAAAAAAGCATAAAAGTTAGA
* * *
44240 AAAAAAAG-GTGAAAA-CTAGT
1 AAAAAAAGCAT-AAAAGTTAGA
*
44260 AAAAAAA-CATAAAAGTTAATA
1 AAAAAAAGCATAAAAGTT-AGA
*
44281 AAAAGAAAGCATTAAAGTTA
1 AAAA-AAAGCATAAAAGTTA
44301 CTAGAAAGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
19 7 0.15
20 21 0.46
21 5 0.11
22 4 0.09
23 9 0.20
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAAAAAGCATAAAAGTTAGA
Found at i:44275 original size:39 final size:40
Alignment explanation
Indices: 44206--44284 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
44196 TACGTATAGG
44206 AGGTGAAAACTAGTAAAAAAAGCATAAAAGTTAAAAAAAA
1 AGGTGAAAACTAGTAAAAAAAGCATAAAAGTTAAAAAAAA
*
44246 AGGTGAAAACTAGTAAAAAAA-CATAAAAGTTAATAAAAA
1 AGGTGAAAACTAGTAAAAAAAGCATAAAAGTTAAAAAAAA
44285 GAAAGCATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 17 0.45
40 21 0.55
ACGTcount: A:0.65, C:0.05, G:0.14, T:0.16
Consensus pattern (40 bp):
AGGTGAAAACTAGTAAAAAAAGCATAAAAGTTAAAAAAAA
Found at i:44308 original size:23 final size:23
Alignment explanation
Indices: 44254--44308 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
44244 AAAGGTGAAA
44254 ACTAGTAAA-AAAACATAAAAGTT
1 ACTAG-AAAGAAAACATAAAAGTT
* * * *
44277 AATAAAAAGAAAGCATTAAAGTT
1 ACTAGAAAGAAAACATAAAAGTT
44300 ACTAGAAAG
1 ACTAGAAAG
44309 GAGGTCACCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (23 bp):
ACTAGAAAGAAAACATAAAAGTT
Found at i:46218 original size:4 final size:4
Alignment explanation
Indices: 46204--46238 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
46194 AGGCGCACAG
*
46204 AATA TATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT
46239 GACTCACTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AATA
Found at i:47363 original size:2 final size:2
Alignment explanation
Indices: 47356--47402 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
47346 GTTTAGAGGC
*
47356 TA TA TA TA TA -A TA -A TA TA CA 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
47396 TA TA TA T
1 TA TA TA T
47403 GACAAGGACA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:47881 original size:20 final size:19
Alignment explanation
Indices: 47852--47894 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
47842 TCGGTAAAAA
*
47852 CAAAAAATGACAACGATAT
1 CAAAAAATGACAACGAAAT
*
47871 CAAACAAATGATAACGAAAT
1 CAAA-AAATGACAACGAAAT
47891 CAAA
1 CAAA
47895 GGATTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.14
Consensus pattern (19 bp):
CAAAAAATGACAACGAAAT
Done.