Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020107.1 Corchorus olitorius cultivar O-4 contig20140, 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: 13168
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:90 original size:17 final size:18
Alignment explanation
Indices: 68--101 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58 TTTTTTTATT
68 TTTGTTTT-TTGAGTCAA
1 TTTGTTTTATTGAGTCAA
85 TTTGTTTTATTGAGTCA
1 TTTGTTTTATTGAGTCA
102 GTTTCTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.59
Consensus pattern (18 bp):
TTTGTTTTATTGAGTCAA
Found at i:110 original size:18 final size:17
Alignment explanation
Indices: 72--110 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
62 TTTATTTTTG
*
72 TTTTTTGAGTCAATTTG
1 TTTTTTGAGTCAATTTC
*
89 TTTTATTGAGTCAGTTTC
1 TTTT-TTGAGTCAATTTC
107 TTTT
1 TTTT
111 CTAGTCTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (17 bp):
TTTTTTGAGTCAATTTC
Found at i:120 original size:18 final size:18
Alignment explanation
Indices: 99--152 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 18
89 TTTTATTGAG
99 TCAGTTTCTTTTCTAGTC
1 TCAGTTTCTTTTCTAGTC
*
117 TCAG-TTCTTTTTTAGTC
1 TCAGTTTCTTTTCTAGTC
* * *
134 TGAGTTTTTTTTCGAGTC
1 TCAGTTTCTTTTCTAGTC
152 T
1 T
153 GAATCTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.57
Consensus pattern (18 bp):
TCAGTTTCTTTTCTAGTC
Found at i:153 original size:18 final size:17
Alignment explanation
Indices: 101--154 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
91 TTATTGAGTC
* *
101 AGTTTCTTTTCTAGTCTC
1 AGTTTTTTTTC-AGTCTG
119 AGTTCTTTTTT-AGTCTG
1 AGTT-TTTTTTCAGTCTG
136 AGTTTTTTTTCGAGTCTG
1 AGTTTTTTTTC-AGTCTG
154 A
1 A
155 ATCTTATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 6 0.19
17 9 0.29
18 11 0.35
19 5 0.16
ACGTcount: A:0.13, C:0.15, G:0.17, T:0.56
Consensus pattern (17 bp):
AGTTTTTTTTCAGTCTG
Found at i:1018 original size:21 final size:21
Alignment explanation
Indices: 989--1030 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
979 TCGCTCGGTC
*
989 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
1009 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
1031 CACACCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:1935 original size:21 final size:21
Alignment explanation
Indices: 1906--1947 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1896 TCGCTCGGTC
*
1906 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
1926 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
1948 CACACCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:2288 original size:2 final size:2
Alignment explanation
Indices: 2281--2312 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2271 TTAGAATTCG
2281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2313 TTGTAGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2348 original size:3 final size:3
Alignment explanation
Indices: 2334--2376 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
2324 GGGAGCAAAT
2334 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2377 AACAATACTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2488 original size:68 final size:69
Alignment explanation
Indices: 2372--2525 Score: 184
Period size: 68 Copynumber: 2.2 Consensus size: 69
2362 TTATTATTAT
* * *
2372 TATTAAACAATACTGATATCTATATTATGTTAAGTGGAAAAAGCTCAATACCCTCAACTAAGGTC
1 TATTAAACAATACTGATATC-ATATTAAGTTAAGTAGAAAAAGCTCAATACCCTCAAATAAGGTC
2437 TCGGC
65 TCGGC
* * * * ** * *
2442 TATTAAATAATATTGATATC-TATTAAGTTAAGTAGAAAGAGTTCAATGTCTTTAAATAAGGTCT
1 TATTAAACAATACTGATATCATATTAAGTTAAGTAGAAAAAGCTCAATACCCTCAAATAAGGTCT
2506 CGGC
66 CGGC
*
2510 TGTTAAACAATACTGA
1 TATTAAACAATACTGA
2526 GATTTATTGA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
68 52 0.74
70 18 0.26
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (69 bp):
TATTAAACAATACTGATATCATATTAAGTTAAGTAGAAAAAGCTCAATACCCTCAAATAAGGTCT
CGGC
Found at i:4330 original size:216 final size:213
Alignment explanation
Indices: 3867--4647 Score: 880
Period size: 205 Copynumber: 3.7 Consensus size: 213
3857 TTTTTGTTAT
* *
3867 TGCTTTTGCGACATTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAAT
1 TGCTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAAC
* * * * ** * *
3932 AAACTTCATTTTAAGATAGATTTTTCTGACATTTATAACAACATTTTTCGGAAACATCGTTCAAT
66 AAACGTCACTTTAAAATAGACTTTTCCAACATTTATAACAACGTTTTTCGGAAACATCGTTTAAT
* * * * **
3997 ATATGACATTTTCATAAACGTCGCAAAAAATAGCGACTCTTTTTAAAAATTAAGTGATGTTTTTT
131 ATATGACATTTTAATAAACGTCGCAAAAACTTGCGACTCTTTTT-TAAATTAAGTGACATTTTTT
*
4062 AATAACGTCGCTCTTGTTTA
195 AATAATGTCGCTCTT-TTTA
** *
4082 TATTTTTGCGACGGTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTTAA
1 TGCTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACA-TTTTTTAA
* * * *
4147 CAAACATCGCTTTAAAATAGACTTTTCCAACATTTATAACAACGTTTTTTGGAAACGTCGTTGTA
65 CAAACGTCACTTTAAAATAGACTTTTCCAACATTTATAACAACGTTTTTCGGAAACATCGTT-TA
* * * * **
4212 ATATATAACATTTTAATATACGTCGCAATACCTTGCGACTCTTTTTTATCTTAAGTGACATTTTT
129 ATATATGACATTTTAATAAACGTCGCAAAAACTTGCGACTCTTTTTTAAATTAAGTGACATTTTT
* *
4277 AAATAATGTCACTCTTATTTA
194 TAATAATGTCGCTCTT-TTTA
***
4298 TGCTTTTGCGACGTTTGTAGAGATACTTTTCTCAAACGTCGTTCAATCAT--G-CA------AAC
1 TGCTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAAC
* * * * ***
4354 AAATGTCACTTT-AAGTAAACTTTTCCAACATTTATAACAATGTTTTTCGGAATTGTCGTTGTAA
66 AAACGTCACTTTAAAATAGACTTTTCCAACATTTATAACAACGTTTTTCGGAAACATCGTT-TAA
* * * * *
4418 TATATGGCATTTTATTAAACGTCGCAAAATCTTGCGACTCTTTCTTAAGTTAAGTGACATTTTTT
130 TATATGACATTTTAATAAACGTCGCAAAAACTTGCGACTCTTTTTTAAATTAAGTGACATTTTTT
* *
4483 AATAATGTCGCTATTTCTTG
195 AATAATGTCGCTCTTT-TTA
* * * * *
4503 CGCTTTTGCGACGTTTGTAAAGACGTTTTTTTCAAATGTCGTTCAATCATTCGACATTTTTTAAC
1 TGCTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAAC
* * * * * *
4568 AAACGTCGCTTTTAGATAGACTTTTCCGACATTTATAACAACGTTTTTCGGAAAATATTGTTTAA
66 AAACGTCACTTTAAAATAGACTTTTCCAACATTTATAACAACGTTTTTCGG-AAACATCGTTTAA
4633 TATATGACATTTTAA
130 TATATGACATTTTAA
4648 ACTTAAACTA
Statistics
Matches: 473, Mismatches: 79, Indels: 28
0.82 0.14 0.05
Matches are distributed among these distances:
204 1 0.00
205 159 0.34
206 12 0.03
207 1 0.00
208 2 0.00
213 2 0.00
214 14 0.03
215 101 0.21
216 141 0.30
217 40 0.08
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (213 bp):
TGCTTTTGCGACGTTTGTAGAGACGTTTTTCTCAAACGTCGTTCAATCATGCGACATTTTTTAAC
AAACGTCACTTTAAAATAGACTTTTCCAACATTTATAACAACGTTTTTCGGAAACATCGTTTAAT
ATATGACATTTTAATAAACGTCGCAAAAACTTGCGACTCTTTTTTAAATTAAGTGACATTTTTTA
ATAATGTCGCTCTTTTTA
Found at i:4881 original size:11 final size:11
Alignment explanation
Indices: 4846--4899 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
4836 CTGTTTGGCA
*
4846 TTGTTTCTGTT
1 TTGTTTTTGTT
* *
4857 TTCTTGTT-TT
1 TTGTTTTTGTT
4867 TTGTTTTTGTT
1 TTGTTTTTGTT
4878 TTGTTTTTGTT
1 TTGTTTTTGTT
*
4889 TTGCTTTTGTT
1 TTGTTTTTGTT
4900 ACGTTGTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
10 8 0.22
11 28 0.78
ACGTcount: A:0.00, C:0.06, G:0.17, T:0.78
Consensus pattern (11 bp):
TTGTTTTTGTT
Found at i:4886 original size:17 final size:17
Alignment explanation
Indices: 4864--4899 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
4854 GTTTTCTTGT
4864 TTTTTGTTTTTG-TTTTG
1 TTTTTG-TTTTGCTTTTG
4881 TTTTTGTTTTGCTTTTG
1 TTTTTGTTTTGCTTTTG
4898 TT
1 TT
4900 ACGTTGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.81
Consensus pattern (17 bp):
TTTTTGTTTTGCTTTTG
Found at i:8774 original size:125 final size:124
Alignment explanation
Indices: 8530--8877 Score: 349
Period size: 125 Copynumber: 2.8 Consensus size: 124
8520 TTAACAAATA
* * * * * * * *
8530 TCACAATATAACATCTATATCAACGCTTATAGATGTC-GAAATATGTCAAAATCAAAATGATGTA
1 TCACAATATAATATCTATAACAACACTTACAAATGCCAG-AATACGTCGAAATC-AAATGATGTA
* *
8594 ATGACTTGTTCCGACATTTGTAATCGTCGGTATAATGTTCTATAACGACGCTTAATAAAGG
64 ATAACTTGTTCCGACATTTGCAATCGTCGGTATAATGTTCTATAACGACGCTTAATAAAGG
** * * * *
8655 TCATGATATAATATTTATAACAACTCTTACAAATGTCGGAATACGTCGAAA-CAAATGATGTAAA
1 TCACAATATAATATCTATAACAACACTTACAAATGCCAGAATACGTCGAAATCAAATGATGT-AA
* * * * * * ** *
8719 TAACTTGTTCTGACTTTTGCAATTGTCGGTATAATATTTTTTTTGCGACGTTTAATAAAGG
65 TAACTTGTTCCGACATTTGCAATCGTCGGTATAAT-GTTCTATAACGACGCTTAATAAAGG
* * *
8780 TCACAATATAATATCTATACCAACACTTACAAATGCCAGAATACTTCGAAATCAAATGATATGAA
1 TCACAATATAATATCTATAACAACACTTACAAATGCCAGAATACGTCGAAATCAAATGATGT-AA
* * * *
8845 GAACTTGTTCCGACATTTACAAACGTCGATATA
65 TAACTTGTTCCGACATTTGCAATCGTCGGTATA
8878 GTGTATATAT
Statistics
Matches: 181, Mismatches: 38, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
123 9 0.05
124 33 0.18
125 101 0.56
126 38 0.21
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (124 bp):
TCACAATATAATATCTATAACAACACTTACAAATGCCAGAATACGTCGAAATCAAATGATGTAAT
AACTTGTTCCGACATTTGCAATCGTCGGTATAATGTTCTATAACGACGCTTAATAAAGG
Found at i:12773 original size:42 final size:42
Alignment explanation
Indices: 12714--12794 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
12704 GCTAAGTCTT
12714 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* *
12756 GAAAATTCTTTGTAAATTAAGAAATACTCAACTGAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
12795 CTGATCTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:12960 original size:56 final size:57
Alignment explanation
Indices: 12860--12974 Score: 178
Period size: 56 Copynumber: 2.0 Consensus size: 57
12850 TTTATTTTGT
* *
12860 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAAGATTTATTATAACATTTATTATGTAAA
* * *
12917 AGAATAATTAAGTAGAGATA-TGTGGATAAGATTTATTATAACATTTATTGTGTAAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAAGATTTATTATAACATTTATTATGTAAA
12973 AG
1 AG
12975 GAAACAGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 33 0.62
57 20 0.38
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.35
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGGGGGATAAGATTTATTATAACATTTATTATGTAAA
Done.