Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024491.1 Corchorus olitorius cultivar O-4 contig24524, 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: 11950
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1526 original size:40 final size:40
Alignment explanation
Indices: 1467--1961 Score: 348
Period size: 40 Copynumber: 11.7 Consensus size: 40
1457 CTTTACCCAA
1467 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
* * * *
1507 TTTGCCCTTCCTCATCGGAAGGTGTTGTCTTAGTCTACTTTACCCAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGT-TTA----A-ATT-CTCAG
* *
1554 TTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
* * * * *
1594 TTTGTCCTTCCTCATCGGAAGGTGTTGTCTAAATTCCCAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
* * * *
1634 TTTGCCCTTCCTCATCAGAAGGTGTTGTTTAAGTCTTCTTTACCTAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA--ATTC--T--C-AG
* *
1681 TTTGTCCTTCCCCACCGGAAGGTGTTGTCTAAATTCTCAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
* * * ** * *
1721 TTTTCCCTTCTCCATCGGAAGGTGTTGTCGAAGTCTACTTTACCAAA
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAAT-T-C--T--C-AG
*
1768 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCACAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
* * *
1808 TATGTCCTTCCCCACCGGAAGGTGTTGTTTAAGTTTAGTT-TACCAA
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA----A-TTCT--CAG
1854 TTT-CCCTTCCCCACCGGAAGGTGTTGTTTAAATTGC-CAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT-CTCAG
* ** * ** * * *
1893 CTTGCCCTTCCTAACTGGAAGGCATGGTTTGAATTCCCAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
* * *
1933 TCTGCCCTTCCTCATCGGAAGGTGTTGTT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTT
1962 CTCACTCCCT
Statistics
Matches: 363, Mismatches: 60, Indels: 64
0.75 0.12 0.13
Matches are distributed among these distances:
39 5 0.01
40 208 0.57
41 9 0.02
42 5 0.01
43 1 0.00
44 2 0.01
45 34 0.09
46 11 0.03
47 88 0.24
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (40 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAG
Found at i:1551 original size:87 final size:87
Alignment explanation
Indices: 1325--1625 Score: 523
Period size: 87 Copynumber: 3.5 Consensus size: 87
1315 TGCCTTGTCT
*
1325 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTAGTTTACCCAATTTGCCCTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTT
1390 CCCCACCGGAAGGTGTTGTTTA
66 CCCCACCGGAAGGTGTTGTTTA
* *
1412 AATT-CCAGTTTGCGCTTCCGCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTT
1476 CCCCACCGGAAGGTGTTGTTTA
66 CCCCACCGGAAGGTGTTGTTTA
* * *
1498 AATTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTTAGTCTACTTTACCCAGTTTGCCCTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTT
*
1563 CCCCACCGGAAGGTGTTGTCTA
66 CCCCACCGGAAGGTGTTGTTTA
*
1585 AATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTCTAA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAA
1626 ATTCCCAGTT
Statistics
Matches: 201, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
86 83 0.41
87 118 0.59
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (87 bp):
AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTT
CCCCACCGGAAGGTGTTGTTTA
Found at i:1635 original size:127 final size:126
Alignment explanation
Indices: 1319--1749 Score: 475
Period size: 127 Copynumber: 3.4 Consensus size: 126
1309 CAGTCTTGCC
*
1319 TTGTCT-AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTAGTTTACCCAATT
1 TTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAA----A--TT-CCCAGTT
* * * * * *
1383 TGCCCTTCCCCACCGGAAGGTGTTGTTTA----A-ATT--CCAGTTTGCGCTTCCGCATCGGAAG
59 TGCCCTTCCTCATCGGAAGGTGTTGTTTAGTCTACTTTACCCAGTTTGCCCTTCCCCACCGGAAG
1441 GTG
124 GTG
* * * * *
1444 TTGTCTAAGTCTACTTTACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAGTT
1 TTGTCTAA----A--TT-CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAATTCCCAGTT
1509 TGCCCTTCCTCATCGGAAGGTGTTGTCTTAGTCTACTTTACCCAGTTTGCCCTTCCCCACCGGAA
59 TGCCCTTCCTCATCGGAAGGTGTTGT-TTAGTCTACTTTACCCAGTTTGCCCTTCCCCACCGGAA
1574 GGTG
123 GGTG
*
1578 TTGTCTAAATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTT
1 TTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTT
* * * *
1643 CCTCATCAGAAGGTGTTGTTTAAGTCTTCTTTACCTAGTTTGTCCTTCCCCACCGGAAGGTG
66 CCTCATCGGAAGGTGTTGTTT-AGTCTACTTTACCCAGTTTGCCCTTCCCCACCGGAAGGTG
* *
1705 TTGTCTAAATTCTCAGTTTTCCCTT-CTCCATCGGAAGGTGTTGTC
1 TTGTCTAAATTCCCAGTTTGCCCTTCCT-CATCGGAAGGTGTTGTC
1750 GAAGTCTACT
Statistics
Matches: 263, Mismatches: 25, Indels: 34
0.82 0.08 0.11
Matches are distributed among these distances:
125 6 0.02
126 34 0.13
127 147 0.56
128 2 0.01
129 1 0.00
130 2 0.01
131 1 0.00
132 4 0.02
133 33 0.13
134 33 0.13
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.36
Consensus pattern (126 bp):
TTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTT
CCTCATCGGAAGGTGTTGTTTAGTCTACTTTACCCAGTTTGCCCTTCCCCACCGGAAGGTG
Found at i:1683 original size:87 final size:86
Alignment explanation
Indices: 1549--1904 Score: 379
Period size: 87 Copynumber: 4.2 Consensus size: 86
1539 GTCTACTTTA
* * * * * * *
1549 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAA--ATTC----CCAGTTTGTCCTTCCTCA
1 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTTCTTTACCAATTTGCCCTTCCCCA
*
1608 TCGGAAGGTGTTGTCTAAATT
66 CCGGAAGGTGTTGTCTAAATT
* * *
1629 CCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTAAGTCTTCTTTACCTAGTTTGTCCTTCCCC
1 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTTCTTTACC-AATTTGCCCTTCCCC
1694 ACCGGAAGGTGTTGTCTAAATT
65 ACCGGAAGGTGTTGTCTAAATT
* * ** *
1716 CTCAGTTTTCCCTT-CTCCATCGGAAGGTGTTGTCGAAGTCTACTTTACCAAATTTGCCCTTCCC
1 CCCAGTTTGCCCTTCCT-CATCGGAAGGTGTTGTTTAAGTCTTCTTTACC-AATTTGCCCTTCCC
*
1780 CACCGGAAGGTGTTGTTTAAATT
64 CACCGGAAGGTGTTGTCTAAATT
* * * * * *
1803 CACAGTATGTCCTTCCCCACCGGAAGGTGTTGTTTAAGT-TTAGTTTACCAATTT-CCCTTCCCC
1 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTT-CTTTACCAATTTGCCCTTCCCC
*
1866 ACCGGAAGGTGTTGTTTAAATT
65 ACCGGAAGGTGTTGTCTAAATT
* *
1888 GCCAGCTTGCCCTTCCT
1 CCCAGTTTGCCCTTCCT
1905 AACTGGAAGG
Statistics
Matches: 233, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
80 33 0.14
82 3 0.01
85 42 0.18
86 10 0.04
87 144 0.62
88 1 0.00
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (86 bp):
CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTTCTTTACCAATTTGCCCTTCCCCA
CCGGAAGGTGTTGTCTAAATT
Found at i:1704 original size:214 final size:213
Alignment explanation
Indices: 1329--1835 Score: 710
Period size: 214 Copynumber: 2.3 Consensus size: 213
1319 TTGTCTAATT
* * * *
1329 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTAGTTTACCCAATTTGCCCTTCCCC
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAA----A--TT-CCCAGTTTGTCCTTCCCC
* * *
1394 ACCGGAAGGTGTTGTTTAAATTCCAGTTTGCGCTTCCGCATCGGAAGGTGTTGTCTAAGTCTACT
59 ACCGGAAGGTGTTGTCTAAATTCCAGTTTGCCCTTCCGCATCAGAAGGTGTTGTCTAAGTCTACT
*
1459 TTACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCTCAGTTTGCCCTTC-CTCATC
124 TTACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCTCAGTTTGCCCTTCTC-CATC
**
1523 GGAAGGTGTTGTCTTAGTCTACTTTA
188 GGAAGGTGTTGTCGAAGTCTACTTTA
* *
1549 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGTCCTTCCTCATCGGAA
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGTCCTTCCCCACCGGAA
* * * *
1614 GGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTAAGTCTTCTTTACCT
66 GGTGTTGTCTAAATT-CCAGTTTGCCCTTCCGCATCAGAAGGTGTTGTCTAAGTCTACTTTACCC
* * *
1679 AGTTTGTCCTTCCCCACCGGAAGGTGTTGTCTAAATTCTCAGTTTTCCCTTCTCCATCGGAAGGT
130 AATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCTCAGTTTGCCCTTCTCCATCGGAAGGT
1744 GTTGTCGAAGTCTACTTTA
195 GTTGTCGAAGTCTACTTTA
* * * * *
1763 CCAAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCACAGTATGTCCTTCCCCACCGGAA
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGTCCTTCCCCACCGGAA
1828 GGTGTTGT
66 GGTGTTGT
1836 TTAAGTTTAG
Statistics
Matches: 259, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
213 35 0.14
214 187 0.72
215 1 0.00
216 1 0.00
220 35 0.14
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (213 bp):
CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGTCCTTCCCCACCGGAA
GGTGTTGTCTAAATTCCAGTTTGCCCTTCCGCATCAGAAGGTGTTGTCTAAGTCTACTTTACCCA
ATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCTCAGTTTGCCCTTCTCCATCGGAAGGTG
TTGTCGAAGTCTACTTTA
Found at i:1814 original size:127 final size:125
Alignment explanation
Indices: 1319--1835 Score: 461
Period size: 127 Copynumber: 4.0 Consensus size: 125
1309 CAGTCTTGCC
*
1319 TTGTCT-AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTAGTTTACCCAATT
1 TTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGT-TA-CTT-CCCAATT
* *
1383 TGCCCTTCCCCACCGGAAGGTGTTGTTTAA-ATTC-CAGTTTG-CGCTTCCGCATCGGAAGGTG
63 TGCCCTTCCCCACCGGAAGGTGTTGTTTAACATTCACAGTTTGTC-CTTCCCCACCGGAAGGTG
* * * * *
1444 TTGTCTAAGTCTACTTTACCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA---A-TTCTC
1 TTGTCTAA----A--TT-CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTTACTTCCC
* * * * * *
1505 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTTAGTCTACTTTACCCAGTTTGCCCTTCCCCACC
59 AATTTGCCCTTCCCCACCGGAAGGTGTTGT-TTA----ACATT-CACAGTTTGTCCTTCCCCACC
1570 GGAAGGTG
118 GGAAGGTG
* *
1578 TTGTCTAAATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTCTAA---A-TTCCCAGTTTGC
1 TTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTTACTTCCCAATTTGC
* * *
1639 CCTTCCTCATCAGAAGGTGTTGTTTAAGTC-TTCTTTACCTAGTTTGTCCTTCCCCACCGGAAGG
66 CCTTCCCCACCGGAAGGTGTTGTTTAA--CATTC---A-C-AGTTTGTCCTTCCCCACCGGAAGG
1703 TG
124 TG
* * * *
1705 TTGTCTAAATTCTCAGTTTTCCCTT-CTCCATCGGAAGGTGTTGTCGAAGTCTACTTTACCAAAT
1 TTGTCTAAATTCCCAGTTTGCCCTTCCT-CATCGGAAGGTGTTGTCTAAGT-TAC-TT-CCCAAT
*
1769 TTGCCCTTCCCCACCGGAAGGTGTTGTTTAA-ATTCACAGTATGTCCTTCCCCACCGGAAGGTG
62 TTGCCCTTCCCCACCGGAAGGTGTTGTTTAACATTCACAGTTTGTCCTTCCCCACCGGAAGGTG
1832 TTGT
1 TTGT
1836 TTAAGTTTAG
Statistics
Matches: 329, Mismatches: 30, Indels: 64
0.78 0.07 0.15
Matches are distributed among these distances:
122 2 0.01
123 2 0.01
124 1 0.00
125 6 0.02
126 36 0.11
127 166 0.50
128 3 0.01
129 2 0.01
130 2 0.01
131 2 0.01
132 7 0.02
133 36 0.11
134 63 0.19
135 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (125 bp):
TTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTTACTTCCCAATTTGC
CCTTCCCCACCGGAAGGTGTTGTTTAACATTCACAGTTTGTCCTTCCCCACCGGAAGGTG
Found at i:3251 original size:11 final size:11
Alignment explanation
Indices: 3235--3266 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3225 TTTTTCAGTT
3235 TTTTGTTTTTG
1 TTTTGTTTTTG
3246 TTTTGTTTTTG
1 TTTTGTTTTTG
*
3257 CTTTGTTTTT
1 TTTTGTTTTT
3267 ATTGTGCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:4892 original size:30 final size:30
Alignment explanation
Indices: 4833--4896 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
4823 AAGTTCGTGT
* *
4833 TTGAATACTTATTGAAGATAATTTGAAGAA
1 TTGAAGACTTATTGAAGATAATTTCAAGAA
*
4863 TTGAAGAC-TATTGAAGAATTATTTCAAGAA
1 TTGAAGACTTATTGAAG-ATAATTTCAAGAA
4893 TTGA
1 TTGA
4897 GGATTGAGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (30 bp):
TTGAAGACTTATTGAAGATAATTTCAAGAA
Found at i:8941 original size:20 final size:21
Alignment explanation
Indices: 8888--8941 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
8878 TTTTCTTCTT
* *
8888 TTGCTTTGATTTGATTGATTA
1 TTGCCTTGATTTGATTGACTA
* *
8909 TTGCTTTGA-TTGATTGCCTA
1 TTGCCTTGATTTGATTGACTA
8929 TT-CCTTGATTTGA
1 TTGCCTTGATTTGA
8942 ATCAGTTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 15 0.52
21 9 0.31
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.54
Consensus pattern (21 bp):
TTGCCTTGATTTGATTGACTA
Found at i:11430 original size:21 final size:21
Alignment explanation
Indices: 11404--11558 Score: 235
Period size: 21 Copynumber: 7.4 Consensus size: 21
11394 TGCTAGAAGT
11404 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
11425 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
11446 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
11467 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
*
11488 TCATTGGAG-AAGGTTCCAAGT
1 TCATTGGAGCAA-GTTCCAAGC
*
11509 TCATTGGAG-AAGGTTCCAAGT
1 TCATTGGAGCAA-GTTCCAAGC
*
11530 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
11551 TCATTGGA
1 TCATTGGA
11559 ATTGCCTAAG
Statistics
Matches: 130, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
20 2 0.02
21 128 0.98
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.