Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017655.1 Corchorus olitorius cultivar O-4 contig17688, 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: 19736
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:299 original size:21 final size:21
Alignment explanation
Indices: 269--308 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
259 CTAAAAACAG
*
269 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
*
290 GACAACTCCTGCCCTGGAC
1 GACAACTCCTGCCCAGGAC
309 CTGGTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.17
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:364 original size:71 final size:71
Alignment explanation
Indices: 261--451 Score: 276
Period size: 71 Copynumber: 2.7 Consensus size: 71
251 ATTGAAGCCT
* * *
261 AAAAA-CAGGACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCTGGACCTGGTCTGTTGAAAGA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
325 CGGAAG
66 CGGAAG
* * * *
331 AAAAATCAGAACAACTCCCGCCCAAGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
*
396 GGGAAG
66 CGGAAG
* *
402 AAAATTCAGAACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGAC
1 AAAAATCAGAACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGAC
452 TTGTTGCGGA
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
70 5 0.05
71 82 0.77
72 19 0.18
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.17
Consensus pattern (71 bp):
AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
CGGAAG
Found at i:367 original size:21 final size:21
Alignment explanation
Indices: 341--382 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
331 AAAAATCAGA
341 ACAACTCCCGCCCAAGACTTG
1 ACAACTCCCGCCCAAGACTTG
* *
362 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCCGCCCAAGACTTG
383 GTCTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.40, G:0.17, T:0.17
Consensus pattern (21 bp):
ACAACTCCCGCCCAAGACTTG
Found at i:442 original size:22 final size:22
Alignment explanation
Indices: 412--454 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
402 AAAATTCAGA
* *
412 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
434 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
455 TTGCGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:1472 original size:14 final size:14
Alignment explanation
Indices: 1445--1483 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1435 TAAAAAAATG
1445 AATGAAAAATTGAAAA
1 AATG-AAAA-TGAAAA
1461 AATGAAAATGAAAA
1 AATGAAAATGAAAA
*
1475 AAGGAAAAT
1 AATGAAAAT
1484 AAAGGCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 4 0.18
16 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AATGAAAATGAAAA
Found at i:1481 original size:22 final size:20
Alignment explanation
Indices: 1437--1482 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1427 AATCAAAATA
**
1437 AAAAAATGAATGAAAAATTG
1 AAAAAATGAATGAAAAAAGG
1457 AAAAAATGAAAATGAAAAAAGG
1 AAAAAATG--AATGAAAAAAGG
1479 AAAA
1 AAAA
1483 TAAAGGCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAAAATGAATGAAAAAAGG
Found at i:1878 original size:13 final size:13
Alignment explanation
Indices: 1875--1912 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1865 AAAAAAAATC
1875 AAAAAATCAAAAA
1 AAAAAATCAAAAA
1888 AAAAAATCAAAAA
1 AAAAAATCAAAAA
*
1901 AATCAAATCAAA
1 AA-AAAATCAAA
1913 TCAAAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAAATCAAAAA
Found at i:1879 original size:14 final size:14
Alignment explanation
Indices: 1875--1912 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1865 AAAAAAAATC
1875 AAAAAATC-AAAAA
1 AAAAAATCAAAAAA
1888 AAAAAATCAAAAAA
1 AAAAAATCAAAAAA
**
1902 ATCAAATCAAA
1 AAAAAATCAAA
1913 TCAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAATCAAAAAA
Found at i:1887 original size:22 final size:22
Alignment explanation
Indices: 1860--1907 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
1850 ATTAAGAAAT
1860 TCAAAAAAAAAAATC-AAAAAA
1 TCAAAAAAAAAAATCAAAAAAA
1881 TCAAAAAAAAAAATCAAAAAAA
1 TCAAAAAAAAAAATCAAAAAAA
1903 TCAAA
1 TCAAA
1908 TCAAATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (22 bp):
TCAAAAAAAAAAATCAAAAAAA
Found at i:1929 original size:12 final size:11
Alignment explanation
Indices: 1891--1930 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1881 TCAAAAAAAA
1891 AAATCAAAA--
1 AAATCAAAATC
1900 AAATC-AAATC
1 AAATCAAAATC
1910 AAATCAAAATC
1 AAATCAAAATC
1921 AATATCAAAA
1 AA-ATCAAAA
1931 GAGAATGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 3 0.11
9 5 0.19
10 5 0.19
11 7 0.26
12 7 0.26
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATCAAAATC
Found at i:2597 original size:50 final size:50
Alignment explanation
Indices: 2522--2725 Score: 266
Period size: 50 Copynumber: 4.0 Consensus size: 50
2512 AAGTTTTATT
* *
2522 ATAAGATTGCATTCCGTTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAA
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
* *
2572 ATAAGATTGCATTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTCCAAA
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
* * *
2622 GTGAA-ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTTGCTTGTCAAAA
1 AT-AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTC-AAA
* * * *
2673 ATAAGATTGCACTCCATTTGTGAGACCAAGACCAAAAGCTCGCTTTTTCAAA
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAA-TTCGC-TTTTCAAA
2725 A
1 A
2726 GGCATTTTAG
Statistics
Matches: 135, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
50 89 0.66
51 35 0.26
52 7 0.05
53 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (50 bp):
ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
Found at i:3469 original size:69 final size:69
Alignment explanation
Indices: 3374--3851 Score: 715
Period size: 69 Copynumber: 6.9 Consensus size: 69
3364 AAATAGCAAC
* *
3374 ATAGGCTTTTTCATCAAGCCAAACTCGTTTTCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAA
1 ATAGGCTTTTCCAT-AAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAA
* *
3439 GCGAC
65 GCCAT
* *
3444 GTAGGCTTTTCCATAAGCCAAACTCGTTTCCATATGAGTCAGTTTAAGCCTTGGTTCCATCCAAG
1 ATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAG
3509 CCAT
66 CCAT
* * *
3513 GTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCATTGGTTCCATCCAAG
1 ATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAG
3578 CCAT
66 CCAT
* * * *
3582 ACAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCTATCCAAG
1 ATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAG
3647 CCAT
66 CCAT
* *
3651 AT-GGACTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAA
1 ATAGG-CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAA
3715 GCCAT
65 GCCAT
* * * * *
3720 ATAGACTTTTCCATAAGTCAAACTCGTTTCCATACAAATCAGTTCAAGCCTTGGTTCCATCCAAG
1 ATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAG
3785 CCAT
66 CCAT
* * * *
3789 ATAGACTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTTAAACATTGGTTCCATCCA
1 ATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCA
3852 TATAGCAGAG
Statistics
Matches: 380, Mismatches: 26, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
68 2 0.01
69 365 0.96
70 13 0.03
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (69 bp):
ATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAG
CCAT
Found at i:4273 original size:30 final size:30
Alignment explanation
Indices: 4230--4416 Score: 252
Period size: 30 Copynumber: 6.2 Consensus size: 30
4220 ACTTTGTCAA
*
4230 TTTATTTTCAATCCTGGTTGAGGATCATTG-
1 TTTATTTT-AATCCTGGTTTAGGATCATTGC
* *
4260 TTGCATTTTAATCCTGATTTAGGATCATTGC
1 TT-TATTTTAATCCTGGTTTAGGATCATTGC
*
4291 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
4321 TTTATTTTAATCCTGGTTTAAGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
4351 TTTATTTTAATCCTGGTTTAGGGTCATTAC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
4381 TTTATTTCAAAATCCT-GTTTAGGATCATTGC
1 TTTATTT--TAATCCTGGTTTAGGATCATTGC
4412 TTTAT
1 TTTAT
4417 CATTTTATTT
Statistics
Matches: 139, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
30 108 0.78
31 25 0.18
32 6 0.04
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTTAGGATCATTGC
Found at i:4868 original size:27 final size:27
Alignment explanation
Indices: 4832--4919 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
4822 GGAATTTTGG
* *
4832 GTCATTTGCACGTTCAGGGGCATTTTA
1 GTCATTTGCACATCCAGGGGCATTTTA
4859 GTCATTTGCACATCCAGGGGCATTTTA
1 GTCATTTGCACATCCAGGGGCATTTTA
* *
4886 GTCATTTGCACATCCAGGGGCATGTTG
1 GTCATTTGCACATCCAGGGGCATTTTA
4913 GTCATTT
1 GTCATTT
4920 TAAGCTCACT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (27 bp):
GTCATTTGCACATCCAGGGGCATTTTA
Found at i:7904 original size:41 final size:41
Alignment explanation
Indices: 7823--7925 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 41
7813 TTTTTCCGTT
* * * *
7823 TTCAATATAGTCCCTGATTTAGGTTTATGTTTGTTAATTGA
1 TTCAATTTAGTCCCTGATTTAGGTTAATATTTATTAATTGA
* *
7864 TTCAATTTTGTCCCTGATTTAGAG-TAATATTTATTTATTGA
1 TTCAATTTAGTCCCTGATTTAG-GTTAATATTTATTAATTGA
* *
7905 TTC-ATATTCGCCCCTGATTTA
1 TTCAAT-TTAGTCCCTGATTTA
7926 AGATTTTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
40 2 0.04
41 49 0.94
42 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (41 bp):
TTCAATTTAGTCCCTGATTTAGGTTAATATTTATTAATTGA
Found at i:15610 original size:25 final size:25
Alignment explanation
Indices: 15576--15654 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
15566 TATTTATTCA
15576 CTATTTATTTATTTTTAACTATCAT
1 CTATTTATTTATTTTTAACTATCAT
* *
15601 CTATTTATTTACTATT---TATCA-
1 CTATTTATTTATTTTTAACTATCAT
* *
15622 --ATTTATTTATTTTTAACCATTAT
1 CTATTTATTTATTTTTAACTATCAT
15645 CTATTTATTT
1 CTATTTATTT
15655 GCTATTTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 12 0.29
22 8 0.19
25 22 0.52
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (25 bp):
CTATTTATTTATTTTTAACTATCAT
Found at i:15636 original size:44 final size:44
Alignment explanation
Indices: 15576--15796 Score: 307
Period size: 44 Copynumber: 4.9 Consensus size: 44
15566 TATTTATTCA
*
15576 CTATTTATTTATTTTTAACTATCATCTATTTATTTACTATTTAT
1 CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
* * *
15620 CAATTTATTTATTTTTAACCATTATCTATTTATTTGCTATTTAT
1 CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
* *
15664 CTTTTTATTTATTTTTAACTATTATCTATATATTTACTATTTAT
1 CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
* *
15708 CTTTTTATTTATTAATTTAACTATTATCTATTTACTTACTATTTAT
1 CTATTTATTTATT--TTTAACTATTATCTATTTATTTACTATTTAT
* * *
15754 CTATTTATTTATTAATTTAGCTATTATCTATTTAGTTATTATT
1 CTATTTATTTATT--TTTAACTATTATCTATTTATTTACTATT
15797 ATTTTTTTCA
Statistics
Matches: 160, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
44 92 0.57
46 68 0.43
ACGTcount: A:0.28, C:0.10, G:0.01, T:0.61
Consensus pattern (44 bp):
CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
Found at i:15665 original size:19 final size:18
Alignment explanation
Indices: 15641--15763 Score: 76
Period size: 19 Copynumber: 6.8 Consensus size: 18
15631 TTTTTAACCA
15641 TTATCTATTTATTTGCTAT
1 TTATCTATTTATTT-CTAT
* * *
15660 TTATCTTTTTATTTATTT
1 TTATCTATTTATTTCTAT
* *
15678 TTAACTA-TTATCTATATAT
1 TTATCTATTTAT-T-TCTAT
*
15697 TTA-CTATTTA--TCTTT
1 TTATCTATTTATTTCTAT
* *
15712 TTATTTATTAATTTAACTA-
1 TTATCTATTTATTT--CTAT
*
15731 TTATCTATTTACTTACTAT
1 TTATCTATTTA-TTTCTAT
15750 TTATCTATTTATTT
1 TTATCTATTTATTT
15764 ATTAATTTAG
Statistics
Matches: 79, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
15 6 0.08
16 5 0.06
17 4 0.05
18 17 0.22
19 43 0.54
20 4 0.05
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (18 bp):
TTATCTATTTATTTCTAT
Found at i:15725 original size:27 final size:26
Alignment explanation
Indices: 15695--15794 Score: 88
Period size: 27 Copynumber: 4.0 Consensus size: 26
15685 TTATCTATAT
*
15695 ATTTACTATTTATCTTTTTATTTATTA
1 ATTTACTA-TTATCTATTTATTTATTA
*
15722 ATTTAACTATTATCTATTTA---CTT-
1 ATTT-ACTATTATCTATTTATTTATTA
*
15745 A-CTA-T-TTATCTATTTATTTATTA
1 ATTTACTATTATCTATTTATTTATTA
*
15768 ATTTAGCTATTATCTATTTAGTTATTA
1 ATTTA-CTATTATCTATTTATTTATTA
15795 TTATTTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
19 11 0.19
20 1 0.02
21 1 0.02
22 3 0.05
23 2 0.03
24 4 0.07
26 1 0.02
27 31 0.53
28 4 0.07
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTACTATTATCTATTTATTTATTA
Found at i:15740 original size:15 final size:15
Alignment explanation
Indices: 15722--15800 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
15712 TTATTTATTA
15722 ATTTAACTATTATCT
1 ATTTAACTATTATCT
15737 ATTTACTTACTATTTATCT
1 ATTTA---ACTA-TTATCT
15756 ATTT-A-T-TTAT-T
1 ATTTAACTATTATCT
*
15767 AATTTAGCTATTATCT
1 -ATTTAACTATTATCT
**
15783 ATTTAGTTATTAT-T
1 ATTTAACTATTATCT
15797 ATTT
1 ATTT
15801 TTTTCAGCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
11 1 0.02
12 8 0.15
14 7 0.13
15 22 0.42
16 1 0.02
18 4 0.08
19 10 0.19
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTAACTATTATCT
Found at i:15839 original size:24 final size:24
Alignment explanation
Indices: 15809--15874 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
15799 TTTTTTCAGC
*
15809 TACCTATTTATCTATTATTCTCTG
1 TACCTATTTATCTATTATTCTCTA
*
15833 TATCTATTTATCTATTCA-TCTCTA
1 TACCTATTTATCTATT-ATTCTCTA
*
15857 TACCTATTT-TTTATTATT
1 TACCTATTTATCTATTATT
15875 ATTATTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.03
23 6 0.17
24 28 0.78
25 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.02, T:0.58
Consensus pattern (24 bp):
TACCTATTTATCTATTATTCTCTA
Done.