Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016755.1 Corchorus olitorius cultivar O-4 contig16788, 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: 37997
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:463 original size:21 final size:19
Alignment explanation
Indices: 433--477 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
423 TTTTTCTTCC
433 TTTTTCTTTTCCAT-TCATTT
1 TTTTTCTTTTCC-TCT-ATTT
453 TTTTTCTTTTTCCTCTATTT
1 TTTTTC-TTTTCCTCTATTT
473 TTTTT
1 TTTTT
478 TATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTCTTTTCCTCTATTT
Found at i:577 original size:29 final size:29
Alignment explanation
Indices: 545--600 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
535 TGGGCCGCGT
* *
545 GCTGGTCTGCCAATGTGCAGGCCCAGCAC
1 GCTGGCCTGCCAATGCGCAGGCCCAGCAC
**
574 GCTGGCCTGCCTGTGCGCAGGCCCAGC
1 GCTGGCCTGCCAATGCGCAGGCCCAGC
601 GGCCTGCTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.12, C:0.38, G:0.34, T:0.16
Consensus pattern (29 bp):
GCTGGCCTGCCAATGCGCAGGCCCAGCAC
Found at i:10194 original size:20 final size:20
Alignment explanation
Indices: 10153--10195 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
10143 CTCTCACAAG
* *
10153 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
10173 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
10193 TTT
1 TTT
10196 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:11837 original size:30 final size:30
Alignment explanation
Indices: 11792--11900 Score: 166
Period size: 30 Copynumber: 3.7 Consensus size: 30
11782 CATGAACTTC
*
11792 AATTTTAGACATTTTGCCCCTTCAACTCTT
1 AATTTTGGACATTTTGCCCCTTCAACTCTT
* * *
11822 AATTTTGGACGTTTTGCCCCATGAACT-TT
1 AATTTTGGACATTTTGCCCCTTCAACTCTT
11851 AATTTTGGACATTTTGCCCCTTCAACTCTT
1 AATTTTGGACATTTTGCCCCTTCAACTCTT
*
11881 AATTTTGGACGTTTTGCCCC
1 AATTTTGGACATTTTGCCCC
11901 CTCTCAAACG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 26 0.37
30 44 0.63
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (30 bp):
AATTTTGGACATTTTGCCCCTTCAACTCTT
Found at i:11855 original size:59 final size:59
Alignment explanation
Indices: 11771--11900 Score: 226
Period size: 59 Copynumber: 2.2 Consensus size: 59
11761 GTAGCGTTTA
*
11771 GACG-TTTGTCCCATGAACTTCAATTTTAGACATTTTGCCCCTTCAACTCTTAATTTTG
1 GACGTTTTGCCCCATGAACTTCAATTTTAGACATTTTGCCCCTTCAACTCTTAATTTTG
* *
11829 GACGTTTTGCCCCATGAACTTTAATTTTGGACATTTTGCCCCTTCAACTCTTAATTTTG
1 GACGTTTTGCCCCATGAACTTCAATTTTAGACATTTTGCCCCTTCAACTCTTAATTTTG
11888 GACGTTTTGCCCC
1 GACGTTTTGCCCC
11901 CTCTCAAACG
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
58 4 0.06
59 64 0.94
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (59 bp):
GACGTTTTGCCCCATGAACTTCAATTTTAGACATTTTGCCCCTTCAACTCTTAATTTTG
Found at i:16405 original size:36 final size:36
Alignment explanation
Indices: 16365--16502 Score: 141
Period size: 36 Copynumber: 3.8 Consensus size: 36
16355 CCCTGCTTCC
* ** *
16365 TCCCAACCCTTTGCTTCCGCCGCCACCTCCACTCAT
1 TCCCAACCCTTTCCAGCCACCGCCACCTCCACTCAT
* *
16401 TCCCAACCCTTTCCAGCCACCGCCAGCTCCACTTAT
1 TCCCAACCCTTTCCAGCCACCGCCACCTCCACTCAT
* * * ** *
16437 TCCAAACCCTTTCCAGCCTCCTCCGGCTCCACTTAT
1 TCCCAACCCTTTCCAGCCACCGCCACCTCCACTCAT
* * *
16473 TCCAAACCCTTTCCAGCCACCACCAGCTCC
1 TCCCAACCCTTTCCAGCCACCGCCACCTCC
16503 TCCGTCTCCA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.18, C:0.51, G:0.08, T:0.23
Consensus pattern (36 bp):
TCCCAACCCTTTCCAGCCACCGCCACCTCCACTCAT
Found at i:16503 original size:45 final size:45
Alignment explanation
Indices: 16449--16640 Score: 235
Period size: 45 Copynumber: 4.2 Consensus size: 45
16439 CAAACCCTTT
* *
16449 CCAGCCTCCTCCGGCTCCACTTATTCCAAACCCTTTCCAGCCACCA
1 CCAG-CTCCTCCGGCTCCACTTATTCCGAACCCTTTCCAGCCTCCA
*
16495 CCAGCTCCTCCGTCTCCACTTATTCCGAACCCTTTCCAGCCTCCA
1 CCAGCTCCTCCGGCTCCACTTATTCCGAACCCTTTCCAGCCTCCA
* * * * *
16540 CCAGCTCCGCCGGCTCCGCTCATCCCGAACCCATTT-CAGCCTCCT
1 CCAGCTCCTCCGGCTCCACTTATTCCGAACCC-TTTCCAGCCTCCA
* * *
16585 CCAGCACCTCCGGCTCC-GTTCATTCCGAACCCTTTCCAGCCTCCT
1 CCAGCTCCTCCGGCTCCACTT-ATTCCGAACCCTTTCCAGCCTCCA
*
16630 CCAGCACCTCC
1 CCAGCTCCTCC
16641 ATCAAGGCCT
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
44 4 0.03
45 118 0.91
46 7 0.05
ACGTcount: A:0.16, C:0.51, G:0.11, T:0.22
Consensus pattern (45 bp):
CCAGCTCCTCCGGCTCCACTTATTCCGAACCCTTTCCAGCCTCCA
Found at i:21159 original size:9 final size:9
Alignment explanation
Indices: 21145--21188 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
21135 AGCAAGGTTT
*
21145 TGGAAAACC
1 TGGAAAATC
*
21154 TGGAAATTC
1 TGGAAAATC
* *
21163 TGCAAATTC
1 TGGAAAATC
21172 TGGAAAATC
1 TGGAAAATC
21181 TGGAAAAT
1 TGGAAAAT
21189 TCCAGAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (9 bp):
TGGAAAATC
Found at i:22760 original size:27 final size:26
Alignment explanation
Indices: 22730--22798 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 26
22720 AAAGAGAAAG
*
22730 GATCTTGATGATCAAATTGAAAGCATT
1 GATCTT-ATGATCAAACTGAAAGCATT
*
22757 GATCTTAATGATCAAACTGAAGGCATT
1 GATCTT-ATGATCAAACTGAAAGCATT
22784 GATCTTAGTGATCAA
1 GATCTTA-TGATCAA
22799 GTTGTTTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (26 bp):
GATCTTATGATCAAACTGAAAGCATT
Found at i:26853 original size:30 final size:29
Alignment explanation
Indices: 26817--26912 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 29
26807 AAGGAAGCAG
*
26817 CAGCAGTTTCATTTCCTATGGTCAAAACAA
1 CAGCAGTTTCATTTCCTTTGGT-AAAACAA
* * *
26847 CAGCAGTTTCAGTTCGTTTGGTGAAAACAG
1 CAGCAGTTTCATTTCCTTTGGT-AAAACAA
*
26877 CAGCAGTTTCATTTCTTTTGGTATAAACAA
1 CAGCAGTTTCATTTCCTTTGGTA-AAACAA
26907 CAGCAG
1 CAGCAG
26913 CAATTTCAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.02
30 56 0.98
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (29 bp):
CAGCAGTTTCATTTCCTTTGGTAAAACAA
Found at i:26914 original size:33 final size:33
Alignment explanation
Indices: 26814--26920 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 33
26804 AGCAAGGAAG
*
26814 CAGCAGCAGTTTCATTTCCTATGGTCA-AAAC-A
1 CAGCAGCAGTTTCATTTCCTTTGGT-ATAAACAA
* * *
26846 -A-CAGCAGTTTCAGTTCGTTTGG--TGAA-AA
1 CAGCAGCAGTTTCATTTCCTTTGGTATAAACAA
*
26874 CAGCAGCAGTTTCATTTCTTTTGGTATAAACAA
1 CAGCAGCAGTTTCATTTCCTTTGGTATAAACAA
*
26907 CAGCAGCAATTTCA
1 CAGCAGCAGTTTCA
26921 ACAGTAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.05
29 1 0.02
30 37 0.62
31 1 0.02
32 3 0.05
33 15 0.25
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (33 bp):
CAGCAGCAGTTTCATTTCCTTTGGTATAAACAA
Found at i:34256 original size:66 final size:65
Alignment explanation
Indices: 34128--34351 Score: 163
Period size: 65 Copynumber: 3.4 Consensus size: 65
34118 GTAGAAATAT
* * * * *
34128 TGATAACAACACTGTGAAAATTTGATAA-CTTCATTATGAAATTTCGATTACCTTCCTATGAAAG
1 TGATAACCACACTGTGAAATTTTGATAATC-ACACTATGAAATTTCGATAACCTTCCTATGAAA-
34192 TC
64 TC
* * * *
34194 TGATAACCACACTGTGAAATTTTGATAATCACACTATGAAATTTTGATAATC-TCAGTGTGAAAT
1 TGATAACCACACTGTGAAATTTTGATAATCACACTATGAAATTTCGATAACCTTC-CTATGAAAT
*
34258 T
65 C
* * * * * * *
34259 TGATAATCTCCCTATGAAATTTTGATAATCACACAAT-ATAA-TT-GGTAACC-GCACTATGAAA
1 TGATAACCACACTGTGAAATTTTGATAATCACACTATGA-AATTTCGATAACCTTC-CTATG-AA
*
34320 ATTT
63 A-TC
* *
34324 TGATAACCACACTATGAAATTTCGATAA
1 TGATAACCACACTGTGAAATTTTGATAA
34352 CCTTCTTATG
Statistics
Matches: 129, Mismatches: 24, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
63 10 0.08
64 6 0.05
65 63 0.49
66 49 0.38
67 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (65 bp):
TGATAACCACACTGTGAAATTTTGATAATCACACTATGAAATTTCGATAACCTTCCTATGAAATC
Found at i:34353 original size:22 final size:21
Alignment explanation
Indices: 34121--34353 Score: 148
Period size: 22 Copynumber: 10.7 Consensus size: 21
34111 CTCAAACGTA
* *
34121 GAAATATTGATAACAACACTGT
1 GAAAT-TTGATAACCACACTAT
** *
34143 GAAAATTTGATAACTTCATTAT
1 G-AAATTTGATAACCACACTAT
* *
34165 GAAATTTCGATTACCTTC-CTAT
1 GAAATTT-GATAACC-ACACTAT
* *
34187 GAAAGTCTGATAACCACACTGT
1 GAAA-TTTGATAACCACACTAT
*
34209 GAAATTTTGATAATCACACTAT
1 GAAA-TTTGATAACCACACTAT
* * * *
34231 GAAATTTTGATAATCTCAGTGT
1 GAAA-TTTGATAACCACACTAT
* * *
34253 GAAATTTGATAATCTCCCTAT
1 GAAATTTGATAACCACACTAT
* *
34274 GAAATTTTGATAATCACACAAT
1 GAAA-TTTGATAACCACACTAT
* *
34296 -ATAA-TTGGTAACCGCACTAT
1 GA-AATTTGATAACCACACTAT
34316 GAAAATTTTGATAACCACACTAT
1 G-AAA-TTTGATAACCACACTAT
34339 GAAATTTCGATAACC
1 GAAATTT-GATAACC
34354 TTCTTATGAG
Statistics
Matches: 169, Mismatches: 30, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.07
21 31 0.18
22 103 0.61
23 23 0.14
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (21 bp):
GAAATTTGATAACCACACTAT
Found at i:34609 original size:22 final size:22
Alignment explanation
Indices: 34365--34724 Score: 115
Period size: 22 Copynumber: 16.5 Consensus size: 22
34355 TCTTATGAGA
* * *
34365 ATGAAATTATGATATCCTCTCT
1 ATGAAATTTTGATAACCTTTCT
* * *
34387 AT-ATAATTATGATAACCTCTCC
1 ATGA-AATTTTGATAACCTTTCT
* * **
34409 ATAAAATTTTCATAACCTCCCT
1 ATGAAATTTTGATAACCTTTCT
*
34431 ATGAAATTTTGCTAACC--TCT
1 ATGAAATTTTGATAACCTTTCT
* *
34451 AGGAAATTTTGATAA----GC-
1 ATGAAATTTTGATAACCTTTCT
* **
34468 A-CAAATTTTGATAATCTCCCTCCCT
1 ATGAAATTTTGATAA----CCTTTCT
* * *
34493 ATGATATTTTGTTAACCTTTTTT
1 ATGAAATTTTGATAACC-TTTCT
*
34516 ATGAAATTTTGATAA--TTACACT
1 ATGAAATTTTGATAACCTT--TCT
*
34538 AT-AAACTTTCGATAACC-TTCGT
1 ATGAAA-TTTTGATAACCTTTC-T
* * **
34560 ATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAACCTTTCT
* *
34582 AAGAAATTTTGATAACCTTTTT
1 ATGAAATTTTGATAACCTTTCT
* * *
34604 ATGAAATTTTGGTAACCTCTGT
1 ATGAAATTTTGATAACCTTTCT
*
34626 ATGAAATTTTGATAA-CTATACT
1 ATGAAATTTTGATAACCT-TTCT
* * *
34648 TTGAAGTTTTGATAACC-TCCAT
1 ATGAAATTTTGATAACCTTTC-T
* **
34670 ATGAAATTTTTG-CAA-CTACACT
1 ATGAAA-TTTTGATAACCT-TTCT
* *
34692 ATGAAATTTTGATAAACTTCCT
1 ATGAAATTTTGATAACCTTTCT
*
34714 ATGTAATTTTG
1 ATGAAATTTTG
34725 GTTTGATTGT
Statistics
Matches: 251, Mismatches: 58, Indels: 58
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.05
17 1 0.00
18 1 0.00
20 17 0.07
21 15 0.06
22 163 0.65
23 30 0.12
24 1 0.00
25 1 0.00
26 10 0.04
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTTTCT
Found at i:34658 original size:44 final size:44
Alignment explanation
Indices: 34486--34679 Score: 162
Period size: 44 Copynumber: 4.4 Consensus size: 44
34476 TGATAATCTC
* * * *
34486 CCTCCCTATGATATTTTGTTAACCTTTTTTATGAAATTTTGATAA
1 CCTCCATATGAAATTTTGATAACC-TTCTTATGAAATTTTGATAA
* * * * *
34531 -TTACACTAT-AAACTTTCGATAACCTTCGTATGAAATTTTGTTAA
1 CCTCCA-TATGAAA-TTTTGATAACCTTCTTATGAAATTTTGATAA
* * * * *
34575 TCTCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTTGGTAA
1 CCTCCATATGAAATTTTGATAACCTTCTTATGAAATTTTGATAA
** *
34619 CCTCTGTATGAAATTTTGATAA-CTATACTT-TGAAGTTTTGATAA
1 CCTCCATATGAAATTTTGATAACCT-T-CTTATGAAATTTTGATAA
34663 CCTCCATATGAAATTTT
1 CCTCCATATGAAATTTT
34680 TGCAACTACA
Statistics
Matches: 117, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
43 2 0.02
44 96 0.82
45 19 0.16
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (44 bp):
CCTCCATATGAAATTTTGATAACCTTCTTATGAAATTTTGATAA
Found at i:34687 original size:44 final size:44
Alignment explanation
Indices: 34603--34723 Score: 129
Period size: 44 Copynumber: 2.7 Consensus size: 44
34593 ATAACCTTTT
* * * *
34603 TATGAAATTTTGGTAACCTCTGTATGAAA-TTTTGATAACTATAC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTTGACAACTACAC
* *
34647 TTTGAAGTTTTGATAACCTCCATATGAAATTTTTG-CAACTACAC
1 TATGAAATTTTGATAACCTCC-TATGAAATTTTTGACAACTACAC
* *
34691 TATGAAATTTTGATAAACTTCCTATGTAATTTT
1 TATGAAATTTTGAT-AACCTCCTATGAAATTTT
34724 GGTTTGATTG
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
44 53 0.83
45 11 0.17
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCTATGAAATTTTTGACAACTACAC
Found at i:34724 original size:66 final size:65
Alignment explanation
Indices: 34559--34724 Score: 156
Period size: 66 Copynumber: 2.5 Consensus size: 65
34549 ATAACCTTCG
* * * * *** * *
34559 TATGAAATTTTGTTAATCTCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTTGGTAACCTCT
1 TATGAAATTTTGATAAACTTCCTATG-AATTTTGATAACCTCCATATGAAATTTTGGCAACCTCA
*
34624 G
65 C
* * *
34625 TATGAAATTTTGAT-AACTATACTTTGAAGTTTTGATAACCTCCATATGAAATTTTTGCAA-CTA
1 TATGAAATTTTGATAAACT-TCCTATGAA-TTTTGATAACCTCCATATGAAATTTTGGCAACCT-
34688 CAC
63 CAC
34691 TATGAAATTTTGATAAACTTCCTATGTAATTTTG
1 TATGAAATTTTGATAAACTTCCTATG-AATTTTG
34725 GTTTGATTGT
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
65 7 0.09
66 67 0.84
67 6 0.08
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (65 bp):
TATGAAATTTTGATAAACTTCCTATGAATTTTGATAACCTCCATATGAAATTTTGGCAACCTCAC
Done.