Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012992.1 Corchorus olitorius cultivar O-4 contig13025, 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: 11244
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1075 original size:203 final size:202
Alignment explanation
Indices: 669--1075 Score: 692
Period size: 204 Copynumber: 2.0 Consensus size: 202
659 CTTAATAACT
669 TTATCAATGGTGAATGTTATTAATTTTTTAAGCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
1 TTATCAATGGTGAATGTTATTAATTTTTTAAGCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
* *
734 TACAGCACATTATTATTATTATACATAAAACTATACCAAAAAAAAGTGTTGAACATTAGTGGTTG
66 TACAACACATTACTATTATTATACATAAAACTATACCAAAAAAAAGTGTTGAACATTAGTGGTTG
*
799 ATTTATTGAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
**
864 TGATTTA
196 CAATTTA
871 TTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTATCAATGGTGAATGTTATTAATTTTTTAAG-CTAAGATTACTAACAAAGTTGTAGTGAATAAG
* * * *
936 ATACAACACATTACTATTA-TATATATAGAATTATACCAAAAAAAAATTAGTTGAACATTAGTGG
65 ATACAACACATTACTATTATTATACATAAAACTATACC-AAAAAAAAGT-GTTGAACATTAGTGG
1000 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAG
128 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
1064 ATCCAATTTA
193 ATCCAATTTA
1074 TT
1 TT
1076 TATTATTAAG
Statistics
Matches: 193, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
202 47 0.24
203 71 0.37
204 75 0.39
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (202 bp):
TTATCAATGGTGAATGTTATTAATTTTTTAAGCTAAGATTACTAACAAAGTTGTAGTGAATAAGA
TACAACACATTACTATTATTATACATAAAACTATACCAAAAAAAAGTGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
CAATTTA
Found at i:1498 original size:6 final size:6
Alignment explanation
Indices: 1480--1526 Score: 85
Period size: 6 Copynumber: 7.7 Consensus size: 6
1470 GTTTAGACTT
1480 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
1527 GTATTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 34 0.85
7 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:2622 original size:21 final size:22
Alignment explanation
Indices: 2576--2623 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2566 CCATTATATC
*
2576 CTTTCTTATCTTTCCTTTCATT
1 CTTTGTTATCTTTCCTTTCATT
2598 -TTTGTTATCTTT-CTTTC-TGT
1 CTTTGTTATCTTTCCTTTCAT-T
2618 CTTTGT
1 CTTTGT
2624 GTGTTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 6 0.26
21 16 0.70
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.67
Consensus pattern (22 bp):
CTTTGTTATCTTTCCTTTCATT
Found at i:7301 original size:6 final size:6
Alignment explanation
Indices: 7286--7340 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
7276 AGCTTTACGT
*
7286 AAAAAA AAAAAC AAAAAC AAAAA- AAAAAC AAAAAC AAAAAC -AAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
7332 AAAAAC AAA
1 AAAAAC AAA
7341 GTACGTAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
5 10 0.22
6 36 0.78
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:7307 original size:11 final size:11
Alignment explanation
Indices: 7287--7340 Score: 81
Period size: 11 Copynumber: 4.8 Consensus size: 11
7277 GCTTTACGTA
*
7287 AAAAAAAAAAC
1 AAAAACAAAAC
*
7298 AAAAACAAAAA
1 AAAAACAAAAC
7309 AAAAACAAAAAC
1 AAAAAC-AAAAC
7321 AAAAACAAAAC
1 AAAAACAAAAC
7332 AAAAACAAA
1 AAAAACAAA
7341 GTACGTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
11 29 0.74
12 10 0.26
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:7309 original size:17 final size:17
Alignment explanation
Indices: 7287--7340 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
7277 GCTTTACGTA
7287 AAAAAAAAAACAAAAAC
1 AAAAAAAAAACAAAAAC
7304 AAAAAAAAAACAAAAAC
1 AAAAAAAAAACAAAAAC
*
7321 AAAAACAAAACAAAAAC
1 AAAAAAAAAACAAAAAC
7338 AAA
1 AAA
7341 GTACGTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAC
Found at i:7318 original size:23 final size:23
Alignment explanation
Indices: 7286--7340 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
7276 AGCTTTACGT
7286 AAAAAA-AAAAACAAAAACAAAA
1 AAAAAACAAAAACAAAAACAAAA
7308 AAAAAACAAAAACAAAAACAAAA
1 AAAAAACAAAAACAAAAACAAAA
*
7331 CAAAAACAAA
1 AAAAAACAAA
7341 GTACGTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAAACAAAAACAAAAACAAAA
Found at i:8179 original size:44 final size:44
Alignment explanation
Indices: 8131--8231 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
8121 GAACGATTAT
** * * *
8131 CAAAATTTTGTAGTGTGGTTACCAAAATTTCATATAGAGGTTAA
1 CAAAATTTCATAGTGTAGTGACCAAAATTTCATACAGAGGTTAA
* * *
8175 CAAAACTTCATAGTGTAGTGATCAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGTAGTGACCAAAATTTCATACAGAGGTTAA
8219 CAAAATTTCATAG
1 CAAAATTTCATAG
8232 GGAGGGAGGT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (44 bp):
CAAAATTTCATAGTGTAGTGACCAAAATTTCATACAGAGGTTAA
Found at i:8236 original size:22 final size:22
Alignment explanation
Indices: 8107--8344 Score: 100
Period size: 22 Copynumber: 10.9 Consensus size: 22
8097 TGACAATCAA
* *
8107 ACCAAAATTACATAGA-ACGATT
1 ACCAAAATTTCATAGAGA-GGTT
* ** * *
8129 ATCAAAATTTTGTAGTGTGGTT
1 ACCAAAATTTCATAGAGAGGTT
*
8151 ACCAAAATTTCATATAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* * * *
8173 AACAAAACTTCATAGTGTA-GTG
1 ACCAAAATTTCATAGAG-AGGTT
* *
8195 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
8217 ACCAAAATTTCATAGGGAGGGAGGTT
1 ACCAAAATTTCATA--GA--GAGGTT
* *
8243 ACCAAAA-TT--T---GTGCTT
1 ACCAAAATTTCATAGAGAGGTT
* *
8259 ATCAAAATTTCCTAGAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* *
8281 AGCAAAATTTTATA-AGGAGGTT
1 ACCAAAATTTCATAGA-GAGGTT
** * *
8303 ATGAAAATTTTATGGAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* *
8325 ATCGAAAA-TACATAGAGAGG
1 A-CCAAAATTTCATAGAGAGG
8345 ATATCACAGT
Statistics
Matches: 160, Mismatches: 40, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
19 1 0.01
21 2 0.01
22 121 0.76
23 8 0.05
24 1 0.01
25 2 0.01
26 13 0.08
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (22 bp):
ACCAAAATTTCATAGAGAGGTT
Found at i:8515 original size:22 final size:22
Alignment explanation
Indices: 8362--8605 Score: 135
Period size: 22 Copynumber: 11.1 Consensus size: 22
8352 AGTTTCATTC
* *
8362 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGTGGTTATCGAAATT
* * *
8384 TCATGGTTTGGTTATCAAAATTT
1 TCATAGTGTGGTTATCGAAA-TT
*
8407 TCATAGTGCGGTTATC--AATT
1 TCATAGTGTGGTTATCGAAATT
* * **
8427 TTATTTAGTGTGATTATTAAAATT
1 TCA--TAGTGTGGTTATCGAAATT
* * * *
8451 TTATAG-GCAGATTATCAAAATT
1 TCATAGTG-TGGTTATCGAAATT
* * * *
8473 TCACACTGAGATTATCGAAATT
1 TCATAGTGTGGTTATCGAAATT
* *
8495 TCATAGTGTGGTTACCCAAATT
1 TCATAGTGTGGTTATCGAAATT
* *
8517 TCACAGTGTGGTTATCGAATTT
1 TCATAGTGTGGTTATCGAAATT
*
8539 TCATA-TGAAGGTTATCGAAATT
1 TCATAGTG-TGGTTATCGAAATT
8561 TCATA-T-TAGGTTATC-AAATT
1 TCATAGTGT-GGTTATCGAAATT
* *
8581 TGCAAAATGTGGTTATC-AATATT
1 T-CATAGTGTGGTTATCGAA-ATT
8604 TC
1 TC
8606 TACATTGGAG
Statistics
Matches: 176, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.06
21 15 0.09
22 123 0.70
23 21 0.12
24 7 0.04
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (22 bp):
TCATAGTGTGGTTATCGAAATT
Found at i:9021 original size:168 final size:169
Alignment explanation
Indices: 8738--9048 Score: 398
Period size: 168 Copynumber: 1.8 Consensus size: 169
8728 AGTTTTCTAA
*
8738 AAAGCCTAAAACCTCAACTTCCTGATTTAGCACGTTTGAGCGCCAAACGTTGTTCTTAGGAAAAT
1 AAAGCCTAAAACCTAAACTTCCTGATTTAGCACGTTTGAGCGCCAAACGTTGTTCTTAGGAAAAT
* * * *
8803 GCTCATTCCAAGTACATTATTTGTGAAACCAACGCTCAAATGTTATGTTTCAGAGTGAGTA-AGC
66 GCTAATTCCAAGTACATTATTTGTGAAACCAACGCTCAAATGTCATGTTTCAGAGTCAATAGAGC
8867 TAATTGGAAAGTGGGTTTGCTGAAAAAAAAACTTTCTTC
131 TAATTGGAAAGTGGGTTTGCTGAAAAAAAAACTTTCTTC
* * ** *
8906 AAAGCCTAAAACTTAAACTTCAC-GATTTTGCGTGTTTGTGCG-CAGAACGTTGTTCTT-GAGAA
1 AAAGCCTAAAACCTAAACTTC-CTGATTTAGCACGTTTGAGCGCCA-AACGTTGTTCTTAG-GAA
* * * * * *
8968 AATGTTAATTCCGAA-TGCATTATTTGTGTAACCATCGTTCATATGTCATGTTTCAGAGTCAATA
63 AATGCTAATTCC-AAGTACATTATTTGTGAAACCAACGCTCAAATGTCATGTTTCAGAGTCAATA
*
9032 GAGCTCATTGGAAAGTG
127 GAGCTAATTGGAAAGTG
9049 ACTTGCCAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
167 3 0.02
168 100 0.83
169 18 0.15
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (169 bp):
AAAGCCTAAAACCTAAACTTCCTGATTTAGCACGTTTGAGCGCCAAACGTTGTTCTTAGGAAAAT
GCTAATTCCAAGTACATTATTTGTGAAACCAACGCTCAAATGTCATGTTTCAGAGTCAATAGAGC
TAATTGGAAAGTGGGTTTGCTGAAAAAAAAACTTTCTTC
Found at i:10365 original size:22 final size:22
Alignment explanation
Indices: 10324--10866 Score: 159
Period size: 22 Copynumber: 24.4 Consensus size: 22
10314 ACAATCAAAC
* *
10324 CAAAATTACATAGTAAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
10346 TAAAATTTCATAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
10368 CAAAATTTCATA-TGGAGGTTAT
1 CAAAATTTCATAGT-GAGGTTAT
* *
10390 CAAAACTTCATAGTGTA-ATTAT
1 CAAAATTTCATAGTG-AGGTTAT
** *
10412 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
***
10434 CAAAATTTCATAAAAAAAAAGGTTAT
1 CAAAATTTCAT----AGTGAGGTTAT
* * *
10460 CAAAATCTCTTA-TGGAGATTAT
1 CAAAATTTCATAGT-GAGGTTAT
*
10482 CAAAATTTCATACG-AAGGTTAT
1 CAAAATTTCATA-GTGAGGTTAT
** * * *
10504 TGAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
10526 CAAAATTAATCA-A--AACGTTAT
1 CAAAATT--TCATAGTGAGGTTAT
* ***
10547 CAAGA--T--T-G-GTTCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
10563 CAAAATTTCCTAG-GATGGTTAA
1 CAAAATTTCATAGTGA-GGTTAT
* *
10585 CAAAATTTCATAGGGAGCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
10607 GAAAATATT-ATGGAGAGGTTAT
1 CAAAAT-TTCATAGTGAGGTTAT
* **
10629 CAAAATTACATA-TAGAGAATAT
1 CAAAATTTCATAGT-GAGGTTAT
* * *
10651 CACAATTTCATTCTTATAGGGAAGTTAT
1 CA-AA----ATT-TCATAGTGAGGTTAT
* * *
10679 CGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
10701 CAAAATTTTCATAGTGCGATTA-
1 CAAAA-TTTCATAGTGAGGTTAT
* * * ***
10723 C-CAATTTTATAATGTTATTAT
1 CAAAATTTCATAGTGAGGTTAT
10744 CAAAATTTCATAGACAATGAGGTTAT
1 CAAAATTTCATAG----TGAGGTTAT
* * *
10770 CAAAACTTCATTGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
10792 CAGAATTTCACAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
10814 CAAATTTTCATAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
10836 CGAAATTTCACAATGAGATTAT
1 CAAAATTTCATAGTGAGGTTAT
*
10858 CAAATTTTC
1 CAAAATTTC
10867 GCGGTGTGGT
Statistics
Matches: 371, Mismatches: 110, Indels: 80
0.66 0.20 0.14
Matches are distributed among these distances:
16 8 0.02
17 1 0.00
18 1 0.00
20 13 0.04
21 17 0.05
22 256 0.69
23 25 0.07
24 2 0.01
26 34 0.09
27 5 0.01
28 9 0.02
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAT
Found at i:10824 original size:44 final size:45
Alignment explanation
Indices: 10757--10881 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 45
10747 AATTTCATAG
** *
10757 ACAATGAGGTTATCAAAACTTCATTGTGTGGTTATCAG-AATTTC
1 ACAATGAGGTTATCAAATTTTCATAGTGTGGTTATCAGAAATTTC
* * * *
10801 ACAGTGTGGTTATCAAATTTTCATAGGGAGGTTATC-GAAATTTC
1 ACAATGAGGTTATCAAATTTTCATAGTGTGGTTATCAGAAATTTC
* ***
10845 ACAATGAGATTATCAAATTTTCGCGGTGTGGTTATCA
1 ACAATGAGGTTATCAAATTTTCATAGTGTGGTTATCA
10882 ATATTTCTAC
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
43 1 0.02
44 63 0.98
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (45 bp):
ACAATGAGGTTATCAAATTTTCATAGTGTGGTTATCAGAAATTTC
Found at i:10879 original size:22 final size:22
Alignment explanation
Indices: 10764--10887 Score: 99
Period size: 22 Copynumber: 5.6 Consensus size: 22
10754 TAGACAATGA
** **
10764 GGTTATCAAAACTTCATTGTGT
1 GGTTATCAAATTTTCACAGTGT
10786 GGTTATCAGAA-TTTCACAGTGT
1 GGTTATCA-AATTTTCACAGTGT
* * *
10808 GGTTATCAAATTTTCATAGGGA
1 GGTTATCAAATTTTCACAGTGT
* *
10830 GGTTATCGAAA-TTTCACAATGA
1 GGTTATC-AAATTTTCACAGTGT
* * *
10852 GATTATCAAATTTTCGCGGTGT
1 GGTTATCAAATTTTCACAGTGT
10874 GGTTATCAATATTT
1 GGTTATCAA-ATTT
10888 CTACGTTGGA
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
21 5 0.06
22 68 0.83
23 9 0.11
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (22 bp):
GGTTATCAAATTTTCACAGTGT
Done.