Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021112.1 Corchorus olitorius cultivar O-4 contig21145, 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: 32970
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:2273 original size:671 final size:650
Alignment explanation
Indices: 903--2375 Score: 1748
Period size: 671 Copynumber: 2.2 Consensus size: 650
893 ACTGAACCGG
* * * **
903 GGCTAAAAGCTGACCA-AAATATTTTTTTCTCATTTTTTTGGTGCAATACTCAG-AAAAATATAT
1 GGCTAAAAACTGACCAGAAA-A-CTTTTTCTCAATTTTTT-GCACAATACTCAGAAAAAATATAT
* * *
966 AATTTAACACCAAAAAGATTGATGGGA-TTTTCACGTTTCTAATATTGTTTTTCCATTTTTTTCT
63 AATTCAACACCAAAAAGATTGAT-GGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCT
* ** *
1030 GAATTAATTTTTAATTAAATCGAAACAAGATTAAGATTCTCATCAAAACAAATCCTTAAATCCAA
127 GAATTAATTTCTAATTAAATCGAAACAAGATTAAGATTCTCAAAAAAACAAATCATTAAATCCAA
* * *
1095 TGTGGGTGGGATTTGGTTCGATAAATATAGATATTTCAAGAAGTCTTTAAGCCAAAAATCATGCA
192 TGTGGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGAAGTCTTTAAGCAAAAAATCATGCA
* *
1160 AAAGTGACCCAGGACCCCGAAACATATTTTTAGCAAAAAACCGTGATGGGTACACGATTTCGGCT
257 AAAGTGACCCAGGACCCCGAAACACATTTTTAGCAAAAAACCGTAATGGGTACACGATTTCGGCT
* * * *
1225 AAAATTTTGCAAAAACTGACTCAGAAAATTTTTTTCTCAATTCTTTGCCACAATATTCAGAAAAG
322 AAAATTTTGCAAAAACTGACTCAGAAAAGTTTTTCCTCAATTCTTTGCCAAAATACTCAGAAAAG
* * *
1290 ATATACAATTCAAACCAAAAAAAAATGAAGGGTTTTTCACGCTTCTAATATCGATTTTCTATTTT
387 ATATACAATTAAAACCAAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGATTTTCCATTTT
* *
1355 TTTCGAATTTATTTCTAATTAAATCGAAACAAGACTCAGATGCTTGTAAAAAACAAATCCTTAAA
452 TTTCGAATTTATTTCTAATAAAATCGAAACAAGACTCAGATGCTCGTAAAAAACAAATCCTTAAA
* * * * * * * *
1420 TCCAAGGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTTTTTTTGCCAGAAATC
517 TCCAAGGTGGCTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTGTATGCCAAAAACC
* * *
1485 ATGCAAAACCGAGTCGGGATCCCGAAACGCGTTTTTAGTCCAAAAACCGTAATCGTAGTACATGA
582 ATGCAAAACCGAGTCGGGACCCCGAAACGCGTTTTTAGTCCAAAAACAGTAATCGTAGTACACGA
1550 TTTC
647 TTTC
*
1554 GGCTAAAAACTGACCAGAAAATTTTTTCTTCTGAATTTTTTGCACAATACTCAGAAAAAATATAT
1 GGCTAAAAACTGACCAGAAAACTTTTTC-TC--AATTTTTTGCACAATACTCAGAAAAAATATAT
* **
1619 AATTCAACACCAAAAAGATTGGTGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCA
63 AATTCAACACCAAAAAGATTGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTG
* * * *
1684 AATTAATTTCTAACTAAATCGAAACAAGATTCTAATGCTTGT-AAAAAAACAAATCATTATATCC
128 AATTAATTTCTAATTAAATCGAAACAAGA-T-TAA-GATTCTCAAAAAAACAAATCATTAAATCC
* * **
1748 AATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATG
190 AATGTGGCTGAGATTTGGTTCGATAAATATAGATATTTCAAGAAGTCTTTAAGCAAAAAATCATG
* ** * * * * * * *
1813 C-AAAGTTGAGCTGGGTCTCCGGAACGCGTTTTTAGCCAAAAATCGTAATGGTTAGTACACGATT
255 CAAAAG-TGACCCAGGACCCCGAAACACATTTTTAGCAAAAAACCGTAATGG---GTACACGATT
* *
1877 TCGGCTAAAATTTTGCAAAAACTGA-TCCGAAAAGTTTTTCCTCAATTTTTTGCCAAAATACTCA
316 TCGGCTAAAATTTTGCAAAAACTGACTCAGAAAAGTTTTTCCTCAATTCTTTGCCAAAATACTCA
* * * *
1941 GAATTAATATATATATATATATATATAATTTAACGCCAAAAAAATTGAAGGGGTTTTCACGCTT-
381 G-----A-A-A-AGATATACA-AT-TAA---AAC-CAAAAAAAAATGAAGGGGTTTTCACGCTTC
* * *
2005 TCAATATCGTTTTTCCATTTTTTTCTGAATTTATTTTTAATAAAATCGAAACAAGATTCAGATGC
432 T-AATATCGATTTTCCATTTTTTTC-GAATTTATTTCTAATAAAATCGAAACAAGACTCAGATGC
* * * * *
2070 TCGT-AAAAACAAATCCTTAAATTCAATGTGGCTTAGATTTGATTACATTAATATTGATATTTCA
495 TCGTAAAAAACAAATCCTTAAATCCAAGGTGGCTGAGATTTGATTACATGAATATAGATATTTCA
* *
2134 AGGAGTCTGTATGCCAAAAACCATGCAAAACTGAGTCGAGG-CCCCGAAACGTGTTTTTAG-CCA
560 AGGAGTCTGTATGCCAAAAACCATGCAAAACCGAGTCG-GGACCCCGAAACGCGTTTTTAGTCC-
* *
2197 AAAAACAGTGATGGTTAGTACACGATTTC
623 AAAAACAGTAATCG-TAGTACACGATTTC
* *
2226 GGCTAAAAACTTA-CACGAAAAACTTTTTCTCAATTTTTTGCCACAATATTCAGAAAAAATATAT
1 GGCTAAAAACTGACCA-G-AAAACTTTTTCTCAATTTTTTG-CACAATACTCAGAAAAAATATAT
* * * *
2290 AATTGC-ACACCAAAAATATTGAAGGATTTTTCACGCTTCTAATATC-ATTTTCCTGTTTATTTT
63 AATT-CAACACCAAAAAGATTGATGGATTTTTCACGCTTCTAATATCGTTTTTCC-ATTT-TTTT
*
2353 ATGAATTAATTTCTAATTAAATC
125 CTGAATTAATTTCTAATTAAATC
2376 TACACGATTC
Statistics
Matches: 697, Mismatches: 87, Indels: 55
0.83 0.10 0.07
Matches are distributed among these distances:
650 7 0.01
651 18 0.03
652 17 0.02
653 99 0.14
654 5 0.01
655 113 0.16
656 4 0.01
657 34 0.05
658 35 0.05
662 1 0.00
663 1 0.00
664 1 0.00
665 7 0.01
666 2 0.00
667 2 0.00
670 21 0.03
671 227 0.33
672 93 0.13
673 10 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (650 bp):
GGCTAAAAACTGACCAGAAAACTTTTTCTCAATTTTTTGCACAATACTCAGAAAAAATATATAAT
TCAACACCAAAAAGATTGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAAT
TAATTTCTAATTAAATCGAAACAAGATTAAGATTCTCAAAAAAACAAATCATTAAATCCAATGTG
GCTGAGATTTGGTTCGATAAATATAGATATTTCAAGAAGTCTTTAAGCAAAAAATCATGCAAAAG
TGACCCAGGACCCCGAAACACATTTTTAGCAAAAAACCGTAATGGGTACACGATTTCGGCTAAAA
TTTTGCAAAAACTGACTCAGAAAAGTTTTTCCTCAATTCTTTGCCAAAATACTCAGAAAAGATAT
ACAATTAAAACCAAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGATTTTCCATTTTTTTC
GAATTTATTTCTAATAAAATCGAAACAAGACTCAGATGCTCGTAAAAAACAAATCCTTAAATCCA
AGGTGGCTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTGTATGCCAAAAACCATGC
AAAACCGAGTCGGGACCCCGAAACGCGTTTTTAGTCCAAAAACAGTAATCGTAGTACACGATTTC
Found at i:2880 original size:14 final size:16
Alignment explanation
Indices: 2840--2880 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2830 TCATTTATAA
2840 ATATAATTATTTAATT
1 ATATAATTATTTAATT
2856 ATATTATATTATTT-A-T
1 ATA-TA-ATTATTTAATT
2872 ATATAATTA
1 ATATAATTA
2881 CGGGCTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.17
15 2 0.09
16 7 0.30
17 3 0.13
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATAATTATTTAATT
Found at i:3804 original size:333 final size:337
Alignment explanation
Indices: 3174--3971 Score: 831
Period size: 333 Copynumber: 2.4 Consensus size: 337
3164 TCGTAAAAGA
* * * *
3174 AAATCCTTAAATCAATATAGCTGAGATTTGGTTAGATGAATATAAATA-TTTCAGGGAGTC-TTG
1 AAATCCTTAAATCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTCAAGGAGTCTTTG
* * * * * * *
3237 GCACCAAAAATCATGCAAAACTTA-GTCG-GGCCCCGGTACGCATTTTTAGCC-GAAAACCGTGA
66 GCACCAAAAATCATGCAAAACTGACCT-GAGGCCCCAGAACGCGTTTTTAACCAAAAAACCGTGA
*
3299 TGGTTAGTTAAATGATTTCGGCTAAAAATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTT
130 TGG-T-GTTAAACGATTTCGGCTAAAAATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTT
* * *
3364 CTAGCGAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAAACTGAAAGCCTTTTTCACG
193 CTAGCCAAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAAAACTGAAAGCCTTTCTCACG
* ** * *
3429 CCTCTAATATTGTTTTTCCTATTTTATTTCCAAATTAATTTTTGA-TTAAAAGGAAACAAGATTT
258 CCTCTAATATTGTTTTTCCAATTTTATTTCCAAATTAATTTTT-ATTTAAAACAAAACAACATTC
* *
3493 AGATACTCATAAAATC
322 AAATACTCATAAAAAC
* * *
3509 AAATCCTTAAATACAATGTGGTTGAGATTTGGTTAGATAAATATAGATATGTTTTAAGGAGTCTT
1 AAATCCTTAAAT-CAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT-TTTCAAGGAGTCTT
*
3574 TGGCGCCAAAAATCATGCAAAACTGACCTGAGGCCCCAGAACGCGTTTTTAACCAAAAAACCGTG
64 TGGCACCAAAAATCATGCAAAACTGACCTGAGGCCCCAGAACGCGTTTTTAACCAAAAAACCGTG
* * * * * * * *
3639 AT-G-G-TACACGATTTCGGCTGAAATTTTGCAAAAGTTGACGCGAAATATTTTT-TTCAATTTT
129 ATGGTGTTAAACGATTTCGGCTAAAAATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTC
* * * * * * * * * *
3700 TAGCCATATTACTGATAAAATATATATAATTCAAAGGC-AAAAAGATTGAACGGC-TTCTCATGC
194 TAGCCAAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAAAACTGAAAGCCTTTCTCACGC
* * * **
3763 TTCTAATATTGTTTTTCCAAATTTT-TTTTCAAATTAATTTTTATTTAAATCAAAACTTCATTCA
259 CTCTAATATTGTTTTTCC-AATTTTATTTCCAAATTAATTTTTATTTAAAACAAAACAACATTCA
* *
3827 AATGCTCGTAAAAAC
323 AATACTCATAAAAAC
* *
3842 AAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATA-TTTCAATGAGT-TTT
1 AAATCCTTAAAT-CAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTCAAGGAGTCTTT
* * * * * *
3905 -GCAACAAAAAATCATGCAACACTGAACC-GAGTCCCGAAAACGCGTTTTTAGGA-AAAAAAACC
65 GGC-ACCAAAAATCATGCAAAACTG-ACCTGAGGCCCCAGAACGCGTTTTTA--ACCAAAAAACC
3967 GTGAT
126 GTGAT
3972 TTCGACTAAA
Statistics
Matches: 386, Mismatches: 64, Indels: 30
0.80 0.13 0.06
Matches are distributed among these distances:
329 2 0.01
330 40 0.10
331 25 0.06
332 2 0.01
333 109 0.28
334 17 0.04
335 50 0.13
336 72 0.19
337 1 0.00
338 10 0.03
339 26 0.07
340 21 0.05
341 11 0.03
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (337 bp):
AAATCCTTAAATCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTCAAGGAGTCTTTG
GCACCAAAAATCATGCAAAACTGACCTGAGGCCCCAGAACGCGTTTTTAACCAAAAAACCGTGAT
GGTGTTAAACGATTTCGGCTAAAAATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTCTA
GCCAAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAAAACTGAAAGCCTTTCTCACGCCT
CTAATATTGTTTTTCCAATTTTATTTCCAAATTAATTTTTATTTAAAACAAAACAACATTCAAAT
ACTCATAAAAAC
Found at i:4041 original size:51 final size:49
Alignment explanation
Indices: 3986--4085 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 49
3976 ACTAAAATAC
* * *
3986 ACGATTTCGGCTAATATTTTGTAAAAAATTGA-CCAGAAATATTTTTCCTCA
1 ACGATTTCGGCTAAAATTTTGCAAAAAA-TGATCCA-AAA-AATTTTCCTCA
*
4037 ACGATTTTGGCTAAAATTTTGCAAAAAATGATCCAAAAAATTTTCCTCA
1 ACGATTTCGGCTAAAATTTTGCAAAAAATGATCCAAAAAATTTTCCTCA
4086 TTTTTTTTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
49 10 0.23
50 6 0.14
51 28 0.64
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (49 bp):
ACGATTTCGGCTAAAATTTTGCAAAAAATGATCCAAAAAATTTTCCTCA
Found at i:4741 original size:23 final size:24
Alignment explanation
Indices: 4694--4741 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4684 TTTATTTTAA
*
4694 AAAGTTGAATCATCTAAAAAAAAT
1 AAAGTTAAATCATCTAAAAAAAAT
* *
4718 AAAGTTAAATGAT-TAAAAAGAAT
1 AAAGTTAAATCATCTAAAAAAAAT
4741 A
1 A
4742 CTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.25
Consensus pattern (24 bp):
AAAGTTAAATCATCTAAAAAAAAT
Found at i:6437 original size:3 final size:3
Alignment explanation
Indices: 6422--6454 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
6412 ACCTATAAGG
6422 ATT ATT ATAT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT AT
6455 ATAATTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:16765 original size:7 final size:7
Alignment explanation
Indices: 16731--16778 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
16721 CACAATACAA
*
16731 AAAGTTC
1 AAAGTTT
*
16738 AAAGTTC
1 AAAGTTT
*
16745 AAACTTT
1 AAAGTTT
16752 AAAGTTT
1 AAAGTTT
16759 AAAGTTT
1 AAAGTTT
*
16766 GAAGTTT
1 AAAGTTT
*
16773 AGAGTT
1 AAAGTT
16779 GTAACTTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (7 bp):
AAAGTTT
Found at i:19884 original size:14 final size:14
Alignment explanation
Indices: 19862--19891 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19852 CGAATTGACA
19862 AACAAAATAATGAT
1 AACAAAATAATGAT
*
19876 AACAGAATAATGAT
1 AACAAAATAATGAT
19890 AA
1 AA
19892 TAATAAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (14 bp):
AACAAAATAATGAT
Found at i:20242 original size:24 final size:24
Alignment explanation
Indices: 20186--20251 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
20176 AAATTAACCT
**
20186 GAAATACTGGAAATATAAAACTGTG
1 GAAATACTGGAAATATAAAAC-GAA
20211 GAAA-ACTGGAAATATGAAAAC-AA
1 GAAATACTGGAAATAT-AAAACGAA
20234 GAAATACT-GAAATATAAA
1 GAAATACTGGAAATATAAA
20252 GCAATCGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
22 3 0.08
23 11 0.30
24 14 0.38
25 9 0.24
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.20
Consensus pattern (24 bp):
GAAATACTGGAAATATAAAACGAA
Found at i:21363 original size:80 final size:85
Alignment explanation
Indices: 21231--21387 Score: 218
Period size: 80 Copynumber: 1.9 Consensus size: 85
21221 AATTAATTTA
* * * *
21231 AAAAATGGACATGTGTCAACTCTACAAACCGCTTGTGGAGTCTAAAATTTACACCG-CCG-ATGT
1 AAAAATGGACATGTGTCAACTCTACAAACCGCTTGTGGAGTCCAAAAATTACACCGTCAGTATAT
21294 ATCAAATAATTACCCATTCT
66 ATCAAATAATTACCCATTCT
*
21314 AAAAAT-GA-ATGTGTCAACTTCT-C-ACCCGCTTGTGGAGTCCAAAAATTACACCGTCAGTATA
1 AAAAATGGACATGTGTCAAC-TCTACAAACCGCTTGTGGAGTCCAAAAATTACACCGTCAGTATA
21375 TATCAAATAATTA
65 TATCAAATAATTA
21388 ACCTAATTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
80 27 0.41
81 13 0.20
82 20 0.30
83 6 0.09
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (85 bp):
AAAAATGGACATGTGTCAACTCTACAAACCGCTTGTGGAGTCCAAAAATTACACCGTCAGTATAT
ATCAAATAATTACCCATTCT
Found at i:32325 original size:151 final size:154
Alignment explanation
Indices: 32145--32443 Score: 399
Period size: 153 Copynumber: 2.0 Consensus size: 154
32135 TTTTTTTATA
* *
32145 AAATTTAAATACTTATATTTATCCTCTAATTGGT-AGTTTTATTTAAGATTGA-TAGTTTTTATT
1 AAATTTAAATACTTATATTTATCCTCTAATGGGTAAGTTTTATTTAA-AATGAGTAGTTTTTATT
* * * * * * * *
32208 TTGTTTTAAA-TTTTTAAAGACTGGGTTTGTGTATGAGTCAACTCGTGACACAGACTCAGGACTT
65 TTATTTTAAATTTTTTAAAAACTGAGTTTGTCTATAAATCAACTCGTGACACAAACTCAAGACTT
*
32272 GATTTTATAATTAGTATAGATAAAT
130 GACTTTATAATTAGTATAGATAAAT
* *
32297 AAATTTAAATA-TTATATTTATCCTCTAATGGGTAATTTTTATTTAAAATGAGTATTTTTTATTT
1 AAATTTAAATACTTATATTTATCCTCTAATGGGTAAGTTTTATTTAAAATGAGTAGTTTTTATTT
* * * **
32361 TATTTTAAATTTTTTAAAAACTGAGTTTGTCTCTAAATTAACTCGTGAGACAAACTCAAGTTTTG
66 TATTTTAAATTTTTTAAAAACTGAGTTTGTCTATAAATCAACTCGTGACACAAACTCAAGACTTG
32426 ACTTTATAATTAGTATAG
131 ACTTTATAATTAGTATAG
32444 CTAATTGTAC
Statistics
Matches: 126, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
151 25 0.20
152 41 0.33
153 60 0.48
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (154 bp):
AAATTTAAATACTTATATTTATCCTCTAATGGGTAAGTTTTATTTAAAATGAGTAGTTTTTATTT
TATTTTAAATTTTTTAAAAACTGAGTTTGTCTATAAATCAACTCGTGACACAAACTCAAGACTTG
ACTTTATAATTAGTATAGATAAAT
Done.