Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013676.1 Corchorus capsularis cultivar CVL-1 contig13697, 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: 13517
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1158 original size:333 final size:328
Alignment explanation
Indices: 9--2983 Score: 2014
Period size: 333 Copynumber: 9.1 Consensus size: 328
1 GAAAAATG
* * **
9 TTTCCTAAATTTTTGGCTAGAATACTCAT--AATATATATATAATTTAACGTGAAAAAGATTGGA
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTTAACGCCAAAAAGATTGGA
** * *
72 ATACTTTTCACGC-TTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAA
66 GGATTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTTTAATTAAATCGAAA
* * * *
136 CAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGCTGATATTTGGTTAGATGAA
131 CAAGATTCAGATGCTCGTAAAAA-AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
** * * * *
201 TACGGATATCTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTT-AGCCGGGGCCCCGAAACG
195 TATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA-TTAAGCCGGGGCCTCGAAACG
* * * * *
265 CGTTTTTAGCCAAAAATCGCGATGAT-TATTACATGATTACGACTAAAATTTTGCAAAAATTGAC
259 CGTTTTTAG-CAAAAAAC-C-ATGATGTATTAC--GATTTCGGCTAAAATTTTGCAAAAAATGAT
*
329 CCAAAAG-TT
319 CCGAAAGATT
* * * * * *
338 ATTTTCTCAATTTTTAGCTATAATACTCATAAAA-AT-TATATTATTCAACGCCAAAAAGATTGA
1 -TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTTAACGCCAAAAAGATTGG
* * * * * *
401 AGGGTTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCCGAATTAATTTTTAATTAAATTG
65 AGGATTTTTCACGCTTTTAATATCGTTTTTCATA-T-TTTTCTGAATTAATTTTTAATTAAATCG
* * * *** * * * **
466 AAACATGATTCAGATGGTAGTTTTACAAATCCTTAAATCTAATGTGTCTGAGATTTGGCTAGATG
128 AAACAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * * *
531 AATATAGATATTTCAAGTAGTTTCGGCGCGAAAAATCATGCAACATTAAACCGGGGCCTCGGAAC
193 AATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTAAGCCGGGGCCTCGAAAC
**** * ** *** * * * * * * *
596 GCGTAAAAATCGTGATTTCGACTAACGTA-CACAATTTCGGCTAATATTTTGCAAAAATTG-TCC
258 GCGTTTTTAGC-AAAAAACCA-TGATGTATTACGATTTCGGCTAAAATTTTGCAAAAAATGATCC
*
659 AGAAATATT
321 -GAAAGATT
* *
668 TTTCCTCAATTTTTGTCTAAAATACTCATAAAATATATA-A-AATTTAACTCCAAAAAGATTGGA
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTTAACGCCAAAAAGATTGGA
* * * * * * * *
731 AGAGTTTTCACCCTTTTAATATCATTTTTCATA-TTCTATAAATTAATTTTTATTTAAATCGAAA
66 GGATTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTTTAATTAAATCGAAA
* * * *
795 CAAGATTAAGATGCTCGTAAAAACAAATCCATAAATGCAAAGTGGCTGAGATTTGATTAGATGAA
131 CAAGATTCAGATGCTCGTAAAAA-AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * * *
860 TATATATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACTT-AGTCGGAGTCC-CGAAAT
195 TATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA-TTAAGCCGG-GGCCTCGAAAC
*
923 GCGTTTTTAGCAAAAAACCATGATGTA-TACGATTTTGGCTAAAATTTTGCAAAAAATGATCCGG
258 GCGTTTTTAGCAAAAAACCATGATGTATTACGATTTCGGCTAAAATTTTGCAAAAAATGATCC-G
987 AAA-ATT
322 AAAGATT
* * * *
993 TTTCCTTAATTTTTGGCTGAAATACTAATGAAATATATATATATATATAATTTAACGCCAAAAAT
1 TTTCCTCAATTTTTGGCTAAAATACTCAT---A-A-A-ATATATATATAATTTAACGCCAAAAAG
* * * **
1058 ATTGGAGGATTTTTCACGCTTTTCATATCATTTTTCATATTTTTCTGAATTAATTTCTGTTTAAA
60 ATTGGAGGATTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTTTAATTAAA
* * * * * *
1123 TCGAAATAAGATTCAGATGCTCGTAAAAAAAATCCATAAATGCAATATTGCTGAGATTTGATTGG
125 TCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAG
* * * * * * * *
1188 ATGAATATGGATATCTGAAGGAGTCTTGGTGCAAAAAATCATGCAAAATTGA-CACGGGGCCTTG
190 ATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTAAGC-CGGGGCCTCG
* * * * *
1252 GAATGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGGTTTCGGCTAAAATTTTGC-AAAAA
254 AAACGCGTTTTTAGCAAAAAACCATGATG--TATT--ACGATTTCGGCTAAAATTTTGCAAAAAA
* * * *
1316 TTAACCTAAAAGATA
315 TGATCC-GAAAGATT
** * *
1331 TTTCCTCAATTTTTGGCTAAAATACTCATAAAA-A-ATATATAATTTAACGATAAAAAGATCGAA
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTTAACGCCAAAAAGATTGGA
* * * *
1394 GGGATTTTTTAAC-CTTCTAATATCGTTTTTCCTACTTTTTCTAAATTAATTTTTAATTAAATCG
66 -GGA-TTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTTTAATTAAATCG
* * * *
1458 AAACAAGATTTAGATGCTCGTAAAATCAATTTCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
128 AAACAAGATTCAGATGCTCGTAAAA-AAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* * ** * * * * * * * *
1523 AAATATAGATATTTCAAGGAGTTTTAGTGCAAAAAATTATGCAAAACTGACCCGGGGCCCCGGAA
192 GAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTAAGCCGGGGCCTCGAAA
* * * * * *
1588 -GTCGTTTTTAGGGAAAAAAACCGTGATGGTA-CACGATTTCGGCTAACATTTTG-TAAAAATTA
257 CG-CGTTTTTA--GCAAAAAACCATGAT-GTATTACGATTTCGGCTAAAATTTTGCAAAAAATGA
* *
1650 ACCCAAA-ATAT
318 TCCGAAAGAT-T
* * * * ** * **
1661 TTTCTCTCAATTTTTAGCCACAATATTCATAAAA-A-ATATATAATTCCATGCCAAAAAGATTTA
1 TTTC-CTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTTAACGCCAAAAAGATTGG
** * * * * * *
1724 AGGGCTTTTGATGCTTTTAATATCATTTTTCCTATTTTTTTCGAATTCAATTTAT-ATTAAATCG
65 AGGATTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GAATT-AATTTTTAATTAAATCG
* * * *
1788 AAACAGGATTCAAATGCTTGT-----AAA-----AAA---AATG-GG--GAGATTTGGTTAGATG
128 AAACAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * * *
1837 AATATAGATATTTCGAGGAGTCTCAGTGGCAAAAATCATGCAAAACTGAA-CC-GGGCCTCTAAA
193 AATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA-TTAAGCCGGGGCCTCGAAA
* ** * * ** *
1900 CGCGTTTTTAGCCAAAAGTCGTGATG-ATTAC--TTCACGG-T----TTCGGC-CAAAA-G-TCG
257 CGCGTTTTTAGCAAAAAACCATGATGTATTACGATT-TCGGCTAAAATTTTGCAAAAAATGATC-
*
1954 TGAAAGA-T
320 CGAAAGATT
* * * * * * * * *
1962 ATTCCTCAATTATTAGCCACAATACTC-TACAAA-AAATATATAATTCAATGACAAAAAGATT-G
1 TTTCCTCAATTTTTGGCTAAAATACTCATA-AAATATATATATAATTTAACGCCAAAAAGATTGG
* * * *
2024 AAGAGCTTTTCACGCTTTTAATA-CAGATTTTCATATTTTTCTGAATTAATTTCTAATTAAATCG
65 AGGA-TTTTTCACGCTTTTAATATC-GTTTTTCATATTTTTCTGAATTAATTTTTAATTAAATCG
* * * *
2088 AAACAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGAT
128 AAACAAGATTCAGATGCTCGTAAAAA-AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* * * * * * * * *
2153 GAATATAGGTATTTCAAGGAGTCCCGACGTCAAAAATCATACAAAAATGAGTCGTGGCCTCG-AA
192 GAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTAAGCCGGGGCCTCGAAA
*** * * * * *
2217 C-CG----T-G-----ATGGAT-A-GTA-CACAATTTCAGCTAAAATTTTGCAGAAAAAAAAGAC
257 CGCGTTTTTAGCAAAAAACCATGATGTATTACGATTTCGGCTAAAATTTTGC---AAAAAATGAT
2268 CCGAAA-ATTTT
319 CCGAAAGA--TT
* * *
2279 TTTCCTCAATTTTTGGATAAAATACTCATAAAAT-TA-ATATAATTTAACCCCAAAAAGATTGTA
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTTAACGCCAAAAAGATTGGA
* * * *
2342 GGACTTTTCACGATTTTAATATCATTTTTCATATTTTTTCTGAATTAGTTTTTAATTAAATCGAA
66 GGATTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTTTAATTAAATCGAA
* * *
2407 ACAAGATTCAAATGCTCG-AAAAAAAAT-CATAAATCCAATGTGGCTGAGATTTGATTAGATAAA
130 ACAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * * * * * * *
2470 TATGGATATCTCAAGGAGTTTTGACGCCAAAAATCATGCAAAATTGAGTCAGGGCC-CCAGAACG
195 TATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTAAGCCGGGGCCTCGA-AACG
* ** * * * *
2534 CGTTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAACTTTTGTAAAAATTGAC
259 CG-TTTTTAGCAAAAAACCATGAT-G-TATT--ACGATTTCGGCTAAAATTTTGCAAAAAATGAT
*
2599 CCGGAAGATAT
319 CCGAAAGAT-T
* * * *
2610 TTT-CTTAATTTTTGGATATAATACTCCTAAAA-A-ATATAT-ATTTCAACGCCAAAAAGATTGG
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTT-AACGCCAAAAAGATTGG
* * * * * * * *
2671 A-GAGCTTTTGA-GGTTTCAAATATCATTTTTCCTATTTTTTCAGAATTAATTTATAATTAAATC
65 AGGA-TTTTTCACGCTTT-TAATATCGTTTTTCATA-TTTTTCTGAATTAATTTTTAATTAAATC
* * * *
2734 GAAACAAGATACAGATGCTCGTAAAAACAAATCATTAAATCCAATATGGCTGAGTTTTGATTAGA
127 GAAACAAGATTCAGATGCTCGTAAAAA-AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGA
* * ** **** * * * *
2799 TTAATATAGATATTTCAAGTAGTCTTAGATTAAAAAATCATGCAAAATTAAGGCGCGTCC-CCAG
191 TGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTAAGCCGGGGCCTCGA-
* * * *
2863 AACGCG-TTTTAGCGAAAAACCGTAATGGTTAGTTAGTACATGATTTCGGCTAAAATTTTACAAA
255 AACGCGTTTTTAGCAAAAAACC---AT-GAT-G-TATTAC--GATTTCGGCTAAAATTTTGCAAA
* *
2927 AATTGA-CACAGAAATATT
312 AAATGATC-C-GAAAGATT
* *
2945 TCTCCTCAATTTTTGCCTAAAATACTCATAAAATATATA
1 TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATA
2984 GTTCAATGCC
Statistics
Matches: 2085, Mismatches: 415, Indels: 282
0.75 0.15 0.10
Matches are distributed among these distances:
299 8 0.00
300 61 0.03
301 58 0.03
302 3 0.00
303 8 0.00
304 3 0.00
305 4 0.00
306 8 0.00
307 3 0.00
308 4 0.00
309 3 0.00
310 15 0.01
311 4 0.00
312 17 0.01
313 57 0.03
314 86 0.04
315 16 0.01
316 60 0.03
317 129 0.06
318 8 0.00
319 3 0.00
321 1 0.00
322 1 0.00
324 2 0.00
325 59 0.03
326 50 0.02
327 87 0.04
328 9 0.00
329 125 0.06
330 259 0.12
331 177 0.08
332 164 0.08
333 374 0.18
334 71 0.03
335 53 0.03
336 31 0.01
337 13 0.01
338 51 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (328 bp):
TTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATATAATTTAACGCCAAAAAGATTGGA
GGATTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTTTAATTAAATCGAAA
CAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
ATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAATTAAGCCGGGGCCTCGAAACGCG
TTTTTAGCAAAAAACCATGATGTATTACGATTTCGGCTAAAATTTTGCAAAAAATGATCCGAAAG
ATT
Found at i:3765 original size:8 final size:8
Alignment explanation
Indices: 3752--3798 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
3742 TTTTATATAG
3752 TAGTAAGA
1 TAGTAAGA
3760 TAGTAAG-
1 TAGTAAGA
3767 -A-TAAGA
1 TAGTAAGA
3773 TAGTAAGA
1 TAGTAAGA
3781 TAGTAAGA
1 TAGTAAGA
3789 TAGTAAGA
1 TAGTAAGA
3797 TA
1 TA
3799 TACGATGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 1 0.03
8 30 0.83
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (8 bp):
TAGTAAGA
Found at i:4370 original size:15 final size:16
Alignment explanation
Indices: 4345--4374 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4335 AAAAAATCAC
4345 TTTCAAATTAGATTAT
1 TTTCAAATTAGATTAT
4361 TTTC-AATTAGATTA
1 TTTCAAATTAGATTA
4375 ATGAGAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
TTTCAAATTAGATTAT
Found at i:6017 original size:24 final size:24
Alignment explanation
Indices: 5981--6031 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
5971 TTATAATTAA
* *
5981 TTTAAATTTATTTAAAACAT-ATTT
1 TTTAAAATAATTTAAAA-ATAATTT
6005 TTTAAAATAATTTAAAAATAATTT
1 TTTAAAATAATTTAAAAATAATTT
6029 TTT
1 TTT
6032 TAGATAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAAAATAATTTAAAAATAATTT
Found at i:9017 original size:43 final size:44
Alignment explanation
Indices: 8956--9042 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 44
8946 TATTAAATGC
8956 CTTTTACCAAAAAATGCCAACATTGCTGTC-AATCAATCAATTA
1 CTTTTACCAAAAAATGCCAACATTGCTGTCGAATCAATCAATTA
8999 CTTTTACCAAAAAATGCCAACATTGCTGTCGAATCAATCAATTA
1 CTTTTACCAAAAAATGCCAACATTGCTGTCGAATCAATCAATTA
9043 TTGCTATTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 30 0.70
44 13 0.30
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (44 bp):
CTTTTACCAAAAAATGCCAACATTGCTGTCGAATCAATCAATTA
Found at i:9808 original size:29 final size:28
Alignment explanation
Indices: 9758--9816 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
9748 ATTATGTGTG
* *
9758 TTTTAATTTTTAAATTTATTTTGAAATAA
1 TTTTAATTATTAAATTTATTTT-AAAAAA
** *
9787 TTTTAATTATTATTTTTGTTTTAAAAAA
1 TTTTAATTATTAAATTTATTTTAAAAAA
9815 TT
1 TT
9817 AAATATGAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTTAATTATTAAATTTATTTTAAAAAA
Done.