Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010775.1 Corchorus capsularis cultivar CVL-1 contig10796, 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: 50299
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:15848 original size:2 final size:2
Alignment explanation
Indices: 15841--15871 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15831 ACGAGAAGAT
15841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15872 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22960 original size:146 final size:146
Alignment explanation
Indices: 22687--22960 Score: 361
Period size: 146 Copynumber: 1.9 Consensus size: 146
22677 GACACATCGA
* * ** * *
22687 GTTTATCGATTTGTGAGAATCTGTCGATCAGTAAAGTTGTTTGTCGTATTTAAAATGAATGTATG
1 GTTTATCGATTTGTGACAATCTGCCGATCAGTAAAGCAGTTTGTCATATTTAAAATGAACGTATG
* * * * *
22752 AACCGTTTCAAATGTTAAAAATTTTGATTCTTTCTGACTTTCATTGATTTTCACTATGAAACTGA
66 AACCATTTCAAATGATAAAAATATTGATTCTTTCTGACTTTCATTGAATTTCACTATAAAACTGA
22817 TGTAAAAAGAACTCAT
131 TGTAAAAAGAACTCAT
* * * * *
22833 GTTTGTCGATTTGTGACAATCTGCCGTTCTGTATAGCAGTTTGTCATTTTTAAAATGAACGTATG
1 GTTTATCGATTTGTGACAATCTGCCGATCAGTAAAGCAGTTTGTCATATTTAAAATGAACGTATG
* * *
22898 AACTATTTCAAATGATAAAAATATTGACTT-TTTCTGACTTTCATTGAATTTCATTGTAAAACT
66 AACCATTTCAAATGATAAAAATATTGA-TTCTTTCTGACTTTCATTGAATTTCACTATAAAACT
22961 ATTAAACTGA
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
146 106 0.98
147 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (146 bp):
GTTTATCGATTTGTGACAATCTGCCGATCAGTAAAGCAGTTTGTCATATTTAAAATGAACGTATG
AACCATTTCAAATGATAAAAATATTGATTCTTTCTGACTTTCATTGAATTTCACTATAAAACTGA
TGTAAAAAGAACTCAT
Found at i:23839 original size:2 final size:2
Alignment explanation
Indices: 23832--23857 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23822 TTCAAATGTA
23832 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
23858 GATTCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25960 original size:32 final size:31
Alignment explanation
Indices: 25863--26085 Score: 125
Period size: 26 Copynumber: 7.7 Consensus size: 31
25853 ACTTATGAAT
* *
25863 TGCCTTTGTGTTT-GAGGACTTCTG--AGAGA
1 TGCCTCTGTGTTTAG-GGACTTTTGATAGAGA
25892 TGCCTCTGTGTTTAGGGAC--TT-AT-GA-A
1 TGCCTCTGTGTTTAGGGACTTTTGATAGAGA
25918 TGCC-CATGTGTTT-GAGGACTTTTTGATAGAGA
1 TGCCTC-TGTGTTTAG-GGAC-TTTTGATAGAGA
25950 TGCCTCTGTGTTTAGGGAC--TT-AT-GA-A
1 TGCCTCTGTGTTTAGGGACTTTTGATAGAGA
*
25976 TGCC-CAGGTGTTT-GAGGACTTTTTGATAGAGA
1 TGCCTC-TGTGTTTAG-GGAC-TTTTGATAGAGA
*
26008 TGCATCTGTGTTTAGGGAC--TT-AT-GA-A
1 TGCCTCTGTGTTTAGGGACTTTTGATAGAGA
* *
26034 TGCC-CAGGTGTTT-GAGGACTTTTAATAGAGA
1 TGCCTC-TGTGTTTAG-GGACTTTTGATAGAGA
**
26065 TGTATCTGTGTTTAGGGACTT
1 TGCCTCTGTGTTTAGGGACTT
26086 ATGAATGCCC
Statistics
Matches: 152, Mismatches: 10, Indels: 62
0.68 0.04 0.28
Matches are distributed among these distances:
25 6 0.04
26 45 0.30
27 7 0.05
28 6 0.04
29 26 0.17
30 7 0.05
31 19 0.12
32 32 0.21
33 4 0.03
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.38
Consensus pattern (31 bp):
TGCCTCTGTGTTTAGGGACTTTTGATAGAGA
Found at i:26089 original size:57 final size:57
Alignment explanation
Indices: 25844--26112 Score: 398
Period size: 58 Copynumber: 4.7 Consensus size: 57
25834 AAATTGCCTT
*** * *
25844 TGTTTAGGGACTTATGAATTGCCTTTGTGTTTGAGGACTTCTG--AGAGATGCCTCTG
1 TGTTTAGGGACTTATGAA-TGCCCAGGTGTTTGAGGACTTTTGATAGAGATGCATCTG
* *
25900 TGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAGATGCCTCTG
1 TGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGAC-TTTTGATAGAGATGCATCTG
25958 TGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTGATAGAGATGCATCTG
1 TGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGAC-TTTTGATAGAGATGCATCTG
* *
26016 TGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTAATAGAGATGTATCTG
1 TGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTGATAGAGATGCATCTG
* *
26073 TGTTTAGGGACTTATGAATGCCCTGGTATTTGAGGACTTT
1 TGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTT
26113 AGTTATTGGG
Statistics
Matches: 201, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
55 17 0.08
56 22 0.11
57 56 0.28
58 106 0.53
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (57 bp):
TGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTGATAGAGATGCATCTG
Found at i:27108 original size:309 final size:301
Alignment explanation
Indices: 26336--27803 Score: 993
Period size: 304 Copynumber: 4.8 Consensus size: 301
26326 TGTTCTCCCT
* *
26336 ATTCAATCTACTTTTTTTCTGTGTGCTTTCAAAATTTTCAAATTCACCTTTATAGAATAGAACAC
1 ATTCAATCTACTTTTTTT-T-TATGCTTTCAAAATTTT-AAACTCACCTTTATAGAATAGAACAC
*
26401 ATCTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAGAACGACACATCAAGTTTGTCG
63 ATCTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAAAACGACACATCAAGTTTGTCG
*
26466 ATTTGTGAGAATCTGCCTATCTATAAAGCAGTTTG-CAGTATTTAAAATTAATGCATGAACCGTT
128 ATTTGTGAGAATCTG-CTATCTATAAAGCAGTTTGTC-GTATTTAAAATTAATGTATGAACCGTT
* * * ** * * *
26530 TCAAACGTTAAAATTTTTTTATTTTTTCTGACTTTCATTGAATGTCACTGTGAAATTGGTGTAAA
191 TCAAACGTTAAAATATTTTGATTCTTTCTGACTTTCATTG-ATGAAACTATGAAACTGGTGCAAA
* * ** *
26595 ACATAACTCATGTTTTTGAATTAGCGGTTTTCGTCCCTTTTTTCCTT
255 ACATAACACATGCTTTTGAATTAGAAGTTTTCGTCCCTTTTTTCCTC
* * *
26642 ATTCAATCTACTTTTTTTTTGTGCTTTCAAAATTTTCAAATTCACCTTTATAGAATAGAATACAT
1 ATTCAATCTACTTTTTTTTTATGCTTTCAAAATTTT-AAACTCACCTTTATAGAATAGAACACAT
*
26707 CTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAAAACGACACATCATGTTTGTCGAT
65 CTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAAAACGACACATCAAGTTTGTCGAT
* * * * *
26772 TTTTGAGAATCTGCCGATCTGTAAAGCAGGTTGTCGTATTTAAAATGAATGTATGAACCGTTTCA
130 TTGTGAGAATCTG-CTATCTATAAAGCAGTTTGTCGTATTTAAAATTAATGTATGAACCGTTTCA
26837 AACGTTAAAA-ATTTTGATTCTTTCTGACTTTCATTG-TGAAACTATGAAACTGGTGCAAGAA-A
194 AACGTTAAAATATTTTGATTCTTTCTGACTTTCATTGATGAAACTATGAAACTGGTGCAA-AACA
* * ** *
26899 TAACACATGCTTTTGAGTTAGTAATTTTTTTTCCCCGTTTTTGTTCTCC
258 TAACACATGCTTTTGAATTAG-AAGTTTTCGT-CCC-TTTTT-TCCT-C
* * * *
26948 ATCCTCAATCTACTTTCCTTTTTTTTATGTTTTCAATATTTT-AACTCGCCTTTATAGAATAAAA
1 AT--TCAATCTAC--T--TTTTTTTTATGCTTTCAAAATTTTAAACTCACCTTTATAGAATAGAA
* * * *
27012 GACAT-TTTGCAGTCCTTTTTATTTTTCTCACCAAACTCTGATATAAAACGACATATCAAGTTTG
60 CACATCTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAAAACGACACATCAAGTTTG
* * * * ** * *
27076 TCGATTTGTGAGAACCCGTTAATCTATAAAGCAATTTGTTTTGTTTAAAATTAATGTATGAACCA
125 TCGATTTGTGAGAATCTGCT-ATCTATAAAGCAGTTTGTCGTATTTAAAATTAATGTATGAACCG
*** * **** * * *
27141 TTTCAAATGCAAAAAAAAAAAAAAAAAGATTCTTTCTTACTTTCATTGAATTTCGTTGTTTAATT
189 TTTCAAA--C----GTTAAAATATTTTGATTCTTTCTGACTTTCATTG-A------TG--AAACT
* * * * * *
27206 ACGAAATTAGTGTAATAA-ATAACTCATGCTTTTGAATTACTAGTAA-TTTTCTTCCCTTTTTTT
239 ATGAAACTGGTGCAA-AACATAACACATGCTTTTGAA-T--TAG-AAGTTTTCGTCCC-TTTTTT
27269 CTTCTCCC
298 C--CT--C
* * * * * *
27277 TCTTCAATCTATTTTCTTTTTTTATTTTTATGTTTTCAACATTTTAAACACACCATTATAGAAAA
1 -ATTCAATCTA----C---TTTT-TTTTTATGCTTTCAAAATTTTAAACTCACCTTTATAGAATA
** * * * * *
27342 TG-AGTCATTTTTGCGCTCCTTTTTATTTTTCTCACCAAACTCTGAAACAAAATGACACATCGAG
57 -GAACACATCTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAAAACGACACATCAAG
* * *
27406 TTTGTCGA--T-T--G-----G-----TA-AAA-CAATTTGTCGTATTTAAAATGAAT-TCTTGA
121 TTTGTCGATTTGTGAGAATCTGCTATCTATAAAGCAGTTTGTCGTATTTAAAATTAATGT-ATGA
* * * * * *** *
27453 GCTGTTTCAAACG-TAAAAAATTGTGATTCTTTCTGACTTTCACTGAATTTCACTGTGAAACTGG
185 ACCGTTTCAAACGTTAAAATATTTTGATTCTTTCTGACTTTCATTG-ATGAAACTATGAAACTGG
* * * * * * * * *
27517 TGTAAAACATAACTCGTGTTTTTGAATTAGTAGTTTACTTCCTATTTTGTTCTCCC
249 TGCAAAACATAACACATGCTTTTGAATTAGAAGTTTTCGTCC-CTTTT-TTC-CTC
* * * * * * *
27573 TATTCATTTTACATTTTTTTTTTTTGCTCTCAACATTTTCAAACCCACCTTTATAGAGTAGAACA
1 -ATTCAATCTAC--TTTTTTTTTATGCTTTCAAAATTTT-AAACTCACCTTTATAGAATAGAACA
** * * *
27638 CATCTTTGCACTCCTTTTTATTTTTCTCAATAAACTCTGATACACAACGACACATCGAGTTTGTT
62 CATCTTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAAAACGACACATCAAGTTTGTC
* * * * * * * * * *
27703 GA-TTGTTAGAATCT--AATCTGTAAAGGAATTTGTCATGTTTGAAATGAATATATGAACCGTTT
127 GATTTGTGAGAATCTGCTATCTATAAAGCAGTTTGTCGTATTTAAAATTAATGTATGAACCGTTT
* * ** * *
27765 CAAATGGTAAAA-AAATTGATTCTTTTTTACTTTCATTGA
192 CAAACGTTAAAATATTTTGATTCTTTCTGACTTTCATTGA
27804 ATTTCACTGT
Statistics
Matches: 940, Mismatches: 151, Indels: 144
0.76 0.12 0.12
Matches are distributed among these distances:
290 19 0.02
291 81 0.09
292 2 0.00
293 1 0.00
295 1 0.00
296 9 0.01
297 1 0.00
298 17 0.02
299 3 0.00
300 3 0.00
301 66 0.07
302 7 0.01
303 28 0.03
304 184 0.20
305 58 0.06
306 26 0.03
308 9 0.01
309 140 0.15
310 24 0.03
311 1 0.00
312 21 0.02
314 1 0.00
315 5 0.01
316 52 0.06
317 3 0.00
318 2 0.00
324 3 0.00
326 33 0.04
327 9 0.01
328 16 0.02
329 9 0.01
330 1 0.00
331 4 0.00
332 22 0.02
333 23 0.02
334 56 0.06
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (301 bp):
ATTCAATCTACTTTTTTTTTATGCTTTCAAAATTTTAAACTCACCTTTATAGAATAGAACACATC
TTTGCACTCCTTTTTATTTTTCTCACCAAACTCTGATACAAAACGACACATCAAGTTTGTCGATT
TGTGAGAATCTGCTATCTATAAAGCAGTTTGTCGTATTTAAAATTAATGTATGAACCGTTTCAAA
CGTTAAAATATTTTGATTCTTTCTGACTTTCATTGATGAAACTATGAAACTGGTGCAAAACATAA
CACATGCTTTTGAATTAGAAGTTTTCGTCCCTTTTTTCCTC
Found at i:44593 original size:112 final size:112
Alignment explanation
Indices: 44395--44613 Score: 402
Period size: 112 Copynumber: 2.0 Consensus size: 112
44385 GCAACACAAC
44395 AAGTATACAATACAATTTCCTATGAAAGCCTTCCAAAGGAAACATCATCACTGCATTGTTGAGAA
1 AAGTATACAATACAATTTCCTATGAAAGCCTTCCAAAGGAAACATCATCACTGCATTGTTGAGAA
*
44460 ATGCTAAACAAGTATACAATACAATTTCCTATGTGAAATTTGTATGA
66 ATGCTAAACAAGTATAAAATACAATTTCCTATGTGAAATTTGTATGA
*
44507 AAGTATACAATACAATTTCCTATGAAAGCCTTTCAAAGGAAACATCATCACTGCATTGTTGAGAA
1 AAGTATACAATACAATTTCCTATGAAAGCCTTCCAAAGGAAACATCATCACTGCATTGTTGAGAA
* *
44572 ATGCTAAACAAGTATAAAATACAATTTTCTATGTGAGATTTG
66 ATGCTAAACAAGTATAAAATACAATTTCCTATGTGAAATTTG
44614 CTTTTTCACT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 103 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (112 bp):
AAGTATACAATACAATTTCCTATGAAAGCCTTCCAAAGGAAACATCATCACTGCATTGTTGAGAA
ATGCTAAACAAGTATAAAATACAATTTCCTATGTGAAATTTGTATGA
Found at i:44664 original size:35 final size:33
Alignment explanation
Indices: 44610--44677 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 33
44600 CTATGTGAGA
44610 TTTGCTTTTTCACTCCTCAATCTTGTATGTTAT
1 TTTGCTTTTTCACTCCTCAATCTTGTATGTTAT
* *
44643 TTTGCCTTTTATCACTGCTCAATCTTTTATGTTAT
1 TTTG-CTTTT-TCACTCCTCAATCTTGTATGTTAT
44678 ATTTTTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 4 0.13
34 5 0.16
35 22 0.71
ACGTcount: A:0.16, C:0.21, G:0.09, T:0.54
Consensus pattern (33 bp):
TTTGCTTTTTCACTCCTCAATCTTGTATGTTAT
Done.