Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020831.1 Corchorus olitorius cultivar O-4 contig20864, 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: 100386
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:758 original size:319 final size:318
Alignment explanation
Indices: 2--1435 Score: 1826
Period size: 319 Copynumber: 4.5 Consensus size: 318
1 A
* *
2 AAAAAATTGAAGCGTTTTTCACGT-TTCTAATATCGTTTTTCCATTTTTTTTCAAATTTATATCT
1 AAAAAATTGAAGCGCTTTTCAC-TCTTCTAATATCGTTTTTCCA-TTTTTTTCGAATTTATATCT
* * *
66 AATTAT-TACGAAACAAGACTCAGATGCTCGTAAAAACAAATTCGTAAATCCATTGCGGCTGAGA
64 AATTATAT-CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGA
* * * *
130 TTGGGTTCGATTAATATAGATATTTGAAGGAGTCTTTCTGCCAAAAATTATGGAAAACTCAGCCG
128 TTTGGTTCGATTAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTCAGCC-
* *
195 GGGCCCCGAAACGCCTTTTTA-ACAAAAACCGTGATGGTAAGTACACAATTTC-GCT-AAAACTG
192 GGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGGCTAAAAACTG
* * *
257 ACCCGGAAATTTTTTTCTAAATTTTTTTCCACAATACTCAGAAAAAATATATAATTTGTAACC
257 ACCCGAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTGT-GCC
* * * * *
320 AAAAAATTGAAG-GGTTTTTACGCTTCTAATATCGTTTTACCATTTTTTTCCTAATTTATATCTA
1 AAAAAATTGAAGCGCTTTTCACTCTTCTAATATCGTTTTTCCATTTTTTT-CGAATTTATATCTA
* * * *
384 ATTATATCGAAACAACATTCAGATGCTTGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGGTT
65 ATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATT
* * * * * * *
449 TGGTTTGATGAATATAGACATTTCAGGGAGTGTTTCTGCGAAAAATTATGCAAAACTCAGTCCGG
130 TGGTTCGATTAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTCAG-CCGG
* * * *
514 GCCCCGAAACACATTTTTAGCCCAAAACCGTGATGGTAAGTACACGATTTCGGCTAAAAACTGAC
194 GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGGCTAAAAACTGAC
** * * *
579 CCGAAAATTTTTTTCTCTATTGTTTGGCACAATACTCGGAAAAAATATATAATTTTGTGCC
259 CCGAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAA-TTTGTGCC
* * * * * *
640 AAAAAATTCAAGAGCTTTTCACTCTTATAAAATCATTTTTCCATTTTTTT-GAATTTATTTCTAA
1 AAAAAATTGAAGCGCTTTTCACTCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATATCTAA
* * *
704 TTATATCGAAACAAGATTCAGATGCTCGTCAAAACAAATCCGTAAATTCATTGTGGTTGAGATTT
66 TTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTT
* *
769 AGTTCGATTAATATAGATATTTCAAGGAGTCTTTCTTCCAAAAATCATGCAAAACTCAGCCGGAG
131 GGTTCGATTAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTCAGCCGG-G
* * * *
834 CCCCGAAACGTGTTTTTAGCCAAAAACCGTGATAGTAAGTACACGATTTCGGCTAAAAACTGACT
195 CCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGGCTAAAAACTGACC
* * * *
899 CGAAAA-TTTTTTCTCAATTTTTTGGCACATTACTCGGAAAAAATATATAATTTGATGCC
260 CGAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTG-TGCC
* * *
958 AAAAAAATTGAAGCGCTTCTCACGCTTTTAATATCGTTTTTCCATTTTTTTCGAATTTATATCTA
1 -AAAAAATTGAAGCGCTTTTCACTCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATATCTA
* *
1023 ATTATAACGAAACAAGATTCAGATGCTCGTAAAAACAAATCTGTAAATCCATTGTGGCTGAGATT
65 ATTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATT
* ** *
1088 TAGTTCGATTAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGGGAAACTCAGTCGGG
130 TGGTTCGATTAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTCAGCCGGG
* * *
1153 GCCCGAAATGCGTTTTTAGCCAAAAACCGTGACGGTAAGTACACAATTTCGGCTAAAAACTGACC
195 CCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGGCTAAAAACTGACC
* * * * * **
1218 TGAAAAATTTTTTCTAAATTTTTTACCACAATACTTAGAAAACATATATAATTTAAAGCC
260 CGAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTT-GTGCC
* * * * ** * * *
1278 AGAAAAATGGAAGGGTTTTTCACGAC-TCTTCTATCATTTTACCATTTTTTTTCCGAATTTATTT
1 A-AAAAATTGAAGCGCTTTTCAC-TCTTCTAATATCGTTTTTCCA-TTTTTTT-CGAATTTATAT
* *
1342 CTAATTATATCGAAACAAAATTCA-ATTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
62 CTAATTATATCGAAACAAGATTCAGA-TGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGA
* * *
1406 GATTTGGTTTGATAAATATTGATATTTCAA
126 GATTTGGTTCGATTAATATAGATATTTCAA
1436 TAAAAATATA
Statistics
Matches: 974, Mismatches: 122, Indels: 36
0.86 0.11 0.03
Matches are distributed among these distances:
316 7 0.01
317 168 0.17
318 92 0.09
319 297 0.30
320 272 0.28
321 44 0.05
322 94 0.10
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (318 bp):
AAAAAATTGAAGCGCTTTTCACTCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATATCTAA
TTATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCGTAAATCCATTGTGGCTGAGATTT
GGTTCGATTAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTCAGCCGGGC
CCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACAATTTCGGCTAAAAACTGACCC
GAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTTGTGCC
Found at i:14535 original size:4 final size:4
Alignment explanation
Indices: 14526--14562 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
14516 ACTTCTTTTC
*
14526 CTTT CTTT CTTT CTTT CTTT CCTT CTTT ACTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT
14563 TTTTTGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:17566 original size:2 final size:2
Alignment explanation
Indices: 17561--17610 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
17551 AGTTATGCGA
* * *
17561 AT AT AT AT AT AT AT AT AT AT ACT -T AT AA AG A- AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
17602 AT AT AT AT A
1 AT AT AT AT A
17611 ATAATTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.93
3 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:38440 original size:22 final size:21
Alignment explanation
Indices: 38411--38454 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
38401 CTCACTGTAA
*
38411 GAGAAACT-TCTTAGAGTTCTT
1 GAGAAACTGTCTTA-AGATCTT
38432 GAGATAACTGTCTTAAGATCTT
1 GAGA-AACTGTCTTAAGATCTT
38454 G
1 G
38455 TGGTTGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (21 bp):
GAGAAACTGTCTTAAGATCTT
Found at i:48523 original size:23 final size:23
Alignment explanation
Indices: 48493--48544 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
48483 ATTTTGAGTG
*
48493 ATTTCTCTAACACTTTATCTTTT
1 ATTTCTCTAACAATTTATCTTTT
48516 ATTTCTCTAACAATTTATCTTTT
1 ATTTCTCTAACAATTTATCTTTT
48539 ATTTCT
1 ATTTCT
48545 TGGTTAGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTCTCTAACAATTTATCTTTT
Found at i:65349 original size:17 final size:17
Alignment explanation
Indices: 65327--65366 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
65317 GTTGAAATTA
65327 CTATATCTTAGTCTCTT
1 CTATATCTTAGTCTCTT
65344 CTATATC-TAGTCTCTT
1 CTATATCTTAGTCTCTT
65360 CT-TATCT
1 CTATATCT
65367 CGAGCCGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 11 0.50
17 7 0.32
ACGTcount: A:0.17, C:0.25, G:0.05, T:0.53
Consensus pattern (17 bp):
CTATATCTTAGTCTCTT
Found at i:69358 original size:21 final size:19
Alignment explanation
Indices: 69334--69391 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
69324 GCTGCTCTAA
*
69334 TAATTTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
69355 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
69374 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
69392 TGTTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:82415 original size:9 final size:8
Alignment explanation
Indices: 82397--82433 Score: 51
Period size: 7 Copynumber: 4.8 Consensus size: 8
82387 CATATATGAC
82397 CTTTTTTT
1 CTTTTTTT
82405 CTTTCTTTT
1 CTTT-TTTT
82414 CTTTTTTT
1 CTTTTTTT
82422 -TTTTTTT
1 CTTTTTTT
82429 -TTTTT
1 CTTTTT
82434 AAGAAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 12 0.43
8 8 0.29
9 8 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
CTTTTTTT
Found at i:97139 original size:87 final size:89
Alignment explanation
Indices: 96968--97163 Score: 270
Period size: 87 Copynumber: 2.2 Consensus size: 89
96958 GACATGACAT
* * * * *
96968 AGAATAAAATTAAACATCATGTTCATGATCACGTGGCTGAATTCGACAAATTTAGCTGACATTGT
1 AGAATAAAATTAAACATTATGCTCATGATCAC-TGACTGAATTCGACAAACTTAGCTGACATTAT
* *
97033 TGGCATCTTATGTAAAAAGAAAAAG
65 TGACATCTTATATAAAAAGAAAAAG
* *
97058 AGAATAAAATTAAACATTATGCTCATGA-CA-TGACTGAATTCGATAAACTTAGTTGACATTATT
1 AGAATAAAATTAAACATTATGCTCATGATCACTGACTGAATTCGACAAACTTAGCTGACATTATT
* *
97121 GACATCTTATATATAAAGAAAGAG
66 GACATCTTATATAAAAAGAAAAAG
97145 AGAATAAAATTAAACATTA
1 AGAATAAAATTAAACATTA
97164 ACTATTCACT
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
87 67 0.71
89 2 0.02
90 26 0.27
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.30
Consensus pattern (89 bp):
AGAATAAAATTAAACATTATGCTCATGATCACTGACTGAATTCGACAAACTTAGCTGACATTATT
GACATCTTATATAAAAAGAAAAAG
Found at i:98923 original size:18 final size:17
Alignment explanation
Indices: 98878--98914 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
98868 AAAGATTGGG
98878 AAAG-AAAGAAGAAGCA
1 AAAGAAAAGAAGAAGCA
98894 AAAGAAGAAGAAGAAG-A
1 AAAGAA-AAGAAGAAGCA
98911 AAAG
1 AAAG
98915 GTAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAGAAGCA
Found at i:100355 original size:2 final size:2
Alignment explanation
Indices: 100348--100382 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
100338 TTGGACTTCA
100348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
100383 GTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.