Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011172.1 Corchorus capsularis cultivar CVL-1 contig11193, 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: 23220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:371 original size:82 final size:84
Alignment explanation
Indices: 285--443 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 84
275 TCTATTTTTA
*
285 TTTAATTAAATCTAAT-TCTTTATAACTAATTTATTTTTACCA-TTTTACTATTTTAATTAAAAA
1 TTTAATTAAATCTAATCTCTTTATAACTAATTTATTTTTACCATTTTTACTACTTTAATTAAAAA
348 ACTTAGATATATTAGATTT
66 ACTTAGATATATTAGATTT
* * *
367 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTACTTTAATTACATA
1 TTTAATTAAATCTAATCTCTTTATAACTAATTTATTTTTACCATTTTTACTACTTTAATTAAAAA
432 ACTTAGATATAT
66 ACTTAGATATAT
444 ATTATAATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
82 16 0.23
83 25 0.35
84 30 0.42
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (84 bp):
TTTAATTAAATCTAATCTCTTTATAACTAATTTATTTTTACCATTTTTACTACTTTAATTAAAAA
ACTTAGATATATTAGATTT
Found at i:3379 original size:30 final size:31
Alignment explanation
Indices: 3343--3421 Score: 124
Period size: 30 Copynumber: 2.5 Consensus size: 31
3333 ATTCCCGTAC
3343 AAAAGTCAAACAAAAACTTGTTCAT-AAAAA
1 AAAAGTCAAACAAAAACTTGTTCATAAAAAA
*
3373 ATAAGTCAAACAAAAACTTGTTCATAAAAAAAA
1 AAAAGTCAAACAAAAACTTGTTCAT--AAAAAA
3406 AAAAGTCAAACAAAAA
1 AAAAGTCAAACAAAAA
3422 TTTCAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 24 0.55
33 20 0.45
ACGTcount: A:0.63, C:0.13, G:0.06, T:0.18
Consensus pattern (31 bp):
AAAAGTCAAACAAAAACTTGTTCATAAAAAA
Found at i:3402 original size:15 final size:15
Alignment explanation
Indices: 3354--3403 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3344 AAAGTCAAAC
3354 AAAAACTTGTTCATA
1 AAAAACTTGTTCATA
* *
3369 AAAAA-TAAG-TCAAA
1 AAAAACT-TGTTCATA
3383 CAAAAACTTGTTCATA
1 -AAAAACTTGTTCATA
3399 AAAAA
1 AAAAA
3404 AAAAAAGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
14 5 0.19
15 17 0.63
16 5 0.19
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAACTTGTTCATA
Found at i:4231 original size:33 final size:35
Alignment explanation
Indices: 4194--4260 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
4184 ATTTTAAATA
4194 AATTGTCCTCT-G-ATTCTAATAATAAGAAATTAG
1 AATTGTCCTCTGGAATTCTAATAATAAGAAATTAG
*
4227 AATTGTCCTTTGGAAATTCTAATAATAAGAAATT
1 AATTGTCCTCTGG-AATTCTAATAATAAGAAATT
4261 GTCCTCTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 10 0.33
34 1 0.03
36 19 0.63
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (35 bp):
AATTGTCCTCTGGAATTCTAATAATAAGAAATTAG
Found at i:4718 original size:91 final size:91
Alignment explanation
Indices: 4563--4786 Score: 310
Period size: 91 Copynumber: 2.5 Consensus size: 91
4553 TCTTTGATAA
* * * *
4563 TTTGAAAGAAGAATCCTCCACATACGTGGATCTTCTTTCAATAATTTCCCGATAATTGGGTCTTC
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTC
* *
4628 AGTAGTTCTGCAATAATTG-GATCTTT-
66 AGTAATTCTCCAATAATTGAG-T-TTTC
*
4654 TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAATAA-CTCCCAAATAACTGGGTCTT
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCC-AATAACTGGGTCTT
4718 CAGTAATTCTCCAATAATTGAGTTTTC
65 CAGTAATTCTCCAATAATTGAGTTTTC
* **
4745 TTTGAAAGAAAAATTTTCCACATACGTGGATCTTCTTTCAAT
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAAT
4787 CTTCTTAAGC
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
90 7 0.06
91 111 0.93
92 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (91 bp):
TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTC
AGTAATTCTCCAATAATTGAGTTTTC
Found at i:7957 original size:91 final size:90
Alignment explanation
Indices: 7787--8009 Score: 297
Period size: 91 Copynumber: 2.5 Consensus size: 90
7777 TCTTTGATAA
* * * *
7787 TTTGAAAGAAGAATCCTCCACATATGTGGTTCTTCTTTCAATAATTTCCCAATAATTGGGTCTTC
1 TTTGAAAGAAGAAT-CTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTC
* * *
7852 AGTAGTTTTGCAATAATTG-GATCTTC
65 AGTAATTCTCCAATAATTGAG-TCTTC
*
7878 TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAATAA-CTCCCAAATAACTGGGTCTT
1 TTTGAAAGAAGAAT-CTCCACATACGTGGATCTTCTTTCAATAATCTCCC-AATAACTGGGTCTT
* *
7942 TAGTAATTCTCCAATAATTGAGTCTTT
64 CAGTAATTCTCCAATAATTGAGTCTTC
*
7969 TTTGAAAGAAGAATTTCCACATACGTGGATCTTCTTTCAAT
1 TTTGAAAGAAGAATCTCCACATACGTGGATCTTCTTTCAAT
8010 CTTCTTAAGC
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
90 29 0.25
91 87 0.74
92 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (90 bp):
TTTGAAAGAAGAATCTCCACATACGTGGATCTTCTTTCAATAATCTCCCAATAACTGGGTCTTCA
GTAATTCTCCAATAATTGAGTCTTC
Found at i:11045 original size:22 final size:22
Alignment explanation
Indices: 11012--11066 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
11002 CATGAAAATG
11012 AAATTAC-ATAGTTCATAACAA
1 AAATTACAATAGTTCATAACAA
*
11033 AAATTGCAATAGTTCATAACAA
1 AAATTACAATAGTTCATAACAA
11055 AAATTACAATAG
1 AAATTACAATAG
11067 ATTGAATGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (22 bp):
AAATTACAATAGTTCATAACAA
Found at i:13654 original size:44 final size:44
Alignment explanation
Indices: 13604--13726 Score: 201
Period size: 44 Copynumber: 2.8 Consensus size: 44
13594 CTTCACATCG
13604 CCTTGGTCAAATTGAAAAGCCAACATGGCTTTTTATCACAGCCA
1 CCTTGGTCAAATTGAAAAGCCAACATGGCTTTTTATCACAGCCA
*
13648 CCTTGGTCAAATTGAAAAGCCAACATGCCTTTTTATCACAGCCA
1 CCTTGGTCAAATTGAAAAGCCAACATGGCTTTTTATCACAGCCA
** * *
13692 CCTTGGTCAAATTGAAATCCCGACATGGCCTTTTA
1 CCTTGGTCAAATTGAAAAGCCAACATGGCTTTTTA
13727 AAATTCTCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (44 bp):
CCTTGGTCAAATTGAAAAGCCAACATGGCTTTTTATCACAGCCA
Found at i:14850 original size:6 final size:6
Alignment explanation
Indices: 14839--14920 Score: 100
Period size: 6 Copynumber: 14.3 Consensus size: 6
14829 TGGGTTCTTC
14839 ATGTAT ATGTAT ATGTAT ATGTAT ATG--T ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
* * * *
14885 A--TAT ATATAT ATATAT ATGTAT ATATAT ATATAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
14921 ATATGTGTGT
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
4 8 0.11
6 62 0.89
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:14871 original size:22 final size:22
Alignment explanation
Indices: 14842--14926 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
14832 GTTCTTCATG
* *
14842 TATATGTATATGTATATGTATA
1 TATATATATATATATATGTATA
* * *
14864 TGTATGTATATGTATATGTATA
1 TATATATATATATATATGTATA
14886 TATATATATATATATATGTATA
1 TATATATATATATATATGTATA
14908 TATATATATATATATATGT
1 TATATATATATATATATGT
14927 GTGTGTGTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.51
Consensus pattern (22 bp):
TATATATATATATATATGTATA
Found at i:15308 original size:20 final size:20
Alignment explanation
Indices: 15257--15315 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
15247 AATATATATT
**
15257 TATATTATTAGTAAATTAGTA
1 TATATTATTA-TTTATTAGTA
*
15278 AATA-T-TTATTTATTAGTA
1 TATATTATTATTTATTAGTA
15296 TATATTATTATTTATTAGTA
1 TATATTATTATTTATTAGTA
15316 AAACATATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.34
19 4 0.12
20 14 0.44
21 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
TATATTATTATTTATTAGTA
Found at i:19149 original size:15 final size:15
Alignment explanation
Indices: 19118--19159 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
19108 TTTCATCTAT
19118 ATTT-CATTATTTCAG
1 ATTTACATTA-TTCAG
*
19133 ATTTACATTATTGAG
1 ATTTACATTATTCAG
19148 ATTTACATTATT
1 ATTTACATTATT
19160 AATGTTGCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (15 bp):
ATTTACATTATTCAG
Found at i:20969 original size:18 final size:18
Alignment explanation
Indices: 20946--20980 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20936 CTTGATTGCC
*
20946 ATTAAATTCATTTCCTTG
1 ATTAAATCCATTTCCTTG
*
20964 ATTAAATCCTTTTCCTT
1 ATTAAATCCATTTCCTT
20981 TGGAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.20, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTAAATCCATTTCCTTG
Found at i:22429 original size:15 final size:16
Alignment explanation
Indices: 22402--22446 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
22392 TTAAGAAAGC
22402 AATCTAAACTAAAATA
1 AATCTAAACTAAAATA
* *
22418 AAT-TAAAGTAAATTA
1 AATCTAAACTAAAATA
22433 AATCTAAATCTAAA
1 AATCTAAA-CTAAA
22447 GAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (16 bp):
AATCTAAACTAAAATA
Done.