Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018531.1 Corchorus olitorius cultivar O-4 contig18564, 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: 21235
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:6076 original size:123 final size:118
Alignment explanation
Indices: 5875--6269 Score: 410
Period size: 123 Copynumber: 3.3 Consensus size: 118
5865 TTTTGATCAT
*
5875 TTTCATAATTCATTAAGGTTTAAGTGAATCTCTAATTGAATATGAAA-CTAAGGTTAAGTGACCT
1 TTTCATAATTCATTAAGATTTAAGTGAATCTCTAATTGAAT-TGAAATC-AAGGTTAAGTGACCT
5939 TAAAACTTTAGGTTTAATTAAGTAATTAAAGCCTTTAGTTTAAAAGCTTTTGGCAAGTAA
64 TAAAAC-TTAGGTTTAATTAAGTAATTAAA-CCTTTAGTTTAAAA-CTTTTGG-AAG-AA
* *
5999 TTTCATAATTCATTAAGATTTAAGTGAATC-CTTA-TCAGATTGGAAATCAAGGTTAAGTGACCT
1 TTTCATAATTCATTAAGATTTAAGTGAATCTCTAATTGA-ATT-GAAATCAAGGTTAAGTGACCT
* * * * * *
6062 TAAAACTCTAGGTTTAATTAGGTGATTATACCTATAGTTATTAAA-TTTTGG--GAG
64 TAAAACT-TAGGTTTAATTAAGTAATTAAACCTTTAGTT-TAAAACTTTTGGAAGAA
* *
6116 TTTCATAATTCTTTTAAGATTTAAGTGAATCTCTAATTGAATTTGAAATCAAGGTTAAGTAACC-
1 TTTCATAATTC-ATTAAGATTTAAGTGAATCTCTAATTGAA-TTGAAATCAAGGTTAAGTGACCT
* * *
6180 TAAAACTTAAGGTTTAATTAAGTAATTAAAACCTTTAGTTAATAAACCCTTTGGGAA-AC
64 TAAAACTT-AGGTTTAATTAAGTAATT-AAACCTTTAGTT--TAAA-ACTTTTGGAAGAA
* * *
6239 TTTCATAATTCCTTTAAGATTCAAGTAAATC
1 TTTCATAATT-CATTAAGATTTAAGTGAATC
6270 CTTCAATGAA
Statistics
Matches: 231, Mismatches: 23, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
117 13 0.06
118 42 0.18
119 33 0.14
120 8 0.03
121 6 0.03
122 17 0.07
123 81 0.35
124 31 0.13
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (118 bp):
TTTCATAATTCATTAAGATTTAAGTGAATCTCTAATTGAATTGAAATCAAGGTTAAGTGACCTTA
AAACTTAGGTTTAATTAAGTAATTAAACCTTTAGTTTAAAACTTTTGGAAGAA
Found at i:7449 original size:2 final size:2
Alignment explanation
Indices: 7436--7480 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
7426 TATTCAAATA
7436 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7479 AT
1 AT
7481 GTGTGTATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9515 original size:21 final size:20
Alignment explanation
Indices: 9468--9517 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
9458 TCTTCTAATT
9468 ACAAAAAA-AAAAAAAAGAA
1 ACAAAAAAGAAAAAAAAGAA
*
9487 ACTAAAAAGAATAAAAAA-AA
1 ACAAAAAAGAA-AAAAAAGAA
9507 ACCAAAAAAGA
1 A-CAAAAAAGA
9518 TGAGCAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 7 0.27
20 5 0.19
21 14 0.54
ACGTcount: A:0.82, C:0.08, G:0.06, T:0.04
Consensus pattern (20 bp):
ACAAAAAAGAAAAAAAAGAA
Found at i:10156 original size:42 final size:43
Alignment explanation
Indices: 10110--10199 Score: 110
Period size: 45 Copynumber: 2.1 Consensus size: 43
10100 TATTACCTAA
* * * *
10110 ATTCTACTCC-ATCTCTAGGTCGTTCATTAAAATAAAGTTAAT
1 ATTCTACTCCTATCTCTAGATAGTTCATCAAAAAAAAGTTAAT
*
10152 ATTCTACTCCTTAATCTCTAGATATTTCATCAAAAAAAAGTTAAT
1 ATTCTACTCC-T-ATCTCTAGATAGTTCATCAAAAAAAAGTTAAT
10197 ATT
1 ATT
10200 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 10 0.25
45 30 0.75
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.39
Consensus pattern (43 bp):
ATTCTACTCCTATCTCTAGATAGTTCATCAAAAAAAAGTTAAT
Found at i:11405 original size:42 final size:43
Alignment explanation
Indices: 11354--11447 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
11344 AGTGCATTAC
* *
11354 CTAA-ATTCTA-CTCCATCTCTAGGTGATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
11395 CTAATATTCTACTCCTCCATCTCTATATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
11440 CTAATATT
1 CTAATATT
11448 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:13260 original size:385 final size:380
Alignment explanation
Indices: 12543--13292 Score: 969
Period size: 385 Copynumber: 2.0 Consensus size: 380
12533 ATAATATTTA
*** *
12543 AACTAGATATTATCCCTTTGCATTCGCGTCGGGGTTTTTGGTTTATGATTGGAACTGAGTAATTT
1 AACTAGATATTATCCCCACGCATTCGCGTCGGGGTTTTTGGTTTATGATTGAAACTGAGTAATTT
* * *
12608 TAATTCGAAGTAAAAATTTTATGGTAATAGCAATTAACTTAAATGGAAGGAAATATTCTTAGAAT
66 CAATTCGAAATAAAAATCTTATGGTAATAGCAATTAACTTAAATGGAAGGAAATATTCTTAGAAT
* * *
12673 TCTGATGTGTATTCAAATAATTATGTACTGGAAAAAGGAAATGACGTTTTACTTTGATTATTATT
131 TCTAATGTGTATTCAAATAATTATCTACTGGAAAAAGGAAATGACGTTTTACTTTGATTATAATT
* *
12738 CAATATTCTAAATATTATTTAAAAATATTATTTGGCATTCCAAATATATAGTAATATATATTAAT
196 CAATATTCTAAATATTATTTAAAAATATTATTTGGAATTCCAAATATATAATAATATATATT-AT
* ** * * **
12803 TAGTTTTCTCCGGACCAATCAACGTTGGACAAATGTTAGCATGAGAAGAGTCAAATACTGAGCTT
260 GAGTTTTCTCCCAACCAATCAACGTTGGACAAATGTCAACATGAGAAGAGTCAAATACTGAGCAC
*
12868 ACAGCAGTTT-AGGGATAACTTTAATAGT-AATATAAATAATAAATAATAACTAGAT
325 ACAGCAGTTTGA-GAATAACTTTAATAGTAAATATAAATAATAAATAATAACTAGAT
* *
12923 AACTAGATATTTTCCCCACGCATTCGTGT-GGGGTTTTTCGGTTTATGATTGAAACTGAGTAATT
1 AACTAGATATTATCCCCACGCATTCGCGTCGGGGTTTTT-GGTTTATGATTGAAACTGAGTAATT
* * *
12987 TCAATTCTAAATAAAATTTAATCTTAT-GTAATCGCAATTAAGTTAAATTATGGAAGGAAATATT
65 TCAATTCGAAAT-AAA---AATCTTATGGTAATAGCAATTAACTT-AA--ATGGAAGGAAATATT
* * * *
13051 GTTAGAATTCTAATGTTTATTCAAATAATTATCTGCTGGAAAAAAGGAAATTGA-GTTTTAGTTT
123 CTTAGAATTCTAATGTGTATTCAAATAATTATCTACTGG-AAAAAGGAAA-TGACGTTTTACTTT
* * * *
13115 GATTATAATTCAATGTTCTAACTATTATTTATAAATATTATATTTGGAATTCTAAATATATAATA
186 GATTATAATTCAATATTCTAAATATTATTTAAAAATA-T-TATTTGGAATTCCAAATATATAATA
*
13180 ATATATA-T-TGA-TTTTCTCCCAACCAATCAACGTTGGACAAATGTCAATATGAGAAGAG-CTA
249 ATATATATTATGAGTTTTCTCCCAACCAATCAACGTTGGACAAATGTCAACATGAGAAGAGTC-A
* * *
13241 AATATTTAGCACACAGCAGTTTGAGAATAACTTTAATAGTAAATATATATAA
313 AATACTGAGCACACAGCAGTTTGAGAATAACTTTAATAGTAAATATAAATAA
13293 GGTAAGGTAT
Statistics
Matches: 318, Mismatches: 37, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
379 9 0.03
380 57 0.18
381 3 0.01
383 15 0.05
384 10 0.03
385 76 0.24
386 62 0.19
387 52 0.16
388 5 0.02
389 29 0.09
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (380 bp):
AACTAGATATTATCCCCACGCATTCGCGTCGGGGTTTTTGGTTTATGATTGAAACTGAGTAATTT
CAATTCGAAATAAAAATCTTATGGTAATAGCAATTAACTTAAATGGAAGGAAATATTCTTAGAAT
TCTAATGTGTATTCAAATAATTATCTACTGGAAAAAGGAAATGACGTTTTACTTTGATTATAATT
CAATATTCTAAATATTATTTAAAAATATTATTTGGAATTCCAAATATATAATAATATATATTATG
AGTTTTCTCCCAACCAATCAACGTTGGACAAATGTCAACATGAGAAGAGTCAAATACTGAGCACA
CAGCAGTTTGAGAATAACTTTAATAGTAAATATAAATAATAAATAATAACTAGAT
Found at i:18049 original size:20 final size:22
Alignment explanation
Indices: 18010--18050 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
18000 GCTGGAATGT
*
18010 AAGTTTCTTCTGTTTTTTGTGC
1 AAGTTTCTTCTGTATTTTGTGC
18032 AAGTTT-TT-TGTATTTTGTG
1 AAGTTTCTTCTGTATTTTGTG
18051 GACATTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (22 bp):
AAGTTTCTTCTGTATTTTGTGC
Found at i:21096 original size:25 final size:26
Alignment explanation
Indices: 21061--21110 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
21051 ACACTTAACT
*
21061 TAAAATCCTAATTCTAATAGGAAAAG
1 TAAAATCCTAATCCTAATAGGAAAAG
*
21087 TAAAA-CCTAATCCTACTAGGAAAA
1 TAAAATCCTAATCCTAATAGGAAAA
21111 ACCTTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (26 bp):
TAAAATCCTAATCCTAATAGGAAAAG
Done.