Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013526.1 Corchorus olitorius cultivar O-4 contig13559, 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: 17059
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4569 original size:13 final size:13
Alignment explanation
Indices: 4551--4577 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4541 AAACGGAAAA
4551 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
4564 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
4577 T
1 T
4578 TCAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:5840 original size:42 final size:43
Alignment explanation
Indices: 5789--5882 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
5779 AGTGCATTAT
*
5789 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
5830 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
5875 CTAATATT
1 CTAATATT
5883 ACTTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:6476 original size:20 final size:20
Alignment explanation
Indices: 6427--6467 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6417 TTTTAAAAAA
*
6427 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
6447 TTAAAAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
6467 T
1 T
6468 ATANGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:11539 original size:16 final size:17
Alignment explanation
Indices: 11512--11587 Score: 79
Period size: 16 Copynumber: 4.7 Consensus size: 17
11502 GTCGGGTTGA
11512 TCGGGTTCGGGTCACTT
1 TCGGGTTCGGGTCACTT
* *
11529 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCACTT
*
11545 TCGGGTTCGGGTC-GTT
1 TCGGGTTCGGGTCACTT
* *
11561 T-GGATTCGGGT-AATT
1 TCGGGTTCGGGTCACTT
11576 TCGGGTTCGGGT
1 TCGGGTTCGGGT
11588 ACCCAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.24
16 26 0.53
17 11 0.22
ACGTcount: A:0.07, C:0.14, G:0.39, T:0.39
Consensus pattern (17 bp):
TCGGGTTCGGGTCACTT
Found at i:13471 original size:50 final size:48
Alignment explanation
Indices: 13392--13669 Score: 351
Period size: 50 Copynumber: 5.6 Consensus size: 48
13382 CTTGTTTTGT
* * *
13392 TTCCAAAAATGCCCGTTCCCGGTCAGAAGGTCCAAGATTTACTTTATTTA
1 TTCCAAAAATGCCC-TTTCCGGTCGGAAGGTCCCAG-TTTACTTTATTTA
* * *
13442 TTACAAAAATGCCCTTTCCGGGTTGGAAGGGCCCAGGTTTACTTTATTTA
1 TTCCAAAAATGCCCTTTCC-GGTCGGAAGGTCCCA-GTTTACTTTATTTA
*
13492 TTCCAAAAATGCCCTTTCCTGGTCGGAAGGTCCCAGTTTTGCTTTATTTA
1 TTCCAAAAATGCCCTTTCC-GGTCGGAAGGTCCCAG-TTTACTTTATTTA
* *
13542 TTCCAAAAATGCCCGTTCCCGTTCGGAAGGTCCCAGTTTCACTTTATTTA
1 TTCCAAAAATGCCC-TTTCCGGTCGGAAGGTCCCAGTTT-ACTTTATTTA
* * *
13592 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTCACTTT-
1 TTCCAAAAATG-CCCTTTCCGGTCGGAAGGTCCCAGTTTACTTTA-TTTA
13641 TTCCAAAAATGCCCTTTCCGGTCGGAAGG
1 TTCCAAAAATGCCCTTTCCGGTCGGAAGG
13670 AGCCAGATTT
Statistics
Matches: 203, Mismatches: 18, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
48 17 0.08
49 23 0.11
50 155 0.76
51 8 0.04
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (48 bp):
TTCCAAAAATGCCCTTTCCGGTCGGAAGGTCCCAGTTTACTTTATTTA
Found at i:14353 original size:28 final size:27
Alignment explanation
Indices: 14312--14386 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
14302 TAGGGATATA
* *
14312 AAATTACCGA-TTTACCCTTGGAGTTGAT
1 AAATTACC-ATTTTACCCTTAGAG-GGAT
*
14340 AAATTACCATTTTACCCTTAGAGGGGT
1 AAATTACCATTTTACCCTTAGAGGGAT
*
14367 AAAGTTACAATTTTACCCTT
1 AAA-TTACCATTTTACCCTT
14387 TTAACCTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.15
28 35 0.85
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (27 bp):
AAATTACCATTTTACCCTTAGAGGGAT
Found at i:16165 original size:22 final size:22
Alignment explanation
Indices: 16137--16276 Score: 190
Period size: 22 Copynumber: 6.2 Consensus size: 22
16127 TCGAAAATGT
*
16137 AATTCTTCAATGTTTCAATTTC
1 AATTCTTCAATGCTTCAATTTC
16159 AATTCTTCAATGCTTCAATTTC
1 AATTCTTCAATGCTTCAATTTC
*
16181 AATTCTTCAATTCTTCAATTCTTC
1 AATTCTTCAATGCTTCAA-T-TTC
*
16205 AATTCTTCAATACTTCAATTTC
1 AATTCTTCAATGCTTCAATTTC
*
16227 AATTCTTCAATGCTTCAAATTC
1 AATTCTTCAATGCTTCAATTTC
* *
16249 AATTCTTAAATTCTTCAATACTTC
1 AATTCTTCAATGCTTCAAT--TTC
16273 AATT
1 AATT
16277 TCAATTCCCA
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
22 77 0.73
23 2 0.02
24 27 0.25
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTCTTCAATGCTTCAATTTC
Found at i:16250 original size:68 final size:68
Alignment explanation
Indices: 16137--16276 Score: 235
Period size: 68 Copynumber: 2.1 Consensus size: 68
16127 TCGAAAATGT
** * * *
16137 AATTCTTCAATGTTTCAATTTCAATTCTTCAATGCTTCAATTTCAATTCTTCAATTCTTCAATTC
1 AATTCTTCAATACTTCAATTTCAATTCTTCAATGCTTCAAATTCAATTCTTAAATTCTTCAATAC
16202 TTC
66 TTC
16205 AATTCTTCAATACTTCAATTTCAATTCTTCAATGCTTCAAATTCAATTCTTAAATTCTTCAATAC
1 AATTCTTCAATACTTCAATTTCAATTCTTCAATGCTTCAAATTCAATTCTTAAATTCTTCAATAC
16270 TTC
66 TTC
16273 AATT
1 AATT
16277 TCAATTCCCA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.46
Consensus pattern (68 bp):
AATTCTTCAATACTTCAATTTCAATTCTTCAATGCTTCAAATTCAATTCTTAAATTCTTCAATAC
TTC
Found at i:16282 original size:22 final size:23
Alignment explanation
Indices: 16140--16411 Score: 114
Period size: 22 Copynumber: 12.0 Consensus size: 23
16130 AAAATGTAAT
16140 TCTTCAATGT-TTCAAT--TTCAA
1 TCTTCAAT-TCTTCAATGCTTCAA
*
16161 TTCTTCAATGCTTCAAT--TTCAA
1 -TCTTCAATTCTTCAATGCTTCAA
*
16183 TTCTTCAATTCTTCAATTCTTCAA
1 -TCTTCAATTCTTCAATGCTTCAA
*
16207 TTCTTCAATACTTCAAT--TTCAA
1 -TCTTCAATTCTTCAATGCTTCAA
* *
16229 TTCTTCAATGCTTCAA--ATTCAA
1 -TCTTCAATTCTTCAATGCTTCAA
* *
16251 TTCTTAAATTCTTCAATACTTCAA
1 -TCTTCAATTCTTCAATGCTTCAA
* *
16275 T-TTCAATTC--CCATACTTCAA
1 TCTTCAATTCTTCAATGCTTCAA
* *
16295 TGCTTCAA-T-TTCAATTCTCCAA
1 T-CTTCAATTCTTCAATGCTTCAA
* *
16317 TGCTTCAATT-TAC-ATACTTCAA
1 T-CTTCAATTCTTCAATGCTTCAA
* **
16339 TGCTTCAGTTCTTCAATTATTCAA
1 T-CTTCAATTCTTCAATGCTTCAA
*
16363 TGC-TCTAATTCTTAAAT--TATCTAA
1 T-CTTC-AATTCTTCAATGCT-TC-AA
* *
16387 TGTTTCAATTCTTCAATTCTTCAA
1 T-CTTCAATTCTTCAATGCTTCAA
16411 T
1 T
16412 TATTCAAAGT
Statistics
Matches: 208, Mismatches: 23, Indels: 36
0.78 0.09 0.13
Matches are distributed among these distances:
20 11 0.05
21 1 0.00
22 119 0.57
23 10 0.05
24 62 0.30
25 4 0.02
26 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.45
Consensus pattern (23 bp):
TCTTCAATTCTTCAATGCTTCAA
Found at i:16302 original size:8 final size:8
Alignment explanation
Indices: 16137--16468 Score: 229
Period size: 8 Copynumber: 43.5 Consensus size: 8
16127 TCGAAAATGT
16137 AATTCTTC
1 AATTCTTC
16145 AATGT-TTC
1 AAT-TCTTC
16153 AA-T-TTC
1 AATTCTTC
16159 AATTCTTC
1 AATTCTTC
*
16167 AATGCTTC
1 AATTCTTC
16175 AA-T-TTC
1 AATTCTTC
16181 AATTCTTC
1 AATTCTTC
16189 AATTCTTC
1 AATTCTTC
16197 AATTCTTC
1 AATTCTTC
16205 AATTCTTC
1 AATTCTTC
*
16213 AATACTTC
1 AATTCTTC
16221 AA-T-TTC
1 AATTCTTC
16227 AATTCTTC
1 AATTCTTC
*
16235 AATGCTTC
1 AATTCTTC
*
16243 AA--ATTC
1 AATTCTTC
*
16249 AATTCTTA
1 AATTCTTC
16257 AATTCTTC
1 AATTCTTC
*
16265 AATACTTC
1 AATTCTTC
16273 AA-T-TTC
1 AATTCTTC
16279 AATTC--C
1 AATTCTTC
* *
16285 CATACTTC
1 AATTCTTC
*
16293 AATGCTTC
1 AATTCTTC
16301 AA-T-TTC
1 AATTCTTC
*
16307 AATTCTCC
1 AATTCTTC
*
16315 AATGCTTC
1 AATTCTTC
*
16323 AATT-TAC
1 AATTCTTC
*
16330 -ATACTTC
1 AATTCTTC
*
16337 AATGCTTC
1 AATTCTTC
*
16345 AGTTCTTC
1 AATTCTTC
*
16353 AATTATTC
1 AATTCTTC
*
16361 AATGC-TC
1 AATTCTTC
*
16368 TAATTCTTA
1 -AATTCTTC
*
16377 AATT-ATC
1 AATTCTTC
16384 TAATGT-TTC
1 -AAT-TCTTC
16393 AATTCTTC
1 AATTCTTC
16401 AATTCTTC
1 AATTCTTC
*
16409 AATTATTC
1 AATTCTTC
*
16417 AAAGT-TTC
1 -AATTCTTC
* *
16425 AATTATTA
1 AATTCTTC
*
16433 AATTATTC
1 AATTCTTC
*
16441 AATACTTC
1 AATTCTTC
16449 AATTCTTC
1 AATTCTTC
* *
16457 AGTGCTTC
1 AATTCTTC
16465 AATT
1 AATT
16469 TTTATTTCAA
Statistics
Matches: 253, Mismatches: 47, Indels: 48
0.73 0.14 0.14
Matches are distributed among these distances:
6 37 0.15
7 16 0.06
8 192 0.76
9 8 0.03
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (8 bp):
AATTCTTC
Done.