Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009055.1 Corchorus capsularis cultivar CVL-1 contig09076, 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: 27736
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:4229 original size:28 final size:28
Alignment explanation
Indices: 4189--4250 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
4179 AGTTAAAGGT
* *
4189 TTTTGTAATTTTGGCTAGTTGCGGCAAA
1 TTTTGGAATTTTGGCTACTTGCGGCAAA
* *
4217 TTTTGGAATTTTGGGTACTTGCGGCAAT
1 TTTTGGAATTTTGGCTACTTGCGGCAAA
4245 TTTTGG
1 TTTTGG
4251 GTTGCTGCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.18, C:0.10, G:0.27, T:0.45
Consensus pattern (28 bp):
TTTTGGAATTTTGGCTACTTGCGGCAAA
Found at i:7715 original size:31 final size:31
Alignment explanation
Indices: 7680--7767 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 31
7670 TATCACATTA
*
7680 TTAGGGGTTAAATGTCTTGAATTTGAGAAGT
1 TTAGGGGTTAAATGTCTTGAATTTGAGAAAT
** * *
7711 TTAGGAAATTAATTGTCTTAAATTTG-GAAAT
1 TTAGG-GGTTAAATGTCTTGAATTTGAGAAAT
*
7742 TTAGAGGG-TAAATTGTCGTG-ATTTGA
1 TTAG-GGGTTAAA-TGTCTTGAATTTGA
7768 AGTCTAGGGA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
30 8 0.19
31 18 0.42
32 17 0.40
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.40
Consensus pattern (31 bp):
TTAGGGGTTAAATGTCTTGAATTTGAGAAAT
Found at i:8899 original size:2 final size:2
Alignment explanation
Indices: 8892--8918 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8882 TACTATTAAC
8892 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 A
8919 GGAGTTCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10578 original size:5 final size:5
Alignment explanation
Indices: 10568--10603 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
10558 ACAATATTAC
10568 ATAAA ATAAA ATAAA ATAAAA CATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA AT-AAA -ATAAA ATAAA ATAA
10604 TATCTAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 21 0.72
6 6 0.21
7 2 0.07
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:19754 original size:395 final size:389
Alignment explanation
Indices: 18830--19983 Score: 1661
Period size: 390 Copynumber: 2.9 Consensus size: 389
18820 AATTTGATTC
* * * *
18830 TGTTGGGAGATGAACCCGGGACTTGTCAGGGTTCAAGGGCCACCGAGTAGCCCATATACATGTCG
1 TGTTGGGAGAGGAACCCGGGCCTTGTCAGGGTCCAAGGCCCACCGAGTAGCCCATATACATGTCG
*
18895 GACACCAATCATGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGCCA
66 GACACCAATC-CGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGCCA
18960 CTCAAACAACCCATCTCTTTATGATGTGGGATGTTTCCCTCACATGTAAATCCTCAACAATCTCC
130 CTCAAACAACCCATCTCTTTATGATGTGGGATGTTTCCCTCACATGTAAATCCTCAACAATCTCC
*
19025 CCCGATTTACATGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCCGTCAAGTTTTAAGCCAAT
195 CCCGATTTACATGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCCGTCAAGTCTTAAGCCAAT
19090 TACCGGCTATCCAAGACTTAACCCATGGAGTGGTACAAGCTACGAACACTCCACAATCGCACACC
260 TACCGGCTATCCAAGACTTAACCCATGGAGTGGTACAAGCTACGAACACTCCACAATCGCACACC
* *
19155 ACTGGCGGATTGGAGACACCAAGTTCACCGTGCTCATGGGCCACACCGATCAAGCTCAGATACCA
325 ACT-G-GGATTGGACACACCAAGTTCACCGTGCTCATGAGCCACACCGATCAAGCTCAGATACCA
19220 CT
388 CT
* * *
19222 TGATGGGAGAGGAA-CCGGGCCCTGTCAGGGTCCAAGGCCCATCGAGTAGCCCATATACATGTCG
1 TGTTGGGAGAGGAACCCGGGCCTTGTCAGGGTCCAAGGCCCACCGAGTAGCCCATATACATGTCG
19286 GACACCAA-CCTGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGCCA
66 GACACCAATCC-GAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGCCA
* *
19350 CTCAAACAACCCATC-CTTTTATGATGTGAGATGTTT-CCTCACATGTAAATCCTCAACAATNTC
130 CTCAAACAACCCATCTC-TTTATGATGTGGGATGTTTCCCTCACATGTAAATCCTCAACAATCTC
* * *
19413 CCCTGATTTACATAGTGAGT-C-C-TNT-ACCCCCGTGCGG-CCAACCCCCCGTTCAAG-CTTAA
194 CCCCGATTTACAT-GTGAGTCCTCATCTCTCCCCCGTGCGGCCCAA---CCCG-TCAAGTCTTAA
** * * * *
19472 GCC-ATTAAGGGCTATCCAAGACTTAACCCCTGGAGTGGTGCAAGCTACGAAAACTCCACAATTG
254 GCCAATTACCGGCTATCCAAGACTTAACCCATGGAGTGGTACAAGCTACGAACACTCCACAATCG
* * *
19536 CGCACCCCT-GGA-TGGTCACA-CAAGGTTCACCGTGCTCATGAGCCACACTGATCGAGTTCAAC
319 CACACCACTGGGATTGGACACACCAA-GTTCACCGTGCTCATGAGCCACAC----CGA--TC-A-
*
19598 CAGGCTCTGATACCACT
375 -A-GCTCAGATACCACT
* * * * *
19615 TGTTGGAAGAGGAACCCGAGCCTTGTCAGGGTCCGAGGCCCACCGAGCAGCCTATATACATGTCG
1 TGTTGGGAGAGGAACCCGGGCCTTGTCAGGGTCCAAGGCCCACCGAGTAGCCCATATACATGTCG
19680 GACACCAATTCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGCCA
66 GACACCAA-TCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGCCA
19745 CTCAAACAACCCATCTCTTTATGATGTGGGATGTTTCCCTCACATGTAAATCCTCAACAATCTCC
130 CTCAAACAACCCATCTCTTTATGATGTGGGATGTTTCCCTCACATGTAAATCCTCAACAATCTCC
*
19810 CCCGATTTACATGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCCGTGAAGTCTTAAGCCAAT
195 CCCGATTTACATGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCCGTCAAGTCTTAAGCCAAT
19875 TACCGGCTATCCAAGACTTAACCCATGGAGTGGTACAAGCTACGAACACTCCACAATCGCACACC
260 TACCGGCTATCCAAGACTTAACCCATGGAGTGGTACAAGCTACGAACACTCCACAATCGCACACC
* * * * *
19940 TCTGGCGGATTGGAGACACCAAGTTCATCGTCCTCATGGGCCAC
325 ACT-G-GGATTGGACACACCAAGTTCACCGTGCTCATGAGCCAC
19984 TGTAGACACC
Statistics
Matches: 674, Mismatches: 53, Indels: 60
0.86 0.07 0.08
Matches are distributed among these distances:
382 3 0.00
383 29 0.04
384 3 0.00
385 4 0.01
386 11 0.02
387 67 0.10
388 12 0.02
389 47 0.07
390 94 0.14
391 53 0.08
392 13 0.02
393 25 0.04
394 52 0.08
395 92 0.14
396 46 0.07
397 13 0.02
398 64 0.09
399 11 0.02
400 4 0.01
401 3 0.00
402 25 0.04
403 3 0.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (389 bp):
TGTTGGGAGAGGAACCCGGGCCTTGTCAGGGTCCAAGGCCCACCGAGTAGCCCATATACATGTCG
GACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGCCAC
TCAAACAACCCATCTCTTTATGATGTGGGATGTTTCCCTCACATGTAAATCCTCAACAATCTCCC
CCGATTTACATGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCCGTCAAGTCTTAAGCCAATT
ACCGGCTATCCAAGACTTAACCCATGGAGTGGTACAAGCTACGAACACTCCACAATCGCACACCA
CTGGGATTGGACACACCAAGTTCACCGTGCTCATGAGCCACACCGATCAAGCTCAGATACCACT
Found at i:21236 original size:19 final size:17
Alignment explanation
Indices: 21205--21243 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
21195 TTTACTTTTT
21205 TTTTCTTTTTTCTTCCA
1 TTTTCTTTTTTCTTCCA
*
21222 TTTTCTTCTTCTTCTTTCA
1 TTTTCTT-TT-TTCTTCCA
21241 TTT
1 TTT
21244 CCTCCATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTCTTTTTTCTTCCA
Found at i:21447 original size:26 final size:26
Alignment explanation
Indices: 21411--21466 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
21401 ATCAACGAAG
* *
21411 ACAAAAAAATTGCAACACCAGATTCA
1 ACAAAAAAATTACAACACCAAATTCA
* *
21437 ACAACAAAATTACAACATCAAATTCA
1 ACAAAAAAATTACAACACCAAATTCA
21463 ACAA
1 ACAA
21467 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.57, C:0.23, G:0.04, T:0.16
Consensus pattern (26 bp):
ACAAAAAAATTACAACACCAAATTCA
Found at i:22814 original size:16 final size:16
Alignment explanation
Indices: 22793--22831 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
22783 ATGCATGTAT
* *
22793 GAGTCATTTGGGTTTC
1 GAGTCATTCGGATTTC
22809 GAGTCATTCGGATTTC
1 GAGTCATTCGGATTTC
*
22825 GGGTCAT
1 GAGTCAT
22832 CTGGATTACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (16 bp):
GAGTCATTCGGATTTC
Done.