Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004913.1 Corchorus capsularis cultivar CVL-1 contig04931, 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: 17262
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:23 original size:5 final size:5
Alignment explanation
Indices: 13--52 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
3 TGATCATATA
13 TATCT TATCT TATCT TA-C- TATCT TATCT TATCT TATCT TA
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TA
53 CTATTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 29 0.88
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (5 bp):
TATCT
Found at i:36 original size:18 final size:18
Alignment explanation
Indices: 13--47 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3 TGATCATATA
13 TATCTTATCTTATCTTAC
1 TATCTTATCTTATCTTAC
31 TATCTTATCTTATCTTA
1 TATCTTATCTTATCTTA
48 TCTTACTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TATCTTATCTTATCTTAC
Found at i:43 original size:23 final size:23
Alignment explanation
Indices: 13--56 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3 TGATCATATA
13 TATCTTATCTTATCTTACTATCT
1 TATCTTATCTTATCTTACTATCT
36 TATCTTATCTTATCTTACTAT
1 TATCTTATCTTATCTTACTAT
57 TATATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (23 bp):
TATCTTATCTTATCTTACTATCT
Found at i:259 original size:19 final size:21
Alignment explanation
Indices: 216--262 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
206 GTAATTAATA
216 ATTTATTTTTCAAAATTATTT
1 ATTTATTTTTCAAAATTATTT
*
237 -TTTATTTTT-AAGA-TATTT
1 ATTTATTTTTCAAAATTATTT
255 ATTTATTT
1 ATTTATTT
263 AATAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTTATTTTTCAAAATTATTT
Found at i:912 original size:23 final size:23
Alignment explanation
Indices: 886--935 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
876 TACTAAAGGT
886 ATTTCTAAAATTTCCCAATTAAG
1 ATTTCTAAAATTTCCCAATTAAG
* * **
909 ATTTTTGAGTTTTCCCAATTAAG
1 ATTTCTAAAATTTCCCAATTAAG
932 ATTT
1 ATTT
936 TTGAGTTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (23 bp):
ATTTCTAAAATTTCCCAATTAAG
Found at i:936 original size:23 final size:23
Alignment explanation
Indices: 896--942 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
886 ATTTCTAAAA
896 TTTCCCAATTAAGATTTTTGAGT
1 TTTCCCAATTAAGATTTTTGAGT
919 TTTCCCAATTAAGATTTTTGAGT
1 TTTCCCAATTAAGATTTTTGAGT
942 T
1 T
943 GTAGTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (23 bp):
TTTCCCAATTAAGATTTTTGAGT
Found at i:957 original size:8 final size:8
Alignment explanation
Indices: 944--969 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
934 TTTTGAGTTG
944 TAGTAAGA
1 TAGTAAGA
952 TAGTAAGA
1 TAGTAAGA
960 TAGTAAGA
1 TAGTAAGA
968 TA
1 TA
970 TGATAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (8 bp):
TAGTAAGA
Found at i:1290 original size:93 final size:93
Alignment explanation
Indices: 1131--1311 Score: 254
Period size: 93 Copynumber: 1.9 Consensus size: 93
1121 AACCTTCAAC
1131 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCATAGATGCCCACCC
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCATAGATGCCCACCC
1196 TCAATTAATTAACTCGTCAAAATGCTCA
66 TCAATTAATTAACTCGTCAAAATGCTCA
* * ** ** * **
1224 TTTCTTAATATTTTGTATGTAATTTTACATGGTGTTCACCCTTATTTGGTCCTAGATGTTCACCC
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCATAGATGCCCACCC
* * *
1289 TCAATTGATTAATTTGTCAAAAT
66 TCAATTAATTAACTCGTCAAAAT
1312 ATCTTTGAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (93 bp):
TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTACATGGTCATAGATGCCCACCC
TCAATTAATTAACTCGTCAAAATGCTCA
Found at i:2635 original size:12 final size:13
Alignment explanation
Indices: 2618--2651 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2608 CGATGAAGTA
2618 AAGGAGGAGG-AG
1 AAGGAGGAGGTAG
2630 AAGGA-GAGGTAG
1 AAGGAGGAGGTAG
2642 AAGGAGGAGG
1 AAGGAGGAGG
2652 GAGAGAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 12 0.60
13 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.03
Consensus pattern (13 bp):
AAGGAGGAGGTAG
Found at i:8154 original size:22 final size:24
Alignment explanation
Indices: 8120--8203 Score: 111
Period size: 24 Copynumber: 3.5 Consensus size: 24
8110 TTTATTAATT
8120 TATATATAATAAAAACATATATAA
1 TATATATAATAAAAACATATATAA
*
8144 TATAT-T-TTAAATAA-ATATATAA
1 TATATATAATAAA-AACATATATAA
8166 TATATATAATAAAAACATATATAA
1 TATATATAATAAAAACATATATAA
8190 TATAATATATATAA
1 TAT-ATATA-ATAA
8204 TATATTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
22 17 0.33
23 6 0.12
24 20 0.38
25 5 0.10
26 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TATATATAATAAAAACATATATAA
Found at i:8169 original size:29 final size:29
Alignment explanation
Indices: 8136--8230 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 29
8126 TAATAAAAAC
8136 ATATATAATATATTTTAAATAAATATATA
1 ATATATAATATATTTTAAATAAATATATA
*** *
8165 ATATAT-ATA-ATAAAAACATATATAATATAA
1 ATATATAATATATTTTAA-ATAAAT-ATAT-A
*
8195 TATATATAATATATTTTAAATACATAT-T-
1 -ATATATAATATATTTTAAATAAATATATA
8223 ATATATAA
1 ATATATAA
8231 AAATATCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
27 12 0.23
28 8 0.15
29 10 0.19
30 2 0.04
31 8 0.15
32 8 0.15
33 4 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATATAATATATTTTAAATAAATATATA
Found at i:8207 original size:36 final size:35
Alignment explanation
Indices: 8153--8230 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
8143 ATATATTTTA
8153 AATA-AATATATAATATATATAATAAAAACATATAT
1 AATATAATATATAATATATATAATAAAAACATAT-T
** *
8188 AATATAATATAT-ATAATATATTTTAAATACATATT
1 AATATAATATATAAT-ATATATAATAAAAACATATT
8223 ATATATAA
1 A-ATATAA
8231 AAATATCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 8 0.22
36 29 0.78
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (35 bp):
AATATAATATATAATATATATAATAAAAACATATT
Found at i:14945 original size:25 final size:26
Alignment explanation
Indices: 14917--14968 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
14907 AAAACAACAA
14917 TCAAGCTCC-GTGCTTTC-AATCTCTT
1 TCAAGC-CCTGTGCTTTCAAATCTCTT
14942 TCAAGCCCTGTGCTTTCAAATCTCTT
1 TCAAGCCCTGTGCTTTCAAATCTCTT
14968 T
1 T
14969 TGTAGATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 2 0.08
25 14 0.56
26 9 0.36
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (26 bp):
TCAAGCCCTGTGCTTTCAAATCTCTT
Found at i:15356 original size:27 final size:27
Alignment explanation
Indices: 15318--15376 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
15308 TTACTACCTC
* *
15318 TGTTCCTTTTTAATTGTTCCTTTCCCT
1 TGTTTCTTTTTAATTGTCCCTTTCCCT
15345 TGTTTCTTTTTAATTGTCCCTTTCCCT
1 TGTTTCTTTTTAATTGTCCCTTTCCCT
15372 TGTTT
1 TGTTT
15377 TCCAGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.07, C:0.24, G:0.08, T:0.61
Consensus pattern (27 bp):
TGTTTCTTTTTAATTGTCCCTTTCCCT
Found at i:15428 original size:24 final size:25
Alignment explanation
Indices: 15396--15442 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
15386 ACCCTTCTTG
15396 AAACATGCATTTAATTA-AAAGATC
1 AAACATGCATTTAATTAGAAAGATC
15420 AAACATGCATTTAATTAGAAAGA
1 AAACATGCATTTAATTAGAAAGA
15443 AGCAATGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (25 bp):
AAACATGCATTTAATTAGAAAGATC
Found at i:16047 original size:15 final size:14
Alignment explanation
Indices: 16022--16051 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
16012 AGAAATATGC
16022 ATGTAACATAATTA
1 ATGTAACATAATTA
16036 ATGTACACATAATTA
1 ATGTA-ACATAATTA
16051 A
1 A
16052 CGTGAGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (14 bp):
ATGTAACATAATTA
Done.