Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019016.1 Corchorus olitorius cultivar O-4 contig19049, 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: 32996
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:10626 original size:35 final size:35
Alignment explanation
Indices: 10587--10660 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
10577 ACTTTTGTAA
* *
10587 GCTTTGTTGTTGGTTTGTTGATGGAGACGAACTTT
1 GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
10622 GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
1 GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
10657 GCTT
1 GCTT
10661 CAGATCTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.15, C:0.09, G:0.30, T:0.46
Consensus pattern (35 bp):
GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
Found at i:10671 original size:35 final size:35
Alignment explanation
Indices: 10600--10690 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
10590 TTGTTGTTGG
* * * *
10600 TTTGTTGATGGAGACGAACTTTGCTTTGTTGTTGC
1 TTTGTTGATGGAGAAGAACTTTGCTTAGATGCTGC
10635 TTTGTTGATGGAGAAGAACTTTGCTTCAGAT-CTGC
1 TTTGTTGATGGAGAAGAACTTTGCTT-AGATGCTGC
10670 --T-TTGATGGAGAAGAACTTTGC
1 TTTGTTGATGGAGAAGAACTTTGC
10691 CTTGAATTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
32 20 0.39
33 1 0.02
35 28 0.55
36 2 0.04
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (35 bp):
TTTGTTGATGGAGAAGAACTTTGCTTAGATGCTGC
Found at i:10680 original size:32 final size:32
Alignment explanation
Indices: 10639--10746 Score: 115
Period size: 32 Copynumber: 3.6 Consensus size: 32
10629 TGTTGCTTTG
10639 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
1 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
**
10671 TTGATGGAGAAGAACTTTGC--C---T-TGAA
1 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
* *
10697 TT--TGGAGAAAAACTTTGCTTCAGATCTACT
1 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
*
10727 TTGATGGAGAAGAAATTTGC
1 TTGATGGAGAAGAACTTTGC
10747 CTTGAATTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
24 15 0.25
26 5 0.08
27 1 0.02
29 1 0.02
30 4 0.07
32 34 0.57
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (32 bp):
TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
Found at i:10711 original size:56 final size:56
Alignment explanation
Indices: 10643--10759 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
10633 GCTTTGTTGA
* * *
10643 TGGAGAAGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATT
1 TGGAGAAAAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
10699 TGGAGAAAAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
1 TGGAGAAAAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
10755 TGGAG
1 TGGAG
10760 TGGCTTGAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (56 bp):
TGGAGAAAAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
Found at i:13232 original size:45 final size:46
Alignment explanation
Indices: 13118--13331 Score: 301
Period size: 46 Copynumber: 4.7 Consensus size: 46
13108 CCTTTCAACA
13118 TTGGCGGGGTTGATTATTTATCGCCCTCTACCTCTGCATCGAC-T-
1 TTGGCGGGGTTGATTATTTATCGCCCTCTACCTCTGCATCGACTTC
* * *
13162 TTGACAGGGTTGATTATTTATCGCCCTCTACCTGTGCAT-GACTTC
1 TTGGCGGGGTTGATTATTTATCGCCCTCTACCTCTGCATCGACTTC
*
13207 TTGGCGGGGTTGATTATTTATCGCCCTCTACCTCTGCATCGACTTA
1 TTGGCGGGGTTGATTATTTATCGCCCTCTACCTCTGCATCGACTTC
* * * * *
13253 TTGGCAGGGTTGA-TATTTTGTCACCATCTACCTCTGCATCGGCTTC
1 TTGGCGGGGTTGATTA-TTTATCGCCCTCTACCTCTGCATCGACTTC
*
13299 TTGGCGGGGTTGATTTTTTATCGCCCTCTACCT
1 TTGGCGGGGTTGATTATTTATCGCCCTCTACCT
13332 TTTGCTTCAG
Statistics
Matches: 147, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
43 3 0.02
44 37 0.25
45 38 0.26
46 68 0.46
47 1 0.01
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (46 bp):
TTGGCGGGGTTGATTATTTATCGCCCTCTACCTCTGCATCGACTTC
Found at i:16807 original size:35 final size:35
Alignment explanation
Indices: 16768--16841 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
16758 GCTTTTGTAA
* *
16768 GCTTTGTTGTTGGTTTGTTGATGGAGACGAGCTTT
1 GCTTTGTTGTTGGTTTGTTGATGGAGAAGAACTTT
*
16803 GCTTTGTTGTTGTTTTGTTGATGGAGAAGAACTTT
1 GCTTTGTTGTTGGTTTGTTGATGGAGAAGAACTTT
16838 GCTT
1 GCTT
16842 CAGATCTGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.14, C:0.08, G:0.31, T:0.47
Consensus pattern (35 bp):
GCTTTGTTGTTGGTTTGTTGATGGAGAAGAACTTT
Found at i:16861 original size:32 final size:32
Alignment explanation
Indices: 16820--16927 Score: 124
Period size: 32 Copynumber: 3.6 Consensus size: 32
16810 TGTTGTTTTG
16820 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
1 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
**
16852 TTGATGGAGAAGAACTTTGC--C---T-TGAA
1 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
*
16878 TT--TGGAGAAGAACTTTGCTTCAGATCTACT
1 TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
*
16908 TTGATGGAGAAGAAATTTGC
1 TTGATGGAGAAGAACTTTGC
16928 CTTGAATTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
24 16 0.26
26 5 0.08
27 1 0.02
29 1 0.02
30 4 0.06
32 35 0.56
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (32 bp):
TTGATGGAGAAGAACTTTGCTTCAGATCTGCT
Found at i:16890 original size:56 final size:56
Alignment explanation
Indices: 16824--16941 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 56
16814 GTTTTGTTGA
* *
16824 TGGAGAAGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATT
1 TGGAGAAGAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
16880 TGGAGAAGAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
1 TGGAGAAGAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
16936 TGGAGA
1 TGGAGA
16942 GATTGCTGGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (56 bp):
TGGAGAAGAACTTTGCTTCAGATCTACTTTGATGGAGAAGAAATTTGCCTTGAATT
Found at i:19107 original size:16 final size:18
Alignment explanation
Indices: 19082--19125 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
19072 AGGTCATTTG
19082 GGTTTC-GGTCAATTTT-
1 GGTTTCGGGTCAATTTTC
*
19098 GG-TTCGGGTC-TTTTTC
1 GGTTTCGGGTCAATTTTC
19114 GGTTTCGGGTCA
1 GGTTTCGGGTCA
19126 TATGGTTCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 7 0.30
16 8 0.35
17 8 0.35
ACGTcount: A:0.07, C:0.16, G:0.32, T:0.45
Consensus pattern (18 bp):
GGTTTCGGGTCAATTTTC
Found at i:19863 original size:17 final size:19
Alignment explanation
Indices: 19826--19863 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19816 GGTCTACTAT
*
19826 TTTTAGCCATGTGGAATTG
1 TTTTAGCCACGTGGAATTG
19845 TTTT-GCCACGTGG-ATTG
1 TTTTAGCCACGTGGAATTG
19862 TT
1 TT
19864 GATATGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (19 bp):
TTTTAGCCACGTGGAATTG
Found at i:24972 original size:22 final size:21
Alignment explanation
Indices: 24947--25488 Score: 191
Period size: 22 Copynumber: 25.0 Consensus size: 21
24937 ATTTTTTATG
24947 ACCTCCTTATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
*
24969 ACCTTCCTATGAAATTTTAATAA
1 ACC-TCCTATGAAATTTTGAT-A
** * * ** *
24992 AGATACTATGGAATTTCAAGA
1 ACCTCCTATGAAATTTTGATA
** * **
25013 ACCTTTTTAT-AATTTTTTTTA
1 ACC-TCCTATGAAATTTTGATA
*
25034 ACCT--TATGAAATTTTGTTA
1 ACCTCCTATGAAATTTTGATA
* *
25053 ACCTCCCTAAGGAATTTTGA-A
1 ACCT-CCTATGAAATTTTGATA
25074 GACCTCACTATGAAATTTTGATA
1 -ACCTC-CTATGAAATTTTGATA
* *
25097 ACTTCCCAATGAAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
*
25119 ACCAACACTATG-AATTGTTGATA
1 ACC-TC-CTATGAAATT-TTGATA
25142 ACCT-CTAT-AAGATATATTGATA
1 ACCTCCTATGAA-AT-T-TTGATA
** * * *
25164 ACAACGTTATGGAAA-TTTAAAA
1 ACCTC-CTAT-GAAATTTTGATA
*
25186 ACCTTCATATG-AATTATT-AGTA
1 ACC-TCCTATGAAATT-TTGA-TA
* * *
25208 ATCACACTCTGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
* * *
25230 ATCACACTATGAAATTGTGATA
1 ACCTC-CTATGAAATTTTGATA
* *
25252 ACCTCGCTATAAAATTTTGATTC
1 ACCTC-CTATGAAATTTTGA-TA
*
25275 ACCTTCCTAT-AATATTTTAATAA
1 ACC-TCCTATGAA-ATTTTGAT-A
* *
25298 ACCTCCCTATAAAATTTCGATA
1 ACCT-CCTATGAAATTTTGATA
* *
25320 ACCTCCTTATGAAATCTTGACA
1 ACCTCC-TATGAAATTTTGATA
*
25342 A----CTA-CAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
**
25358 ACCTCCCTATGATTTTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* * *
25380 AACTCATTATGAAATTTTGTTA
1 ACCTC-CTATGAAATTTTGATA
* *
25402 ATCTCCCTATGAAATTTTGATCT
1 ACCT-CCTATGAAATTTTGAT-A
* *
25425 ACATACTATGAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
*
25446 ACCCTCTTATGAAATTTTGA-A
1 A-CCTCCTATGAAATTTTGATA
* *
25467 AACTAAACTATGAAATTTTGAT
1 ACCT--CCTATGAAATTTTGAT
25489 TTTGATATCC
Statistics
Matches: 387, Mismatches: 85, Indels: 95
0.68 0.15 0.17
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 4 0.01
19 13 0.03
20 10 0.03
21 27 0.07
22 253 0.65
23 58 0.15
24 7 0.02
25 1 0.00
26 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
ACCTCCTATGAAATTTTGATA
Found at i:25284 original size:23 final size:23
Alignment explanation
Indices: 25251--25314 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
25241 AAATTGTGAT
* * *
25251 AACCTCGCTATAAAATTTTGATT
1 AACCTCCCTATAAAATTTTAATA
* * *
25274 CACCTTCCTATAATATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
25297 AACCTCCCTATAAAATTT
1 AACCTCCCTATAAAATTT
25315 CGATAACCTC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTTAATA
Found at i:25413 original size:82 final size:84
Alignment explanation
Indices: 25263--25421 Score: 187
Period size: 82 Copynumber: 1.9 Consensus size: 84
25253 CCTCGCTATA
* * * *
25263 AAATTTTGATTCACCTTCCTATAATATTTTAATAAACCTCCCTATAAAATTTCGATAACCTCCTT
1 AAATTTTGATTAACCTCCCTATAATATTTTAATAAACCTCACTATAAAATTTCGATAACCTCCCT
25328 ATGAAATCTTGACAACTAC
66 ATGAAATCTTGACAACTAC
* * * * * * * *
25347 AAATTTTGA-TAACCTCCCTATGATTTTTTGATAAA-CTCATTATGAAATTTTGTTAATCTCCCT
1 AAATTTTGATTAACCTCCCTATAATATTTTAATAAACCTCACTATAAAATTTCGATAACCTCCCT
*
25410 ATGAAATTTTGA
66 ATGAAATCTTGA
25422 TCTACATACT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
82 32 0.52
83 21 0.34
84 9 0.15
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (84 bp):
AAATTTTGATTAACCTCCCTATAATATTTTAATAAACCTCACTATAAAATTTCGATAACCTCCCT
ATGAAATCTTGACAACTAC
Found at i:25649 original size:21 final size:22
Alignment explanation
Indices: 25620--26016 Score: 212
Period size: 22 Copynumber: 17.9 Consensus size: 22
25610 AATCACATTT
* *
25620 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
25642 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
25664 TAAAATTTTGTTGACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
*
25686 TGAAATTTTGATAA-TTACAT-TA
1 TGAAATTTTGATAACCT-C-TCTA
* ** *
25708 TGTAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
25730 TGGAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
*
25752 T-AAATTATGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* *
25776 TGAAATTTTGATAATCAT-TATA
1 TGAAATTTTGATAA-CCTCTCTA
*
25798 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
*
25818 TAAAATTTTGAT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
25838 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
25866 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
** * * *
25888 AAAAATTTTGATGACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
25910 TGAAATTTTCATAACCTC-CACA
1 TGAAATTTTGATAACCTCTC-TA
*
25932 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
25954 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
25976 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
* *
25998 TGACATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
26017 TTGATAACTG
Statistics
Matches: 290, Mismatches: 56, Indels: 58
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.01
20 15 0.05
21 30 0.10
22 200 0.69
23 6 0.02
24 5 0.02
25 14 0.05
26 5 0.02
27 2 0.01
28 10 0.03
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:32320 original size:26 final size:26
Alignment explanation
Indices: 32291--32340 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
32281 CTCTGAAAAA
*
32291 AAAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAAGAGAGTTAGTAACCTC
* *
32317 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAAAAAAAAGAGAGTTAGTAACC
32341 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.20, T:0.16
Consensus pattern (26 bp):
AAAAAAAAAAGAGAGTTAGTAACCTC
Done.