Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021328.1 Corchorus olitorius cultivar O-4 contig21361, 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: 64066
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:936 original size:19 final size:19
Alignment explanation
Indices: 896--936 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
886 AGATCATAGT
* *
896 AAAACCAAGATAATCAATC
1 AAAACCAAGATAATAAACC
*
915 AAAACCAGGATAATAAACC
1 AAAACCAAGATAATAAACC
934 AAA
1 AAA
937 TCAATCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAACCAAGATAATAAACC
Found at i:2023 original size:15 final size:15
Alignment explanation
Indices: 1989--2022 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1979 TTCCTTCTTT
*
1989 CTTTTCTTTCCTTTC
1 CTTTTCTTTCCATTC
2004 CTTTTCTTTCCATT-
1 CTTTTCTTTCCATTC
2018 CTTTT
1 CTTTT
2023 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (15 bp):
CTTTTCTTTCCATTC
Found at i:10285 original size:13 final size:13
Alignment explanation
Indices: 10267--10291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10257 GTTTTTTTAT
10267 TTTTTTATTATTA
1 TTTTTTATTATTA
10280 TTTTTTATTATT
1 TTTTTTATTATT
10292 CATTGATTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTATTATTA
Found at i:11774 original size:2 final size:2
Alignment explanation
Indices: 11767--11849 Score: 52
Period size: 2 Copynumber: 44.5 Consensus size: 2
11757 AGGTTTAGGT
* * * *
11767 TA TA TA TA TA AA TA TA AA TA TA TA -A AA TA TA -A AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
11807 AA TA TA TA AA TA AA TA TA -A AA TA T- TA TA TA TA T- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11845 TA TA T
1 TA TA T
11850 GGGTCGGTCA
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
1 6 0.10
2 56 0.90
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (2 bp):
TA
Found at i:11814 original size:32 final size:34
Alignment explanation
Indices: 11768--11849 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 34
11758 GGTTTAGGTT
11768 ATATATATAA-ATATAAAT-ATATAAAATATAAA
1 ATATATATAATATATAAATAATATAAAATATAAA
* *
11800 ATATATA-AATATATAAATAAATATAAAATATTAT
1 ATATATATAATATATAAAT-AATATAAAATATAAA
11834 ATATATTATAATATAT
1 ATATA-TATAATATAT
11850 GGGTCGGTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 2 0.05
32 15 0.35
34 17 0.40
35 2 0.05
36 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
ATATATATAATATATAAATAATATAAAATATAAA
Found at i:11834 original size:10 final size:9
Alignment explanation
Indices: 11779--11849 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
11769 TATATATAAA
11779 TATAAATA-
1 TATAAATAT
11787 TATAAA-A-
1 TATAAATAT
11794 TATAAA-AT
1 TATAAATAT
11802 ATATAAATA-
1 -TATAAATAT
*
11811 TATAAATAAA
1 TATAAAT-AT
11821 TATAAAATAT
1 TAT-AAATAT
*
11831 TATATATAT
1 TATAAATAT
11840 TATAATATAT
1 TATAA-ATAT
11850 GGGTCGGTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
7 8 0.15
8 13 0.25
9 16 0.30
10 12 0.23
11 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TATAAATAT
Found at i:17341 original size:40 final size:40
Alignment explanation
Indices: 17290--17365 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
17280 TTTTATTTTA
*
17290 TAAGTGCTTTTAAGAAAATTTAGTTAAGAAAATGAATATT
1 TAAGTGCTTTTAAGAAAATTCAGTTAAGAAAATGAATATT
*
17330 TAAGTGCTTTTAAGAAAATTCAGTTATGAAAATGAA
1 TAAGTGCTTTTAAGAAAATTCAGTTAAGAAAATGAA
17366 ACCATTAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.36
Consensus pattern (40 bp):
TAAGTGCTTTTAAGAAAATTCAGTTAAGAAAATGAATATT
Found at i:19346 original size:2 final size:2
Alignment explanation
Indices: 19339--19363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19329 TTTATGTTTA
19339 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 A
19364 ATAAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27355 original size:18 final size:18
Alignment explanation
Indices: 27334--27394 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
27324 AAGAGGTCGA
27334 AAAACAAAAACAGGACCT
1 AAAACAAAAACAGGACCT
* * * **
27352 AAAACAGAAAGAGGTCAG
1 AAAACAAAAACAGGACCT
* *
27370 AATAAGAAAAACTGGACCT
1 AA-AACAAAAACAGGACCT
27389 AAAACA
1 AAAACA
27395 GAGAGAGGTC
Statistics
Matches: 29, Mismatches: 13, Indels: 2
0.66 0.30 0.05
Matches are distributed among these distances:
18 18 0.62
19 11 0.38
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.08
Consensus pattern (18 bp):
AAAACAAAAACAGGACCT
Found at i:27389 original size:37 final size:37
Alignment explanation
Indices: 27308--27410 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
27298 AAAAAAGGAG
* *
27308 CTGGGCCTAAAACAGTAAGAGGTC-GAAAAACAAAAA
1 CTGGACCTAAAACAGAAAGAGGTCAGAAAAACAAAAA
* * *
27344 CAGGACCTAAAACAGAAAGAGGTCAGAATAAGAAAAA
1 CTGGACCTAAAACAGAAAGAGGTCAGAAAAACAAAAA
* *
27381 CTGGACCTAAAACAGAGAGAGGTCATAAAA
1 CTGGACCTAAAACAGAAAGAGGTCAGAAAA
27411 TTTAAAAGGG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
36 21 0.37
37 36 0.63
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (37 bp):
CTGGACCTAAAACAGAAAGAGGTCAGAAAAACAAAAA
Found at i:28391 original size:58 final size:58
Alignment explanation
Indices: 28236--28451 Score: 360
Period size: 58 Copynumber: 3.7 Consensus size: 58
28226 ACAGACTCTT
28236 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
1 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
*
28294 ATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTATTAGAGAGTTTTCAATTCAAAATATC
1 ATCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* *
28353 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTT
1 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* * * *
28411 ATCTTGTTTTAAAATCTTGGTCGAGGTCTTTGTTTGAGAGT
1 ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
28452 CCATGTTTCA
Statistics
Matches: 149, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
58 92 0.62
59 57 0.38
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (58 bp):
ATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
Found at i:28727 original size:28 final size:28
Alignment explanation
Indices: 28695--28860 Score: 206
Period size: 29 Copynumber: 5.8 Consensus size: 28
28685 TTCGCACACT
28695 CAGGGGCATTTTGGTCATTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTGCATATC
28723 CAGGGGCATTTTGGTCATTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTGCATATC
* * *
28751 CAAGGGAATTTTGGTCGTGTTTGCATATC
1 CAGGGGCATTTTGGTCAT-TTTGCATATC
** * *
28780 CAAAGGCATTTTGGTCATATTTACACATC
1 CAGGGGCATTTTGGTCAT-TTTGCATATC
* * **
28809 TAGGGACATTTTGGTCATTTTTGCACGTC
1 CAGGGGCATTTTGGTCA-TTTTGCATATC
28838 CAGGGGCATTTTGGTCATTTTGC
1 CAGGGGCATTTTGGTCATTTTGC
28861 GTACTCTGGG
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
28 49 0.41
29 69 0.58
30 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (28 bp):
CAGGGGCATTTTGGTCATTTTGCATATC
Found at i:39948 original size:40 final size:38
Alignment explanation
Indices: 39904--39982 Score: 88
Period size: 40 Copynumber: 2.0 Consensus size: 38
39894 CAATCACTTA
39904 TTCCTTATT-TTCATTCTCCTTTTTCTTTTATTTTCCTTTT
1 TTCCTTATTCTTCATT-TCC-TTTTCTTTTATTTT-CTTTT
* * *
39944 TTCCTTTTTCCTTTATTTCCTTTTCTTTTCTTTTCTTTT
1 TTCCTTATT-CTTCATTTCCTTTTCTTTTATTTTCTTTT
39983 CTTTTCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 5 0.15
40 21 0.62
41 3 0.09
42 5 0.15
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (38 bp):
TTCCTTATTCTTCATTTCCTTTTCTTTTATTTTCTTTT
Found at i:39952 original size:25 final size:25
Alignment explanation
Indices: 39920--40005 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 25
39910 ATTTTCATTC
39920 TCCTTTTTCTTTTATTTTCCTTTTT
1 TCCTTTTTCTTTTATTTTCCTTTTT
*
39945 TCCTTTTTCCTTTA-TTTCC--TTT
1 TCCTTTTTCTTTTATTTTCCTTTTT
* *
39967 T-C-TTTTCTTTTCTTTTCTTTTCTTT
1 TCCTTTTTCTTTTATTTTC-CTT-TTT
39992 TCCTTTTTCCTTTT
1 TCCTTTTT-CTTTT
40006 TCCTTCTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
20 8 0.16
21 5 0.10
22 4 0.08
24 5 0.10
25 17 0.35
26 1 0.02
27 4 0.08
28 5 0.10
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (25 bp):
TCCTTTTTCTTTTATTTTCCTTTTT
Found at i:39954 original size:15 final size:15
Alignment explanation
Indices: 39934--40010 Score: 70
Period size: 15 Copynumber: 5.1 Consensus size: 15
39924 TTTTCTTTTA
39934 TTTTCCTTTTTTCCT
1 TTTTCCTTTTTTCCT
39949 TTTTCCTTTATTTCC-
1 TTTTCCTTT-TTTCCT
* *
39964 TTTTCTTTTCTTTTC-
1 TTTTCCTTT-TTTCCT
*
39979 TTTTCTTTTCTTTTCCT
1 TTTTC-CTT-TTTTCCT
39996 TTTTCC-TTTTTCCT
1 TTTTCCTTTTTTCCT
40010 T
1 T
40011 CTTTTTTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
14 8 0.15
15 27 0.51
16 12 0.23
17 6 0.11
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCCTTTTTTCCT
Found at i:39962 original size:9 final size:8
Alignment explanation
Indices: 39934--40015 Score: 54
Period size: 7 Copynumber: 10.5 Consensus size: 8
39924 TTTTCTTTTA
39934 TTTTCCTT
1 TTTTCCTT
39942 TTTTCC-T
1 TTTTCCTT
39949 TTTTCCTT
1 TTTTCCTT
39957 TATTTCCTT
1 T-TTTCCTT
39966 TTCTT--TT
1 TT-TTCCTT
39973 CTTTT-CTT
1 -TTTTCCTT
39981 TTCTT--TT
1 TT-TTCCTT
39988 CTTTTCC-T
1 -TTTTCCTT
39996 TTTTCC-T
1 TTTTCCTT
40003 TTTTCCTT
1 TTTTCCTT
40011 CTTTT
1 -TTTT
40016 TTTTCTTTGG
Statistics
Matches: 63, Mismatches: 0, Indels: 21
0.75 0.00 0.25
Matches are distributed among these distances:
7 30 0.48
8 19 0.30
9 14 0.22
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTCCTT
Found at i:39973 original size:5 final size:5
Alignment explanation
Indices: 39924--39998 Score: 71
Period size: 5 Copynumber: 14.8 Consensus size: 5
39914 TCATTCTCCT
* * * * * *
39924 TTTTC TTTTA TTTTC CTTT- TTTCC TTTTTC CTTTA TTTCC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC
39974 TTTTC TTTTC TTTTC TTTTCC TTTT
1 TTTTC TTTTC TTTTC TTTT-C TTTT
39999 TCCTTTTTCC
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
4 2 0.04
5 44 0.80
6 9 0.16
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:42502 original size:31 final size:32
Alignment explanation
Indices: 42457--42522 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
42447 TTGGTCCGCG
*
42457 GAACTTCGAATAAATCTTCAATCACGAACTTC
1 GAACTTCGAATAAATATTCAATCACGAACTTC
42489 GAACTTC-AATAAATATTCAATCACGAACTTC
1 GAACTTCGAATAAATATTCAATCACGAACTTC
42520 GAA
1 GAA
42523 TCTCTAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (32 bp):
GAACTTCGAATAAATATTCAATCACGAACTTC
Found at i:48605 original size:28 final size:27
Alignment explanation
Indices: 48449--48603 Score: 222
Period size: 27 Copynumber: 5.7 Consensus size: 27
48439 TATGAACTTA
*
48449 AAATGA-TCAAAATGTCCCTGAATGTGC
1 AAATGACT-AAAATGCCCCTGAATGTGC
48476 AAATGACTAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
48503 AAATGACTAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
48530 AAATGACTAAAATGCCCCTGAATATGC
1 AAATGACTAAAATGCCCCTGAATGTGC
* * *
48557 AAATGACTAAAATGCCCCTAGATTTTGA
1 AAATGACTAAAATGCCCCT-GAATGTGC
**
48585 AAATGACCGAAATGCCCCT
1 AAATGACTAAAATGCCCCT
48604 AGTTGATCCT
Statistics
Matches: 119, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
27 96 0.81
28 23 0.19
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAATGTGC
Found at i:50372 original size:11 final size:11
Alignment explanation
Indices: 50356--50385 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
50346 CATTGGTACT
50356 GAAATCTTTGA
1 GAAATCTTTGA
50367 GAAATCTTTGA
1 GAAATCTTTGA
*
50378 TAAATCTT
1 GAAATCTT
50386 CTGTAGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (11 bp):
GAAATCTTTGA
Found at i:55461 original size:21 final size:21
Alignment explanation
Indices: 55413--55453 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
55403 ATTTTGTTAA
55413 AAAAAAAAACCAAACCTTTTC
1 AAAAAAAAACCAAACCTTTTC
55434 AATAAAAAAACCAAA-CTTTT
1 AA-AAAAAAACCAAACCTTTT
55454 AGCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAAAAACCAAACCTTTTC
Done.