Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008126.1 Corchorus capsularis cultivar CVL-1 contig08147, 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: 43772
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:507 original size:41 final size:42
Alignment explanation
Indices: 461--544 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
451 CGTGTGGCTG
*
461 TTTTATTTTATAAATTCTTTTAAGAAAGA-TCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
502 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
544 T
1 T
545 GAAATTTTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 28 0.68
42 13 0.32
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (42 bp):
TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
Found at i:871 original size:11 final size:11
Alignment explanation
Indices: 857--894 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
847 ATTCATAACA
857 AATTTATAATT
1 AATTTATAATT
868 AATTTATAATT
1 AATTTATAATT
879 -ATTTGATAATT
1 AATTT-ATAATT
*
890 TATTT
1 AATTT
895 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:3725 original size:2 final size:2
Alignment explanation
Indices: 3720--3754 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3710 ACACACAAAC
*
3720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3755 AGAAGTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:10151 original size:2 final size:2
Alignment explanation
Indices: 10144--10195 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
10134 TACCTTTCAA
* *
10144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
10186 AT GT AT AT AT
1 AT AT AT AT AT
10196 TTGACGACAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15270 original size:101 final size:100
Alignment explanation
Indices: 15116--15296 Score: 326
Period size: 101 Copynumber: 1.8 Consensus size: 100
15106 AAGATACACC
*
15116 TATCAAATAGATCATCTATAAAATCCCTAATTTCATGAATAAGAACACCTCCCTCCCACCAACAA
1 TATCAAATAGATCATCTACAAAATCCCTAATTTCATGAATAAGAACACCTCCCTCCCACCAACAA
15181 GGGCCAGTCCCTTTGAGTAAAGATACACCTATCAAA
66 GGGCCAGT-CCTTTGAGTAAAGATACACCTATCAAA
*
15217 TATCAAATAGATCATCTACCAAATCCCTAATTTCATGAATAAGAACACCTCCCTCCCACCAACAA
1 TATCAAATAGATCATCTACAAAATCCCTAATTTCATGAATAAGAACACCTCCCTCCCACCAACAA
*
15282 GGGTCAGTCCTTTGA
66 GGGCCAGTCCTTTGA
15297 TGTCATTTTG
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
100 7 0.09
101 70 0.91
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (100 bp):
TATCAAATAGATCATCTACAAAATCCCTAATTTCATGAATAAGAACACCTCCCTCCCACCAACAA
GGGCCAGTCCTTTGAGTAAAGATACACCTATCAAA
Found at i:15831 original size:21 final size:21
Alignment explanation
Indices: 15805--15855 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
15795 AAATATTATA
*
15805 TTTATCTTATAATGGGTAGTT
1 TTTATCTTATAATGAGTAGTT
*
15826 TTTATC-TAAAATGAGTAGTT
1 TTTATCTTATAATGAGTAGTT
*
15846 TTTATTTTAT
1 TTTATCTTAT
15856 TTTGAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTATCTTATAATGAGTAGTT
Found at i:16119 original size:31 final size:31
Alignment explanation
Indices: 16081--16140 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
16071 TATGAGCAGG
16081 ATAATTAGCCTAACACATGATTAATCTACAT
1 ATAATTAGCCTAACACATGATTAATCTACAT
16112 ATAATTAGCCTAACACATGATTAATCTAC
1 ATAATTAGCCTAACACATGATTAATCTAC
16141 TAAATGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (31 bp):
ATAATTAGCCTAACACATGATTAATCTACAT
Found at i:22271 original size:102 final size:104
Alignment explanation
Indices: 22109--22371 Score: 372
Period size: 107 Copynumber: 2.5 Consensus size: 104
22099 AGTAAAATTT
** * * *
22109 AATTTTAATTT-GGTATAAGCTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCATATAACA
* *
22172 AT-ATTATTAATTATGGAATTTACCCTT-ATAAAAATAA
66 ATAATTATTAATTATGAAATTTACACTTAATAAAAATAA
* * *
22209 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTACTTGTAAAACCATATAACA
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCATATAACA
*
22274 ATAAATTATTAATTTTGAAATTTACACTTAAAATAAAAATAA
66 AT-AATTATTAATTATGAAATTTACACTT--AATAAAAATAA
22316 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
22372 TCTATAATAA
Statistics
Matches: 142, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
100 11 0.08
101 12 0.08
102 34 0.24
104 22 0.15
107 63 0.44
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (104 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCATATAACA
ATAATTATTAATTATGAAATTTACACTTAATAAAAATAA
Found at i:25324 original size:10 final size:11
Alignment explanation
Indices: 25299--25357 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 11
25289 ATTATGCATG
25299 TTTTTATAGCTA
1 TTTTTATA-CTA
25311 TTTTTATA-TA
1 TTTTTATACTA
*
25321 TTTTT-TGCTA
1 TTTTTATACTA
* *
25331 CTTTTATATGTA
1 TTTTTATA-CTA
*
25343 TTTTTATCCTA
1 TTTTTATACTA
25354 TTTT
1 TTTT
25358 GCTAGTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
9 1 0.03
10 13 0.35
11 7 0.19
12 16 0.43
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.66
Consensus pattern (11 bp):
TTTTTATACTA
Found at i:25346 original size:20 final size:20
Alignment explanation
Indices: 25307--25346 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
25297 TGTTTTTATA
* *
25307 GCTATTTTTATATATTTTTT
1 GCTACTTTTATATATATTTT
*
25327 GCTACTTTTATATGTATTTT
1 GCTACTTTTATATATATTTT
25347 TATCCTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.65
Consensus pattern (20 bp):
GCTACTTTTATATATATTTT
Found at i:26091 original size:10 final size:11
Alignment explanation
Indices: 26062--26094 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
26052 CTCATGTATC
*
26062 ACTTTTCATAT
1 ACTTTTCACAT
26073 ACTTTTCACAT
1 ACTTTTCACAT
26084 AC-TTTCACAT
1 ACTTTTCACAT
26094 A
1 A
26095 GATATAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (11 bp):
ACTTTTCACAT
Found at i:30459 original size:27 final size:27
Alignment explanation
Indices: 30429--30533 Score: 165
Period size: 27 Copynumber: 3.9 Consensus size: 27
30419 ATTAGGGTCG
* *
30429 CCCAAGGGTATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
30456 CCCAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
*
30483 CCCAGGGGCATTTTGGTAATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
* *
30510 CTCAGGGGCATTTTAGTCATTTTT
1 CCCAGGGGCATTTTGGTCATTTTT
30534 AAGTTCACCT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTTGCA
Found at i:31211 original size:2 final size:2
Alignment explanation
Indices: 31204--31239 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31194 AGTTGATTGA
31204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31240 GCGCTGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33325 original size:49 final size:49
Alignment explanation
Indices: 33266--33599 Score: 456
Period size: 49 Copynumber: 6.8 Consensus size: 49
33256 AATAACTTAG
33266 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
1 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
33315 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
1 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
* *
33364 GTAAAAATGCCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGCAA
1 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
33413 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
1 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
* * * *
33462 GTAAAAATGCCATCTTTGGGTAAAAGATTGAAACTTTTAGTGATTATTAA
1 GTAAAAATGTCATCTTTGGGTAAAAGATTG-AATTTTTAGTAATTAGTAA
* * * *
33512 GTAAAGATGTCA-CCTTGGAGCAAAAGATTG-ATTTTTAGAGCAATTAGTAA
1 GTAAAAATGTCATCTTTGG-GTAAAAGATTGAATTTTT--AGTAATTAGTAA
* * * * * ** *
33562 ATAGAGATGTAACCTTTGAATAAAAGATTGAAGTTTTA
1 GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTA
33600 AAAAGTAATT
Statistics
Matches: 255, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
48 5 0.02
49 178 0.70
50 63 0.25
51 9 0.04
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (49 bp):
GTAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAA
Found at i:34499 original size:47 final size:51
Alignment explanation
Indices: 34408--34662 Score: 239
Period size: 55 Copynumber: 4.8 Consensus size: 51
34398 TCAGAATAGA
* * * * *
34408 AATCAGTCAATTAGTAATTAAGTAAAAAAAAAAGGTTAATCAGAGTC-AAG-GA
1 AATCAGTAAATCAGTAATTAAGT---AAAAAGAGATTAATCAGAGTCAAAGAGT
*
34460 AAT-AGT-AATCAGTAACTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAG----AGT
*
34513 AATCAATAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAG----AGT
*
34568 AATCAGTAAATCAGTAATTAAATAAAAAGAGATTAATCAGAGTCAAAGTAATGGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAG--A--GT
* * * *
34623 AATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
34663 TAAATTGATA
Statistics
Matches: 177, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
47 19 0.11
48 3 0.02
50 13 0.07
51 3 0.02
52 3 0.02
53 5 0.03
54 2 0.01
55 129 0.73
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.24
Consensus pattern (51 bp):
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGAGT
Found at i:34535 original size:55 final size:55
Alignment explanation
Indices: 34466--34662 Score: 322
Period size: 55 Copynumber: 3.6 Consensus size: 55
34456 AGGAAATAGT
* *
34466 AATCAGTAACTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
34521 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* *
34576 AATCAGTAATTAAATAAAAAGAGATTAATCAGAGTCAAAGTAATGGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
* * * *
34631 AATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAG
34663 TAAATTGATA
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 133 1.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.24
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
Found at i:34725 original size:37 final size:36
Alignment explanation
Indices: 34612--34739 Score: 113
Period size: 34 Copynumber: 3.6 Consensus size: 36
34602 AATCAGAGTC
* * * * *
34612 AAAGTAATGGTAATCAGTAAATCAGTAATCAGGTAA
1 AAAGTAATAGTAATCAGTAAATTAGTAATTAAGAAA
**
34648 AAAG--ATAGTAATCAGTAAATT-GATAATTAAGAGT
1 AAAGTAATAGTAATCAGTAAATTAG-TAATTAAGAAA
**
34682 CCAGATAATAGTAATCAGTAAATTAGTAATTAAGAAA
1 AAAG-TAATAGTAATCAGTAAATTAGTAATTAAGAAA
*
34719 AAAG--ATAGTAATCAATAAATT
1 AAAGTAATAGTAATCAGTAAATT
34740 GATAATAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
33 1 0.01
34 39 0.53
36 4 0.05
37 28 0.38
38 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (36 bp):
AAAGTAATAGTAATCAGTAAATTAGTAATTAAGAAA
Found at i:35334 original size:27 final size:26
Alignment explanation
Indices: 35063--35328 Score: 151
Period size: 27 Copynumber: 10.1 Consensus size: 26
35053 AAGTAAAATA
*
35063 AAAAAGAGTAAAAGA-GAGTAATTAGT
1 AAAAAGAGTAAAAAATG-GTAATTAGT
* * *
35089 AATAAAGAGTAAGAAATGGTGATCAGT
1 AA-AAAGAGTAAAAAATGGTAATTAGT
*
35116 AAAAAAGAGTAAAAAGTGGT-ATTCAGT
1 -AAAAAGAGTAAAAAATGGTAATT-AGT
*
35143 AAAAAG-GGATAAAAATGGT-A--A--
1 AAAAAGAGTA-AAAAATGGTAATTAGT
*
35164 AAAAAGAG-CAAAAATGGT-ATTAAGT
1 AAAAAGAGTAAAAAATGGTAATT-AGT
35189 AAAAAGGGAGAGTAAAAAATGGTAATTAAGT
1 -AAAA---AGAGTAAAAAATGGTAATT-AGT
*
35220 AAAAAGAGTAAAAAGTGGT-ATTCAGT
1 AAAAAGAGTAAAAAATGGTAATT-AGT
* * * * *
35246 -AGAAGCAGAAAGAAAAGAGGTGATCAGT
1 AAAAAG-AGTAA-AAAA-TGGTAATTAGT
* * *
35274 AAGAAAGGGTAAAATATGGTAATCAGT
1 AA-AAAGAGTAAAAAATGGTAATTAGT
*
35301 ACAAAGAGTAAAAAATGGTAATTAGT
1 AAAAAGAGTAAAAAATGGTAATTAGT
35327 AA
1 AA
35329 TCAAGAAATA
Statistics
Matches: 188, Mismatches: 29, Indels: 46
0.71 0.11 0.17
Matches are distributed among these distances:
20 10 0.05
21 6 0.03
22 1 0.01
23 2 0.01
25 6 0.03
26 55 0.29
27 63 0.34
28 12 0.06
29 10 0.05
30 16 0.09
31 7 0.04
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.20
Consensus pattern (26 bp):
AAAAAGAGTAAAAAATGGTAATTAGT
Found at i:35860 original size:23 final size:21
Alignment explanation
Indices: 35830--35878 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
35820 ACATTAAGCA
*
35830 ATGCCCGGCCTTGTCCGCGCACT
1 ATGCCCGGCCATG-CC-CGCACT
*
35853 ATGCCCGGCCATGCCCGCCCT
1 ATGCCCGGCCATGCCCGCACT
35874 ATGCC
1 ATGCC
35879 GCGCCATCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 2 0.08
23 12 0.50
ACGTcount: A:0.10, C:0.47, G:0.24, T:0.18
Consensus pattern (21 bp):
ATGCCCGGCCATGCCCGCACT
Found at i:38279 original size:10 final size:11
Alignment explanation
Indices: 38250--38282 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
38240 CTCCTGTATC
*
38250 ACTTTTCATAT
1 ACTTTTCACAT
38261 ACTTTTCACAT
1 ACTTTTCACAT
38272 AC-TTTCACAT
1 ACTTTTCACAT
38282 A
1 A
38283 GATATAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (11 bp):
ACTTTTCACAT
Done.