Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009919.1 Corchorus capsularis cultivar CVL-1 contig09940, 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: 40122
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:81 original size:14 final size:14
Alignment explanation
Indices: 48--104 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
38 CGCGACCCGC
*
48 TGTTCTTCTTCTTCT
1 TGTTTTTCTTCTT-T
* *
63 TGTTTTTTTTTTTT
1 TGTTTTTCTTCTTT
77 TGTTTTTCTTCTTT
1 TGTTTTTCTTCTTT
91 TGTTTTTCTTCTTT
1 TGTTTTTCTTCTTT
105 ATAGGCTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 27 0.73
15 10 0.27
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TGTTTTTCTTCTTT
Found at i:8428 original size:2 final size:2
Alignment explanation
Indices: 8421--8449 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8411 TTGTCTTCAA
8421 AT 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 AT A
8450 CTGTCAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12391 original size:62 final size:62
Alignment explanation
Indices: 12294--12424 Score: 235
Period size: 62 Copynumber: 2.1 Consensus size: 62
12284 TTATAACTTA
* * *
12294 GGGGGGCTAAAGCTAAATTTATCCAATTTTGTTAAGACTTATGTAAGATATGGAGGAGGTTT
1 GGGGGGCTAAAGCTAAATTTATCCAATTTTATTAAGACTCATGTAAGATATGCAGGAGGTTT
12356 GGGGGGCTAAAGCTAAATTTATCCAATTTTATTAAGACTCATGTAAGATATGCAGGAGGTTT
1 GGGGGGCTAAAGCTAAATTTATCCAATTTTATTAAGACTCATGTAAGATATGCAGGAGGTTT
12418 GGGGGGC
1 GGGGGGC
12425 GATGGCCCCT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.30, C:0.10, G:0.29, T:0.31
Consensus pattern (62 bp):
GGGGGGCTAAAGCTAAATTTATCCAATTTTATTAAGACTCATGTAAGATATGCAGGAGGTTT
Found at i:12875 original size:5 final size:5
Alignment explanation
Indices: 12867--12925 Score: 55
Period size: 5 Copynumber: 10.8 Consensus size: 5
12857 AAGTTTATTG
* *
12867 ATAAT ATAAT ATAAT AAAAAT AATAAT ATAAT ATAAC ATAATT ATCAAT
1 ATAAT ATAAT ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAA-T AT-AAT
12916 ATATAT ATAA
1 ATA-AT ATAA
12926 AGATTGAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 25 0.54
6 19 0.41
7 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:19255 original size:23 final size:26
Alignment explanation
Indices: 19229--19281 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 26
19219 AATCATTGAA
19229 TTATGATCA-TTAT-TATATAA-A-TT
1 TTATGAT-ATTTATATATATAATAGTT
*
19252 TTATTATATTTATATATATAATAGTT
1 TTATGATATTTATATATATAATAGTT
19278 TTAT
1 TTAT
19282 TTAGTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 10 0.40
24 7 0.28
25 1 0.04
26 6 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
TTATGATATTTATATATATAATAGTT
Found at i:19816 original size:32 final size:32
Alignment explanation
Indices: 19775--19839 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
19765 CCGAAGGAGT
19775 AGTGGATGTACTTTAGGAAGCAATGGCTTCCA
1 AGTGGATGTACTTTAGGAAGCAATGGCTTCCA
*
19807 AGTGGATGTATTTTAGGAAGCAATGGCTTCCA
1 AGTGGATGTACTTTAGGAAGCAATGGCTTCCA
19839 A
1 A
19840 AGCAGGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (32 bp):
AGTGGATGTACTTTAGGAAGCAATGGCTTCCA
Found at i:22404 original size:179 final size:180
Alignment explanation
Indices: 21996--22425 Score: 473
Period size: 179 Copynumber: 2.4 Consensus size: 180
21986 CGAAATAACA
* * * *
21996 AATA-TTTCGGAAGCATTTTTTATATTTGAAACATCAAATTTAACTTCCGAGTCCTTCATGAAAG
1 AATATTTTCGGAAGCATTTTTTATATTTGAAACATTAAATTTAGCTTTCGAGTCATTCATGAAAG
* * * * *
22060 TTGTAGATTATGAAACAACCTTCAACCAGATACTTGAATCACCTTAATCGGACATCTGGAGCAAA
66 TTGTAGATAATGAAACAACCTTCAACCAGACACTTGAATCACCTCAATCAGACATATGGAGCAAA
**
22125 AATTATGTAATATTAAGTAGACCATCCATTCCCGCACTAACCAAAACAACT
131 AATTAACTAATATTAAGTAGACCATCCATTCCCG-ACTAACCAAAACAACT
* * *
22176 AATATTTT-GGTAATG--TTTTTTATATTTGAAACGTTAAA-TTAGCTTTCGAGTCGTACATGAA
1 AATATTTTCGG-AA-GCATTTTTTATATTTGAAACATTAAATTTAGCTTTCGAGTCATTCATGAA
* * * *
22237 AGTTGTAGATAATGGAACAACCTTTTAA-GAGACACTTGAATCACCTCAATCAGACATATGGAGT
64 AGTTGTAGATAATGAAACAACC-TTCAACCAGACACTTGAATCACCTCAATCAGACATATGGAGC
* * * * * **
22301 AAAAGTTAACTAATATTAAGTAGACCGTCTATTCTCG-TTAACTGAAACAACT
128 AAAAATTAACTAATATTAAGTAGACCATCCATTCCCGACTAACCAAAACAACT
* * * **
22353 AACT-TTTCTCGG-AGCATTTTTTATACTCGAAACATTAAATTTAGTTTTCGAGTCATTTGTGAA
1 AA-TATTT-TCGGAAGCATTTTTTATATTTGAAACATTAAATTTAGCTTTCGAGTCATTCATGAA
22416 AGTTGTAGAT
64 AGTTGTAGAT
22426 CATACGATAA
Statistics
Matches: 208, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
176 1 0.00
177 18 0.09
178 22 0.11
179 130 0.62
180 31 0.15
181 5 0.02
182 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (180 bp):
AATATTTTCGGAAGCATTTTTTATATTTGAAACATTAAATTTAGCTTTCGAGTCATTCATGAAAG
TTGTAGATAATGAAACAACCTTCAACCAGACACTTGAATCACCTCAATCAGACATATGGAGCAAA
AATTAACTAATATTAAGTAGACCATCCATTCCCGACTAACCAAAACAACT
Found at i:27965 original size:27 final size:27
Alignment explanation
Indices: 27927--27981 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
27917 GGGATCAATG
27927 AAATTTATGCAGATTTGGAATATCTAT
1 AAATTTATGCAGATTTGGAATATCTAT
27954 AAATTTATGCAGATTTGGAATATCTAT
1 AAATTTATGCAGATTTGGAATATCTAT
27981 A
1 A
27982 TGCAGATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (27 bp):
AAATTTATGCAGATTTGGAATATCTAT
Found at i:27985 original size:21 final size:21
Alignment explanation
Indices: 27932--28003 Score: 90
Period size: 21 Copynumber: 3.1 Consensus size: 21
27922 CAATGAAATT
27932 TATGCAGATTTGGAATATCTATAAA
1 TATGCAGATTTGGAATATC--T--A
27957 TTTATGCAGATTTGGAATATCTA
1 --TATGCAGATTTGGAATATCTA
27980 TATGCAGATTTGGAATATCTA
1 TATGCAGATTTGGAATATCTA
28001 TAT
1 TAT
28004 CATTAAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 24 0.53
23 1 0.02
25 1 0.02
27 19 0.42
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (21 bp):
TATGCAGATTTGGAATATCTA
Found at i:28003 original size:27 final size:27
Alignment explanation
Indices: 27932--28004 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
27922 CAATGAAATT
** *
27932 TATGCAGATTTGGAATATCTATAAATT
1 TATGCAGATTTGGAATATCTATATCTA
27959 TATGCAGATTTGG---A---ATATCTA
1 TATGCAGATTTGGAATATCTATATCTA
27980 TATGCAGATTTGGAATATCTATATC
1 TATGCAGATTTGGAATATCTATATC
28005 ATTAAGAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 17 0.46
24 2 0.05
27 18 0.49
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (27 bp):
TATGCAGATTTGGAATATCTATATCTA
Found at i:30203 original size:2 final size:2
Alignment explanation
Indices: 30196--30222 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30186 TCAATGGCAT
30196 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
30223 ACCAAAAAAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30877 original size:3 final size:3
Alignment explanation
Indices: 30869--30903 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30859 CTTTGTTTAC
30869 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
30904 ATATCTATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:31056 original size:13 final size:13
Alignment explanation
Indices: 31038--31062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31028 TTAGAATTCC
31038 AAATAATATTTAT
1 AAATAATATTTAT
31051 AAATAATATTTA
1 AAATAATATTTA
31063 GAACATTGAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:34111 original size:54 final size:53
Alignment explanation
Indices: 34029--34135 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 53
34019 GATTTACATG
*
34029 TGAGTCCTCATCTCTCCCCCGTGCGACCCAACTGGCCATCCAAGACTTAACCCT
1 TGAGTCCTCATCTCTCCCCCGTGCGACCCAACCGG-CATCCAAGACTTAACCCT
34083 TGAGTCCTCATCTCTCCCCCGTGCGACCCAACCGGCATCCAAGACTTAACCCT
1 TGAGTCCTCATCTCTCCCCCGTGCGACCCAACCGGCATCCAAGACTTAACCCT
34136 GAAGTGGTGC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 18 0.35
54 34 0.65
ACGTcount: A:0.21, C:0.43, G:0.15, T:0.21
Consensus pattern (53 bp):
TGAGTCCTCATCTCTCCCCCGTGCGACCCAACCGGCATCCAAGACTTAACCCT
Found at i:36090 original size:6 final size:6
Alignment explanation
Indices: 36079--36120 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
36069 ATGTGTTATA
36079 TATATC TATATC TATATC TATATC TATATC TATATAC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT-C TATAT
36121 AAGTCTAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:36281 original size:24 final size:23
Alignment explanation
Indices: 36257--36320 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
36247 ATTTCTTAAT
36257 ATATCCTAATCCTTTTAC-AAAA
1 ATATCCTAATCCTTTTACAAAAA
36279 ATA----AAT-CTTTTCACAAAAA
1 ATATCCTAATCCTTTT-ACAAAAA
36298 ATATCCTAATCCTTTTACAAAAA
1 ATATCCTAATCCTTTTACAAAAA
36321 TAAATCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
17 5 0.14
18 5 0.14
19 7 0.20
22 3 0.09
23 10 0.29
24 5 0.14
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATCCTAATCCTTTTACAAAAA
Found at i:36331 original size:18 final size:18
Alignment explanation
Indices: 36264--36330 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 18
36254 AATATATCCT
36264 AATCCTTTTACAAAAATA
1 AATCCTTTTACAAAAATA
36282 AAT-CTTTTCACAAAAAATA
1 AATCCTTTT-AC-AAAAATA
36301 TCCTAATCCTTTTACAAAAATA
1 ----AATCCTTTTACAAAAATA
36323 AAT-CTTTT
1 AATCCTTTT
36331 TTATCAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
17 10 0.24
18 8 0.19
19 7 0.17
22 7 0.17
23 5 0.12
24 5 0.12
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (18 bp):
AATCCTTTTACAAAAATA
Found at i:36441 original size:32 final size:32
Alignment explanation
Indices: 36375--36446 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
36365 TCAAGGAACA
**
36375 TTAAAATTCCAATAGTTAAAATTATTAACAAG
1 TTAAAATTCCAATAGTTAAAATTACCAACAAG
*
36407 TTAAAATTCCAATAGTGATAAAATT-CCAA-TAG
1 TTAAAATTCCAATAGT--TAAAATTACCAACAAG
36439 TTAAAATT
1 TTAAAATT
36447 ACCATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 26 0.74
33 2 0.06
34 7 0.20
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.35
Consensus pattern (32 bp):
TTAAAATTCCAATAGTTAAAATTACCAACAAG
Done.