Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016576.1 Corchorus olitorius cultivar O-4 contig16609, 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: 55855
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2148 original size:22 final size:22
Alignment explanation
Indices: 2120--2168 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2110 AATACATACC
2120 GTCAATGGGGGTGACTAAAGTG
1 GTCAATGGGGGTGACTAAAGTG
*
2142 GTCAATGGGGGTGACTAATGTG
1 GTCAATGGGGGTGACTAAAGTG
2164 GTCAA
1 GTCAA
2169 GGTTTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.39, T:0.24
Consensus pattern (22 bp):
GTCAATGGGGGTGACTAAAGTG
Found at i:13402 original size:16 final size:16
Alignment explanation
Indices: 13383--13417 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13373 AAATTCGGTA
13383 GAATTAAGGGGGAATT
1 GAATTAAGGGGGAATT
*
13399 GAATTGAGGGGGAATT
1 GAATTAAGGGGGAATT
13415 GAA
1 GAA
13418 AATAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (16 bp):
GAATTAAGGGGGAATT
Found at i:17239 original size:13 final size:13
Alignment explanation
Indices: 17221--17245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17211 CAAAAACAAT
17221 AGAAAATGGTAGA
1 AGAAAATGGTAGA
17234 AGAAAATGGTAG
1 AGAAAATGGTAG
17246 TAGTATGGTA
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (13 bp):
AGAAAATGGTAGA
Found at i:22444 original size:78 final size:78
Alignment explanation
Indices: 22300--22456 Score: 172
Period size: 78 Copynumber: 2.0 Consensus size: 78
22290 TCTTTAGAAA
* * * * *
22300 GTGTTGGTCCAAACAACTTGCAGAAAACAGATACCGTGATATCTGAAAGCCATGACTTAAAATCT
1 GTGTTGGTACAAACAACTTGCAGAAAACAGATACCATAATATCTGAAAACAATGACTTAAAATCT
*
22365 AACTCTCTAAATG
66 AAATCTCTAAATG
** * * * * *
22378 GTGTTGGTACAAACGCCTTTCAGAAAGCAGATACCATAAT-TGCTGAAAACAATGAGTTAGACTC
1 GTGTTGGTACAAACAACTTGCAGAAAACAGATACCATAATAT-CTGAAAACAATGACTTAAAATC
*
22442 TAAATCTTTAAATG
65 TAAATCTCTAAATG
22456 G
1 G
22457 CGTCGGTCCA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
77 1 0.02
78 63 0.98
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (78 bp):
GTGTTGGTACAAACAACTTGCAGAAAACAGATACCATAATATCTGAAAACAATGACTTAAAATCT
AAATCTCTAAATG
Found at i:22480 original size:78 final size:78
Alignment explanation
Indices: 22316--22480 Score: 172
Period size: 78 Copynumber: 2.1 Consensus size: 78
22306 GTCCAAACAA
* * * * * *
22316 CTTGCAGAAAACAGATACCGTGATATCTGAAAGCCATGACTTAAAATCTAACTCTCTAAATGGTG
1 CTTGCAGAAAACAGATACCATAATATCTGAAAACAATGACTTAAAATCTAAATCTCTAAATGGCG
*
22381 TTGGTACAAACGC
66 TCGGTACAAACGC
* * * * * *
22394 CTTTCAGAAAGCAGATACCATAAT-TGCTGAAAACAATGAGTTAGACTCTAAATCTTTAAATGGC
1 CTTGCAGAAAACAGATACCATAATAT-CTGAAAACAATGACTTAAAATCTAAATCTCTAAATGGC
*
22458 GTCGGTCCAAA-GTC
65 GTCGGTACAAACG-C
22472 CTTGCAGAA
1 CTTGCAGAA
22481 TTCAGATTTT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
77 2 0.03
78 68 0.97
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (78 bp):
CTTGCAGAAAACAGATACCATAATATCTGAAAACAATGACTTAAAATCTAAATCTCTAAATGGCG
TCGGTACAAACGC
Found at i:26276 original size:31 final size:31
Alignment explanation
Indices: 26241--26308 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
26231 TTAAGGAGCT
* **
26241 AATTGACTCAATCTTGT-GAGTATGGAGACTA
1 AATTGACCCAATCTTGTGGA-TATACAGACTA
26272 AATTGACCCAATCTTGTGGATATACAGACTA
1 AATTGACCCAATCTTGTGGATATACAGACTA
26303 AATTGA
1 AATTGA
26309 TTACTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (31 bp):
AATTGACCCAATCTTGTGGATATACAGACTA
Found at i:31783 original size:30 final size:30
Alignment explanation
Indices: 31749--32262 Score: 551
Period size: 30 Copynumber: 16.7 Consensus size: 30
31739 ACTCCCTAAA
*
31749 TGACACCAGAAATTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
31779 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
31809 TGACACCAGAAGTTGTCACGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
31839 TGACACCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
31869 TGACGCCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
** * * * *
31899 TGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
* * *
31931 TGAAACCAGAAGTTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAAT
** ** * * *
31964 TGACACTTGAAAATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
*
31996 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
32026 TGACACTAGAAGTTGTCATGATTTTCCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
32056 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
32086 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
32116 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
** * * * *
32146 TGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
** *
32178 TGACACCAGAAGTTGTCATGATAAATCCAAT
1 TGACACCAGAAGTTGTCATGAT-CTTGCAAT
* ** * * * *
32209 AGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
32241 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
32263 TTTACCTTTC
Statistics
Matches: 409, Mismatches: 63, Indels: 23
0.83 0.13 0.05
Matches are distributed among these distances:
30 267 0.65
31 33 0.08
32 86 0.21
33 20 0.05
34 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:31842 original size:60 final size:62
Alignment explanation
Indices: 31749--32262 Score: 612
Period size: 60 Copynumber: 8.4 Consensus size: 62
31739 ACTCCCTAAA
* * * * * *
31749 TGACACCAGAAATTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
* * * * * * *
31809 TGACACCAGAAGTTGTCACGATCTTGCAATTGACACCATAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
* * *
31869 TGACGCCATAAGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
* * * * *
31931 TGAAACCAGAAGTTGTCATGATAAATTTCCAATTGACACTTGAAAATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
* * * *
31996 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACTAGAAGTTGTCATGA-TTT-TCCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
* * * * *
32056 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
*
32116 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
** * * *
32178 TGACACCAGAAGTTGTCATGATAAATCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGAT-CTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
32241 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
32263 TTTACCTTTC
Statistics
Matches: 406, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
60 208 0.51
61 7 0.02
62 75 0.18
63 58 0.14
65 58 0.14
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (62 bp):
TGACACCAGAAGTTGTCATGATCTTGCAATTGACACTAGAAGATGTCATAATTTTATTCAAT
Found at i:32188 original size:247 final size:245
Alignment explanation
Indices: 31749--32265 Score: 908
Period size: 247 Copynumber: 2.1 Consensus size: 245
31739 ACTCCCTAAA
* * *
31749 TGACACCAGAAATTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACA
1 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTCCAATTGACA
* * *
31814 CCAGAAGTTGTCACGATCTTGCAATTGACACCATAAGTTGTCATGATCTTGCAATTGACGCCATA
66 CCAGAAGTTGTCACGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGA
31879 AGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATTCAATTGAAACCAGAAGT
131 AGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATTCAATTGAAACCAGAAGT
*
31944 TGTCATGATAAATTTCCAATTGACACTTGAAAATGTCATAATTTTATTCAAT
196 TGTCATGATAAA--TCCAATAGACACTTGAAAATGTCATAATTTTATTCAAT
* *
31996 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACTAGAAGTTGTCATGATTTTCCAATTGACA
1 TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTCCAATTGACA
*
32061 CCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGA
66 CCAGAAGTTGTCACGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGA
*
32126 AGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATTCAATTGACACCAGAAGT
131 AGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATTCAATTGAAACCAGAAGT
*
32191 TGTCATGATAAATCCAATAGACACTTGAAGATGTCATAATTTTATTCAAT
196 TGTCATGATAAATCCAATAGACACTTGAAAATGTCATAATTTTATTCAAT
32241 TGACACCAGAAGTTGTCATGATTTT
1 TGACACCAGAAGTTGTCATGATTTT
32266 ACCTTTCAAA
Statistics
Matches: 258, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
245 61 0.24
247 197 0.76
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (245 bp):
TGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTCCAATTGACA
CCAGAAGTTGTCACGATCTTGCAATTGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGA
AGTTGTCATGATCTTGCAATTGACACTTGAAGATGTCATAATTTTATTCAATTGAAACCAGAAGT
TGTCATGATAAATCCAATAGACACTTGAAAATGTCATAATTTTATTCAAT
Found at i:34376 original size:33 final size:33
Alignment explanation
Indices: 34313--34376 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
34303 ATACTGAATA
* **
34313 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCAAAAACCCATGAGC
* *
34346 ATATTGCCCCTGTAGTGGCAAAAACCCATGA
1 ATATTGCCCCTGAAGAGGCAAAAACCCATGA
34377 AAAGATCACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCAAAAACCCATGAGC
Found at i:36348 original size:119 final size:123
Alignment explanation
Indices: 36048--36361 Score: 351
Period size: 126 Copynumber: 2.6 Consensus size: 123
36038 TAAAGTGCGT
* *
36048 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACAGGGTTTTCCGACTTAAGGTTTTTAATGA
1 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACATAAGGTTTTTAATGA
* * * * *
36113 GACAACAATAGCACATTTAGATGTAATTGTCCTGAAGACATATACATGGACTTAATTGCTC
66 GGCAACAAGAGCACATGTAGA-GTAATTGTCCAGAAGACA-ATACATGAACTTAATTGC-C
* *
36174 TAGCACTCTTTTTCCCTT-TAGTTCGGTTTT-TCCCACTGGGTTTTCCGACACAAGGTTTTTAAT
1 T-GCACTCTTTTTCCCTTAT-GATCGGTTTTGTCCCACTGGGTTTTCCGACATAAGGTTTTTAAT
* *
36237 GAGGCAACAAAGAGCACATGTA-A-TATTTGTCCAGAAGAC-A-A-ATGAACTTGATATG-C
64 GAGGCAAC-AAGAGCACATGTAGAGTAATTGTCCAGAAGACAATACATGAACTTAAT-TGCC
* * *
36293 TGCACTCTTTTTTCCTTATGA-CTGGTTTTGTCCCATTGGGTTTTCC-AGCATAAGGTTTTTAAC
1 TGCACTCTTTTTCCCTTATGATC-GGTTTTGTCCCACTGGGTTTTCCGA-CATAAGGTTTTTAAT
36356 GAGGCA
64 GAGGCA
36362 CTAGCTACAT
Statistics
Matches: 164, Mismatches: 16, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
117 1 0.01
118 23 0.14
119 37 0.23
120 9 0.05
121 3 0.02
122 1 0.01
124 14 0.09
126 40 0.24
127 36 0.22
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (123 bp):
TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACATAAGGTTTTTAATGA
GGCAACAAGAGCACATGTAGAGTAATTGTCCAGAAGACAATACATGAACTTAATTGCC
Found at i:46646 original size:21 final size:20
Alignment explanation
Indices: 46595--46658 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
46585 TTGACACTGT
*
46595 TTAGATACCGTACAGATAAGA
1 TTAGATACTGTACAGATAA-A
*
46616 TT--ACACTGTACAGATCAAA
1 TTAGATACTGTACAGAT-AAA
*
46635 TTAGATACTGTACATATGAAA
1 TTAGATACTGTACAGAT-AAA
46656 TTA
1 TTA
46659 TTGTTGGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 14 0.40
20 2 0.06
21 19 0.54
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
TTAGATACTGTACAGATAAA
Found at i:53344 original size:2 final size:2
Alignment explanation
Indices: 53339--53368 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53329 TACTTGCTTC
53339 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
53369 TGGTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.