Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013473.1 Corchorus olitorius cultivar O-4 contig13506, 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: 75176
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:10804 original size:457 final size:457
Alignment explanation
Indices: 9950--10868 Score: 1707
Period size: 457 Copynumber: 2.0 Consensus size: 457
9940 ATTATTATAA
9950 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
10015 AAAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTAT
66 AAAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTAT
10080 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAAGTCTTTTTTTTTGAAGA
131 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAAGTCTTTTTTTTTGAAGA
*
10145 ATTTTTTAAGTTTTAGAATCCAAAAGCCTTTCAATCATAGTTGGGTAAGTTTGTTTAGTCTTAAT
196 ATTTTTTAAGTTTTAGAATCCAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAAT
*
10210 GTTTCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGAC
261 GTTTCTGTTTTTTGTTGGAATAATCAATTATTCTTCACAGCTTATTATTGCTTAACTTTCTTGAC
10275 AACTTCTTAGCTTCGGCGTTTTGATAAATATATTTAAAGCAGTTTAAAGTTAGAATCATGAGGCG
326 AACTTCTTAGCTTCGGCGTTTTGATAAATATATTTAAAGCAGTTTAAAGTTAGAATCATGAGGCG
*
10340 AAAAAGTTTAAAAACTTACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTT
391 AAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTT
10405 AC
456 AC
10407 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATT-TC
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCT-
* *
10471 GAAAAGTTAAAAAGTTGCCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTG
65 GAAAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTA
*
10536 TTCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAA-TTTTTTTTTTTGGAA
130 TTCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAAGTCTTTTTTTTT-GAA
*
10600 GAATTTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTA
194 GAATTTTTTAAGTTTTAGAATCCAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTA
10665 ATGTTTCTGTTTTTTGTTGGAATAATCAATTATTCTTCACAGCTTATTATTGCTTAACTTTCTTG
259 ATGTTTCTGTTTTTTGTTGGAATAATCAATTATTCTTCACAGCTTATTATTGCTTAACTTTCTTG
* *
10730 ACAACTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAGG
324 ACAACTTCTTAGCTTCGGCGTTTTGATAAATATATTTAAAGCAGTTTAAAGTTAGAATCATGAGG
* *
10795 CGAAAAAGTTTAAAAACTGACTCTTGAGAGGTATTTTTAAGTTAAAAAGCTTCCATCTGATATCT
389 CGAAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCT
10860 TTAC
454 TTAC
10864 ATAAA
1 ATAAA
10869 TCGTACTTAA
Statistics
Matches: 449, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
456 11 0.02
457 438 0.98
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (457 bp):
ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
AAAAGTTAAAAAGTTGACATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTAT
TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAAGTCTTTTTTTTTGAAGA
ATTTTTTAAGTTTTAGAATCCAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAAT
GTTTCTGTTTTTTGTTGGAATAATCAATTATTCTTCACAGCTTATTATTGCTTAACTTTCTTGAC
AACTTCTTAGCTTCGGCGTTTTGATAAATATATTTAAAGCAGTTTAAAGTTAGAATCATGAGGCG
AAAAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTT
AC
Found at i:10931 original size:16 final size:16
Alignment explanation
Indices: 10912--10943 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10902 TGATTGGTAT
10912 TAAAGTCATTATATTA
1 TAAAGTCATTATATTA
*
10928 TAAATTCATTATATTA
1 TAAAGTCATTATATTA
10944 ATCTCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAAGTCATTATATTA
Found at i:12068 original size:2 final size:2
Alignment explanation
Indices: 12061--12095 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
12051 ACTAAAAATA
12061 AT AT AT AT A- AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12096 ATGCAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12072 original size:9 final size:9
Alignment explanation
Indices: 12058--12097 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
12048 GCCACTAAAA
12058 ATAATATAT
1 ATAATATAT
12067 ATAATATAT
1 ATAATATAT
12076 ATAATATAT
1 ATAATATAT
12085 AT-ATATAT
1 ATAATATAT
12093 ATAAT
1 ATAAT
12098 GCAATTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATAATATAT
Found at i:13011 original size:16 final size:16
Alignment explanation
Indices: 12975--13035 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
12965 CTTCTCCAAC
12975 CTTCAACAAACAACAATTT
1 CTTCAACAAACAAC---TT
12994 CTTCAACAAACAACTT
1 CTTCAACAAACAACTT
*** *
13010 CTTCAACCTTCAATTT
1 CTTCAACAAACAACTT
13026 CTTCAACAAA
1 CTTCAACAAA
13036 TCCTCAAGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
16 21 0.60
19 14 0.40
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (16 bp):
CTTCAACAAACAACTT
Found at i:13138 original size:40 final size:40
Alignment explanation
Indices: 13092--13195 Score: 181
Period size: 40 Copynumber: 2.6 Consensus size: 40
13082 AAGATTTACA
*
13092 AGTTTTAGATCTAGATCTGTTGAAATGGTTTGAATTTGGT
1 AGTTTTAGATCTAGATCTGTTGAAATGGTTTGAATTTGGG
*
13132 AGTTTTAGATCTAGATCTATTGAAATGGTTTGAATTTGGG
1 AGTTTTAGATCTAGATCTGTTGAAATGGTTTGAATTTGGG
*
13172 AGTTTTAGATCTAGATTTGTTGAA
1 AGTTTTAGATCTAGATCTGTTGAA
13196 TTTCGGGTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (40 bp):
AGTTTTAGATCTAGATCTGTTGAAATGGTTTGAATTTGGG
Found at i:13417 original size:22 final size:22
Alignment explanation
Indices: 13372--13421 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
13362 AAATTTAATG
* * * *
13372 AATTATTTAGTTTATTAGTTTT
1 AATTAGTTAGTTTATGACTGTT
13394 AATTAGTTAGTTTATGACTGTT
1 AATTAGTTAGTTTATGACTGTT
13416 AATTAG
1 AATTAG
13422 AACTAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (22 bp):
AATTAGTTAGTTTATGACTGTT
Found at i:15514 original size:18 final size:18
Alignment explanation
Indices: 15491--15526 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15481 TAAATAAATC
15491 ATTTCTTTGACTTATTAT
1 ATTTCTTTGACTTATTAT
*
15509 ATTTCTTTTACTTATTAT
1 ATTTCTTTGACTTATTAT
15527 GTTTTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTCTTTGACTTATTAT
Found at i:17941 original size:18 final size:18
Alignment explanation
Indices: 17918--17953 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17908 TAAATAAATC
17918 ATTTCTTTGACTAATTAT
1 ATTTCTTTGACTAATTAT
* *
17936 ATTTCTTTTACTTATTAT
1 ATTTCTTTGACTAATTAT
17954 GTTTTGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTTCTTTGACTAATTAT
Found at i:20459 original size:19 final size:19
Alignment explanation
Indices: 20437--20493 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
20427 ATAAATGAAT
20437 ACATTAATAAATAATAATA
1 ACATTAATAAATAATAATA
*
20456 ACATTAAT-AATAAATACT-
1 ACATTAATAAAT-AATAATA
*
20474 ACGACTAATAAATAATAATA
1 AC-ATTAATAAATAATAATA
20494 CCACCTGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.16
19 23 0.74
20 3 0.10
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (19 bp):
ACATTAATAAATAATAATA
Found at i:21701 original size:14 final size:15
Alignment explanation
Indices: 21669--21707 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
21659 TACAACAAAA
21669 AAAAATAATTTACTC
1 AAAAATAATTTACTC
21684 AAAAATAATTTACT-
1 AAAAATAATTTACTC
*
21698 AAAAAAAATT
1 AAAAATAATT
21708 AATTGTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAATAATTTACTC
Found at i:23869 original size:5 final size:5
Alignment explanation
Indices: 23847--23890 Score: 70
Period size: 5 Copynumber: 8.4 Consensus size: 5
23837 TTTGTGTTTG
23847 ATATA TATATA TATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATATA AT
23891 CAATAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.71
6 11 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:27413 original size:51 final size:52
Alignment explanation
Indices: 27313--27413 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
27303 AACAAGAATT
*
27313 GCAGGACAACTTCGGCCCATAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
* * *
27365 GCAGGACAACTTTGGCCTAGAACTTGTT-GACTTCGGGACAGAAGTTGTT
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTT
27414 ACGGAAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 20 0.44
52 25 0.56
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (52 bp):
GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
Found at i:31626 original size:8 final size:8
Alignment explanation
Indices: 31613--31637 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31603 TCGAACTCAT
31613 CTTGAAGA
1 CTTGAAGA
31621 CTTGAAGA
1 CTTGAAGA
31629 CTTGAAGA
1 CTTGAAGA
31637 C
1 C
31638 CATTGAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (8 bp):
CTTGAAGA
Found at i:50954 original size:16 final size:16
Alignment explanation
Indices: 50933--50974 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
50923 CTCTATTTAT
50933 GTGGCATGGCCTAGAG
1 GTGGCATGGCCTAGAG
*
50949 GTGGCATGGGCTAGAG
1 GTGGCATGGCCTAGAG
*
50965 GTGTCATGGC
1 GTGGCATGGC
50975 GTGGATGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (16 bp):
GTGGCATGGCCTAGAG
Found at i:57066 original size:18 final size:18
Alignment explanation
Indices: 57043--57089 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
57033 TGAAATTTAT
57043 TAATTATTAAATAAATAA
1 TAATTATTAAATAAATAA
***
57061 TAATTATTTTCTAAATAA
1 TAATTATTAAATAAATAA
*
57079 TTATTATTAAA
1 TAATTATTAAA
57090 ATCATCATTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTATTAAATAAATAA
Found at i:70952 original size:24 final size:24
Alignment explanation
Indices: 70920--70967 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
70910 GAAAGCAAAC
70920 TAGGTAATGGGCTTTTCAATGATG
1 TAGGTAATGGGCTTTTCAATGATG
*
70944 TAGGTAATGGGTTTTTCAATGATG
1 TAGGTAATGGGCTTTTCAATGATG
70968 AAAAAGCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.06, G:0.29, T:0.40
Consensus pattern (24 bp):
TAGGTAATGGGCTTTTCAATGATG
Done.