Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022972.1 Corchorus olitorius cultivar O-4 contig23005, 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: 76774
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1362 original size:51 final size:52
Alignment explanation
Indices: 1261--1362 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 52
1251 GTTCTTCATA
* **
1261 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
*
1313 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
1363 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 2 0.05
51 37 0.84
52 5 0.11
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
Found at i:4163 original size:13 final size:13
Alignment explanation
Indices: 4145--4170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4135 AAGGTAACAA
4145 CAAAAATCATCAC
1 CAAAAATCATCAC
4158 CAAAAATCATCAC
1 CAAAAATCATCAC
4171 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:20740 original size:21 final size:21
Alignment explanation
Indices: 20691--20740 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
20681 ACTGAGATTG
*
20691 TGAGATTAAACACTGTACAGA
1 TGAGATTAAACACTATACAGA
* * * *
20712 TCAAATTAGATACTATACAGA
1 TGAGATTAAACACTATACAGA
20733 TGAGATTA
1 TGAGATTA
20741 TAATCAGCGA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (21 bp):
TGAGATTAAACACTATACAGA
Found at i:21105 original size:13 final size:12
Alignment explanation
Indices: 21074--21115 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
21064 ACTCCATTAC
*
21074 AAAAATCCAAAA
1 AAAAATACAAAA
21086 AAAAATACAAAA
1 AAAAATACAAAA
21098 GAAAAATA-AAGAA
1 -AAAAATACAA-AA
21111 AAAAA
1 AAAAA
21116 GTTTCACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.81, C:0.07, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAAATACAAAA
Found at i:27367 original size:23 final size:21
Alignment explanation
Indices: 27340--27395 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
27330 AATTTTAACG
27340 CAAAAAGCAGAGATTTTTTTTTT
1 CAAAAAGCA-A-ATTTTTTTTTT
* * *
27363 GAAAACGCAACTTTTTTTTTT
1 CAAAAAGCAAATTTTTTTTTT
27384 CAAAAACGCAAA
1 CAAAAA-GCAAA
27396 AACTAAATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 14 0.54
22 5 0.19
23 7 0.27
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (21 bp):
CAAAAAGCAAATTTTTTTTTT
Found at i:27379 original size:21 final size:22
Alignment explanation
Indices: 27353--27394 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
27343 AAAGCAGAGA
*
27353 TTTTTTTTTT-GAAAACGCAAC
1 TTTTTTTTTTCAAAAACGCAAC
27374 TTTTTTTTTTCAAAAACGCAA
1 TTTTTTTTTTCAAAAACGCAA
27395 AAACTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTTTTTTTTCAAAAACGCAAC
Found at i:29111 original size:19 final size:18
Alignment explanation
Indices: 29076--29115 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
29066 CCCTTGAAAT
29076 AATTCTTCAATTATCTTC
1 AATTCTTCAATTATCTTC
*
29094 AATTCTTCAAATTGTCTTC
1 AATTCTTC-AATTATCTTC
29113 AAT
1 AAT
29116 AAATTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTCTTCAATTATCTTC
Found at i:30871 original size:2 final size:2
Alignment explanation
Indices: 30864--30892 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30854 CCATTGAATA
30864 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
30893 GAAGTTTATT
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:32898 original size:75 final size:75
Alignment explanation
Indices: 32811--33023 Score: 363
Period size: 75 Copynumber: 2.8 Consensus size: 75
32801 CCTCTAAATC
* *
32811 ATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTCATCCTTCCTTTGCTCACA
1 ATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTTATCATTCCTTTGCTCACA
*
32876 TCTCGAAACA
66 CCTCGAAACA
32886 ATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTTATCATTCCTTTGCTCACA
1 ATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTTATCATTCCTTTGCTCACA
* *
32951 CCTCGAATCC
66 CCTCGAAACA
* *
32961 ATTGCTTTGACTAAAACTGATTTTGAAACATTTTTTGACTAAAACTTATCATTCCTTTGCTCA
1 ATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTTATCATTCCTTTGCTCA
33024 TAGTCCAAAT
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 131 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (75 bp):
ATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTTATCATTCCTTTGCTCACA
CCTCGAAACA
Found at i:33191 original size:3 final size:3
Alignment explanation
Indices: 33171--33232 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
33161 TTTTATTCAT
* * * * *
33171 TTA TTA CTA TTG TTA TTA TTA TTT TTA TTT TTA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
33219 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
33233 TAATGCAAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33199 original size:18 final size:18
Alignment explanation
Indices: 33178--33234 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
33168 CATTTATTAC
33178 TATTGTTATTATTATTTT
1 TATTGTTATTATTATTTT
* *
33196 TATTTTTATTATTATTAT
1 TATTGTTATTATTATTTT
33214 TATTGTTATTATTATTATT
1 TATTGTTATTATTATT-TT
33233 TA
1 TA
33235 ATGCAAACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 31 0.91
19 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
TATTGTTATTATTATTTT
Found at i:37886 original size:62 final size:63
Alignment explanation
Indices: 37815--37934 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 63
37805 ACACTAATGG
* * *
37815 GAACTTTCCCAATTTGAAAACTG-AAACCTGATAGGAACTTTTCTCA-TTTGAAAACTTGATCA
1 GAACTTTCCCAATTCGAAAACCGAAAACCTGATAGGAAC-TTTCCCATTTTGAAAACTTGATCA
* * *
37877 GAACTTTCCCAATTCGAAAACCGAAAACTTGGTGGGAACTTTCCCATTTTGAAAACTT
1 GAACTTTCCCAATTCGAAAACCGAAAACCTGATAGGAACTTTCCCATTTTGAAAACTT
37935 TGAAAACTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 27 0.54
63 23 0.46
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (63 bp):
GAACTTTCCCAATTCGAAAACCGAAAACCTGATAGGAACTTTCCCATTTTGAAAACTTGATCA
Found at i:37916 original size:35 final size:36
Alignment explanation
Indices: 37864--37962 Score: 119
Period size: 35 Copynumber: 2.8 Consensus size: 36
37854 TTTCTCATTT
* *
37864 GAAAACTTGATCAGAACTTTCCCAATTCGAAAAC-C
1 GAAAACTTGGTGAGAACTTTCCCAATTCGAAAACTC
* * * *
37899 GAAAACTTGGTGGGAACTTTCCCATTTTGAAAACTTT
1 GAAAACTTGGTGAGAACTTTCCCAATTCGAAAAC-TC
*
37936 GAAAACTTGGTGAGAATTTTCCCAATT
1 GAAAACTTGGTGAGAACTTTCCCAATT
37963 TAAAAACAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 29 0.55
37 24 0.45
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (36 bp):
GAAAACTTGGTGAGAACTTTCCCAATTCGAAAACTC
Found at i:37957 original size:37 final size:37
Alignment explanation
Indices: 37861--37969 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 37
37851 ACTTTTCTCA
* * *
37861 TTTGAAAACTTGATCAGAACTTTCCCAATTCGAAAAC
1 TTTGAAAACTTGGTGAGAACTTTCCCAATTTGAAAAC
* * *
37898 --CGAAAACTTGGTGGGAACTTTCCCATTTTGAAAAC
1 TTTGAAAACTTGGTGAGAACTTTCCCAATTTGAAAAC
* *
37933 TTTGAAAACTTGGTGAGAATTTTCCCAATTTAAAAAC
1 TTTGAAAACTTGGTGAGAACTTTCCCAATTTGAAAAC
37970 AGCTAAATTG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 29 0.49
37 30 0.51
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (37 bp):
TTTGAAAACTTGGTGAGAACTTTCCCAATTTGAAAAC
Found at i:53476 original size:18 final size:18
Alignment explanation
Indices: 53453--53489 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53443 CTCCTCTTGC
*
53453 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
53471 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
53489 A
1 A
53490 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:59848 original size:19 final size:18
Alignment explanation
Indices: 59815--59850 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
59805 TTGAGATAAT
59815 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
59833 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
59851 TAAGTCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:64055 original size:21 final size:21
Alignment explanation
Indices: 64031--64076 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
64021 AAGTTTTCGG
64031 TTTTGCG-ATAAAAAGAAAAAT
1 TTTTGCGCATAAAAA-AAAAAT
*
64052 TTTTGCGTCATAAAAAAAATAT
1 TTTTGCG-CATAAAAAAAAAAT
64074 TTT
1 TTT
64077 GTTTCTGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (21 bp):
TTTTGCGCATAAAAAAAAAAT
Done.