Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016142.1 Corchorus olitorius cultivar O-4 contig16175, 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: 5225
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Found at i:2303 original size:77 final size:78
Alignment explanation
Indices: 2173--2343 Score: 224
Period size: 77 Copynumber: 2.2 Consensus size: 78
2163 TTCATTTGAG
* *
2173 TAAACCTGCTTAGG-CCTCTGCTTAGATTTTTGTTTAATCAAACCTGCTTAGGTCCTTGTTTAG-
1 TAAACCTGCTTAGGTCCTCTGCTTAGACTTTCGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGA
* **
2236 AGTTTCGTTT-AA
66 ACTCCCGTTTAAA
* * *
2248 TCAAACCTGCTTAGGTCCT-TGTTTAGAACTTTCGTTTAATCGAACTTGCTTAGGTCCTTGTTTA
1 T-AAACCTGCTTAGGTCCTCTGCTTAG-ACTTTCGTTTAATCAAACCTGCTTAGGTCCTTGTTTA
2312 GAACTCCCGTTTAAA
64 GAACTCCCGTTTAAA
2327 TAAACCTGCTTAGGTCC
1 TAAACCTGCTTAGGTCC
2344 ACATTTAGAG
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
75 1 0.01
76 19 0.23
77 37 0.45
78 23 0.28
79 3 0.04
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (78 bp):
TAAACCTGCTTAGGTCCTCTGCTTAGACTTTCGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGA
ACTCCCGTTTAAA
Found at i:2376 original size:78 final size:77
Alignment explanation
Indices: 2207--2377 Score: 177
Period size: 78 Copynumber: 2.2 Consensus size: 77
2197 GATTTTTGTT
* ** ***
2207 TAATCAAACCTGCTTAGGTCCTTGTTTAGAGTTTCGTTTAATCAAACCTGCTTAGGTCCTTGTTT
1 TAATCAAACCTGCTTAGGTCCTTGTTTAGACTCCCGTTTAATCAAACCTGCTTAGGTCCACATTT
* * *
2272 AGAACTTTCGTT
66 AGAACTTCCATC
* *
2284 TAATCGAACTTGCTTAGGTCCTTGTTTAGAACTCCCGTTTAAAT-AAACCTGCTTAGGTCCACAT
1 TAATCAAACCTGCTTAGGTCCTTGTTTAG-ACTCCCGTTT-AATCAAACCTGCTTAGGTCCACAT
*
2348 TTAG-AGTTGCCATC
64 TTAGAACTT-CCATC
2362 TAAGT-AAACCTGCTTA
1 TAA-TCAAACCTGCTTA
2378 AGTTTATGTT
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
77 30 0.39
78 42 0.55
79 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (77 bp):
TAATCAAACCTGCTTAGGTCCTTGTTTAGACTCCCGTTTAATCAAACCTGCTTAGGTCCACATTT
AGAACTTCCATC
Found at i:2490 original size:33 final size:33
Alignment explanation
Indices: 2443--2505 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2433 TCATTTAAGA
* *
2443 AAACCTGCTTAGGTCT-CTACTTAGAATTTCTGT
1 AAACCTGCTGAGGTCTAC-ACGTAGAATTTCTGT
2476 AAACCTGCTGAGGTCTACACGTAGAATTTC
1 AAACCTGCTGAGGTCTACACGTAGAATTTC
2506 GTTTAATCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (33 bp):
AAACCTGCTGAGGTCTACACGTAGAATTTCTGT
Found at i:2578 original size:39 final size:38
Alignment explanation
Indices: 2058--2579 Score: 258
Period size: 38 Copynumber: 13.7 Consensus size: 38
2048 TCTATCTTAG
* **
2058 TAAACCTGTTTAGGT-CCTCGTTTAGAATTTCCATTTAA
1 TAAACCTGCTTAGGTCCCT-GTTTAGAATTTCTGTTTAA
* * * *
2096 GTACACCTGCTTAGGTCCATGTTTAGAATTTCAG-ATAA
1 -TAAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTTAA
* * * *
2134 GTAAACCTGCTTAGGACCCCTGCTTT-G-AGTTCAT-TTGAG
1 -TAAACCTGCTTAGG-TCCCTG-TTTAGAATTTC-TGTTTAA
* *
2173 TAAACCTGCTTAGG-CCTCTGCTTAG-ATTTTTGTTTAA
1 TAAACCTGCTTAGGTCC-CTGTTTAGAATTTCTGTTTAA
* *
2210 TCAAACCTGCTTAGGTCCTTGTTTAGAGTTTC-GTTTAA
1 T-AAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTTAA
*
2248 TCAAACCTGCTTAGGTCCTTGTTTAGAACTTTC-GTTTAA
1 T-AAACCTGCTTAGGTCCCTGTTTAGAA-TTTCTGTTTAA
* * * * * *
2287 TCGAACTTGCTTAGGTCCTTGTTTAGAACTCCCGTTTAAA
1 T-AAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTT-AA
* * * ** *
2327 TAAACCTGCTTAGGTCCAC-ATTTAGAGTTGCCATCTAA
1 TAAACCTGCTTAGGTCC-CTGTTTAGAATTTCTGTTTAA
* *** * * *
2365 GTAAACCTGCTTAAGTTTATGTTTGGAATCTC-ATTTAA
1 -TAAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTTAA
* * * ** *
2403 GGAAATCTCCTTAGGTCAATGTTTAGAATTTC-ATTTAA
1 -TAAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTTAA
* * **
2441 GAAAACCTGCTTAGGTCTCTACTTAGAATTTCTG-----
1 -TAAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTTAA
*
2475 TAAACCTGCTGAGGTCTACAC-G--TAGAATTTC-GTTTAA
1 TAAACCTGCTTAGGTC--C-CTGTTTAGAATTTCTGTTTAA
* * *
2512 TCGAACCTGCTTAGGTCCTTGTTTAGAAGTTCTGTTTAA
1 T-AAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTTAA
*
2551 TCAAACCTGCTTAGGTCCCTCTTTAGAAT
1 T-AAACCTGCTTAGGTCCCTGTTTAGAAT
2580 CTCACATTAG
Statistics
Matches: 377, Mismatches: 75, Indels: 62
0.73 0.15 0.12
Matches are distributed among these distances:
32 1 0.00
33 23 0.06
36 8 0.02
37 12 0.03
38 172 0.46
39 153 0.41
40 8 0.02
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (38 bp):
TAAACCTGCTTAGGTCCCTGTTTAGAATTTCTGTTTAA
Found at i:3031 original size:21 final size:21
Alignment explanation
Indices: 3001--3041 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2991 TTTATATGTT
3001 TGAGTAACTTGTTTCATTTCA
1 TGAGTAACTTGTTTCATTTCA
*
3022 TGAGTTACTTGTTTCATTTC
1 TGAGTAACTTGTTTCATTTC
3042 GTTACTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (21 bp):
TGAGTAACTTGTTTCATTTCA
Found at i:3050 original size:21 final size:21
Alignment explanation
Indices: 3007--3050 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2997 TGTTTGAGTA
*
3007 ACTTGTTTCATTTCATGAGTT
1 ACTTGTTTCATTTCATGACTT
* *
3028 ACTTGTTTCATTTCGTTACTT
1 ACTTGTTTCATTTCATGACTT
3049 AC
1 AC
3051 GTTTCTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.52
Consensus pattern (21 bp):
ACTTGTTTCATTTCATGACTT
Found at i:3103 original size:36 final size:36
Alignment explanation
Indices: 3056--3129 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
3046 CTTACGTTTC
* *
3056 TTTTAAATTTCCTAAATTCCTAGTCATAACCTTAGT
1 TTTTAAATTTCCTAAATTCCTAATCATAACCATAGT
*
3092 TTTTAAATTTCCTAAATTCCTAATCATAATCATAGT
1 TTTTAAATTTCCTAAATTCCTAATCATAACCATAGT
3128 TT
1 TT
3130 ATTCTCTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTAAATTTCCTAAATTCCTAATCATAACCATAGT
Found at i:4024 original size:17 final size:17
Alignment explanation
Indices: 3984--4132 Score: 181
Period size: 17 Copynumber: 8.4 Consensus size: 17
3974 TTGATACAAA
*
3984 AAAAATACAGTTCATACAAA
1 AAAAA-ACAGTTCATAC--C
*
4004 AAAAAATAGTTCATACC
1 AAAAAACAGTTCATACC
4021 AAAAAAACAGTTCATACC
1 -AAAAAACAGTTCATACC
*
4039 AAAAAACAGTTCATACA
1 AAAAAACAGTTCATACC
* *
4056 AAAAAACAATTCATACAAA
1 AAAAAACAGTTCATAC--C
4075 AAAAAACAGTTCATACC
1 AAAAAACAGTTCATACC
*
4092 AAAAAACATTTCATACC
1 AAAAAACAGTTCATACC
4109 AAAAAACAGTTCATACCC
1 AAAAAACAGTTCATA-CC
4127 AAAAAA
1 AAAAAA
4133 AAACAGTCAT
Statistics
Matches: 116, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
17 61 0.53
18 24 0.21
19 26 0.22
20 5 0.04
ACGTcount: A:0.58, C:0.19, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAAAACAGTTCATACC
Found at i:4076 original size:71 final size:71
Alignment explanation
Indices: 3983--4133 Score: 241
Period size: 70 Copynumber: 2.1 Consensus size: 71
3973 GTTGATACAA
* *
3983 AAAAAATACAGTTCATACAAAAAAAAATAGTTCATACCAAAAAAACAGTTCATACCAAAAAACAG
1 AAAAAA-ACAATTCATACAAAAAAAAACAGTTCATACC-AAAAAACAGTTCATACCAAAAAACAG
4048 TTCATA-C
64 TTCATACC
*
4055 AAAAAAACAATTCATACAAAAAAAAACAGTTCATACCAAAAAACATTTCATACCAAAAAACAGTT
1 AAAAAAACAATTCATACAAAAAAAAACAGTTCATACCAAAAAACAGTTCATACCAAAAAACAGTT
4120 CATACCC
66 CATA-CC
4127 AAAAAAA
1 AAAAAAA
4134 AACAGTCATT
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
70 31 0.42
71 29 0.39
72 14 0.19
ACGTcount: A:0.59, C:0.19, G:0.04, T:0.18
Consensus pattern (71 bp):
AAAAAAACAATTCATACAAAAAAAAACAGTTCATACCAAAAAACAGTTCATACCAAAAAACAGTT
CATACC
Found at i:4082 original size:53 final size:53
Alignment explanation
Indices: 3984--4139 Score: 215
Period size: 53 Copynumber: 2.9 Consensus size: 53
3974 TTGATACAAA
* *
3984 AAAAATACAGTTCATACAAAAAAAAATAGTTCATAC-CAAAAAAACAGTTCATACC
1 AAAAA-ACAGTTCATACAAAAAAACA-A-TTCATACAAAAAAAAACAGTTCATACC
4039 AAAAAACAGTTCATACAAAAAAACAATTCATACAAAAAAAAACAGTTCATACC
1 AAAAAACAGTTCATACAAAAAAACAATTCATACAAAAAAAAACAGTTCATACC
* * *
4092 AAAAAACATTTCATACCAAAAAACAGTTCATACCCAAAAAAAAACAGT
1 AAAAAACAGTTCATACAAAAAAACAATTCATA--CAAAAAAAAACAGT
4140 CATTGAGCAA
Statistics
Matches: 93, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
52 7 0.08
53 48 0.52
54 19 0.20
55 19 0.20
ACGTcount: A:0.58, C:0.19, G:0.04, T:0.18
Consensus pattern (53 bp):
AAAAAACAGTTCATACAAAAAAACAATTCATACAAAAAAAAACAGTTCATACC
Found at i:4868 original size:15 final size:15
Alignment explanation
Indices: 4848--4878 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4838 GCAGAGGTTG
4848 AAAGAAAACAATTAA
1 AAAGAAAACAATTAA
*
4863 AAAGAAAGCAATTAA
1 AAAGAAAACAATTAA
4878 A
1 A
4879 CTAGAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAGAAAACAATTAA
Done.