Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013821.1 Corchorus olitorius cultivar O-4 contig13854, 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: 34138
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:11843 original size:19 final size:18
Alignment explanation
Indices: 11810--11845 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11800 TTGAGATAAT
11810 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
11828 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
11846 TAAGTCTTCA
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:20154 original size:54 final size:54
Alignment explanation
Indices: 20075--20462 Score: 469
Period size: 54 Copynumber: 7.2 Consensus size: 54
20065 TTCATAAGCC
*
20075 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGCTTACTCT
1 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* * * * * *
20129 TTCTTTTAATTTTTATCTTAATTACTCCGAATTAAATTAATTATTGTTTACTCT
1 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* * * *
20183 TTCTTTTACTTTTTAGCTTAATTACTCTGAAGTAAACTAATTATTGTTTACTCT
1 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* *
20237 TTCTTTTACTCTTTAGCCTAATTACTCAGAATTAAACTAATTACTGCTTACTCT
1 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* * *
20291 TTCTTTTACTCTTTAGCTTAATTACTCATAATTAAACT--TTACTGTTTACGCC
1 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* * * *
20343 TTCTTTTACT-TCTTAG-TTTATTAACCCTGAATTAAACTAATTACTGTTTGCTCT
1 TTCTTTTACTCT-TTAGCTTAATT-ACTCAGAATTAAACTAATTACTGTTTACTCT
* * * * * * *
20397 TTCTTTTACTCTATAGCTTAATTACTCTTGAATCAAATTAATCTTCCGATTACTCT
1 TTCTTTTACTCTTTAGCTTAATTACTC-AGAATTAAACTAAT-TACTGTTTACTCT
20453 TTCTTTTACT
1 TTCTTTTACT
20463 TCTGATTACT
Statistics
Matches: 287, Mismatches: 39, Indels: 14
0.84 0.11 0.04
Matches are distributed among these distances:
51 6 0.02
52 37 0.13
54 207 0.72
55 18 0.06
56 19 0.07
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (54 bp):
TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
Found at i:20269 original size:108 final size:107
Alignment explanation
Indices: 20075--20940 Score: 521
Period size: 108 Copynumber: 8.3 Consensus size: 107
20065 TTCATAAGCC
* * *
20075 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGCTTACTCTTTCTTTTAATT
1 TTCTTTTACTCTTTAGCTTAATTACTCTGAATTAAACTAATTACTGTTTACTCTTTCTTTT-ACT
* * * *
20140 TTTATCTTAATTACTCCGAATTAAATTAATTATTGTTTACTCT
65 TTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* * *
20183 TTCTTTTACTTTTTAGCTTAATTACTCTGAAGTAAACTAATTATTGTTTACTCTTTCTTTTACTC
1 TTCTTTTACTCTTTAGCTTAATTACTCTGAATTAAACTAATTACTGTTTACTCTTTCTTTTACT-
* *
20248 TTTAGCCTAATTACTCAGAATTAAACTAATTACTGCTTACTCT
65 TTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* *
20291 TTCTTTTACTCTTTAGCTTAATTACTCAT-AATTAAACT--TTACTGTTTACGCCTTCTTTTACT
1 TTCTTTTACTCTTTAGCTTAATTACTC-TGAATTAAACTAATTACTGTTTACTCTTTCTTTTACT
* * * *
20353 TCTTAG-TTTATTAACCCTGAATTAAACTAATTACTGTTTGCTCT
65 T-TTAGCTTAATT-ACTCAGAATTAAACTAATTACTGTTTACTCT
* * * * * *
20397 TTCTTTTACTCTATAGCTTAATTACTCTTGAATCAAATTAATCTTCCGATTACTCTTTCTTTTAC
1 TTCTTTTACTCTTTAGCTTAATTACTC-TGAATTAAACTAAT-TACTGTTTACTCTTTCTTTTAC
* * *** * * *
20462 --TT--C-TGATTACTC---TTTCTTCTACTT-CTGATTACTCC
64 TTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* * * * ** * * * *
20497 TTCTTCTACTTCTGATTA-CTCT--TTA-TTTTACTT---CCGATCACTCTTT-CT-TCTACTCT
1 TTCTTTTAC-TCT--TTAGCT-TAATTACTCTGAATTAAACTAATTACTGTTTACTCT-TTCTTT
* * *
20553 T--TTTTAGTTTAATTACTCTTGAATTAAACTAATCTACTGCTTACTCT
61 TACTTTTAGCTTAATTACTC-AGAATTAAACTAAT-TACTGTTTACTCT
* * * *
20600 TTCTTTTACTCTTTAGCTTAATTACCCTGAATTAAACTAACTACCGATTAC-C-TTCTTTTTACT
1 TTCTTTTACTCTTTAGCTTAATTACTCTGAATTAAACTAATTACTGTTTACTCTTTC-TTTTACT
* * * * *
20663 TCTTAGTTTAATTTCTCTGAATTAAACTAACTACTGATTAC-C-
65 T-TTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
* * * * * *
20705 ATC-TTTACTCTTTTTAGTTTAACTT-CTCTGAATTAAACTAACTACTGATCAC-C-ATCTTTTA
1 TTCTTTTACTC--TTTAGCTTAA-TTACTCTGAATTAAACTAATTACTGTTTACTCTTTCTTTTA
* * * *
20766 CTTTTTAGCTTAACTT-CTCTGAATTAAATTAACTACTGATTAC-C-
63 C-TTTTAGCTTAA-TTACTCAGAATTAAACTAATTACTGTTTACTCT
* * * * *
20810 ATCTTTTACTTTTTAGCTT-ATCTTCTCTGAACT---CT--TT-CT-TTTACTTCTTT-GTTT--
1 TTCTTTTACTCTTTAGCTTAAT-TACTCTGAATTAAACTAATTACTGTTTAC-TCTTTCTTTTAC
* *
20864 TTTTAGCTTAATTACTCTGAATTAAACTAATTACTGATTACTCT
64 TTTTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
*
20908 TT-TCTTTACTTTTTTTAGCTTAATTACTCTGAA
1 TTCT-TTTAC--TCTTTAGCTTAATTACTCTGAA
20941 ATAAGTCTTT
Statistics
Matches: 598, Mismatches: 104, Indels: 120
0.73 0.13 0.15
Matches are distributed among these distances:
93 1 0.00
94 9 0.02
95 5 0.01
96 38 0.06
97 13 0.02
98 8 0.01
99 8 0.01
100 40 0.07
101 25 0.04
102 10 0.02
103 26 0.04
104 25 0.04
105 57 0.10
106 135 0.23
107 23 0.04
108 142 0.24
109 16 0.03
110 17 0.03
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (107 bp):
TTCTTTTACTCTTTAGCTTAATTACTCTGAATTAAACTAATTACTGTTTACTCTTTCTTTTACTT
TTAGCTTAATTACTCAGAATTAAACTAATTACTGTTTACTCT
Found at i:20326 original size:162 final size:160
Alignment explanation
Indices: 20075--20462 Score: 517
Period size: 162 Copynumber: 2.4 Consensus size: 160
20065 TTCATAAGCC
* *
20075 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGCTTACTCTTTCTTTTAATT
1 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGCTTACTCTTTCTTTTACTC
* * * * * * *
20140 TTTATCTTAATTACTCCGAATTAAATTAATTATTGTTTACTCTTTCTTTTACTTTTTAGCTTAAT
66 TTTAGCTTAATTACTCAGAATTAAACT--TTACTGTTTACGCCTTCTTTTACTTCTTAG-TTAAT
* *
20205 T-ACTCTGAAGTAAACTAATTATTGTTTACTCT
128 TAACCCTGAAGTAAACTAATTACTGTTTACTCT
*
20237 TTCTTTTACTCTTTAGCCTAATTACTCAGAATTAAACTAATTACTGCTTACTCTTTCTTTTACTC
1 TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGCTTACTCTTTCTTTTACTC
* *
20302 TTTAGCTTAATTACTCATAATTAAACTTTACTGTTTACGCCTTCTTTTACTTCTTAGTTTATTAA
66 TTTAGCTTAATTACTCAGAATTAAACTTTACTGTTTACGCCTTCTTTTACTTCTTAGTTAATTAA
* *
20367 CCCTGAATTAAACTAATTACTGTTTGCTCT
131 CCCTGAAGTAAACTAATTACTGTTTACTCT
* * * * * * *
20397 TTCTTTTACTCTATAGCTTAATTACTCTTGAATCAAATTAATCTTCCGATTACTCTTTCTTTTAC
1 TTCTTTTACTCTTTAGCTTAATTACTC-AGAATTAAACTAAT-TACTGCTTACTCTTTCTTTTAC
20462 T
64 T
20463 TCTGATTACT
Statistics
Matches: 199, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
159 5 0.03
160 78 0.39
161 11 0.06
162 105 0.53
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (160 bp):
TTCTTTTACTCTTTAGCTTAATTACTCAGAATTAAACTAATTACTGCTTACTCTTTCTTTTACTC
TTTAGCTTAATTACTCAGAATTAAACTTTACTGTTTACGCCTTCTTTTACTTCTTAGTTAATTAA
CCCTGAAGTAAACTAATTACTGTTTACTCT
Found at i:20469 original size:22 final size:22
Alignment explanation
Indices: 20439--20550 Score: 161
Period size: 22 Copynumber: 5.1 Consensus size: 22
20429 TCAAATTAAT
* *
20439 CTTCCGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTCTA
20461 CTTCTGATTACTCTTTCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
*
20483 CTTCTGATTACTCCTTCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
* *
20505 CTTCTGATTACTCTTTATTTTA
1 CTTCTGATTACTCTTTCTTCTA
* *
20527 CTTCCGATCACTCTTTCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
20549 CT
1 CT
20551 CTTTTTTAGT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 80 1.00
ACGTcount: A:0.14, C:0.29, G:0.04, T:0.53
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTCTA
Found at i:20792 original size:52 final size:52
Alignment explanation
Indices: 20553--20840 Score: 348
Period size: 53 Copynumber: 5.4 Consensus size: 52
20543 CTTCTACTCT
* * *
20553 TTTTTAGTTTAA-TTACTCTTGAATTAAACTAATCTACTGCTTACTCTTTCTTTTAC
1 TTTTTAGCTTAACTT-CTC-TGAATTAAACTAA-CTACTGATTAC-C-ATCTTTTAC
* * * *
20609 TCTTTAGCTTAA-TTACCCTGAATTAAACTAACTACCGATTACCTTCTTTTTAC
1 TTTTTAGCTTAACTT-CTCTGAATTAAACTAACTACTGATTACCATC-TTTTAC
* * *
20662 TTCTTAGTTTAATTTCTCTGAATTAAACTAACTACTGATTACCATC-TTTACTC
1 TTTTTAGCTTAACTTCTCTGAATTAAACTAACTACTGATTACCATCTTTTA--C
* *
20715 TTTTTAGTTTAACTTCTCTGAATTAAACTAACTACTGATCACCATCTTTTAC
1 TTTTTAGCTTAACTTCTCTGAATTAAACTAACTACTGATTACCATCTTTTAC
*
20767 TTTTTAGCTTAACTTCTCTGAATTAAATTAACTACTGATTACCATCTTTTAC
1 TTTTTAGCTTAACTTCTCTGAATTAAACTAACTACTGATTACCATCTTTTAC
*
20819 TTTTTAGCTTATCTTCTCTGAA
1 TTTTTAGCTTAACTTCTCTGAA
20841 CTCTTTCTTT
Statistics
Matches: 209, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
51 4 0.02
52 74 0.35
53 88 0.42
54 15 0.07
55 13 0.06
56 15 0.07
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (52 bp):
TTTTTAGCTTAACTTCTCTGAATTAAACTAACTACTGATTACCATCTTTTAC
Found at i:20799 original size:105 final size:105
Alignment explanation
Indices: 20553--20840 Score: 345
Period size: 105 Copynumber: 2.7 Consensus size: 105
20543 CTTCTACTCT
* *
20553 TTTTTAGTTTAATTACTCTTGAATTAAACTAATCTACTGCTTACTCTTTCTTTTACTC--TTTAG
1 TTTTTAGTTTAATT-CTC-TGAATTAAACTAA-CTACTGATTAC-C-ATC-TTTACTCTTTTTAG
* * *
20616 CTTAA-TTACCCTGAATTAAACTAACTACCGATTACCTTCTTTTTAC
60 CTTAACTT-CTCTGAATTAAACTAACTACCGATCACCATCTTTTTAC
* *
20662 TTCTTAGTTTAATTTCTCTGAATTAAACTAACTACTGATTACCATCTTTACTCTTTTTAGTTTAA
1 TTTTTAGTTTAA-TTCTCTGAATTAAACTAACTACTGATTACCATCTTTACTCTTTTTAGCTTAA
*
20727 CTTCTCTGAATTAAACTAACTACTGATCACCATC-TTTTAC
65 CTTCTCTGAATTAAACTAACTACCGATCACCATCTTTTTAC
* *
20767 TTTTTAGCTTAACTTCTCTGAATTAAATTAACTACTGATTACCATCTTT--TACTTTTTAGCTTA
1 TTTTTAGTTTAA-TTCTCTGAATTAAACTAACTACTGATTACCATCTTTACT-CTTTTTAGCTTA
*
20830 TCTTCTCTGAA
64 ACTTCTCTGAA
20841 CTCTTTCTTT
Statistics
Matches: 160, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
103 1 0.01
104 28 0.17
105 53 0.33
106 37 0.23
107 12 0.08
108 13 0.08
109 14 0.09
110 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (105 bp):
TTTTTAGTTTAATTCTCTGAATTAAACTAACTACTGATTACCATCTTTACTCTTTTTAGCTTAAC
TTCTCTGAATTAAACTAACTACCGATCACCATCTTTTTAC
Found at i:20966 original size:36 final size:37
Alignment explanation
Indices: 20920--21026 Score: 94
Period size: 40 Copynumber: 2.8 Consensus size: 37
20910 TCTTTACTTT
20920 TTTTAGCTTAATTACTCTGAAATAAGTCTTTGA-C-TAC
1 TTTTA-CTTAATTAC-CTGAAATAAGTCTTTGACCTTAC
* ** *
20957 TTTTACTTAATTTCCTTGAGTTAAGTCTTTGACTGCTTGC
1 TTTTACTTAATTACC-TGAAATAAGTCTTTGAC--CTTAC
20997 TTTTACTTAATTACCCT-AAATTAAGTCTTT
1 TTTTACTTAATTA-CCTGAAA-TAAGTCTTT
21027 ACTGATTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
35 1 0.02
36 22 0.39
37 5 0.09
39 2 0.04
40 24 0.43
41 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (37 bp):
TTTTACTTAATTACCTGAAATAAGTCTTTGACCTTAC
Found at i:23914 original size:19 final size:18
Alignment explanation
Indices: 23890--23925 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23880 TGAAGACTTA
23890 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
23909 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
23926 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:29010 original size:29 final size:31
Alignment explanation
Indices: 28978--29040 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
28968 AGGATTAGTT
28978 ATTTAATTTATG-CCTTAATTTTCAA-TTTC
1 ATTTAATTTATGTCCTTAATTTTCAAGTTTC
* *
29007 ATTTATTTTATGTCTTTAATTTTCAAGTTTC
1 ATTTAATTTATGTCCTTAATTTTCAAGTTTC
29038 ATT
1 ATT
29041 AATAAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.37
30 12 0.40
31 7 0.23
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (31 bp):
ATTTAATTTATGTCCTTAATTTTCAAGTTTC
Found at i:29391 original size:22 final size:20
Alignment explanation
Indices: 29345--29398 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
29335 TTATTTCCCC
29345 AATTTTTGAAAAAAAAATCG
1 AATTTTTGAAAAAAAAATCG
* **
29365 GATTTTTGAAGATAAAATTTCG
1 AATTTTTGAA-A-AAAAAATCG
*
29387 AATTTTTCAAAA
1 AATTTTTGAAAA
29399 CCTTTTGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.37
21 2 0.07
22 15 0.56
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTTTTGAAAAAAAAATCG
Found at i:29706 original size:17 final size:18
Alignment explanation
Indices: 29684--29719 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29674 AAAGGGGAAT
*
29684 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
29701 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
29719 T
1 T
29720 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:31215 original size:18 final size:19
Alignment explanation
Indices: 31187--31224 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
31177 CTCTTCTTCT
31187 TTTTCTCTTCTAGTTCTAG
1 TTTTCTCTTCTAGTTCTAG
*
31206 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTCTAG
31224 T
1 T
31225 GTCACGCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.63
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTCTAG
Found at i:33696 original size:29 final size:29
Alignment explanation
Indices: 33633--33711 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
33623 GGAGAATTGT
33633 GAGAATTGTGAAGCCTAAATT-AGGAGGG
1 GAGAATTGTGAAGCCTAAATTAAGGAGGG
33661 GAGAATTGTGAAGCCTAAATTAAGGAGGG
1 GAGAATTGTGAAGCCTAAATTAAGGAGGG
33690 GAGAATTGTGAAGCCTAAATTA
1 GAGAATTGTGAAGCCTAAATTA
33712 GTATTTTCCT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 21 0.42
29 29 0.58
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.23
Consensus pattern (29 bp):
GAGAATTGTGAAGCCTAAATTAAGGAGGG
Done.