Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012726.1 Corchorus olitorius cultivar O-4 contig12759, 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: 20707
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4100 original size:43 final size:42
Alignment explanation
Indices: 4046--4139 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 42
4036 TTGATAAAAG
* *
4046 ACCTCAATTGAAATTTTGATAACAACCTTATGTAACTTTGATA
1 ACCTCATTTGAAATTTTGATAACAACCTT-TATAACTTTGATA
* * * *
4089 ACCTCATTTGAAATTTTGGTAACCATCTTTATAATTTTGATA
1 ACCTCATTTGAAATTTTGATAACAACCTTTATAACTTTGATA
4131 ACCTTCATT
1 ACC-TCATT
4140 AAAAATTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
42 14 0.32
43 30 0.68
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (42 bp):
ACCTCATTTGAAATTTTGATAACAACCTTTATAACTTTGATA
Found at i:4104 original size:82 final size:82
Alignment explanation
Indices: 3967--4118 Score: 189
Period size: 82 Copynumber: 1.9 Consensus size: 82
3957 TTTAATAACT
* ** * *
3967 TCAATTGAAATTTTGGCAACTGCCTTTTGAAACTTTGAAACCACCCTTGGAAATTTTGAAAACCA
1 TCAATTGAAATTTTGACAACAACCTTATGAAACTTTGAAACCACCATTGGAAATTTTGAAAACCA
4032 TCTTTTGATAAAAGACC
66 TCTTTTGATAAAAGACC
* * * * **
4049 TCAATTGAAATTTTGATAACAACCTTATGTAACTTTGATAACC-TCATTTGAAATTTTGGTAACC
1 TCAATTGAAATTTTGACAACAACCTTATGAAACTTTGA-AACCACCATTGGAAATTTTGAAAACC
4113 ATCTTT
65 ATCTTT
4119 ATAATTTTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
82 54 0.93
83 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (82 bp):
TCAATTGAAATTTTGACAACAACCTTATGAAACTTTGAAACCACCATTGGAAATTTTGAAAACCA
TCTTTTGATAAAAGACC
Found at i:4111 original size:21 final size:21
Alignment explanation
Indices: 4046--4139 Score: 75
Period size: 21 Copynumber: 4.4 Consensus size: 21
4036 TTGATAAAAG
*
4046 ACCTCAATTGAAATTTTGATA
1 ACCTCATTTGAAATTTTGATA
** * * *
4067 ACAACCTTATGTAACTTTGATA
1 ACCTCATT-TGAAATTTTGATA
*
4089 ACCTCATTTGAAATTTTGGTA
1 ACCTCATTTGAAATTTTGATA
4110 ACCATC-TTT-ATAATTTTGATA
1 ACC-TCATTTGA-AATTTTGATA
4131 ACCTTCATT
1 ACC-TCATT
4140 AAAAATTTGA
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 20 0.36
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
ACCTCATTTGAAATTTTGATA
Found at i:4148 original size:21 final size:20
Alignment explanation
Indices: 4082--4149 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
4072 CTTATGTAAC
*
4082 TTTGATAACCTCATTTGAAAT
1 TTTGATAACCTCA-TTAAAAT
* * *
4103 TTTGGTAACCATCTTTATAAT
1 TTTGATAACC-TCATTAAAAT
*
4124 TTTGATAACCTTCATTAAAAA
1 TTTGATAACC-TCATTAAAAT
4145 TTTGA
1 TTTGA
4150 AAATACCTCT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (20 bp):
TTTGATAACCTCATTAAAAT
Found at i:12008 original size:18 final size:19
Alignment explanation
Indices: 11985--12021 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11975 CACTACCCAA
11985 TAATGTTC-TACATTTTAT
1 TAATGTTCTTACATTTTAT
*
12003 TAATGTTCTTATATTTTAT
1 TAATGTTCTTACATTTTAT
12022 ATTCTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.59
Consensus pattern (19 bp):
TAATGTTCTTACATTTTAT
Found at i:13641 original size:9 final size:9
Alignment explanation
Indices: 13627--13670 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
13617 CACGTTAACT
13627 ATATATATA
1 ATATATATA
13636 ATATATATA
1 ATATATATA
13645 ATA-ATATA
1 ATATATATA
13653 ATA-ATATTA
1 ATATATA-TA
*
13662 ATATTTATA
1 ATATATATA
13671 TTGCGTCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 11 0.34
9 19 0.59
10 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATATA
Found at i:13665 original size:14 final size:16
Alignment explanation
Indices: 13626--13665 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
13616 CCACGTTAAC
13626 TATAT-ATATAATATA
1 TATATAATATAATATA
13641 TATAATAATATAATA-A
1 TAT-ATAATATAATATA
13657 TAT-TAATAT
1 TATATAATAT
13666 TTATATTGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 3 0.13
16 6 0.26
17 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATAATATAATATA
Found at i:15117 original size:22 final size:22
Alignment explanation
Indices: 15092--15146 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
15082 TTAAAATTCC
*
15092 ATAGGAAGGTTAATAGAAGTTA
1 ATAGGAAGGTTAATAAAAGTTA
* * *
15114 ATAGGAAAGTTAATAAAATTTC
1 ATAGGAAGGTTAATAAAAGTTA
*
15136 ATAGAAAGGTT
1 ATAGGAAGGTT
15147 CTCGAAATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (22 bp):
ATAGGAAGGTTAATAAAAGTTA
Found at i:15123 original size:12 final size:12
Alignment explanation
Indices: 15092--15128 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
15082 TTAAAATTCC
*
15092 ATAGGAAGGTTA
1 ATAGGAAAGTTA
15104 ATA-G-AAGTTA
1 ATAGGAAAGTTA
15114 ATAGGAAAGTTA
1 ATAGGAAAGTTA
15126 ATA
1 ATA
15129 AAATTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (12 bp):
ATAGGAAAGTTA
Found at i:17590 original size:143 final size:143
Alignment explanation
Indices: 17332--17759 Score: 696
Period size: 143 Copynumber: 3.0 Consensus size: 143
17322 GCCTCCAAAG
*
17332 AGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCAATT
1 AGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATTT
*
17397 GATTATAAAGAACCAATATATTAAGAGGTAGCTTAAATCATGGTGGCCGGTTTAGAATGGTAAAT
66 GATTATAAAGAACCCATATATTAAGAGGTAGCTTAAATCATGGTGGCCGGTTTAGAATGGTAAAT
17462 CCCCCATGGTTTA
131 CCCCCATGGTTTA
* * *
17475 AGTGTCCTTATTCGTCTTCAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATTT
1 AGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATTT
17540 GATTATAAAGAACCCATATATTAAGAGGTAGCTTAAATCATGGTGGCCGGTTTAGAATGGTAAAT
66 GATTATAAAGAACCCATATATTAAGAGGTAGCTTAAATCATGGTGGCCGGTTTAGAATGGTAAAT
17605 -CCCCAGTGGTTTA
131 CCCCCA-TGGTTTA
* * * *
17618 AGTGTCTTTATTCTTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACAATGGTGGTTACCATTT
1 AGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATTT
* * * ** **
17683 GATTATAAAGAACCCGTATATCAAGAAGTAGCTTAAATCATGGTAACCGGCCTAGAATGGTAAAT
66 GATTATAAAGAACCCATATATTAAGAGGTAGCTTAAATCATGGTGGCCGGTTTAGAATGGTAAAT
17748 CCCCCATGGTTT
131 CCCCCATGGTTT
17760 CCTTTTCCTT
Statistics
Matches: 265, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
142 5 0.02
143 255 0.96
144 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (143 bp):
AGTGTCTTTATTCCTCTTGAAGGCTACCATTGTGGTGGTAACTCCAACTAGGGTGGTCACCATTT
GATTATAAAGAACCCATATATTAAGAGGTAGCTTAAATCATGGTGGCCGGTTTAGAATGGTAAAT
CCCCCATGGTTTA
Found at i:18001 original size:72 final size:70
Alignment explanation
Indices: 17832--18033 Score: 250
Period size: 72 Copynumber: 2.9 Consensus size: 70
17822 TCATCTTAAG
* * *
17832 GTCCACTTATGTGGCAAGGCTTTGGTGATCATG-AGCGCCT-TAGCTCTCACCTAGTCTTT-ATT
1 GTCCACTTATGTGGCAAGGCATTGGTGAT--TGTAGCGTCTATAGCTCTCACCTTGTCTTTAATT
*
17894 TGCAAAA
64 TACAAAA
*
17901 GTCCACTTACGTGGCAAGGCATTGGTGATTGTAGCGGTCTATAGCTCTCACCTTGTCTTTAAAAT
1 GTCCACTTATGTGGCAAGGCATTGGTGATTGTAGC-GTCTATAGCTCTCACCTTGTCTTT--AAT
*
17966 TTACAAAT
63 TTACAAAA
* *
17974 GTCCAC-TATGTGGCAAGGCATTGGTGATTGTAGCAATCTATTGCTCTCACCTTGTCTTTA
1 GTCCACTTATGTGGCAAGGCATTGGTGATTGTAGC-GTCTATAGCTCTCACCTTGTCTTTA
18034 TTGTTATGGC
Statistics
Matches: 117, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
67 2 0.02
68 3 0.03
69 30 0.26
70 19 0.16
72 49 0.42
73 14 0.12
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (70 bp):
GTCCACTTATGTGGCAAGGCATTGGTGATTGTAGCGTCTATAGCTCTCACCTTGTCTTTAATTTA
CAAAA
Found at i:18424 original size:147 final size:147
Alignment explanation
Indices: 18204--18483 Score: 375
Period size: 147 Copynumber: 1.9 Consensus size: 147
18194 CTGGAGAGAT
* ** * * * *
18204 ACTGTTCATGACCTCTGATGGGATGTTGGACCCACTATCTAGTACTGTTGGGACTCACAGCAAGT
1 ACTGCTCATGACCTCTGATGGGATGCCGGACCCACTATCAAGCACTGTTGGGACCCACAGCAAGC
* * * * *
18269 TGATGTGGCAACACCCGAAACATGCTGATGGTGTAGCTCACTAATA-GATGAGTTTATTGTTTTC
66 TGACGTGGCAACACCCGAAACATGCTGATAGTGGAGCTCACTAATAGGA-GAGTTTATTATTGTC
18333 GGCCCCTGTTGGAAGGTC
130 GGCCCCTGTTGGAAGGTC
*
18351 ACTGCTCATGACCTCT-ACTGGGATGCCGGACCCACTGTCAAGCACTGTTGGGACCCACAGCAAG
1 ACTGCTCATGACCTCTGA-TGGGATGCCGGACCCACTATCAAGCACTGTTGGGACCCACAGCAAG
* * * *
18415 CTGACGTGGCAACACCCGAGATATGCTGATAGTGGGGCTCGCTAATAGGAGAGTTTATTATTGTC
65 CTGACGTGGCAACACCCGAAACATGCTGATAGTGGAGCTCACTAATAGGAGAGTTTATTATTGTC
18480 GGCC
130 GGCC
18484 TTTGCTGGAA
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
146 1 0.01
147 111 0.97
148 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (147 bp):
ACTGCTCATGACCTCTGATGGGATGCCGGACCCACTATCAAGCACTGTTGGGACCCACAGCAAGC
TGACGTGGCAACACCCGAAACATGCTGATAGTGGAGCTCACTAATAGGAGAGTTTATTATTGTCG
GCCCCTGTTGGAAGGTC
Found at i:18650 original size:21 final size:20
Alignment explanation
Indices: 18624--18663 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18614 CTCTAAATTC
*
18624 CATTATCTATTCATCTATTTT
1 CATTATCTATT-ATCCATTTT
*
18645 CATTATTTATTATCCATTT
1 CATTATCTATTATCCATTT
18664 ATTAAAGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.57
Consensus pattern (20 bp):
CATTATCTATTATCCATTTT
Found at i:20363 original size:124 final size:124
Alignment explanation
Indices: 20093--20322 Score: 311
Period size: 124 Copynumber: 1.9 Consensus size: 124
20083 TGTGGGACTG
* ** * * * *
20093 CCTTGCTGGCGTGTCACTCTGTTGAGAAGCAGGTTCCGCTGCTGGAAAGTGATGCTGGGTACTTT
1 CCTTGCTGACGTGTCACTCTGCCGAGAAGGACGTTCCGCTGCTGGAAAGTGATGCTGGGCACTTC
*
20158 AAACAAAGTCTTATCCTTCATCAACAAAGGAGGTCAATAGCATGGCTAACCCGGTTCAA
66 AAACAAAGTCGTATCCTTCATCAACAAAGGAGGTCAATAGCATGGCTAACCCGGTTCAA
*
20217 CCTTGCTGACGTGTCACTCTGCCGAGAAGGACGTTCCGCTGCT-GAGAAGTGCTGCTGGGCACTT
1 CCTTGCTGACGTGTCACTCTGCCGAGAAGGACGTTCCGCTGCTGGA-AAGTGATGCTGGGCACTT
* * * *
20281 CAATCGAAGTTCGTCT-CTTCATCAACAAAGGAGGTCAGTAGC
65 CAAACAAAG-TCGTATCCTTCATCAACAAAGGAGGTCAATAGC
20323 GTGGTTCCCG
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
123 2 0.02
124 85 0.93
125 4 0.04
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (124 bp):
CCTTGCTGACGTGTCACTCTGCCGAGAAGGACGTTCCGCTGCTGGAAAGTGATGCTGGGCACTTC
AAACAAAGTCGTATCCTTCATCAACAAAGGAGGTCAATAGCATGGCTAACCCGGTTCAA
Found at i:20656 original size:2 final size:2
Alignment explanation
Indices: 20649--20698 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
20639 GACCCCCAAC
20649 AT AT AT AT AT AT 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 AT AT AT AT AT AT
20691 ACT AT AT A
1 A-T AT AT A
20699 GTANATACT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.