Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022490.1 Corchorus olitorius cultivar O-4 contig22523, 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: 92652
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2274 original size:10 final size:11
Alignment explanation
Indices: 2246--2273 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2236 CTTATTGTGG
2246 TTTTTTTCTTT
1 TTTTTTTCTTT
2257 TTTTTTTCTTT
1 TTTTTTTCTTT
2268 TTTTTT
1 TTTTTT
2274 CCTCATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:4666 original size:21 final size:23
Alignment explanation
Indices: 4627--4668 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
4617 CTTGTTAATA
4627 ACAGACAAAAGAGTAAGCAAAAG
1 ACAGACAAAAGAGTAAGCAAAAG
*
4650 ACAGA-AAAAGA-TGAGCAAA
1 ACAGACAAAAGAGTAAGCAAA
4669 CTTTTGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.62, C:0.12, G:0.21, T:0.05
Consensus pattern (23 bp):
ACAGACAAAAGAGTAAGCAAAAG
Found at i:20222 original size:36 final size:36
Alignment explanation
Indices: 20182--20254 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
20172 AATTCCAATG
* *
20182 TCTATAATTTGGCGCAAACACAGAAGTAAACCCATT
1 TCTATAATTTGGCACAAACACAAAAGTAAACCCATT
20218 TCTATAATTTGGCACAAACACAAAAGTAAACCCATT
1 TCTATAATTTGGCACAAACACAAAAGTAAACCCATT
20254 T
1 T
20255 GACCATTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (36 bp):
TCTATAATTTGGCACAAACACAAAAGTAAACCCATT
Found at i:30281 original size:21 final size:22
Alignment explanation
Indices: 30233--30281 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
30223 GATTCACCGT
*
30233 TTCATCATCATTATTACTGATA
1 TTCATCATCATTATTACTCATA
* *
30255 AT-ATCATCATTATTA-TCATC
1 TTCATCATCATTATTACTCATA
30275 TTCATCA
1 TTCATCA
30282 GCATCGTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.18
21 17 0.77
22 1 0.05
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (22 bp):
TTCATCATCATTATTACTCATA
Found at i:31979 original size:124 final size:129
Alignment explanation
Indices: 31696--31979 Score: 303
Period size: 124 Copynumber: 2.2 Consensus size: 129
31686 AAATATATTT
* *
31696 AAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT
1 AAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGT---AATAAAAT--GTAT
* *
31761 AATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTACTTTTAGTTGAGTAAAACTGTAA
61 AAT-A-GATATTAGATTTAATTAAATAAAAATAGAG---TTA-TTTTAGTTAAGTAAAACTATAA
**
31826 AAGTATATGC
120 AAGTATAAAC
* *
31836 AAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-TATAAT-
1 AAAAAATTCTAAGAAATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAATAAAATGTATAATA
*
31897 GATATTAGATTTAATTAAATAAAAATAGAG-T-TTTTAGTTAAGTAAAACTATAAAAGTTTAAAC
65 GATATTAGATTTAATTAAATAAAAATAGAGTTATTTTAGTTAAGTAAAACTATAAAAGTATAAAC
* *
31960 AATGACATT-TAAGAAATATA
1 AA-AAAATTCTAAGAAATATA
31980 TTCGAAAAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
124 38 0.29
125 4 0.03
126 1 0.01
130 30 0.23
133 6 0.05
136 5 0.04
137 1 0.01
140 22 0.17
141 26 0.20
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (129 bp):
AAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAATAAAATGTATAATAG
ATATTAGATTTAATTAAATAAAAATAGAGTTATTTTAGTTAAGTAAAACTATAAAAGTATAAAC
Found at i:32349 original size:1 final size:1
Alignment explanation
Indices: 32343--32368 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
32333 CTCCTTTGCC
32343 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
32369 CAAAGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:56044 original size:11 final size:11
Alignment explanation
Indices: 56028--56062 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
56018 TTTTTCTGTT
56028 TTTTGTTTTTG
1 TTTTGTTTTTG
**
56039 TTTTGTTTTCA
1 TTTTGTTTTTG
56050 TTTTGTTTTTG
1 TTTTGTTTTTG
56061 TT
1 TT
56063 GCACTGTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.03, C:0.03, G:0.14, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:68327 original size:41 final size:41
Alignment explanation
Indices: 68270--68352 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
68260 GGCAACCCAC
68270 AAGAAAGCTAACCAACTAATTAAACGGCCACAGCGCACCAA
1 AAGAAAGCTAACCAACTAATTAAACGGCCACAGCGCACCAA
*
68311 AAGAAAGCTAACCAACTAATTAAACGGCCACAGCGCGCCAA
1 AAGAAAGCTAACCAACTAATTAAACGGCCACAGCGCACCAA
68352 A
1 A
68353 CTTAACGAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.10
Consensus pattern (41 bp):
AAGAAAGCTAACCAACTAATTAAACGGCCACAGCGCACCAA
Found at i:71618 original size:19 final size:20
Alignment explanation
Indices: 71592--71648 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
71582 AGGTAATATA
71592 TAAAAAAAAAAGTGATGCTT
1 TAAAAAAAAAAGTGATGCTT
71612 TAAAAAAAAAAGTGATGCTT
1 TAAAAAAAAAAGTGATGCTT
71632 T-AAAAAAAAAGTGATGC
1 TAAAAAAAAAAGTGATGC
71649 GGACATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (20 bp):
TAAAAAAAAAAGTGATGCTT
Found at i:72852 original size:43 final size:44
Alignment explanation
Indices: 72791--72889 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 44
72781 TTATAAAATA
* * * *
72791 TTGTCCGTACATCCATACAGGTTAGCTGGCAGGCCATGCC-TTG
1 TTGTCCGTACACCCATACAGGTTAGCTGACAAGCCACGCCATTG
*
72834 TTGTCCGTATACCCATACAGGTTAGCTGACAAGCCACGCCATTG
1 TTGTCCGTACACCCATACAGGTTAGCTGACAAGCCACGCCATTG
72878 TTGTCCGTACAC
1 TTGTCCGTACAC
72890 GATACACATG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
43 35 0.71
44 14 0.29
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.27
Consensus pattern (44 bp):
TTGTCCGTACACCCATACAGGTTAGCTGACAAGCCACGCCATTG
Found at i:76068 original size:19 final size:19
Alignment explanation
Indices: 76031--76089 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
76021 TATGAGTAGT
* *
76031 TATT-AAGTGAAAATATAA
1 TATTAAAGTAAAAATTTAA
76049 TATGTAAA-TAAAAATTTAA
1 TAT-TAAAGTAAAAATTTAA
*
76068 TATTAAAGTAATAAAATTAA
1 TATTAAAGTAA-AAATTTAA
76088 TA
1 TA
76090 ACCGGATTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.21
19 16 0.47
20 11 0.32
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
TATTAAAGTAAAAATTTAA
Found at i:87228 original size:6 final size:7
Alignment explanation
Indices: 87211--87235 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
87201 AGAAGAATAG
87211 AAAAAAT
1 AAAAAAT
87218 AAAAAAT
1 AAAAAAT
87225 AAAAAAT
1 AAAAAAT
87232 AAAA
1 AAAA
87236 GAAATCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:90447 original size:12 final size:12
Alignment explanation
Indices: 90430--90454 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90420 AAAAAACATT
90430 ACAGAAACTCCA
1 ACAGAAACTCCA
90442 ACAGAAACTCCA
1 ACAGAAACTCCA
90454 A
1 A
90455 ATTTCATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.08, T:0.08
Consensus pattern (12 bp):
ACAGAAACTCCA
Found at i:92121 original size:3 final size:3
Alignment explanation
Indices: 92113--92200 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
92103 TAAGTCAAAG
92113 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
92161 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
92201 CCTCAAAATG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.