Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022998.1 Corchorus olitorius cultivar O-4 contig23031, 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: 48119
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2035 original size:29 final size:31
Alignment explanation
Indices: 1971--2035 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1961 GCTTATTACC
1971 CAAATTAGCCCCTTAACTATCTATTTTGGGA
1 CAAATTAGCCCCTTAACTATCTATTTTGGGA
* * *
2002 CAAATTGGCCCCTTGACT-T-TTTTTTGGGA
1 CAAATTAGCCCCTTAACTATCTATTTTGGGA
2031 CAAAT
1 CAAAT
2036 AAATCCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
30 1 0.03
31 16 0.52
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (31 bp):
CAAATTAGCCCCTTAACTATCTATTTTGGGA
Found at i:2379 original size:25 final size:25
Alignment explanation
Indices: 2345--2395 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2335 TGAGAAAGGA
2345 TAATAAAGAAAATAACCAATGCCGG
1 TAATAAAGAAAATAACCAATGCCGG
2370 TAATAAAGAAAATAACCAATGCCGG
1 TAATAAAGAAAATAACCAATGCCGG
2395 T
1 T
2396 CTACTGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (25 bp):
TAATAAAGAAAATAACCAATGCCGG
Found at i:2749 original size:29 final size:30
Alignment explanation
Indices: 2717--2781 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
2707 TATGGGATTT
2717 ATTTGTCCCAAAA-AAAAGTTAAGGGGCCA
1 ATTTGTCCCAAAAGAAAAGTTAAGGGGCCA
* * * *
2746 ATTTATCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCCAAAA-GAAAAGTTAAGGGGCCA
2777 ATTTG
1 ATTTG
2782 GGTATTAAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (30 bp):
ATTTGTCCCAAAAGAAAAGTTAAGGGGCCA
Found at i:15050 original size:17 final size:17
Alignment explanation
Indices: 15028--15060 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15018 TTTTTATACC
15028 ATAATA-TTATATGTATA
1 ATAATAGTTA-ATGTATA
15045 ATAATAGTTAATGTAT
1 ATAATAGTTAATGTAT
15061 TTTAGAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
ATAATAGTTAATGTATA
Found at i:19508 original size:3 final size:3
Alignment explanation
Indices: 19493--19556 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
19483 GGGTATCATA
*
19493 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19541 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
19557 AATATGTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20253 original size:24 final size:24
Alignment explanation
Indices: 20226--20274 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
20216 AAAGGCTTAA
*
20226 GTAATGTGAATAGAGAAAATAGAT
1 GTAATATGAATAGAGAAAATAGAT
20250 GTAATATGAATAGAGAAAATAGAT
1 GTAATATGAATAGAGAAAATAGAT
20274 G
1 G
20275 AGAGGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (24 bp):
GTAATATGAATAGAGAAAATAGAT
Found at i:21415 original size:21 final size:21
Alignment explanation
Indices: 21390--21440 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
21380 TATCTTAGAT
21390 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
21411 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
21432 ATAAATAAT
1 AT-AATAAT
21441 GAGTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 11 0.41
22 9 0.33
23 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:21423 original size:25 final size:25
Alignment explanation
Indices: 21392--21440 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21382 TCTTAGATAT
*
21392 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
21417 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
21441 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:25780 original size:5 final size:5
Alignment explanation
Indices: 25765--25854 Score: 98
Period size: 5 Copynumber: 18.2 Consensus size: 5
25755 TGTTTTGGGG
* *
25765 TTATCA TTATA TTATA TTATA TTATA TTGTA TCATA TTATA TTATA TTATA
1 TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
*
25816 TTATA TAATA -TA-A TTATA -TATA -TATA TATATA TCTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T-TATA T-TATA T
25855 ACTATATAAG
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
3 1 0.01
4 11 0.15
5 47 0.64
6 14 0.19
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (5 bp):
TTATA
Found at i:26134 original size:39 final size:40
Alignment explanation
Indices: 26078--26158 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
26068 TTTAATTCCT
26078 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
26118 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
26157 AT
1 AT
26159 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:26630 original size:203 final size:203
Alignment explanation
Indices: 26239--26649 Score: 738
Period size: 203 Copynumber: 2.0 Consensus size: 203
26229 TTCCTTAATA
*
26239 ATAAATAAATTGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
26304 AATTTAATAAATTAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAGT
66 AATTTAATAAATTAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAAT
*
26369 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTGAAAAATTAATAACATT
131 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
*
26434 CACCATTG
196 CACCAATG
26442 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
26507 AATTTAAT-AATTCAACCACTAATGTTCAACTAA-TTTTTTTTGGTATAGTT-TAATATATAATA
66 AATTTAATAAATT-AACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCT-ATATATAATA
26569 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAGAATTAATAAC
129 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAA-AATTAATAAC
26634 ATTCACCAATG
193 ATTCACCAATG
26645 ATAAA
1 ATAAA
26650 GTTATTAAGC
Statistics
Matches: 201, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
201 1 0.00
202 83 0.41
203 117 0.58
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATTAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
CACCAATG
Found at i:27211 original size:36 final size:36
Alignment explanation
Indices: 27164--27233 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
27154 GAGATTTTGG
* *
27164 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
27200 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
27234 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:30130 original size:2 final size:2
Alignment explanation
Indices: 30101--30160 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
30091 CTTTAATTAG
30101 TA TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
30139 TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
30161 GATAGGTATA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
1 4 0.08
2 48 0.92
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30165 original size:10 final size:10
Alignment explanation
Indices: 30126--30170 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
30116 ATTATATTAT
*
30126 ATATATATAT
1 ATATATATAG
*
30136 ATATATATAT
1 ATATATATAG
30146 ATATATATAG
1 ATATATATAG
*
30156 ATATAGATAG
1 ATATATATAG
*
30166 GTATA
1 ATATA
30171 GATAAGGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (10 bp):
ATATATATAG
Found at i:34649 original size:28 final size:28
Alignment explanation
Indices: 34616--34672 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
34606 TACTATTAAT
*
34616 TTTTATCAA-CAAATTCATTAATAATTGA
1 TTTTATCAAGC-AATTCATCAATAATTGA
* *
34644 TTTTATTAAGCATTTCATCAATAATTGA
1 TTTTATCAAGCAATTCATCAATAATTGA
34672 T
1 T
34673 ATAATCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.46
Consensus pattern (28 bp):
TTTTATCAAGCAATTCATCAATAATTGA
Found at i:35166 original size:26 final size:27
Alignment explanation
Indices: 35110--35167 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
35100 TATAAAAAGA
*
35110 TTATGGTATTTTTATTATTAATGATCGTT
1 TTATGGTATTTTTATTATCAATGA-C-TT
*
35139 TTATGGTATTTTTATTATCAATGATTT
1 TTATGGTATTTTTATTATCAATGACTT
35166 TT
1 TT
35168 TAAGGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
29 23 0.85
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.60
Consensus pattern (27 bp):
TTATGGTATTTTTATTATCAATGACTT
Found at i:37411 original size:1 final size:1
Alignment explanation
Indices: 37377--37404 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
37367 ACTTTTTGTC
37377 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
37405 CGTTTTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42749 original size:14 final size:14
Alignment explanation
Indices: 42727--42782 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
42717 ATTTGTTGGG
*
42727 TTTTAGGGTTTCAA
1 TTTTGGGGTTTCAA
42741 TTTTGGGGTTTCAGAA
1 TTTTGGGGTTTC--AA
*
42757 TTTTTGGGGTTTTAA
1 -TTTTGGGGTTTCAA
*
42772 CTTTGGGGTTT
1 TTTTGGGGTTT
42783 AAAAATGGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 21 0.58
15 2 0.06
16 2 0.06
17 11 0.31
ACGTcount: A:0.14, C:0.05, G:0.29, T:0.52
Consensus pattern (14 bp):
TTTTGGGGTTTCAA
Done.