Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022999.1 Corchorus olitorius cultivar O-4 contig23032, 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: 17721
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:829 original size:36 final size:36
Alignment explanation
Indices: 782--851 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
772 GAGATTTTGG
* *
782 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
818 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
852 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:2182 original size:57 final size:58
Alignment explanation
Indices: 2112--2223 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 58
2102 AGCATCATGC
*
2112 CTCGGTCCTAAAACGTC-TTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT
1 CTCGGTCCGAAAACGTCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT
* * *
2169 CTCGGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 CTCGGTCCGAAAACGTCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
2224 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 16 0.32
58 34 0.68
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (58 bp):
CTCGGTCCGAAAACGTCTTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGT
Found at i:6543 original size:3 final size:3
Alignment explanation
Indices: 6535--6565 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6525 ATATATATAT
6535 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6566 AGATCAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7462 original size:31 final size:30
Alignment explanation
Indices: 7396--7482 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 30
7386 TTTCATCAAA
*
7396 GACATTTTGTCCC-TGAACTTT-AAA-TCAT
1 GACATTTTG-CCCTTGAACTTTCAAATTCAG
7424 GACATTTTGCCTCTTGAACTTTCAAATTCAG
1 GACATTTTGCC-CTTGAACTTTCAAATTCAG
7455 GACATTTTGCCCTCTGAACTTTTCAAAT
1 GACATTTTGCCCT-TGAAC-TTTCAAAT
7483 CGAGAAGGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
27 2 0.04
28 10 0.19
29 8 0.15
30 5 0.10
31 19 0.37
32 8 0.15
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.39
Consensus pattern (30 bp):
GACATTTTGCCCTTGAACTTTCAAATTCAG
Found at i:7556 original size:29 final size:30
Alignment explanation
Indices: 7487--7556 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
7477 TCAAATCGAG
7487 AAGGGACAAAATGTCCTGAATTTGAAAGTTA
1 AAGGG-CAAAATGTCCTGAATTTGAAAGTTA
**
7518 AAGGATAAAATGTCCTG-ATTTG-AAGTTTA
1 AAGGGCAAAATGTCCTGAATTTGAAAG-TTA
*
7547 GAGGGCAAAA
1 AAGGGCAAAA
7557 CATTCTTGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 3 0.09
29 15 0.45
30 11 0.33
31 4 0.12
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (30 bp):
AAGGGCAAAATGTCCTGAATTTGAAAGTTA
Found at i:9906 original size:18 final size:19
Alignment explanation
Indices: 9883--9918 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9873 TTTTTCAAAC
9883 TTTCTAAT-TTCAAGAACA
1 TTTCTAATCTTCAAGAACA
9901 TTTCTAATCTTCAAGAAC
1 TTTCTAATCTTCAAGAAC
9919 GCTAAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (19 bp):
TTTCTAATCTTCAAGAACA
Found at i:10219 original size:33 final size:33
Alignment explanation
Indices: 10145--10209 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
10135 TTGGTCGGCG
* *
10145 CCGAGGGCGCCATGGCCAAGTCCATGCCGCCCA
1 CCGAGGGCGCCATGGACAAGTCCACGCCGCCCA
10178 CCGAGGGCGCCATGGACATAG-CCACGCCGCCC
1 CCGAGGGCGCCATGGACA-AGTCCACGCCGCCC
10210 TAGCAGGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.18, C:0.43, G:0.31, T:0.08
Consensus pattern (33 bp):
CCGAGGGCGCCATGGACAAGTCCACGCCGCCCA
Found at i:12881 original size:11 final size:11
Alignment explanation
Indices: 12865--12892 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12855 TCCAACGTAA
12865 AAATTTTCAAT
1 AAATTTTCAAT
12876 AAATTTTCAAT
1 AAATTTTCAAT
12887 AAATTT
1 AAATTT
12893 GTATGTCATT
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:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (11 bp):
AAATTTTCAAT
Found at i:12963 original size:18 final size:18
Alignment explanation
Indices: 12920--12975 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
12910 GATAATGATG
12920 TGAAAATTTGATAACATCATTA
1 TGAAAATTTGATAAC--C--TA
12942 TG-AAATTTCGATAACCTA
1 TGAAAATTT-GATAACCTA
12960 TGAAAATTTGATAACC
1 TGAAAATTTGATAACC
12976 ACACTGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 1 0.03
21 6 0.19
22 8 0.25
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (18 bp):
TGAAAATTTGATAACCTA
Found at i:12986 original size:40 final size:40
Alignment explanation
Indices: 12920--12995 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
12910 GATAATGATG
*
12920 TGAAAATTTGATAACATCATTATGAAATTTCGATAACCTA
1 TGAAAATTTGATAACATCACTATGAAATTTCGATAACCTA
* *
12960 TGAAAATTTGATAACCA-CACTGTGAAATTTTGATAA
1 TGAAAATTTGATAA-CATCACTATGAAATTTCGATAA
12996 TCACACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (40 bp):
TGAAAATTTGATAACATCACTATGAAATTTCGATAACCTA
Found at i:13009 original size:22 final size:22
Alignment explanation
Indices: 12957--13084 Score: 84
Period size: 22 Copynumber: 5.9 Consensus size: 22
12947 TTTCGATAAC
12957 CTATGAAAA-TTTGATAACCACA
1 CTAT-AAAATTTTGATAACCACA
* * *
12979 CTGTGAAATTTTGATAATCACA
1 CTATAAAATTTTGATAACCACA
* * *
13001 CTATAAAA--TCGGTAACCGCA
1 CTATAAAATTTTGATAACCACA
* *
13021 TTATGAAAATTTTGATAACCTC-
1 CTAT-AAAATTTTGATAACCACA
*
13043 TTCATAAAATTTTGATAACCACA
1 CT-ATAAAATTTTGATAACCACA
* * * *
13066 CCATTAAGTTTCGATAACC
1 CTATAAAATTTTGATAACC
13085 TCCCTATGAG
Statistics
Matches: 81, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
20 11 0.14
21 7 0.09
22 53 0.65
23 10 0.12
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (22 bp):
CTATAAAATTTTGATAACCACA
Found at i:13228 original size:21 final size:20
Alignment explanation
Indices: 13202--13280 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 20
13192 CCTCCGTATG
13202 AAATTTTGATAACTACACTAT
1 AAATTTTGATAACTAC-CTAT
* * *
13223 AAATTTTAATAACCTTCGTAT
1 AAATTTTGATAA-CTACCTAT
* *
13244 AAATTTTGTTAACGATACTCTAAG
1 AAATTTTGATAAC--TAC-CT-AT
13268 AAATTTTGATAAC
1 AAATTTTGATAAC
13281 CCTTTTATGA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.02
21 24 0.55
22 5 0.11
23 1 0.02
24 13 0.30
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.39
Consensus pattern (20 bp):
AAATTTTGATAACTACCTAT
Found at i:13362 original size:22 final size:21
Alignment explanation
Indices: 13192--13362 Score: 55
Period size: 22 Copynumber: 7.8 Consensus size: 21
13182 TGATAACCTC
*
13192 CCTCCGTATGAAATTTTGATAA
1 CCTCCATAT-AAATTTTGATAA
* *
13214 -CTACACTATAAATTTTAATAA
1 CCTCCA-TATAAATTTTGATAA
* * *
13235 CCTTCGTATAAATTTTGTTAA
1 CCTCCATATAAATTTTGATAA
* *
13256 CGATACTC-TAAGAAATTTTGATAA
1 C-CT-C-CAT-ATAAATTTTGATAA
** *
13280 CC-CTTTTATGAAATTTTGGTAA
1 CCTC-CATAT-AAATTTTGATAA
*
13302 CGTCTGCATA-AAATTTTGAT-A
1 C--CTCCATATAAATTTTGATAA
* * *
13323 TCTACACTATAACGTTTTGATAA
1 CCTCCA-TATAA-ATTTTGATAA
13346 CCTCCATATGAAATTTT
1 CCTCCATAT-AAATTTT
13363 AGCAACCATA
Statistics
Matches: 108, Mismatches: 25, Indels: 32
0.65 0.15 0.19
Matches are distributed among these distances:
19 4 0.04
20 2 0.02
21 34 0.31
22 43 0.40
23 8 0.07
24 17 0.16
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (21 bp):
CCTCCATATAAATTTTGATAA
Found at i:13770 original size:56 final size:56
Alignment explanation
Indices: 13700--13811 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
13690 CAAAATTTAC
13700 CAAAGAAAAGTTATGCTTGCAGGAATATTGCATACTTCTTATCAATAGTATTATTA
1 CAAAGAAAAGTTATGCTTGCAGGAATATTGCATACTTCTTATCAATAGTATTATTA
* *
13756 CAAAGAAAAGTTATGCTTGCAGGAATATTGCATACTTTTTATTAATAGTATTATTA
1 CAAAGAAAAGTTATGCTTGCAGGAATATTGCATACTTCTTATCAATAGTATTATTA
13812 TTCATATTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (56 bp):
CAAAGAAAAGTTATGCTTGCAGGAATATTGCATACTTCTTATCAATAGTATTATTA
Found at i:14787 original size:119 final size:118
Alignment explanation
Indices: 14547--14901 Score: 559
Period size: 118 Copynumber: 3.0 Consensus size: 118
14537 TATTGTTAAC
* *
14547 GCGTTTGGGATCTAAGAATTAAGAAGTAATTTATACTATTTTTACTGGAAGAATTGGTTTGAAGT
1 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTACTGGAAGAGTTGGTTTGAAGT
14612 GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
* * *
14665 GCGTTTGGGACCTAAAAATTAAGGAGTAATTTATACTATTTTTA-TGGAATAGTTGGTTTGAAGT
1 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTACTGGAAGAGTTGGTTTGAAGT
* *
14729 GGAAAATTTAAGTACTTGAGAAATTCCTCAAAACAATATTCATGGTTGTGGTGTA
66 GGAAAATTTAAGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
* * * * *
14784 GCGTTTGGAATCTAAGAATTAAAGAGTAATTTATACTACTTTTATTGGAAGAGTTGGTTTGAAAT
1 GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTACTGGAAGAGTTGGTTTGAAGT
* *
14849 GGAAAATTGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGATGGA
66 GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
14902 TGTTCTTCCA
Statistics
Matches: 216, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
117 34 0.16
118 75 0.35
119 74 0.34
120 33 0.15
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.35
Consensus pattern (118 bp):
GCGTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTACTGGAAGAGTTGGTTTGAAGT
GGAAAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
Found at i:16774 original size:16 final size:16
Alignment explanation
Indices: 16753--16783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16743 TTATCCGATG
16753 TAGTAGCTTTGTTTTC
1 TAGTAGCTTTGTTTTC
*
16769 TAGTAGTTTTGTTTT
1 TAGTAGCTTTGTTTT
16784 GTCGAATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.06, G:0.19, T:0.61
Consensus pattern (16 bp):
TAGTAGCTTTGTTTTC
Found at i:17417 original size:16 final size:15
Alignment explanation
Indices: 17356--17419 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
17346 AAGTTGCAAT
17356 AGAAAATAAAT-TGCA
1 AGAAAATAAATAT-CA
17371 A-ATAAATAAATATTCA
1 AGA-AAATAAATA-TCA
*
17387 AGAAAAT-ATTAATCA
1 AGAAAATAAAT-ATCA
17402 AGAGAAATAAATATCA
1 AGA-AAATAAATATCA
17418 AG
1 AG
17420 CGATGGAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 1 0.03
15 17 0.43
16 18 0.45
17 4 0.10
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.23
Consensus pattern (15 bp):
AGAAAATAAATATCA
Done.