Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018423.1 Corchorus olitorius cultivar O-4 contig18456, 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: 58358
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2106 original size:5 final size:5
Alignment explanation
Indices: 2096--2145 Score: 77
Period size: 5 Copynumber: 10.4 Consensus size: 5
2086 TATATAGCAG
*
2096 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TGAGA TAAGA T-AG- TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
2144 TA
1 TA
2146 TGTCTCATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 1 0.02
4 4 0.10
5 36 0.88
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:2947 original size:6 final size:6
Alignment explanation
Indices: 2936--2962 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2926 TGGCTATAGA
2936 GAATTG GAATTG GAATTG GAATTG GAA
1 GAATTG GAATTG GAATTG GAATTG GAA
2963 GAGGTGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (6 bp):
GAATTG
Found at i:8062 original size:51 final size:51
Alignment explanation
Indices: 7974--8080 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
7964 GTTCTTCATA
* * *
7974 TTTT-TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCTCTTGTTTAGATCTTGTCTCAGAACAATAAAACACTCTATTAGTGT
* * *
8024 TTTTCTCTTGTTTCA-ATCTTGTCTCCGAAC-ATAAAAACACTGTATTCGTGT
1 TTTTCTCTTGTTT-AGATCTTGTCTCAGAACAAT-AAAACACTCTATTAGTGT
8075 TTTTCT
1 TTTTCT
8081 TCAGAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
50 6 0.12
51 41 0.85
52 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (51 bp):
TTTTCTCTTGTTTAGATCTTGTCTCAGAACAATAAAACACTCTATTAGTGT
Found at i:8454 original size:78 final size:76
Alignment explanation
Indices: 8325--8488 Score: 301
Period size: 78 Copynumber: 2.1 Consensus size: 76
8315 GCAAATTGAC
*
8325 TGGCACGCCCTTATGCTGTCATGAAGAATTCTCCGCGAAAACTCTAGCAAGAGATTTTTTGGCCC
1 TGGCACGCCCTTATGCTGTCATAAAGAATTCTCCGCGAAAACTCTAGCAAGAGA-TTTTTGGCCC
8390 AACATCTCTTTTT
65 AACATCTC-TTTT
8403 TGGCACGCCCTTATGCTGTCATAAAGAATTCTCCGCGAAAACTCTAGCAAGAGATTTTTGGCCCA
1 TGGCACGCCCTTATGCTGTCATAAAGAATTCTCCGCGAAAACTCTAGCAAGAGATTTTTGGCCCA
8468 ACATCTCTTTT
66 ACATCTCTTTT
8479 TGGCACGCCC
1 TGGCACGCCC
8489 AGTGGGACAC
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
76 14 0.16
77 18 0.21
78 53 0.62
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (76 bp):
TGGCACGCCCTTATGCTGTCATAAAGAATTCTCCGCGAAAACTCTAGCAAGAGATTTTTGGCCCA
ACATCTCTTTT
Found at i:14550 original size:51 final size:51
Alignment explanation
Indices: 14462--14568 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
14452 GTTCTTCATA
* * *
14462 TTTT-TCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCTCTTGTTTAGATCTTGTCTCAGAACAATAAAACACTCTATTAGTGT
* * *
14512 TTTTCTCTTGTTTCA-ATCTTGTCTCCGAAC-ATAAAAACACTGTATTCGTGT
1 TTTTCTCTTGTTT-AGATCTTGTCTCAGAACAAT-AAAACACTCTATTAGTGT
14563 TTTTCT
1 TTTTCT
14569 TTCAGAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
50 6 0.12
51 41 0.85
52 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (51 bp):
TTTTCTCTTGTTTAGATCTTGTCTCAGAACAATAAAACACTCTATTAGTGT
Found at i:18936 original size:49 final size:52
Alignment explanation
Indices: 18827--18936 Score: 149
Period size: 49 Copynumber: 2.2 Consensus size: 52
18817 AAATAATTAC
*
18827 TATTAA-TTTAGACTTTTTTTAATATGAAAATAAAATATGGTTGGATCACAT
1 TATTAATTTTAGACTTCTTTTAATATGAAAATAAAATATGGTTGGATCACAT
* *
18878 TAATT-ATTTTAGA-TTCTTTTAATATGGAAAT-AAA-ATGGTTGGATTACAT
1 T-ATTAATTTTAGACTTCTTTTAATATGAAAATAAAATATGGTTGGATCACAT
18927 TATTAATTTT
1 TATTAATTTT
18937 TTAAATAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
48 3 0.06
49 20 0.38
50 3 0.06
51 18 0.34
52 9 0.17
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (52 bp):
TATTAATTTTAGACTTCTTTTAATATGAAAATAAAATATGGTTGGATCACAT
Found at i:30299 original size:15 final size:15
Alignment explanation
Indices: 30279--30309 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30269 CTTAGTTACC
30279 GGAACTAAGAGATCA
1 GGAACTAAGAGATCA
30294 GGAACTAAGAGATCA
1 GGAACTAAGAGATCA
30309 G
1 G
30310 TACCTTACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.29, T:0.13
Consensus pattern (15 bp):
GGAACTAAGAGATCA
Found at i:31807 original size:28 final size:30
Alignment explanation
Indices: 31762--31822 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
31752 ATTATTATGT
31762 TTTTTTTTTTATAAAAAACATTAAATTGAA
1 TTTTTTTTTTATAAAAAACATTAAATTGAA
* *
31792 TTTTTTTTTT-T-GAAAACTTTAAATTGAA
1 TTTTTTTTTTATAAAAAACATTAAATTGAA
31820 TTT
1 TTT
31823 AGAAACTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 18 0.62
29 1 0.03
30 10 0.34
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTTTTTTTTATAAAAAACATTAAATTGAA
Found at i:39912 original size:15 final size:15
Alignment explanation
Indices: 39892--39920 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39882 GATGGCTGCT
39892 GGGGAAGTCAGTGCC
1 GGGGAAGTCAGTGCC
39907 GGGGAAGTCAGTGC
1 GGGGAAGTCAGTGC
39921 TAGATCGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.17, G:0.48, T:0.14
Consensus pattern (15 bp):
GGGGAAGTCAGTGCC
Found at i:43492 original size:19 final size:19
Alignment explanation
Indices: 43464--43502 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
43454 TGTTTGACTA
43464 ATTAGAATCAACTGTAATT
1 ATTAGAATCAACTGTAATT
* *
43483 ATTAGGATCAATTGTAATT
1 ATTAGAATCAACTGTAATT
43502 A
1 A
43503 GTAATTACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (19 bp):
ATTAGAATCAACTGTAATT
Found at i:51549 original size:123 final size:128
Alignment explanation
Indices: 51330--51585 Score: 405
Period size: 123 Copynumber: 2.0 Consensus size: 128
51320 ATTTAAGAAA
*
51330 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATGGTAAAATGGTAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---
* *
51395 ATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTGTAAA
63 ATA-GTATAAGGATATTAAATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAA
51460 AG
127 AG
51462 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
*
51525 -TA-AA-GATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 GTATAAGGATATTAAATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAG
51585 T
1 T
51586 TTAAACAATG
Statistics
Matches: 120, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
123 54 0.45
124 2 0.02
125 2 0.02
127 2 0.02
131 31 0.26
132 29 0.24
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
GTATAAGGATATTAAATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAG
Found at i:52031 original size:18 final size:18
Alignment explanation
Indices: 52008--52043 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
51998 ACCTATTGAG
52008 CTCGAGCTCGAGCTCGAA
1 CTCGAGCTCGAGCTCGAA
* *
52026 CTCGAGTTCGAGTTCGAA
1 CTCGAGCTCGAGCTCGAA
52044 TTTTAGCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (18 bp):
CTCGAGCTCGAGCTCGAA
Found at i:52822 original size:41 final size:41
Alignment explanation
Indices: 52745--52824 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
52735 ATTTGACTCT
* *
52745 CCTAATAATTAAGGAAATAAATTAAATCTAAGTTTAGCCTC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTAGCCTC
*
52786 CCTAATAATTAAGGTAAGAAATTAAATCC-AGATTTAGCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAAG-TTTAGCC
52825 CCTAATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 33 0.94
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTAGCCTC
Found at i:55591 original size:29 final size:31
Alignment explanation
Indices: 55559--55617 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
55549 GTTTTGCTCT
*
55559 ATGAACTT-CAAA-TCAAGATATTTTACCTC
1 ATGAACTTCCAAATTCAAGACATTTTACCTC
55588 ATGAACTTCCCAAATTCAAGACATTTTACC
1 ATGAACTT-CCAAATTCAAGACATTTTACC
55618 CTTTAACAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
31 4 0.15
32 14 0.54
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (31 bp):
ATGAACTTCCAAATTCAAGACATTTTACCTC
Done.