Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015961.1 Corchorus olitorius cultivar O-4 contig15994, 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: 40243
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1138 original size:21 final size:21
Alignment explanation
Indices: 1114--1164 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1104 GGCACTGAAT
**
1114 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATAACC
* *
1135 GGTGGTGGCACGGGCTTAACC
1 GGTGATGGCACGGGCATAACC
1156 GGTGATGGC
1 GGTGATGGC
1165 TTGGTAGTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.18
Consensus pattern (21 bp):
GGTGATGGCACGGGCATAACC
Found at i:4273 original size:27 final size:29
Alignment explanation
Indices: 4223--4280 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 29
4213 ACGCAGGAAC
*
4223 AAGAAATTTTTTTTTTTTAGAAAACGCAA
1 AAGAAATTTTTTTTTTTCAGAAAACGCAA
4252 AAGAAA-TTTTTTTTTTCA-AAAACGCAA
1 AAGAAATTTTTTTTTTTCAGAAAACGCAA
4279 AA
1 AA
4281 CTAATAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 11 0.39
28 11 0.39
29 6 0.21
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (29 bp):
AAGAAATTTTTTTTTTTCAGAAAACGCAA
Found at i:4713 original size:16 final size:16
Alignment explanation
Indices: 4676--4716 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
4666 CAGAGATTGA
*
4676 TAGAAAGCAATTAAAC
1 TAGAAAACAATTAAAC
4692 -AGAAAACAATTAAAC
1 TAGAAAACAATTAAAC
4707 TAGAAAACAA
1 TAGAAAACAA
4717 AGCAGAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
TAGAAAACAATTAAAC
Found at i:14311 original size:18 final size:17
Alignment explanation
Indices: 14278--14315 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
14268 CTAAAAGGCC
14278 TTTGGGTTGAGTTTGTG
1 TTTGGGTTGAGTTTGTG
*
14295 TTTGGGTTTGTGTTTGTG
1 TTTGGG-TTGAGTTTGTG
14313 TTT
1 TTT
14316 TAGATGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.03, C:0.00, G:0.37, T:0.61
Consensus pattern (17 bp):
TTTGGGTTGAGTTTGTG
Found at i:15758 original size:2 final size:2
Alignment explanation
Indices: 15751--15785 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15741 TTTGAGAACA
15751 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
15786 GATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16276 original size:2 final size:2
Alignment explanation
Indices: 16269--16325 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
16259 GTCTAGCTTC
16269 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16311 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
16326 ATTGAAGTGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:17062 original size:26 final size:26
Alignment explanation
Indices: 17026--17078 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
17016 GAGAGAATGG
17026 CCACATGAACAATCTACATTTTGTAA
1 CCACATGAACAATCTACATTTTGTAA
*
17052 CCACATGAACAATCTGCATTTTGTAA
1 CCACATGAACAATCTACATTTTGTAA
17078 C
1 C
17079 TTGTAAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (26 bp):
CCACATGAACAATCTACATTTTGTAA
Found at i:27804 original size:2 final size:2
Alignment explanation
Indices: 27797--27831 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27787 TCTGTCCATT
27797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27832 TAAACATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29548 original size:19 final size:19
Alignment explanation
Indices: 29524--29582 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
29514 CTGTTCAACA
29524 ACTGTACAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
* *
29543 ACTGTACAGATTAGATTAGAT
1 ACTGTACAAATGAGATT--AT
29564 ACTGTACAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
29583 TAGAGCAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAT
Found at i:29567 original size:21 final size:20
Alignment explanation
Indices: 29524--29581 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
29514 CTGTTCAACA
29524 ACTGTACAAATGAGATT-AT
1 ACTGTACAAATGAGATTAAT
* *
29543 ACTGTACAGATTAGATTAGAT
1 ACTGTACAAATGAGATTA-AT
29564 ACTGTACAAATGAGATTA
1 ACTGTACAAATGAGATTA
29582 TTAGAGCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (20 bp):
ACTGTACAAATGAGATTAAT
Found at i:34098 original size:67 final size:67
Alignment explanation
Indices: 33965--34397 Score: 701
Period size: 67 Copynumber: 6.5 Consensus size: 67
33955 TTGCCCTTTT
* * * * * *
33965 GACCGAAAGGGCATTTTTGG-AA-AGAAAA-ACTAAACCTGAACGCCAGAAGATGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATG-CAAAAGACGAAAATGACCC
34027 TTC
65 TTC
* *
34030 GACCGAAAGGGTATTTTTGGAAATAGAAAATACCAAACTTAAATACAAAAGACGAAAATGACCCT
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCT
34095 TC
66 TC
*
34097 GACCGAAAGGGTATTTTTGGAAACAGAAAATACTAAACTTAAATGCAAGAAGACGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAA-AAGACGAAAATGACCC
34162 TTC
65 TTC
* *
34165 GACCAAAAGGGTATTTTTGGAAATAGAAAACACTAAACTTAAATGCAAAAGACGAAAATGACCCT
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCT
34230 TC
66 TC
* *
34232 GATCGAAAGGGTATTTTTGGAAATAGAAAACACTAAACTTAAATGCAAAAGACGAAAATGACCCT
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCT
34297 TC
66 TC
*
34299 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCATAAGACGAAAATGACCCT
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCT
34364 TC
66 TC
34366 GACCGAAAGGGTATTTTTGGAAATAGAAAATA
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATA
34398 GAGCTTTACT
Statistics
Matches: 345, Mismatches: 19, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
65 19 0.06
66 2 0.01
67 251 0.73
68 73 0.21
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (67 bp):
GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGACCCT
TC
Found at i:34159 original size:135 final size:135
Alignment explanation
Indices: 33965--34397 Score: 712
Period size: 135 Copynumber: 3.2 Consensus size: 135
33955 TTGCCCTTTT
* * * * * *
33965 GACCGAAAGGGCATTTTTGG-AA-AGAAAA-ACTAAACCTGAACGCCAGAAGATGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAGAAGACGAAAATGACCC
* *
34027 TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACCAAACTTAAATACAAAAGACGAAAATGAC
66 TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGAC
34092 CCTTC
131 CCTTC
*
34097 GACCGAAAGGGTATTTTTGGAAACAGAAAATACTAAACTTAAATGCAAGAAGACGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAGAAGACGAAAATGACCC
* *
34162 TTCGACCAAAAGGGTATTTTTGGAAATAGAAAACACTAAACTTAAATGCAAAAGACGAAAATGAC
66 TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGAC
34227 CCTTC
131 CCTTC
* *
34232 GATCGAAAGGGTATTTTTGGAAATAGAAAACACTAAACTTAAATGCAA-AAGACGAAAATGACCC
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAGAAGACGAAAATGACCC
*
34296 TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCATAAGACGAAAATGAC
66 TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGAC
34361 CCTTC
131 CCTTC
34366 GACCGAAAGGGTATTTTTGGAAATAGAAAATA
1 GACCGAAAGGGTATTTTTGGAAATAGAAAATA
34398 GAGCTTTACT
Statistics
Matches: 280, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
132 19 0.07
133 2 0.01
134 119 0.43
135 140 0.50
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (135 bp):
GACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAGAAGACGAAAATGACCC
TTCGACCGAAAGGGTATTTTTGGAAATAGAAAATACTAAACTTAAATGCAAAAGACGAAAATGAC
CCTTC
Found at i:35180 original size:19 final size:21
Alignment explanation
Indices: 35141--35180 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
35131 TAACCAAGCC
35141 CAAGACCCAACAGAAAATTTA
1 CAAGACCCAACAGAAAATTTA
*
35162 CAAG-CCCAA-AGAAAGTTTA
1 CAAGACCCAACAGAAAATTTA
35181 GAGAAGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.50, C:0.23, G:0.12, T:0.15
Consensus pattern (21 bp):
CAAGACCCAACAGAAAATTTA
Done.