Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020243.1 Corchorus olitorius cultivar O-4 contig20276, 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: 46303
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1636 original size:24 final size:24
Alignment explanation
Indices: 1602--1649 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1592 TTGTCAGTCT
* *
1602 AAACCAGGATAATATACCAAAATA
1 AAACCAAGATAATAAACCAAAATA
*
1626 AAACCAAGATAATAAACGAAAATA
1 AAACCAAGATAATAAACCAAAATA
1650 TCAAATCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (24 bp):
AAACCAAGATAATAAACCAAAATA
Found at i:4233 original size:22 final size:23
Alignment explanation
Indices: 4194--4237 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4184 TTGTTTTCAA
* *
4194 AAAACTGACAACGTAACAAAAAT
1 AAAACTGAAAACGAAACAAAAAT
4217 AAAA-TGAAAACGAAACAAAAA
1 AAAACTGAAAACGAAACAAAAA
4238 CAGAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.14, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAACTGAAAACGAAACAAAAAT
Found at i:9757 original size:72 final size:71
Alignment explanation
Indices: 9602--9821 Score: 270
Period size: 73 Copynumber: 3.0 Consensus size: 71
9592 GTTTAGAAGT
*
9602 ATATTTGACAAATAAGGGTATAATAGGT-GATTCAAAAGTTTTACAGGTGAA-CGTACTTTT-TA
1 ATATTTGA-AAATAAGGGTATAATAGGTCGATTCAAAAGTTTTACA---AAATCGTACTTTTAT-
9664 ATATAGTATAG
61 ATATAGTATAG
*
9675 ATATTCGAAAACTAAGGGTATAAT-GGTCGATTCAAAAGTTTTACAAAATTCGTACTTTTATATA
1 ATATTTGAAAA-TAAGGGTATAATAGGTCGATTCAAAAGTTTTACAAAA-TCGTACTTTTATATA
*
9739 TAATATAG
64 TAGTATAG
* *
9747 ATATTTGAAAAATAAGGGTATAATAGG-CGATTTAAAAGTTTTACAACAACTCCTACTTTTATAT
1 ATATTTG-AAAATAAGGGTATAATAGGTCGATTCAAAAGTTTTACAA-AA-TCGTACTTTTATAT
9811 ATAGTATAG
63 ATAGTATAG
9820 AT
1 AT
9822 GGTAATCAAT
Statistics
Matches: 131, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
70 2 0.02
72 61 0.47
73 68 0.52
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (71 bp):
ATATTTGAAAATAAGGGTATAATAGGTCGATTCAAAAGTTTTACAAAATCGTACTTTTATATATA
GTATAG
Found at i:22509 original size:2 final size:2
Alignment explanation
Indices: 22502--22538 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22492 AGTTTGATAG
22502 TA 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 TA T
22539 CCATGTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23166 original size:25 final size:25
Alignment explanation
Indices: 23132--23180 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
23122 CCAAACAATC
23132 TTGAGCACTCTCGCTCAGTCTCTAT
1 TTGAGCACTCTCGCTCAGTCTCTAT
*
23157 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCAGTCTCTA
23181 CAAACCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCAGTCTCTAT
Found at i:24050 original size:30 final size:32
Alignment explanation
Indices: 24011--24090 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 32
24001 GGCAATGCCA
24011 TGACTTTTTGATCATATTT-TCTTTTGGCATC
1 TGACTTTTTGATCATATTTATCTTTTGGCATC
*
24042 TGAC-TTTTGATCATATTTATTTTTTGGCATC
1 TGACTTTTTGATCATATTTATCTTTTGGCATC
24073 TGACTTTTTGATCATATT
1 TGACTTTTTGATCATATT
24091 AAGCTATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
30 14 0.30
31 19 0.41
32 13 0.28
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.55
Consensus pattern (32 bp):
TGACTTTTTGATCATATTTATCTTTTGGCATC
Found at i:27196 original size:11 final size:11
Alignment explanation
Indices: 27172--27206 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
27162 TTGACAGCGC
27172 AACAAAAACAA
1 AACAAAAACAA
* *
27183 AACGAAAACGA
1 AACAAAAACAA
27194 AACAAAAACAA
1 AACAAAAACAA
27205 AA
1 AA
27207 AACAGAAAAA
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:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:27356 original size:19 final size:18
Alignment explanation
Indices: 27323--27358 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
27313 TTGAAATAAT
27323 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
27341 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
27359 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:27366 original size:11 final size:10
Alignment explanation
Indices: 27323--27369 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
27313 TTGAAATAAT
27323 TCTTCAATGA
1 TCTTCAATGA
27333 TCTTCAA--A
1 TCTTCAATGA
*
27341 TCTTCAAATTA
1 TCTTC-AATGA
27352 TCTTCAATGA
1 TCTTCAATGA
27362 GTCTTCAA
1 -TCTTCAA
27370 ACACGAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:30241 original size:31 final size:31
Alignment explanation
Indices: 30182--30260 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
30172 ATTTTTAGCC
* **
30182 ACCAATTTGAGTCTAAACCTTTTGAAAG-TT
1 ACCAATTTGAGCCTAAACCTTTCAAAAGTTT
*
30212 GCTCAATTTGAGCCTAAACCTTTCAAAAGTTT
1 AC-CAATTTGAGCCTAAACCTTTCAAAAGTTT
*
30244 ACCCATTTGAGCCTAAA
1 ACCAATTTGAGCCTAAA
30261 AACAGAAACG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 37 0.90
32 3 0.07
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (31 bp):
ACCAATTTGAGCCTAAACCTTTCAAAAGTTT
Found at i:36350 original size:6 final size:6
Alignment explanation
Indices: 36339--36401 Score: 105
Period size: 6 Copynumber: 11.0 Consensus size: 6
36329 CTAATTAATC
36339 TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA
1 TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA
36387 -T--TA TTACTA TTACTA
1 TTACTA TTACTA TTACTA
36402 CTATATAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 50 0.93
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
TTACTA
Found at i:43729 original size:22 final size:22
Alignment explanation
Indices: 43677--43723 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
43667 TCTTATGAGG
*
43677 TTTTGATAACAATCCTTTGTCA
1 TTTTGATAACAATCCTTTGTAA
*
43699 TTTTGATAACTATCCTTTGTAA
1 TTTTGATAACAATCCTTTGTAA
43721 TTT
1 TTT
43724 ATATAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTGATAACAATCCTTTGTAA
Found at i:44233 original size:133 final size:133
Alignment explanation
Indices: 43912--44329 Score: 791
Period size: 133 Copynumber: 3.1 Consensus size: 133
43902 AGTTATTAAA
* *
43912 ATTATAAAGGATGGTTATCATAATTATATACGACAATTGTCAAAATTCTAATCGAGATTATCAAA
1 ATTACAAAGGATGGTTATCATAATTATATAGGACAATTGTCAAAATTCTAATCGAGATTATCAAA
43977 ATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTTGATATGGCGTTTGATTAT
66 ATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAA-TTTGATATGGCGTTTGATTAT
44042 CAAG
130 CAAG
*
44046 ATTACAAAGGATTGTTATCATAATTATATAGGACAATTGTCAAAATTCTAATCGAGATTATCAAA
1 ATTACAAAGGATGGTTATCATAATTATATAGGACAATTGTCAAAATTCTAATCGAGATTATCAAA
*
44111 ATCTCAAAGGGCAGTTATCAGCAATATAGGGCGATTATCAAAATTTGATATGGCGTTTGATTATC
66 ATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATGGCGTTTGATTATC
44176 AAG
131 AAG
44179 ATTACAAAGGATGGTTATCATAATTATATAGGACAATTGTCAAAATTCTAATCGAGATTATCAAA
1 ATTACAAAGGATGGTTATCATAATTATATAGGACAATTGTCAAAATTCTAATCGAGATTATCAAA
44244 ATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATGGCGTTTGATTATC
66 ATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATGGCGTTTGATTATC
44309 AAG
131 AAG
44312 ATTACAAAGGATGGTTAT
1 ATTACAAAGGATGGTTAT
44330 AAAAAATACA
Statistics
Matches: 278, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
133 174 0.63
134 104 0.37
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (133 bp):
ATTACAAAGGATGGTTATCATAATTATATAGGACAATTGTCAAAATTCTAATCGAGATTATCAAA
ATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATGGCGTTTGATTATC
AAG
Found at i:44349 original size:23 final size:22
Alignment explanation
Indices: 44314--44359 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
44304 TTATCAAGAT
44314 TACAAAGGATGGTTATA-AAAAA
1 TACAAAGGATGGTTA-ACAAAAA
*
44336 TACATAAGGGTGGTTAACAAAAA
1 TACA-AAGGATGGTTAACAAAAA
44359 T
1 T
44360 TTCATTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.24
Consensus pattern (22 bp):
TACAAAGGATGGTTAACAAAAA
Found at i:45081 original size:9 final size:9
Alignment explanation
Indices: 45067--45109 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
45057 AATTACTTAT
45067 GGAAATTAA
1 GGAAATTAA
*
45076 GGAAATTAT
1 GGAAATTAA
45085 GGAAATT-A
1 GGAAATTAA
45093 GGAAATT-A
1 GGAAATTAA
45101 GGAAATTAA
1 GGAAATTAA
45110 ATGAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 15 0.48
9 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (9 bp):
GGAAATTAA
Found at i:45086 original size:18 final size:18
Alignment explanation
Indices: 45063--45109 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
45053 CCCAAATTAC
45063 TTATGGAAATTAAGGAAA
1 TTATGGAAATTAAGGAAA
45081 TTATGGAAATT-AGGAAA
1 TTATGGAAATTAAGGAAA
45098 TTA-GGAAATTAA
1 TTATGGAAATTAA
45110 ATGAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.25
17 10 0.36
18 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (18 bp):
TTATGGAAATTAAGGAAA
Found at i:45098 original size:8 final size:8
Alignment explanation
Indices: 45067--45108 Score: 66
Period size: 8 Copynumber: 5.0 Consensus size: 8
45057 AATTACTTAT
45067 GGAAATTAA
1 GGAAATT-A
45076 GGAAATTA
1 GGAAATTA
45084 TGGAAATTA
1 -GGAAATTA
45093 GGAAATTA
1 GGAAATTA
45101 GGAAATTA
1 GGAAATTA
45109 AATGAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 17 0.53
9 15 0.47
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (8 bp):
GGAAATTA
Done.