Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021111.1 Corchorus olitorius cultivar O-4 contig21144, 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: 64742
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:5514 original size:80 final size:80
Alignment explanation
Indices: 5402--5554 Score: 211
Period size: 80 Copynumber: 1.9 Consensus size: 80
5392 CACATCAAAT
* *
5402 CAATTTTAGTTCAAGTTTAGGGTTTTAGAAAATATTAAG-ATATCATTAG-AATAAGCTTTTAAA
1 CAATTTTAGTTCAAGTTTAAGGTTTTAGAAAATATCAAGAATATCATTAGAAATAAGCTTTTAAA
5465 AATATGATTTAGGCA
66 AATATGATTTAGGCA
* *
5480 CAATTTTAGTTCAAGTATTTAAGGTTTTTGAAAATATCAAGATATATATCATTCGAAATAAGCTT
1 CAATTTTAGTTCAAG--TTTAAGGTTTTAGAAAATATCAAG--A-ATATCATTAGAAATAAGCTT
5545 TTAAAAATAT
61 TTAAAAATAT
5555 TTTTTGAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
78 15 0.23
80 21 0.33
84 9 0.14
85 19 0.30
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (80 bp):
CAATTTTAGTTCAAGTTTAAGGTTTTAGAAAATATCAAGAATATCATTAGAAATAAGCTTTTAAA
AATATGATTTAGGCA
Found at i:7289 original size:31 final size:31
Alignment explanation
Indices: 7227--7292 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
7217 AAAAGCGATT
* **
7227 AATTTAGTCCCTTTAATCACAATTTTAGGTC
1 AATTTAGTCCCTATAATCACAAAATTAGGTC
*
7258 AATTTAGTCCCTATACTCACAAGAATT-GGTC
1 AATTTAGTCCCTATAATCACAA-AATTAGGTC
7289 AATT
1 AATT
7293 GAGTTCTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (31 bp):
AATTTAGTCCCTATAATCACAAAATTAGGTC
Found at i:7360 original size:31 final size:31
Alignment explanation
Indices: 7325--7392 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
7315 GATTGGACTC
* *
7325 AATTGACTTAATCTTATGAGTATATGAACTA
1 AATTGACTCAATCTTATGAGTACATGAACTA
* *
7356 AATTGACTCAATCTTGTGAGTACATGGACTA
1 AATTGACTCAATCTTATGAGTACATGAACTA
7387 AATTGA
1 AATTGA
7393 TCGCTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (31 bp):
AATTGACTCAATCTTATGAGTACATGAACTA
Found at i:8515 original size:9 final size:9
Alignment explanation
Indices: 8501--8532 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
8491 TATACATATT
8501 TAAAAAAAA
1 TAAAAAAAA
8510 T-AAAAAAA
1 TAAAAAAAA
8518 TAAAAAAAA
1 TAAAAAAAA
8527 TAAAAA
1 TAAAAA
8533 CAGAAACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:8516 original size:8 final size:8
Alignment explanation
Indices: 8503--8532 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
8493 TACATATTTA
8503 AAAAAAAT
1 AAAAAAAT
8511 AAAAAAAT
1 AAAAAAAT
8519 AAAAAAAAT
1 -AAAAAAAT
8528 AAAAA
1 AAAAA
8533 CAGAAACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:11503 original size:24 final size:23
Alignment explanation
Indices: 11464--11511 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
11454 AAATTATGAG
11464 AAAAATACTTGTCCATCTTTATC
1 AAAAATACTTGTCCATCTTTATC
11487 AAAAATACTT-TCGCCATCTTTATC
1 AAAAATACTTGT--CCATCTTTATC
11511 A
1 A
11512 GGTATATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.04
23 10 0.43
24 12 0.52
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAAATACTTGTCCATCTTTATC
Found at i:13073 original size:154 final size:154
Alignment explanation
Indices: 12792--13257 Score: 851
Period size: 154 Copynumber: 3.0 Consensus size: 154
12782 ACTTACCAGA
*
12792 TTCAACAAAAGTATGCAAGTTGGTAAAGTCTCTATATGGTTTGAAACAAGCTAGTCGGCAGTGGA
1 TTCAACAAAAGTATGCAAGTTGGTGAAGTCTCTATATGGTTTGAAACAAGCTAGTCGGCAGTGGA
* *
12857 ACATAAAACTGACAAAGAGTCTATTCAGCAAAGGTTTTGTGCAATCACAAGCTGATCGTAGCTTA
66 ACATAAAACTGACAGAGAGTCTATTCAGCAAAGGTTTTGTGCAATCACAAGCTGATCATAGCTTA
12922 TTCACAAAGAAAACAGGTGACAAC
131 TTCACAAAGAAAACAGGTGACAAC
* *
12946 TTCAACAAAAGTATGCAAGTTGGTGAAGTCTCTATATGGTTTGAAACAAGCTAGTCGACAATGGA
1 TTCAACAAAAGTATGCAAGTTGGTGAAGTCTCTATATGGTTTGAAACAAGCTAGTCGGCAGTGGA
*
13011 ACATAAAACTGACAGAGAGTCTATTCAGCAAAGGTTTTGTGCAATCACAAACTGATCATAGCTTA
66 ACATAAAACTGACAGAGAGTCTATTCAGCAAAGGTTTTGTGCAATCACAAGCTGATCATAGCTTA
*
13076 TTCACAAATAAAACAGGTGACAAC
131 TTCACAAAGAAAACAGGTGACAAC
13100 TTCAACAAAAGTATGCAAGTTGGTGAAGTCTCTATATGGTTTGAAACAAGCTAGTCGGCAGTGGA
1 TTCAACAAAAGTATGCAAGTTGGTGAAGTCTCTATATGGTTTGAAACAAGCTAGTCGGCAGTGGA
*
13165 ACATAAAACTGACAGAGAGTCTATTCAGCAAAGGTTTTGTGCAACCACAAGCTGATCATAGCTTA
66 ACATAAAACTGACAGAGAGTCTATTCAGCAAAGGTTTTGTGCAATCACAAGCTGATCATAGCTTA
*
13230 TTCACAAAGAAAACGGGTGACAAC
131 TTCACAAAGAAAACAGGTGACAAC
13254 TTCA
1 TTCA
13258 TAGCTTTGCT
Statistics
Matches: 299, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
154 299 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (154 bp):
TTCAACAAAAGTATGCAAGTTGGTGAAGTCTCTATATGGTTTGAAACAAGCTAGTCGGCAGTGGA
ACATAAAACTGACAGAGAGTCTATTCAGCAAAGGTTTTGTGCAATCACAAGCTGATCATAGCTTA
TTCACAAAGAAAACAGGTGACAAC
Found at i:17021 original size:23 final size:21
Alignment explanation
Indices: 16980--17034 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 21
16970 CAACAATTAA
16980 TTAATCCATA-TTCTGAACCT
1 TTAATCCATATTTCTGAACCT
17000 TTAATCCATATTAATCTGAACCT
1 TTAATCCATATT--TCTGAACCT
17023 TTAATCCATATT
1 TTAATCCATATT
17035 GATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.31
21 1 0.03
23 21 0.66
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.42
Consensus pattern (21 bp):
TTAATCCATATTTCTGAACCT
Found at i:21868 original size:31 final size:31
Alignment explanation
Indices: 21817--21908 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 31
21807 ACATTTTGAA
21817 ACACATGGTCACTTTTTTGGTACACATGGCGTG
1 ACACAT-GTCAC-TTTTTGGTACACATGGCGTG
* **
21850 ATATGTGTCACTTTTTGGTACACATGGCGTG
1 ACACATGTCACTTTTTGGTACACATGGCGTG
* * *
21881 CCACATGTCGCTTTTTGGTACACGTGGC
1 ACACATGTCACTTTTTGGTACACATGGC
21909 ATGCCATCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 42 0.84
32 5 0.10
33 3 0.06
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (31 bp):
ACACATGTCACTTTTTGGTACACATGGCGTG
Found at i:27527 original size:15 final size:15
Alignment explanation
Indices: 27507--27543 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
27497 GAGTCCTGAA
**
27507 GATGATGAAGATGGT
1 GATGATGAAGATAAT
27522 GATGATGAAGATAAT
1 GATGATGAAGATAAT
27537 GATGATG
1 GATGATG
27544 CGGATGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.27
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:34441 original size:28 final size:29
Alignment explanation
Indices: 34398--34453 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
34388 GGAAGTTTCC
*
34398 TTTTTTGGGGGTTAATTTCAGGAAACTTA
1 TTTTTTGGCGGTTAATTTCAGGAAACTTA
34427 TTTTTTGGCGG-TAATTTCAGGAAACTT
1 TTTTTTGGCGGTTAATTTCAGGAAACTT
34454 TTAGTTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (29 bp):
TTTTTTGGCGGTTAATTTCAGGAAACTTA
Found at i:39620 original size:36 final size:36
Alignment explanation
Indices: 39301--39645 Score: 357
Period size: 36 Copynumber: 9.6 Consensus size: 36
39291 CTCTGTCTGC
* * *
39301 GACTGTGCACAGACCTATCGAGGTGCATCCTCAGGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
* *
39337 GACTATGCACAGACCTATCGAGGTACATCCTCAGGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
* *
39373 GACTATGCACAGACCTATCGAGGTACATCCTCAGGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
*
39409 GACTATGCACAGACCTATTGAGGTACATCCTCAGGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
* *
39445 GACTTTGCGCAGACCTATTGAGGTACTTCCTCAGGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
** * * *
39481 GACTTTGCGTAGACCTATGGAGGTACTTCCTCAAGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
** * ** ** *
39517 GACTTTGCGGAGACCTATCGAATTATTTCCTCAGGC
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
** * ** *
39553 GACTTTGCGTAGACATATTGACTTACTTCCTCAGGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
* *** *
39589 GGCTTTGCACAGACCTATTGAGGTGGGTCCTCATGA
1 GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
** *
39625 CCCATTGCACAGACCTATTGA
1 GACTTTGCACAGACCTATTGA
39646 TGTTATTGTT
Statistics
Matches: 274, Mismatches: 35, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 274 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (36 bp):
GACTTTGCACAGACCTATTGAGGTACATCCTCAGGA
Found at i:39659 original size:108 final size:105
Alignment explanation
Indices: 39331--39681 Score: 297
Period size: 108 Copynumber: 3.3 Consensus size: 105
39321 AGGTGCATCC
* ** * * * * *
39331 TCAGGAGACTATGCACAGACCTATCGAGGTACATCCTCAGGAGACTATGCACAGACCTATCGAGG
1 TCAGGAGACTTTGCGTAGACATATTGACGTACTTCCTCAGGAGACTTTGCACAGACCTATCGAGG
* * **
39396 TACATCCTCAGGAGACTATGCACAGACCTATTGAGGTACATCC
66 TACATCCTCAAGAGACT-TGCACAGACCTATTGA-GT-TATTT
* * * ** *
39439 TCAGGAGACTTTGCGCAGACCTATTGAGGTACTTCCTCAGGAGACTTTGCGTAGACCTATGGAGG
1 TCAGGAGACTTTGCGTAGACATATTGACGTACTTCCTCAGGAGACTTTGCACAGACCTATCGAGG
* ** * *
39504 TACTTCCTCAAGAGACTTTGCGGAGACCTATCGAATTATTT
66 TACATCCTCAAGAGAC-TTGCACAGACCTATTGAGTTATTT
* * * *
39545 CCTCAGGCGACTTTGCGTAGACATATTGACTTACTTCCTCAGGAGGCTTTGCACAGACCTATTGA
1 --TCAGGAGACTTTGCGTAGACATATTGACGTACTTCCTCAGGAGACTTTGCACAGACCTATCGA
*** * **
39610 GGTGGGTCCTCATGACCCATTGCACAGACCTATTGATGTTATTGT
64 GGTACATCCTCAAGAGAC-TTGCACAGACCTATTGA-GTTATT-T
** *
39655 TCAGGATTCCTTGCGTAGACATATTGA
1 TCAGGAGACTTTGCGTAGACATATTGA
39682 GGTTTCTTCG
Statistics
Matches: 197, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
106 2 0.01
107 1 0.01
108 187 0.95
109 6 0.03
110 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (105 bp):
TCAGGAGACTTTGCGTAGACATATTGACGTACTTCCTCAGGAGACTTTGCACAGACCTATCGAGG
TACATCCTCAAGAGACTTGCACAGACCTATTGAGTTATTT
Found at i:47185 original size:1 final size:1
Alignment explanation
Indices: 47179--47209 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
47169 ACTAGTGTAG
47179 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47210 AAATTGATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47306 original size:27 final size:27
Alignment explanation
Indices: 47268--47321 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
47258 TCATGTTGGC
47268 AAAGATGAGAAAATAAGTTCGATTTTT
1 AAAGATGAGAAAATAAGTTCGATTTTT
47295 AAAGATGAGAAAATAAGTTCGATTTTT
1 AAAGATGAGAAAATAAGTTCGATTTTT
47322 TAGAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (27 bp):
AAAGATGAGAAAATAAGTTCGATTTTT
Found at i:50522 original size:141 final size:141
Alignment explanation
Indices: 50268--50552 Score: 520
Period size: 141 Copynumber: 2.0 Consensus size: 141
50258 GTCTTTTCGT
50268 TATTTAATTGCATGAAGACACGATAGAGCATACTATGAGATGATTGGAAGTCCTCTAACTTTTTC
1 TATTTAATTGCATGAAGACACGATAGAGCATACTATGAGATGATTGGAAGTCCTCTAACTTTTTC
50333 TTAATGTGTTCTATTAATACTAATAATATTTAGTCCCGCAAGATTATGATTAATCCTTGTCACTG
66 TTAATGTGTTCTATTAATACTAATAATATTTAGTCCCGCAAGATTATGATTAATCCTTGTCACTG
50398 TTAGAAAGGCA
131 TTAGAAAGGCA
*
50409 TATTTAATTGCATGAAGACATGATAGAGCATACTATGAGATGATTGGAAGTCCTCTTAACTTTTT
1 TATTTAATTGCATGAAGACACGATAGAGCATACTATGAGATGATTGGAAGTCCTC-TAACTTTTT
*
50474 CTTAATGTGTT-TAATTAATATTAATAATATTTAGTCCCGCAAG-TTATGATTAATCCTTGTCAC
65 CTTAATGTGTTCT-ATTAATACTAATAATATTTAGTCCCGCAAGATTATGATTAATCCTTGTCAC
50537 TGTTAGAAAGGCA
129 TGTTAGAAAGGCA
50550 TAT
1 TAT
50553 ATAAACAAGT
Statistics
Matches: 140, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
141 91 0.65
142 49 0.35
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (141 bp):
TATTTAATTGCATGAAGACACGATAGAGCATACTATGAGATGATTGGAAGTCCTCTAACTTTTTC
TTAATGTGTTCTATTAATACTAATAATATTTAGTCCCGCAAGATTATGATTAATCCTTGTCACTG
TTAGAAAGGCA
Found at i:60056 original size:21 final size:22
Alignment explanation
Indices: 60012--60057 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
60002 ACCATGAACC
* *
60012 AACTTTTTACAGATTATGTAAA
1 AACTTTTTACAAATCATGTAAA
60034 AACTTTTTACAAATCATGTAAA
1 AACTTTTTACAAATCATGTAAA
60056 AA
1 AA
60058 GATGAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (22 bp):
AACTTTTTACAAATCATGTAAA
Found at i:62533 original size:79 final size:79
Alignment explanation
Indices: 62445--62590 Score: 238
Period size: 79 Copynumber: 1.8 Consensus size: 79
62435 CAATAATTAA
* * *
62445 AGCCAAATTTTGCGTATATATTAACCCACGGAATAGCAACTAGTTTAAAGCCAATTGAATTATAT
1 AGCCAAATTTTGAGTATATATTAACCCACGAAATAGCAACTAGTTTAAAGCAAATTGAATTATAT
62510 ATATTATATTATAT
66 ATATTATATTATAT
* * *
62524 AGCCAAATTTTGAGTATATTTTAATCCACGAAATAGCAACTAGTTTTAAGCAAATTGAATTATAT
1 AGCCAAATTTTGAGTATATATTAACCCACGAAATAGCAACTAGTTTAAAGCAAATTGAATTATAT
62589 AT
66 AT
62591 TAAATTATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (79 bp):
AGCCAAATTTTGAGTATATATTAACCCACGAAATAGCAACTAGTTTAAAGCAAATTGAATTATAT
ATATTATATTATAT
Found at i:64714 original size:2 final size:2
Alignment explanation
Indices: 64707--64739 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64697 CACAATACCA
64707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64740 AAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.