Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024178.1 Corchorus olitorius cultivar O-4 contig24211, 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: 24548
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:462 original size:27 final size:27
Alignment explanation
Indices: 432--518 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
422 AATGAGCCAC
432 ATGCCCCTGAATATGCAAATGACCAAA
1 ATGCCCCTGAATATGCAAATGACCAAA
* * * **
459 ATG-CCCTTATTGTAAAAATGACCAAA
1 ATGCCCCTGAATATGCAAATGACCAAA
* * * *
485 ATGACCCTGAACATGCGAATGATCAAA
1 ATGCCCCTGAATATGCAAATGACCAAA
*
512 ACGCCCC
1 ATGCCCC
519 CTGGGTGACC
Statistics
Matches: 44, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
26 21 0.48
27 23 0.52
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (27 bp):
ATGCCCCTGAATATGCAAATGACCAAA
Found at i:4925 original size:16 final size:15
Alignment explanation
Indices: 4887--4928 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
4877 ACACAGATTG
4887 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
4902 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
4917 ACTAGAAAACAA
1 AC-AGAAAACAA
4929 AGCAGAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:8217 original size:21 final size:21
Alignment explanation
Indices: 8188--8254 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
8178 GACATGGAAT
*
8188 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATGGCC
* **
8209 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATGGCC
*
8230 GGTGGTGGCACGGTGAATGGCC
1 GGTGGTGGCACGG-GCATGGCC
8252 GGT
1 GGT
8255 AATGGCTTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 30 0.81
22 7 0.19
ACGTcount: A:0.13, C:0.21, G:0.48, T:0.18
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATGGCC
Found at i:8411 original size:21 final size:21
Alignment explanation
Indices: 8387--8428 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8377 GGCACGGCTA
8387 GCCGGGCAGG-TGGCGCGGATG
1 GCCGGGC-GGATGGCGCGGATG
*
8408 GCCGGTCGGATGGCGCGGATG
1 GCCGGGCGGATGGCGCGGATG
8429 AGGTCTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.10, C:0.24, G:0.55, T:0.12
Consensus pattern (21 bp):
GCCGGGCGGATGGCGCGGATG
Found at i:10654 original size:25 final size:25
Alignment explanation
Indices: 10626--10738 Score: 81
Period size: 25 Copynumber: 4.3 Consensus size: 25
10616 CAGACACAAA
*
10626 TTTTTTTTTATGACGCAAAAACTCT
1 TTTTTTTTTATGACGCAAAAACTAT
10651 TTTTTTTTT-TAGAAAAAAATCGCAAAAAC--T
1 TTTTTTTTTAT-G------A-CGCAAAAACTAT
* *
10681 -TTTTTTTTATGACGCAGAAACAAT
1 TTTTTTTTTATGACGCAAAAACTAT
*
10705 TTTTTTTTTATGACGCAAAACAATAT
1 TTTTTTTTTATGACGCAAAA-ACTAT
10731 TTTTTTTT
1 TTTTTTTT
10739 CGACGCAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
22 8 0.11
23 1 0.01
24 2 0.03
25 28 0.39
26 11 0.15
29 9 0.13
30 2 0.03
31 1 0.01
32 9 0.13
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (25 bp):
TTTTTTTTTATGACGCAAAAACTAT
Found at i:10667 original size:54 final size:53
Alignment explanation
Indices: 10598--10714 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 53
10588 AAAGAAAATA
* **
10598 TTTTTTTTAA-TAAAAA-CGCAGACACAAATTTTTTTTTATGACGCAAAAACTCTT
1 TTTTTTTTAAGAAAAAATCGCA-A-A-AAATTTTTTTTTATGACGCAAAAACAATT
* * *
10652 TTTTTTTTTAGAAAAAAATCGCAAAAACTTTTTTTTTATGACGCAGAAACAATT
1 TTTTTTTTAAG-AAAAAATCGCAAAAAATTTTTTTTTATGACGCAAAAACAATT
10706 TTTTTTTTA
1 TTTTTTTTA
10715 TGACGCAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
54 42 0.79
55 1 0.02
56 6 0.11
57 4 0.08
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (53 bp):
TTTTTTTTAAGAAAAAATCGCAAAAAATTTTTTTTTATGACGCAAAAACAATT
Found at i:10707 original size:24 final size:24
Alignment explanation
Indices: 10680--10750 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 24
10670 TCGCAAAAAC
10680 TTTTTTTTTATGACGCAGAAACAAT
1 TTTTTTTTTATGACGCA-AAACAAT
10705 TTTTTTTTTATGACGCAAAACAAT
1 TTTTTTTTTATGACGCAAAACAAT
*
10729 ATTTTTTTTT-CGACGCAAAACA
1 -TTTTTTTTTATGACGCAAAACA
10751 CAAAATAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
24 18 0.41
25 26 0.59
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (24 bp):
TTTTTTTTTATGACGCAAAACAAT
Found at i:10763 original size:79 final size:79
Alignment explanation
Indices: 10613--10767 Score: 188
Period size: 79 Copynumber: 2.0 Consensus size: 79
10603 TTTAATAAAA
* ** * *
10613 ACGCAGACACAAATTTTTTTTTATGACGCAAAAACTCTTTTTTTTTTTAGAAAAAAATCGCAAAA
1 ACGCAGAAACAAATTTTTTTTTATGACGCAAAAACAATATTTTTTTTTAGAAAAAAATCACAAAA
*
10678 ACTTTTTTTTTATG
66 AATTTTTTTTTATG
* * **
10692 ACGCAGAAACAATTTTTTTTTTATGACGC-AAAACAATATTTTTTTTTCGACGCAAAA-CACAAA
1 ACGCAGAAACAAATTTTTTTTTATGACGCAAAAACAATATTTTTTTTTAGA-AAAAAATCACAAA
10755 ATAATTTTTTTTT
65 A-AATTTTTTTTT
10768 TTAGATTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 23 0.36
79 41 0.64
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.41
Consensus pattern (79 bp):
ACGCAGAAACAAATTTTTTTTTATGACGCAAAAACAATATTTTTTTTTAGAAAAAAATCACAAAA
AATTTTTTTTTATG
Found at i:11092 original size:16 final size:15
Alignment explanation
Indices: 11054--11095 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
11044 ACAGAGATTG
*
11054 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
11069 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
11084 ACTAGAAAACAA
1 AC-AGAAAACAA
11096 AGTAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:15669 original size:34 final size:34
Alignment explanation
Indices: 15631--15715 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
15621 AAAAATTGAA
**
15631 TGGGAACTTTCCCAATTTGAAAACTTAAAACCGG
1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG
* * * *
15665 TGGGAACTTTCTCGATTACAAAACTTGAAACTGG
1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG
*
15699 TGGGAATCTTTTCCAAT
1 TGGGAA-CTTTCCCAAT
15716 AAAAAAAACT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 34 0.83
35 7 0.17
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (34 bp):
TGGGAACTTTCCCAATTACAAAACTTAAAACCGG
Found at i:21646 original size:38 final size:38
Alignment explanation
Indices: 21605--21678 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 38
21595 AAAGAGCTAA
21605 AAAAAAAC-TGGACCTAAAATAGAAAGAGGTC-GAAAAG
1 AAAAAAACTTGG-CCTAAAATAGAAAGAGGTCAGAAAAG
*
21642 AAAAAAACTTGGCCTAAAATAGAGAGAGGTCAGAAAA
1 AAAAAAACTTGGCCTAAAATAGAAAGAGGTCAGAAAA
21679 AAGAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 26 0.76
38 8 0.24
ACGTcount: A:0.55, C:0.11, G:0.22, T:0.12
Consensus pattern (38 bp):
AAAAAAACTTGGCCTAAAATAGAAAGAGGTCAGAAAAG
Found at i:22603 original size:59 final size:59
Alignment explanation
Indices: 22518--23331 Score: 1360
Period size: 59 Copynumber: 13.8 Consensus size: 59
22508 TAGATTACCA
**
22518 TATCTTGTTTTTTAAAATATTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
1 TATCTTG-TTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
*
22578 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAGTTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
* * *
22637 TATCTTGTTTTTAAAATCCTGTTTGAGGTCTCTGTTAGAGAGTTTTCAAATCAAAACCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
* * *
22696 TATCTTGTTTTTAAAATCCTGTTCGAGGTTTCTGTTAGTGAGTTTTCAATTGAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
*
22755 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTATTAGAGAGTTTTCAATTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
*
22814 TATCTTGTTTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
*
22873 TATCTTCG-TTTTAAAATCCTGTTCGAGGTCTCTATTAGAGAGTTTTCAATTCAAAATCT
1 TATCTT-GTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
* *
22932 TATCTTCTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAGTTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
* * * *
22991 TATCTTATTTTTAAAATCCTGTTCGAGGTCTCTATTAGAGAGTTTTCAAATCAAAACCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
* *
23050 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGTGAGTTTACAATTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
*
23109 TATCTTGTTTTTAAACTCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
* * *
23168 TATCTTGTTTTTAAAATCCTGTTCGAGGTTTCTGTTAGTGAGTTGTCAATTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
*
23227 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAATTTTTCAATTCAAAATCT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAG-AGTTTTCAATTCAAAATCT
*
23287 TATCTTGTTCTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTT
1 TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTT
23332 ATATTTCAGA
Statistics
Matches: 703, Mismatches: 48, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
59 639 0.91
60 64 0.09
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (59 bp):
TATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCT
Found at i:23835 original size:145 final size:145
Alignment explanation
Indices: 23561--23890 Score: 464
Period size: 145 Copynumber: 2.3 Consensus size: 145
23551 TCTTAATTGG
** * * *
23561 TCATATTTGCAGGTCCAGGGGCATTTTTGTCATTTTTGCTTACTCAGGGGTATTTTGGTCATTTT
1 TCATATTTGCACTTCCAGGGGCATTTTGGTCATTTTTGCTTACTCAGGGGCATTCTGGTCATTTT
* * *
23626 TGCTTCCTCAGGGGCATTCTGGTCATTTTTGCACATCCTAGGGCATTTTGATCATATTTGCACAT
66 TGCTTCCTCAGGGGCATTCTGGTCAATTTTGCACAGCCTAGGGCATTTTGATCATATTTACACAT
* *
23691 CCCATGGCATTTTGA
131 CCAAGGGCATTTTGA
23706 TCATATTTGCACTTCCAGGGGCATTTTGGTCATTTTTGCTTACTCAGGGGCATTCTGGTCATTTT
1 TCATATTTGCACTTCCAGGGGCATTTTGGTCATTTTTGCTTACTCAGGGGCATTCTGGTCATTTT
* * ** *
23771 TGCTTCCTTAGTGGCATTCTGGTCAATTTTGCACAGCCTAGGGCATTTTTTTCATGTTTACACAT
66 TGCTTCCTCAGGGGCATTCTGGTCAATTTTGCACAGCCTAGGGCATTTTGATCATATTTACACAT
*
23836 CCAAGGGCATTTTGG
131 CCAAGGGCATTTTGA
* * *
23851 TCATTTTTTGCACATT-CAGGGACATTATGGTCATTTTTGC
1 TCA-TATTTGCAC-TTCCAGGGGCATTTTGGTCATTTTTGC
23891 ATGTCTAGGA
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
145 132 0.80
146 30 0.18
147 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (145 bp):
TCATATTTGCACTTCCAGGGGCATTTTGGTCATTTTTGCTTACTCAGGGGCATTCTGGTCATTTT
TGCTTCCTCAGGGGCATTCTGGTCAATTTTGCACAGCCTAGGGCATTTTGATCATATTTACACAT
CCAAGGGCATTTTGA
Found at i:23965 original size:29 final size:29
Alignment explanation
Indices: 23557--23965 Score: 267
Period size: 29 Copynumber: 14.1 Consensus size: 29
23547 TTTTTCTTAA
* ** *
23557 TTGGTCATATTTGCAGGTCCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* ** * *
23586 TTTGTCATTTTTGCTTACTCAGGGGTATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* *
23615 TTGGTCATTTTTGCTTC-CTCAGGGGCATT
1 TTGGTCATTTTTGC-ACATTCAGGGGCATT
* *
23644 CTGGTCATTTTTGCACATCCTA-GGGCATT
1 TTGGTCATTTTTGCACATTC-AGGGGCATT
* * * *
23673 TTGATCATATTTGCACATCCCA-TGGCATT
1 TTGGTCATTTTTGCACAT-TCAGGGGCATT
* *
23702 TTGATCATATTTGCAC-TTCCAGGGGCATT
1 TTGGTCATTTTTGCACATT-CAGGGGCATT
** *
23731 TTGGTCATTTTTGCTTACTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* * * *
23760 CTGGTCATTTTTGCTTCCTT-AGTGGCATT
1 TTGGTCATTTTTGC-ACATTCAGGGGCATT
* * **
23789 CTGGTCAATTTTGCACAGCCTA-GGGCATT
1 TTGGTCATTTTTGCACATTC-AGGGGCATT
** * * * *
23818 TTTTTCATGTTTACACATCCAAGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
*
23847 TTGGTCATTTTTTGCACATTCAGGGACATT
1 TTGGTCA-TTTTTGCACATTCAGGGGCATT
* *
23877 ATGGTCATTTTTG--CATGTCTAGGAGCATT
1 TTGGTCATTTTTGCACAT-TC-AGGGGCATT
* * * * * **
23906 TTGATAATCTTTGCACATCCAAGGGTGTT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
23935 TTGGTCATTTTTGCACATTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
23964 TT
1 TT
23966 TAATGCTTTA
Statistics
Matches: 294, Mismatches: 70, Indels: 32
0.74 0.18 0.08
Matches are distributed among these distances:
27 3 0.01
28 8 0.03
29 248 0.84
30 32 0.11
31 3 0.01
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (29 bp):
TTGGTCATTTTTGCACATTCAGGGGCATT
Done.