Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013896.1 Corchorus olitorius cultivar O-4 contig13929, 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: 57682
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:116 original size:29 final size:28
Alignment explanation
Indices: 77--132 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
67 GTTATTCCAC
*
77 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
106 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
133 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:2060 original size:31 final size:30
Alignment explanation
Indices: 2025--2190 Score: 113
Period size: 31 Copynumber: 5.5 Consensus size: 30
2015 GGCTAATTGC
*
2025 TCAAATAAGGGCCTAATGTTTAATAAAATGT
1 TCAAATAAGGGCCTAATGTTT-ATAAAATGA
* * * **
2056 TCAAATAAGGGTCTGATCTTT-TAATTTGA
1 TCAAATAAGGGCCTAATGTTTATAAAATGA
*
2085 TCAAATAAGGGCCTAATGTTTGCA-AAAATGC
1 TCAAATAAGGGCCTAATGTTT--ATAAAATGA
* * * **
2116 TCAAATAAGGGCTTGATCTTT-TAATTTGA
1 TCAAATAAGGGCCTAATGTTTATAAAATGA
* * * ** *
2145 CCAAATGAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTT-ATAAAATGA
2176 TCAAATAAGGGCCTA
1 TCAAATAAGGGCCTA
2191 GTATCGAAAA
Statistics
Matches: 99, Mismatches: 30, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
29 42 0.42
31 57 0.58
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (30 bp):
TCAAATAAGGGCCTAATGTTTATAAAATGA
Found at i:2093 original size:60 final size:59
Alignment explanation
Indices: 2025--2187 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 59
2015 GGCTAATTGC
*
2025 TCAAATAAGGGCCTAATGTTTAATAAAATGTTCAAATAAGGG-TCTGATCTTTTAATTTGA
1 TCAAATAAGGGCCTAATGTTTAA-AAAATGCTCAAATAAGGGCT-TGATCTTTTAATTTGA
*
2085 TCAAATAAGGGCCTAATGTTTGCAAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGA
1 TCAAATAAGGGCCTAATGTTT-AAAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGA
* * * **
2145 CCAAATGAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
1 TCAAATAAGGGCCTAATGTTT-AAAAAATGCTCAAATAAGGGC
2188 CTAGTATCGA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
60 93 0.98
61 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (59 bp):
TCAAATAAGGGCCTAATGTTTAAAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGA
Found at i:2095 original size:29 final size:28
Alignment explanation
Indices: 2056--2156 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 28
2046 AATAAAATGT
2056 TCAAATAAGGGTCTGATCTTTTAATTTGA
1 TCAAATAAGGG-CTGATCTTTTAATTTGA
* * * ** *
2085 TCAAATAAGGGCCTAATGTTTGCAAAAATGC
1 TCAAATAAGGG-CTGATCTTT--TAATTTGA
2116 TCAAATAAGGGCTTGATCTTTTAATTTGA
1 TCAAATAAGGGC-TGATCTTTTAATTTGA
* *
2145 CCAAATGAGGGC
1 TCAAATAAGGGC
2157 CTAACGTTTG
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
29 32 0.59
30 1 0.02
31 21 0.39
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (28 bp):
TCAAATAAGGGCTGATCTTTTAATTTGA
Found at i:2330 original size:61 final size:61
Alignment explanation
Indices: 2227--2393 Score: 212
Period size: 61 Copynumber: 2.8 Consensus size: 61
2217 AAACTGATGC
* * **
2227 CAGGCCCTTATTTGAGCATTTTCAAT-AACGTTAGGCCCTTATTTGGTCAAATTAAAAGAT
1 CAGGCACTTATTTGAGCATTTTCGATAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT
*
2287 CAGGTACTTATTTGAGCATTTTCGATAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT
1 CAGGCACTTATTTGAGCATTTTCGATAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT
* * * ** * *
2348 CGGGCCCTTATTTGAACATTTT-GGCAAACCTTAGACCCTTATTTGA
1 CAGGCACTTATTTGAGCATTTTCGATAAACGTTAGGCCCTTATTTGA
2394 GCAATTAGCC
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 43 0.46
61 50 0.54
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (61 bp):
CAGGCACTTATTTGAGCATTTTCGATAAACGTTAGGCCCTTATTTGACCAAATTAAAAGAT
Found at i:2437 original size:30 final size:30
Alignment explanation
Indices: 2401--2460 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2391 TGAGCAATTA
2401 GCCTATTTCATTAGCTTGCTTCTACCATAT
1 GCCTATTTCATTAGCTTGCTTCTACCATAT
2431 GCCTATTTCATTAGCTTGCTTCTACCATAT
1 GCCTATTTCATTAGCTTGCTTCTACCATAT
2461 ACCATTAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.43
Consensus pattern (30 bp):
GCCTATTTCATTAGCTTGCTTCTACCATAT
Found at i:2983 original size:19 final size:18
Alignment explanation
Indices: 2936--2983 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
2926 AATTAATTAT
*
2936 TTTAATATTATATTTTTA
1 TTTAATATTATATTTTAA
2954 TTTATATATTATATTTTAA
1 TTTA-ATATTATATTTTAA
*
2973 CTTTAAAATTA
1 -TTTAATATTA
2984 CTCCTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATATTATATTTTAA
Found at i:5786 original size:40 final size:40
Alignment explanation
Indices: 5742--5822 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
5732 TTTTTTTTTG
5742 TGATTTGAGTAATTCTATCTTTGTCTTCTAGTCATTAGAA
1 TGATTTGAGTAATTCTATCTTTGTCTTCTAGTCATTAGAA
*
5782 TGATTTGAGTAATTTTATCTTTGTCTTCTAGTCATTAGAA
1 TGATTTGAGTAATTCTATCTTTGTCTTCTAGTCATTAGAA
5822 T
1 T
5823 ACTAACAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (40 bp):
TGATTTGAGTAATTCTATCTTTGTCTTCTAGTCATTAGAA
Found at i:5833 original size:40 final size:40
Alignment explanation
Indices: 5749--5834 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
5739 TTGTGATTTG
***
5749 AGTAATTCTATCTTTGTCTTCTAGTCATTAGAATGATTTG
1 AGTAATTCTATCTTTGTCTTCTAGTCATTAGAATGATAAC
*
5789 AGTAATTTTATCTTTGTCTTCTAGTCATTAGAAT-ACTAAC
1 AGTAATTCTATCTTTGTCTTCTAGTCATTAGAATGA-TAAC
5829 AGTAAT
1 AGTAAT
5835 CTAACTGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (40 bp):
AGTAATTCTATCTTTGTCTTCTAGTCATTAGAATGATAAC
Found at i:27807 original size:2 final size:2
Alignment explanation
Indices: 27802--27840 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
27792 GGAAACATGA
27802 AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27840 A
1 A
27841 ATTATAATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:27817 original size:10 final size:10
Alignment explanation
Indices: 27802--27840 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
27792 GGAAACATGA
27802 ATATATATAT
1 ATATATATAT
27812 ATATATA-AT
1 ATATATATAT
27821 ATA-ATATA-
1 ATATATATAT
27829 ATATA-ATAT
1 ATATATATAT
27838 ATA
1 ATA
27841 ATTATAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 9 0.35
9 10 0.38
10 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:27824 original size:5 final size:5
Alignment explanation
Indices: 27801--27838 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
27791 AGGAAACATG
27801 AATAT ATATAT ATATAT AATAT AATAT AATAT AATAT A
1 AATAT A-ATAT A-ATAT AATAT AATAT AATAT AATAT A
27839 TAATTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 21 0.66
6 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:35618 original size:18 final size:18
Alignment explanation
Indices: 35595--35630 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35585 ACTCTTGTAC
35595 ATTATGGAAATCTAATAG
1 ATTATGGAAATCTAATAG
35613 ATTATGGAAATCTAATAG
1 ATTATGGAAATCTAATAG
35631 TAATAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
ATTATGGAAATCTAATAG
Found at i:38967 original size:8 final size:8
Alignment explanation
Indices: 38954--39001 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
38944 TGTAGGTAAG
38954 TTGTTATT
1 TTGTTATT
38962 TTGTTAATT
1 TTGTT-ATT
38971 TTGTTATAT
1 TTGTTAT-T
* *
38980 TAGTTACT
1 TTGTTATT
*
38988 TTGTTATC
1 TTGTTATT
38996 TTGTTA
1 TTGTTA
39002 ACTTATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.19, C:0.04, G:0.12, T:0.65
Consensus pattern (8 bp):
TTGTTATT
Found at i:38976 original size:17 final size:17
Alignment explanation
Indices: 38954--39005 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
38944 TGTAGGTAAG
*
38954 TTGTTATTTTGTTAATT
1 TTGTTATTTTGTTAACT
*
38971 TTGTTATATTAGTT-ACT
1 TTGTTAT-TTTGTTAACT
*
38988 TTGTTATCTTGTTAACT
1 TTGTTATTTTGTTAACT
39005 T
1 T
39006 ATATAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.14
17 20 0.69
18 5 0.17
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.63
Consensus pattern (17 bp):
TTGTTATTTTGTTAACT
Found at i:41456 original size:3 final size:3
Alignment explanation
Indices: 41448--41522 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
41438 ATTTATTTTC
41448 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41496 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
41523 TTCCTTTTCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:49572 original size:21 final size:21
Alignment explanation
Indices: 49546--49616 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
49536 TGCTAGGAGA
49546 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
49567 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
49588 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
49609 TCATTGGA
1 TCATTGGA
49617 ATTGTCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:50891 original size:17 final size:17
Alignment explanation
Indices: 50840--50891 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
50830 TGTAGGTAAG
* *
50840 TTGTTATTTTGTTAATT
1 TTGTTATATTGTTAACT
*
50857 TTGTTTTATTAGTT-ACT
1 TTGTTATATT-GTTAACT
*
50874 TTGTTATCTTGTTAACT
1 TTGTTATATTGTTAACT
50891 T
1 T
50892 ATCTGATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.17, C:0.06, G:0.12, T:0.65
Consensus pattern (17 bp):
TTGTTATATTGTTAACT
Found at i:51138 original size:28 final size:28
Alignment explanation
Indices: 51107--51164 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
51097 TAAATAGGAA
*
51107 TTTTTTTATG-GACAAAAATAATATATAT
1 TTTTTTTA-GAGAAAAAAATAATATATAT
*
51135 TTTTTTTAGATAAAAAAATAATATATAT
1 TTTTTTTAGAGAAAAAAATAATATATAT
51163 TT
1 TT
51165 AAGATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
TTTTTTTAGAGAAAAAAATAATATATAT
Done.