Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024314.1 Corchorus olitorius cultivar O-4 contig24347, 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: 15594
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:438 original size:2 final size:2
Alignment explanation
Indices: 427--484 Score: 84
Period size: 2 Copynumber: 29.5 Consensus size: 2
417 TACTTTTTTA
427 AT AT AGT AT AT AT AT AT AT AT AT -T AT AT AT AT AT -T AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
468 AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT A
485 CTAATTATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1734 original size:22 final size:22
Alignment explanation
Indices: 1709--2282 Score: 149
Period size: 22 Copynumber: 26.4 Consensus size: 22
1699 ATTTTTTATG
1709 ACCTCCATATGAAATTTTGATA
1 ACCTCCATATGAAATTTTGATA
*
1731 ACCTTCC-TATGAAATTTTAATA
1 ACC-TCCATATGAAATTTTGATA
* * * **
1753 ACGATAC-TATGGAATTTTGGGA
1 AC-CTCCATATGAAATTTTGATA
*** * **
1775 ACCTTTTTAT-AATTTTTTTTA
1 ACCTCCATATGAAATTTTGATA
* * *
1796 ACCTTCTTATGAAATTTTGTTA
1 ACCTCCATATGAAATTTTGATA
* * *
1818 ACCTCCCTAAGGAATTTTGA-A
1 ACCTCCATATGAAATTTTGATA
1839 GACCT-CACTATGAAATTTTGATA
1 -ACCTCCA-TATGAAATTTTGATA
* *
1862 ACTTCCCA-ATGAAATTTTGGTA
1 ACCT-CCATATGAAATTTTGATA
** * *
1884 ACCAACACTATGAGATGTTGATA
1 ACCTCCA-TATGAAATTTTGATA
* * *
1907 ACCTCCATATGATATATCGATA
1 ACCTCCATATGAAATTTTGATA
* ** * * * *
1929 ACCACGTTAAGAAAATTTAAAA
1 ACCTCCATATGAAATTTTGATA
* *
1951 ACATTCATATG-AATTGTT-AGTA
1 ACCTCCATATGAAATT-TTGA-TA
* * *
1973 A-TTTCACTTTGAAATTTTGATA
1 ACCTCCA-TATGAAATTTTGATA
1995 A--TCACACTATG-AATTTGTGATA
1 ACCTC-CA-TATGAAATTT-TGATA
** * *
2017 ACCTCGC-TAAAAAAATTCGATAA
1 ACCTC-CATATGAAATTTTGAT-A
*
2040 ACCTTCC-TATAAAATTTTGATAA
1 ACC-TCCATATGAAATTTTGAT-A
* * *
2063 ATCTCCCTATAAAATTTTGATA
1 ACCTCCATATGAAATTTTGATA
* * *
2085 ATCTCCTTATGAAATCTTGATA
1 ACCTCCATATGAAATTTTGATA
* *
2107 A----C-TA-CAAATTTTGCTA
1 ACCTCCATATGAAATTTTGATA
* *
2123 ACCT-CATTATGAAATTTCGTTA
1 ACCTCCA-TATGAAATTTTGATA
** * * *
2145 ATTTCCCTATGAAACTTTGATCT
1 ACCTCCATATGAAATTTTGAT-A
* * *
2168 ACATAC-TATGAAACTTTGATA
1 ACCTCCATATGAAATTTTGATA
*
2189 ACC-CTCTTATGAAATTTTGA-A
1 ACCTC-CATATGAAATTTTGATA
* **
2210 AACTAAACTATGAAATTTTGATA
1 ACCTCCA-TATGAAATTTTGATA
*
2233 ACCTTCATATGAAATTTTGATA
1 ACCTCCATATGAAATTTTGATA
* * *
2255 TCCTCC--CTGAAATTTTGATT
1 ACCTCCATATGAAATTTTGATA
2275 A-CTCCATA
1 ACCTCCATA
2283 ATAAAAGTTT
Statistics
Matches: 407, Mismatches: 106, Indels: 79
0.69 0.18 0.13
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
18 1 0.00
19 5 0.01
20 12 0.03
21 42 0.10
22 256 0.63
23 72 0.18
24 7 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
ACCTCCATATGAAATTTTGATA
Found at i:2053 original size:23 final size:23
Alignment explanation
Indices: 2006--2107 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
1996 TCACACTATG
* *
2006 AATTTGTGAT-AACCTCGCTAAAA
1 AATTT-TGATAAACCTCCCTATAA
* * *
2029 AAATTCGATAAACCTTCCTATAA
1 AATTTTGATAAACCTCCCTATAA
*
2052 AATTTTGATAAATCTCCCTATAA
1 AATTTTGATAAACCTCCCTATAA
* * *
2075 AATTTTGAT-AATCTCCTTATGA
1 AATTTTGATAAACCTCCCTATAA
*
2097 AATCTTGATAA
1 AATTTTGATAA
2108 CTACAAATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 22 0.34
23 43 0.66
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (23 bp):
AATTTTGATAAACCTCCCTATAA
Found at i:2468 original size:22 final size:22
Alignment explanation
Indices: 2359--2482 Score: 90
Period size: 22 Copynumber: 5.6 Consensus size: 22
2349 TACCACTATT
* * *
2359 AAATTTTGGTAATCACATTTTG
1 AAATTTTGATAACCACATTATG
* * *
2381 AAAATTTGATAACCTCTTTATG
1 AAATTTTGATAACCACATTATG
* * *
2403 AAATTTGGATAACCTC-TCTATA
1 AAATTTTGATAACCACAT-TATG
* * *
2425 AAATTTTGTTGACC-CCTCTATG
1 AAATTTTGATAACCACAT-TATG
*
2447 AAATTTTGATAATCACATTATG
1 AAATTTTGATAACCACATTATG
*
2469 TAATTTTGATAACC
1 AAATTTTGATAACC
2483 TTGCTTTGAA
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
21 2 0.03
22 76 0.95
23 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCACATTATG
Found at i:2474 original size:44 final size:44
Alignment explanation
Indices: 2354--2543 Score: 135
Period size: 44 Copynumber: 4.4 Consensus size: 44
2344 AAAAATACCA
* * * * *
2354 CTATTAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * * *
2398 TTATGAAATTTGGATAACCTC-TCTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
* *
2442 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAA-CCTT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * *
2485 GCTTTG-AATTTTGATAA-CAC--TATGGAATTTTGATAA-TCTT
1 -CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
2525 CCTAT-AAATTTTGATAATC
1 -CTATGAAATTTTGATAATC
2544 CGATCTCTAT
Statistics
Matches: 115, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
40 32 0.28
41 1 0.01
42 3 0.03
43 15 0.13
44 63 0.55
45 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:2520 original size:40 final size:42
Alignment explanation
Indices: 2442--2543 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 42
2432 GTTGACCCCT
* *
2442 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTTG
1 CTAT-AAATTTTGATAATCACA-TATGGAATTTTGATAACCTTC
* * *
2486 CTTTGAATTTTGATAA-CAC-TATGGAATTTTGATAATCTTC
1 CTATAAATTTTGATAATCACATATGGAATTTTGATAACCTTC
2526 CTATAAATTTTGATAATC
1 CTATAAATTTTGATAATC
2544 CGATCTCTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 32 0.64
41 1 0.02
42 3 0.06
43 11 0.22
44 3 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (42 bp):
CTATAAATTTTGATAATCACATATGGAATTTTGATAACCTTC
Found at i:2558 original size:25 final size:22
Alignment explanation
Indices: 2442--2567 Score: 93
Period size: 22 Copynumber: 5.8 Consensus size: 22
2432 GTTGACCCCT
2442 CTATGAAATTTTGATAATCA-C
1 CTATGAAATTTTGATAATCATC
* * * * *
2463 ATTATGTAATTTTGATAACCTTG
1 -CTATGAAATTTTGATAATCATC
*
2486 CTTTG-AATTTTGATAA-CA--
1 CTATGAAATTTTGATAATCATC
* *
2504 CTATGGAATTTTGATAATCTTC
1 CTATGAAATTTTGATAATCATC
2526 CTAT-AAATTTTGATAATCCGATC
1 CTATGAAATTTTGATAAT-C-ATC
*
2549 TCTATGAAATTTCGATAAT
1 -CTATGAAATTTTGATAAT
2568 TACTTTATGA
Statistics
Matches: 82, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
18 4 0.05
19 11 0.13
20 2 0.02
21 23 0.28
22 24 0.29
23 2 0.02
24 4 0.05
25 12 0.15
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCATC
Found at i:2697 original size:21 final size:22
Alignment explanation
Indices: 2641--2785 Score: 120
Period size: 22 Copynumber: 6.7 Consensus size: 22
2631 ATAACCTTCA
2641 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
** *
2663 TAAAAAATTTTGATGACCACAC
1 TATGAAATTTTGATAACCACAC
* *
2685 TATGAAA-TTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * *
2706 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
2727 T-TGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCACAC
* * *
2748 TATG-AATTTCTTATAACCTCGC
1 TATGAAATTT-TGATAACCACAC
*
2770 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
2786 TCTCTTTGAT
Statistics
Matches: 96, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
20 14 0.15
21 26 0.27
22 52 0.54
23 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:2922 original size:22 final size:23
Alignment explanation
Indices: 2894--2989 Score: 103
Period size: 22 Copynumber: 4.3 Consensus size: 23
2884 TAACCACATT
2894 ATGAAATTTTGATAAACTTCC-C
1 ATGAAATTTTGATAAACTTCCAC
*
2916 ATGAAATTTTGAT-AACTTCCAT
1 ATGAAATTTTGATAAACTTCCAC
* *
2938 ATGAAATTTTGGTAACCTT--AC
1 ATGAAATTTTGATAAACTTCCAC
* *
2959 TATGAAATTTTGATAATC-TCCTC
1 -ATGAAATTTTGATAAACTTCCAC
2982 ATGAAATT
1 ATGAAATT
2990 ATAATAGCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
21 9 0.15
22 48 0.77
23 5 0.08
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
ATGAAATTTTGATAAACTTCCAC
Found at i:3007 original size:66 final size:66
Alignment explanation
Indices: 2893--3020 Score: 161
Period size: 66 Copynumber: 1.9 Consensus size: 66
2883 GTAACCACAT
* * * *
2893 TATGAAATTTTGATAAACTTCCCATGAAATTTTGATAACTTCCATATGAAATTTTGGTAACCTTA
1 TATGAAATTTTGATAAACTTCCCATGAAATTATAATAACATCCATATGAAATTTTGATAACCTTA
2958 C
66 C
* * *
2959 TATGAAATTTTGATAATC-TCCTCATGAAATTATAATAGCAAT-CTTATGAAATTTTGATAACC
1 TATGAAATTTTGATAAACTTCC-CATGAAATTATAATAAC-ATCCATATGAAATTTTGATAACC
3021 ACACAGAGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 3 0.06
66 49 0.92
67 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (66 bp):
TATGAAATTTTGATAAACTTCCCATGAAATTATAATAACATCCATATGAAATTTTGATAACCTTA
C
Found at i:3218 original size:19 final size:20
Alignment explanation
Indices: 3185--3224 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3175 TTATTGACAT
3185 TTAAAAAATTGAAATTAAAA
1 TTAAAAAATTGAAATTAAAA
*
3205 TTAAAATATT-AAATTAAAA
1 TTAAAAAATTGAAATTAAAA
3224 T
1 T
3225 AATAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TTAAAAAATTGAAATTAAAA
Found at i:3231 original size:19 final size:19
Alignment explanation
Indices: 3196--3236 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3186 TAAAAAATTG
*
3196 AAATTAAAATTAAAATATT
1 AAATTAAAATTAAAATAAT
3215 AAATTAAAA-TAATAATAAT
1 AAATTAAAATTAA-AATAAT
3234 AAA
1 AAA
3237 GGAAATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTAAAATTAAAATAAT
Found at i:3513 original size:13 final size:13
Alignment explanation
Indices: 3477--3515 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
3467 TCTAAATTGA
3477 AATTTT-ATAATT
1 AATTTTAATAATT
3489 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
3504 AATTTTAATAAT
1 AATTTTAATAAT
3516 GCCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 4 0.17
15 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:5787 original size:51 final size:51
Alignment explanation
Indices: 5706--5810 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
5696 CAACCAACTC
*
5706 AGTAACTTTGAGTTTGAGGTGGGTTTTGCTCTTAATGTTTTGGGCCATGAT
1 AGTAACTTTGAGTTTGAGGTGGGTTCTGCTCTTAATGTTTTGGGCCATGAT
*
5757 AGTAGCTTTGAGTTTGAGGTGGGTTCTGCTCTTAATGTTTTGGGCCATGAT
1 AGTAACTTTGAGTTTGAGGTGGGTTCTGCTCTTAATGTTTTGGGCCATGAT
5808 AGT
1 AGT
5811 GGAGTTGTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.17, C:0.10, G:0.30, T:0.42
Consensus pattern (51 bp):
AGTAACTTTGAGTTTGAGGTGGGTTCTGCTCTTAATGTTTTGGGCCATGAT
Found at i:10523 original size:31 final size:31
Alignment explanation
Indices: 10485--10580 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
10475 AAGTACCTAA
*
10485 TTAGTCCCTGTACTATTGAAAAAAGATCAAT
1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT
* ***
10516 TTAGTCCCTCCA-TCA-TGAAATCTG-TCAAT
1 TTAGTCCCTCTACT-ATTGAAAAAAGATCAAT
* **
10545 TTAGTCCCTTTACTATTGAAAAGCGATCAAT
1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT
10576 TTAGT
1 TTAGT
10581 TCCAAGTGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
29 16 0.31
30 14 0.27
31 21 0.41
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (31 bp):
TTAGTCCCTCTACTATTGAAAAAAGATCAAT
Done.