Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016412.1 Corchorus capsularis cultivar CVL-1 contig16433, 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: 66254
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:602 original size:18 final size:18
Alignment explanation
Indices: 564--603 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
554 CCAAGTTAAG
**
564 TAATAAACTAAGTAATTT
1 TAATAAACTAAGTAAAAT
*
582 TAATAAACTAATTAAAAT
1 TAATAAACTAAGTAAAAT
600 TAAT
1 TAAT
604 CATAAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
TAATAAACTAAGTAAAAT
Found at i:650 original size:18 final size:19
Alignment explanation
Indices: 615--652 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
605 ATAAACATTA
*
615 AAAATAATTAAATTTTTTT
1 AAAATAATTAAATATTTTT
*
634 AAAA-AATTAAGTATTTTT
1 AAAATAATTAAATATTTTT
652 A
1 A
653 TGTAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAAATAATTAAATATTTTT
Found at i:658 original size:22 final size:20
Alignment explanation
Indices: 626--665 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
616 AAATAATTAA
626 ATTTTTTTAAAAAATTAAGT
1 ATTTTTTTAAAAAATTAAGT
*
646 ATTTTTATGTAAATAATTAA
1 ATTTTT-T-TAAAAAATTAA
666 TTAATGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTTTTTAAAAAATTAAGT
Found at i:786 original size:22 final size:22
Alignment explanation
Indices: 758--801 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
748 TGAGTTTGAA
758 GAAGTTGTTAGAAATGAAGTTT
1 GAAGTTGTTAGAAATGAAGTTT
780 GAAGTTGTTAGAAATGAAGTTT
1 GAAGTTGTTAGAAATGAAGTTT
802 AGGCTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (22 bp):
GAAGTTGTTAGAAATGAAGTTT
Found at i:13941 original size:22 final size:22
Alignment explanation
Indices: 13735--13971 Score: 60
Period size: 22 Copynumber: 10.7 Consensus size: 22
13725 TTAACTTTCT
* * *
13735 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAATCACAC
* * * * *
13757 TACGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ATCACAC
13779 TATGAAATTTTGATAACTTC-C-C
1 TATGAAATTTTGATAA--TCACAC
* * *
13801 AATAAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAATC-ACAC
* *
13824 TATGAGATGTTGATAA-CATC-C
1 TATGAAATTTTGATAATCA-CAC
* * **
13845 ATATGATATATTGATAATCACTT
1 -TATGAAATTTTGATAATCACAC
* * * *
13868 TATAAAAATTTAAAAACCTC-CA-
1 TATGAAATTTTGATAA--TCACAC
*
13890 TATG-AATTTTTAGTAATCACAC
1 TATGAAATTTTGA-TAATCACAC
* * *
13912 TTTAAAATTTTGATAATCACAG
1 TATGAAATTTTGATAATCACAC
* * *
13934 TATGAAATTGTGATAA-CTTCGC
1 TATGAAATTTTGATAATC-ACAC
*
13956 TATTAAATTTTGATAA
1 TATGAAATTTTGATAA
13972 ATATTCCTAT
Statistics
Matches: 154, Mismatches: 43, Indels: 36
0.66 0.18 0.15
Matches are distributed among these distances:
20 3 0.02
21 12 0.08
22 111 0.72
23 25 0.16
24 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAC
Found at i:13986 original size:23 final size:22
Alignment explanation
Indices: 13938--14039 Score: 80
Period size: 23 Copynumber: 4.5 Consensus size: 22
13928 TCACAGTATG
* * *
13938 AAATTGTGAT-AACTTCGCTATT
1 AAATTTTGATAAATTTC-CTATA
13960 AAATTTTGATAAATATTCCTATA
1 AAATTTTGATAAAT-TTCCTATA
* * *
13983 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGATAAA-TTTCCTATA
* * *
14006 AAATTTTGATAACTTTCTTATG
1 AAATTTTGATAAATTTCCTATA
*
14028 AAATCTTGATAA
1 AAATTTTGATAA
14040 CTACAAATTT
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
22 25 0.39
23 36 0.56
24 3 0.05
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAAATTTCCTATA
Found at i:14199 original size:22 final size:22
Alignment explanation
Indices: 14127--14208 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
14117 GATCTACATA
* *
14127 ATATGAAATTTTGATAACCCTC
1 ATATGAAAATTTGATAACCTTC
* * **
14149 TTAT-AAAATTCTGA-AAACTAA
1 ATATGAAAATT-TGATAACCTTC
14170 ACTATGAAAATTTGATAACCTTC
1 A-TATGAAAATTTGATAACCTTC
*
14193 ATATGAAAGTTTGATA
1 ATATGAAAATTTGATA
14209 TCCTCACTGA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
21 8 0.18
22 26 0.58
23 11 0.24
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (22 bp):
ATATGAAAATTTGATAACCTTC
Found at i:14252 original size:19 final size:19
Alignment explanation
Indices: 14202--14252 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
14192 CATATGAAAG
*
14202 TTTGATATCCTCACTGAAT
1 TTTGATATCCTCCCTGAAT
* *
14221 TTCGATATTCTCCCTGAAT
1 TTTGATATCCTCCCTGAAT
*
14240 TTTGGTATCCTCC
1 TTTGATATCCTCC
14253 ATCATAAAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (19 bp):
TTTGATATCCTCCCTGAAT
Found at i:14494 original size:88 final size:88
Alignment explanation
Indices: 14330--14496 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
14320 AGAAATACCA
** * * *
14330 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
14395 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * *
14418 CTATGAAATTTTAATAATCACATTATGTAATTTTGATAATCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTAATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
**
14482 CACTATGTAATTTTG
65 CACTATAAAATTTTG
14497 ATAATCTTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
88 64 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (88 bp):
CTATGAAATTTTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:14707 original size:22 final size:22
Alignment explanation
Indices: 14328--14889 Score: 177
Period size: 22 Copynumber: 26.0 Consensus size: 22
14318 CTAGAAATAC
*
14328 CACTATGAAATTTTTG-TAATCA
1 CACTATGAAA-TTTTGATAACCA
* * * *
14350 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
**
14372 CTTTATGAAATTTTGATAA-CA
1 CACTATGAAATTTTGATAACCA
** * * * *
14393 TCTTTATAAAATTTTGTTGACCC
1 -CACTATGAAATTTTGATAACCA
* * *
14416 CTCTATGAAATTTTAATAATCA
1 CACTATGAAATTTTGATAACCA
* * * *
14438 CATTATGTAATTTTGATAATCT
1 CACTATGAAATTTTGATAACCA
* * *
14460 CGCTTTGAAATTTTGATAACAA
1 CACTATGAAATTTTGATAACCA
* **
14482 CACTATGTAATTTTGATAATCTT
1 CACTATGAAATTTTGATAA-CCA
14505 CA-TAT-AAATTTTGATAATCCTA
1 CACTATGAAATTTTGATAA-CC-A
** * *
14527 TCTTTATGAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAACCA
* *
14550 CTCTATGAGA-TTTGATAACC-
1 CACTATGAAATTTTGATAACCA
** * *
14570 TTCTATCAAATTTTGGT-ACTCA
1 CACTATGAAATTTTGATAAC-CA
* * *
14592 -AAT-TGAGACTTTT-ATAACCTT
1 CACTATGA-AATTTTGATAACC-A
14613 CA-TATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
* *
14634 CACTATAAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * * * *
14656 CCCGATGAAGTATTAATAACC-
1 CACTATGAAATTTTGATAACCA
** *
14677 TTCTAATGAAATTTTGTTAACCA
1 CACT-ATGAAATTTTGATAACCA
* *
14700 CACTATGAAA-TTCGTATAACCT
1 CACTATGAAATTTTG-ATAACCA
* * *
14722 CGCTATGACATTTTGA-AA--T
1 CACTATGAAATTTTGATAACCA
** *
14741 CTTTTTGATAACCTTTCT-ATAA--A
1 CACTATGA-AA--TTT-TGATAACCA
* *
14764 -ATTGTGATAA---T--TAACCA
1 CACTATGA-AATTTTGATAACCA
* **
14781 CCCTATGAAATTTCAATAACCA
1 CACTATGAAATTTTGATAACCA
*
14803 -ACCTATGAAATTTTGGTAACCA
1 CA-CTATGAAATTTTGATAACCA
* *
14825 CTCTATGAAATTTTGGTAACCA
1 CACTATGAAATTTTGATAACCA
* *
14847 CACTATGAAATTTTGGTAACCT
1 CACTATGAAATTTTGATAACCA
*
14869 CACTATGGAATTTTGATAACC
1 CACTATGAAATTTTGATAACC
14890 TCCTCATGGA
Statistics
Matches: 401, Mismatches: 102, Indels: 74
0.69 0.18 0.13
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 3 0.01
18 4 0.01
19 6 0.01
20 14 0.03
21 54 0.13
22 287 0.72
23 14 0.03
24 4 0.01
25 11 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:14911 original size:22 final size:22
Alignment explanation
Indices: 14864--14911 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
14854 AAATTTTGGT
* * *
14864 AACCTCACTATGGAATTTTGAT
1 AACCTCACTATGGAATTATAAC
14886 AACCTC-CTCATGGAATTATAAC
1 AACCTCACT-ATGGAATTATAAC
14908 AACC
1 AACC
14912 ATCTTATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (22 bp):
AACCTCACTATGGAATTATAAC
Found at i:16343 original size:109 final size:109
Alignment explanation
Indices: 16190--16484 Score: 457
Period size: 109 Copynumber: 2.6 Consensus size: 109
16180 TAAATTAAAA
** *
16190 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
16254 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
16301 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
16366 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
16410 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
16475 GTAGAATAAA
61 GTAGAATAAA
16485 CTATAATAGT
Statistics
Matches: 172, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
109 121 0.70
110 13 0.08
111 11 0.06
114 27 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:22132 original size:11 final size:11
Alignment explanation
Indices: 22118--22150 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
22108 ATTCATAACA
22118 AATTTATAATT
1 AATTTATAATT
22129 AATTTATAATT
1 AATTTATAATT
22140 -ATTTGATAATT
1 AATTT-ATAATT
22151 TAGATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:22338 original size:24 final size:24
Alignment explanation
Indices: 22311--22360 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
22301 TGCTTATAAA
22311 TTGGATTGAATCTAAGTGTCTAAT
1 TTGGATTGAATCTAAGTGTCTAAT
22335 TTGGATTGAATCTAAGTGTCTAAT
1 TTGGATTGAATCTAAGTGTCTAAT
22359 TT
1 TT
22361 CAAAGAGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (24 bp):
TTGGATTGAATCTAAGTGTCTAAT
Found at i:22763 original size:16 final size:16
Alignment explanation
Indices: 22742--22777 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
22732 AATCACACAC
*
22742 AATTAAACTTACTATT
1 AATTAAACCTACTATT
22758 AATTAAACCTACTATT
1 AATTAAACCTACTATT
22774 AATT
1 AATT
22778 TTATAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAAACCTACTATT
Found at i:22886 original size:15 final size:15
Alignment explanation
Indices: 22851--22879 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22841 TAATTTTCTA
22851 ATATTT-TATTTATT
1 ATATTTGTATTTATT
22865 ATATTTGTATTTATT
1 ATATTTGTATTTATT
22880 TAGTTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATATTTGTATTTATT
Found at i:23786 original size:22 final size:21
Alignment explanation
Indices: 23761--23817 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 21
23751 TTAAATTCTG
*
23761 AAATTAAATTAATTAAAAAAGT
1 AAATAAAATTAATTAAAAAA-T
23783 AAATAAAAATTAATTAAAAAAT
1 AAAT-AAAATTAATTAAAAAAT
23805 AAATAAACATTAA
1 AAATAAA-ATTAA
23818 CCCACTCCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 3 0.09
22 14 0.44
23 15 0.47
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
AAATAAAATTAATTAAAAAAT
Found at i:23800 original size:11 final size:11
Alignment explanation
Indices: 23766--23817 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
23756 TTCTGAAATT
*
23766 AAATTAATTAAA
1 AAATTAAAT-AA
*
23778 AAAGTAAATAA
1 AAATTAAATAA
*
23789 AAATTAATTAA
1 AAATTAAATAA
*
23800 AAAATAAATAA
1 AAATTAAATAA
*
23811 ACATTAA
1 AAATTAA
23818 CCCACTCCCC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 25 0.78
12 7 0.22
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (11 bp):
AAATTAAATAA
Found at i:24042 original size:32 final size:32
Alignment explanation
Indices: 23999--24060 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
23989 AAGACCCATT
23999 TGCCCAAAATTTCTTCCTCTTAAAAAAAAATC
1 TGCCCAAAATTTCTTCCTCTTAAAAAAAAATC
*
24031 TGCCCAGAATTTCTTCCTCTTAAAAAAAAA
1 TGCCCAAAATTTCTTCCTCTTAAAAAAAAA
24061 AAGGCAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (32 bp):
TGCCCAAAATTTCTTCCTCTTAAAAAAAAATC
Found at i:28970 original size:30 final size:29
Alignment explanation
Indices: 28908--28977 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
28898 GCCGAACCGT
****
28908 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
28937 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
28967 CAAATAAGCCC
1 CAAATAAGCCC
28978 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:36254 original size:15 final size:16
Alignment explanation
Indices: 36234--36271 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
36224 CGATGAAATG
36234 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
36249 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
36266 T-GGGTC
1 TCGGGTC
36272 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:36651 original size:2 final size:2
Alignment explanation
Indices: 36639--36681 Score: 61
Period size: 2 Copynumber: 21.0 Consensus size: 2
36629 GTCTCTGATT
36639 TA TA CTA TA TA TA TA TA TA TA CTA TA TA TA TA TA TA TA -A TA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
36682 ATAGACTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 33 0.87
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:36661 original size:17 final size:17
Alignment explanation
Indices: 36639--36681 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
36629 GTCTCTGATT
36639 TATACTATATATATATA
1 TATACTATATATATATA
36656 TATACTATATATATATA
1 TATACTATATATATATA
*
36673 TATAATATA
1 TATACTATA
36682 ATAGACTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TATACTATATATATATA
Found at i:36664 original size:15 final size:15
Alignment explanation
Indices: 36646--36674 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36636 ATTTATACTA
36646 TATATATATATATAC
1 TATATATATATATAC
36661 TATATATATATATA
1 TATATATATATATA
36675 TAATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAC
Found at i:37943 original size:60 final size:60
Alignment explanation
Indices: 37850--37969 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
37840 TCTAAATGTA
*
37850 TGGAGTCTATATGTGTTCGCGCCAAAAAAATCTCTTTGGAGATCTTGGTGAAAGGGTACC
1 TGGAGTCTATATATGTTCGCGCCAAAAAAATCTCTTTGGAGATCTTGGTGAAAGGGTACC
37910 TGGAGTCTATATATGTTCGCGCCAAAAAAATCTCTTTGGAGATCTTGGTGAAAGGGTACC
1 TGGAGTCTATATATGTTCGCGCCAAAAAAATCTCTTTGGAGATCTTGGTGAAAGGGTACC
37970 GAGCGTGCCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (60 bp):
TGGAGTCTATATATGTTCGCGCCAAAAAAATCTCTTTGGAGATCTTGGTGAAAGGGTACC
Found at i:38390 original size:25 final size:26
Alignment explanation
Indices: 38343--38392 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
38333 GATTCACAAG
**
38343 AGAGATTTGAAAGCACAGGGCTTGAA
1 AGAGATTTGAAAGCACAAAGCTTGAA
38369 AGAGATTT-AAAGCACAAAGCTTGA
1 AGAGATTTGAAAGCACAAAGCTTGA
38393 TTGTTGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (26 bp):
AGAGATTTGAAAGCACAAAGCTTGAA
Found at i:42051 original size:14 final size:13
Alignment explanation
Indices: 42020--42048 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42010 ATGGAAAAAC
42020 AAAA-AAAAACAA
1 AAAACAAAAACAA
42032 AAAACAAAAACAA
1 AAAACAAAAACAA
42045 AAAA
1 AAAA
42049 ACAGTAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAACAA
Found at i:53296 original size:22 final size:20
Alignment explanation
Indices: 53265--53309 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
53255 AACCTTTTCA
53265 CCAAAAAAAATAATCAAACAAC
1 CCAAAAAAAAT-ATCAAAC-AC
* *
53287 CCAAATAAAATTTCAAACAC
1 CCAAAAAAAATATCAAACAC
53307 CCA
1 CCA
53310 TAACACGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (20 bp):
CCAAAAAAAATATCAAACAC
Found at i:56517 original size:2 final size:2
Alignment explanation
Indices: 56504--56534 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
56494 GTTAAAAATA
56504 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
56535 TTCCTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60611 original size:30 final size:30
Alignment explanation
Indices: 60575--60688 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 30
60565 CTCGTCAGCT
*
60575 AAAACAGATTTATTTTCAATGCTATCAACC
1 AAAACAGAATTATTTTCAATGCTATCAACC
* *
60605 AAAACAGGATTATTTGCAATGCTATAATCAACC
1 AAAACAGAATTATTTTCAATGC--T-ATCAACC
* *
60638 AAAACAGAATTGTTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTA---TCAACC
*
60671 AAAACAGAATTGTTTTCA
1 AAAACAGAATTATTTTCA
60689 TCACAATTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
30 20 0.29
31 1 0.01
32 1 0.01
33 48 0.69
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAACAGAATTATTTTCAATGCTATCAACC
Found at i:60749 original size:33 final size:33
Alignment explanation
Indices: 60724--60832 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
60714 TAGTTTTATT
60724 GCAAACAACACTCAAATTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
* * * *
60757 GCAAACAACA-TCTAAAATAGATTTAGTGTCATT
1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC
*
60790 GCAAACAACACTCAATTTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
60823 GCAAACAACA
1 GCAAACAACA
60833 TCTAAAAGAC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 61 0.94
34 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (33 bp):
GCAAACAACACTCAAATTAGGTTTAGTATCATC
Found at i:60756 original size:66 final size:66
Alignment explanation
Indices: 60699--60839 Score: 210
Period size: 66 Copynumber: 2.1 Consensus size: 66
60689 TCACAATTAG
* * *
60699 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
60764 A
66 A
* * * *
60765 CATCTAAAATAGATTTAGTGTCATTGCAAACAACACTCAATTTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
60830 A
66 A
*
60831 CATCTAAAA
1 CATCCAAAA
60840 GACTCTTTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (66 bp):
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
A
Found at i:62347 original size:5 final size:5
Alignment explanation
Indices: 62337--62362 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
62327 TCGAAAATTT
62337 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
62363 ATTTTTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:64468 original size:2 final size:2
Alignment explanation
Indices: 64461--64491 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
64451 ACATACATAC
*
64461 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64492 CGTAGTGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.