Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013051.1 Corchorus capsularis cultivar CVL-1 contig13072, 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: 13204
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:4763 original size:13 final size:13
Alignment explanation
Indices: 4745--4769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4735 TTATAATTTC
4745 AAATAATATTTAT
1 AAATAATATTTAT
4758 AAATAATATTTA
1 AAATAATATTTA
4770 CAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:8645 original size:36 final size:36
Alignment explanation
Indices: 8605--8673 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
8595 GATTAAATTC
** *
8605 TTTATTGATTCCACTTAATTGCCCTGAATTAAGCCT
1 TTTATTGACGCCACTTAATTACCCTGAATTAAGCCT
* *
8641 TTTATTGACGCTATTTAATTACCCTGAATTAAG
1 TTTATTGACGCCACTTAATTACCCTGAATTAAG
8674 TCCCTGACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTATTGACGCCACTTAATTACCCTGAATTAAGCCT
Found at i:8719 original size:30 final size:32
Alignment explanation
Indices: 8655--8720 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
8645 TTGACGCTAT
*
8655 TTAATTACCCTGAATTAAGTCCCTGACTTGAC
1 TTAACTACCCTGAATTAAGTCCCTGACTTGAC
*
8687 TTAACTACCCTGAATTAAGT-CC-GACTTTAC
1 TTAACTACCCTGAATTAAGTCCCTGACTTGAC
8717 TTAA
1 TTAA
8721 TTTCCTTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 11 0.34
31 2 0.06
32 19 0.59
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (32 bp):
TTAACTACCCTGAATTAAGTCCCTGACTTGAC
Found at i:8871 original size:37 final size:37
Alignment explanation
Indices: 8714--8890 Score: 250
Period size: 37 Copynumber: 4.8 Consensus size: 37
8704 AGTCCGACTT
* * * *
8714 TACTTAATTTCCTTCCTTGAAATTAAGTCATTTACTC
1 TACTTAATTCCCTTCCTTGGAATCAAGTCCTTTACTC
8751 TACTTAATTCCCTTCCTTGGAATCAAGTCCTTTACTC
1 TACTTAATTCCCTTCCTTGGAATCAAGTCCTTTACTC
* *
8788 TTCTTAATT-CCTTCCCTTGGAAACAAGTCCTTTACTC
1 TACTTAATTCCCTT-CCTTGGAATCAAGTCCTTTACTC
*
8825 TACTTAATTCTCTTCCTTGGAATCAAGTCCTTTACTC
1 TACTTAATTCCCTTCCTTGGAATCAAGTCCTTTACTC
*
8862 TACTTAATTCCCCTT-CTTGGAATGAAGTC
1 TACTTAATT-CCCTTCCTTGGAATCAAGTC
8891 TTTGACCAAT
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
36 4 0.03
37 115 0.91
38 7 0.06
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (37 bp):
TACTTAATTCCCTTCCTTGGAATCAAGTCCTTTACTC
Found at i:8946 original size:21 final size:21
Alignment explanation
Indices: 8917--9012 Score: 65
Period size: 15 Copynumber: 5.2 Consensus size: 21
8907 CATTTTTGGA
8917 TTAAGTCTTTGCTGATTTTAC
1 TTAAGTCTTTGCTGATTTTAC
* *
8938 TTAATTC-TTG-TGA----AA
1 TTAAGTCTTTGCTGATTTTAC
8953 TTAAGTCTTTGCTGATTTTAC
1 TTAAGTCTTTGCTGATTTTAC
* *
8974 TTAATTC-TTG-TGA----AA
1 TTAAGTCTTTGCTGATTTTAC
8989 TTAAGTCTTTGCTGA-TTTAC
1 TTAAGTCTTTGCTGATTTTAC
9009 TTAA
1 TTAA
9013 TTACCCTGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 23
0.64 0.09 0.26
Matches are distributed among these distances:
15 14 0.25
16 6 0.11
17 6 0.11
19 6 0.11
20 11 0.20
21 13 0.23
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (21 bp):
TTAAGTCTTTGCTGATTTTAC
Found at i:8956 original size:36 final size:36
Alignment explanation
Indices: 8916--9014 Score: 191
Period size: 36 Copynumber: 2.8 Consensus size: 36
8906 TCATTTTTGG
8916 ATTAAGTCTTTGCTGATTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTGATTTTACTTAATTCTTGTGAA
8952 ATTAAGTCTTTGCTGATTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTGATTTTACTTAATTCTTGTGAA
8988 ATTAAGTCTTTGCTGA-TTTACTTAATT
1 ATTAAGTCTTTGCTGATTTTACTTAATT
9015 ACCCTGAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 11 0.17
36 52 0.83
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (36 bp):
ATTAAGTCTTTGCTGATTTTACTTAATTCTTGTGAA
Found at i:9050 original size:71 final size:72
Alignment explanation
Indices: 8916--9293 Score: 191
Period size: 82 Copynumber: 4.9 Consensus size: 72
8906 TCATTTTTGG
** * * *
8916 ATTAAGTCTTTGCTGATTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTGATTTTACTTAATTC
1 ATTAAGTCTTTGCTGATTTTACTTAATTCTCCTGAAATTAAGTCTGTGCTGACTTTACCTAATTC
8981 TTGTGAA
66 TTGTGAA
*
8988 ATTAAGTCTTTGCTGA-TTTACTTAATTAC-CCTG-AATTAAGTCTGTGCTTGCCTTTACCTAAT
1 ATTAAGTCTTTGCTGATTTTACTTAATT-CTCCTGAAATTAAGTCTGTGC-TGACTTTACCTAA-
*
9050 TTCCTTCCTTGAA
63 TT-CTT--GTGAA
* *
9063 ATTAAGT-TTGTACTTG-TCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTG--TTTA
1 ATTAAGTCTT-TGC-TGAT-TTTACTTAA-TT-C-TCC-TGAAATTAAGTCTGTGC-TGACTTTA
*
9124 CCTAATTTCCTTCCTTGAA
58 CCTAA-TT-CTT--GTGAA
* * *
9143 ATTAAGT-TTGTGCTTG-TTCTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTCCTTGTCTTTA
1 ATTAAGTCTT-TGC-TGATT-TTACTTAA-TT-C-TCC-TGAAATTAAGTCTGTGC-TGACTTTA
*
9206 CCTAATTTCCTTCCTTGAA
58 CCTAA-TT-CTT--GTGAA
* * * * *
9225 ATTAAGTCTGTGCTTTACTTTA-TCTAATTTCCTTCCTTGAAATTAAGTTTGTGCTTACTTTACC
1 ATTAAGTCTTTGC-TGATTTTACT-TAA-TT-C-TCC-TGAAATTAAGTCTGTGCTGACTTTACC
9289 TAATT
60 TAATT
9294 TCCTTCCCTG
Statistics
Matches: 265, Mismatches: 20, Indels: 34
0.83 0.06 0.11
Matches are distributed among these distances:
70 13 0.05
71 23 0.09
72 19 0.07
73 3 0.01
74 2 0.01
75 13 0.05
76 2 0.01
77 8 0.03
78 3 0.01
79 1 0.00
80 80 0.30
81 13 0.05
82 83 0.31
83 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.48
Consensus pattern (72 bp):
ATTAAGTCTTTGCTGATTTTACTTAATTCTCCTGAAATTAAGTCTGTGCTGACTTTACCTAATTC
TTGTGAA
Found at i:9084 original size:41 final size:41
Alignment explanation
Indices: 9021--9320 Score: 466
Period size: 41 Copynumber: 7.4 Consensus size: 41
9011 AATTACCCTG
*
9021 AATTAAGTCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
* *
9062 AATTAAGTTTGTACTTGTCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
9103 AATTAAGTCTGTGCTTG--TTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
*
9142 AATTAAGTTTGTGCTTGT-TCTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTGTCT-TTACCTAATTTCCTTCCTTGA
*
9183 AATTAAGTCTGTCCTTGTCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
*
9224 AATTAAGTCTGTGCTT-TACTTTATCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTGT-CTTTACCTAATTTCCTTCCTTGA
* * *
9265 AATTAAGTTTGTGCTT-ACTTTACCTAATTTCCTTCCCTGA
1 AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
9305 AATTAAGTCTGTGCTT
1 AATTAAGTCTGTGCTT
9321 CACTTAATTA
Statistics
Matches: 240, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
39 38 0.16
40 38 0.16
41 163 0.68
42 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (41 bp):
AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGA
Found at i:9171 original size:121 final size:122
Alignment explanation
Indices: 9021--9316 Score: 472
Period size: 121 Copynumber: 2.4 Consensus size: 122
9011 AATTACCCTG
* * *
9021 AATTAAGTCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTTTGTACTTGTCTTTAC
1 AATTAAGTTTGTGCTTGTC-TTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTTGTCTTTAC
*
9086 CTAATTTCCTTCCTTGAAATTAAGTCTGTGC-TT-GTTTACCTAATTTCCTTCCTTGA
65 CTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
*
9142 AATTAAGTTTGTGCTTGTTCTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTCCTTGTCTTTAC
1 AATTAAGTTTGTGCTTG-TCTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTTGTCTTTAC
*
9207 CTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTATCTAATTTCCTTCCTTGA
65 CTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
* *
9265 AATTAAGTTTGTGCTT-ACTTTACCTAATTTCCTTCCCTGAAATTAAGTCTGT
1 AATTAAGTTTGTGCTTGTC-TTACCTAATTTCCTTCCTTGAAATTAAGTCTGT
9317 GCTTCACTTA
Statistics
Matches: 163, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
121 91 0.56
122 35 0.21
123 37 0.23
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (122 bp):
AATTAAGTTTGTGCTTGTCTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTTGTCTTTACC
TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
Found at i:9209 original size:162 final size:163
Alignment explanation
Indices: 9021--9320 Score: 496
Period size: 162 Copynumber: 1.8 Consensus size: 163
9011 AATTACCCTG
* *
9021 AATTAAGTCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTTTGTACTTGT-CTTTA
1 AATTAAGTCTGTCCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTT-TACTTTA
* *
9085 CCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTT-GTTTACCTAATTTCCTTCCTTGAAATTAAG
65 CCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCCTGAAATTAAG
*
9149 TTTGTGCTTGTTCTTACCTAATTTCCTTCCTTGA
130 TCTGTGCTTGTTCTTACCTAATTTCCTTCCTTGA
* * *
9183 AATTAAGTCTGTCCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTAT
1 AATTAAGTCTGTCCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTTTACTTTAC
*
9248 CTAATTTCCTTCCTTGAAATTAAGTTTGTGCTTACTTTACCTAATTTCCTTCCCTGAAATTAAGT
66 CTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCCTGAAATTAAGT
9313 CTGTGCTT
131 CTGTGCTT
9321 CACTTAATTA
Statistics
Matches: 127, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
161 1 0.01
162 90 0.71
163 36 0.28
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (163 bp):
AATTAAGTCTGTCCTTGCCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTTTACTTTAC
CTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCCTGAAATTAAGT
CTGTGCTTGTTCTTACCTAATTTCCTTCCTTGA
Found at i:9365 original size:37 final size:36
Alignment explanation
Indices: 9322--9395 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
9312 TCTGTGCTTC
*
9322 ACTTAATTACCTTGAATTAAATCCTTTAACTGCTTTT
1 ACTTAATTACCCTGAATTAAATCCTTT-ACTGCTTTT
* *
9359 ACTTAATTTCCCTGAATTAAGTCCTTTACTGCTTTT
1 ACTTAATTACCCTGAATTAAATCCTTTACTGCTTTT
9395 A
1 A
9396 TGGGCCTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 10 0.29
37 24 0.71
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAATCCTTTACTGCTTTT
Found at i:11508 original size:50 final size:50
Alignment explanation
Indices: 11454--11745 Score: 267
Period size: 50 Copynumber: 5.8 Consensus size: 50
11444 AAGATGTAAC
11454 CTTTGAATAAAAGATTGAATTTTTAAGTAATT-GATAAATAAAAATGTCAT
1 CTTTGAATAAAAGATTGAATTTTTAAGTAATTAG-TAAATAAAAATGTCAT
** * * * * * *
11504 CTTTGGGTAAAAGATTGAA-CTTTAGAGTGATTAGTAAATAAAATTTTAAG
1 CTTTGAATAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATGTCAT
*
11554 CTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAAATGTCAT
1 CTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAAT-AAAAATGTCAT
** * * *
11605 CTTTGGGTAAAAGATTG-ATTCTTTAGAGTGATTAGTAAAT-AAAATTTCAAC
1 CTTTGAATAAAAGATTGAATT-TTTA-AGTAATTAGTAAATAAAAATGTC-AT
*
11656 CTTTGATTAAAAGATTGAATTTTTAAGT--TTAGTAAAT-AAAATGTCA-
1 CTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCAT
* * * * **
11702 CATTTGAATTAGAAGTTTGAACTTTTAGGCCATTAGTAAATAAA
1 C-TTTGAA-TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAA
11746 TTGATTGGTT
Statistics
Matches: 197, Mismatches: 32, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
46 1 0.01
47 6 0.03
48 32 0.16
49 4 0.02
50 86 0.44
51 53 0.27
52 15 0.08
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (50 bp):
CTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCAT
Found at i:11672 original size:102 final size:101
Alignment explanation
Indices: 11451--11696 Score: 408
Period size: 102 Copynumber: 2.5 Consensus size: 101
11441 TAAAAGATGT
*
11451 AACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGATAAAT-AAAAATGTCATCTTTGGGTAAA
1 AACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAAATGTCATCTTTGGGTAAA
*
11515 AGATTGAACTTTAGAGTGATTAGTAAATAAAATTTT
66 AGATTGAACTTTAGAGTGATTAGTAAATAAAATTTC
*
11551 AAGCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAAATGTCATCTTTGGGTAAA
1 AACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAAATGTCATCTTTGGGTAAA
*
11616 AGATTGATTCTTTAGAGTGATTAGTAAATAAAATTTC
66 AGATTGA-ACTTTAGAGTGATTAGTAAATAAAATTTC
* *
11653 AACCTTTGATTAAAAGATTGAATTTTTAAGT--TTAGTAAATAAAA
1 AACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAA
11697 TGTCACATTT
Statistics
Matches: 137, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
100 52 0.38
101 29 0.21
102 56 0.41
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (101 bp):
AACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAAATGTCATCTTTGGGTAAA
AGATTGAACTTTAGAGTGATTAGTAAATAAAATTTC
Found at i:12280 original size:38 final size:38
Alignment explanation
Indices: 12248--12570 Score: 248
Period size: 38 Copynumber: 8.6 Consensus size: 38
12238 AATTAAGGAC
* *
12248 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
12286 CAAAGTAAGAATAATCAGTAAAATTGATAATTACGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
12324 C--A--AAG--TAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
12356 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
* * *
12394 CAAGGTAACG-GTAATCAGT-AAA-TCAGTAATTAAGTAG-
1 CAAAGTAA-GAATAATCAGTAAAATTGA-TAATTAAG-AGT
* * * *
12431 -AAAG--GGATTAATCAGT--AATTCGGTAATCAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATT-GATAATTAAGAGT
* * * * *
12465 CAAGGTAATAGATTAATCAGTGAAATCGGTAATTAAAGAGT
1 CAAAGT-A-AGAATAATCAGTAAAATTGATAATT-AAGAGT
*
12506 CAAAGTAAAAGAAGTAATCAGTAAAA-TGGTAATTAAGAGT
1 CAAAGT--AAGAA-TAATCAGTAAAATTGATAATTAAGAGT
12546 -AAGAGTAAAAGAAGTAATCAGTAAA
1 CAA-AGT--AAGAA-TAATCAGTAAA
12571 TCGGTAAAGA
Statistics
Matches: 238, Mismatches: 23, Indels: 46
0.78 0.07 0.15
Matches are distributed among these distances:
32 27 0.11
33 5 0.02
34 20 0.08
35 3 0.01
36 9 0.04
37 10 0.04
38 79 0.33
39 14 0.06
40 34 0.14
41 24 0.10
42 13 0.05
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (38 bp):
CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
Found at i:12340 original size:70 final size:70
Alignment explanation
Indices: 12257--12401 Score: 263
Period size: 70 Copynumber: 2.1 Consensus size: 70
12247 CCAAAGTAAT
* *
12257 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTACGA
1 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
12322 GTCAA
66 GTCAA
12327 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
1 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
12392 GTCAA
66 GTCAA
*
12397 GGTAA
1 AGTAA
12402 CGGTAATCAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (70 bp):
AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
GTCAA
Found at i:12553 original size:40 final size:42
Alignment explanation
Indices: 12439--12577 Score: 175
Period size: 40 Copynumber: 3.5 Consensus size: 42
12429 AGAAAGGGAT
* * * *
12439 TAATCAGT-AATTCGGTAATCAAGAGTCAAG-GTAATAG-AT
1 TAATCAGTAAAATCGGTAATTAAGAGTCAAGAGTAAAAGAAG
*
12478 TAATCAGTGAAATCGGTAATTAAAGAGTCAA-AGTAAAAGAAG
1 TAATCAGTAAAATCGGTAATT-AAGAGTCAAGAGTAAAAGAAG
12520 TAATCAGTAAAAT-GGTAATTAAGAGT-AAGAGTAAAAGAAG
1 TAATCAGTAAAATCGGTAATTAAGAGTCAAGAGTAAAAGAAG
12560 TAATCAGT-AAATCGGTAA
1 TAATCAGTAAAATCGGTAA
12578 AGAGTAAAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
39 14 0.16
40 40 0.45
41 22 0.25
42 13 0.15
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.24
Consensus pattern (42 bp):
TAATCAGTAAAATCGGTAATTAAGAGTCAAGAGTAAAAGAAG
Found at i:12594 original size:16 final size:17
Alignment explanation
Indices: 12568--12602 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12558 AGTAATCAGT
*
12568 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
12585 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
12601 AA
1 AA
12603 GGGTAATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:12643 original size:43 final size:43
Alignment explanation
Indices: 12590--12990 Score: 339
Period size: 43 Copynumber: 9.4 Consensus size: 43
12580 AGTAAAAATG
* ** * * *
12590 GTAAAAAGTAAAAGGGTAATCGGTAAGAGCAAAATGGTAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
* *
12633 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
12676 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAAAAT-A
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGT--AATCA
* * * *
12720 GTAAAAAGT--GAT-GATAATCCGTAAAAGGTAAAATGGTAATCA
1 GTAAAGAGTAAAATAG-TAATCAGTAAAA-GCAAAATGGTAATCA
* *
12762 GT-AAGAGCAAAATAGTAATCAGTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAATCA
** ** *
12805 GTAAAGAGTAAAATAGTAA--A--AAAAG--TGATGACAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
* * * *
12842 GTAAA-AGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCA
1 GTAAAGA-GTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
*
12885 GTAAAGAGCAAAA-AGGTAATCAGTAAGAA-CAAAATGGTAATCA
1 GTAAAGAGTAAAATA-GTAATCAGTAA-AAGCAAAATGGTAATCA
* * * *
12928 ATAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAA-GATGATCA
1 GTAAAGAGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAATCA
12972 GTAAAGAGTAAAATAGTAA
1 GTAAAGAGTAAAATAGTAA
12991 AAAGTAATCA
Statistics
Matches: 291, Mismatches: 41, Indels: 51
0.76 0.11 0.13
Matches are distributed among these distances:
36 2 0.01
37 21 0.07
39 6 0.02
41 12 0.04
42 17 0.06
43 167 0.57
44 62 0.21
45 4 0.01
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (43 bp):
GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
Found at i:12645 original size:22 final size:22
Alignment explanation
Indices: 12590--12990 Score: 284
Period size: 22 Copynumber: 18.9 Consensus size: 22
12580 AGTAAAAATG
* * *
12590 GTAAAAAGTAAAAGGGTAATCG
1 GTAAAGAGTAAAATGGTAATCA
* *
12612 GT-AAGAGCAAAATGGTAACCA
1 GTAAAGAGTAAAATGGTAATCA
*
12633 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
12655 GTAAA-AGCAAAATGGGAACCA
1 GTAAAGAGTAAAATGGTAATCA
*
12676 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
12698 GTAAA-AGCAAAATGGTAAAAT-A
1 GTAAAGAGTAAAATGGT--AATCA
* * * *
12720 GTAAAAAGT--GATGATAATCC
1 GTAAAGAGTAAAATGGTAATCA
12740 GTAAA-AGGTAAAATGGTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
* *
12762 GT-AAGAGCAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
12783 GTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAA-AATGGTAATCA
*
12805 GTAAAGAGTAAAATAGTAA--A
1 GTAAAGAGTAAAATGGTAATCA
* ** *
12825 --AAA-AGT--GATGACAACCA
1 GTAAAGAGTAAAATGGTAATCA
12842 GTAAA-AGGTAAAATGGTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
** *
12864 GT-AAGAGCGAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
12885 GTAAAGAGCAAAAAGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
**
12907 GT-AAGAACAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
12928 ATAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
12950 GTAAAAAGTAAGAA-GATGATCA
1 GTAAAGAGTAA-AATGGTAATCA
*
12972 GTAAAGAGTAAAATAGTAA
1 GTAAAGAGTAAAATGGTAA
12991 AAAGTAATCA
Statistics
Matches: 293, Mismatches: 61, Indels: 50
0.73 0.15 0.12
Matches are distributed among these distances:
15 4 0.01
17 4 0.01
18 3 0.01
19 8 0.03
20 10 0.03
21 101 0.34
22 154 0.53
23 9 0.03
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:12877 original size:102 final size:101
Alignment explanation
Indices: 12628--12910 Score: 340
Period size: 102 Copynumber: 2.7 Consensus size: 101
12618 GCAAAATGGT
* * * * * *
12628 AACCAGT-AAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAACCAGTAAAGAGTAAAATAG
1 AACCAGTAAAAG-GTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAAAA-GG
*
12692 TAATCAGTAAAAGCAAAATGGTAAAATAGTAAAAAGTGATGAT
64 TAATCAGT-AAAG---AA-GGTAAAATAGTAAAAAGTGATGAC
*
12735 AATCC-GTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGG
1 AA-CCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAA-AAGG
12799 TAATCAGTAAAG-A-GTAAAATAGTAAAAAAAGTGATGAC
64 TAATCAGTAAAGAAGGTAAAATAGT--AAAAAGTGATGAC
* *
12837 AACCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAAAGGT
1 AACCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAG-TAAAAGGT
12902 AATCAGTAA
65 AATCAGTAA
12911 GAACAAAATG
Statistics
Matches: 158, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
100 10 0.06
101 2 0.01
102 78 0.49
103 2 0.01
106 4 0.03
107 54 0.34
108 8 0.05
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.19
Consensus pattern (101 bp):
AACCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAAAAGGTA
ATCAGTAAAGAAGGTAAAATAGTAAAAAGTGATGAC
Found at i:12972 original size:65 final size:64
Alignment explanation
Indices: 12851--12975 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 64
12841 AGTAAAAGGT
* * * *
12851 AAAATGGTAATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAAAGGTAATCAGTAAGAAC
1 AAAATGGTAATCAATAAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAAGAAC
* * * *
12915 AAAATGGTAATCAATAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGATGATCAGTAA
1 AAAATGGTAATCAAT-AAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAA
12976 AGAGTAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
64 14 0.27
65 38 0.73
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (64 bp):
AAAATGGTAATCAATAAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAAGAAC
Found at i:12996 original size:22 final size:21
Alignment explanation
Indices: 12929--13019 Score: 56
Period size: 22 Copynumber: 4.1 Consensus size: 21
12919 TGGTAATCAA
**
12929 TAAAGAGTAAAATAGTAATCAG
1 TAAAGAGTAAAA-AGTAAAAAG
* * * **
12951 TAAAAAGTAAGAAGATGATCAG
1 TAAAGAGTAAAAAG-TAAAAAG
12973 TAAAGAGTAAAATAGTAAAAAG
1 TAAAGAGTAAAA-AGTAAAAAG
** *
12995 TAATCAGTAAAAGGTAAAATAG
1 TAAAGAGTAAAAAGTAAAA-AG
13017 TAA
1 TAA
13020 TCAGTAGGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
21 8 0.15
22 45 0.82
23 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.19, T:0.21
Consensus pattern (21 bp):
TAAAGAGTAAAAAGTAAAAAG
Found at i:13025 original size:29 final size:29
Alignment explanation
Indices: 12949--13019 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
12939 AATAGTAATC
* *
12949 AGTAAAA-AGTAAGAAGATGATCAGTAAAG
1 AGTAAAATAGTAAAAAG-TAATCAGTAAAG
12978 AGTAAAATAGTAAAAAGTAATCAGTAAA-
1 AGTAAAATAGTAAAAAGTAATCAGTAAAG
13006 AGGTAAAATAGTAA
1 A-GTAAAATAGTAA
13020 TCAGTAGGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 1 0.03
29 29 0.76
30 8 0.21
ACGTcount: A:0.58, C:0.03, G:0.20, T:0.20
Consensus pattern (29 bp):
AGTAAAATAGTAAAAAGTAATCAGTAAAG
Done.