Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000985.1 Hibiscus syriacus cultivar Beakdansim tig00001970_pilon, 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: 82098
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1933 original size:88 final size:88
Alignment explanation
Indices: 1767--1991 Score: 337
Period size: 88 Copynumber: 2.5 Consensus size: 88
1757 CTAAGGATAT
* *
1767 GGCCCCAAGGAATATTCTTAGGTTGGTTTCCTTTTTGCTGTGTGCTTAAGGTACCCTACGGATCT
1 GGCCCCAAGGAATATCCTTAGGTTGGTTTCC-TTTTGCTGTGTACTTAAGGTACCCTACGGATCT
*
1832 AAGGATATCCTTGGGTAGGCCCATA
65 AAGGATACCCTTGGGTAGG-CCATA
*
1857 GGCCCC-AGGAATATCCTTAGGTTGGTTTCC-TTTGTTGTGTACTTAAGGTAACCCTACGGATCT
1 GGCCCCAAGGAATATCCTTAGGTTGGTTTCCTTTTGCTGTGTACTTAAGGT-ACCCTACGGATCT
1920 AAGGATACCCTTGGGTAGGCCATA
65 AAGGATACCCTTGGGTAGGCCATA
* * *
1944 GGCCCCAAGGAATATCCTTAGGTTGGCTCCCTTTTTGCTGTGTGCTTA
1 GGCCCCAAGGAATATCCTTAGGTTGGTTTCC-TTTTGCTGTGTACTTA
1992 GCGTAAGCTC
Statistics
Matches: 123, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
87 28 0.23
88 53 0.43
89 23 0.19
90 19 0.15
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (88 bp):
GGCCCCAAGGAATATCCTTAGGTTGGTTTCCTTTTGCTGTGTACTTAAGGTACCCTACGGATCTA
AGGATACCCTTGGGTAGGCCATA
Found at i:7988 original size:18 final size:19
Alignment explanation
Indices: 7953--8001 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
7943 ACAAACTTTT
*
7953 TGTTTATAA-TAT-TGTTA
1 TGTTTATAAGTTTGTGTTA
7970 TG-TTATAAGTTTGTGTTA
1 TGTTTATAAGTTTGTGTTA
*
7988 TGTTTATAATTTTG
1 TGTTTATAAGTTTG
8002 ATTATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.22
17 4 0.15
18 7 0.26
19 10 0.37
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (19 bp):
TGTTTATAAGTTTGTGTTA
Found at i:8006 original size:18 final size:17
Alignment explanation
Indices: 7953--8006 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
7943 ACAAACTTTT
*
7953 TGTTTATAATATTGTTA
1 TGTTTATAATTTTGTTA
7970 TG-TTATAAGTTTGTGTTA
1 TGTTTATAA-TTT-TGTTA
7988 TGTTTATAATTTTGATTA
1 TGTTTATAATTTTG-TTA
8006 T
1 T
8007 AAATTTCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 14 0.44
19 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (17 bp):
TGTTTATAATTTTGTTA
Found at i:13263 original size:224 final size:226
Alignment explanation
Indices: 12840--13285 Score: 573
Period size: 224 Copynumber: 2.0 Consensus size: 226
12830 TAAACTATAC
*
12840 AAAAAATTCAATTATATTTAACAGTAAAATAAAATATTAAAAATATATCAATTACCTGGATATTG
1 AAAAAATTCAATTATATTTAACAGTAAAATAAAATATTAAAAATATATCAATTACCTGAATATTG
** * * *
12905 AAATTGATGAACCACTTCTAGTACTATAATCTGGTGCAAAATAAAAAAATTTGCAAAAATAATAC
66 AAATTGACAAACCACTTC-A-TACTATAATCTGGAGCAAAACAAAAAAAATTGCAAAAATAATAC
* * * * * * * *
12970 AACTCTAAAACAATATTATTTCAAAAGTAAAATACATAAAATAAGATTTCTATTTCACTTTCTTG
129 AACTCTAAAACAAGATCATCTCAAAAGTAAAATAAAGAAAAGAAAATTTCTATTTCACTTACTTG
*
13035 ATAATCTTTTTAACCCTAAATCAAATCTTTTAT
194 ATAATCTTATTAACCCTAAATCAAATCTTTTAT
* *
13068 AAAAAATTCAATTATATTTATCAGTAAAATAAAAATAAATTAAAAA-A-ACTTAATTA-CTGAAT
1 AAAAAATTCAATTATATTTAACAGTAAAAT-AAAAT--ATTAAAAATATA-TCAATTACCTGAAT
* * *
13130 ATTGAAATTGGCAAACCGCTTC-TACTATAATCTGGAGCAAAACAAAAAAAATTG-TAAAATAAT
62 ATTGAAATTGACAAACCACTTCATACTATAATCTGGAGCAAAACAAAAAAAATTGCAAAAATAAT
* * *
13193 AGAATTCTAAAACAAGATCA-CTCAAAAGTAAAATAAAGAGAAGAATAATTT-TATTTCACTTAC
127 ACAACTCTAAAACAAGATCATCTCAAAAGTAAAATAAAGAAAAGAA-AATTTCTATTTCACTTAC
13256 TTGATAATCTTATTAACCCTAAATCAAATC
191 TTGATAATCTTATTAACCCTAAATCAAATC
13286 GAATATGTAG
Statistics
Matches: 190, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
224 60 0.32
225 28 0.15
226 29 0.15
228 29 0.15
229 29 0.15
230 7 0.04
231 8 0.04
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (226 bp):
AAAAAATTCAATTATATTTAACAGTAAAATAAAATATTAAAAATATATCAATTACCTGAATATTG
AAATTGACAAACCACTTCATACTATAATCTGGAGCAAAACAAAAAAAATTGCAAAAATAATACAA
CTCTAAAACAAGATCATCTCAAAAGTAAAATAAAGAAAAGAAAATTTCTATTTCACTTACTTGAT
AATCTTATTAACCCTAAATCAAATCTTTTAT
Found at i:15947 original size:29 final size:30
Alignment explanation
Indices: 15915--15989 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
15905 TTCATTTGAT
*
15915 AAATATTAAAAATTATAAT-TAATATTA-TA
1 AAATA-TAAAAATTATAATATAATAATATTA
*
15944 AAATAATAAAAATTACAATATAATAATATTA
1 AAAT-ATAAAAATTATAATATAATAATATTA
15975 AAA-ATAAAAA-TATAA
1 AAATATAAAAATTATAA
15990 ATTTGATTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 4 0.10
29 23 0.57
30 8 0.20
31 5 0.12
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (30 bp):
AAATATAAAAATTATAATATAATAATATTA
Found at i:15971 original size:23 final size:22
Alignment explanation
Indices: 15940--15990 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
15930 TAATTAATAT
* *
15940 TATAAAATAATAAAAATTACAA
1 TATAAAATAATAAAAATAAAAA
*
15962 TATAATAATATTAAAAATAAAAA
1 TATAA-AATAATAAAAATAAAAA
15985 TATAAA
1 TATAAA
15991 TTTGATTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
TATAAAATAATAAAAATAAAAA
Found at i:16090 original size:44 final size:44
Alignment explanation
Indices: 16026--16127 Score: 186
Period size: 44 Copynumber: 2.3 Consensus size: 44
16016 TTGATGTTTT
*
16026 TATTTCTAAAAGAATATTAATGATATATTTATTATTATGATTTAA
1 TATTT-TAAAAGAATATTAATGATATATTTATTACTATGATTTAA
16071 TATTTTAAAAGAATATTAATGATATATTTATTACTATGATTTAA
1 TATTTTAAAAGAATATTAATGATATATTTATTACTATGATTTAA
16115 TATTTTAAAAGAA
1 TATTTTAAAAGAA
16128 GTAGGAGGGT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
44 51 0.91
45 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (44 bp):
TATTTTAAAAGAATATTAATGATATATTTATTACTATGATTTAA
Found at i:19031 original size:21 final size:21
Alignment explanation
Indices: 18987--19031 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
18977 AAACTACGTC
*
18987 TTTAGTATCTAAATTATCAGT
1 TTTAGTATCTAAATTATCAAT
*
19008 TTTAGTATCTGAACTT-TCAAT
1 TTTAGTATCT-AAATTATCAAT
19029 TTT
1 TTT
19032 TTCAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTAGTATCTAAATTATCAAT
Found at i:21275 original size:75 final size:75
Alignment explanation
Indices: 21131--21348 Score: 332
Period size: 75 Copynumber: 2.9 Consensus size: 75
21121 GAACCATAAA
21131 CAAATCTCAAGACTCAAACCACAATATTAAGTCT--AACAATAAAATTCATAAACAAACCACAAT
1 CAAATCTCAAGACTCAAACCACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
* *
21194 ACTAAAATGT
66 ATTAAAATAT
* * * *
21204 CAAATCTTAAGACTGAAACTACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACGAT
1 CAAATCTCAAGACTCAAACCACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
21269 ATTAAAATAT
66 ATTAAAATAT
* * * *
21279 CAAATCTCAAGATTCAAACCACAATATTAACTCTAGAACAATAAAATCCATAAACAAACCATAAT
1 CAAATCTCAAGACTCAAACCACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
21344 ATTAA
66 ATTAA
21349 GTATAAAACA
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
73 31 0.24
75 98 0.76
ACGTcount: A:0.52, C:0.20, G:0.05, T:0.23
Consensus pattern (75 bp):
CAAATCTCAAGACTCAAACCACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
ATTAAAATAT
Found at i:21337 original size:40 final size:40
Alignment explanation
Indices: 21293--21388 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
21283 TCTCAAGATT
* * * *
21293 CAAACCACAATATTAACTCTAGAACAATAAAATCCATAAA
1 CAAACCATAATATTAACTATAAAACAATAAAATCCACAAA
*
21333 CAAACCATAATATTAAGTATAAAACAATAAAATCCACAAA
1 CAAACCATAATATTAACTATAAAACAATAAAATCCACAAA
*
21373 CAAACCATAGTATTAA
1 CAAACCATAATATTAA
21389 AGTGTCAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.21
Consensus pattern (40 bp):
CAAACCATAATATTAACTATAAAACAATAAAATCCACAAA
Found at i:24116 original size:19 final size:19
Alignment explanation
Indices: 24092--24129 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24082 ACCACCAATC
*
24092 CTAAATGGGTAGAGGAAAA
1 CTAAATAGGTAGAGGAAAA
24111 CTAAATAGGTAGAGGAAAA
1 CTAAATAGGTAGAGGAAAA
24130 ATCAAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.29, T:0.16
Consensus pattern (19 bp):
CTAAATAGGTAGAGGAAAA
Found at i:26046 original size:27 final size:27
Alignment explanation
Indices: 26016--26085 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
26006 AATTGAATGG
* * *
26016 AATGATCGAAATACCTCTGAA-CTCTAA
1 AATGATCGAAATACCCCAGAATC-CAAA
26043 AATGATCGAAATACCCCAGAATCCAAA
1 AATGATCGAAATACCCCAGAATCCAAA
*
26070 AATGATCAAAATACCC
1 AATGATCGAAATACCC
26086 ATGCTCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.46, C:0.24, G:0.10, T:0.20
Consensus pattern (27 bp):
AATGATCGAAATACCCCAGAATCCAAA
Found at i:33162 original size:26 final size:26
Alignment explanation
Indices: 33126--33175 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
33116 CTTTTTATAA
*
33126 ATTGCTACTGCTAAAAAAGCTAACAG
1 ATTGCTACTGCTAAAAAACCTAACAG
*
33152 ATTGCTACTGCTAAACAACCTAAC
1 ATTGCTACTGCTAAAAAACCTAAC
33176 TCAGATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (26 bp):
ATTGCTACTGCTAAAAAACCTAACAG
Found at i:33457 original size:21 final size:21
Alignment explanation
Indices: 33431--33471 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33421 ACAAGGCTTG
*
33431 GAATTTTAAATTATAATGTCA
1 GAATTTCAAATTATAATGTCA
*
33452 GAATTTCAAATTATGATGTC
1 GAATTTCAAATTATAATGTC
33472 TAAAATAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (21 bp):
GAATTTCAAATTATAATGTCA
Found at i:36651 original size:26 final size:26
Alignment explanation
Indices: 36611--36665 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
36601 AGAGTCAATA
*
36611 TCAGATCGGTTGATTTTTGGATTGGT
1 TCAGATCGGTGGATTTTTGGATTGGT
36637 TCAGATCGGTGGATTTTTGGATTGGT
1 TCAGATCGGTGGATTTTTGGATTGGT
36663 TCA
1 TCA
36666 CTATTAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.09, G:0.31, T:0.44
Consensus pattern (26 bp):
TCAGATCGGTGGATTTTTGGATTGGT
Found at i:43429 original size:32 final size:32
Alignment explanation
Indices: 43393--43468 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
43383 AGGGCCACGA
*
43393 GGCCTACCTAAGAACAT-ATCTTAGGGCCGTAG
1 GGCCTACCTAAGAA-ATGATCTCAGGGCCGTAG
**
43425 GGCCTACCCGAG-AATGATCTCAGGGCCGTAG
1 GGCCTACCTAAGAAATGATCTCAGGGCCGTAG
*
43456 AGCCTACCTAAGA
1 GGCCTACCTAAGA
43469 GTCACATTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 2 0.06
31 24 0.67
32 10 0.28
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (32 bp):
GGCCTACCTAAGAAATGATCTCAGGGCCGTAG
Found at i:49844 original size:29 final size:29
Alignment explanation
Indices: 49802--49873 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
49792 GCTTGTACTG
*
49802 TAATTTGTAGAAAAAAATTGGGATGATATTA
1 TAATTTGT--AAAAAAATTGGGATGATATCA
** * *
49833 TAATTTGTAAAAAGTTTGGGTTGTTATCA
1 TAATTTGTAAAAAAATTGGGATGATATCA
*
49862 TAATTTGGAAAA
1 TAATTTGTAAAA
49874 GTTTGATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 27 0.77
31 8 0.23
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.39
Consensus pattern (29 bp):
TAATTTGTAAAAAAATTGGGATGATATCA
Found at i:49900 original size:56 final size:55
Alignment explanation
Indices: 49828--50084 Score: 209
Period size: 56 Copynumber: 4.6 Consensus size: 55
49818 ATTGGGATGA
* * **
49828 TATTATAATTTGTAAAAAGTTTGGGTTGTTATCATAATTTGGAAAAGTTTGATCTT
1 TATTATAATTTATAAAAAGTTTGGGTTATTAT-ATAATTTGGAAAAGTTTGGGCTT
* * * * *
49884 TATTATAATTTATAAAAAAGTTTGGGTTGTTGTTTAATATGTAAAATGTTT-GGCTT
1 TATTATAATTTAT-AAAAAGTTTGGGTTATTATATAATTTGGAAAA-GTTTGGGCTT
* * * * *
49940 CATTATAATTTTTTAAATAGTTTTGG-TATTATTGTAATTTATGG-AAAGTTTGGGCATT
1 TATTATAA-TTTATAAAAAGTTTGGGTTATTA-TATAA-TT-TGGAAAAGTTTGGGC-TT
* * *
49998 TATTATGATTTATAAAAAGTTTGGGTTATTAATATAATTTATGAAAACTTTGGGCTT
1 TATTATAATTTATAAAAAGTTTGGGTTATT-ATATAATTT-GGAAAAGTTTGGGCTT
* * *
50055 TACTGTAATATAT-AAAAGTTTGGGTT-TTAT
1 TATTATAATTTATAAAAAGTTTGGGTTATTAT
50085 TGCAATTTTA
Statistics
Matches: 161, Mismatches: 28, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
54 2 0.01
55 5 0.03
56 64 0.40
57 61 0.38
58 28 0.17
59 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.47
Consensus pattern (55 bp):
TATTATAATTTATAAAAAGTTTGGGTTATTATATAATTTGGAAAAGTTTGGGCTT
Found at i:50000 original size:29 final size:28
Alignment explanation
Indices: 49828--50092 Score: 139
Period size: 29 Copynumber: 9.4 Consensus size: 28
49818 ATTGGGATGA
* * *
49828 TATTATAATTTGTAAAAAGTTTGGGTTGT
1 TATTGTAATTTATGAAAAGTTTGGGTT-T
** * *
49857 TATCATAATTT-GGAAAAGTTT-GATCTT
1 TATTGTAATTTATGAAAAGTTTGGGT-TT
* *
49884 TATTATAATTTATAAAAAAGTTTGGGTTGT
1 TATTGTAATTTAT-GAAAAGTTTGGGTT-T
* *
49914 TGTT-TAA--TATGTAAAATGTTT-GGCTT
1 TATTGTAATTTATG-AAAA-GTTTGGGTTT
* * * * * *
49940 CATTATAATTTTTTAAATAGTTTTGGTAT
1 TATTGTAATTTATGAAA-AGTTTGGGTTT
* *
49969 TATTGTAATTTATGGAAAGTTTGGGCATT
1 TATTGTAATTTATGAAAAGTTTGGG-TTT
* * *
49998 TATTATGATTTATAAAAAGTTTGGGTTAT
1 TATTGTAATTTATGAAAAGTTTGGGTT-T
* * * *
50027 TAATATAATTTATGAAAACTTTGGGCTT
1 TATTGTAATTTATGAAAAGTTTGGGTTT
* *
50055 TACTGTAATATAT-AAAAGTTTGGGTTT
1 TATTGTAATTTATGAAAAGTTTGGGTTT
*
50082 TATTGCAATTT
1 TATTGTAATTT
50093 TATAAAATTT
Statistics
Matches: 179, Mismatches: 43, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
26 3 0.02
27 46 0.26
28 39 0.22
29 85 0.47
30 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (28 bp):
TATTGTAATTTATGAAAAGTTTGGGTTT
Found at i:57314 original size:19 final size:20
Alignment explanation
Indices: 57275--57314 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
57265 TAAGTGTTAA
*
57275 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
57295 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
57314 T
1 T
57315 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:57539 original size:21 final size:21
Alignment explanation
Indices: 57515--57579 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
57505 AGAGGGAACA
57515 GATTCCCCCCTAGGGGGTACC
1 GATTCCCCCCTAGGGGGTACC
*
57536 GATT--CCCCT---GGATA--
1 GATTCCCCCCTAGGGGGTACC
*
57550 TATTCCCCCCTAGGGGGTACC
1 GATTCCCCCCTAGGGGGTACC
57571 GATTCCCCC
1 GATTCCCCC
57580 ACAGGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
14 3 0.09
16 9 0.27
19 9 0.27
21 12 0.36
ACGTcount: A:0.15, C:0.38, G:0.23, T:0.23
Consensus pattern (21 bp):
GATTCCCCCCTAGGGGGTACC
Found at i:60131 original size:3 final size:3
Alignment explanation
Indices: 60123--60153 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
60113 CATGTTTTTA
*
60123 ATT ATT ATT ATT ATT ATT TTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
60154 GTATCATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:62449 original size:19 final size:20
Alignment explanation
Indices: 62410--62449 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
62400 TAAGTGTTAA
*
62410 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
62430 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
62449 T
1 T
62450 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:67661 original size:6 final size:6
Alignment explanation
Indices: 67650--67684 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
67640 GACACGTATT
* *
67650 ACCACG ACCACG ACCACG ACCACA ATCACG ACCAC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCAC
67685 TACCCGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.37, C:0.49, G:0.11, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:68444 original size:21 final size:22
Alignment explanation
Indices: 68419--68680 Score: 203
Period size: 21 Copynumber: 12.3 Consensus size: 22
68409 ATTTTGGACT
68419 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
* *
68440 ATCGCAACGCGAACTTCGACT--
1 ATCGCAAC-CGAACTTGGAATAA
*
68461 ATCACAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
* *
68482 ATCGCAACGCGAACTTCGACT--
1 ATCGCAAC-CGAACTTGGAATAA
*
68503 ATCGCAACGCGAATTTGGAATAA
1 ATCGCAAC-CGAACTTGGAATAA
*
68526 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
* *
68547 ATCGCAACGCGAACTTCGACT--
1 ATCGCAAC-CGAACTTGGAATAA
*
68568 ATCGCAACGCGAATTTGGAATAA
1 ATCGCAAC-CGAACTTGGAATAA
* * *
68591 ATCGTAA-TGAATTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
* * *
68612 ATTGCAACGCGAACTTCGACT--
1 ATCGCAAC-CGAACTTGGAATAA
68633 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGGAATAA
*
68654 ATCGCAACGCGAATTTGG-A-AA
1 ATCGCAAC-CGAACTTGGAATAA
68675 ATCGCA
1 ATCGCA
68681 TTGCGATAGT
Statistics
Matches: 194, Mismatches: 29, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
19 20 0.10
21 115 0.59
22 1 0.01
23 58 0.30
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (22 bp):
ATCGCAACCGAACTTGGAATAA
Found at i:68474 original size:42 final size:42
Alignment explanation
Indices: 68415--68666 Score: 278
Period size: 42 Copynumber: 5.9 Consensus size: 42
68405 TGCGATTTTG
68415 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
68457 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
68499 GACTATCGCAACGCGAATTTGGAATAAATCGCAA--CGAATTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * * *
68541 GAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGCGAATTTG
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * * *
68585 GAATAAATCGTAATGAATTTGGAATAAATTGCAACGCGAACTTC
1 GACT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
68629 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
68667 TTTGGAAAAT
Statistics
Matches: 180, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
42 105 0.58
44 75 0.42
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:68545 original size:65 final size:65
Alignment explanation
Indices: 68440--68680 Score: 341
Period size: 65 Copynumber: 3.8 Consensus size: 65
68430 CTTGGAATAA
* * * *
68440 ATCGCAACGCGAACTTCGACT--ATCACAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
68503 ATCGCAACGCGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
68568 ATCGCAACGCGAATTTGGAATAAATCGTAATGAATTTGGAATAAATTGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
68633 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAATTTGG-A-AAATCGCA
1 ATCGCAACGCGAACTTGGAATAAATCGCAA--CGAATTTGGAATAAATCGCA
68681 TTGCGATAGT
Statistics
Matches: 162, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
63 44 0.27
64 1 0.01
65 117 0.72
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (65 bp):
ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:68637 original size:86 final size:84
Alignment explanation
Indices: 68406--68680 Score: 290
Period size: 86 Copynumber: 3.2 Consensus size: 84
68396 ACCAGTCGTT
* * * *
68406 GCGATTTTGGACTATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACG
1 GCGAATTTGGAATATCGCAACCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
68470 AACTTGGAATAAATCGCAAC
66 AACTTGGAAT-AATCGCAAC
* * * * * *
68490 GCGAACTTCGACTATCGCAACGCGAATTTGGAATAAATCGCAA--CGAATTTGGAATAAATCGCA
1 GCGAATTTGGAATATCGCAAC-CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCA
* *
68553 ACGCGAACTTCGACT-ATCGCAAC
63 A--CGAACTTGGAATAATCGCAAC
* * *
68576 GCGAATTTGGAATAAATCGTAA-TGAATTTGGAATAAATTGCAACGCGAACTTCGACTATCGCAA
1 GCGAATTTGGAAT--ATCGCAACCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
68640 CGAACTTGGAATAAATCGCAAC
64 CGAACTTGGAAT-AATCGCAAC
*
68662 GCGAATTTGGAAAATCGCA
1 GCGAATTTGGAATATCGCA
68681 TTGCGATAGT
Statistics
Matches: 156, Mismatches: 23, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
84 41 0.26
86 90 0.58
88 25 0.16
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (84 bp):
GCGAATTTGGAATATCGCAACCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
AACTTGGAATAATCGCAAC
Found at i:71459 original size:46 final size:46
Alignment explanation
Indices: 71409--71534 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 46
71399 GTAATTGGGA
* * *
71409 TTATCACCCACTAAGGATGCACCAGCCTATATATCGATAATTAGAT
1 TTATCATCCAGTAAGGATGCACCAGCCTGTATATCGATAATTAGAT
* * * * * * * *
71455 TTATCATCCGGTAAGGTTGCACTAGCATGTATTTTGGTAATTGGAT
1 TTATCATCCAGTAAGGATGCACCAGCCTGTATATCGATAATTAGAT
* *
71501 TTATCATCTAGTAAGGATACACCAGCCTGTATAT
1 TTATCATCCAGTAAGGATGCACCAGCCTGTATAT
71535 TGATTATTCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (46 bp):
TTATCATCCAGTAAGGATGCACCAGCCTGTATATCGATAATTAGAT
Found at i:75007 original size:32 final size:32
Alignment explanation
Indices: 74958--75112 Score: 116
Period size: 32 Copynumber: 4.9 Consensus size: 32
74948 TTGGTTTAGG
* *
74958 TTGCTTTCGATTCGGGTTATTTTCGATTCAGA
1 TTGCTTTCGATTTGGGTTAATTTCGATTCAGA
* *
74990 TTGCTTTCGGTTTGGGTTAATTTC-ATT-TGA
1 TTGCTTTCGATTTGGGTTAATTTCGATTCAGA
* ** * * *
75020 TTTACTTTCGAACTGGGTTAAATTCGATTTAGT
1 -TTGCTTTCGATTTGGGTTAATTTCGATTCAGA
* * * ** * * *
75053 TTGCTTTCGGTTCGCGTTGTTTTCGGTTCGGG
1 TTGCTTTCGATTTGGGTTAATTTCGATTCAGA
*
75085 TTACTTTCGATTTGGGTTAATTTCGATT
1 TTGCTTTCGATTTGGGTTAATTTCGATT
75113 GAATTATTTT
Statistics
Matches: 89, Mismatches: 31, Indels: 6
0.71 0.25 0.05
Matches are distributed among these distances:
30 2 0.02
31 22 0.25
32 64 0.72
33 1 0.01
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (32 bp):
TTGCTTTCGATTTGGGTTAATTTCGATTCAGA
Found at i:75076 original size:95 final size:95
Alignment explanation
Indices: 74952--75125 Score: 233
Period size: 95 Copynumber: 1.8 Consensus size: 95
74942 TTGCTTTTGG
* * *
74952 TTTAGGTTGCTTTCGATTCGGGTTATTTTCGATTCAGATTGCTTTCGGTTTGGGTTAATTTC-AT
1 TTTAGGTTGCTTTCGATTCGCGTTATTTTCGATTCAGATTACTTTCGATTTGGGTTAATTTCGA-
*
75016 TTGATTTACTTTCGAACTGGGTTAAATTCGA
65 TTGAATTACTTTCGAACTGGGTTAAATTCGA
* * * * * *
75047 TTTAGTTTGCTTTCGGTTCGCGTTGTTTTCGGTTCGGGTTACTTTCGATTTGGGTTAATTTCGAT
1 TTTAGGTTGCTTTCGATTCGCGTTATTTTCGATTCAGATTACTTTCGATTTGGGTTAATTTCGAT
*
75112 TGAATTATTTTCGA
66 TGAATTACTTTCGA
75126 TTCGAGTCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
95 66 0.99
96 1 0.01
ACGTcount: A:0.16, C:0.13, G:0.23, T:0.49
Consensus pattern (95 bp):
TTTAGGTTGCTTTCGATTCGCGTTATTTTCGATTCAGATTACTTTCGATTTGGGTTAATTTCGAT
TGAATTACTTTCGAACTGGGTTAAATTCGA
Found at i:75110 original size:16 final size:16
Alignment explanation
Indices: 74956--75112 Score: 73
Period size: 16 Copynumber: 9.9 Consensus size: 16
74946 TTTTGGTTTA
* *
74956 GGTTGCTTTCGATTCG
1 GGTTACTTTCGATTTG
* **
74972 GGTTATTTTCGATTCA
1 GGTTACTTTCGATTTG
* * *
74988 GATTGCTTTCGGTTTG
1 GGTTACTTTCGATTTG
*
75004 GGTTAATTTC-ATTTG
1 GGTTACTTTCGATTTG
** **
75019 ATTTACTTTCGAACTG
1 GGTTACTTTCGATTTG
** *
75035 GGTTAAATTCGATTTA
1 GGTTACTTTCGATTTG
* * * *
75051 GTTTGCTTTCGGTTCG
1 GGTTACTTTCGATTTG
* ** * *
75067 CGTTGTTTTCGGTTCG
1 GGTTACTTTCGATTTG
75083 GGTTACTTTCGATTTG
1 GGTTACTTTCGATTTG
*
75099 GGTTAATTTCGATT
1 GGTTACTTTCGATT
75113 GAATTATTTT
Statistics
Matches: 99, Mismatches: 41, Indels: 2
0.70 0.29 0.01
Matches are distributed among these distances:
15 11 0.11
16 88 0.89
ACGTcount: A:0.14, C:0.13, G:0.24, T:0.48
Consensus pattern (16 bp):
GGTTACTTTCGATTTG
Found at i:75605 original size:2 final size:2
Alignment explanation
Indices: 75598--75658 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
75588 TTTTTCCTTT
75598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
75640 TA TA TA TA TA -A TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
75659 GGACTTTTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:79022 original size:54 final size:53
Alignment explanation
Indices: 78946--79294 Score: 464
Period size: 54 Copynumber: 6.5 Consensus size: 53
78936 GTAAGTTCTT
* * * * *
78946 TGGGTTGCGCACGTAGTACCGATACAGTCATTCATAAACTTATTATGAATTTCA
1 TGGGTTGCACACTTAGTGCCGATAC-GTCATTCATAAACTTATTATGAATTCCG
** * *
79000 TGGGTTGCACACTTAGTGCCGATACAGTTGTTCCTAAACTTATTATGAATTTTCG
1 TGGGTTGCACACTTAGTGCCGATAC-GTCATTCATAAACTTATTATGAA-TTCCG
79055 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACG-TCATTCATAAACTTATTATGAATTCCG
* * **
79109 TGGGCTGCACACTTAGTGTCGATACGGTCATTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATAC-GTCATTCATAAACTTATTATGAATTCCG
* * *
79163 TGGGTTGCACATTTAGTGCCGATACGATCGTTCATAAACTTATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACG-TCATTCATAAACTTATTATGAATTCCG
* * *
79217 TAGATTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATAC-GTCATTCATAAACTTATTATGAATTCCG
79271 TGGGTTGCACACTTAGTGCCGATA
1 TGGGTTGCACACTTAGTGCCGATA
79295 GTACATATAG
Statistics
Matches: 262, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
53 1 0.00
54 211 0.81
55 50 0.19
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (53 bp):
TGGGTTGCACACTTAGTGCCGATACGTCATTCATAAACTTATTATGAATTCCG
Found at i:79172 original size:163 final size:162
Alignment explanation
Indices: 78959--79294 Score: 512
Period size: 163 Copynumber: 2.1 Consensus size: 162
78949 GTTGCGCACG
*
78959 TAGTACCGATACAGTCATTCATAAACTTATTATGAATTTCATGGGTTGCACACTTAGTGCCGATA
1 TAGTGCCGATACAGTCATTCATAAACTTATTATGAATTTCATGGGTTGCACACTTAGTGCCGATA
* * * * * *
79024 C-AGTTGTTCCTAAACTTATTATGAATTTTCGTGGGTTGCACACTTAGTGCCGATACGATCATTC
66 CGA-TCGTTCATAAACTTATTATGAA-TTCCATAGATTGCACACTTAGTGCCGATACGATCATTC
79088 ATAAACTTATTATGAATTCCGTGGGCTGCACACT
129 ATAAACTTATTATGAATTCCGTGGGCTGCACACT
* * ** *
79122 TAGTGTCGATACGGTCATTCATAAACTTATTATGAATTTTGTGGGTTGCACATTTAGTGCCGATA
1 TAGTGCCGATACAGTCATTCATAAACTTATTATGAATTTCATGGGTTGCACACTTAGTGCCGATA
* *
79187 CGATCGTTCATAAACTTATTATGAATTCCATAGATTGCACACTTAGTGCCGATACGGTCGTTCAT
66 CGATCGTTCATAAACTTATTATGAATTCCATAGATTGCACACTTAGTGCCGATACGATCATTCAT
*
79252 AAACTTATTATGAATTCCGTGGGTTGCACACT
131 AAACTTATTATGAATTCCGTGGGCTGCACACT
79284 TAGTGCCGATA
1 TAGTGCCGATA
79295 GTACATATAG
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 75 0.48
163 80 0.51
164 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (162 bp):
TAGTGCCGATACAGTCATTCATAAACTTATTATGAATTTCATGGGTTGCACACTTAGTGCCGATA
CGATCGTTCATAAACTTATTATGAATTCCATAGATTGCACACTTAGTGCCGATACGATCATTCAT
AAACTTATTATGAATTCCGTGGGCTGCACACT
Found at i:79214 original size:108 final size:108
Alignment explanation
Indices: 78946--79294 Score: 520
Period size: 108 Copynumber: 3.2 Consensus size: 108
78936 GTAAGTTCTT
* * * *
78946 TGGGTTGCGCACGTAGTACCGATAC-AGTCATTCATAAACTTATTATGAATTTCATGGGTTGCAC
1 TGGGTTGCACACTTAGTGCCGATACGA-TCATTCATAAACTTATTATGAATTCCATGGGTTGCAC
* * *
79010 ACTTAGTGCCGATACAGTTGTTCCTAAACTTATTATGAATTTTCG
65 ACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTT-G
* *
79055 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCGTGGGCTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCATGGGTTGCACA
* *
79120 CTTAGTGTCGATACGGTCATTCATAAACTTATTATGAATTTTG
66 CTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
* * * *
79163 TGGGTTGCACATTTAGTGCCGATACGATCGTTCATAAACTTATTATGAATTCCATAGATTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCATGGGTTGCACA
**
79228 CTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
66 CTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
79271 TGGGTTGCACACTTAGTGCCGATA
1 TGGGTTGCACACTTAGTGCCGATA
79295 GTACATATAG
Statistics
Matches: 217, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
108 122 0.56
109 94 0.43
110 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (108 bp):
TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCATGGGTTGCACA
CTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
Done.