Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007912.1 Hibiscus syriacus cultivar Beakdansim tig00110313_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: 1361188
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 6 of 6
Found at i:1204374 original size:14 final size:14
Alignment explanation
Indices: 1204355--1204390 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1204345 ATTGTTTAAT
1204355 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1204369 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1204383 TGATTTGT
1 TGATTTGT
1204391 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1204581 original size:19 final size:19
Alignment explanation
Indices: 1204507--1204571 Score: 112
Period size: 19 Copynumber: 3.4 Consensus size: 19
1204497 ATCGCAACGA
*
1204507 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCGAAAT
1204526 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1204545 GAAAATCCCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1204564 GAAAATCG
1 GAAAATCG
1204572 TAACGAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.49, C:0.17, G:0.18, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1204592 original size:33 final size:33
Alignment explanation
Indices: 1204478--1204593 Score: 124
Period size: 33 Copynumber: 3.4 Consensus size: 33
1204468 AAAACAGACT
* ***
1204478 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
1204511 ATCGCAATGCAAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
* *
1204549 ATCCCAATGCGAAATGAAAATCGTAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1204582 ATCGCAATGCGA
1 ATCGCAATGCGA
1204594 TTTTCATTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
33 36 0.52
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 27 0.39
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1204637 original size:20 final size:20
Alignment explanation
Indices: 1204612--1204649 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1204602 TCGCATTGCG
*
1204612 ATTTTCGCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1204632 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1204650 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1205733 original size:24 final size:24
Alignment explanation
Indices: 1205706--1205759 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1205696 GTATTCGAAA
* *
1205706 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1205730 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1205754 TTTGAT
1 TTTGAT
1205760 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1205951 original size:12 final size:12
Alignment explanation
Indices: 1205934--1205958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1205924 ATATAATCCT
1205934 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1205946 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1205958 G
1 G
1205959 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1208272 original size:19 final size:19
Alignment explanation
Indices: 1208250--1208308 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1208240 GGAAATTACT
1208250 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1208269 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1208283 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1208302 ATCGCAA
1 ATCGCAA
1208309 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1208454 original size:14 final size:14
Alignment explanation
Indices: 1208435--1208471 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1208425 CATCAATTAA
1208435 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1208449 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1208463 ACAAATCAA
1 ACAAATCAA
1208472 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1209894 original size:21 final size:21
Alignment explanation
Indices: 1209828--1209894 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1209818 GTGAATCGGG
*
1209828 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1209848 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1209870 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1209891 CTCT
1 CTCT
1209895 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1209913 original size:42 final size:41
Alignment explanation
Indices: 1209828--1209950 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1209818 GTGAATCGGG
* * * *
1209828 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1209870 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1209912 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1209951 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1212037 original size:33 final size:33
Alignment explanation
Indices: 1211983--1212067 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
1211973 AGATAATGAG
* * *
1211983 AATCGCAACGCGGAAATGACTATCATAACGAGAT
1 AATCGCAACGC-GAAATGACTATCACAACCAGAC
* *
1212017 AATCGCAACGCGAAATGACTATCGCGACCAGAC
1 AATCGCAACGCGAAATGACTATCACAACCAGAC
*
1212050 AATCGCAACGTGAAATGA
1 AATCGCAACGCGAAATGA
1212068 AAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 34 0.76
34 11 0.24
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCACAACCAGAC
Found at i:1212074 original size:19 final size:20
Alignment explanation
Indices: 1212050--1212095 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1212040 GCGACCAGAC
* *
1212050 AATCGCAA-CGTGAAATGAA
1 AATCGCAACCGCGAAATAAA
1212069 AATCGCAACCGCGAAATAAA
1 AATCGCAACCGCGAAATAAA
1212089 AATCGCA
1 AATCGCA
1212096 GTTATTTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACCGCGAAATAAA
Found at i:1212666 original size:20 final size:20
Alignment explanation
Indices: 1212633--1212685 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1212623 GCGCTATGTA
1212633 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1212653 AATCGTGTTTCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1212673 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1212686 TTTTGTATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1212723 original size:20 final size:20
Alignment explanation
Indices: 1212694--1212747 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1212684 GATTTTGTAT
1212694 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
1212714 TATGGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1212734 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1212748 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1212842 original size:21 final size:21
Alignment explanation
Indices: 1212818--1212913 Score: 174
Period size: 21 Copynumber: 4.6 Consensus size: 21
1212808 ACTGTATACC
*
1212818 ATCGCAACGCGATTTCCAACA
1 ATCGCAATGCGATTTCCAACA
1212839 ATCGCAATGCGATTTCCAACA
1 ATCGCAATGCGATTTCCAACA
1212860 ATCGCAATGCGATTTCCAACA
1 ATCGCAATGCGATTTCCAACA
1212881 ATCGCAATGCGATTTCCAACA
1 ATCGCAATGCGATTTCCAACA
*
1212902 ATCGCAACGCGA
1 ATCGCAATGCGA
1212914 AATGCAATGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (21 bp):
ATCGCAATGCGATTTCCAACA
Found at i:1215122 original size:13 final size:13
Alignment explanation
Indices: 1215104--1215133 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1215094 GGTCAACGGC
1215104 GGTCAACAGGTCG
1 GGTCAACAGGTCG
*
1215117 GGTCAACGGGTCG
1 GGTCAACAGGTCG
1215130 GGTC
1 GGTC
1215134 GGGTTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:1219565 original size:61 final size:61
Alignment explanation
Indices: 1219481--1219595 Score: 185
Period size: 61 Copynumber: 1.9 Consensus size: 61
1219471 TAAGGTGGAT
* *
1219481 ACGACCTAATGTATCATGTCCGGATTAGCACTATAGCGTAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTAATGTATCATATCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
* * *
1219542 ACGACCTTATGTTTCATATCCGGATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ACGACCTAATGTATCATATCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGT
1219596 TTAGAACTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (61 bp):
ACGACCTAATGTATCATATCCGGATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGC
Found at i:1219740 original size:47 final size:47
Alignment explanation
Indices: 1219668--1220100 Score: 706
Period size: 47 Copynumber: 9.2 Consensus size: 47
1219658 TATTGTCTAT
* *
1219668 GAGCTTATGGAATTTAAATGTCAAGTATATAT-ATAAAATAAGCTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATAT-TGGTAAAATAAGCTTAC
* *
1219715 GAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGTTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
*
1219762 GAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
* *
1219809 GAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
*
1219856 GAGATTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
1219903 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
** * *
1219950 GAGCTTATGGAATTTAAATGATAACTATTTTGGTAAAATAAGCTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
*
1219997 GAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCTTAC
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
* * *
1220044 GAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTAT
1 GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
1220091 GAGCTTATGG
1 GAGCTTATGG
1220101 GATAAATGGT
Statistics
Matches: 362, Mismatches: 23, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
46 1 0.00
47 361 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (47 bp):
GAGCTTATGGAATTTAAATGGCAAGTATATTGGTAAAATAAGCTTAC
Found at i:1226878 original size:47 final size:47
Alignment explanation
Indices: 1226825--1227161 Score: 537
Period size: 47 Copynumber: 7.3 Consensus size: 47
1226815 GGCTATTGTC
1226825 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
*
1226872 TACGAGCTTATAGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
* *
1226919 TACGAGCTTATGGAATTTAAATGGCAAGTATTTTGGTAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
* * *
1226966 TACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
*
1227013 TACGAGCTTATGGAATTTAAATGGCAAGTATATTTATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
* *
1227060 TACGAGCTTATGGAATTTAAATGGTAAGTATTTTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1227107 T---A-C----GGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1227146 TACGAGCTTATGGAAT
1 TACGAGCTTATGGAAT
1227162 AAATGGTAAA
Statistics
Matches: 268, Mismatches: 14, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.13
42 1 0.00
43 2 0.01
44 1 0.00
47 229 0.85
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (47 bp):
TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
Found at i:1227148 original size:39 final size:39
Alignment explanation
Indices: 1227064--1227149 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
1227054 TAAGCTTACG
* * *
1227064 AGCTTATGGAATTTAAATGGTAAGTATTTTGATAAAATA
1 AGCTTACGGAATTTAAATGGCAAGTATATTGATAAAATA
1227103 AGCTTACGGAATTTAAATGGCAAGTATATTGATAAAATA
1 AGCTTACGGAATTTAAATGGCAAGTATATTGATAAAATA
1227142 AGCTTACG
1 AGCTTACG
1227150 AGCTTATGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (39 bp):
AGCTTACGGAATTTAAATGGCAAGTATATTGATAAAATA
Found at i:1228942 original size:96 final size:96
Alignment explanation
Indices: 1228782--1228971 Score: 245
Period size: 96 Copynumber: 2.0 Consensus size: 96
1228772 CAATAGATTT
* ** * *
1228782 CATGATCCATAAATTAAGAATGATCATATTTTACAGTGAAAACAGGAAACCCGATAACACATTTC
1 CATGATCCATAAATCAAGAACAATCATATTTTACAGTGAAAACAGGAAACCAGAGAACACATTTC
** *
1228847 AGGTAACCATAGTTCATAAACCAGTAAATTC
66 AAATAACCATAGTTCATAAAACAGTAAATTC
* * * * * **
1228878 CATGATCCATAAATCAGGAACAATCATATTTTACAGTGAAAATATGTAATCAGAGAACTTATTTC
1 CATGATCCATAAATCAAGAACAATCATATTTTACAGTGAAAACAGGAAACCAGAGAACACATTTC
1228943 AAATAACCATAGTTCATAAAACAGTAAAT
66 AAATAACCATAGTTCATAAAACAGTAAAT
1228972 CAAGAAATTT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (96 bp):
CATGATCCATAAATCAAGAACAATCATATTTTACAGTGAAAACAGGAAACCAGAGAACACATTTC
AAATAACCATAGTTCATAAAACAGTAAATTC
Found at i:1233046 original size:23 final size:23
Alignment explanation
Indices: 1233018--1233077 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1233008 AATTGACTTT
*
1233018 TTGGTCAAAGTCAACGATCAAAC
1 TTGGTCAAAGTCAACAATCAAAC
*
1233041 TTGGTCAAAGTCAATAATCAAAC
1 TTGGTCAAAGTCAACAATCAAAC
*
1233064 TTGGTCAAAATCAA
1 TTGGTCAAAGTCAA
1233078 AGTTAAAGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (23 bp):
TTGGTCAAAGTCAACAATCAAAC
Found at i:1233160 original size:20 final size:20
Alignment explanation
Indices: 1233137--1233185 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1233127 AGTTGGTTTT
*
1233137 AGGTGACTTAGTATGGTTCA
1 AGGTGACTTAGTATGCTTCA
1233157 AGGTGACTTAGTATGCTTCA
1 AGGTGACTTAGTATGCTTCA
*
1233177 AGTTGACTT
1 AGGTGACTT
1233186 GGACCGATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (20 bp):
AGGTGACTTAGTATGCTTCA
Found at i:1248602 original size:12 final size:12
Alignment explanation
Indices: 1248565--1248603 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1248555 AACTGATACT
1248565 TGACATGGATTC
1 TGACATGGATTC
*
1248577 TGATAT-GATATC
1 TGACATGGAT-TC
1248589 TGACATGGATTC
1 TGACATGGATTC
1248601 TGA
1 TGA
1248604 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1248681 original size:24 final size:24
Alignment explanation
Indices: 1248549--1248667 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
1248539 TTAGATTTGA
1248549 ATTCTGA-ACTGATACTTGACATGG
1 ATTCTGATA-TGATACTTGACATGG
1248573 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
1248597 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
1248621 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
1248645 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
1248668 AATTATGTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.01
24 83 0.97
25 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1248844 original size:43 final size:43
Alignment explanation
Indices: 1248783--1248877 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
1248773 AGGCTTTACT
*
1248783 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1248826 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1248869 TGGTGTGTT
1 TGGTGTGTT
1248878 CGATTGGAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:1253584 original size:24 final size:24
Alignment explanation
Indices: 1253493--1253591 Score: 123
Period size: 24 Copynumber: 4.1 Consensus size: 24
1253483 TTTTATTTGA
1253493 ATTCTGAA-CTGATACTTGA-TATGG
1 ATTCT-AATCTGATACTTGACT-TGG
* *
1253517 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTAATCTGATACT-TGACTTGG
1253541 ATTCTAATCTGATACTTGACTTGG
1 ATTCTAATCTGATACTTGACTTGG
*
1253565 ATTCTAATCTGATACTTGACTTAG
1 ATTCTAATCTGATACTTGACTTGG
1253589 ATT
1 ATT
1253592 TTGATATGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
23 2 0.03
24 63 0.95
25 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (24 bp):
ATTCTAATCTGATACTTGACTTGG
Found at i:1253601 original size:24 final size:24
Alignment explanation
Indices: 1253540--1253603 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
1253530 ATCTGACATG
* *
1253540 GATTCTAATCTGATACTTGACTTG
1 GATTCTAATATGATACTTGACTTA
*
1253564 GATTCTAATCTGATACTTGACTTA
1 GATTCTAATATGATACTTGACTTA
* *
1253588 GATTTTGATATGATAC
1 GATTCTAATATGATAC
1253604 GACAATTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (24 bp):
GATTCTAATATGATACTTGACTTA
Found at i:1253602 original size:48 final size:48
Alignment explanation
Indices: 1253502--1253603 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
1253492 AATTCTGAAC
* * *
1253502 TGATACTTGATATGGATTCTGATCTGATATCTGACATGGATTCTAATC
1 TGATACTTGATATGGATTCTAATCTGATATCTGACATAGATTCTAATA
* * *
1253550 TGATACTTGACT-TGGATTCTAATCTGATA-CTTGACTTAGATTTTGATA
1 TGATACTTGA-TATGGATTCTAATCTGATATC-TGACATAGATTCTAATA
1253598 TGATAC
1 TGATAC
1253604 GACAATTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 1 0.02
48 44 0.96
49 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (48 bp):
TGATACTTGATATGGATTCTAATCTGATATCTGACATAGATTCTAATA
Found at i:1255261 original size:13 final size:13
Alignment explanation
Indices: 1255242--1255286 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1255232 AACCTGACCC
1255242 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
1255255 TACCCGAACCGTT
1 GACCCGACCCGTT
* *
1255268 GACCTGACTCGTT
1 GACCCGACCCGTT
1255281 GACCCG
1 GACCCG
1255287 TTGACTGTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1255298 original size:7 final size:7
Alignment explanation
Indices: 1255262--1255307 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
1255252 GTTTACCCGA
1255262 ACCGTTG
1 ACCGTTG
1255269 ACC--TG
1 ACCGTTG
1255274 ACTCGTTG
1 AC-CGTTG
1255282 ACCCGTTG
1 A-CCGTTG
*
1255290 ACTGTTG
1 ACCGTTG
1255297 ACCGTTG
1 ACCGTTG
1255304 ACCG
1 ACCG
1255308 ACGTTGACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
5 4 0.12
6 1 0.03
7 18 0.55
8 9 0.27
9 1 0.03
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.28
Consensus pattern (7 bp):
ACCGTTG
Found at i:1257848 original size:24 final size:24
Alignment explanation
Indices: 1257813--1257931 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
1257803 TTTTATTTGA
* *
1257813 ATTCTGAACTGATACTTGATATGG
1 ATTCTGATCTGATACTTGACATGG
*
1257837 ATTTTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
1257861 ATTCTAATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1257885 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1257909 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
1257932 AATTATGTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1258108 original size:43 final size:43
Alignment explanation
Indices: 1258047--1258141 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
1258037 AGGCTTTACT
*
1258047 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1258090 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1258133 TGGTGTGTT
1 TGGTGTGTT
1258142 CGGTTGGAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:1260224 original size:13 final size:13
Alignment explanation
Indices: 1260196--1260251 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
1260186 GTTGATCCGA
*
1260196 CCTGACCCGTTTAC
1 CCTGA-CCGTTGAC
*
1260210 CCTAACCGTTGAC
1 CCTGACCGTTGAC
1260223 CC-GACTCGTTGAC
1 CCTGAC-CGTTGAC
1260236 CCGTTGACCGTTGAC
1 CC--TGACCGTTGAC
1260251 C
1 C
1260252 GGCGTTGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 2 0.06
13 18 0.51
14 4 0.11
15 8 0.23
16 3 0.09
ACGTcount: A:0.16, C:0.39, G:0.20, T:0.25
Consensus pattern (13 bp):
CCTGACCGTTGAC
Found at i:1262783 original size:24 final size:24
Alignment explanation
Indices: 1262756--1262874 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
1262746 TTCGATTTGA
** *
1262756 ATTCTGACCTGATACTTTACATGG
1 ATTCTGATATGATACTTGACATGG
*
1262780 ATTCTGATATGATA-TCTGACATAG
1 ATTCTGATATGATACT-TGACATGG
* * *
1262804 ATTCTGATCTGATACTTGACTTAG
1 ATTCTGATATGATACTTGACATGG
*
1262828 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
1262852 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
1262875 AAATATGTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1263052 original size:43 final size:43
Alignment explanation
Indices: 1262991--1263084 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 43
1262981 GGCCTTACTA
*
1262991 GGTGTGTTGGTGGGTGTATGGTTATGGGGAACCTACACATTAT
1 GGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTAT
*
1263034 GGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTAT
1 GGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTAT
1263077 GGTGTGTT
1 GGTGTGTT
1263085 TATGGTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.17, C:0.10, G:0.37, T:0.36
Consensus pattern (43 bp):
GGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTAT
Found at i:1284816 original size:699 final size:700
Alignment explanation
Indices: 1283444--1284834 Score: 2453
Period size: 699 Copynumber: 2.0 Consensus size: 700
1283434 TTTTAACACA
*
1283444 TTCATGTTTAAATGTTTTAGACATTAACTTTTTAAGCAAAAAGTAGAAGATTCTTGAATATCACA
1 TTCATGTTTAAATGTTTTAGACATTAACTTTTTAAGCAAAAAATAGAAGATTCTTGAATATCACA
* *
1283509 AGTCAATGTACAAAATATATTATTTGAATAAGGCTCATACATGTAATCCATATATATTTTGTATA
66 AGTCAACGTACAAAATATATTATTTGAACAAGGCTCATACATGTAATCCATATATATTTTGTATA
* *
1283574 CAATATACTTGAGTATATATATACCTTCAATGTCTAATATATATTAACTATGAAGTTTTTATCTC
131 CAATATACTTGAGCATATATATACCTTCAATGTCTAATATATATTAACTATGAAGATTTTATCTC
* * *
1283639 CAGTAAGATAAACATCCATAAAATCGACCTTGTGGATTTTACCTTATTCACAATGAAGGGTTATT
196 CAGTAAGACAAACATCCATAAAATCGACCTTGTGGAGTTTACCTTATTCAAAATGAAGGGTTATT
*
1283704 ATAAAATGTAAGATCATTTGTGATGGTGAGGATAAGGGCCACTTTGACTTTGCCTATTTGAAAAC
261 ATAAAATGTAAGATCATTTGTGATGGTGAGGATAAGGGCCACTTGGACTTTGCCTATTTGAAAAC
*
1283769 CAAAGGATTCCCTATGTTTCTTTTTATGCTAGCTTTATTAGCTTCCCTTCCATCCTTTACGAATG
326 CAAAGGATTCCCTATGTTTCTTTTTATGCTAGCTTTATTAGCTTCCCTTACATCCTTTACGAATG
* * *
1283834 CACATTTCTTCTGACTTTTTTATTTATCTCAATAGTTGGTGTAACAGATGTTTCTTTAGTCAATC
391 CACATTTCTTCTGACTTTTTTATTTATCTAAATAGTTGGTGTAACAGACGTTTCTGTAGTCAATC
* *
1283899 CTATTGAATTTTAAGGAAGAGATCTAAAATTATTAATTGGAGATCGAACTTTTGCTTCGTTTTCA
456 CTATTGAATTTTAAGGAAGAGATCTAAAATTATTAATTGGAGATCGAACTTTTGCTTCATTTTAA
* *
1283964 ATTCAGTTGACTAGATATTGAAAATGTATGAAGTGAACGTACTACAGAGATCAAATCCACTAACA
521 ATTCAGTTGACAAGATATTGAAAATGTATGAAGTGAACGTACTACAGAGATCAAAACCACTAACA
* *
1284029 TAACCTGTAGGGAAAGCTAAAAGAAATAAATTGAAACTAGCAATTCGAATATTGAAATAAGGTCT
586 TAACATGTAGGGAAAGCTAAAAGAAAAAAATTGAAACTAGCAATTCGAATATTGAAATAAGGTCT
1284094 GACAATGTCCTTATCATGGGTTAAAGGATATATTTATAAACTAGCATTTC
651 GACAATGTCCTTATCATGGGTTAAAGGATATATTTATAAACTAGCATTTC
* *
1284144 TTCATGTTTAAATGTTTTAGACATTAACTTTTTAAGGAAAAAATAGAAGATTCTTGAATATTACA
1 TTCATGTTTAAATGTTTTAGACATTAACTTTTTAAGCAAAAAATAGAAGATTCTTGAATATCACA
1284209 AGTCAACGTACAAAATATATTATTTGAACAAGGCTCATACATGTAATCCATATATATTTTGTATA
66 AGTCAACGTACAAAATATATTATTTGAACAAGGCTCATACATGTAATCCATATATATTTTGTATA
1284274 CAATATACTTGAGCATATATATACCTTCAATGTCTAATATATATTAACTATGAAGATTTTATCTC
131 CAATATACTTGAGCATATATATACCTTCAATGTCTAATATATATTAACTATGAAGATTTTATCTC
* *
1284339 CCGTAAGACAAACATCCATAAAATCGACGTTGTGGAGTTTACCTTATTCAAAATGAAGGGTTATT
196 CAGTAAGACAAACATCCATAAAATCGACCTTGTGGAGTTTACCTTATTCAAAATGAAGGGTTATT
1284404 ATAAAATGTAAGATCATTTGTGATGGTGAGGATAAGGGCCACTTGGACTTTGCCTATTTG-AAAC
261 ATAAAATGTAAGATCATTTGTGATGGTGAGGATAAGGGCCACTTGGACTTTGCCTATTTGAAAAC
1284468 CAAAGGATTCCCTATGTTTCTTTTTATGCTAGCTTTATTAGCTTCCCTTACATCCTTTACGAATG
326 CAAAGGATTCCCTATGTTTCTTTTTATGCTAGCTTTATTAGCTTCCCTTACATCCTTTACGAATG
* * * *
1284533 CACGTTTGTTCT-ATTTTTTTTATTTATCTAAATAGTTGGTGTAACAGACGTTTCTGTAGTCAGT
391 CACATTTCTTCTGA-CTTTTTTATTTATCTAAATAGTTGGTGTAACAGACGTTTCTGTAGTCAAT
* *
1284597 CCTATTGAATTTTGAGGGAGAGATCTAAAATTATTAATTGGAGATCGAACTTTTGCTTCATTTTA
455 CCTATTGAATTTTAAGGAAGAGATCTAAAATTATTAATTGGAGATCGAACTTTTGCTTCATTTTA
* **
1284662 AATTCAGTTGACAAGATATTGAAAATGTATGAAGTGAATGTACTGTAGAGATCAAAACCACTAAC
520 AATTCAGTTGACAAGATATTGAAAATGTATGAAGTGAACGTACTACAGAGATCAAAACCACTAAC
* *
1284727 ATAACATGTAGGGAAAGCTAAAAGAAAAAAATTGAAACTAGCCATTCGAATATTGAAATAAGGTT
585 ATAACATGTAGGGAAAGCTAAAAGAAAAAAATTGAAACTAGCAATTCGAATATTGAAATAAGGTC
1284792 TGACAATGTCCTTATCATGGGTTAAAGGATATATTTATAAACT
650 TGACAATGTCCTTATCATGGGTTAAAGGATATATTTATAAACT
1284835 GGATATCATA
Statistics
Matches: 656, Mismatches: 34, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
698 1 0.00
699 348 0.53
700 307 0.47
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (700 bp):
TTCATGTTTAAATGTTTTAGACATTAACTTTTTAAGCAAAAAATAGAAGATTCTTGAATATCACA
AGTCAACGTACAAAATATATTATTTGAACAAGGCTCATACATGTAATCCATATATATTTTGTATA
CAATATACTTGAGCATATATATACCTTCAATGTCTAATATATATTAACTATGAAGATTTTATCTC
CAGTAAGACAAACATCCATAAAATCGACCTTGTGGAGTTTACCTTATTCAAAATGAAGGGTTATT
ATAAAATGTAAGATCATTTGTGATGGTGAGGATAAGGGCCACTTGGACTTTGCCTATTTGAAAAC
CAAAGGATTCCCTATGTTTCTTTTTATGCTAGCTTTATTAGCTTCCCTTACATCCTTTACGAATG
CACATTTCTTCTGACTTTTTTATTTATCTAAATAGTTGGTGTAACAGACGTTTCTGTAGTCAATC
CTATTGAATTTTAAGGAAGAGATCTAAAATTATTAATTGGAGATCGAACTTTTGCTTCATTTTAA
ATTCAGTTGACAAGATATTGAAAATGTATGAAGTGAACGTACTACAGAGATCAAAACCACTAACA
TAACATGTAGGGAAAGCTAAAAGAAAAAAATTGAAACTAGCAATTCGAATATTGAAATAAGGTCT
GACAATGTCCTTATCATGGGTTAAAGGATATATTTATAAACTAGCATTTC
Found at i:1286620 original size:24 final size:24
Alignment explanation
Indices: 1286593--1286692 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
1286583 AGATATCAAA
*
1286593 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1286617 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1286641 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1286665 GTTAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1286689 ATCA
1 ATCA
1286693 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1286692 original size:48 final size:48
Alignment explanation
Indices: 1286587--1286694 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1286577 AAACGGAGAT
* * * *
1286587 ATCA-AAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
1286634 TTTAGGAATCAGAACAGATTTCAGATCAGATGTTAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1286682 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1286695 TAAAATATTC
Statistics
Matches: 46, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
47 2 0.04
48 44 0.96
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1287775 original size:18 final size:18
Alignment explanation
Indices: 1287754--1287789 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1287744 CTTCCATCCG
*
1287754 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1287772 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1287790 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1289104 original size:7 final size:7
Alignment explanation
Indices: 1289092--1289122 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1289082 TGGTCAACTC
1289092 CGGTCAA
1 CGGTCAA
1289099 CGGTCAA
1 CGGTCAA
*
1289106 GGGTCAA
1 CGGTCAA
1289113 CGGTCAA
1 CGGTCAA
1289120 CGG
1 CGG
1289123 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:1289112 original size:14 final size:15
Alignment explanation
Indices: 1289093--1289138 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
1289083 GGTCAACTCC
1289093 GGTCAACGGTCAA-G
1 GGTCAACGGTCAACG
1289107 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1289122 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1289135 GGTC
1 GGTC
1289139 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 12 0.40
14 13 0.43
15 5 0.17
ACGTcount: A:0.22, C:0.24, G:0.39, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1289118 original size:21 final size:20
Alignment explanation
Indices: 1289092--1289135 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
1289082 TGGTCAACTC
1289092 CGGTCAAC-GGTCAAGGGTCAA
1 CGGTCAACGGGTC--GGGTCAA
1289113 CGGTCAACGGGTCGGGTCAA
1 CGGTCAACGGGTCGGGTCAA
1289133 CGG
1 CGG
1289136 GTCGGGTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.23, C:0.25, G:0.39, T:0.14
Consensus pattern (20 bp):
CGGTCAACGGGTCGGGTCAA
Found at i:1289143 original size:18 final size:18
Alignment explanation
Indices: 1289120--1289196 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1289110 CAACGGTCAA
1289120 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1289138 CGGGTCGGGTCAA----T
1 CGGGTCGGGTCAACGGGT
*
1289152 -GGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1289169 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1289187 CGGGTCGGGT
1 CGGGTCGGGT
1289197 TGTGACCGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.21
14 1 0.02
17 1 0.02
18 39 0.75
ACGTcount: A:0.12, C:0.19, G:0.51, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1289149 original size:31 final size:31
Alignment explanation
Indices: 1289114--1289192 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1289104 AAGGGTCAAC
1289114 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
1289145 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1289176 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1289193 GGGTTGTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1289168 original size:13 final size:13
Alignment explanation
Indices: 1289138--1289173 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1289128 GTCAACGGGT
*
1289138 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
1289151 TGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1289164 CGGGTCGGGT
1 CGGGTCGGGT
1289174 CGGGTCAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.50, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1289192 original size:13 final size:13
Alignment explanation
Indices: 1289114--1289143 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1289104 AAGGGTCAAC
1289114 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1289127 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1289140 GGTC
1 GGTC
1289144 GGGTCAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1292498 original size:18 final size:18
Alignment explanation
Indices: 1292477--1292512 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1292467 CTTCCATCCG
*
1292477 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1292495 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1292513 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1293826 original size:7 final size:7
Alignment explanation
Indices: 1293814--1293845 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1293804 TGGTCAACTC
1293814 CGGTCAA
1 CGGTCAA
1293821 CGGTCAA
1 CGGTCAA
1293828 CGGGTCAA
1 C-GGTCAA
1293836 CGGTCAA
1 CGGTCAA
1293843 CGG
1 CGG
1293846 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1293835 original size:8 final size:8
Alignment explanation
Indices: 1293815--1293861 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1293805 GGTCAACTCC
1293815 GGTCAAC-
1 GGTCAACG
1293822 GGTCAACG
1 GGTCAACG
1293830 GGTCAAC-
1 GGTCAACG
1293837 GGTCAACG
1 GGTCAACG
1293845 GGT---CG
1 GGTCAACG
1293850 GGTCAACG
1 GGTCAACG
1293858 GGTC
1 GGTC
1293862 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1293835 original size:15 final size:15
Alignment explanation
Indices: 1293815--1293861 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1293805 GGTCAACTCC
1293815 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1293830 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1293845 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1293858 GGTC
1 GGTC
1293862 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1293866 original size:18 final size:18
Alignment explanation
Indices: 1293843--1293919 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1293833 CAACGGTCAA
1293843 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1293861 CGGGTCGGGTCAA----T
1 CGGGTCGGGTCAACGGGT
*
1293875 -GGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1293892 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1293910 CGGGTCGGGT
1 CGGGTCGGGT
1293920 TGTGACCGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.21
14 1 0.02
17 1 0.02
18 39 0.75
ACGTcount: A:0.12, C:0.19, G:0.51, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1293879 original size:31 final size:31
Alignment explanation
Indices: 1293837--1293915 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1293827 ACGGGTCAAC
1293837 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
1293868 GGTCAATGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1293899 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1293916 GGGTTGTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1293891 original size:13 final size:13
Alignment explanation
Indices: 1293861--1293896 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1293851 GTCAACGGGT
*
1293861 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
1293874 TGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1293887 CGGGTCGGGT
1 CGGGTCGGGT
1293897 CGGGTCAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.50, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1293915 original size:13 final size:13
Alignment explanation
Indices: 1293822--1293866 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1293812 TCCGGTCAAC
*
1293822 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1293837 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1293850 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1293863 GGTC
1 GGTC
1293867 GGGTCAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1300106 original size:22 final size:23
Alignment explanation
Indices: 1300064--1300107 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1300054 TTATGGTTTT
*
1300064 TTTTATAATATCAATAGTTCTTA
1 TTTTATAATATCAAGAGTTCTTA
1300087 TTTTATATATAT-AAGA-TTCTT
1 TTTTATA-ATATCAAGAGTTCTT
1300108 CGTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTATAATATCAAGAGTTCTTA
Found at i:1306191 original size:22 final size:23
Alignment explanation
Indices: 1306149--1306192 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1306139 TTATGGTTTT
*
1306149 TTTTATAATATCAATAGTTCTTA
1 TTTTATAATATCAAGAGTTCTTA
1306172 TTTTATATATAT-AAGA-TTCTT
1 TTTTATA-ATATCAAGAGTTCTT
1306193 CGTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTATAATATCAAGAGTTCTTA
Found at i:1315714 original size:27 final size:24
Alignment explanation
Indices: 1315673--1315726 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 24
1315663 ATGTTAAAGG
*
1315673 TACTTGGATGGAAAATTATGAGAA
1 TACTTGGATGGAAAATTATGAAAA
1315697 TACTCTGGTATGGTAAAATTATGAAAA
1 TACT-TGG-ATGG-AAAATTATGAAAA
1315724 TAC
1 TAC
1315727 CCTTATGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 3 0.12
26 4 0.15
27 15 0.58
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (24 bp):
TACTTGGATGGAAAATTATGAAAA
Found at i:1315739 original size:27 final size:26
Alignment explanation
Indices: 1315680--1315733 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1315670 AGGTACTTGG
* *
1315680 ATGG-AAAATTATGAGAATACTCTGGT
1 ATGGTAAAATTATGAAAATACCCT-GT
1315706 ATGGTAAAATTATGAAAATACCCT-T
1 ATGGTAAAATTATGAAAATACCCTGT
1315731 ATG
1 ATG
1315734 TTGTAAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 4 0.16
27 17 0.68
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (26 bp):
ATGGTAAAATTATGAAAATACCCTGT
Found at i:1324970 original size:27 final size:26
Alignment explanation
Indices: 1324940--1324990 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1324930 TTACTTTTAA
* * *
1324940 AGTTTTCGATTTCGAGTCGAGCTCAGC
1 AGTTCTCGAGTTCGACTCG-GCTCAGC
1324967 AGTTCTCGAGTTCGACTCGGCTCA
1 AGTTCTCGAGTTCGACTCGGCTCA
1324991 TTTAACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (26 bp):
AGTTCTCGAGTTCGACTCGGCTCAGC
Found at i:1332072 original size:11 final size:13
Alignment explanation
Indices: 1332040--1332069 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1332030 TGGCCAAAGA
1332040 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1332053 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1332065 TGAAA
1 TGAAA
1332070 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1336926 original size:24 final size:24
Alignment explanation
Indices: 1336891--1336937 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1336881 ATACTAGAGG
*
1336891 CAGGAGGCAGATCGGTCGGGCTCA
1 CAGGAGGAAGATCGGTCGGGCTCA
*
1336915 CAGGAGGAAGATCTGTCGGGCTC
1 CAGGAGGAAGATCGGTCGGGCTC
1336938 GTATGAGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.40, T:0.15
Consensus pattern (24 bp):
CAGGAGGAAGATCGGTCGGGCTCA
Found at i:1344991 original size:25 final size:25
Alignment explanation
Indices: 1344940--1344999 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
1344930 GAGTCGAGCT
* * *
1344940 GAGCTAAGACAAGCCGAGCTGAGCC
1 GAGCTAAGCCAAGCCAAGCTGAACC
* *
1344965 GAGCTAAGCCATGCCAAGTTGAACC
1 GAGCTAAGCCAAGCCAAGCTGAACC
*
1344990 GAGCTGAGCC
1 GAGCTAAGCC
1345000 GAGTTAAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.12
Consensus pattern (25 bp):
GAGCTAAGCCAAGCCAAGCTGAACC
Found at i:1345071 original size:15 final size:15
Alignment explanation
Indices: 1345053--1345093 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1345043 CCGAATCGAT
* *
1345053 CCGAGCCGAGTCAAG
1 CCGAGCCAAGCCAAG
1345068 CCGAGCCAAGCCAAG
1 CCGAGCCAAGCCAAG
*
1345083 CCGAACCAAGC
1 CCGAGCCAAGC
1345094 TGAGCCGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.39, G:0.27, T:0.02
Consensus pattern (15 bp):
CCGAGCCAAGCCAAG
Found at i:1351488 original size:16 final size:16
Alignment explanation
Indices: 1351464--1351503 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1351454 TTACAAAGCC
*
1351464 AAGCAACACTTTTGCA
1 AAGCCACACTTTTGCA
1351480 AAGCCACACTTTTGCA
1 AAGCCACACTTTTGCA
1351496 AAGCCACA
1 AAGCCACA
1351504 GTTCATCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (16 bp):
AAGCCACACTTTTGCA
Found at i:1356317 original size:24 final size:24
Alignment explanation
Indices: 1356290--1356365 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
1356280 TTCCGATTGA
* *
1356290 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACCTGACCTGG
*
1356314 ATTCTGATCTGATA-CTGACATGG
1 ATTCTGATCTGATACCTGACCTGG
*
1356337 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACCTGACCTGG
1356361 ATTCT
1 ATTCT
1356366 AATATAATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 22 0.48
24 24 0.52
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACCTGACCTGG
Done.