Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 25 of 32
Found at i:12422168 original size:15 final size:16
Alignment explanation
Indices: 12422148--12422188 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
12422138 TCAGAAGAAT
12422148 AAAAAATAATAAAA-A
1 AAAAAATAATAAAATA
*
12422163 ATAAAATAA-AAAATA
1 AAAAAATAATAAAATA
12422178 AAAAAATAATA
1 AAAAAATAATA
12422189 CCTTAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 17 0.77
16 1 0.05
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAATAATAAAATA
Found at i:12422170 original size:12 final size:12
Alignment explanation
Indices: 12422145--12422180 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
12422135 AACTCAGAAG
12422145 AATAAAAAAT--
1 AATAAAAAATAA
12422155 AATAAAAAATAA
1 AATAAAAAATAA
12422167 AATAAAAAATAA
1 AATAAAAAATAA
12422179 AA
1 AA
12422181 AAATAATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:12424796 original size:23 final size:23
Alignment explanation
Indices: 12424770--12424815 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12424760 TAGACAGTAT
* * *
12424770 GTTAGTAAAGCATTGCGTGACTA
1 GTTAGCAAAGCATTACATGACTA
*
12424793 GTTAGCAAGGCATTACATGACTA
1 GTTAGCAAAGCATTACATGACTA
12424816 TTTTTTATGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (23 bp):
GTTAGCAAAGCATTACATGACTA
Found at i:12427045 original size:20 final size:21
Alignment explanation
Indices: 12427006--12427045 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12426996 TGCCTCCTCA
*
12427006 GCTGCAGAAACTGCCTGATCG
1 GCTGCAGAAACAGCCTGATCG
*
12427027 GCTGCATAAACAG-CTGATC
1 GCTGCAGAAACAGCCTGATC
12427046 TTGTTTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (21 bp):
GCTGCAGAAACAGCCTGATCG
Found at i:12439152 original size:81 final size:81
Alignment explanation
Indices: 12439056--12439258 Score: 307
Period size: 81 Copynumber: 2.5 Consensus size: 81
12439046 TTAAATAGGT
* * * *
12439056 TCAATTAAAAATTAGTTATTGGTCATCCAATTTGTCTCTAAATAAATCAAGATAATTTAGAGATA
1 TCAATTAAAATTTAGTTATTGGTCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGACATA
12439121 ATATTCATATTTTTGA
66 ATATTCATATTTTTGA
* *
12439137 TCAATTAAAATTTAGTTATTGGTCATCCAATTTATCTTTAAATAAATTAAAATAATTTAGACATA
1 TCAATTAAAATTTAGTTATTGGTCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGACATA
12439202 ATATTCATATTTTTGA
66 ATATTCATATTTTTGA
* * * **
12439218 CCAATCAAAATTTAATTATTGGTCATTTAATTTATCTCTAA
1 TCAATTAAAATTTAGTTATTGGTCATCCAATTTATCTCTAA
12439259 TAATTATACT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 110 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (81 bp):
TCAATTAAAATTTAGTTATTGGTCATCCAATTTATCTCTAAATAAATCAAAATAATTTAGACATA
ATATTCATATTTTTGA
Found at i:12439627 original size:29 final size:29
Alignment explanation
Indices: 12439591--12439651 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
12439581 TTCTGAAGTG
** *
12439591 AAGATCAAGCGGCCGCGAATTTCGTGATC
1 AAGATCAAGCGGCAACGAAGTTCGTGATC
12439620 AAGATCAAGCGGCAACGAAGTTCGTGATC
1 AAGATCAAGCGGCAACGAAGTTCGTGATC
12439649 AAG
1 AAG
12439652 CGACAACGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (29 bp):
AAGATCAAGCGGCAACGAAGTTCGTGATC
Found at i:12439652 original size:23 final size:23
Alignment explanation
Indices: 12439622--12439674 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
12439612 TCGTGATCAA
*
12439622 GATCAAGCGGCAACGAAGTTCGT
1 GATCAAGCGACAACGAAGTTCGT
12439645 GATCAAGCGACAACGAAGTTCGT
1 GATCAAGCGACAACGAAGTTCGT
12439668 GATCAAG
1 GATCAAG
12439675 ATATCAAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (23 bp):
GATCAAGCGACAACGAAGTTCGT
Found at i:12439731 original size:51 final size:51
Alignment explanation
Indices: 12439672--12439778 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
12439662 GTTCGTGATC
* * * * *
12439672 AAGATATCAAGTGTTCGTGATCAAAATTAAGTCGTGAAGACCATTGAAATG
1 AAGATATCAAGTATTCATAATCAAAATTAAGTCCTAAAGACCATTGAAATG
* *
12439723 AAGATATCAAGTATTCATAATCAAGATTAAGTCCTAAAGACCTTTGAAATG
1 AAGATATCAAGTATTCATAATCAAAATTAAGTCCTAAAGACCATTGAAATG
12439774 AAGAT
1 AAGAT
12439779 CAAGCAAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (51 bp):
AAGATATCAAGTATTCATAATCAAAATTAAGTCCTAAAGACCATTGAAATG
Found at i:12439805 original size:51 final size:49
Alignment explanation
Indices: 12439684--12439810 Score: 123
Period size: 51 Copynumber: 2.5 Consensus size: 49
12439674 GATATCAAGT
* * *
12439684 GTTCGTGATCAAA-ATTAAGTCGTGAAGACCATTGAAATGAAGATATCAA
1 GTTCGTGAT-AAAGATTAAGTCCTAAAGACCATTGAAATGAAGATAGCAA
* * * *
12439733 GTATTCATAATCAAGATTAAGTCCTAAAGACCTTTGAAATGAAGATCAAGCAA
1 G--TTCGTGATAAAGATTAAGTCCTAAAGACCATTGAAATGAAGAT--AGCAA
*
12439786 GTTCGTGATAAAGACTAAGT-CTAAA
1 GTTCGTGATAAAGATTAAGTCCTAAA
12439811 TTTGTGACTG
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
49 1 0.02
50 7 0.11
51 49 0.79
53 5 0.08
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (49 bp):
GTTCGTGATAAAGATTAAGTCCTAAAGACCATTGAAATGAAGATAGCAA
Found at i:12440090 original size:27 final size:27
Alignment explanation
Indices: 12440059--12440110 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
12440049 TTGCCTCATT
12440059 AGCCTCTTTCTTCAAGTTTTAGTTAAC
1 AGCCTCTTTCTTCAAGTTTTAGTTAAC
*
12440086 AGCCTCTTTCTTCAGGTTTTAGTTA
1 AGCCTCTTTCTTCAAGTTTTAGTTA
12440111 GCAGTTGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.46
Consensus pattern (27 bp):
AGCCTCTTTCTTCAAGTTTTAGTTAAC
Found at i:12448642 original size:21 final size:22
Alignment explanation
Indices: 12448607--12448650 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
12448597 NNNNNNNNNT
12448607 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
12448629 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
12448650 A
1 A
12448651 TTAAACACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:12451224 original size:28 final size:28
Alignment explanation
Indices: 12451184--12451244 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
12451174 GACACCCTAG
* *
12451184 CTAGCGAGGGG-AAGTGGGGTAAATGGCA
1 CTAGTGAGGGGAAAG-GGAGTAAATGGCA
12451212 CTAGTGAGGGGAAAGGGAGTAAATGGCA
1 CTAGTGAGGGGAAAGGGAGTAAATGGCA
12451240 CTAGT
1 CTAGT
12451245 CTTCTGGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.90
29 3 0.10
ACGTcount: A:0.31, C:0.10, G:0.43, T:0.16
Consensus pattern (28 bp):
CTAGTGAGGGGAAAGGGAGTAAATGGCA
Found at i:12452471 original size:20 final size:20
Alignment explanation
Indices: 12452448--12452491 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12452438 TAATGAGGTT
12452448 ATTTTT-ATTAAGTTATTTTA
1 ATTTTTCATTAA-TTATTTTA
* *
12452468 ATTTTTCATTTATTTTTTTA
1 ATTTTTCATTAATTATTTTA
12452488 ATTT
1 ATTT
12452492 ACCTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTTCATTAATTATTTTA
Found at i:12462958 original size:76 final size:77
Alignment explanation
Indices: 12462798--12462965 Score: 250
Period size: 76 Copynumber: 2.2 Consensus size: 77
12462788 TAACTATGGT
* * **
12462798 GTGTAACGTGTTTTTGTGTATGACGTGTAACAACAGTATTTTTTTTTCAACATGACGTATAACAA
1 GTGTAACATGTTTTTATCCATGACGTGTAACAACAGTATTTTTTTTTCAACATGACGTATAACAA
12462863 CCTAACCATGAC
66 CCTAACCATGAC
*
12462875 ATGTAACATGTTTTTATCCATGACGTGTAACAACAGTA-TTTTTTTTCAACAT-AGCGTATAACA
1 GTGTAACATGTTTTTATCCATGACGTGTAACAACAGTATTTTTTTTTCAACATGA-CGTATAACA
* *
12462938 ACTTGACCATGAC
65 ACCTAACCATGAC
12462951 GTGTAACATGTTTTT
1 GTGTAACATGTTTTT
12462966 GTACATAACC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 1 0.01
76 48 0.59
77 33 0.40
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (77 bp):
GTGTAACATGTTTTTATCCATGACGTGTAACAACAGTATTTTTTTTTCAACATGACGTATAACAA
CCTAACCATGAC
Found at i:12465856 original size:2 final size:2
Alignment explanation
Indices: 12465849--12465879 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12465839 AAGTCTAATC
12465849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12465880 TATGAATGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12471897 original size:20 final size:21
Alignment explanation
Indices: 12471864--12471908 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
12471854 CGATCACATG
*
12471864 ACAT-CACAATAATAATCAAA
1 ACATACACAATAATAAGCAAA
*
12471884 ACATACACAA-AATAAGCATA
1 ACATACACAATAATAAGCAAA
12471904 ACATA
1 ACATA
12471909 AATTAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.60, C:0.20, G:0.02, T:0.18
Consensus pattern (21 bp):
ACATACACAATAATAAGCAAA
Found at i:12475784 original size:9 final size:9
Alignment explanation
Indices: 12475772--12475799 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12475762 TTCATGTATC
12475772 GATACATGG
1 GATACATGG
12475781 GATACATGG
1 GATACATGG
12475790 GATACATGG
1 GATACATGG
12475799 G
1 G
12475800 TGCATGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (9 bp):
GATACATGG
Found at i:12475788 original size:21 final size:21
Alignment explanation
Indices: 12475747--12475817 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
12475737 TTGAGGAATC
** *
12475747 TATCGATACATGTTATTCATG
1 TATCGATACATGGGATACATG
12475768 TATCGATACATGGGATACATG
1 TATCGATACATGGGATACATG
* *
12475789 ---GGATACATGGG-TGCATG
1 TATCGATACATGGGATACATG
12475806 TATCGATACATG
1 TATCGATACATG
12475818 AACCTTTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.12
18 10 0.24
20 8 0.20
21 18 0.44
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (21 bp):
TATCGATACATGGGATACATG
Found at i:12478574 original size:17 final size:17
Alignment explanation
Indices: 12478552--12478584 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12478542 CTAACATTTG
12478552 TTATTTT-ATACTCTTTC
1 TTATTTTCA-ACTCTTTC
12478569 TTATTTTCAACTCTTT
1 TTATTTTCAACTCTTT
12478585 TGCAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTTTCAACTCTTTC
Found at i:12481501 original size:37 final size:36
Alignment explanation
Indices: 12481429--12481501 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
12481419 TTGATCAAGA
* * * *
12481429 TTCAATATAATGCCTTTTATGGATCAAGTATAACCT
1 TTCAATACAATGCCTTTTATGGATAAAATACAACCT
*
12481465 TTCAATACAATGCCTTTTTATGGTTAAAATACAACCT
1 TTCAATACAATGCC-TTTTATGGATAAAATACAACCT
12481502 CTTTGCCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (36 bp):
TTCAATACAATGCCTTTTATGGATAAAATACAACCT
Found at i:12482106 original size:14 final size:15
Alignment explanation
Indices: 12482087--12482117 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12482077 TATCGATAAA
12482087 TTGAG-TTTGACTTT
1 TTGAGTTTTGACTTT
12482101 TTGAGTTTTGACTTT
1 TTGAGTTTTGACTTT
12482116 TT
1 TT
12482118 TACAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.13, C:0.06, G:0.19, T:0.61
Consensus pattern (15 bp):
TTGAGTTTTGACTTT
Found at i:12487589 original size:23 final size:21
Alignment explanation
Indices: 12487545--12487589 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
12487535 TAACTGAATA
*
12487545 ATTTCCAATTTAATCTTTTTT
1 ATTTCCAATTTAATCTTGTTT
*
12487566 ATTTCCGAATTTAGTTCTTGTTT
1 ATTTCC-AATTTA-ATCTTGTTT
12487589 A
1 A
12487590 GTTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 6 0.30
23 8 0.40
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTTCCAATTTAATCTTGTTT
Found at i:12499639 original size:41 final size:40
Alignment explanation
Indices: 12499592--12499671 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
12499582 AAATTTTCTG
*
12499592 TTTGGTTTTACTATTCTATTCTTTATATTTATTTCAATTTC
1 TTTGGTTTTAATATTCTATTCTTTAT-TTTATTTCAATTTC
* * *
12499633 TTTGGTTTTAATATTCTGTTCTTTATTTTTTTTCGATTT
1 TTTGGTTTTAATATTCTATTCTTTATTTTATTTCAATTT
12499672 GGTTTCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 11 0.31
41 24 0.69
ACGTcount: A:0.16, C:0.10, G:0.07, T:0.66
Consensus pattern (40 bp):
TTTGGTTTTAATATTCTATTCTTTATTTTATTTCAATTTC
Found at i:12508794 original size:16 final size:15
Alignment explanation
Indices: 12508768--12508798 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
12508758 ATATTATTAA
12508768 AAACATATAACATTC
1 AAACATATAACATTC
12508783 AAACACTATAACATTC
1 AAACA-TATAACATTC
12508799 TTTTTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACATATAACATTC
Found at i:12518424 original size:9 final size:9
Alignment explanation
Indices: 12518393--12518417 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12518383 TCTCATCCAT
12518393 TTTTTTTAG
1 TTTTTTTAG
12518402 TTTTTTTAG
1 TTTTTTTAG
12518411 TTTTTTT
1 TTTTTTT
12518418 CTTTTTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTAG
Found at i:12519015 original size:7 final size:7
Alignment explanation
Indices: 12519003--12519031 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12518993 GCAGAGACAA
12519003 CCTAAAC
1 CCTAAAC
12519010 CCTAAAC
1 CCTAAAC
12519017 CCTAAAC
1 CCTAAAC
12519024 CCTAAAC
1 CCTAAAC
12519031 C
1 C
12519032 ACGAACCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.45, G:0.00, T:0.14
Consensus pattern (7 bp):
CCTAAAC
Found at i:12524777 original size:64 final size:63
Alignment explanation
Indices: 12524698--12524849 Score: 196
Period size: 64 Copynumber: 2.4 Consensus size: 63
12524688 AACATAGATA
* * * ** * * *
12524698 AAAACAATAATAAATAGTCTTGAGTAAATAACAATAAATCATTAACAGTATTCAATAATGGATT
1 AAAACAACAACAAATAATCTTGAACAAAAAACAACAAATCATTAACAGTATTCAACAATGGA-T
* *
12524762 AAAACAACAACAAATAATCTTCAACAAAAAACAACAAATCATTAACAGTCTTCAACAATGGAT
1 AAAACAACAACAAATAATCTTGAACAAAAAACAACAAATCATTAACAGTATTCAACAATGGAT
12524825 AACAACAACAACAAATAATCTTGAA
1 AA-AACAACAACAAATAATCTTGAA
12524850 TGCAAATAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
63 3 0.04
64 73 0.96
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.23
Consensus pattern (63 bp):
AAAACAACAACAAATAATCTTGAACAAAAAACAACAAATCATTAACAGTATTCAACAATGGAT
Found at i:12535893 original size:21 final size:21
Alignment explanation
Indices: 12535867--12535910 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
12535857 CCATTCCATT
12535867 TTGAAATATGGAAG-GGGACAA
1 TTGAAATATGGAAGAGGG-CAA
12535888 TTGAAATATGGAAGAGGGCAA
1 TTGAAATATGGAAGAGGGCAA
12535909 TT
1 TT
12535911 CAAAAAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.23
Consensus pattern (21 bp):
TTGAAATATGGAAGAGGGCAA
Found at i:12543234 original size:15 final size:14
Alignment explanation
Indices: 12543197--12543254 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
12543187 AAATTATAAT
12543197 TATTTTAAAATTAA
1 TATTTTAAAATTAA
**
12543211 TAAAGTTAATAATTAA
1 T-ATTTTAA-AATTAA
* *
12543227 TTTTTTAACATTAA
1 TATTTTAAAATTAA
12543241 TATTTTAAATATTA
1 TATTTTAAA-ATTA
12543255 TATGTAAGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 13 0.39
15 13 0.39
16 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
TATTTTAAAATTAA
Found at i:12543689 original size:27 final size:28
Alignment explanation
Indices: 12543649--12543718 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
12543639 CTTTGAGAAC
* * *
12543649 ATATAAATTTA-TTTATTTTTTTACAAA
1 ATATAAATTAATTTTAATCTTTTACAAA
*
12543676 ATATGAATTAATTTTAATCTTTTACAAA
1 ATATAAATTAATTTTAATCTTTTACAAA
*
12543704 ATGA-AAACTAATTTT
1 AT-ATAAATTAATTTT
12543719 TTTTATTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 9 0.26
28 25 0.71
29 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (28 bp):
ATATAAATTAATTTTAATCTTTTACAAA
Found at i:12548716 original size:28 final size:28
Alignment explanation
Indices: 12548685--12548738 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
12548675 TATTACAAAC
12548685 AAATAAATTACAC-CAAACATAAATAAGT
1 AAATAAATTAC-CTCAAACATAAATAAGT
*
12548713 AAATACATTACCTCAAACATAAATAA
1 AAATAAATTACCTCAAACATAAATAA
12548739 AATTTCAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.59, C:0.17, G:0.02, T:0.22
Consensus pattern (28 bp):
AAATAAATTACCTCAAACATAAATAAGT
Found at i:12553147 original size:42 final size:41
Alignment explanation
Indices: 12553101--12553211 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
12553091 TTATAATATC
** * *
12553101 TAAATTATAAATAAAGTATTAATATTTTAATTTTTTAATGGT
1 TAAATTATAAAT-AAGTATTAATATTTTAAAATATTAATAGT
* * * *
12553143 TAAATTATAAGTAAGATGTTAATATTTAAAAATATTAATATT
1 TAAATTATAAATAAG-TATTAATATTTTAAAATATTAATAGT
12553185 TAAATTATAAAT---TATTAATATTTTAAA
1 TAAATTATAAATAAGTATTAATATTTTAAA
12553212 TAAATTATGA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
38 13 0.23
41 3 0.05
42 41 0.72
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (41 bp):
TAAATTATAAATAAGTATTAATATTTTAAAATATTAATAGT
Found at i:12553217 original size:27 final size:27
Alignment explanation
Indices: 12553185--12553242 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
12553175 TATTAATATT
12553185 TAAATTATAAATTATTAATATTTTA-AA
1 TAAATTATAAATTATTAATA-TTTAGAA
*
12553212 TAAATTATGAATTATTAATATTTAGAA
1 TAAATTATAAATTATTAATATTTAGAA
12553239 TAAA
1 TAAA
12553243 ATAACATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
TAAATTATAAATTATTAATATTTAGAA
Found at i:12554841 original size:15 final size:15
Alignment explanation
Indices: 12554821--12554851 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12554811 GTTGATTTTG
12554821 TTTTTTATGAAATTA
1 TTTTTTATGAAATTA
12554836 TTTTTTATGAAATTA
1 TTTTTTATGAAATTA
12554851 T
1 T
12554852 GGATGAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTTTATGAAATTA
Found at i:12560689 original size:15 final size:17
Alignment explanation
Indices: 12560647--12560682 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12560637 AATATTATAA
12560647 TATAATCA-TA-TTTTT
1 TATAATCATTACTTTTT
12560662 TATAATCATTACTTTTT
1 TATAATCATTACTTTTT
12560679 TATA
1 TATA
12560683 TTATACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 9 0.47
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (17 bp):
TATAATCATTACTTTTT
Found at i:12560754 original size:15 final size:15
Alignment explanation
Indices: 12560734--12560771 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
12560724 TCACATACTC
*
12560734 AATAATTATATTATT
1 AATAATTATATTAAT
12560749 AATAATTATATTAAT
1 AATAATTATATTAAT
12560764 AATAATTA
1 AATAATTA
12560772 CATTCTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAATTATATTAAT
Found at i:12562264 original size:25 final size:25
Alignment explanation
Indices: 12562207--12562259 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
12562197 AGAAAATTTT
12562207 TAAAATTTTTATAAAAACGAAATTA
1 TAAAATTTTTATAAAAACGAAATTA
*
12562232 TAAAATTTTTAT-AAAA-TAAATTA
1 TAAAATTTTTATAAAAACGAAATTA
12562255 TAAAA
1 TAAAA
12562260 AATTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 11 0.41
24 4 0.15
25 12 0.44
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
TAAAATTTTTATAAAAACGAAATTA
Found at i:12563177 original size:19 final size:19
Alignment explanation
Indices: 12563129--12563180 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
12563119 TTTTAAAATA
12563129 AAAAATTATATCATATAAT
1 AAAAATTATATCATATAAT
*
12563148 AAAAAAT-TATC-T-TAATT
1 AAAAATTATATCATATAA-T
12563165 CAAAAATTATATCATA
1 -AAAAATTATATCATA
12563181 AAGAGTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
16 3 0.12
17 2 0.08
18 10 0.38
19 10 0.38
20 1 0.04
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTATATCATATAAT
Found at i:12572328 original size:20 final size:20
Alignment explanation
Indices: 12572282--12572339 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
12572272 AAAATATTTT
* *
12572282 ATAATATTATAATTAAAATAA
1 ATAATATTA-AAATAAAACAA
* *
12572303 AAAATATTAAAATAAAACAC
1 ATAATATTAAAATAAAACAA
*
12572323 ATAATATAAAAATAAAA
1 ATAATATTAAAATAAAA
12572340 AATAAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAATATTAAAATAAAACAA
Found at i:12572406 original size:28 final size:26
Alignment explanation
Indices: 12572298--12572418 Score: 95
Period size: 27 Copynumber: 4.5 Consensus size: 26
12572288 TTATAATTAA
* *
12572298 AATAAAAAATATTAAAATAAAACACAT
1 AATAAAAAA-ATTAAAATAAAATATAT
* *
12572325 AATATAAAAATAAAAAATAAAATA-A-
1 AATAAAAAAAT-TAAAATAAAATATAT
* **
12572350 AATATAAGAAATTAAAAT-TTATATAAT
1 AATA-AAAAAATTAAAATAAAATAT-AT
12572377 AAGTAAAAGAAATTAAAATAAAATATAT
1 AA-TAAAA-AAATTAAAATAAAATATAT
12572405 AATATAAAAAATTA
1 AATA-AAAAAATTA
12572419 TATTAAAGAA
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
24 3 0.04
25 9 0.12
26 9 0.12
27 30 0.41
28 19 0.26
29 4 0.05
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (26 bp):
AATAAAAAAATTAAAATAAAATATAT
Found at i:12572474 original size:33 final size:33
Alignment explanation
Indices: 12572392--12572485 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
12572382 AAAGAAATTA
* * *
12572392 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAATA-A-AATATATAATATTATAATAAAG
*
12572427 AAATTAAAACAAAATATATAATATTATAAT-AAG
1 AAA-TAAAATAAAATATATAATATTATAATAAAG
*
12572460 AAATGAAAATAAAATATATGATATTA
1 AAAT-AAAATAAAATATATAATATTA
12572486 AAAAATATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 1 0.02
33 25 0.49
34 15 0.29
35 4 0.08
36 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (33 bp):
AAATAAAATAAAATATATAATATTATAATAAAG
Found at i:12574385 original size:3 final size:3
Alignment explanation
Indices: 12574362--12574406 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
12574352 TTTAAATTAT
* *
12574362 ATA ATA TTA AAA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12574407 TAAAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12581813 original size:238 final size:238
Alignment explanation
Indices: 12581395--12581867 Score: 858
Period size: 238 Copynumber: 2.0 Consensus size: 238
12581385 TTTCATGTTG
*
12581395 AATTGGGTGAAGTAGTAAACATAAAAGTTGTATATTTTTCTTTTATCTTTCCAATGGTATAAAAA
1 AATTGGGTGAAGTAGCAAACATAAAAGTTGTATATTTTTCTTTTATCTTTCCAATGGTATAAAAA
12581460 TCACTTTACTTGAAACCCTGTAGAGAGAGTTATGGCCAAAATACCAAAACATGTGTAGTGTAAGT
66 TCACTTTACTTGAAACCCTGTAGAGAGAGTTATGGCCAAAATACCAAAACATGTGTAGTGTAAGT
*
12581525 TTACACCTTGAAATTGCTCTTCTTCTTTTACTAAAATTTTTCTTTCATCAAATACCTATAAAAGC
131 TTACACCTTGAAATTGCTCTTCTTCTTTTACTAAAATTTTTCTTTCATCAAATACCTACAAAAGC
*
12581590 ACAAATAAATTAATAACAACCTATCTTAACCACATTAACACCA
196 ACAAATAAATCAATAACAACCTATCTTAACCACATTAACACCA
12581633 AATTGGGTGAAGTAGCAAACATAAAAGTTGTATATTTTT-TTCTTATCTTTCCAATGGTATAAAA
1 AATTGGGTGAAGTAGCAAACATAAAAGTTGTATATTTTTCTT-TTATCTTTCCAATGGTATAAAA
* *
12581697 ATCACTTTATTTGAAACTCTGTAGAGAGAGTTATGGCCAAAATACCAAAACATGTGTAGTGTAAG
65 ATCACTTTACTTGAAACCCTGTAGAGAGAGTTATGGCCAAAATACCAAAACATGTGTAGTGTAAG
*
12581762 TTTACATCTTGAAATTGCTCTTCTTCTTTTACTAAAATTTTTCTTTCATCAAATACCTACAAAAG
130 TTTACACCTTGAAATTGCTCTTCTTCTTTTACTAAAATTTTTCTTTCATCAAATACCTACAAAAG
* *
12581827 CACAAATAAATCAATAATAACCTATCTTAATCACATTAACA
195 CACAAATAAATCAATAACAACCTATCTTAACCACATTAACA
12581868 TTAAATTAAG
Statistics
Matches: 226, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
237 2 0.01
238 224 0.99
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (238 bp):
AATTGGGTGAAGTAGCAAACATAAAAGTTGTATATTTTTCTTTTATCTTTCCAATGGTATAAAAA
TCACTTTACTTGAAACCCTGTAGAGAGAGTTATGGCCAAAATACCAAAACATGTGTAGTGTAAGT
TTACACCTTGAAATTGCTCTTCTTCTTTTACTAAAATTTTTCTTTCATCAAATACCTACAAAAGC
ACAAATAAATCAATAACAACCTATCTTAACCACATTAACACCA
Found at i:12586018 original size:54 final size:54
Alignment explanation
Indices: 12585959--12586063 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
12585949 TTTTTTATTC
12585959 TCCTAAAAAGGCCCTTTTGTTGTAAATACTAACAAATGCTATTCCCATTCCCAT
1 TCCTAAAAAGGCCCTTTTGTTGTAAATACTAACAAATGCTATTCCCATTCCCAT
12586013 TCCTAAAAAGGCCCTTTTGTTGTAAATACTAACAAATGCTATTCCCATTCC
1 TCCTAAAAAGGCCCTTTTGTTGTAAATACTAACAAATGCTATTCCCATTCC
12586064 TAACATGGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (54 bp):
TCCTAAAAAGGCCCTTTTGTTGTAAATACTAACAAATGCTATTCCCATTCCCAT
Found at i:12589050 original size:2 final size:2
Alignment explanation
Indices: 12589043--12589068 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12589033 TCATTTTGCA
12589043 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
12589069 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12589073 original size:2 final size:2
Alignment explanation
Indices: 12589068--12589098 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12589058 GTGTGTGTGT
12589068 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
12589099 GTGTGATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12591827 original size:23 final size:23
Alignment explanation
Indices: 12591801--12591873 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
12591791 AGGGTTTAAC
*
12591801 ATTGTGAGACTGGTTGATATGTA
1 ATTGTGAGACTGGTTGATAGGTA
* **
12591824 ATTG-CATGACTTATTGATAGGTA
1 ATTGTGA-GACTGGTTGATAGGTA
* * *
12591847 TTTGTGTGACTGGTTGATAGGTT
1 ATTGTGAGACTGGTTGATAGGTA
12591870 ATTG
1 ATTG
12591874 CATAAATATT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.23, C:0.05, G:0.29, T:0.42
Consensus pattern (23 bp):
ATTGTGAGACTGGTTGATAGGTA
Found at i:12592785 original size:13 final size:13
Alignment explanation
Indices: 12592767--12592795 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12592757 GTGACGATAC
12592767 AACAAGTTTTAGA
1 AACAAGTTTTAGA
12592780 AACAAGTTTTAGA
1 AACAAGTTTTAGA
12592793 AAC
1 AAC
12592796 GTTCAAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (13 bp):
AACAAGTTTTAGA
Found at i:12595028 original size:18 final size:19
Alignment explanation
Indices: 12594985--12595033 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
12594975 TTAATATTTT
*
12594985 AATAATATTTTATTAATAAA
1 AATATTATTTTATT-ATAAA
12595005 AATATTATTTTATT-TAAA
1 AATATTATTTTATTATAAA
* *
12595023 ACTATTCTTTT
1 AATATTATTTT
12595034 TACCTACCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTATAAA
Found at i:12595833 original size:12 final size:12
Alignment explanation
Indices: 12595816--12595841 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12595806 TCGCTACTGT
12595816 TGAGGCCTCGGG
1 TGAGGCCTCGGG
12595828 TGAGGCCTCGGG
1 TGAGGCCTCGGG
12595840 TG
1 TG
12595842 CTGCTGAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (12 bp):
TGAGGCCTCGGG
Found at i:12598224 original size:69 final size:68
Alignment explanation
Indices: 12598132--12598330 Score: 220
Period size: 69 Copynumber: 2.9 Consensus size: 68
12598122 GAATCGCGTG
** * *
12598132 ACTAGTTGATATGGAATAACGTGAGTAGTAAAAATGGAATTACGTTACTAGTTATTATGGAGT-C
1 ACTAGTTGATATGGAATCGCGTGAGTAGTAAATATGGAATCACGTTACTAGTTATTATGGAGTAC
12598196 GCTCC
66 G-T-C
* * * ** ** *
12598201 AGTATTTGATAGGGAATCGCGTGAGTAGTAAATATGGAATCATATTACTAGTTATTATAAAATTA
1 ACTAGTTGATATGGAATCGCGTGAGTAGTAAATATGGAATCACGTTACTAGTTATTAT-GGAGTA
*
12598266 CGTG
65 CGTC
* * *
12598270 ACTAGTTGATATGGAATCGCGCGAGTAGTAAATATGGAATCGCGTTACTAGCTATTATGGA
1 ACTAGTTGATATGGAATCGCGTGAGTAGTAAATATGGAATCACGTTACTAGTTATTATGGA
12598331 ATCATAAAAT
Statistics
Matches: 105, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
68 1 0.01
69 99 0.94
70 3 0.03
71 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (68 bp):
ACTAGTTGATATGGAATCGCGTGAGTAGTAAATATGGAATCACGTTACTAGTTATTATGGAGTAC
GTC
Found at i:12598239 original size:23 final size:23
Alignment explanation
Indices: 12598076--12598333 Score: 122
Period size: 23 Copynumber: 11.2 Consensus size: 23
12598066 CATTAAGACA
* * * *
12598076 GAATCGCTTGACTAGTTGATATT
1 GAATCGCGTGAGTAGTTAATATG
* * *
12598099 GAATTGCATGAGTAGTAAATATG
1 GAATCGCGTGAGTAGTTAATATG
* *
12598122 GAATCGCGTGACTAGTTGATATG
1 GAATCGCGTGAGTAGTTAATATG
** * *
12598145 GAATAACGTGAGTAGTAAAAATG
1 GAATCGCGTGAGTAGTTAATATG
** * * *
12598168 GAATTACGTTACTAGTTATTATG
1 GAATCGCGTGAGTAGTTAATATG
* * * * *
12598191 GAGTCGC-TCCAGTATTTGATAGG
1 GAATCGCGT-GAGTAGTTAATATG
*
12598214 GAATCGCGTGAGTAGTAAATATG
1 GAATCGCGTGAGTAGTTAATATG
*** * * * *
12598237 GAATCATATTACTAGTTATTATA
1 GAATCGCGTGAGTAGTTAATATG
* ** * *
12598260 AAATTACGTGACTAGTTGATATG
1 GAATCGCGTGAGTAGTTAATATG
* *
12598283 GAATCGCGCGAGTAGTAAATATG
1 GAATCGCGTGAGTAGTTAATATG
* * * *
12598306 GAATCGCGTTACTAGCTATTATG
1 GAATCGCGTGAGTAGTTAATATG
12598329 GAATC
1 GAATC
12598334 ATAAAATTAT
Statistics
Matches: 166, Mismatches: 67, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
22 1 0.01
23 164 0.99
24 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (23 bp):
GAATCGCGTGAGTAGTTAATATG
Found at i:12598320 original size:46 final size:46
Alignment explanation
Indices: 12598076--12598333 Score: 171
Period size: 46 Copynumber: 5.6 Consensus size: 46
12598066 CATTAAGACA
* * *
12598076 GAATCGCTTGACTAGTTGATATTGAATTGCATGAGTAGTAAATATG
1 GAATCGCGTGACTAGTTGATATGGAATCGCATGAGTAGTAAATATG
** * *
12598122 GAATCGCGTGACTAGTTGATATGGAATAACGTGAGTAGTAAAAATG
1 GAATCGCGTGACTAGTTGATATGGAATCGCATGAGTAGTAAATATG
** * * * * ** *
12598168 GAATTACGTTACTAGTT-ATTATGGAGTCGC-TCCAGTATTTGATAGG
1 GAATCGCGTGACTAGTTGA-TATGGAATCGCAT-GAGTAGTAAATATG
* ** ** * * * * *
12598214 GAATCGCGTGAGTAGTAAATATGGAATCATATTACTAGTTATTATA
1 GAATCGCGTGACTAGTTGATATGGAATCGCATGAGTAGTAAATATG
* ** **
12598260 AAATTACGTGACTAGTTGATATGGAATCGCGCGAGTAGTAAATATG
1 GAATCGCGTGACTAGTTGATATGGAATCGCATGAGTAGTAAATATG
* *
12598306 GAATCGCGTTACTAGCT-ATTATGGAATC
1 GAATCGCGTGACTAGTTGA-TATGGAATC
12598334 ATAAAATTAT
Statistics
Matches: 154, Mismatches: 53, Indels: 10
0.71 0.24 0.05
Matches are distributed among these distances:
45 3 0.02
46 149 0.97
47 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (46 bp):
GAATCGCGTGACTAGTTGATATGGAATCGCATGAGTAGTAAATATG
Found at i:12598423 original size:23 final size:23
Alignment explanation
Indices: 12598384--12598432 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
12598374 GAAACGTGTT
*
12598384 ACTAGTTATTATGGAATAACATG
1 ACTAGTTATTATAGAATAACATG
* *
12598407 ACTAGTTGA-TATAGAATCACGTG
1 ACTAGTT-ATTATAGAATAACATG
12598430 ACT
1 ACT
12598433 TTTTTATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (23 bp):
ACTAGTTATTATAGAATAACATG
Found at i:12604364 original size:189 final size:189
Alignment explanation
Indices: 12604116--12604549 Score: 534
Period size: 189 Copynumber: 2.3 Consensus size: 189
12604106 TCACATACTG
* * * *
12604116 CCAATATCGCAATACC-ACATAATAAGTCACTCAATGCCTAATATCCATTCATGTTATGCCAACA
1 CCAATCTCGAAATACCTA-ATAATAAGTCACTCAATGCCTAATATCCACTCATATTATGCCAACA
* * *
12604180 TAACCAGTAACATACTAGCCCAACGTCACA-CAATACATAACAACAAGTCACGCAATACATAAAA
65 TAACCAGTAACATACTAGCCCAACATCA-AGCAATAAACAACAACAAGTCACGCAATACATAAAA
** *** *
12604244 ATTAGTCATGTAAT-GTCTCAACACAAGATATGCATTGCACAATTCACACAGTGCCTATAAC
129 ACCAGTCACACAATAG-CTCAACACAAGATATGCATTGCACAATTCACACAGCGCCTATAAC
* * * *
12604305 CTAGTCTCGCAATACCTAATAACT-GGTCACTCAATGCCTAATATCCACTCATATTATGCCAACA
1 CCAATCTCGAAATACCTAATAA-TAAGTCACTCAATGCCTAATATCCACTCATATTATGCCAACA
* * * * * * * *
12604369 TAACGAGTCACGTATTGGCCCAACATCAAGCAATAAACAACAACAGGTCATGCAATACATAAAAC
65 TAACCAGTAACATACTAGCCCAACATCAAGCAATAAACAACAACAAGTCACGCAATACATAAAAA
* *
12604434 CCAGTCACACAATAGCTCAACACAAGATATGCATTGCATAATTCACGCAGCGCCTATAAC
130 CCAGTCACACAATAGCTCAACACAAGATATGCATTGCACAATTCACACAGCGCCTATAAC
* * *
12604494 CCAATCTCGAAATACCTAATAATAAGTCACACAATGCCTAACATCCACTCACATTA
1 CCAATCTCGAAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCATATTA
12604550 CACCAAAATA
Statistics
Matches: 208, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
188 2 0.01
189 203 0.98
190 3 0.01
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (189 bp):
CCAATCTCGAAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCATATTATGCCAACAT
AACCAGTAACATACTAGCCCAACATCAAGCAATAAACAACAACAAGTCACGCAATACATAAAAAC
CAGTCACACAATAGCTCAACACAAGATATGCATTGCACAATTCACACAGCGCCTATAAC
Found at i:12604664 original size:22 final size:22
Alignment explanation
Indices: 12604632--12604673 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12604622 ATCAGATACG
*
12604632 CAATGCCTAATATCCATTCAGA
1 CAATGCATAATATCCATTCAGA
12604654 CAATGCATAATATCCATTCA
1 CAATGCATAATATCCATTCA
12604674 CTTAATTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (22 bp):
CAATGCATAATATCCATTCAGA
Found at i:12605572 original size:22 final size:22
Alignment explanation
Indices: 12605478--12605572 Score: 111
Period size: 22 Copynumber: 4.3 Consensus size: 22
12605468 ATAAAGCAAT
12605478 GCAATGCCTACAAACCAA-TCAC
1 GCAATGCCTACAAA-CAAGTCAC
* *
12605500 ACAATCCCTACAAACAAGTCAC
1 GCAATGCCTACAAACAAGTCAC
12605522 GCAATGCCTACAAACAAGTCAC
1 GCAATGCCTACAAACAAGTCAC
* * * *
12605544 CCTATGCCTGCAAACCAGTCAC
1 GCAATGCCTACAAACAAGTCAC
*
12605566 GTAATGC
1 GCAATGC
12605573 ACAACTCACG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 3 0.05
22 58 0.95
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.16
Consensus pattern (22 bp):
GCAATGCCTACAAACAAGTCAC
Found at i:12605986 original size:38 final size:38
Alignment explanation
Indices: 12605908--12605987 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
12605898 GTTGGATAGC
* * *
12605908 GATATAGACCTCAATGGCGTTGGAGAGCTAGACGGCGA
1 GATATAGACCCCAATGGCGTTAGAGAGCTAGACGGAGA
* *
12605946 GATATAGACCCCGATGGCGTTAGAGAGCT-GAATGGAGA
1 GATATAGACCCCAATGGCGTTAGAGAGCTAG-ACGGAGA
12605984 GATA
1 GATA
12605988 GTCAAATTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.31, C:0.16, G:0.34, T:0.19
Consensus pattern (38 bp):
GATATAGACCCCAATGGCGTTAGAGAGCTAGACGGAGA
Found at i:12609769 original size:17 final size:15
Alignment explanation
Indices: 12609747--12609780 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
12609737 CTGTCTTTCC
12609747 TTCTTTCTTTTTTCTTT
1 TTCTTT-TTTTTT-TTT
12609764 TTCTTTTTTTTTTTT
1 TTCTTTTTTTTTTTT
12609779 TT
1 TT
12609781 ACATACTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTCTTTTTTTTTTTT
Found at i:12616097 original size:21 final size:22
Alignment explanation
Indices: 12616072--12616113 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12616062 CTTACAGTGT
12616072 AATGTGATT-ATAAGGAATGTA
1 AATGTGATTGATAAGGAATGTA
* *
12616093 AATGTTATTGTTAAGGAATGT
1 AATGTGATTGATAAGGAATGT
12616114 GATTATTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (22 bp):
AATGTGATTGATAAGGAATGTA
Found at i:12616838 original size:29 final size:29
Alignment explanation
Indices: 12616806--12616861 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
12616796 AAAGGAAGTT
12616806 GAATAAAAGATA-AAAAAGAAAGAAAACAA
1 GAATAAAAGA-AGAAAAAGAAAGAAAACAA
** *
12616835 GAATGTAAGAAGAAGAAGAAAGAAAAC
1 GAATAAAAGAAGAAAAAGAAAGAAAAC
12616862 CCTCCATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (29 bp):
GAATAAAAGAAGAAAAAGAAAGAAAACAA
Found at i:12621533 original size:2 final size:2
Alignment explanation
Indices: 12621526--12621557 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12621516 CCATGAGATC
12621526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12621558 TTGAGCCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12622729 original size:45 final size:45
Alignment explanation
Indices: 12622667--12622760 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
12622657 ATTAAATTTA
* *
12622667 AATAATACTAAATAATATTCTTTATTACATTTATTATAGTCAGAT
1 AATAATACTAAATAATATTCTTTATAACATTTATTATAGTCAAAT
* * *
12622712 AATAATATTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
1 AATAATACTAAATAATATTCTTTATAACATTTATTATAGTCAAAT
12622757 AATA
1 AATA
12622761 TTAATATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (45 bp):
AATAATACTAAATAATATTCTTTATAACATTTATTATAGTCAAAT
Found at i:12622774 original size:18 final size:19
Alignment explanation
Indices: 12622735--12622780 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
12622725 AATATTCTTT
*
12622735 ATAATATTTATTATAGTTAA
1 ATAATA-TTAATATAGTTAA
12622755 ATAATATTAATATA-TTAA
1 ATAATATTAATATAGTTAA
*
12622773 ATAGTATT
1 ATAATATT
12622781 TAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 7 0.29
20 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
ATAATATTAATATAGTTAA
Found at i:12628265 original size:2 final size:2
Alignment explanation
Indices: 12628258--12628289 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12628248 TACAGGTAGA
12628258 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12628290 GTGTGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12636319 original size:5 final size:5
Alignment explanation
Indices: 12636309--12636337 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12636299 TTCCAAGAGT
12636309 TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
12636338 ATGCCAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCCC
Found at i:12636928 original size:92 final size:92
Alignment explanation
Indices: 12636771--12636954 Score: 305
Period size: 92 Copynumber: 2.0 Consensus size: 92
12636761 TTGGATTACT
* *
12636771 TAATCCAAGGCATTTGTGATAGTGGAGGACTTCAATTTAGCATATTTAGTAGCAACTTGGAAGGA
1 TAATCCAAGGCATTTGTGATAGTAGAGGACTTCAATGTAGCATATTTAGTAGCAACTTGGAAGGA
*
12636836 AAATATGACCTCCAACCACCTTGATAA
66 AAATATGACCTCCAACCACCTCGATAA
* * *
12636863 TAATCCAGGGCATTTGTGATAGTATAGGACTTCAATGTAGCGTATTTAGTAGCAACTTGGAAGGA
1 TAATCCAAGGCATTTGTGATAGTAGAGGACTTCAATGTAGCATATTTAGTAGCAACTTGGAAGGA
*
12636928 AAATGTGACCTCCAACCACCTCGATAA
66 AAATATGACCTCCAACCACCTCGATAA
12636955 CATCTTTCAA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (92 bp):
TAATCCAAGGCATTTGTGATAGTAGAGGACTTCAATGTAGCATATTTAGTAGCAACTTGGAAGGA
AAATATGACCTCCAACCACCTCGATAA
Found at i:12641932 original size:109 final size:109
Alignment explanation
Indices: 12641738--12641936 Score: 301
Period size: 109 Copynumber: 1.8 Consensus size: 109
12641728 CAAGACACAC
* *
12641738 CAAGCCTTTCATCTCCTCTTTTCTATTCTCTACATATTTTCTCTGATTTATTTCCTTCCTTACCG
1 CAAGCCTTTCATCTCATATTTTCTATTCTCTACATATTTTCTCTGATTTATTTCCTTCCTTACCG
*
12641803 GGCTATTATTTTTCTCAAAAAAAAAAAAATCTTTCTTCTATCGT
66 GGCTATTATTTTTCTAAAAAAAAAAAAAATCTTTCTTCTATCGT
* * * *
12641847 CAAGCCTTTCATCTCATA-TTTCTTGTTCTCTACATATTTTCTCTGTTTTCTTTCCTTCCTTACT
1 CAAGCCTTTCATCTCATATTTTC-TATTCTCTACATATTTTCTCTGATTTATTTCCTTCCTTACC
* *
12641911 GGGTTCTTATTTTTCTAAAAAAAAAA
65 GGGCTATTATTTTTCTAAAAAAAAAA
12641937 TAATCTTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 4 0.05
109 76 0.95
ACGTcount: A:0.23, C:0.24, G:0.06, T:0.47
Consensus pattern (109 bp):
CAAGCCTTTCATCTCATATTTTCTATTCTCTACATATTTTCTCTGATTTATTTCCTTCCTTACCG
GGCTATTATTTTTCTAAAAAAAAAAAAAATCTTTCTTCTATCGT
Found at i:12642783 original size:20 final size:21
Alignment explanation
Indices: 12642753--12642793 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12642743 AAAGCTTTAC
*
12642753 AAAAGTAAGATGACAAAGATT
1 AAAAGTAAGATAACAAAGATT
*
12642774 AAAA-TAAGATAACAAGGATT
1 AAAAGTAAGATAACAAAGATT
12642794 GTAACCACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAAGTAAGATAACAAAGATT
Found at i:12660765 original size:30 final size:30
Alignment explanation
Indices: 12660729--12660799 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
12660719 AATCATTAAC
* *
12660729 TATAAAAGCTTATTTGATTCAAAATAAAAA
1 TATAAAAACTTATTTGACTCAAAATAAAAA
* * *
12660759 TATAAAAATTTATTTGGCTCAAAATAAAAG
1 TATAAAAACTTATTTGACTCAAAATAAAAA
*
12660789 TACAAAAACTT
1 TATAAAAACTT
12660800 GATTGAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.32
Consensus pattern (30 bp):
TATAAAAACTTATTTGACTCAAAATAAAAA
Found at i:12662462 original size:63 final size:63
Alignment explanation
Indices: 12662345--12662468 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 63
12662335 TCTGTCTTGT
* * * * *
12662345 AAGAATTGATTAGTGCATTCTTGATAAGTCAAATCTTCTTACTTTTGGAGCATTCTATTTTCC
1 AAGAATCGATTAATGCATTCTTGAGAAGTCAAATCTTCTTACTTCTGGACCATTCTATTTTCC
** * * *
12662408 AAGAATCGATTAATGCATTCTTGAGAAGTTGATTCTTCTT-GTGTCTGGACCATTCTGTTTT
1 AAGAATCGATTAATGCATTCTTGAGAAGTCAAATCTTCTTACT-TCTGGACCATTCTATTTT
12662469 TTAGGAATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 1 0.02
63 49 0.98
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (63 bp):
AAGAATCGATTAATGCATTCTTGAGAAGTCAAATCTTCTTACTTCTGGACCATTCTATTTTCC
Found at i:12664137 original size:29 final size:29
Alignment explanation
Indices: 12664104--12664159 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
12664094 AAATATTTAT
12664104 AATATACACAATAGCTAAACAAGATATTC
1 AATATACACAATAGCTAAACAAGATATTC
* * * *
12664133 AATATCCATAGTAGCTAAGCAAGATAT
1 AATATACACAATAGCTAAACAAGATAT
12664160 ATTGAATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (29 bp):
AATATACACAATAGCTAAACAAGATATTC
Found at i:12664168 original size:31 final size:29
Alignment explanation
Indices: 12664115--12664173 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
12664105 ATATACACAA
12664115 TAGCTAAACAAGATATTCAATATCCATAG
1 TAGCTAAACAAGATATTCAATATCCATAG
* *
12664144 TAGCTAAGCAAGATATATTGAATATCCATA
1 TAGCTAAACAAG--ATATTCAATATCCATA
12664174 ATAACTGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 11 0.42
31 15 0.58
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (29 bp):
TAGCTAAACAAGATATTCAATATCCATAG
Found at i:12665624 original size:9 final size:9
Alignment explanation
Indices: 12665610--12665635 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12665600 TACTAATTGG
12665610 ATGAAATCC
1 ATGAAATCC
12665619 ATGAAATCC
1 ATGAAATCC
12665628 ATGAAATC
1 ATGAAATC
12665636 TAAAGGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (9 bp):
ATGAAATCC
Found at i:12675343 original size:21 final size:21
Alignment explanation
Indices: 12675317--12675364 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
12675307 TGTAATTTAG
12675317 TATTTTAAAAAAAATTTAAAT
1 TATTTTAAAAAAAATTTAAAT
** *
12675338 TATTTTTTAATAAATTTAAAT
1 TATTTTAAAAAAAATTTAAAT
*
12675359 AATTTT
1 TATTTT
12675365 TTATTTTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTAAAAAAAATTTAAAT
Found at i:12675365 original size:21 final size:21
Alignment explanation
Indices: 12675328--12675367 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12675318 ATTTTAAAAA
*
12675328 AAATTTAAATTATTTTTTAAT
1 AAATTTAAATAATTTTTTAAT
12675349 AAATTTAAATAATTTTTTA
1 AAATTTAAATAATTTTTTA
12675368 TTTTGAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATTTAAATAATTTTTTAAT
Found at i:12675510 original size:82 final size:81
Alignment explanation
Indices: 12675391--12675644 Score: 325
Period size: 82 Copynumber: 3.1 Consensus size: 81
12675381 TCAATTATGA
* *
12675391 TTTATAT-TTTTTATTTTAAATTAAATAATTTTTTATAATTAATAACAAATTAAGTATTATTTAT
1 TTTATATATTTTTATTTTAAATTAAATAA-ATTTTATAATTAATAA-AAATTAATTATTATTTAT
*
12675455 CAAAATATTACTTATCAT
64 CAAAATATTACTTATTAT
* ** * *
12675473 TTTATATATTTTTATTTTAAATTAAATAAATTTTATAACTAGCAAAAGATTAATTATCT-TCTGT
1 TTTATATATTTTTATTTTAAATTAAATAAATTTTATAATTAATAAAA-ATTAATTAT-TATTTAT
*
12675537 CAAAATATTATTTATTAT
64 CAAAATATTACTTATTAT
**
12675555 TTTATATATTTTTATTTTAAATTAAATAAATTTTTATAATTAATGAATGATTAATTATTATTTAT
1 TTTATATATTTTTATTTTAAATTAAATAAA-TTTTATAATTAAT-AAAAATTAATTATTATTTAT
12675620 CAAAATATCT-CTTATTAT
64 CAAAATAT-TACTTATTAT
12675638 TTTATAT
1 TTTATAT
12675645 CCATATAATG
Statistics
Matches: 148, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
81 2 0.01
82 77 0.52
83 66 0.45
84 3 0.02
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (81 bp):
TTTATATATTTTTATTTTAAATTAAATAAATTTTATAATTAATAAAAATTAATTATTATTTATCA
AAATATTACTTATTAT
Found at i:12680040 original size:21 final size:20
Alignment explanation
Indices: 12680016--12680054 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
12680006 TTTTAAAATT
12680016 AAAAAAATGAAGTGGCAAAAC
1 AAAAAAATGAA-TGGCAAAAC
* *
12680037 AAAATATTGAATGGCAAA
1 AAAAAAATGAATGGCAAA
12680055 GAAAATATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (20 bp):
AAAAAAATGAATGGCAAAAC
Found at i:12680059 original size:19 final size:21
Alignment explanation
Indices: 12680023--12680062 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
12680013 ATTAAAAAAA
12680023 TGAAGTGGCAAAACAAAATAT
1 TGAAGTGGCAAAACAAAATAT
*
12680044 TGAA-TGGC-AAAGAAAATAT
1 TGAAGTGGCAAAACAAAATAT
12680063 CGTTGGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 4 0.22
21 4 0.22
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (21 bp):
TGAAGTGGCAAAACAAAATAT
Found at i:12692457 original size:2 final size:2
Alignment explanation
Indices: 12692450--12692478 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12692440 ATGAATATAA
12692450 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12692479 ATGCGTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12698834 original size:15 final size:15
Alignment explanation
Indices: 12698799--12698831 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12698789 TACTTTGCTA
12698799 AATTAATATTTTATT
1 AATTAATATTTTATT
12698814 AATTAATATTTT-TT
1 AATTAATATTTTATT
12698828 AATT
1 AATT
12698832 TAAAAAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTAATATTTTATT
Found at i:12702698 original size:5 final size:5
Alignment explanation
Indices: 12702688--12702712 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12702678 AAATAATGAA
12702688 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
12702713 CAAATAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:12704981 original size:25 final size:24
Alignment explanation
Indices: 12704946--12704992 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
12704936 ATATTTTATT
12704946 TAATTTTAAA-TAATTTAATTTTA
1 TAATTTTAAATTAATTTAATTTTA
*
12704969 TAATTTTAAAAATTATTTTAATTT
1 TAATTTT--AAATTAATTTAATTT
12704993 AATTTCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
25 3 0.15
26 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATTTTAAATTAATTTAATTTTA
Found at i:12705675 original size:190 final size:190
Alignment explanation
Indices: 12705382--12705731 Score: 439
Period size: 190 Copynumber: 1.8 Consensus size: 190
12705372 ATATGATATG
* * * *
12705382 ATTGACATGATAACGTAACACTGCCATATCACCTCAACATGCTAACGTAGTAATGTCGCCTCACT
1 ATTGACATGATAACGTAACACTGCCATATCACCTCAACATACTAACGTAATAATGTCACATCACT
* ** * * * *
12705447 TTTTATGTTGGAGTTACTAATGTGGCATTACCACGTCAACATATCAAAATAAGGTGGGTATTAAG
66 TTTTAAGTTCAAGTTACTAATGTGGCACTACCACGTCAACATATAAAAACAAGGTGGGCATTAAG
*
12705512 GCTCCACGTCAACATGTCAAAATGATGTGGACATTTTTACTAACATAGTGGCATAGGGTA
131 GCTCCACGTCAACATATCAAAATGATGTGGACATTTTTACTAACATAGTGGCATAGGGTA
* ** * * * * **
12705572 ATTGACATGATAATGTGGCACTGCTATGTCATCTCAACATACTAACGTAATAGTGTCACATTGCT
1 ATTGACATGATAACGTAACACTGCCATATCACCTCAACATACTAACGTAATAATGTCACATCACT
* * * * *
12705637 TTTTAAGTTCAAGTTATTGATGTGGCACTACCACGTCAACCTGTAAAAACGAGGTGGGCATTAAG
66 TTTTAAGTTCAAGTTACTAATGTGGCACTACCACGTCAACATATAAAAACAAGGTGGGCATTAAG
* * *
12705702 GCTCTATGTCAATATATCAAAATGATGTGG
131 GCTCCACGTCAACATATCAAAATGATGTGG
12705732 CAATACCATA
Statistics
Matches: 131, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
190 131 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (190 bp):
ATTGACATGATAACGTAACACTGCCATATCACCTCAACATACTAACGTAATAATGTCACATCACT
TTTTAAGTTCAAGTTACTAATGTGGCACTACCACGTCAACATATAAAAACAAGGTGGGCATTAAG
GCTCCACGTCAACATATCAAAATGATGTGGACATTTTTACTAACATAGTGGCATAGGGTA
Found at i:12716088 original size:21 final size:21
Alignment explanation
Indices: 12716064--12716105 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12716054 TCTTGCTTTA
*
12716064 TTATATGCCTGACCTTTGATT
1 TTATATGCCCGACCTTTGATT
12716085 TTATATGCCCGACCTTTGATT
1 TTATATGCCCGACCTTTGATT
12716106 GAAATGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.45
Consensus pattern (21 bp):
TTATATGCCCGACCTTTGATT
Found at i:12716477 original size:45 final size:45
Alignment explanation
Indices: 12716413--12716506 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
12716403 TATATATATA
*
12716413 TATATAAATAGATAGGGGTATGGCATTGGATACAAAATCAACTCG
1 TATATAAATAGATAAGGGTATGGCATTGGATACAAAATCAACTCG
*
12716458 TATATTAATAGATAAGGGTATGGCATTGGATACAAAATCAACTCG
1 TATATAAATAGATAAGGGTATGGCATTGGATACAAAATCAACTCG
12716503 TATA
1 TATA
12716507 AGATTGAACC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (45 bp):
TATATAAATAGATAAGGGTATGGCATTGGATACAAAATCAACTCG
Found at i:12718883 original size:3 final size:3
Alignment explanation
Indices: 12718875--12718912 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12718865 TTACTCGTGC
12718875 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
12718913 CCCTACTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:12729850 original size:33 final size:34
Alignment explanation
Indices: 12729764--12729859 Score: 113
Period size: 33 Copynumber: 2.8 Consensus size: 34
12729754 ATATAGGTAA
* *
12729764 AATAAATTAAATTAAAATATACAATATAAAAAATTAT
1 AATAAA-TAAATGAAAATA-A-AATATATAAAATTAT
* * *
12729801 ATTAAAGAAATGAAAATAAAATATATAATATTAT
1 AATAAATAAATGAAAATAAAATATATAAAATTAT
12729835 AAT-AATAAATGAAAATAAAATATAT
1 AATAAATAAATGAAAATAAAATATAT
12729860 GACAATAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 21 0.40
34 15 0.29
35 1 0.02
36 10 0.19
37 5 0.10
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (34 bp):
AATAAATAAATGAAAATAAAATATATAAAATTAT
Found at i:12729870 original size:16 final size:16
Alignment explanation
Indices: 12729810--12729875 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 16
12729800 TATTAAAGAA
12729810 ATGAAAAT-AAAATAT
1 ATGAAAATAAAAATAT
* *
12729825 AT-AATATTATAATAATAA
1 ATGAA-A--ATAAAAATAT
12729843 ATGAAAAT-AAAATAT
1 ATGAAAATAAAAATAT
*
12729858 ATGACAATAAAAATAT
1 ATGAAAATAAAAATAT
12729874 AT
1 AT
12729876 TTAAGAGATG
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 2 0.05
15 15 0.38
16 11 0.28
17 2 0.05
18 8 0.20
19 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (16 bp):
ATGAAAATAAAAATAT
Found at i:12730102 original size:15 final size:15
Alignment explanation
Indices: 12730082--12730131 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
12730072 CCCTGTAATG
*
12730082 ACATTACTTGCAATC
1 ACATTACCTGCAATC
*
12730097 ACATTACCTACAATC
1 ACATTACCTGCAATC
*
12730112 ACATTACCTGTAATC
1 ACATTACCTGCAATC
12730127 ACATT
1 ACATT
12730132 GCATTGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (15 bp):
ACATTACCTGCAATC
Found at i:12732428 original size:46 final size:46
Alignment explanation
Indices: 12732350--12732437 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
12732340 GGAAGAGCGG
* *
12732350 CTGAGAGAAAGAGGGAAAGGAGGCACAACGGTTGAGAGAAAGTCGA
1 CTGAAAGAAAGAGGGAAAGGAGGAACAACGGTTGAGAGAAAGTCGA
* * *
12732396 CTGAAAGAAAGAGGGAGAGGAGGAATAGCGGTTGAGAGAAAG
1 CTGAAAGAAAGAGGGAAAGGAGGAACAACGGTTGAGAGAAAG
12732438 AGGGAAAGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.42, C:0.08, G:0.41, T:0.09
Consensus pattern (46 bp):
CTGAAAGAAAGAGGGAAAGGAGGAACAACGGTTGAGAGAAAGTCGA
Found at i:12732436 original size:31 final size:31
Alignment explanation
Indices: 12732401--12732468 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
12732391 GTCGACTGAA
* *
12732401 AGAAAGAGGGAGAGGAGGAATAGCGGTTGAG
1 AGAAAGAGGGAAAGGAGGAACAGCGGTTGAG
* *
12732432 AGAAAGAGGGAAAGGAGGCACATCGGTTGAG
1 AGAAAGAGGGAAAGGAGGAACAGCGGTTGAG
12732463 AGAAAG
1 AGAAAG
12732469 TCGATTGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.44, T:0.09
Consensus pattern (31 bp):
AGAAAGAGGGAAAGGAGGAACAGCGGTTGAG
Found at i:12732463 original size:77 final size:77
Alignment explanation
Indices: 12732332--12732526 Score: 311
Period size: 77 Copynumber: 2.5 Consensus size: 77
12732322 GTGGAATAGT
*
12732332 GGGA-AGGAGGAAGAGCGGCTGAGAGAAAGAGGGAAAGGAGGCACAACGGTTGAGAGAAAGTCGA
1 GGGAGAGGAGGAATAGCGGCTGAGAGAAAGAGGGAAAGGAGGCACAACGGTTGAGAGAAAGTCGA
12732396 CTGAAAGAAAGA
66 CTGAAAGAAAGA
* *
12732408 GGGAGAGGAGGAATAGCGGTTGAGAGAAAGAGGGAAAGGAGGCACATCGGTTGAGAGAAAGTCGA
1 GGGAGAGGAGGAATAGCGGCTGAGAGAAAGAGGGAAAGGAGGCACAACGGTTGAGAGAAAGTCGA
* *
12732473 TTGAGAGAAAGA
66 CTGAAAGAAAGA
* * *
12732485 AGGAGAGGAGGAATAGCGACTGAGAGAAACAGGGAAAGGAGG
1 GGGAGAGGAGGAATAGCGGCTGAGAGAAAGAGGGAAAGGAGG
12732527 AAGAGTGGCT
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
76 4 0.04
77 105 0.96
ACGTcount: A:0.41, C:0.08, G:0.43, T:0.08
Consensus pattern (77 bp):
GGGAGAGGAGGAATAGCGGCTGAGAGAAAGAGGGAAAGGAGGCACAACGGTTGAGAGAAAGTCGA
CTGAAAGAAAGA
Found at i:12732509 original size:31 final size:31
Alignment explanation
Indices: 12732474--12732577 Score: 136
Period size: 31 Copynumber: 3.4 Consensus size: 31
12732464 GAAAGTCGAT
* * * *
12732474 TGAGAGAAAGAAGGAGAGGAGGAATAGCGAC
1 TGAGAGAAAGAGGGAAAGGAGGAAGAGCGGC
* *
12732505 TGAGAGAAACAGGGAAAGGAGGAAGAGTGGC
1 TGAGAGAAAGAGGGAAAGGAGGAAGAGCGGC
* *
12732536 TGAGAGGAAGAGGGAAAGGAAGAAGAGCGGC
1 TGAGAGAAAGAGGGAAAGGAGGAAGAGCGGC
12732567 TGAGAGAAAGA
1 TGAGAGAAAGA
12732578 TGGTTGAGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.44, C:0.06, G:0.44, T:0.06
Consensus pattern (31 bp):
TGAGAGAAAGAGGGAAAGGAGGAAGAGCGGC
Found at i:12732525 original size:108 final size:108
Alignment explanation
Indices: 12732393--12732638 Score: 305
Period size: 108 Copynumber: 2.3 Consensus size: 108
12732383 GAGAGAAAGT
* * * * * *
12732393 CGACTGAAAGAAAGAGGGAGAGGAGGAATAGCGGTTGAGAGAAAGAGGGAAAGGAGGCACATCGG
1 CGACTGAAAGAAAGAGGGAAAGGAGGAAGAGCGGCTGAGAGAAAGAGGGAAAGGAAGAACAGCGG
* * *
12732458 TTGAGAGAAAG-TCGATTGAGAGAAAGAAGGAGAGGAGGAATAG
66 CTGAGAGAAAGAT-GATTGAGAGAAAGAAGGAAAGGAGGAAGAG
* * * * *
12732501 CGACTGAGAGAAACAGGGAAAGGAGGAAGAGTGGCTGAGAGGAAGAGGGAAAGGAAGAAGAGCGG
1 CGACTGAAAGAAAGAGGGAAAGGAGGAAGAGCGGCTGAGAGAAAGAGGGAAAGGAAGAACAGCGG
* *
12732566 CTGAGAGAAAGATGGTTGAGAGAAAGAAGGAAAGGAGGAGGAG
66 CTGAGAGAAAGATGATTGAGAGAAAGAAGGAAAGGAGGAAGAG
* *
12732609 CGGCAGAAAGAAAGAGGGAAAAGGAGGAAG
1 CGACTGAAAGAAAGAGGG-AAAGGAGGAAG
12732639 TGAGAGAAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
108 104 0.90
109 12 0.10
ACGTcount: A:0.43, C:0.06, G:0.43, T:0.07
Consensus pattern (108 bp):
CGACTGAAAGAAAGAGGGAAAGGAGGAAGAGCGGCTGAGAGAAAGAGGGAAAGGAAGAACAGCGG
CTGAGAGAAAGATGATTGAGAGAAAGAAGGAAAGGAGGAAGAG
Found at i:12732610 original size:46 final size:47
Alignment explanation
Indices: 12732527--12732624 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 47
12732517 GGAAAGGAGG
* * * *
12732527 AAGAGTGGCTGAGAGGAAGAGGGAAAGGAAGAAGAGCGGCTGAGAGA
1 AAGAGTGGCTGAGAGAAAGAAGGAAAGGAAGAAGAGCGGCAGAAAGA
* * *
12732574 AAGA-TGGTTGAGAGAAAGAAGGAAAGGAGGAGGAGCGGCAGAAAGA
1 AAGAGTGGCTGAGAGAAAGAAGGAAAGGAAGAAGAGCGGCAGAAAGA
12732620 AAGAG
1 AAGAG
12732625 GGAAAAGGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 39 0.91
47 4 0.09
ACGTcount: A:0.44, C:0.05, G:0.45, T:0.06
Consensus pattern (47 bp):
AAGAGTGGCTGAGAGAAAGAAGGAAAGGAAGAAGAGCGGCAGAAAGA
Found at i:12760471 original size:2 final size:2
Alignment explanation
Indices: 12760466--12760497 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12760456 CCCCCACCTC
12760466 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12760498 GTTTGCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12763060 original size:19 final size:19
Alignment explanation
Indices: 12762980--12763064 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 19
12762970 TATTTGTTGT
12762980 ATTTTAACAAA-TATATCTATA
1 ATTTTAA-AAATTATAT-T-TA
*
12763001 ATTTTCAATAATTATATTT-
1 ATTTT-AAAAATTATATTTA
* * ** *
12763020 GTTGTAAATGTT-TATTTT
1 ATTTTAAAAATTATATTTA
12763038 ATTTTAAAAATTATATTTA
1 ATTTTAAAAATTATATTTA
12763057 ATTTTAAA
1 ATTTTAAA
12763065 CAGTCACTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 16 0.33
20 1 0.02
21 8 0.16
22 7 0.14
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (19 bp):
ATTTTAAAAATTATATTTA
Found at i:12764253 original size:21 final size:20
Alignment explanation
Indices: 12764224--12764263 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12764214 AAATAAATCA
* *
12764224 TCAATATTATATTAGTATAG
1 TCAATATTACATTAATATAG
12764244 TCAATTATTACATTAATATA
1 TCAA-TATTACATTAATATA
12764264 AATAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
TCAATATTACATTAATATAG
Found at i:12769594 original size:26 final size:26
Alignment explanation
Indices: 12769566--12769653 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
12769556 TTTTGATAGT
*
12769566 AAAATTATCCATCCACTTTTGGTGAT
1 AAAATTATCCATCCACTTTTGGTGAC
*
12769592 AAAATTA-CTTATCCACTTCTT-GTGAC
1 AAAATTATC-CATCCACTT-TTGGTGAC
* **
12769618 AAAATTATCTATTTA-TTTTCGGTGAC
1 AAAATTATCCATCCACTTTT-GGTGAC
12769644 AAAATTATCC
1 AAAATTATCC
12769654 TTAATTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 2 0.04
25 3 0.06
26 44 0.85
27 3 0.06
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (26 bp):
AAAATTATCCATCCACTTTTGGTGAC
Found at i:12769862 original size:56 final size:53
Alignment explanation
Indices: 12769785--12769888 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 53
12769775 TATGAAATGA
* *
12769785 TGTCATATTCACTTCAAGGAA-TGAACGAATTTATAATTTTTTATTAGTAGCTCATT
1 TGTCACATTCACTTCAAGGAATTG-AC--A-TTATAATTTTTTATTAATAGCTCATT
* *
12769841 TGTCACATTCACTTTAGGGAATTGACATTATAATTTTTTATTAATAGC
1 TGTCACATTCACTTCAAGGAATTGACATTATAATTTTTTATTAATAGC
12769889 AAAAGATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
53 20 0.47
54 1 0.02
56 20 0.47
57 2 0.05
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (53 bp):
TGTCACATTCACTTCAAGGAATTGACATTATAATTTTTTATTAATAGCTCATT
Found at i:12771418 original size:21 final size:21
Alignment explanation
Indices: 12771393--12771435 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12771383 AAGTGATTAA
12771393 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAG-TATTTTATGTTAAAT
*
12771414 TTTAAGTATTTTATTTTAAAT
1 TTTAAGTATTTTATGTTAAAT
12771435 T
1 T
12771436 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTAAGTATTTTATGTTAAAT
Found at i:12776744 original size:20 final size:21
Alignment explanation
Indices: 12776706--12776749 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12776696 TATTTATGTG
* *
12776706 AATATGAGAAAATGAATTTGA
1 AATACGAGAAAATGAATTTCA
12776727 AATACGAGAAAATG-ATTTCA
1 AATACGAGAAAATGAATTTCA
12776747 AAT
1 AAT
12776750 TTAATGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (21 bp):
AATACGAGAAAATGAATTTCA
Found at i:12790270 original size:32 final size:33
Alignment explanation
Indices: 12790229--12790336 Score: 112
Period size: 32 Copynumber: 3.2 Consensus size: 33
12790219 AATTAAAATT
* *
12790229 TATATAATATAGATAA-AAAAATTAAAATAAAA
1 TATATAATATAAATAATAAAAATAAAAATAAAA
12790261 TATATAATATCAAAAATTATATTAAAAATAAAAATAAAA
1 TATATAATAT---AAA-TA-A-TAAAAATAAAAATAAAA
* *
12790300 TATATAAGAT-TATAATAAAAATAAAAATAAAA
1 TATATAATATAAATAATAAAAATAAAAATAAAA
12790332 TATAT
1 TATAT
12790337 GACATTAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
32 32 0.49
33 1 0.02
34 2 0.03
35 3 0.05
36 2 0.03
37 1 0.02
39 24 0.37
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (33 bp):
TATATAATATAAATAATAAAAATAAAAATAAAA
Found at i:12790311 original size:27 final size:28
Alignment explanation
Indices: 12790280--12790349 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 28
12790270 TCAAAAATTA
*
12790280 TATTAAAAATAAAAATAAAATATATAAGAT
1 TATTAAAAATAAAAATAAAATATAT-A-AC
*
12790310 TATAATAAAAATAAAAATAAAATATATGAC
1 TAT--TAAAAATAAAAATAAAATATATAAC
12790340 -ATTAAAAATA
1 TATTAAAAATA
12790350 TATTTAATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 8 0.22
29 2 0.06
30 4 0.11
32 22 0.61
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (28 bp):
TATTAAAAATAAAAATAAAATATATAAC
Found at i:12790330 original size:12 final size:12
Alignment explanation
Indices: 12790245--12790331 Score: 57
Period size: 12 Copynumber: 6.8 Consensus size: 12
12790235 ATATAGATAA
*
12790245 AAAAATTAAAAT
1 AAAAATAAAAAT
*
12790257 AAAATATATAATAT
1 AAAA-ATA-AAAAT
* * *
12790271 CAAAAATTATATT
1 -AAAAATAAAAAT
12790284 AAAAATAAAAAT
1 AAAAATAAAAAT
*
12790296 AAAATATATAAGAT
1 AAAA-ATA-AAAAT
* *
12790310 TATAATAAAAAT
1 AAAAATAAAAAT
12790322 AAAAATAAAA
1 AAAAATAAAA
12790332 TATATGACAT
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
12 29 0.53
13 10 0.18
14 12 0.22
15 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:12791417 original size:23 final size:23
Alignment explanation
Indices: 12791389--12791464 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
12791379 TGAACTTTGT
*
12791389 CTTGATCACGAACTTCGCCGTCA
1 CTTGATCACGAACTTCGCCGTCG
**
12791412 CTTGATCACGAACTTCGTTGTCG
1 CTTGATCACGAACTTCGCCGTCG
*
12791435 CTTGATCACGAACTTCGCCTTCG
1 CTTGATCACGAACTTCGCCGTCG
12791458 CTTGATC
1 CTTGATC
12791465 TTCACCCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (23 bp):
CTTGATCACGAACTTCGCCGTCG
Found at i:12792446 original size:33 final size:32
Alignment explanation
Indices: 12792360--12792452 Score: 113
Period size: 28 Copynumber: 3.0 Consensus size: 32
12792350 CATAGGTAAG
*
12792360 AAAATTATAACTTTAAAAGATGTATATTGCAAT
1 AAAATTATAA-TTTAAAAGAAGTATATTGCAAT
* *
12792393 AAAA--CT-ATTT-GAAGAAGTATATTGCAAT
1 AAAATTATAATTTAAAAGAAGTATATTGCAAT
12792421 AAAATTATAATTTTAAAAGAAGTATATTGCAA
1 AAAATTATAA-TTTAAAAGAAGTATATTGCAA
12792453 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 20 0.40
29 3 0.06
30 2 0.04
31 2 0.04
32 3 0.06
33 20 0.40
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.34
Consensus pattern (32 bp):
AAAATTATAATTTAAAAGAAGTATATTGCAAT
Found at i:12808421 original size:29 final size:29
Alignment explanation
Indices: 12808378--12808435 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
12808368 TAAATATTTA
*
12808378 GTATATCTTACTTAGCTACTATGGATATT
1 GTATATCTTACTTAGCTACTATGAATATT
** * *
12808407 GTATATCTTGTTTAGTTACTGTGAATATT
1 GTATATCTTACTTAGCTACTATGAATATT
12808436 ATAAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (29 bp):
GTATATCTTACTTAGCTACTATGAATATT
Found at i:12810067 original size:15 final size:15
Alignment explanation
Indices: 12809996--12810070 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 15
12809986 TCTCCTTCCC
*
12809996 TTTTTGTTTTAATTTT
1 TTTTTATTTT-ATTTT
12810012 TTTATTA-TTTATTTT
1 TTT-TTATTTTATTTT
12810027 TTTCTTATTTTTACTCTTTT
1 TTT-TTA-TTTTA---TTTT
12810047 AGTTTTTATTTTATTTT
1 --TTTTTATTTTATTTT
12810064 TTTTTAT
1 TTTTTAT
12810071 CATTAAGACA
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
15 18 0.37
16 6 0.12
17 10 0.20
20 9 0.18
21 3 0.06
22 3 0.06
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTATTTTATTTT
Found at i:12810648 original size:23 final size:23
Alignment explanation
Indices: 12810618--12810693 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
12810608 TGGACTTTGT
** *
12810618 CTTGATCACGAACTTCATTGTTG
1 CTTGATCACGAACTTCACCGTCG
*
12810641 CTTGATCACGAACTTCGCCGTCG
1 CTTGATCACGAACTTCACCGTCG
12810664 CTTGATCACGAACTTCACCGTCG
1 CTTGATCACGAACTTCACCGTCG
12810687 CTTGATC
1 CTTGATC
12810694 TTCACCTCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (23 bp):
CTTGATCACGAACTTCACCGTCG
Found at i:12821769 original size:2 final size:2
Alignment explanation
Indices: 12821762--12821802 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
12821752 CGAACTCGTC
* *
12821762 TA TA TA TA TA TA TG TA TA TA TT TA TA TA -A TA TA T- 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
12821802 T
1 T
12821803 TTTTAGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:12821789 original size:20 final size:20
Alignment explanation
Indices: 12821762--12821804 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 20
12821752 CGAACTCGTC
12821762 TATATATATATATGTATATATT
1 TATATA-ATATAT-TATATATT
12821784 TATATAATATATTATATATT
1 TATATAATATATTATATATT
12821804 T
1 T
12821805 TTAGGGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATAATATATTATATATT
Found at i:12826807 original size:31 final size:30
Alignment explanation
Indices: 12826763--12826836 Score: 132
Period size: 29 Copynumber: 2.5 Consensus size: 30
12826753 GAGAGAAACT
12826763 AAAAAAAGAAGAGAGATAAGGAAAATGA-A
1 AAAAAAAGAAGAGAGATAAGGAAAATGAGA
12826792 AAAAAAAGAAGAGAGATAAGGAAAATGAGA
1 AAAAAAAGAAGAGAGATAAGGAAAATGAGA
12826822 AAAAAAAGAATGAGA
1 AAAAAAAGAA-GAGA
12826837 AATAGAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 28 0.65
30 11 0.26
31 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (30 bp):
AAAAAAAGAAGAGAGATAAGGAAAATGAGA
Found at i:12827889 original size:35 final size:35
Alignment explanation
Indices: 12827849--12827917 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
12827839 TTTAAATTTA
**
12827849 AATAACAAAAAATTAATATATCAAATAACAACTTG
1 AATAACAAAAAACAAATATATCAAATAACAACTTG
* * *
12827884 AATAACCAAAAACAAATATCTGAAATAACAACTT
1 AATAACAAAAAACAAATATATCAAATAACAACTT
12827918 ATAAGTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.23
Consensus pattern (35 bp):
AATAACAAAAAACAAATATATCAAATAACAACTTG
Found at i:12828446 original size:30 final size:30
Alignment explanation
Indices: 12828412--12828468 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
12828402 ATATTTATTA
*
12828412 ATCATATATTAATAT-TAATATATAATTTTT
1 ATCATATA-AAATATATAATATATAATTTTT
* *
12828442 ATCATTTAAAATATATAATTTATAATT
1 ATCATATAAAATATATAATATATAATT
12828469 ACATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
ATCATATAAAATATATAATATATAATTTTT
Found at i:12828564 original size:17 final size:18
Alignment explanation
Indices: 12828518--12828566 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
12828508 AGTAATATGA
12828518 TATTATTTAAATATAATT
1 TATTATTTAAATATAATT
* * *
12828536 AATAATTT-AATA-ATTT
1 TATTATTTAAATATAATT
12828552 TATTATTTAAATATA
1 TATTATTTAAATATA
12828567 TTATTAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
16 9 0.38
17 8 0.33
18 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATTTAAATATAATT
Found at i:12840885 original size:15 final size:15
Alignment explanation
Indices: 12840865--12840906 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
12840855 CCTAAAAATG
*
12840865 TTTTGGAGGGAATTC
1 TTTTGGAGGGAACTC
12840880 TTTTGGAGGGAACTC
1 TTTTGGAGGGAACTC
12840895 TTTTGGAGGGAA
1 TTTTGGAGGGAA
12840907 ATTGGCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (15 bp):
TTTTGGAGGGAACTC
Found at i:12842456 original size:20 final size:21
Alignment explanation
Indices: 12842431--12842470 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12842421 CAATACCCTC
*
12842431 TTAACTATTTAA-ACCTTTTA
1 TTAACTAGTTAAGACCTTTTA
12842451 TTAACTAGTTAAGACCTTTT
1 TTAACTAGTTAAGACCTTTT
12842471 TATCTGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (21 bp):
TTAACTAGTTAAGACCTTTTA
Found at i:12843061 original size:30 final size:31
Alignment explanation
Indices: 12843027--12843090 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
12843017 AACCAGTAAT
*
12843027 ATTGCATC-ACAATAAATACAAACATAT-TTC
1 ATTGCATCAACAA-AAACACAAACATATATTC
*
12843057 ATTGCATCAACAAACACACAAACATATATTC
1 ATTGCATCAACAAAAACACAAACATATATTC
12843088 ATT
1 ATT
12843091 ACACCTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (31 bp):
ATTGCATCAACAAAAACACAAACATATATTC
Done.