Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 9 of 126
Found at i:2445719 original size:45 final size:45
Alignment explanation
Indices: 2445670--2446023 Score: 532
Period size: 45 Copynumber: 7.9 Consensus size: 45
2445660 TCGGCCATGG
* * * * *
2445670 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
2445715 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATG-TGCGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG-GTCAAA
2445760 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATG-TGCGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG-GTCAAA
*
2445805 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * *
2445850 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
2445895 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * *
2445940 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
2445985 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
2446024 TCCACCTCTT
Statistics
Matches: 280, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
44 2 0.01
45 276 0.99
46 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:2445823 original size:90 final size:90
Alignment explanation
Indices: 2445669--2446023 Score: 597
Period size: 90 Copynumber: 3.9 Consensus size: 90
2445659 TTCGGCCATG
* * *
2445669 GTGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCC
1 GTGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCC
2445734 ATGAATTATGCATGATG-TGCGTCAA
66 ATGAATTATGCATGATGTTG-GTCAA
* * * *
2445759 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATG-TGCGTCAAATGCTTCCTCAAATTCTTC
1 GTGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTG-GTCAAATGCTTCCTCAAATTCTTC
2445823 CATGAATTATGCATGATGTTGGTCAA
65 CATGAATTATGCATGATGTTGGTCAA
*
2445849 GTGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCC
1 GTGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCC
2445914 ATGAATTATGCATGATGTTGGTCAA
66 ATGAATTATGCATGATGTTGGTCAA
*
2445939 GTGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCC
1 GTGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCC
2446004 ATGAATTATGCATGATGTTG
66 ATGAATTATGCATGATGTTG
2446024 TCCACCTCTT
Statistics
Matches: 250, Mismatches: 12, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
89 2 0.01
90 244 0.98
91 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (90 bp):
GTGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCC
ATGAATTATGCATGATGTTGGTCAA
Found at i:2446335 original size:20 final size:20
Alignment explanation
Indices: 2446310--2446364 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2446300 ACGAGTTAAA
* *
2446310 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
2446330 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
2446350 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
2446365 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:2447887 original size:57 final size:59
Alignment explanation
Indices: 2447783--2447925 Score: 164
Period size: 57 Copynumber: 2.4 Consensus size: 59
2447773 CTCATCTTCT
* * * * ** *
2447783 TTTTCTTTCATTTTCATTTTCTCGCTCGCGCTCTTTTTCTTTTTCAATCTCTTTTTC-A
1 TTTTCTTTCATTTTCTTTTTCTCGCTCGCACTCTTGTACAATCTCAATCTCTTTTTCAA
*
2447841 -TTTCTTTCATTTTCTTTTTCTCGCTCGCACTCTTGTACAATCTCAATTTCTTTTTCGAA
1 TTTTCTTTCATTTTCTTTTTCTCGCTCGCACTCTTGTACAATCTCAATCTCTTTTTC-AA
2447900 TTTTTTCTCTTCATTTTCTTTTTCTC
1 --TTTTCT-TTCATTTTCTTTTTCTC
2447926 TCACTTTTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
57 48 0.68
59 1 0.01
62 5 0.07
63 17 0.24
ACGTcount: A:0.10, C:0.25, G:0.05, T:0.59
Consensus pattern (59 bp):
TTTTCTTTCATTTTCTTTTTCTCGCTCGCACTCTTGTACAATCTCAATCTCTTTTTCAA
Found at i:2448987 original size:67 final size:68
Alignment explanation
Indices: 2448877--2449023 Score: 251
Period size: 67 Copynumber: 2.1 Consensus size: 68
2448867 TTCCAGACTC
2448877 TTTTTTTTATACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGC-AAAATTTTTTT
1 TTTTTTTT-TACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGCAAAAATTTTTTT
2448941 TTTA
65 TTTA
*
2448945 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAAAAAAATTTTTT
1 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGC--AAAAATTTTTT
2449010 TTTTA
64 TTTTA
2449015 TTTTTTTTT
1 TTTTTTTTT
2449024 TACAAAACCA
Statistics
Matches: 75, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
67 43 0.57
68 8 0.11
70 24 0.32
ACGTcount: A:0.18, C:0.19, G:0.13, T:0.50
Consensus pattern (68 bp):
TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTAGGCAAAAATTTTTTTT
TTA
Found at i:2449697 original size:45 final size:45
Alignment explanation
Indices: 2449648--2449790 Score: 223
Period size: 45 Copynumber: 3.2 Consensus size: 45
2449638 TCGGCCATGG
* * * * *
2449648 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
2449693 TGCTTCCTTAAATTCTTCCATGAATTATCCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
2449738 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
2449783 TGCTTCCT
1 TGCTTCCT
2449791 TAATTTCAGG
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:2449896 original size:20 final size:20
Alignment explanation
Indices: 2449873--2449919 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2449863 AACTGAGCTT
*
2449873 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
2449893 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
2449913 GAATGAG
1 GAATGAG
2449920 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:2450469 original size:18 final size:19
Alignment explanation
Indices: 2450441--2450480 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
2450431 TATTACAAAA
2450441 TTAATTAAAATTCATTATG
1 TTAATTAAAATTCATTATG
2450460 TTAA-TAAAATTCATTATG
1 TTAATTAAAATTCATTATG
2450478 TTA
1 TTA
2450481 GTAATTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAATTAAAATTCATTATG
Found at i:2456116 original size:20 final size:20
Alignment explanation
Indices: 2456077--2456116 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2456067 TCTTTCTTTA
2456077 ACAGCTTTTAAATCTTCCTTG
1 ACAGCTTTTAAA-CTTCCTTG
2456098 ACAGCTTTTACAA-TTCCTT
1 ACAGCTTTTA-AACTTCCTT
2456117 TATCTTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 10 0.56
22 2 0.11
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (20 bp):
ACAGCTTTTAAACTTCCTTG
Found at i:2456702 original size:18 final size:18
Alignment explanation
Indices: 2456676--2456723 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
2456666 TCCCCAGAAC
*
2456676 TTTCATGGAAATTGAGAT
1 TTTCGTGGAAATTGAGAT
2456694 TTTCGTGGAAAATTGAGAT
1 TTTCGTGG-AAATTGAGAT
*
2456713 TTTCGGGGAAA
1 TTTCGTGGAAA
2456724 ATGGTTAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.35
Consensus pattern (18 bp):
TTTCGTGGAAATTGAGAT
Found at i:2456708 original size:19 final size:19
Alignment explanation
Indices: 2456684--2456725 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2456674 ACTTTCATGG
*
2456684 AAATTGAGATTTTCGTGGA
1 AAATTGAGATTTTCGGGGA
2456703 AAATTGAGATTTTCGGGGA
1 AAATTGAGATTTTCGGGGA
2456722 AAAT
1 AAAT
2456726 GGTTAGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (19 bp):
AAATTGAGATTTTCGGGGA
Found at i:2458792 original size:8 final size:9
Alignment explanation
Indices: 2458769--2458796 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2458759 CCTTTTCCTT
2458769 TCTTTTTCA
1 TCTTTTTCA
2458778 TCTTTTTCA
1 TCTTTTTCA
2458787 TCTTTTTCA
1 TCTTTTTCA
2458796 T
1 T
2458797 TGCCATTCCC
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:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (9 bp):
TCTTTTTCA
Found at i:2459987 original size:9 final size:9
Alignment explanation
Indices: 2459975--2460087 Score: 54
Period size: 10 Copynumber: 12.0 Consensus size: 9
2459965 AAAATTGTAA
2459975 AAAAATTAT
1 AAAAATTAT
2459984 -AAAATATAT
1 AAAAAT-TAT
* *
2459993 AGAAATATAG
1 AAAAAT-TAT
2460003 AAAAATTAT
1 AAAAATTAT
*
2460012 -AAAATTTT
1 AAAAATTAT
*
2460020 ATAAATTCAT
1 AAAAATT-AT
2460030 AAGAAAATTAT
1 -A-AAAATTAT
* *
2460041 AGAAAAATGT
1 A-AAAATTAT
2460051 AAAGAA-TAT
1 AAA-AATTAT
*
2460060 -AAAATTCGT
1 AAAAATT-AT
2460069 AAAAAATTAT
1 -AAAAATTAT
2460079 AAAAATTAT
1 AAAAATTAT
2460088 TGTACCAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
7 2 0.03
8 15 0.19
9 24 0.30
10 25 0.31
11 9 0.11
12 5 0.06
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2460079 original size:19 final size:19
Alignment explanation
Indices: 2460012--2460082 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
2460002 GAAAAATTAT
* *
2460012 AAAATTTTATAAATTCATAA
1 AAAATTATA-AAATTCGTAA
*
2460032 GAAAATTATAGAAAAAT-GTAA
1 -AAAATTAT--AAAATTCGTAA
*
2460053 AGAA-TATAAAATTCGTAA
1 AAAATTATAAAATTCGTAA
2460071 AAAATTATAAAA
1 AAAATTATAAAA
2460083 ATTATTGTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 5 0.12
18 7 0.17
19 10 0.25
20 3 0.08
21 10 0.25
22 4 0.10
23 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.30
Consensus pattern (19 bp):
AAAATTATAAAATTCGTAA
Found at i:2460657 original size:88 final size:87
Alignment explanation
Indices: 2460477--2460676 Score: 199
Period size: 88 Copynumber: 2.3 Consensus size: 87
2460467 TCAAAGGGCC
* * *
2460477 TTTTTGATGTATTTTGACAGTTCAAGTACCCAATTGAATATAAAAAAAAGTAATGAACTTAATTG
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAATATAAAAAAAAGTAATGAACTTAATTG
**** *
2460542 TTTTTTTTTTAAGTTTGAGGGA
66 TTTTTTGAAAAAGTTTAAGGGA
* * * * *
2460564 CTTTTTTATGCATTTTGAAAGTTCAAGTAGCCAATTGAGTGTAAAAAAAAATTAATG-GCTTAAT
1 -TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAATAT-AAAAAAAAGTAATGAACTTAAT
2460628 TGCTTGTTTTGAAAAAGTTTAAGGG-
64 TG-TT-TTTTGAAAAAGTTTAAGGGA
2460653 TTTTTT-TGACATATTTTGAAAGTT
1 TTTTTTATG-C--ATTTTGAAAGTT
2460677 TAAATACTCA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
87 2 0.02
88 50 0.54
89 15 0.16
90 26 0.28
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (87 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAATATAAAAAAAAGTAATGAACTTAATTG
TTTTTTGAAAAAGTTTAAGGGA
Found at i:2461297 original size:12 final size:12
Alignment explanation
Indices: 2461280--2461305 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2461270 TCAAGAAAAC
2461280 AACAACAACAAT
1 AACAACAACAAT
2461292 AACAACAACAAT
1 AACAACAACAAT
2461304 AA
1 AA
2461306 TAGTAATACA
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:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (12 bp):
AACAACAACAAT
Found at i:2464495 original size:18 final size:18
Alignment explanation
Indices: 2464472--2464513 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2464462 GTGTTATTTA
2464472 AAAACGAGTATCATTTTG
1 AAAACGAGTATCATTTTG
*
2464490 AAAACGAGTATCGTTTTG
1 AAAACGAGTATCATTTTG
2464508 AAAACG
1 AAAACG
2464514 CGCCCTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (18 bp):
AAAACGAGTATCATTTTG
Found at i:2465642 original size:8 final size:8
Alignment explanation
Indices: 2465625--2465656 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
2465615 TCACAAATGC
2465625 CGGCTTTT
1 CGGCTTTT
*
2465633 CGGCTATT
1 CGGCTTTT
2465641 CGGCTTTT
1 CGGCTTTT
2465649 CGGCTTTT
1 CGGCTTTT
2465657 GTCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:2469764 original size:19 final size:19
Alignment explanation
Indices: 2469740--2469790 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2469730 AAATTTAGTC
2469740 CTATATTTATTTTATTATT
1 CTATATTTATTTTATTATT
*
2469759 CTATATATATTTTATTATT
1 CTATATTTATTTTATTATT
* *
2469778 -TGTTTTTATTTTA
1 CTATATTTATTTTA
2469791 ATTTTACTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
CTATATTTATTTTATTATT
Found at i:2469895 original size:21 final size:21
Alignment explanation
Indices: 2469871--2469935 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
2469861 TTCTCTCATA
2469871 ATTATTATTTTTATATATATT
1 ATTATTATTTTTATATATATT
*
2469892 ATTA-TATTTTTACATATATT
1 ATTATTATTTTTATATATATT
* *
2469912 ATATATT-TATTTATACATATT
1 AT-TATTATTTTTATATATATT
2469933 ATT
1 ATT
2469936 TTTACATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 18 0.47
21 19 0.50
22 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTATTTTTATATATATT
Found at i:2469916 original size:19 final size:18
Alignment explanation
Indices: 2469867--2469945 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 18
2469857 TTAATTCTCT
2469867 CATA-ATTATTATTTTTA
1 CATATATTATTATTTTTA
*
2469884 TATATATTATTATATTTTTA
1 CATATATTA-T-TATTTTTA
2469904 CATATATTATATATTTATT-
1 CATATATTAT-TATTT-TTA
* *
2469923 TATACA-TATTATTTTTA
1 CATATATTATTATTTTTA
2469940 CATATA
1 CATATA
2469946 AATTTTCATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.04
17 12 0.24
18 7 0.14
19 12 0.24
20 18 0.35
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
CATATATTATTATTTTTA
Found at i:2469928 original size:23 final size:24
Alignment explanation
Indices: 2469882--2469931 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
2469872 TTATTATTTT
*
2469882 TATATATATTATTATATTTTTACA
1 TATATATATTATTATATTTATACA
2469906 TATAT-TATATATT-TATTTATACA
1 TATATATAT-TATTATATTTATACA
2469929 TAT
1 TAT
2469932 TATTTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATATATTATTATATTTATACA
Found at i:2474158 original size:15 final size:15
Alignment explanation
Indices: 2474124--2474171 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2474114 ATATTCTTTA
2474124 TGCAT-TCATGCATT
1 TGCATCTCATGCATT
2474138 TGCATCTCATGGCATT
1 TGCATCTCAT-GCATT
*
2474154 T-CATCACAT-CATT
1 TGCATCTCATGCATT
2474167 TGCAT
1 TGCAT
2474172 TCAAAGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.17
14 8 0.27
15 11 0.37
16 6 0.20
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (15 bp):
TGCATCTCATGCATT
Found at i:2478507 original size:47 final size:47
Alignment explanation
Indices: 2478429--2479443 Score: 1861
Period size: 47 Copynumber: 21.6 Consensus size: 47
2478419 CCCTTCGGGA
* * * * * * *
2478429 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
2478476 CCTGTCACATATATACACTTTCACATTCATCACATCGG-TCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCT-ATTAGGC
*
2478523 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478570 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478617 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478664 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478711 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478758 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478805 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478852 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478899 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478946 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2478993 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2479040 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2479087 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2479134 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2479181 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2479228 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
2479275 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
2479322 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
2479369 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
2479418 CTTATCACATACATACACTTTCACAT
1 CTTATCACATATATACACTTTCACAT
2479444 CACAATTATC
Statistics
Matches: 947, Mismatches: 17, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
47 901 0.95
48 1 0.00
49 45 0.05
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:2478508 original size:25 final size:25
Alignment explanation
Indices: 2478480--2478557 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
2478470 CTCGGCCCTG
2478480 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
*** *** *
2478505 TCACATCGGT-CA-TTAGGC-CTCA
1 TCACATATATACACTTTCACATTCA
2478527 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
2478552 TCACAT
1 TCACAT
2478558 CGGCTATTAG
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 10 0.28
23 5 0.14
24 5 0.14
25 16 0.44
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:2485774 original size:11 final size:11
Alignment explanation
Indices: 2485758--2485784 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2485748 AGATGTTTCA
2485758 AAAAAAAAGAG
1 AAAAAAAAGAG
2485769 AAAAAAAAGAG
1 AAAAAAAAGAG
2485780 AAAAA
1 AAAAA
2485785 TAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:2485789 original size:15 final size:15
Alignment explanation
Indices: 2485770--2485808 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
2485760 AAAAAAGAGA
*
2485770 AAAAAAAGAGAAAAAT
1 AAAAAAATA-AAAAAT
2485786 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
2485801 AAAAAAAT
1 AAAAAAAT
2485809 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:2485791 original size:8 final size:8
Alignment explanation
Indices: 2485770--2485808 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2485760 AAAAAAGAGA
*
2485770 AAAAAAAG
1 AAAAAAAT
*
2485778 AGAAAAAT
1 AAAAAAAT
2485786 AAAAAAAT
1 AAAAAAAT
2485794 -AAAAAAT
1 AAAAAAAT
2485801 AAAAAAAT
1 AAAAAAAT
2485809 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2485862 original size:98 final size:98
Alignment explanation
Indices: 2485711--2486041 Score: 644
Period size: 98 Copynumber: 3.4 Consensus size: 98
2485701 GTCTAAGAAG
* *
2485711 GGAGAGTCTAAGGTGAAAACCCGCAAAGGGCGCCTTGAGATGTTTCAAAAAAAAAGAGAAAAAAA
1 GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGATGTTTCAAAAAAAAAGAGAAAAAAA
2485776 AGAGAAAAATAAAAAAATAAAAAATAAAAAAAT
66 AGAGAAAAATAAAAAAATAAAAAATAAAAAAAT
2485809 GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGATGTTTCAAAAAAAAAGAGAAAAAAA
1 GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGATGTTTCAAAAAAAAAGAGAAAAAAA
2485874 AGAGAAAAATAAAAAAATAAAAAATAAAAAAAT
66 AGAGAAAAATAAAAAAATAAAAAATAAAAAAAT
2485907 GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGATGTTTCAAAAAAAAAGAGAAAAAAA
1 GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGATGTTTCAAAAAAAAAGAGAAAAAAA
2485972 AGAGAAAAATAAAAAAATAAAAAATAAAAAAAT
66 AGAGAAAAATAAAAAAATAAAAAATAAAAAAAT
2486005 GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTG
1 GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTG
2486042 TGACCAAAGG
Statistics
Matches: 231, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 231 1.00
ACGTcount: A:0.55, C:0.11, G:0.22, T:0.11
Consensus pattern (98 bp):
GGAGAGGCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGATGTTTCAAAAAAAAAGAGAAAAAAA
AGAGAAAAATAAAAAAATAAAAAATAAAAAAAT
Found at i:2485872 original size:11 final size:11
Alignment explanation
Indices: 2485856--2485882 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2485846 AGATGTTTCA
2485856 AAAAAAAAGAG
1 AAAAAAAAGAG
2485867 AAAAAAAAGAG
1 AAAAAAAAGAG
2485878 AAAAA
1 AAAAA
2485883 TAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:2485887 original size:15 final size:15
Alignment explanation
Indices: 2485868--2485906 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
2485858 AAAAAAGAGA
*
2485868 AAAAAAAGAGAAAAAT
1 AAAAAAATA-AAAAAT
2485884 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
2485899 AAAAAAAT
1 AAAAAAAT
2485907 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:2485889 original size:8 final size:8
Alignment explanation
Indices: 2485868--2485906 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2485858 AAAAAAGAGA
*
2485868 AAAAAAAG
1 AAAAAAAT
*
2485876 AGAAAAAT
1 AAAAAAAT
2485884 AAAAAAAT
1 AAAAAAAT
2485892 -AAAAAAT
1 AAAAAAAT
2485899 AAAAAAAT
1 AAAAAAAT
2485907 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2485970 original size:11 final size:11
Alignment explanation
Indices: 2485954--2485980 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2485944 AGATGTTTCA
2485954 AAAAAAAAGAG
1 AAAAAAAAGAG
2485965 AAAAAAAAGAG
1 AAAAAAAAGAG
2485976 AAAAA
1 AAAAA
2485981 TAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:2485985 original size:15 final size:15
Alignment explanation
Indices: 2485966--2486004 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
2485956 AAAAAAGAGA
*
2485966 AAAAAAAGAGAAAAAT
1 AAAAAAATA-AAAAAT
2485982 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
2485997 AAAAAAAT
1 AAAAAAAT
2486005 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:2485987 original size:8 final size:8
Alignment explanation
Indices: 2485966--2486004 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2485956 AAAAAAGAGA
*
2485966 AAAAAAAG
1 AAAAAAAT
*
2485974 AGAAAAAT
1 AAAAAAAT
2485982 AAAAAAAT
1 AAAAAAAT
2485990 -AAAAAAT
1 AAAAAAAT
2485997 AAAAAAAT
1 AAAAAAAT
2486005 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2487034 original size:119 final size:119
Alignment explanation
Indices: 2486854--2487641 Score: 1423
Period size: 119 Copynumber: 6.6 Consensus size: 119
2486844 AAGAAAATCT
*
2486854 AAGATGATTTGGTATTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
1 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
* * *
2486919 ACGTTCTGAGATATAGCGGATTTAACCTTCAGATGTTTATACTGAAGCAGATCC
66 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
*
2486973 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGTAGATTTGACTCTCAG
1 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
2487038 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
66 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
*
2487092 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCCCAG
1 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
* *
2487157 ACGTTCTCAAATATAGCATATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
66 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
*
2487211 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGTAGATTTGACTCTCAG
1 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
2487276 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
66 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
*
2487330 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGTAGATTTGACTCTCAG
1 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
2487395 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
66 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
* *
2487449 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGGTTTGATTCTCAG
1 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
2487514 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
66 ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
* * * *
2487568 AAGATGATTTGGTATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGAGTGGACTCTCAG
1 AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
*
2487633 ATGTTCTCA
66 ACGTTCTCA
2487642 AACAAACTCA
Statistics
Matches: 646, Mismatches: 23, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 646 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (119 bp):
AAGATGATTTGGTGTTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAG
ACGTTCTCAGATATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCC
Found at i:2487669 original size:83 final size:83
Alignment explanation
Indices: 2487567--2487846 Score: 305
Period size: 83 Copynumber: 3.5 Consensus size: 83
2487557 GAAGCAGATC
* *
2487567 CAAGATGATTTGGTATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGAGTGGACTCTCA
1 CAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGATTGGACTCTCA
2487632 GATGTTCTCAAACAAACT
66 GATGTTCTCAAACAAACT
* *
2487650 CAAGATGATTTGGCATTC-T-TG----C----AACAAATCGAAGACATGGCAGATTGGACTCTCA
1 CAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGATTGGACTCTCA
2487705 GATGTTCTCAAACAAACT
66 GATGTTCTCAAACAAACT
* * * * *
2487723 CAAGATGATTTGGCATTCTTGTGTTCATAAGAAACAAATCAAGGACGTAGCAGATTTGG-CTTTC
1 CAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGA-TTGGACTCTC
* *
2487787 AAATGTTCTCAAACAGAC-
65 AGATGTTCTCAAACAAACT
* * * * * *
2487805 CTAAGATGGTTTGGCATCCTTATGCTTACAAGGAGCAAATCG
1 C-AAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCG
2487847 GAGACGTAGC
Statistics
Matches: 164, Mismatches: 21, Indels: 24
0.78 0.10 0.11
Matches are distributed among these distances:
73 66 0.40
74 1 0.01
75 2 0.01
77 1 0.01
81 2 0.01
82 2 0.01
83 86 0.52
84 4 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (83 bp):
CAAGATGATTTGGCATTCTTGTGTTTACAAGAAACAAATCGAGGACATAGCAGATTGGACTCTCA
GATGTTCTCAAACAAACT
Found at i:2487718 original size:73 final size:73
Alignment explanation
Indices: 2487599--2487743 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
2487589 GTTTACAAGA
*
2487599 AACAAATCGAGGACATAGCAGAGTGGACTCTCAGATGTTCTCAAACAAACTCAAGATGATTTGGC
1 AACAAATCGAAGACATAGCAGAGTGGACTCTCAGATGTTCTCAAACAAACTCAAGATGATTTGGC
2487664 ATTCTTGC
66 ATTCTTGC
* *
2487672 AACAAATCGAAGACATGGCAGATTGGACTCTCAGATGTTCTCAAACAAACTCAAGATGATTTGGC
1 AACAAATCGAAGACATAGCAGAGTGGACTCTCAGATGTTCTCAAACAAACTCAAGATGATTTGGC
2487737 ATTCTTG
66 ATTCTTG
2487744 TGTTCATAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (73 bp):
AACAAATCGAAGACATAGCAGAGTGGACTCTCAGATGTTCTCAAACAAACTCAAGATGATTTGGC
ATTCTTGC
Found at i:2487853 original size:83 final size:83
Alignment explanation
Indices: 2487672--2487870 Score: 217
Period size: 83 Copynumber: 2.4 Consensus size: 83
2487662 GCATTCTTGC
* * * *
2487672 AACAAATCGAAGACATGGCAGA-TTGGACTCTCAGATGTTCTCAAACAAACTCAAGATGATTTGG
1 AACAAATCGAAGACGTAGCAGATTTGG-CTTTCAAATGTTCTCAAACAAACTCAAGATGATTTGG
* * *
2487736 CATTCTTGTGTTCATAAGA
65 CATCCTTATGTTCACAAGA
* *
2487755 AACAAATC-AAGGACGTAGCAGATTTGGCTTTCAAATGTTCTCAAACAGAC-CTAAGATGGTTTG
1 AACAAATCGAA-GACGTAGCAGATTTGGCTTTCAAATGTTCTCAAACAAACTC-AAGATGATTTG
*
2487818 GCATCCTTATGCTT-ACAAGG
64 GCATCCTTATG-TTCACAAGA
* * *
2487838 AGCAAATCGGAGACGTAGCTGATTTGGCTTTCA
1 AACAAATCGAAGACGTAGCAGATTTGGCTTTCA
2487871 CTTTCTTATG
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
82 3 0.03
83 88 0.90
84 7 0.07
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (83 bp):
AACAAATCGAAGACGTAGCAGATTTGGCTTTCAAATGTTCTCAAACAAACTCAAGATGATTTGGC
ATCCTTATGTTCACAAGA
Found at i:2489524 original size:19 final size:19
Alignment explanation
Indices: 2489500--2489550 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2489490 AAATTTAGTC
2489500 CTATATTTATTTTATTATT
1 CTATATTTATTTTATTATT
*
2489519 CTATATATATTTTATTATT
1 CTATATTTATTTTATTATT
* *
2489538 -TGTTTTTATTTTA
1 CTATATTTATTTTA
2489551 ATTTTACTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
CTATATTTATTTTATTATT
Found at i:2489655 original size:21 final size:21
Alignment explanation
Indices: 2489631--2489695 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
2489621 TTCTCTCATA
2489631 ATTATTATTTTTATATATATT
1 ATTATTATTTTTATATATATT
*
2489652 ATTA-TATTTTTACATATATT
1 ATTATTATTTTTATATATATT
* *
2489672 ATATATT-TATTTATACATATT
1 AT-TATTATTTTTATATATATT
2489693 ATT
1 ATT
2489696 TTTACATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 18 0.47
21 19 0.50
22 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTATTTTTATATATATT
Found at i:2489676 original size:19 final size:18
Alignment explanation
Indices: 2489627--2489705 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 18
2489617 TTAATTCTCT
2489627 CATA-ATTATTATTTTTA
1 CATATATTATTATTTTTA
*
2489644 TATATATTATTATATTTTTA
1 CATATATTA-T-TATTTTTA
2489664 CATATATTATATATTTATT-
1 CATATATTAT-TATTT-TTA
* *
2489683 TATACA-TATTATTTTTA
1 CATATATTATTATTTTTA
2489700 CATATA
1 CATATA
2489706 AATTTTCATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.04
17 12 0.24
18 7 0.14
19 12 0.24
20 18 0.35
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
CATATATTATTATTTTTA
Found at i:2489688 original size:23 final size:24
Alignment explanation
Indices: 2489642--2489691 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
2489632 TTATTATTTT
*
2489642 TATATATATTATTATATTTTTACA
1 TATATATATTATTATATTTATACA
2489666 TATAT-TATATATT-TATTTATACA
1 TATATATAT-TATTATATTTATACA
2489689 TAT
1 TAT
2489692 TATTTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATATATTATTATATTTATACA
Found at i:2490074 original size:7 final size:7
Alignment explanation
Indices: 2490062--2490087 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2490052 ATATTCTTGT
2490062 TATTATA
1 TATTATA
2490069 TATTATA
1 TATTATA
2490076 TATTATA
1 TATTATA
2490083 TATTA
1 TATTA
2490088 AATACTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTATA
Found at i:2494091 original size:5 final size:5
Alignment explanation
Indices: 2494083--2494111 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2494073 GAGATGAGAT
2494083 AAAAG AAAAG AAAAG -AAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
2494112 TAGAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2494121 original size:14 final size:14
Alignment explanation
Indices: 2494084--2494111 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2494074 AGATGAGATA
2494084 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
2494098 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
2494112 TAGAAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:2495519 original size:14 final size:14
Alignment explanation
Indices: 2495500--2495526 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2495490 AGAAAAGGTT
2495500 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
2495514 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
2495527 AAGTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:2497344 original size:14 final size:14
Alignment explanation
Indices: 2497325--2497352 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2497315 CAAAAATAAA
2497325 TAAATAATTAAAAC
1 TAAATAATTAAAAC
2497339 TAAATAATTAAAAC
1 TAAATAATTAAAAC
2497353 AGTCCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAATAATTAAAAC
Found at i:2498668 original size:52 final size:52
Alignment explanation
Indices: 2498532--2498679 Score: 172
Period size: 52 Copynumber: 2.8 Consensus size: 52
2498522 GCCTTTTAGC
* * * * *
2498532 TTCAAATTATTATATATATTATTTATTTTAAACTATTTTGTACACTATTTAT
1 TTCAAATTTTTATATATATTATTTATTTTAAATTGTTTTATATACTATTTAT
* * * **
2498584 TTTAAATTGTTT-TATATACTATTTATTTTAAATTGTCTTATATGTTATTTAT
1 TTCAAATT-TTTATATATATTATTTATTTTAAATTGTTTTATATACTATTTAT
* *
2498636 TTCAAATTTTTATATATATTGTTTATTTTAAATGGTTTTATATA
1 TTCAAATTTTTATATATATTATTTATTTTAAATTGTTTTATATA
2498680 TTTGATTTGA
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
51 3 0.04
52 73 0.94
53 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (52 bp):
TTCAAATTTTTATATATATTATTTATTTTAAATTGTTTTATATACTATTTAT
Found at i:2498677 original size:26 final size:25
Alignment explanation
Indices: 2498544--2498681 Score: 141
Period size: 26 Copynumber: 5.3 Consensus size: 25
2498534 CAAATTATTA
*
2498544 TATATATTATTTATTTTAAACTATTT
1 TATATATTATTTATTTTAAA-TGTTT
* * *
2498570 TGTACACTATTTATTTTAAATTGTTT
1 TATATATTATTTATTTTAAA-TGTTT
* *
2498596 TATATACTATTTATTTTAAATTGTCT
1 TATATATTATTTATTTTAAA-TGTTT
* * *
2498622 TATATGTTATTTATTTCAAATTTTT
1 TATATATTATTTATTTTAAATGTTT
*
2498647 ATATATATTGTTTATTTTAAATGGTTT
1 -TATATATTATTTATTTTAAAT-GTTT
2498674 TATATATT
1 TATATATT
2498682 TGATTTGATT
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
25 3 0.03
26 87 0.94
27 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.60
Consensus pattern (25 bp):
TATATATTATTTATTTTAAATGTTT
Found at i:2500050 original size:19 final size:19
Alignment explanation
Indices: 2500023--2500067 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2500013 AATAAGTACG
*
2500023 ATAATAAAT-ATAATGATAT
1 ATAAAAAATGATAAT-ATAT
*
2500042 ATAAAAAATGATACTATAT
1 ATAAAAAATGATAATATAT
2500061 ATAAAAA
1 ATAAAAA
2500068 GGTATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
ATAAAAAATGATAATATAT
Found at i:2500077 original size:18 final size:17
Alignment explanation
Indices: 2500038--2500081 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2500028 AAATATAATG
*
2500038 ATATATA-AAAAATGAT
1 ATATATATAAAAAGGAT
2500054 ACTATATATAAAAAGGTAT
1 A-TATATATAAAAAGG-AT
2500073 ATATATATA
1 ATATATATA
2500082 CATGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.04
17 6 0.25
18 14 0.58
19 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (17 bp):
ATATATATAAAAAGGAT
Found at i:2501952 original size:3 final size:3
Alignment explanation
Indices: 2501944--2501975 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2501934 TTTTAAAACT
2501944 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2501976 TAAACTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2505330 original size:154 final size:152
Alignment explanation
Indices: 2505052--2505353 Score: 448
Period size: 154 Copynumber: 2.0 Consensus size: 152
2505042 GCATTTTGTG
* * * *
2505052 GGATTTTTACTATAATAATATTGAAAAAAAAGTTAAATAGGCTTCCTTTAAAATTATATATAAAA
1 GGATTTTTACTATAATAATATTGAAAAAAAAATAAAATAGGCTTCCTTCAAAATTATATAGAAAA
* * * * *
2505117 TAGATTATTCCAAGTGATGGAGGGTGGTACATAGGCGGTACCATCTTCAATTTTTTGACATCTAT
66 TAGACTATTCCAAGTGATAGAGGGTGGTACATAGGCGGTACCACCTTCAATTTTCTGACATCTAC
2505182 AGGTAAAAAAAACAATAGGTCA
131 AGGTAAAAAAAACAATAGGTCA
2505204 GGATTTTTACTATAATAATATT-AAAAAGAAAATCAAAATAGG-TTGCCTTCAAAATTATATACG
1 GGATTTTTACTATAATAATATTGAAAAA-AAAAT-AAAATAGGCTT-CCTTCAAAATTATATA-G
*
2505267 AAAATAGACTATTCCAAGTGATAGAGGGTGGTGCATAGGCGGTACCACCCTT-AATTTTCTGACA
62 AAAATAGACTATTCCAAGTGATAGAGGGTGGTACATAGGCGGTACCA-CCTTCAATTTTCTGACA
2505331 TCTACAGGTAAAAAAAACAATAG
126 TCTACAGGTAAAAAAAACAATAG
2505354 ATTAAAAAAT
Statistics
Matches: 135, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
151 5 0.04
152 28 0.21
153 22 0.16
154 77 0.57
155 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (152 bp):
GGATTTTTACTATAATAATATTGAAAAAAAAATAAAATAGGCTTCCTTCAAAATTATATAGAAAA
TAGACTATTCCAAGTGATAGAGGGTGGTACATAGGCGGTACCACCTTCAATTTTCTGACATCTAC
AGGTAAAAAAAACAATAGGTCA
Found at i:2505568 original size:6 final size:6
Alignment explanation
Indices: 2505547--2505611 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
2505537 GTGTGTGAGT
* * * * *
2505547 GAAGGA GAA-GA AAAGGG GAAGGA GAA-GA GAAGAA GAAGAA GAAGAA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
* *
2505593 GAAGGA GGAGGA GGAGGA G
1 GAAGGA GAAGGA GAAGGA G
2505612 GCGACATTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
5 9 0.18
6 41 0.82
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:2505569 original size:17 final size:17
Alignment explanation
Indices: 2505547--2505605 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
2505537 GTGTGTGAGT
*
2505547 GAAGGAGAAGAAAAGGG
1 GAAGGAGAAGAAAAGGA
* *
2505564 GAAGGAGAAGAGAAGAA
1 GAAGGAGAAGAAAAGGA
*
2505581 GAAGAAGAAGAAGAAGGA
1 GAAGGAGAAGAA-AAGGA
*
2505599 GGAGGAG
1 GAAGGAG
2505606 GAGGAGGCGA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (17 bp):
GAAGGAGAAGAAAAGGA
Found at i:2505582 original size:3 final size:3
Alignment explanation
Indices: 2505564--2505596 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2505554 AAGAAAAGGG
*
2505564 GAA GGA GAA G-A GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2505597 GAGGAGGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2505652 original size:20 final size:20
Alignment explanation
Indices: 2505627--2505671 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2505617 ATTGGTGAGG
2505627 GAAGAAAAAAAGAAAAAGAA
1 GAAGAAAAAAAGAAAAAGAA
* **
2505647 GAAGAAAAAGAGAAGGAGAA
1 GAAGAAAAAAAGAAAAAGAA
2505667 GAAGA
1 GAAGA
2505672 GGGAGGGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
GAAGAAAAAAAGAAAAAGAA
Found at i:2505733 original size:27 final size:27
Alignment explanation
Indices: 2505702--2505757 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2505692 TAAATTTCTT
2505702 TTTAAGAAAAT-AATT-TTTAGTTGTTAA
1 TTTAAGAAAATAAATTATTTA-TT-TTAA
*
2505729 TTTAAGGAAATAAATTATTTATTTTAA
1 TTTAAGAAAATAAATTATTTATTTTAA
2505756 TT
1 TT
2505758 GTTATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 16 0.62
28 6 0.23
29 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (27 bp):
TTTAAGAAAATAAATTATTTATTTTAA
Found at i:2506531 original size:153 final size:153
Alignment explanation
Indices: 2506218--2506704 Score: 734
Period size: 148 Copynumber: 3.2 Consensus size: 153
2506208 AAAATAATAT
* *
2506218 AAAAATAAAATCCAAAAATAAAAAAATAAAAAAATAAGAACAAATGGCCAAAACCAGAGTTTTTT
1 AAAAATAAAATCCAAAAAT---AAAAT-AAATAATAAAAACAAATGGCCAAAACCAGAGTTTTTT
* * *
2506283 AATAAATTAATATAAAAATACTAAAATAATACATTTAAAACATTATATACTAAAATAATAT-AAA
62 ACTAAATTAATATAAAAATACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAA
* ** *
2506347 AATAAAATACGAAAATAGGGTACTTTA
127 AATAAAATAAGAAAATAGTATATTTTA
*
2506374 AAAAATAAAATCCAAAAATAGAATAAATAATAAAAACAAATGGCCAAAACCAGAGTTTTTTACTA
1 AAAAATAAAATCCAAAAATAAAATAAATAATAAAAACAAATGGCCAAAACCAGAGTTTTTTACTA
2506439 AATTAATATAAAAAATACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAT
66 AATTAATAT-AAAAATACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAT
2506504 AAAATAAGAAAATAGTATATTTTA
130 AAAATAAGAAAATAGTATATTTTA
* * * * **
2506528 AAAAATAAAATTCGAAAATAAAAT---TAAAAAAAACAAACGGCCAAAATTAGAGTTTTTTACTA
1 AAAAATAAAATCCAAAAATAAAATAAATAATAAAAACAAATGGCCAAAACCAGAGTTTTTTACTA
2506590 AATTAATATAAAAA-ACTAAAATAATACATTTGAAACATTA-GTACTAAAATAATATAAAAAATA
66 AATTAATATAAAAATACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATA
2506653 AAATAAGAAAATAGTATATTTTA
131 AAATAAGAAAATAGTATATTTTA
*
2506676 AAAAATAAAATCCGAAAATAAAATAAATA
1 AAAAATAAAATCCAAAAATAAAATAAATA
2506705 CCAAAATATA
Statistics
Matches: 308, Mismatches: 18, Indels: 15
0.90 0.05 0.04
Matches are distributed among these distances:
148 69 0.22
149 26 0.08
150 5 0.02
151 45 0.15
152 47 0.15
153 50 0.16
154 47 0.15
156 19 0.06
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.26
Consensus pattern (153 bp):
AAAAATAAAATCCAAAAATAAAATAAATAATAAAAACAAATGGCCAAAACCAGAGTTTTTTACTA
AATTAATATAAAAATACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATA
AAATAAGAAAATAGTATATTTTA
Found at i:2506558 original size:13 final size:13
Alignment explanation
Indices: 2506525--2506558 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2506515 ATAGTATATT
2506525 TTAAAAAATAAAA
1 TTAAAAAATAAAA
**
2506538 TTCGAAAATAAAA
1 TTAAAAAATAAAA
2506551 TTAAAAAA
1 TTAAAAAA
2506559 AACAAACGGC
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (13 bp):
TTAAAAAATAAAA
Found at i:2506663 original size:25 final size:25
Alignment explanation
Indices: 2506635--2506702 Score: 64
Period size: 30 Copynumber: 2.5 Consensus size: 25
2506625 CATTAGTACT
2506635 AAAATAATATAAAAAATAAAATAAG
1 AAAATAATATAAAAAATAAAATAAG
**
2506660 AAAATAGTATATTTTAAAAAATAAAATCCG
1 AAAATA--ATA---TAAAAAATAAAATAAG
*
2506690 AAAATAAAATAAA
1 AAAATAATATAAA
2506703 TACCAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
25 10 0.29
27 3 0.09
28 2 0.06
30 20 0.57
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (25 bp):
AAAATAATATAAAAAATAAAATAAG
Found at i:2521757 original size:20 final size:20
Alignment explanation
Indices: 2521718--2521773 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
2521708 TTAAATTTAC
*
2521718 ATAAAAAATTAAAATGATTAAA
1 ATAAAATATTAAAA--ATTAAA
* *
2521740 ATAAAATTTTAAAAATTAAT
1 ATAAAATATTAAAAATTAAA
*
2521760 TTAAAATATTAAAA
1 ATAAAATATTAAAA
2521774 TTTTATACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
22 12 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAAAATATTAAAAATTAAA
Found at i:2529049 original size:14 final size:15
Alignment explanation
Indices: 2529030--2529058 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2529020 TCCATCCAAT
2529030 ATAGTTTAT-ATCAA
1 ATAGTTTATGATCAA
2529044 ATAGTTTATGATCAA
1 ATAGTTTATGATCAA
2529059 GTTCAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (15 bp):
ATAGTTTATGATCAA
Found at i:2532023 original size:25 final size:25
Alignment explanation
Indices: 2531991--2532145 Score: 99
Period size: 25 Copynumber: 6.4 Consensus size: 25
2531981 GCTCTTTCAT
*
2531991 GAGCTTCCTGATTAATGGCTCTCTA
1 GAGCTTCCCGATTAATGGCTCTCTA
* *
2532016 GAGCTTCCCGA-T-ATGGCTCGCTT
1 GAGCTTCCCGATTAATGGCTCTCTA
* * * *
2532039 GAACTTCTCGA-TATATGGCTATCCA
1 GAGCTTCCCGATTA-ATGGCTCTCTA
* * *
2532064 GAGCTTCCCGATTAATGGCTTTTTG
1 GAGCTTCCCGATTAATGGCTCTCTA
* * *
2532089 GAGCTACCCG-TTATTGGCTCGC-A
1 GAGCTTCCCGATTAATGGCTCTCTA
* *
2532112 TGAGCTTCCTGATT-ATAGCTCT-TA
1 -GAGCTTCCCGATTAATGGCTCTCTA
2532136 TGAGCTTCCC
1 -GAGCTTCCC
2532146 TTTATATGGC
Statistics
Matches: 97, Mismatches: 27, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
23 19 0.20
24 32 0.33
25 44 0.45
26 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTCTA
Found at i:2532045 original size:23 final size:23
Alignment explanation
Indices: 2532005--2532052 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2531995 TTCCTGATTA
* *
2532005 ATGGCTCTCTAGAGCTTCCCGAT
1 ATGGCTCGCTAGAACTTCCCGAT
* *
2532028 ATGGCTCGCTTGAACTTCTCGAT
1 ATGGCTCGCTAGAACTTCCCGAT
2532051 AT
1 AT
2532053 ATGGCTATCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (23 bp):
ATGGCTCGCTAGAACTTCCCGAT
Found at i:2532141 original size:73 final size:73
Alignment explanation
Indices: 2531968--2532145 Score: 175
Period size: 73 Copynumber: 2.4 Consensus size: 73
2531958 TCTTCGTGAG
* * *
2531968 CTTCTCGATA-AAAGCTCTTTCATGAGCTTCCTGATTAATGGCTCTCTAGAGCTTCCCGATATGG
1 CTTCTCGATATATAGCTC-TT-ATGAGCTTCCCGATTAATGGCTCTCTAGAGCTACCCGATATGG
*
2532032 CTCGCTTGAA
64 CTCGCATGAA
* * * * * * *
2532042 CTTCTCGATATATGGCTATCCA-GAGCTTCCCGATTAATGGCTTTTTGGAGCTACCCGTTATTGG
1 CTTCTCGATATATAGCTCT-TATGAGCTTCCCGATTAATGGCTCTCTAGAGCTACCCGATA-TGG
*
2532106 CTCGCATGAG
64 CTCGCATGAA
2532116 CTTC-CTGAT-TATAGCTCTTATGAGCTTCCC
1 CTTCTC-GATATATAGCTCTTATGAGCTTCCC
2532146 TTTATATGGC
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
72 1 0.01
73 49 0.58
74 30 0.36
75 4 0.05
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (73 bp):
CTTCTCGATATATAGCTCTTATGAGCTTCCCGATTAATGGCTCTCTAGAGCTACCCGATATGGCT
CGCATGAA
Found at i:2538685 original size:21 final size:21
Alignment explanation
Indices: 2538659--2538710 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
2538649 TTTTGACCTG
2538659 CCACACGGCCTAGGCATATTT
1 CCACACGGCCTAGGCATATTT
2538680 CCACACGGCCTAGGCATATTT
1 CCACACGGCCTAGGCATATTT
2538701 CCACACGGCC
1 CCACACGGCC
2538711 AGAGCACACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.19
Consensus pattern (21 bp):
CCACACGGCCTAGGCATATTT
Found at i:2541774 original size:5 final size:5
Alignment explanation
Indices: 2541764--2541797 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
2541754 AAGTAAATAT
2541764 TATTA TATTA TATTA TATTA TATTA TATTA -ATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA
2541798 AATAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:2542002 original size:11 final size:12
Alignment explanation
Indices: 2541979--2542008 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2541969 ATAAATAAAC
2541979 AAAAGAAACAAA
1 AAAAGAAACAAA
2541991 AAAAGAAA-AAA
1 AAAAGAAACAAA
2542002 AAAAGAA
1 AAAAGAA
2542009 GAAGAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAGAAACAAA
Found at i:2542067 original size:25 final size:26
Alignment explanation
Indices: 2542021--2542072 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2542011 AGAACAAAAT
*
2542021 AGAAACGAAAAACAGGGGAGAAAGAA
1 AGAAACGAAAAACAGGGAAGAAAGAA
2542047 AGAAA-GAAAAA-AGGGAAAGAAAGAA
1 AGAAACGAAAAACAGGG-AAGAAAGAA
2542072 A
1 A
2542073 AGGGAGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.67, C:0.04, G:0.29, T:0.00
Consensus pattern (26 bp):
AGAAACGAAAAACAGGGAAGAAAGAA
Found at i:2546251 original size:26 final size:26
Alignment explanation
Indices: 2546215--2547078 Score: 1676
Period size: 26 Copynumber: 33.2 Consensus size: 26
2546205 TGATACAAAT
2546215 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546241 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
2546267 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546293 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546319 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546345 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546371 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546397 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546423 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546449 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546475 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546501 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546527 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546553 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546579 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546605 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546631 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546657 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546683 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546709 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546735 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546761 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546787 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546813 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546839 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546865 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546891 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546917 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546943 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546969 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2546995 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
2547021 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
2547047 TGATAAT-GTGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
2547073 TGATAA
1 TGATAA
2547079 GAATTTCATG
Statistics
Matches: 833, Mismatches: 4, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
25 1 0.00
26 832 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:2548561 original size:28 final size:28
Alignment explanation
Indices: 2548519--2548592 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 28
2548509 AAAAGTAGCT
* * *
2548519 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTATGGATGGA
* *
2548547 AAATTACTGTTATACCCC--TGGGTGTA
1 AAATTACTGTTATACCCCTATGGATGGA
*
2548573 AAATTACCGTTATACCCCTA
1 AAATTACTGTTATACCCCTA
2548593 GGGTTAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 22 0.58
28 16 0.42
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (28 bp):
AAATTACTGTTATACCCCTATGGATGGA
Found at i:2548584 original size:26 final size:27
Alignment explanation
Indices: 2548546--2548596 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
2548536 CTATGTATGG
*
2548546 AAAATTACTGTTATACCCCT-GGGTGT
1 AAAATTACCGTTATACCCCTAGGGTGT
2548572 AAAATTACCGTTATACCCCTAGGGT
1 AAAATTACCGTTATACCCCTAGGGT
2548597 TAATTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (27 bp):
AAAATTACCGTTATACCCCTAGGGTGT
Found at i:2548738 original size:27 final size:27
Alignment explanation
Indices: 2548697--2548809 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
2548687 GAGGAAGCGT
*
2548697 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
2548724 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
2548751 TCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
2548779 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
2548805 TCTGG
1 TCTGG
2548810 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 54 0.74
28 14 0.19
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:2548802 original size:54 final size:54
Alignment explanation
Indices: 2548695--2548818 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
2548685 TGGAGGAAGC
* *
2548695 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCCATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
2548749 GTTCTGGTGGCCCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCCATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
**
2548803 GTTCTGGCAGCCATGC
1 GTTCTGGTGGCCATGC
2548819 TGCAAATTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 42 0.70
55 18 0.30
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (54 bp):
GTTCTGGTGGCCATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:2561932 original size:33 final size:33
Alignment explanation
Indices: 2561886--2562016 Score: 176
Period size: 33 Copynumber: 4.0 Consensus size: 33
2561876 TCAACATAAG
2561886 TGATTGGAACATCTATCAGGGCAGCTTCATCAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAA
* *
2561919 TGATTGGACCATCTA-CAGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCA-GGGCAGCTTCATCAA
* * *
2561952 TGATTGGAACATCTATTAGGGTAGCTTCATCAG
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAA
*
2561985 TGATTGGAATATCTATC-GGGACAGCTTCATCA
1 TGATTGGAACATCTATCAGGG-CAGCTTCATCA
2562017 TTCTGTTCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.06
33 80 0.93
34 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAA
Found at i:2561962 original size:66 final size:66
Alignment explanation
Indices: 2561886--2562018 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 66
2561876 TCAACATAAG
* *
2561886 TGATTGGAACATCTATCAGGGCAGCTTCATCAATGATTGGACCATCTA-CAGGGGCAGCTTCATC
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAATGATTGGAACATCTATC-GGGACAGCTTCATC
2561950 AT
65 AT
* * * *
2561952 TGATTGGAACATCTATTAGGGTAGCTTCATCAGTGATTGGAATATCTATCGGGACAGCTTCATCA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAATGATTGGAACATCTATCGGGACAGCTTCATCA
2562017 T
66 T
2562018 T
1 T
2562019 CTGTTCAACT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 59 0.98
67 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (66 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAATGATTGGAACATCTATCGGGACAGCTTCATCA
T
Found at i:2577836 original size:16 final size:16
Alignment explanation
Indices: 2577815--2577849 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2577805 CCAGATTTTG
2577815 TCTTTCTCTCACTCTC
1 TCTTTCTCTCACTCTC
*
2577831 TCTTTCTCTCTCTCTC
1 TCTTTCTCTCACTCTC
2577847 TCT
1 TCT
2577850 GTTAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (16 bp):
TCTTTCTCTCACTCTC
Found at i:2581263 original size:18 final size:18
Alignment explanation
Indices: 2581240--2581274 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2581230 ATGCAAATAT
*
2581240 ATAAAAACGATAAATAAC
1 ATAAAAACAATAAATAAC
*
2581258 ATAAAAATAATAAATAA
1 ATAAAAACAATAAATAA
2581275 TTTATGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (18 bp):
ATAAAAACAATAAATAAC
Found at i:2581506 original size:39 final size:39
Alignment explanation
Indices: 2581463--2581538 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 39
2581453 TAAAAAATGG
2581463 TTAAT-TA-ATTAATAAAAA-AATACTATATGATATAATAAT
1 TTAATATATATTAATAAAAATAATA-T-TAT-ATATAATAAT
*
2581502 TTAATATATATTTATAAAAATAATATTATATATAATA
1 TTAATATATATTAATAAAAATAATATTATATATAATA
2581539 GGAACAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
39 13 0.39
40 5 0.15
41 11 0.33
42 4 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
TTAATATATATTAATAAAAATAATATTATATATAATAAT
Found at i:2581654 original size:3 final size:3
Alignment explanation
Indices: 2581646--2581734 Score: 62
Period size: 3 Copynumber: 29.3 Consensus size: 3
2581636 AAAATTATAC
* *
2581646 ATA ATA ATAA ATA ATAA ATA ATT AT- ATA ATA TATA ATA A-A ATA AAA
1 ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
*
2581692 ATA AT- ATA ATGA ATA AT- ATA TATA ATA A-A ATG ATA TATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA ATA -ATA ATA A
2581735 AATGTATAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
2 10 0.14
3 42 0.60
4 18 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2581676 original size:15 final size:15
Alignment explanation
Indices: 2581656--2581735 Score: 71
Period size: 15 Copynumber: 5.5 Consensus size: 15
2581646 ATAATAATAA
2581656 ATAATAAATAATTAT
1 ATAATAAATAATTAT
*
2581671 ATAATATATAA-TA-
1 ATAATAAATAATTAT
*
2581684 A-AATAAA-AATAAT
1 ATAATAAATAATTAT
*
2581697 ATAATGAATAATATAT
1 ATAATAAATAAT-TAT
*
2581713 ATAATAAAATGA-TAT
1 ATAAT-AAATAATTAT
2581728 ATAATAAA
1 ATAATAAA
2581736 ATGTATAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
11 2 0.04
12 6 0.12
13 2 0.04
14 10 0.19
15 21 0.40
16 7 0.13
17 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATAATAAATAATTAT
Found at i:2581681 original size:29 final size:27
Alignment explanation
Indices: 2581650--2581818 Score: 95
Period size: 29 Copynumber: 6.1 Consensus size: 27
2581640 TTATACATAA
2581650 TAATAAATAATAAATAATTATATAATATA
1 TAATAAATAATAAATAA-TATATAATA-A
2581679 TAATAAAATAA-AAATAATATAATGAATAA
1 TAAT-AAATAATAAATAATAT-AT-AATAA
* *
2581708 T-ATATATAATAAAATGATATATAATAA
1 TAATAAATAAT-AAATAATATATAATAA
** *
2581735 -AATGTATAAATCAA-AATATATAATAA
1 TAATAAAT-AATAAATAATATATAATAA
*
2581761 -AATGTAAATAATATAATAA-ATAATACACAAA
1 TAA--TAAATAATA-AATAATAT-ATA-A-TAA
*
2581792 TAA-AAATAA-AAATAAAATAT-ATAA
1 TAATAAATAATAAATAATATATAATAA
2581816 TAA
1 TAA
2581819 CTTTTTTACA
Statistics
Matches: 114, Mismatches: 10, Indels: 37
0.71 0.06 0.23
Matches are distributed among these distances:
24 5 0.04
25 1 0.01
26 13 0.11
27 27 0.24
28 20 0.18
29 33 0.29
30 11 0.10
31 2 0.02
32 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
TAATAAATAATAAATAATATATAATAA
Found at i:2581688 original size:12 final size:12
Alignment explanation
Indices: 2581635--2581818 Score: 98
Period size: 12 Copynumber: 15.2 Consensus size: 12
2581625 TACAAATTTT
2581635 TAAAAT-TATACA
1 TAAAATATATA-A
*
2581647 TAATAATAAATAA
1 TAA-AATATATAA
*
2581660 T-AAATA-ATTA
1 TAAAATATATAA
*
2581670 TATAATATATAA
1 TAAAATATATAA
*
2581682 TAAAATA-AAAA
1 TAAAATATATAA
*
2581693 TAATATA-ATGAA
1 TAAAATATAT-AA
*
2581705 TAATATATATAA
1 TAAAATATATAA
2581717 TAAAATGATATATAA
1 T-AAA--ATATATAA
*
2581732 TAAAATGTATAAA
1 TAAAATATAT-AA
2581745 TCAAAATATATAA
1 T-AAAATATATAA
*
2581758 TAAAATGTA-AA
1 TAAAATATATAA
*
2581769 TAATATA-ATAA
1 TAAAATATATAA
* * *
2581780 -ATAATACACAAA
1 TAAAATATA-TAA
*
2581792 TAAAA-ATAAAAA
1 TAAAATAT-ATAA
2581804 TAAAATATATAA
1 TAAAATATATAA
2581816 TAA
1 TAA
2581819 CTTTTTTACA
Statistics
Matches: 135, Mismatches: 20, Indels: 34
0.71 0.11 0.18
Matches are distributed among these distances:
10 9 0.07
11 28 0.21
12 54 0.40
13 21 0.16
14 14 0.10
15 9 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
TAAAATATATAA
Found at i:2581707 original size:26 final size:27
Alignment explanation
Indices: 2581641--2581818 Score: 92
Period size: 26 Copynumber: 6.5 Consensus size: 27
2581631 TTTTTAAAAT
*
2581641 TATACATAATAATAAATAATAAATAATTA
1 TATA-ATAATAAT-AATAATAAATAATAA
2581670 TATAATATATAATAA-AATAAA-AATAA
1 TATAATA-ATAATAATAATAAATAATAA
2581696 TATAATGAATAAT-AT-ATATAATAA-AA
1 TATAAT-AATAATAATAATA-AATAATAA
*
2581722 TGATATATAATAA-AATGTATAAATCAA-AA
1 T-ATA-ATAATAATAAT-AATAAAT-AATAA
*
2581751 TAT-ATAATAA-AAT-GTAAATAAT-A
1 TATAATAATAATAATAATAAATAATAA
* *
2581774 TAATAAATAATACACAAATAA-AAATAAAAA
1 T-AT-AATAATA-A-TAATAATAAATAATAA
*
2581804 TAAAATATATAATAA
1 TATAATA-ATAATAA
2581819 CTTTTTTACA
Statistics
Matches: 122, Mismatches: 6, Indels: 44
0.71 0.03 0.26
Matches are distributed among these distances:
23 4 0.03
24 7 0.06
25 4 0.03
26 36 0.30
27 22 0.18
28 17 0.14
29 30 0.25
30 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
TATAATAATAATAATAATAAATAATAA
Found at i:2581878 original size:26 final size:27
Alignment explanation
Indices: 2581849--2581906 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2581839 ATGTTTATAG
*
2581849 TAAAAATAAAT-AA-TATATATAATATT
1 TAAAAATAAATAAATTATATA-AAAATT
2581875 T-AAAATAAATAAATTATATAAAAATT
1 TAAAAATAAATAAATTATATAAAAATT
2581901 TAAAAA
1 TAAAAA
2581907 GGATTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.32
26 9 0.32
27 10 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAAAATAAATAAATTATATAAAAATT
Found at i:2581879 original size:25 final size:26
Alignment explanation
Indices: 2581851--2581905 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
2581841 GTTTATAGTA
*
2581851 AAAATAAAT-AA-TATATATAATATTT
1 AAAATAAATAAATTATATA-AAAATTT
2581876 AAAATAAATAAATTATATAAAAATTT
1 AAAATAAATAAATTATATAAAAATTT
2581902 AAAA
1 AAAA
2581906 AGGATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.33
26 12 0.44
27 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAATAAATAAATTATATAAAAATTT
Found at i:2589929 original size:14 final size:14
Alignment explanation
Indices: 2589910--2589936 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2589900 GGGCTTTCAA
2589910 ACTTGACAGCATTG
1 ACTTGACAGCATTG
2589924 ACTTGACAGCATT
1 ACTTGACAGCATT
2589937 AACAATATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
ACTTGACAGCATTG
Found at i:2600613 original size:26 final size:26
Alignment explanation
Indices: 2600584--2600638 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2600574 AATTTTATAA
2600584 TTTTAAT-AGTTTATATTTTTAAAATT
1 TTTTAATAAG-TTATATTTTTAAAATT
** *
2600610 TTTTTGTAAGTTATATTTTTATAATT
1 TTTTAATAAGTTATATTTTTAAAATT
2600636 TTT
1 TTT
2600639 ATCGAGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (26 bp):
TTTTAATAAGTTATATTTTTAAAATT
Found at i:2601899 original size:27 final size:27
Alignment explanation
Indices: 2601843--2601900 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
2601833 ATTTTATACG
*
2601843 TTTTTAATATATATATATATTTTAATT
1 TTTTTAATATATATATATATTTTAAAT
*
2601870 TTTTTAAT-T-TATATATATTTATAAAA
1 TTTTTAATATATATATATATTT-TAAAT
2601896 TTTTT
1 TTTTT
2601901 GGAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 11 0.39
26 9 0.32
27 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTAATATATATATATATTTTAAAT
Found at i:2602672 original size:22 final size:22
Alignment explanation
Indices: 2602642--2602707 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
2602632 CTCCTTAAAA
*
2602642 ATAAT-AAAATTTTAATTTAAT
1 ATAATAAAAATTATAATTTAAT
** *
2602663 ATTTTAAAAATTATAATTTTACT
1 ATAATAAAAATTATAA-TTTAAT
2602686 ATAATAAAAATTATAATTTAAT
1 ATAATAAAAATTATAATTTAAT
2602708 TCGACTCTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.08
22 14 0.39
23 19 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATAAAAATTATAATTTAAT
Found at i:2605712 original size:15 final size:16
Alignment explanation
Indices: 2605694--2605723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2605684 ACAAACCATA
2605694 AATAAA-ATAACAAAT
1 AATAAACATAACAAAT
2605709 AATAAACATAACAAA
1 AATAAACATAACAAA
2605724 CACAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (16 bp):
AATAAACATAACAAAT
Found at i:2607964 original size:44 final size:44
Alignment explanation
Indices: 2607856--2607964 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
2607846 ATTTCGGTAA
* * * * *
2607856 AACTTCAAGGAGATAAGGTTGGTGGCTTCAATTTACTCCAATGT
1 AACTTCAAGGAGATAAGATTTGTAGCTTCAATCTACTCCAATGG
* * *
2607900 AATTTCAAGGAGA-AGAGATTTGTAGCTTCGATCTACTCCATTGG
1 AACTTCAAGGAGATA-AGATTTGTAGCTTCAATCTACTCCAATGG
2607944 AACTTCAAGGAGATAAGATTT
1 AACTTCAAGGAGATAAGATTT
2607965 ACTTTCTTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.02
44 52 0.96
45 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (44 bp):
AACTTCAAGGAGATAAGATTTGTAGCTTCAATCTACTCCAATGG
Found at i:2621309 original size:15 final size:16
Alignment explanation
Indices: 2621291--2621320 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2621281 ACAAACCATA
2621291 AATAAA-ATAACAAAT
1 AATAAACATAACAAAT
2621306 AATAAACATAACAAA
1 AATAAACATAACAAA
2621321 CACAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (16 bp):
AATAAACATAACAAAT
Found at i:2621310 original size:19 final size:20
Alignment explanation
Indices: 2621270--2621311 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2621260 CACAAGAATA
*
2621270 AAATAAAATAAACAAACCAT
1 AAATAAAATAAACAAACAAT
*
2621290 AAATAAAAT-AACAAATAAT
1 AAATAAAATAAACAAACAAT
2621309 AAA
1 AAA
2621312 CATAACAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.17
Consensus pattern (20 bp):
AAATAAAATAAACAAACAAT
Found at i:2626041 original size:49 final size:49
Alignment explanation
Indices: 2625946--2626045 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
2625936 TATTGTGATC
* * * * *
2625946 GAATGGTAGCGTAAGAAAGGATGCGGTGCAGTGGCCAGTAACGTGTAGG
1 GAATGGTAGCATAAGAAAGGATACGGTACAATGGCCAGCAACGTGTAGG
**
2625995 GAATGGTAGCATAAGAAAGGATACGGTACAATGGCCAGCAGTGTGTAGG
1 GAATGGTAGCATAAGAAAGGATACGGTACAATGGCCAGCAACGTGTAGG
2626044 GA
1 GA
2626046 GGTAGAGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.32, C:0.12, G:0.38, T:0.18
Consensus pattern (49 bp):
GAATGGTAGCATAAGAAAGGATACGGTACAATGGCCAGCAACGTGTAGG
Found at i:2627344 original size:29 final size:29
Alignment explanation
Indices: 2627300--2627389 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
2627290 TGAGCATGAC
*
2627300 TATAAATGTGAATTGGGCTTGATGGGCCA
1 TATAAATGTGATTTGGGCTTGATGGGCCA
* *
2627329 TATAAATGTGATTTGGGCCTAATGGGCCA
1 TATAAATGTGATTTGGGCTTGATGGGCCA
* * *
2627358 TATAAATGTGATTAGGCCTAG-TGGGCCA
1 TATAAATGTGATTTGGGCTTGATGGGCCA
2627386 TATA
1 TATA
2627390 CAGGTATGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 11 0.21
29 42 0.79
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (29 bp):
TATAAATGTGATTTGGGCTTGATGGGCCA
Found at i:2630879 original size:46 final size:45
Alignment explanation
Indices: 2630812--2631128 Score: 359
Period size: 46 Copynumber: 6.9 Consensus size: 45
2630802 TCTCTGAAAT
*
2630812 GAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGATTA
1 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA-TA
**
2630858 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA
1 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGATA
** * * ** *
2630903 TGAAATGTGTAAAACCATGGTTGAAAGATACCATGGTAATGTGACA
1 -GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGATA
**
2630949 TGAAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGG
1 -GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA-TA
***
2630995 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGTGTGACATA
1 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG--ATA
*
2631042 -AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA
1 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGATA
* * * * * *
2631086 GAAAACGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 G-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
2631129 TCAAAGATAA
Statistics
Matches: 235, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
44 2 0.01
45 38 0.16
46 194 0.83
48 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (45 bp):
GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGATA
Found at i:2631065 original size:137 final size:138
Alignment explanation
Indices: 2630810--2631128 Score: 408
Period size: 137 Copynumber: 2.3 Consensus size: 138
2630800 GCTCTCTGAA
* * ** **
2630810 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGATTAGAAATGTGTAAGACCAT
1 ATGAAACGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAATAAGACCAT
* * ** *
2630875 GGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGT
66 GGTTGAAAGATACCATGGCAACATGACATAAAATGAATAAAACCATGGTTGAAAGATACCATGGC
**
2630940 AATGTGAC
131 AACATGAC
*
2630948 ATGAAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGACCAT
1 ATGAAACGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAATAAGACCAT
*** *
2631012 GGTTGAAAGATACCATGGCAGTGTGACATAAAATGAATAAGACCATGGTTGAAAGATACCATGGC
66 GGTTGAAAGATACCATGGCAACATGACATAAAATGAATAAAACCATGGTTGAAAGATACCATGGC
2631077 AACATGAC
131 AACATGAC
* * * * *
2631085 A-GAAAACGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAACGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
2631129 TCAAAGATAA
Statistics
Matches: 157, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
136 1 0.01
137 118 0.75
138 38 0.24
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (138 bp):
ATGAAACGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAATAAGACCAT
GGTTGAAAGATACCATGGCAACATGACATAAAATGAATAAAACCATGGTTGAAAGATACCATGGC
AACATGAC
Found at i:2633616 original size:34 final size:35
Alignment explanation
Indices: 2633558--2633624 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
2633548 CAAACACCAG
2633558 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2633593 AAAATATTTTCTAG-AAATCATTTTACAGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
2633625 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2636672 original size:7 final size:7
Alignment explanation
Indices: 2636662--2636690 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2636652 TTTTGTTTCT
2636662 AATTTTA
1 AATTTTA
2636669 AATTTTA
1 AATTTTA
2636676 AATTTTA
1 AATTTTA
2636683 AATTTTA
1 AATTTTA
2636690 A
1 A
2636691 TATAACTTGA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:2640586 original size:26 final size:26
Alignment explanation
Indices: 2640555--2640662 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
2640545 TGAAATGTCC
* *
2640555 ATCATGAAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2640581 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
2640607 ATCATGGAATATTTACCTAATCTATT
1 ATCATGGAACATTTACCTAACCCATT
2640633 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2640659 ATCA
1 ATCA
2640663 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2643053 original size:10 final size:10
Alignment explanation
Indices: 2643038--2643063 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2643028 TTTTATTTTA
2643038 ATTTTTATAT
1 ATTTTTATAT
2643048 ATTTTTATAT
1 ATTTTTATAT
2643058 ATTTTT
1 ATTTTT
2643064 TAATGAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:2643515 original size:20 final size:21
Alignment explanation
Indices: 2643489--2643537 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2643479 TGGATGTGGC
2643489 AAAAAAATCTAA-AAA-ATTA
1 AAAAAAATCTAATAAATATTA
*
2643508 ATAAAAAAT-TAATAAATATTT
1 A-AAAAAATCTAATAAATATTA
2643529 AAAAAAATC
1 AAAAAAATC
2643538 ACCTCTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAAATCTAATAAATATTA
Found at i:2643530 original size:11 final size:11
Alignment explanation
Indices: 2643498--2643523 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2643488 CAAAAAAATC
2643498 TAAAAAATTAA
1 TAAAAAATTAA
2643509 TAAAAAATTAA
1 TAAAAAATTAA
2643520 TAAA
1 TAAA
2643524 TATTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAAATTAA
Found at i:2643642 original size:16 final size:16
Alignment explanation
Indices: 2643618--2643649 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2643608 AAGTATTAAA
2643618 ATTTATTAGAAATTAT
1 ATTTATTAGAAATTAT
*
2643634 ATTTTTTAGAAATTAT
1 ATTTATTAGAAATTAT
2643650 TTAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTTATTAGAAATTAT
Found at i:2643669 original size:13 final size:11
Alignment explanation
Indices: 2643569--2643668 Score: 55
Period size: 11 Copynumber: 8.7 Consensus size: 11
2643559 CTCGTGGTTT
2643569 TTTAAATAATTA
1 TTTAAA-AATTA
2643581 --TAAAAA-TA
1 TTTAAAAATTA
2643589 TTGTAGAAAATTA
1 TT-TA-AAAATTA
*
2643602 TTTAAAAAGTA
1 TTTAAAAATTA
*
2643613 -TTAAAATTTA
1 TTTAAAAATTA
* *
2643623 TTAGAAATTATATTT
1 TT-TAAA--A-ATTA
*
2643638 TTTAGAAATTA
1 TTTAAAAATTA
2643649 TTTAAAAATTA
1 TTTAAAAATTA
2643660 TATTAAAAA
1 T-TTAAAAA
2643669 AATAATGTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
8 2 0.03
9 2 0.03
10 12 0.18
11 23 0.34
12 17 0.25
13 4 0.06
14 3 0.04
15 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (11 bp):
TTTAAAAATTA
Found at i:2643939 original size:9 final size:9
Alignment explanation
Indices: 2643925--2643989 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
2643915 GAGTATATAC
2643925 AATTTTTAT
1 AATTTTTAT
*
2643934 AATTTTTGAA
1 AATTTTT-AT
*
2643944 AATTTTAAT
1 AATTTTTAT
2643953 AATTATTTAT
1 AATT-TTTAT
*
2643963 AATTTATA-
1 AATTTTTAT
*
2643971 AATATTTTTT
1 AAT-TTTTAT
2643981 ATATTTTTA
1 A-ATTTTTA
2643990 AACAATTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
8 3 0.07
9 18 0.42
10 20 0.47
11 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
AATTTTTAT
Found at i:2643966 original size:19 final size:19
Alignment explanation
Indices: 2643925--2644001 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 19
2643915 GAGTATATAC
* *
2643925 AATTTTTATAATT-TTTGAA
1 AATTTTAATAATTATTT-AT
2643944 AATTTTAATAATTATTTAT
1 AATTTTAATAATTATTTAT
*
2643963 AATTTATAA-ATATTTTTTAT
1 AATTT-TAATA-ATTATTTAT
* *
2643983 ATTTTTAAACAATTATTTA
1 AATTTT-AATAATTATTTA
2644002 AGAAACCGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 20 0.42
20 27 0.56
21 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
AATTTTAATAATTATTTAT
Found at i:2644095 original size:21 final size:18
Alignment explanation
Indices: 2644060--2644100 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
2644050 TTGTTTTATT
2644060 TTAAAAATTTTATAATTC
1 TTAAAAATTTTATAATTC
2644078 TTAATAAATTTTAAATAATTC
1 TTAA-AAATTTT--ATAATTC
2644099 TT
1 TT
2644101 TATGTTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
21 9 0.45
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAAATTTTATAATTC
Found at i:2645464 original size:3 final size:3
Alignment explanation
Indices: 2645456--2645491 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2645446 TGAAAATTTT
*
2645456 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2645492 TATCAAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2648385 original size:150 final size:150
Alignment explanation
Indices: 2648189--2648488 Score: 582
Period size: 150 Copynumber: 2.0 Consensus size: 150
2648179 GATCTAGCAT
2648189 GAAAAGTTGAGTTCTTACCAAGATGAATAGCACTCTGGCTATCACAGTACAGGACATACTTCTCC
1 GAAAAGTTGAGTTCTTACCAAGATGAATAGCACTCTGGCTATCACAGTACAGGACATACTTCTCC
2648254 TGAGTAAAACCAAGCTCATGCACAAACTTCTTCATCCAAAGCATCTCCTTACACGCTTCAGTTGC
66 TGAGTAAAACCAAGCTCATGCACAAACTTCTTCATCCAAAGCATCTCCTTACACGCTTCAGTTGC
2648319 TGCAATGAACTCTGATTCGG
131 TGCAATGAACTCTGATTCGG
2648339 GAAAAGTTGAGTTCTTACCAAGATGAATAGCACTCTGGCTATCACAGTACAGGACATACTTCTCC
1 GAAAAGTTGAGTTCTTACCAAGATGAATAGCACTCTGGCTATCACAGTACAGGACATACTTCTCC
* *
2648404 TGAGTAAAACCAAGCTCATGCACAAACTTCTTCATCCAAAGCATCTCCTTACATGCTTCGGTTGC
66 TGAGTAAAACCAAGCTCATGCACAAACTTCTTCATCCAAAGCATCTCCTTACACGCTTCAGTTGC
2648469 TGCAATGAACTCTGATTCGG
131 TGCAATGAACTCTGATTCGG
2648489 TGGTGGACAA
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 148 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (150 bp):
GAAAAGTTGAGTTCTTACCAAGATGAATAGCACTCTGGCTATCACAGTACAGGACATACTTCTCC
TGAGTAAAACCAAGCTCATGCACAAACTTCTTCATCCAAAGCATCTCCTTACACGCTTCAGTTGC
TGCAATGAACTCTGATTCGG
Found at i:2652542 original size:131 final size:131
Alignment explanation
Indices: 2652381--2652641 Score: 495
Period size: 131 Copynumber: 2.0 Consensus size: 131
2652371 TGGAAAACCT
*
2652381 CTCTAAATTAAGGGTAAAAACCACGGGACTTTAGAGTCCAATAAAGAGCTCCACTATCATCAAAT
1 CTCTAAATTAAGGGTAAAAACCACAGGACTTTAGAGTCCAATAAAGAGCTCCACTATCATCAAAT
*
2652446 GTTCAACTACAAGATCACAATATCAAGCCTACAATAAGCATTCAACTCCGACAAGGCTAACAACA
66 GTTCAACTACAAGATCACAATATCAAGCCTACAACAAGCATTCAACTCCGACAAGGCTAACAACA
2652511 C
131 C
*
2652512 CTCTAAATTAAGGGTAAAAACCACAGGACTTTAGAGTCCGATAAAGAGCTCCACTATCATCAAAT
1 CTCTAAATTAAGGGTAAAAACCACAGGACTTTAGAGTCCAATAAAGAGCTCCACTATCATCAAAT
2652577 GTTCAACTACAAGATCACAATATCAAGCCTACAACAAGCATTCAACTCCGACAAGGCTAACAACA
66 GTTCAACTACAAGATCACAATATCAAGCCTACAACAAGCATTCAACTCCGACAAGGCTAACAACA
2652642 TGTAATCTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 127 1.00
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.20
Consensus pattern (131 bp):
CTCTAAATTAAGGGTAAAAACCACAGGACTTTAGAGTCCAATAAAGAGCTCCACTATCATCAAAT
GTTCAACTACAAGATCACAATATCAAGCCTACAACAAGCATTCAACTCCGACAAGGCTAACAACA
C
Found at i:2663735 original size:25 final size:27
Alignment explanation
Indices: 2663698--2663750 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2663688 TCAAACATGC
2663698 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
2663724 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
2663750 A
1 A
2663751 AAATTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:2665267 original size:26 final size:26
Alignment explanation
Indices: 2665237--2665292 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
2665227 TGAAATGCCC
2665237 ATCATGGAACATTTACCTAACCCAAT
1 ATCATGGAACATTTACCTAACCCAAT
*
2665263 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCAAT
2665289 ATCA
1 ATCA
2665293 ATTTTTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.29
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCAAT
Found at i:2666610 original size:18 final size:18
Alignment explanation
Indices: 2666587--2666621 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2666577 CCCAACTACT
*
2666587 GTATACGTGAATAGTGCC
1 GTATACATGAATAGTGCC
2666605 GTATACATGAATAGTGC
1 GTATACATGAATAGTGC
2666622 TATAAATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (18 bp):
GTATACATGAATAGTGCC
Found at i:2670863 original size:27 final size:27
Alignment explanation
Indices: 2670793--2670847 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2670783 ACGAATGGGT
2670793 AAAGTCTCCATCTTCTTGACTAAGCTC
1 AAAGTCTCCATCTTCTTGACTAAGCTC
2670820 AAAGTCTCCATCTTCTTGACTAAGCTC
1 AAAGTCTCCATCTTCTTGACTAAGCTC
2670847 A
1 A
2670848 TAATAGCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAGTCTCCATCTTCTTGACTAAGCTC
Found at i:2674205 original size:23 final size:23
Alignment explanation
Indices: 2674178--2674223 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2674168 GGCACACACC
2674178 CATGTGGCTAGGATGTGTGGTAA
1 CATGTGGCTAGGATGTGTGGTAA
2674201 CATGTGGCTAGGATGTGTGGTAA
1 CATGTGGCTAGGATGTGTGGTAA
2674224 ACTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.39, T:0.30
Consensus pattern (23 bp):
CATGTGGCTAGGATGTGTGGTAA
Found at i:2675493 original size:19 final size:17
Alignment explanation
Indices: 2675449--2675495 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2675439 AACACAATAC
*
2675449 CATAATATCAATACTTA
1 CATAATATCAATACATA
2675466 CAT--TATCAATAGCCATA
1 CATAATATCAATA--CATA
2675483 CATAATATCAATA
1 CATAATATCAATA
2675496 ATATGTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 8 0.32
17 9 0.36
19 8 0.32
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (17 bp):
CATAATATCAATACATA
Done.