Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 181 of 284
Found at i:61200682 original size:17 final size:16
Alignment explanation
Indices: 61200660--61200694 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
61200650 TTTTATTCTA
61200660 TTTTTCTATTGCTTTTT
1 TTTTTCTATTG-TTTTT
*
61200677 TTTTTCTTTTGTTTTT
1 TTTTTCTATTGTTTTT
61200693 TT
1 TT
61200695 CTCTGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTCTATTGTTTTT
Found at i:61202671 original size:10 final size:10
Alignment explanation
Indices: 61202639--61202678 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
61202629 TTGTATGAAA
61202639 TTTTATAATT
1 TTTTATAATT
* *
61202649 TTTTTTAAAT
1 TTTTATAATT
*
61202659 TTTGATAATT
1 TTTTATAATT
61202669 TTTTATAATT
1 TTTTATAATT
61202679 ATTAAATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:61202678 original size:19 final size:19
Alignment explanation
Indices: 61202626--61202676 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
61202616 TTCATGTTTT
61202626 TTTTTGTATGAAATTTTATAA
1 TTTTT-TAT-AAATTTTATAA
*
61202647 TTTTTTTTAAATTTTGATAA
1 TTTTTTATAAATTTT-ATAA
61202667 TTTTTTATAA
1 TTTTTTATAA
61202677 TTATTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (19 bp):
TTTTTTATAAATTTTATAA
Found at i:61203448 original size:17 final size:17
Alignment explanation
Indices: 61203416--61203449 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61203406 ATAGAAAATT
* *
61203416 TAATATATATATATAAA
1 TAATATATAAAAATAAA
61203433 TAATATATAAAAATAAA
1 TAATATATAAAAATAAA
61203450 ATATACATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATATATAAAAATAAA
Found at i:61203534 original size:20 final size:20
Alignment explanation
Indices: 61203486--61203534 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
61203476 TAAAACTACA
*
61203486 AATAATAAAAAATATGTTTT
1 AATAAAAAAAAATATGTTTT
61203506 AA-AAGAAAAAAATTAT-TTTT
1 AATAA-AAAAAAA-TATGTTTT
61203526 AATAAAAAA
1 AATAAAAAA
61203535 TAGAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
20 18 0.72
21 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AATAAAAAAAAATATGTTTT
Found at i:61204902 original size:32 final size:31
Alignment explanation
Indices: 61204866--61204925 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
61204856 TACAGCCTAA
61204866 TGACTTAAATAAAAAAATTTTGAATAGTTGAG
1 TGACTTAAAT-AAAAAATTTTGAATAGTTGAG
* **
61204898 TGACTTAAATGAAACCTTTTGAATAGTT
1 TGACTTAAATAAAAAATTTTGAATAGTT
61204926 CAATGACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTTGAATAGTTGAG
Found at i:61209826 original size:28 final size:27
Alignment explanation
Indices: 61209759--61209826 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
61209749 TTATAGCATG
* *
61209759 TTTATTTTTATTTTAAAAATAGGAATTTT
1 TTTA-TTTT-TTTTAAAAATAGGAAATTA
*
61209788 TTGTATTTTTTTTAAACATAGGAAATTA
1 TT-TATTTTTTTTAAAAATAGGAAATTA
*
61209816 TTTATTATTTT
1 TTTATTTTTTT
61209827 ATTAGTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 8 0.24
28 18 0.53
29 6 0.18
30 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTATTTTTTTTAAAAATAGGAAATTA
Found at i:61212135 original size:44 final size:41
Alignment explanation
Indices: 61212087--61212195 Score: 98
Period size: 44 Copynumber: 2.6 Consensus size: 41
61212077 AGTATTATAT
61212087 ATTATGATTTTAGTAAATTCATATAAGAATAAGAATT-TTATTAA
1 ATTAT-ATTTTAGTAAATT-ATAT-AGAATAAGAATTATT-TTAA
* ** *
61212131 ATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAA
1 A-T-TATATT-TTAGTAAATTATATAGAATAAGAATTATTTTAA
61212175 ATTATATTTTAGT--ATTATATA
1 ATTATATTTTAGTAAATTATATA
61212196 TTATGATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
39 7 0.13
41 4 0.07
42 6 0.11
43 1 0.02
44 15 0.27
45 10 0.18
46 12 0.22
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (41 bp):
ATTATATTTTAGTAAATTATATAGAATAAGAATTATTTTAA
Found at i:61212174 original size:26 final size:28
Alignment explanation
Indices: 61212120--61212417 Score: 116
Period size: 27 Copynumber: 10.4 Consensus size: 28
61212110 TAAGAATAAG
* * *
61212120 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
61212148 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
* * *
61212174 AATTATATTTTAGTATTATATATTATGATTT
1 AATTATA-TTTA--ATAATATATTATTATTA
* * *
61212205 TATTAGTAAATTCATATAAGA-A-TATTTATTAA
1 AATTA-T--ATTTA-ATAATATATTA-TTATT-A
* * *
61212237 CAATTTTATTAAATTATATATT-TTATTA
1 -AATTATATTTAATAATATATTATTATTA
* * *
61212265 AATTATATTTTATAACA-ATTA-TGTTA
1 AATTATATTTAATAATATATTATTATTA
* * *
61212291 AATTATATTTTAGTATTATATATTATGATTT
1 AATTATA-TTTA--ATAATATATTATTATTA
* * *
61212322 TATTAGTAAATTCATATAAGA-A-TATTTATTAA
1 AATTA-T--ATTTA-ATAATATATTA-TTATT-A
* * *
61212354 CAATTTTATTAAATTATATATT-TTATTA
1 -AATTATATTTAATAATATATTATTATTA
61212382 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
61212408 AATTATATTT
1 AATTATATTT
61212418 TAGTATCATA
Statistics
Matches: 199, Mismatches: 43, Indels: 58
0.66 0.14 0.19
Matches are distributed among these distances:
26 40 0.20
27 41 0.21
28 16 0.08
29 27 0.14
30 23 0.12
31 24 0.12
32 14 0.07
33 12 0.06
34 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:61212277 original size:15 final size:17
Alignment explanation
Indices: 61212239--61212272 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61212229 TTTATTAACA
61212239 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61212256 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61212273 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:61212286 original size:16 final size:15
Alignment explanation
Indices: 61212239--61212286 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
61212229 TTTATTAACA
*
61212239 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
61212256 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
61212271 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
61212287 GTTAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:61212292 original size:117 final size:117
Alignment explanation
Indices: 61212037--61212526 Score: 795
Period size: 117 Copynumber: 4.3 Consensus size: 117
61212027 AAGTAGATTA
61212037 TAAATTATATTTAATAATAATTAT-TTAAATTATATTTTATAGTATTATATATTATGA--TT-TT
1 TAAATTATATTTAATAATAATTATGTTAAATTATA-TTT-TAGTATTATATATTATGATTTTATT
*
61212098 AGTAAATTCATATAAG---A---A-TAAGAATTTTATTAAATTATATATTATTAT
64 AGTAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATT-TTAT
*
61212146 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
1 TAAATTATATTTAATAATAATTATGTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
61212211 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
66 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
* *
61212263 TAAATTATATTTTATAACAATTATGTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
1 TAAATTATATTTAATAATAATTATGTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
61212328 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
66 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
* *
61212380 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTATCATATATTATGATTTTATTAG
1 TAAATTATATTTAATAATAATTATGTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
*
61212445 TAAATTCATATAAGAATATTTATTAAAAATTTTATTAAATTATATATTTTAT
66 TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
* *
61212497 TAAATTATATTTTATAACAATTATGTTAAA
1 TAAATTATATTTAATAATAATTATGTTAAA
61212527 ATATGATTAA
Statistics
Matches: 358, Mismatches: 12, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
108 18 0.05
109 27 0.08
110 12 0.03
111 18 0.05
114 1 0.00
117 258 0.72
118 24 0.07
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (117 bp):
TAAATTATATTTAATAATAATTATGTTAAATTATATTTTAGTATTATATATTATGATTTTATTAG
TAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATTTTAT
Found at i:61212376 original size:17 final size:17
Alignment explanation
Indices: 61212356--61212389 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61212346 TTTATTAACA
61212356 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61212373 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61212390 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:61212493 original size:17 final size:17
Alignment explanation
Indices: 61212473--61212506 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61212463 TTTATTAAAA
61212473 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61212490 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61212507 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:61212520 original size:16 final size:15
Alignment explanation
Indices: 61212473--61212520 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
61212463 TTTATTAAAA
*
61212473 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
61212490 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
61212505 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
61212521 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:61212698 original size:39 final size:41
Alignment explanation
Indices: 61212654--61212758 Score: 133
Period size: 44 Copynumber: 2.5 Consensus size: 41
61212644 TTCCTTATGT
* *
61212654 TATTACACCTCTATTCCATTCAACCAAACACAAGAA-TACC
1 TATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTACC
61212694 -ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTACC
1 TATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTACC
61212739 TATTACGCCTCTATTCCATT
1 TATTACGCCTCTATTCCATT
61212759 ACGCCTCTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 1 0.02
41 4 0.07
44 19 0.34
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (41 bp):
TATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTACC
Found at i:61212733 original size:44 final size:46
Alignment explanation
Indices: 61212670--61212760 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
61212660 ACCTCTATTC
*
61212670 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
61212714 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
61212760 C
1 C
61212761 GCCTCTATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:61212761 original size:16 final size:16
Alignment explanation
Indices: 61212740--61212776 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
61212730 AGAATTACCT
*
61212740 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTAC
61212756 ATTACGCCTCTATTAC
1 ATTACGCCTCTATTAC
61212772 ATTAC
1 ATTAC
61212777 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTAC
Found at i:61229251 original size:47 final size:47
Alignment explanation
Indices: 61229134--61229334 Score: 215
Period size: 47 Copynumber: 4.2 Consensus size: 47
61229124 TGCACATAGT
* * * ** *
61229134 CACATATCACACACCGAAGCCACAGCCCAGCCATGGTCTTACACAG-AT
1 CACATAT--CACACCGATGCCATATCCCAGATATGGTCTTACACAGAAA
*
61229182 CACATATCACACTGATGCCATATCCCAGATATGGTCTTACACAGAAA
1 CACATATCACACCGATGCCATATCCCAGATATGGTCTTACACAGAAA
* * * *
61229229 CACATATCACACCGACGCCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACACCGATGCCATATCCCAGATATGGTCTTACACAGAAA
* * * * * *
61229276 CTCATATTACACCGATGCCATAACCCAGCTATGGTCTTATACGGAAA
1 CACATATCACACCGATGCCATATCCCAGATATGGTCTTACACAGAAA
61229323 TCACATATCACA
1 -CACATATCACA
61229335 TGTTGCCATG
Statistics
Matches: 131, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
46 31 0.24
47 84 0.64
48 16 0.12
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (47 bp):
CACATATCACACCGATGCCATATCCCAGATATGGTCTTACACAGAAA
Found at i:61243870 original size:49 final size:49
Alignment explanation
Indices: 61243817--61243991 Score: 260
Period size: 49 Copynumber: 3.5 Consensus size: 49
61243807 CTGGTACGCA
*
61243817 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
* * * * * * *
61243866 TAGTAACCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACACG
61243917 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
61243966 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
61243992 CGTGACCTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 65 0.60
50 6 0.06
51 38 0.35
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
Found at i:61243927 original size:51 final size:49
Alignment explanation
Indices: 61243804--61243998 Score: 255
Period size: 49 Copynumber: 3.9 Consensus size: 49
61243794 TAGCCAAAGC
* * *
61243804 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
** * * *
61243853 TATCCGGTACATGTAGTAACCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
* * *
61243904 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* *
61243953 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
61243999 TCACAATAGA
Statistics
Matches: 123, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 79 0.64
50 6 0.05
51 38 0.31
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:61243945 original size:100 final size:100
Alignment explanation
Indices: 61243804--61243996 Score: 359
Period size: 100 Copynumber: 1.9 Consensus size: 100
61243794 TAGCCAAAGC
* *
61243804 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACATGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAG
61243869 TAACCTGCACTTAGTACTACACACGTGATCGAAGT
66 TAACCTGCACTTAGTACTACACACGTGATCGAAGT
61243904 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAG
*
61243969 TAGCCTGCACTTAGTACTACACACGTGA
66 TAACCTGCACTTAGTACTACACACGTGA
61243997 CCTCACAATA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAG
TAACCTGCACTTAGTACTACACACGTGATCGAAGT
Found at i:61244161 original size:5 final size:5
Alignment explanation
Indices: 61244146--61244180 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
61244136 ATTTCATATG
* *
61244146 AAAAC AAAAT ATAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
61244181 CGATAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:61245546 original size:19 final size:18
Alignment explanation
Indices: 61245524--61245593 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
61245514 ATTCTATATA
61245524 TTTTATAATTTTTTACGAT
1 TTTTAT-ATTTTTTACGAT
*** *
61245543 TTTTATAAAAATTTACCAT
1 TTTTAT-ATTTTTTACGAT
61245562 TTTTATATTTTTTACGAT
1 TTTTATATTTTTTACGAT
61245580 TTTTATATTTTTTA
1 TTTTATATTTTTTA
61245594 ATTAAAACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 22 0.51
19 21 0.49
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTATATTTTTTACGAT
Found at i:61247939 original size:19 final size:18
Alignment explanation
Indices: 61247915--61247950 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
61247905 AAAATTTTTG
61247915 CTAAAAAAAATGGAAAAAC
1 CTAAAAAAAA-GGAAAAAC
61247934 CTAAAAAAAAGGAAAAA
1 CTAAAAAAAAGGAAAAA
61247951 GAGAAACGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.72, C:0.08, G:0.11, T:0.08
Consensus pattern (18 bp):
CTAAAAAAAAGGAAAAAC
Found at i:61250492 original size:16 final size:16
Alignment explanation
Indices: 61250473--61250503 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61250463 ATTATTTTAA
61250473 ATTTTAATTAGATAAT
1 ATTTTAATTAGATAAT
*
61250489 ATTTTATTTAGATAA
1 ATTTTAATTAGATAA
61250504 ATGAATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTTTAATTAGATAAT
Found at i:61266238 original size:23 final size:23
Alignment explanation
Indices: 61266208--61266253 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
61266198 AACATTTTAA
61266208 TTTATTATT-TTATTTCTGTTTGG
1 TTTATTATTATT-TTTCTGTTTGG
*
61266231 TTTATTATTATTTTTGTGTTTGG
1 TTTATTATTATTTTTCTGTTTGG
61266254 GTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.70
Consensus pattern (23 bp):
TTTATTATTATTTTTCTGTTTGG
Found at i:61266262 original size:18 final size:19
Alignment explanation
Indices: 61266241--61266277 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
61266231 TTTATTATTA
61266241 TTTTTG-TGTTTGGGTTTT
1 TTTTTGTTGTTTGGGTTTT
*
61266259 TTTTTGTTTTTTGGGTTTT
1 TTTTTGTTGTTTGGGTTTT
61266278 CATGGGCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (19 bp):
TTTTTGTTGTTTGGGTTTT
Found at i:61267580 original size:5 final size:5
Alignment explanation
Indices: 61267570--61267616 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
61267560 TGAAAACACT
61267570 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
61267617 GAGAGTAAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:61268922 original size:46 final size:46
Alignment explanation
Indices: 61268793--61269051 Score: 206
Period size: 46 Copynumber: 5.5 Consensus size: 46
61268783 AGGTCGACAC
* * * *
61268793 CATGTCCCA-ATCATGGTCTTACACTAGCTCTCGCATATCCATGCCGATG
1 CATGTCCCAGA-CAT-GTCTTACACTGGCTCT--CATCTCTAGGCCGATG
** * *
61268842 TCATGTCCCTTACATGGTCTTACACT-G-ACACATCTCGTA-GCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTC-TAGGCCGATG
* *
61268888 CATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAGGCCGATA
1 CATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCTAGGCCGATG
* * * * * *
61268934 CATGTCCCAGACATGTCTTACACTAGCTCTCATTTCAATGTCAATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATCTCTAGGCCGATG
* *
61268980 TCATGTCACAGACATGGTCTTACACTGGCTCTCATAATCT-GGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCTAGGCCGATG
*
61269028 CATGTCCTAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
61269052 AGCACACAAA
Statistics
Matches: 172, Mismatches: 27, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
44 10 0.06
45 14 0.08
46 71 0.41
47 27 0.16
48 24 0.14
49 3 0.02
50 22 0.13
51 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATCTCTAGGCCGATG
Found at i:61269029 original size:140 final size:140
Alignment explanation
Indices: 61268793--61269051 Score: 337
Period size: 140 Copynumber: 1.8 Consensus size: 140
61268783 AGGTCGACAC
* * * **
61268793 CATGTCCCAATCATGGTCTTACACTAGCTCTCGCATATCCATGCCGATGTCATGTCCCTTACATG
1 CATGTCCCAATCATGGTCTTACACTAGCTCTC-CATATCAATGCCAATGTCATGTCACAGACATG
*
61268858 GTCTTACACTGACACATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCT
65 GTCTTACACTGACACATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCT
61268923 CGAGGCCGATA
130 CGAGGCCGATA
* *
61268934 CATGTCCCAGA-CAT-GTCTTACACTAGCTCT-CATTTCAATGTCAATGTCATGTCACAGACATG
1 CATGTCCCA-ATCATGGTCTTACACTAGCTCTCCATATCAATGCCAATGTCATGTCACAGACATG
* * * *
61268996 GTCTTACACTGGCTCTCATAATC-TGGCCGATGCATGTCCTAGACATGTCTTACACT
65 GTCTTACACT-G-ACACAT-ATCGTAGCCGATGCATGTCCCAGACATGTCTTACACT
61269052 AGCACACAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
138 35 0.34
139 1 0.01
140 51 0.50
141 14 0.14
142 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (140 bp):
CATGTCCCAATCATGGTCTTACACTAGCTCTCCATATCAATGCCAATGTCATGTCACAGACATGG
TCTTACACTGACACATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTC
GAGGCCGATA
Found at i:61275426 original size:47 final size:47
Alignment explanation
Indices: 61275354--61275720 Score: 247
Period size: 47 Copynumber: 7.8 Consensus size: 47
61275344 GGTAGAATGC
* *
61275354 CGATGTCATGTCCCAGACATCGTCTTACACTGGCTCATCCATCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGT
*
61275401 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCATCCATCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGT
* ** * * *
61275448 CGATGCCATGTCCCAGACATGGTCTTATACTAACT-ATCGAAATTAAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC--CATCAA-GT
* * * * *
61275497 CAACGCCATGTCCTAGACATGGTCTTACACTAGCTC-TCGCAT-ATCCGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-CATCA--AGT
* * ** * * * *
61275545 GCCGATGTCATATCCCTTACATGGTCTTACACTGACACAT-C-TCGTAGC
1 --CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATC-AAGT
* * *
61275593 CGATG-CATGTTCCAGACAT-GTCTTACACTGGCTTACAT-C-TCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCCATC-AAGT
*
61275639 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTC-T-CATTTCAATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCA--TCAA-GT
* * *
61275685 CGATGTCATGTCACAGACATGGTCTTACATTGGCTC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
61275721 TCATAATCTG
Statistics
Matches: 254, Mismatches: 47, Indels: 37
0.75 0.14 0.11
Matches are distributed among these distances:
43 2 0.01
44 13 0.05
45 12 0.05
46 55 0.22
47 89 0.35
48 22 0.09
49 34 0.13
50 26 0.10
51 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGT
Found at i:61275631 original size:46 final size:46
Alignment explanation
Indices: 61275352--61275761 Score: 216
Period size: 47 Copynumber: 8.7 Consensus size: 46
61275342 GGGGTAGAAT
*
61275352 GCCGATGTCATGTCCCAGACATCGTCTTACACTGG--CTCATC-CATCAA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTC-T-AG
* * *
61275399 GTCGATGCCATGTCCCAGACATGGTCTTACATTGG--CTCATC-CATCAA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTC-T-AG
* * ** * **
61275446 GTCGATGCCATGTCCCAGACATGGTCTTATACTAACTATCGAAAT-TAAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTC-ATCTCT-AG
* * * * * *
61275495 GCCAACGCCATGTCCTAGACATGGTCTTACACTAGCTCTCGCATATC-CG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCT--CATCTCTAG
* ** * *
61275544 TGCCGATGTCATATCCCTTACATGGTCTTACACT-G-ACACATCTCGTA-
1 -GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTC-TAG
* *
61275591 GCCGATGCATGTTCCAGACATGTCTTACACTGGCT-TACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCTAG
* * * *
61275637 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATTTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCTAG
* * * *
61275683 GTCGATGTCATGTCACAGACATGGTCTTACATTGGCTCTCATAATCT-G
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCTAG
*
61275731 GCCGATGCATGTCCCAGACATTTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
61275762 AGCACACAAA
Statistics
Matches: 289, Mismatches: 56, Indels: 37
0.76 0.15 0.10
Matches are distributed among these distances:
44 10 0.03
45 12 0.04
46 71 0.25
47 101 0.35
48 24 0.08
49 40 0.14
50 30 0.10
51 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCTAG
Found at i:61275710 original size:94 final size:95
Alignment explanation
Indices: 61275352--61275764 Score: 295
Period size: 94 Copynumber: 4.4 Consensus size: 95
61275342 GGGGTAGAAT
* * *
61275352 GCCGATGTCATGTCCCAGACATCGTCTTACACTGGCTCATCCA--TCAA-GTCGATGCCATGTCC
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTC-T-CATTTCAATGCCGATGCCATGT-C
* * *
61275414 CAGACATGGTCTTACATTGG--CTCATCCATCAA
63 CAGACATGGTCTTACACTGGCTCTCAT-AATCAG
* * * * * * * * *
61275446 GTCGATGCCATGTCCCAGACATGGTCTTATACTAACTATCGAAATT-AAGGCCAACGCCATGTCC
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATTTCAATGCCGATGCCATGTCC
* *
61275510 TAGACATGGTCTTACACTAGCTCTCGCAT-ATCCG
64 -AGACATGGTCTTACACTGGCTCT--CATAATCAG
* ** * * * *
61275544 TGCCGATGTCATATCCCTTACATGGTCTTACACT-G-ACACATCTC-GTAGCCGATG-CATGTTC
1 -GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATTTCAAT-GCCGATGCCATG-TC
*
61275605 CAGACAT-GTCTTACACTGGCT-TACAT-CTCGAG
63 CAGACATGGTCTTACACTGGCTCT-CATAATC-AG
* *
61275637 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATTTCAATGTCGATGTCATGTCACA
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATTTCAATGCCGATGCCATGTC-CA
* *
61275700 GACATGGTCTTACATTGGCTCTCATAATCTG
65 GACATGGTCTTACACTGGCTCTCATAATCAG
*
61275731 GCCGATG-CATGTCCCAGACAT-TTCTTACACTAGC
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTAGC
61275765 ACACAAATAA
Statistics
Matches: 250, Mismatches: 46, Indels: 46
0.73 0.13 0.13
Matches are distributed among these distances:
90 10 0.04
91 12 0.05
92 27 0.11
93 15 0.06
94 95 0.38
95 19 0.08
96 36 0.14
97 1 0.00
98 5 0.02
99 27 0.11
100 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (95 bp):
GCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATTTCAATGCCGATGCCATGTCCAG
ACATGGTCTTACACTGGCTCTCATAATCAG
Found at i:61284779 original size:23 final size:24
Alignment explanation
Indices: 61284747--61284811 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 24
61284737 TATCAAAATT
61284747 TCATAATCAATCTCATTTTCT-TTC
1 TCAT-ATCAATCTCATTTTCTATTC
*
61284771 TCATATCAATTTCA-TTTCTATTC
1 TCATATCAATCTCATTTTCTATTC
* *
61284794 TCATTTCCACTCTCATTT
1 TCATAT-CAATCTCATTT
61284812 CAGTCTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.15
23 17 0.50
24 10 0.29
25 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (24 bp):
TCATATCAATCTCATTTTCTATTC
Found at i:61284799 original size:12 final size:12
Alignment explanation
Indices: 61284757--61284829 Score: 62
Period size: 12 Copynumber: 6.2 Consensus size: 12
61284747 TCATAATCAA
61284757 TCTCATTTTCT-T
1 TCTCA-TTTCTAT
* *
61284769 TCTCATATCAAT
1 TCTCATTTCTAT
61284781 T-TCATTTCTAT
1 TCTCATTTCTAT
* *
61284792 TCTCATTTCCAC
1 TCTCATTTCTAT
*
61284804 TCTCATTTC-AG
1 TCTCATTTCTAT
61284815 TCTCATTTCATAT
1 TCTCATTTC-TAT
61284828 TC
1 TC
61284830 AAATCATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
11 22 0.45
12 24 0.49
13 3 0.06
ACGTcount: A:0.19, C:0.27, G:0.01, T:0.52
Consensus pattern (12 bp):
TCTCATTTCTAT
Found at i:61287601 original size:11 final size:11
Alignment explanation
Indices: 61287585--61287630 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
61287575 CCATTTTCTA
61287585 AATAAAATAAT
1 AATAAAATAAT
61287596 AAT-AAATATAT
1 AATAAAATA-AT
*
61287607 AAGTAAAATATT
1 AA-TAAAATAAT
61287619 AATAAAATAAT
1 AATAAAATAAT
61287630 A
1 A
61287631 TTTAACTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 5 0.17
11 16 0.53
12 4 0.13
13 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:61289161 original size:36 final size:36
Alignment explanation
Indices: 61289121--61289313 Score: 156
Period size: 36 Copynumber: 5.1 Consensus size: 36
61289111 TAATTATATT
*
61289121 CCCAGCACTAGTCAGATAAACTGACGAAAGTTTGTG
1 CCCAGCACTAGTCAAATAAACTGACGAAAGTTTGTG
** *** * *
61289157 CCCAGTGCTAGTTGGATAAACTGACAAATATTATGGTGTG
1 CCCAGCACTAGTCAAATAAACTGACGAA-AGT-T--TGTG
*
61289197 CCCAGCACAAGTCAAATAAACTGACGAAAGTTTGTG
1 CCCAGCACTAGTCAAATAAACTGACGAAAGTTTGTG
* * *
61289233 CCCAGCGCTAATCAAATAAA-TCGAC-AAATATAATGGTGTG
1 CCCAGCACTAGTCAAATAAACT-GACGAAA-GT--T--TGTG
* *
61289273 CCCAACACTAGTCAAATAAACTGATGAAAGTTTGTG
1 CCCAGCACTAGTCAAATAAACTGACGAAAGTTTGTG
61289309 CCCAG
1 CCCAG
61289314 TGCTAGTTGG
Statistics
Matches: 121, Mismatches: 24, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
35 4 0.03
36 56 0.46
37 2 0.02
38 4 0.03
39 2 0.02
40 49 0.40
41 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (36 bp):
CCCAGCACTAGTCAAATAAACTGACGAAAGTTTGTG
Found at i:61289201 original size:76 final size:76
Alignment explanation
Indices: 61289103--61289357 Score: 332
Period size: 76 Copynumber: 3.4 Consensus size: 76
61289093 TAGACAAATC
** * * * *
61289103 GACAAATATAATTATATTCCCAGCACTAGTCAGATAAACTGACGAAAGTTTGTGCCCAGTGCTAG
1 GACAAATATAATGGTGTGCCCAACACTAGTCAAATAAACTGACGAAAGTTTGTGCCCAGTGCTAG
61289168 TTGGATAAACT
66 TTGGATAAACT
* * * * *
61289179 GACAAATATTATGGTGTGCCCAGCACAAGTCAAATAAACTGACGAAAGTTTGTGCCCAGCGCTAA
1 GACAAATATAATGGTGTGCCCAACACTAGTCAAATAAACTGACGAAAGTTTGTGCCCAGTGCTAG
***
61289244 TCAAATAAA-T
66 TTGGATAAACT
*
61289254 CGACAAATATAATGGTGTGCCCAACACTAGTCAAATAAACTGATGAAAGTTTGTGCCCAGTGCTA
1 -GACAAATATAATGGTGTGCCCAACACTAGTCAAATAAACTGACGAAAGTTTGTGCCCAGTGCTA
*
61289319 GTTGGATAAACC
65 GTTGGATAAACT
* *
61289331 GAAAAATATAATGGTGGGCCCAACACT
1 GACAAATATAATGGTGTGCCCAACACT
61289358 TGTAACAACC
Statistics
Matches: 153, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
75 1 0.01
76 152 0.99
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (76 bp):
GACAAATATAATGGTGTGCCCAACACTAGTCAAATAAACTGACGAAAGTTTGTGCCCAGTGCTAG
TTGGATAAACT
Found at i:61289216 original size:40 final size:40
Alignment explanation
Indices: 61289172--61289296 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
61289162 TGCTAGTTGG
61289172 ATAAACTGACAAATATTATGGTGTGCCCAGCACAAGTCAA
1 ATAAACTGACAAATATTATGGTGTGCCCAGCACAAGTCAA
* * *
61289212 ATAAACTGACGAA-AGT-T--TGTGCCCAGCGCTAA-TCAA
1 ATAAACTGACAAATATTATGGTGTGCCCAGCAC-AAGTCAA
* * *
61289248 ATAAA-TCGACAAATATAATGGTGTGCCCAACACTAGTCAA
1 ATAAACT-GACAAATATTATGGTGTGCCCAGCACAAGTCAA
61289288 ATAAACTGA
1 ATAAACTGA
61289297 TGAAAGTTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
35 1 0.01
36 25 0.37
37 3 0.04
38 2 0.03
39 3 0.04
40 33 0.49
41 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (40 bp):
ATAAACTGACAAATATTATGGTGTGCCCAGCACAAGTCAA
Found at i:61291306 original size:59 final size:53
Alignment explanation
Indices: 61291239--61291372 Score: 151
Period size: 53 Copynumber: 2.4 Consensus size: 53
61291229 TAGGATCTGA
* *
61291239 ATTTAGCCTGGACTGGTAATTCAGACCTAAACTCGTAGGAGTATATGTCATTGTAGGGG
1 ATTTAGCCTGGACTGGTAATCCAGACAT-AACTC-TAGGAGT-TA---CATTGTAGGGG
* * * *
61291298 ATTTAGCCTGGACTGGTAATCCCGACATTACTCTATGAGTTACGTTGTAGGGG
1 ATTTAGCCTGGACTGGTAATCCAGACATAACTCTAGGAGTTACATTGTAGGGG
*
61291351 ATTTAGCCTGGACTAGTAATCC
1 ATTTAGCCTGGACTGGTAATCC
61291373 CACCATAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
53 31 0.46
56 2 0.03
57 6 0.09
58 4 0.06
59 25 0.37
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (53 bp):
ATTTAGCCTGGACTGGTAATCCAGACATAACTCTAGGAGTTACATTGTAGGGG
Found at i:61300950 original size:22 final size:21
Alignment explanation
Indices: 61300925--61300966 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
61300915 AAATTTATTA
61300925 AAAAATCATAAAAAATATAAAC
1 AAAAATCATAAAAAAT-TAAAC
* *
61300947 AAAAGTTATAAAAAATTAAA
1 AAAAATCATAAAAAATTAAA
61300967 ATTATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAATCATAAAAAATTAAAC
Found at i:61301810 original size:4 final size:4
Alignment explanation
Indices: 61301801--61301838 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
61301791 AAATTACTAA
61301801 AAAT AAAT AAAT AAAT ATAGA- AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT A
61301839 TTATAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 27 0.87
5 2 0.06
6 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:61301824 original size:21 final size:21
Alignment explanation
Indices: 61301800--61301839 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
61301790 AAAATTACTA
61301800 AAAATAAATAAATAAATATAG
1 AAAATAAATAAATAAATATAG
61301821 AAAATAAATAAATAAATAT
1 AAAATAAATAAATAAATAT
61301840 TATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAATAAATAAATAAATATAG
Found at i:61301986 original size:27 final size:26
Alignment explanation
Indices: 61301952--61302020 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
61301942 TAAAAGAAGT
*
61301952 AAAA-ATTATAAAAAATTAATAATAC
1 AAAATATTATAAAAAATAAATAATAC
**
61301977 AAAAATATTA-AAAATGAATAAATTTTAC
1 -AAAATATTATAAAA--AATAAATAATAC
61302005 AAAATATTATAAAAAA
1 AAAATATTATAAAAAA
61302021 GCATAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 10 0.28
27 13 0.36
28 13 0.36
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (26 bp):
AAAATATTATAAAAAATAAATAATAC
Found at i:61307718 original size:19 final size:18
Alignment explanation
Indices: 61307694--61307741 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
61307684 TTGTATCTTC
61307694 TTTAAAATTTCATATAATT
1 TTTAAAATTTC-TATAATT
*
61307713 TTTAAAATTTTCTATTATT
1 TTTAAAA-TTTCTATAATT
*
61307732 TTTAATATTT
1 TTTAAAATTT
61307742 TTTGCACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAAATTTCTATAATT
Found at i:61307775 original size:21 final size:19
Alignment explanation
Indices: 61307749--61307809 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
61307739 TTTTTTGCAC
61307749 TTTTCTATATTTTTATAATAA
1 TTTTCTATATTTTTA-AA-AA
61307770 TTTTCTATA-TTTTAAAAA
1 TTTTCTATATTTTTAAAAA
* *
61307788 -TTTCCATATTTTTAACAA
1 TTTTCTATATTTTTAAAAA
61307806 TTTT
1 TTTT
61307810 TTATTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 7 0.19
18 10 0.28
19 5 0.14
20 5 0.14
21 9 0.25
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTCTATATTTTTAAAAA
Found at i:61307913 original size:29 final size:29
Alignment explanation
Indices: 61307881--61307937 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
61307871 ATTTTTGAGA
61307881 CATTTATA-ATATTTTTTACATATTTTTTG
1 CATTTATATATATTTTTTACA-ATTTTTTG
* * *
61307910 CATTTTTATTTATTTTTTATAATTTTTT
1 CATTTATATATATTTTTTACAATTTTTT
61307938 TGTGATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (29 bp):
CATTTATATATATTTTTTACAATTTTTTG
Found at i:61307983 original size:38 final size:35
Alignment explanation
Indices: 61307918--61307993 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 35
61307908 TGCATTTTTA
*
61307918 TTTATTTTTTATAATTTTTTTGTGATTTTGAATAT
1 TTTATTTTTTATAATTTTTTTGTGATTTTCAATAT
*
61307953 TTTAGTTTTTTAATAATTTCTTTTAG-GATTTTCAGTAT
1 TTTA-TTTTTT-ATAATTT-TTTT-GTGATTTTCAATAT
61307991 TTT
1 TTT
61307994 TTTAACAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 4 0.11
36 6 0.17
37 7 0.20
38 17 0.49
39 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.09, T:0.66
Consensus pattern (35 bp):
TTTATTTTTTATAATTTTTTTGTGATTTTCAATAT
Found at i:61310843 original size:18 final size:19
Alignment explanation
Indices: 61310816--61310851 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
61310806 TGTTTTCACC
*
61310816 TTTTTTCTTTTTC-TTTCA
1 TTTTTGCTTTTTCATTTCA
61310834 TTTTTGCTTTTTCATTTC
1 TTTTTGCTTTTTCATTTC
61310852 CAGCAAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTTGCTTTTTCATTTCA
Found at i:61313522 original size:28 final size:29
Alignment explanation
Indices: 61313491--61313557 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 29
61313481 TCTATGTTAT
*
61313491 TTTATTTATATAATTTCTTTT-AAATCTA
1 TTTATATATATAATTTCTTTTCAAATCTA
*
61313519 TTTA-ATATATATTTTCTTTTCAAATCTA
1 TTTATATATATAATTTCTTTTCAAATCTA
*
61313547 -TTATGTATATA
1 TTTATATATATA
61313558 GTTTGTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTATATATATAATTTCTTTTCAAATCTA
Found at i:61313637 original size:3 final size:3
Alignment explanation
Indices: 61313623--61313669 Score: 76
Period size: 3 Copynumber: 15.0 Consensus size: 3
61313613 CTATGGCCAA
61313623 ATT ATAT ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
61313670 TATTTTACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:61318360 original size:15 final size:15
Alignment explanation
Indices: 61318340--61318381 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
61318330 GCTGTAAATG
61318340 GGATTTCCTTATCAT
1 GGATTTCCTTATCAT
* *
61318355 GGATTTCTTTATCTT
1 GGATTTCCTTATCAT
61318370 GGATTTCCTTAT
1 GGATTTCCTTAT
61318382 TCTGGGCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (15 bp):
GGATTTCCTTATCAT
Found at i:61321091 original size:39 final size:39
Alignment explanation
Indices: 61321040--61321257 Score: 301
Period size: 39 Copynumber: 5.6 Consensus size: 39
61321030 GCTCTGATGA
*
61321040 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAGCACTTGCGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGCGT
*
61321079 GCTTTAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGCGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGCGT
* * *
61321118 GCTTCAGTTAGCCTTTGGGCTTCTGTTTAGCATTTGCGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGCGT
* * *
61321157 GCTTCAGTTAGCCTTCGGGCTTTCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGCGT
* * * **
61321196 GCTTCAGTTAGCTTTCGGGCTTCCATTTAGAACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGCGT
* *
61321235 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
61321258 AAATCACGAT
Statistics
Matches: 158, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 158 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGCGT
Found at i:61321153 original size:19 final size:19
Alignment explanation
Indices: 61321047--61321225 Score: 80
Period size: 19 Copynumber: 9.2 Consensus size: 19
61321037 TGAGCTTCAG
*
61321047 TTAGCCTTTGGGCTTCCGT
1 TTAGCATTTGGGCTTCCGT
* **
61321066 TTAGCACTTGCGTGCTTTAG-
1 TTAGCATTTG-G-GCTTCCGT
* *
61321086 TTAGCCTTCGGGCTTCCGT
1 TTAGCATTTGGGCTTCCGT
* *
61321105 TTAGCACTTGCGTGCTTCAG-
1 TTAGCATTTG-G-GCTTCCGT
* *
61321125 TTAGCCTTTGGGCTTCTGT
1 TTAGCATTTGGGCTTCCGT
*
61321144 TTAGCATTTGCGTGCTTCAG-
1 TTAGCATTTG-G-GCTTCCGT
* * *
61321164 TTAGCCTTCGGGCTTTCGT
1 TTAGCATTTGGGCTTCCGT
* * *
61321183 TTAACACTTGTGTGCTTCAG-
1 TTAGCA-TT-TGGGCTTCCGT
*
61321203 TTAGC-TTTCGGGCTTCCAT
1 TTAGCATTT-GGGCTTCCGT
61321222 TTAG
1 TTAG
61321226 AACTTATGTG
Statistics
Matches: 115, Mismatches: 32, Indels: 26
0.66 0.18 0.15
Matches are distributed among these distances:
17 1 0.01
18 24 0.21
19 35 0.30
20 32 0.28
21 23 0.20
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (19 bp):
TTAGCATTTGGGCTTCCGT
Found at i:61322770 original size:52 final size:52
Alignment explanation
Indices: 61322692--61322807 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
61322682 TGGGCACAGG
*
61322692 ACATGGGCGTGTCCCAAGCCACACGGATGTGTGTGACCACACGCCCCAATCC
1 ACATGGGCGTGTCCCAAGCCACACGGATGTGTGTGACCACAAGCCCCAATCC
* *
61322744 ACATGGGCGTGTCCCAAGCCACACGGATGTGTGTGACCACAAGCCCTAATCT
1 ACATGGGCGTGTCCCAAGCCACACGGATGTGTGTGACCACAAGCCCCAATCC
61322796 ACATGGGCGTGT
1 ACATGGGCGTGT
61322808 GACTCTCCGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (52 bp):
ACATGGGCGTGTCCCAAGCCACACGGATGTGTGTGACCACAAGCCCCAATCC
Found at i:61326870 original size:44 final size:43
Alignment explanation
Indices: 61326804--61327093 Score: 167
Period size: 44 Copynumber: 6.5 Consensus size: 43
61326794 GGTTACAAAC
*
61326804 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTGATAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGTGA-AAGT
* * * * *
61326848 CTTATCTCCCTAAAGTTACAGT-GAACAAGCTGAAGATAGCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAG-T-G-AAAGT
* *
61326892 CTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAGAAAAACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAG---T-G---AA-AG-T
* * * * * * * * * *
61326944 CTTATCTCTCTAAAGTTACAATAGAGCA-GATCATAG-CAAA-C
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGA-AGTGAAAGT
61326985 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGTGACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGTGA-AAGT
* * * * * * *
61327029 TTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTCAATATGCAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAA-GTGAAAGT
*
61327073 CTTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAG
61327094 CAGAGCAGAC
Statistics
Matches: 183, Mismatches: 46, Indels: 34
0.70 0.17 0.13
Matches are distributed among these distances:
41 24 0.13
42 4 0.02
43 13 0.07
44 95 0.52
45 15 0.08
47 4 0.02
49 1 0.01
50 1 0.01
51 2 0.01
52 24 0.13
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGTGAAAGT
Found at i:61328819 original size:28 final size:29
Alignment explanation
Indices: 61328788--61328854 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 29
61328778 TCTATGTTAT
* *
61328788 TTTATTTATATAATTTCTTTT-GAATCTA
1 TTTATATATATAATTTCTTTTCAAATCTA
*
61328816 TTTA-ATATATATTTTCTTTTCAAATCTA
1 TTTATATATATAATTTCTTTTCAAATCTA
*
61328844 -TTATGTATATA
1 TTTATATATATA
61328855 GTTTGTTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 17 0.52
28 16 0.48
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTATATATATAATTTCTTTTCAAATCTA
Found at i:61333454 original size:3 final size:3
Alignment explanation
Indices: 61333446--61333472 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
61333436 AATAACATTG
61333446 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
61333473 GTTTCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61335721 original size:6 final size:6
Alignment explanation
Indices: 61335710--61335736 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
61335700 AGGTTTTTTT
61335710 ATTATA ATTATA ATTATA ATTATA ATT
1 ATTATA ATTATA ATTATA ATTATA ATT
61335737 GCTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:61341505 original size:33 final size:33
Alignment explanation
Indices: 61341452--61341516 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
61341442 TAAGGGGTGT
* * * *
61341452 TACATCATTGTTCAATTTTTTTACTTGTATTGA
1 TACATCACTGCTCAAGTTTTTTACTTATATTGA
61341485 TACATCACTGCTCAAGTTTTTTACTTATATTG
1 TACATCACTGCTCAAGTTTTTTACTTATATTG
61341517 GTACTTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (33 bp):
TACATCACTGCTCAAGTTTTTTACTTATATTGA
Found at i:61342025 original size:10 final size:10
Alignment explanation
Indices: 61341987--61342067 Score: 63
Period size: 11 Copynumber: 7.6 Consensus size: 10
61341977 TTATTTAGAT
61341987 AATTACTAAAA
1 AATTA-TAAAA
*
61341998 TATTAATAAAA
1 AATT-ATAAAA
61342009 AACTTATAAAA
1 AA-TTATAAAA
*
61342020 AATTATTTAAA
1 AATTA-TAAAA
* *
61342031 AATTATTAAT
1 AATTATAAAA
*
61342041 AATTAATAAGA
1 AATT-ATAAAA
*
61342052 AATTATAAGA
1 AATTATAAAA
61342062 AATTAT
1 AATTAT
61342068 TAAATTTATT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
10 23 0.39
11 33 0.56
12 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AATTATAAAA
Found at i:61342036 original size:21 final size:21
Alignment explanation
Indices: 61341977--61342068 Score: 69
Period size: 21 Copynumber: 4.2 Consensus size: 21
61341967 TTGGACAAGG
* *
61341977 TTATTTAGATAATTACTAAAATA
1 TTATTTA-AAAATTA-TAAAAAA
* *
61342000 TTAATAAAAAACTTATAAAAAA
1 TTATTTAAAAA-TTATAAAAAA
* *
61342022 TTATTTAAAAATTATTAATAA
1 TTATTTAAAAATTATAAAAAA
* *
61342043 TTA-ATAAGAAATTATAAGAAA
1 TTATTTAA-AAATTATAAAAAA
61342064 TTATT
1 TTATT
61342069 AAATTTATTA
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
20 3 0.06
21 24 0.45
22 18 0.34
23 8 0.15
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.39
Consensus pattern (21 bp):
TTATTTAAAAATTATAAAAAA
Found at i:61342106 original size:10 final size:10
Alignment explanation
Indices: 61341987--61342112 Score: 80
Period size: 10 Copynumber: 12.3 Consensus size: 10
61341977 TTATTTAGAT
*
61341987 AATTACTAAA
1 AATTATTAAA
*
61341997 ATATTAATAAAA
1 A-ATT-ATTAAA
*
61342009 AACTTATAAAA
1 AA-TTATTAAA
61342020 AATTATTTAAA
1 AATTA-TTAAA
*
61342031 AATTATTAAT
1 AATTATTAAA
*
61342041 AATTAATAAGA
1 AATTATTAA-A
61342052 AATTA-TAAGA
1 AATTATTAA-A
61342062 AATTATT-AA
1 AATTATTAAA
*
61342071 ATTTATTAAA
1 AATTATTAAA
**
61342081 GAA-TAACAAA
1 -AATTATTAAA
*
61342091 AA-TATTTAA
1 AATTATTAAA
61342100 AATTATTAAA
1 AATTATTAAA
61342110 AAT
1 AAT
61342113 CATGTCTAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 18
0.74 0.11 0.14
Matches are distributed among these distances:
9 15 0.16
10 43 0.46
11 28 0.30
12 7 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AATTATTAAA
Found at i:61359363 original size:101 final size:100
Alignment explanation
Indices: 61359164--61359536 Score: 414
Period size: 101 Copynumber: 3.8 Consensus size: 100
61359154 CTGTTACGCA
*
61359164 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACGTAGTAGCCTGCAC-T
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACGTAGTAGCCTGCACTT
** * * *
61359228 A-T--TACACAGGTGACCTAACCATCTGATACACG
66 AGTACTACACACATGACCTAACAATTTGGTACACG
* * * * * * * *
61359260 TAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGCTATCGGGTACGCATAGTAGCTTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCTGGTACACGTAGTAGCCTGCACT
*
61359325 TAGTACTACACATATGACCTAACAATTTGGTACACG
65 TAGTACTACACACATGACCTAACAATTTGGTACACG
* * * *
61359361 TAGTAGCCTGCACTTAGTACTTCACACGTGACCTAACCATCTGATATACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACGTAGTAGCCTGCACTT
*** * * * *
61359426 AGTACTACACACATGATGAAAGCTA-TCGAGTACGCA
66 AGTACTACACACATGACCTAA-CAATTTG-GTACACG
* * * *
61359462 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTCGTATCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACGTAGTAGCCTGCACTT
61359527 AGTACTACAC
66 AGTACTACAC
61359537 GACCTAAAAC
Statistics
Matches: 229, Mismatches: 41, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
96 32 0.14
97 22 0.10
98 2 0.01
99 1 0.00
100 41 0.18
101 131 0.57
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (100 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACGTAGTAGCCTGCACTT
AGTACTACACACATGACCTAACAATTTGGTACACG
Found at i:61359373 original size:50 final size:50
Alignment explanation
Indices: 61359164--61359536 Score: 414
Period size: 50 Copynumber: 7.5 Consensus size: 50
61359154 CTGTTACGCA
*
61359164 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * *
61359214 TAGTAGCCTGCAC-TA-T--TACACAGGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * * * * *
61359260 TAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGCTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCTGGTACACG
* ** *
61359311 TAGTAGCTTGCACTTAGTACTACACATATGACCTAACAATTTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * *
61359361 TAGTAGCCTGCACTTAGTACTTCACACGTGACCTAACCATCTGATATACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* *** * * *
61359411 TAGTAGCCTGCACTTAGTACTACACACATGATGAAAGCTATC-GAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCTG-GTACACG
* *
61359462 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* *
61359512 TCGTATCCTGCACTTAGTACTACAC
1 TAGTAGCCTGCACTTAGTACTACAC
61359537 GACCTAAAAC
Statistics
Matches: 263, Mismatches: 52, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
46 40 0.15
47 2 0.01
48 2 0.01
49 2 0.01
50 140 0.53
51 77 0.29
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
Found at i:61359464 original size:151 final size:151
Alignment explanation
Indices: 61359158--61359536 Score: 606
Period size: 151 Copynumber: 2.5 Consensus size: 151
61359148 AGCTCTCTGT
61359158 TACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACGTAGTAGCCT
1 TACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACGTAGTAGCCT
*
61359223 GCAC-TA-T--TACACAGGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACA
66 GCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACA
* * *
61359284 TACGTGATCGAAGCTATCGGG
131 CACATGATCGAAGCTATCGAG
* * *
61359305 TACGCATAGTAGCTTGCACTTAGTACTACACATATGACCTAACAATTTGGTACACGTAGTAGCCT
1 TACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACGTAGTAGCCT
* *
61359370 GCACTTAGTACTTCACACGTGACCTAACCATCTGATATACGTAGTAGCCTGCACTTAGTACTACA
66 GCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACA
61359435 CACATGAT-GAAAGCTATCGAG
131 CACATGATCG-AAGCTATCGAG
* * *
61359456 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTCGTATCCT
1 TACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACGTAGTAGCCT
61359521 GCACTTAGTACTACAC
66 GCACTTAGTACTACAC
61359537 GACCTAAAAC
Statistics
Matches: 211, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
147 66 0.31
148 2 0.01
149 1 0.00
150 1 0.00
151 141 0.67
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (151 bp):
TACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTGGTACACGTAGTAGCCT
GCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACA
CACATGATCGAAGCTATCGAG
Found at i:61363346 original size:25 final size:25
Alignment explanation
Indices: 61363314--61363382 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
61363304 TATTATTAGA
61363314 TATTGTTAGTTTTTATTTTTACTAT
1 TATTGTTAGTTTTTATTTTTACTAT
*
61363339 TATTGTTAGTTTTTATTTTTATTAT
1 TATTGTTAGTTTTTATTTTTACTAT
* *
61363364 TCTTCTTAGGTTTATTATT
1 TATTGTTA-GTTT-TTATT
61363383 ATCCTTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
25 30 0.77
26 4 0.10
27 5 0.13
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (25 bp):
TATTGTTAGTTTTTATTTTTACTAT
Found at i:61372825 original size:47 final size:45
Alignment explanation
Indices: 61372771--61372898 Score: 150
Period size: 44 Copynumber: 2.8 Consensus size: 45
61372761 TACCTTCAGT
* *
61372771 CTGCTCCACTACAAATTCAGGGAGATAAGACTTGTTGTAACTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTG--ACTTCAAC
* ** * * *
61372818 CTGCTCCACTGCAACTTCAGGGAGATAAG-GTTAATGGCTTCGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTGACTTCAAC
*
61372862 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTTG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTG
61372899 GGGTGATTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 34 0.49
45 4 0.06
46 4 0.06
47 27 0.39
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTGACTTCAAC
Found at i:61373953 original size:51 final size:51
Alignment explanation
Indices: 61373854--61373956 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
61373844 ATGCCCCTTT
* * * * **
61373854 GGTCTCAAGGCGCCCTTTGCGGGTTTCACCTTGGCCTCTCCTTTTTTTTAA
1 GGTCCCAAAGCGCCCTTTGCGGGTTTCACATAGGCCTCTCCTCCTTTTTAA
*
61373905 GGTCCCAAAGCGCCCTTTGCGGGTTTTCGCATAGGCCTCTCC-CCTTTTTAA
1 GGTCCCAAAGCGCCCTTTGCGGG-TTTCACATAGGCCTCTCCTCCTTTTTAA
61373956 G
1 G
61373957 TGAAGTACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 29 0.66
52 15 0.34
ACGTcount: A:0.12, C:0.31, G:0.22, T:0.35
Consensus pattern (51 bp):
GGTCCCAAAGCGCCCTTTGCGGGTTTCACATAGGCCTCTCCTCCTTTTTAA
Found at i:61378911 original size:40 final size:40
Alignment explanation
Indices: 61378865--61379089 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
61378855 CTTGCACAAG
* * *
61378865 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
61378905 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
61378945 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
61378985 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
61379025 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
61379066 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
61379090 CATTCGAATA
Statistics
Matches: 159, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 129 0.81
41 29 0.18
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:61378960 original size:80 final size:80
Alignment explanation
Indices: 61378829--61379089 Score: 312
Period size: 80 Copynumber: 3.3 Consensus size: 80
61378819 CTCAAGTAAT
* * * * * * *
61378829 CTTCGGGATTTAG-CCGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
61378892 CACTAGCATAAATGC
66 CACTAGCACAAATGC
* * *
61378907 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTTTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
*
61378971 TCGCTAGCACAAATGC
65 TCACTAGCACAAATGC
* * * * * *
61378987 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
61379052 CACCTAGCACAAAAGC
66 CA-CTAGCACAAATGC
61379068 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
61379090 CATTCGAATA
Statistics
Matches: 155, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
78 12 0.08
79 16 0.10
80 94 0.61
81 33 0.21
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:61382178 original size:18 final size:17
Alignment explanation
Indices: 61382154--61382213 Score: 77
Period size: 18 Copynumber: 3.5 Consensus size: 17
61382144 ATAATCTTCA
61382154 ATGATATGCAATCTTAG
1 ATGATATGCAATCTTAG
61382171 AGTGATATGCAATCTTAG
1 A-TGATATGCAATCTTAG
*
61382189 AT-ATGATACAATCTTAG
1 ATGAT-ATGCAATCTTAG
*
61382206 AAGATATG
1 ATGATATG
61382214 ATTTTCTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.05
17 16 0.43
18 19 0.51
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (17 bp):
ATGATATGCAATCTTAG
Found at i:61382577 original size:7 final size:7
Alignment explanation
Indices: 61382560--61382666 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
61382550 AAATTTGTAA
61382560 ATTAT-T
1 ATTATAT
61382566 ATTATAT
1 ATTATAT
61382573 ATTATAT
1 ATTATAT
61382580 -TT-TA-
1 ATTATAT
61382584 ACTTATAT
1 A-TTATAT
61382592 ATCTTATAT
1 A--TTATAT
*
61382601 ATTTATTT
1 A-TTATAT
61382609 ATT-TAT
1 ATTATAT
*
61382615 ATTATAC
1 ATTATAT
61382622 ATTAT-T
1 ATTATAT
* *
61382628 -TTAAAA
1 ATTATAT
*
61382634 ACTTACAT
1 A-TTATAT
*
61382642 -TTTTAT
1 ATTATAT
61382648 ATTATAT
1 ATTATAT
*
61382655 ATTATAA
1 ATTATAT
61382662 ATTAT
1 ATTAT
61382667 TTCATTTATT
Statistics
Matches: 77, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 35 0.45
8 11 0.14
9 8 0.10
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTATAT
Found at i:61382610 original size:21 final size:21
Alignment explanation
Indices: 61382568--61382702 Score: 65
Period size: 21 Copynumber: 6.7 Consensus size: 21
61382558 AAATTATTAT
*
61382568 TATATATTATAT-TTTAACTTA
1 TATATATTATATATTT-ATTTA
*
61382589 TATATCTTATATATTTATTTA
1 TATATATTATATATTTATTTA
* *
61382610 TTTATATTATACA-TTATTT-
1 TATATATTATATATTTATTTA
* * * * *
61382629 TAAAAACTTACATTTTTATAT-
1 TATATA-TTATATATTTATTTA
*
61382650 TATATATTATA-AATTATTTCA
1 TATATATTATATATTTATTT-A
61382671 T-T-TATTAT-TA-TT-TTTA
1 TATATATTATATATTTATTTA
*
61382687 TATACTATCATATATT
1 TATA-TATTATATATT
61382703 ATCTATTTTA
Statistics
Matches: 84, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
16 2 0.02
17 4 0.05
18 2 0.02
19 20 0.24
20 17 0.20
21 36 0.43
22 3 0.04
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATATTATATATTTATTTA
Found at i:61390802 original size:11 final size:10
Alignment explanation
Indices: 61390780--61390874 Score: 79
Period size: 11 Copynumber: 9.3 Consensus size: 10
61390770 TCTATTTCAG
61390780 AAAAAGAAAA
1 AAAAAGAAAA
61390790 AAAAAG--AA
1 AAAAAGAAAA
*
61390798 GAAAAGAAAA
1 AAAAAGAAAA
61390808 AGAAAAGAAAA
1 A-AAAAGAAAA
61390819 AGAAAAGAAAA
1 A-AAAAGAAAA
* *
61390830 AGAGAGAAAA
1 AAAAAGAAAA
*
61390840 AAGAAAAAAGAGA
1 AA-AAAGAA-A-A
*
61390853 AAAAAG-AGA
1 AAAAAGAAAA
61390862 AAAAAGAAAA
1 AAAAAGAAAA
61390872 AAA
1 AAA
61390875 GAAAAATGGA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.10
9 7 0.10
10 21 0.31
11 26 0.38
12 4 0.06
13 3 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:61390807 original size:16 final size:15
Alignment explanation
Indices: 61390778--61390880 Score: 102
Period size: 16 Copynumber: 6.5 Consensus size: 15
61390768 CTTCTATTTC
*
61390778 AGAAAAAGAAAAAAAA
1 AGAAAAA-AAGAAAAA
*
61390794 AGAAGAAAAG-AAAA
1 AGAAAAAAAGAAAAA
61390808 AGAAAAGAAA-AAGAAA
1 AGAAAA-AAAGAA-AAA
61390824 AGAAAAAGAGAGAAAAA
1 AGAAAAA-A-AGAAAAA
61390841 AGAAAAAAGAGAAAAA
1 AGAAAAAA-AGAAAAA
61390857 AGAGAAAAAAGAAAAAA
1 AGA-AAAAAAG-AAAAA
61390874 AGAAAAA
1 AGAAAAA
61390881 TGGAGAGGCC
Statistics
Matches: 76, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
14 9 0.12
15 7 0.09
16 34 0.45
17 24 0.32
18 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:61390886 original size:25 final size:24
Alignment explanation
Indices: 61390778--61390886 Score: 116
Period size: 25 Copynumber: 4.5 Consensus size: 24
61390768 CTTCTATTTC
* * *
61390778 AGAAAAAGAAAAAAAAAGAAGAAA
1 AGAAAAAGGAGAAAAAAGAAAAAA
*
61390802 AGAAAAA-GA-AAAGAAA-AAGAAA
1 AGAAAAAGGAGAAA-AAAGAAAAAA
61390824 AGAAAAAGAGAGAAAAAAGAAAAAA
1 AGAAAAAG-GAGAAAAAAGAAAAAA
*
61390849 GAGAAAAAAGAGAAAAAAGAAAAAA
1 -AGAAAAAGGAGAAAAAAGAAAAAA
61390874 AGAAAAATGGAGA
1 AGAAAAA-GGAGA
61390887 GGCCAAGGTG
Statistics
Matches: 74, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
22 16 0.22
23 4 0.05
24 19 0.26
25 28 0.38
26 7 0.09
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (24 bp):
AGAAAAAGGAGAAAAAAGAAAAAA
Found at i:61391890 original size:44 final size:44
Alignment explanation
Indices: 61391842--61391928 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
61391832 GATTTTAGTA
* * *
61391842 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAGATT
61391886 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAGAT
1 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAGAT
61391929 CTAACCTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (44 bp):
TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAGATT
Found at i:61392135 original size:119 final size:119
Alignment explanation
Indices: 61391920--61392513 Score: 1035
Period size: 119 Copynumber: 5.0 Consensus size: 119
61391910 CAAATCGAAG
61391920 ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
1 ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
* *
61391985 TTACAAGGAACAAATCGAGGACATAGTAGATTTGACTCTCAGACGTTCTCAAAG
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* *
61392039 ATAGCAGATCTAACCTTTAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
1 ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
* *
61392104 TTACAAGGAACAAATCGAGGACTTAGCAGATTTGACTCTCAAACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* *
61392158 ATAACAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
61392223 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
*
61392277 ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
*
61392342 TTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* * *
61392396 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGC
1 ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
* * * *
61392461 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAA
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAA
61392514 CAGACTCAAG
Statistics
Matches: 452, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 452 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (119 bp):
ATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
Found at i:61392542 original size:83 final size:83
Alignment explanation
Indices: 61392437--61392735 Score: 485
Period size: 83 Copynumber: 3.6 Consensus size: 83
61392427 GAAGCAGATC
*
61392437 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
61392502 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
*
61392520 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCAAGGACATTGCAGATATGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
61392585 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
61392603 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
1 CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
*
61392668 TATGTTCTCAAGA-AGA-T
66 AATGTTCTCAA-ACAGACT
* * * *
61392685 CCAAGATGGTTTAGTATCCTTGTACTTACAAGGAATACAAATCGAAGACAT
1 -CAAGATGGTTTGGCATCCTTGTGCTTACAAGG-A-ACAAATCGAGGACAT
61392736 AGCTGGTTTG
Statistics
Matches: 204, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
82 1 0.00
83 187 0.92
84 2 0.01
85 14 0.07
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (83 bp):
CAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
AATGTTCTCAAACAGACT
Found at i:61393311 original size:19 final size:19
Alignment explanation
Indices: 61393286--61393374 Score: 134
Period size: 17 Copynumber: 4.9 Consensus size: 19
61393276 ATAATCTTCA
61393286 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
61393305 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
61393324 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
61393341 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
61393359 ATGATA--CAATCTTAGA
1 ATGATATGCAATCTTAGA
61393375 AGATATGATT
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
17 26 0.40
18 16 0.25
19 23 0.35
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:61393356 original size:35 final size:36
Alignment explanation
Indices: 61393294--61393381 Score: 146
Period size: 35 Copynumber: 2.5 Consensus size: 36
61393284 CAATGATATG
*
61393294 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
61393330 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
61393365 CAATCTTAGA-A-GATATG
1 CAATCTTAGATATGATATG
61393382 ATTTTGTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
33 3 0.06
34 3 0.06
35 29 0.58
36 15 0.30
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (36 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGATA
Found at i:61396476 original size:21 final size:22
Alignment explanation
Indices: 61396438--61396478 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
61396428 CTCCCGTTTT
* *
61396438 CATTTTTCTTAAAGTCGATTCC
1 CATTTTTCTAAAACTCGATTCC
61396460 CATTTTTC-AAAACTCGATT
1 CATTTTTCTAAAACTCGATT
61396479 TGAAAATGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (22 bp):
CATTTTTCTAAAACTCGATTCC
Found at i:61406658 original size:11 final size:11
Alignment explanation
Indices: 61406642--61406692 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
61406632 TTAGTTAAGG
61406642 TTTTCATTTTT
1 TTTTCATTTTT
61406653 TTTTCA-TTTT
1 TTTTCATTTTT
*
61406663 TTTTCATTTCT
1 TTTTCATTTTT
61406674 TTTT-ATTTTAT
1 TTTTCATTTT-T
61406685 TTTT-ATTT
1 TTTTCATTT
61406693 CTTCATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
10 14 0.39
11 22 0.61
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCATTTTT
Found at i:61406662 original size:10 final size:10
Alignment explanation
Indices: 61406642--61406692 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
61406632 TTAGTTAAGG
61406642 TTTTCATTTTT
1 TTTTCA-TTTT
61406653 TTTTCATTTT
1 TTTTCATTTT
61406663 TTTTCATTTCT
1 TTTTCATTT-T
61406674 TTTT-ATTTT
1 TTTTCATTTT
*
61406683 ATTTTTATTT
1 -TTTTCATTT
61406693 CTTCATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.03
10 21 0.57
11 15 0.41
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:61406668 original size:21 final size:21
Alignment explanation
Indices: 61406642--61406695 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
61406632 TTAGTTAAGG
*
61406642 TTTTCATTTTTTTTTCATTTT-
1 TTTTCATTTCTTTTT-ATTTTA
61406663 TTTTCATTTCTTTTTATTTTA
1 TTTTCATTTCTTTTTATTTTA
*
61406684 TTTTTATTTCTT
1 TTTTCATTTCTT
61406696 CATTTTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTCATTTCTTTTTATTTTA
Found at i:61408467 original size:26 final size:26
Alignment explanation
Indices: 61408432--61408488 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
61408422 TAATTTTTCT
61408432 ATAATATGATTTTTTGGTCACAATGA
1 ATAATATGATTTTTTGGTCACAATGA
61408458 ATAATATGATTTTTTGGTCACAATGA
1 ATAATATGATTTTTTGGTCACAATGA
61408484 ATAAT
1 ATAAT
61408489 GTGACTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (26 bp):
ATAATATGATTTTTTGGTCACAATGA
Found at i:61411404 original size:21 final size:21
Alignment explanation
Indices: 61411365--61411405 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
61411355 TTTCGCTATA
*
61411365 TAATATTTTATTTTTTTGTTT
1 TAATATTTTATTTTCTTGTTT
61411386 TAAT-TTTTATTTTCCTTGTT
1 TAATATTTTATTTT-CTTGTT
61411406 CAAGATTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (21 bp):
TAATATTTTATTTTCTTGTTT
Found at i:61412515 original size:19 final size:20
Alignment explanation
Indices: 61412474--61412515 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
61412464 ATTTTTATTA
**
61412474 TTTTGTTTTTGATATGTTTG
1 TTTTGTTTTTGATATGTGGG
*
61412494 TTTTGTTTTT-CTATGTGGG
1 TTTTGTTTTTGATATGTGGG
61412513 TTT
1 TTT
61412516 ACCTACCGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.07, C:0.02, G:0.21, T:0.69
Consensus pattern (20 bp):
TTTTGTTTTTGATATGTGGG
Found at i:61415086 original size:93 final size:93
Alignment explanation
Indices: 61414974--61415144 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
61414964 GCCCATAAGT
* *
61414974 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61415039 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
61415067 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
61415132 CGAGTTCGGATGC
66 CGAGCTCGGATGC
61415145 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:61415141 original size:46 final size:46
Alignment explanation
Indices: 61414966--61415141 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
61414956 TGTAACCCGC
* *
61414966 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
61415012 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
61415058 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
61415105 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
61415142 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:61416897 original size:22 final size:22
Alignment explanation
Indices: 61416872--61416916 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
61416862 TAATCATATT
*
61416872 TTAAGGTTAAATTAAAT-GTTAA
1 TTAAGCTT-AATTAAATGGTTAA
*
61416894 TTAAGCTTAATTCAATGGTTAA
1 TTAAGCTTAATTAAATGGTTAA
61416916 T
1 T
61416917 CAACTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TTAAGCTTAATTAAATGGTTAA
Found at i:61416923 original size:21 final size:21
Alignment explanation
Indices: 61416881--61416923 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
61416871 TTTAAGGTTA
*
61416881 AATTAAATGTTAATTAAGCTT
1 AATTAAATGTTAATCAAGCTT
*
61416902 AATTCAATGGTTAATCAA-CTT
1 AATTAAAT-GTTAATCAAGCTT
61416923 A
1 A
61416924 TATAAGCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
AATTAAATGTTAATCAAGCTT
Found at i:61431311 original size:15 final size:16
Alignment explanation
Indices: 61431293--61431330 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
61431283 AATTGAAAAG
61431293 ATGAAAATTT-ATTAA
1 ATGAAAATTTAATTAA
*
61431308 ATGACAATTTAATTAA
1 ATGAAAATTTAATTAA
61431324 ATGAAAA
1 ATGAAAA
61431331 AGAAAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (16 bp):
ATGAAAATTTAATTAA
Found at i:61437115 original size:23 final size:23
Alignment explanation
Indices: 61437065--61437124 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
61437055 CAGCTCATTG
** *
61437065 GAGCTTACCGTTTCAGGTCGATA
1 GAGCTTACCGTTTCAACTCAATA
*
61437088 CAGCTTACCGTTTCAACTCAATA
1 GAGCTTACCGTTTCAACTCAATA
*
61437111 GAGCTTATCGTTTC
1 GAGCTTACCGTTTC
61437125 GGCTTATTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (23 bp):
GAGCTTACCGTTTCAACTCAATA
Found at i:61438531 original size:20 final size:20
Alignment explanation
Indices: 61438506--61438576 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
61438496 ACATAGTGAA
61438506 TGAGAATGATTGATATTGAC
1 TGAGAATGATTGATATTGAC
** * *
61438526 TGAGAATAGAAAGTACTTAGTGAA
1 TGAGAAT-GATTG-A--TATTGAC
*
61438550 TGAGAATGATTGATGTTGAC
1 TGAGAATGATTGATATTGAC
61438570 TGAGAAT
1 TGAGAAT
61438577 AGATGTTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
20 18 0.47
21 3 0.08
22 2 0.05
23 3 0.08
24 12 0.32
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (20 bp):
TGAGAATGATTGATATTGAC
Found at i:61438541 original size:44 final size:44
Alignment explanation
Indices: 61438492--61438579 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
61438482 TGCTTTTTTT
61438492 AAGTACATAGTGAATGAGAATGATTGATATTGACTGAGAATAGA
1 AAGTACATAGTGAATGAGAATGATTGATATTGACTGAGAATAGA
* *
61438536 AAGTACTTAGTGAATGAGAATGATTGATGTTGACTGAGAATAGA
1 AAGTACATAGTGAATGAGAATGATTGATATTGACTGAGAATAGA
61438580 TGTTATTGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (44 bp):
AAGTACATAGTGAATGAGAATGATTGATATTGACTGAGAATAGA
Found at i:61440247 original size:34 final size:34
Alignment explanation
Indices: 61440181--61440247 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
61440171 CCAGAAAATA
* *
61440181 TTAAGTTTTGTTTGAATGATGAATTTTAATGGAG
1 TTAAGTTTCGTTTGAATGATGAATTTCAATGGAG
*
61440215 TTAAGTTTCGTTTGAATGATGAATTTCGATGGA
1 TTAAGTTTCGTTTGAATGATGAATTTCAATGGA
61440248 TATATGTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.24, T:0.45
Consensus pattern (34 bp):
TTAAGTTTCGTTTGAATGATGAATTTCAATGGAG
Found at i:61447077 original size:76 final size:74
Alignment explanation
Indices: 61446926--61447202 Score: 271
Period size: 76 Copynumber: 3.7 Consensus size: 74
61446916 TAATTTGAAA
* * *
61446926 TTCAAATTAGGATAAGAAGATAAAAAAATATATGGAACTTTAATTCTATTTAAATTTTAAACAAG
1 TTCAAATTAGGATAAGAAGAT--AATAA-ATA-GGAAATTTAATTCTATTTAAATTTTAAAGAAG
*
61446991 AATAAAATATGAT
62 GATAAAATATGAT
* *
61447004 TTCAAATTAGGATAAGAAGATAATAAGATACGAAAATTTAATTCTATTTAAATTATAAAGAAGGA
1 TTCAAATTAGGATAAGAAGATAATAA-ATA-GGAAATTTAATTCTATTTAAATTTTAAAGAAGGA
*
61447069 TAAGATATGAT
64 TAAAATATGAT
* * ** *
61447080 TTCAAATTATGATAA-AA-A-CAT--AT-GGACTTTTAATTCTATTTTAATTTTTAAAGAAGGAT
1 TTCAAATTAGGATAAGAAGATAATAAATAGGAAATTTAATTCTA-TTTAAATTTTAAAGAAGGAT
*
61447139 AATATATGAT
65 AAAATATGAT
* * *
61447149 TTCAAATTAGGATAAGAAGATAAAAACATATGG-AATTCTATTTCTATTTGAATT
1 TTCAAATTAGGATAAGAAGATAATAA-ATA-GGAAATT-TAATTCTATTTAAATT
61447203 ATCTTTTATT
Statistics
Matches: 164, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
68 12 0.07
69 41 0.25
70 4 0.02
71 1 0.01
72 1 0.01
73 2 0.01
74 1 0.01
75 4 0.02
76 68 0.41
77 9 0.05
78 21 0.13
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (74 bp):
TTCAAATTAGGATAAGAAGATAATAAATAGGAAATTTAATTCTATTTAAATTTTAAAGAAGGATA
AAATATGAT
Found at i:61450488 original size:30 final size:30
Alignment explanation
Indices: 61450454--61450514 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
61450444 TCCTTAACTC
61450454 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
61450484 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
61450514 A
1 A
61450515 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:61478003 original size:21 final size:21
Alignment explanation
Indices: 61477973--61478023 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
61477963 AAGTAGTTAA
* * *
61477973 GGTTCGCATATAATTTCTATG
1 GGTTCACATATAACTTCTACG
61477994 GGTTCACATATAACTTCTACG
1 GGTTCACATATAACTTCTACG
*
61478015 TGTTCACAT
1 GGTTCACAT
61478024 TACAGTTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (21 bp):
GGTTCACATATAACTTCTACG
Found at i:61482136 original size:16 final size:16
Alignment explanation
Indices: 61482100--61482137 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
61482090 AATTATATTC
61482100 AATAATTTTATAGATT
1 AATAATTTTATAGATT
*
61482116 TATAATTTTATTA-ATT
1 AATAATTTTA-TAGATT
61482132 AATAAT
1 AATAAT
61482138 ATATTATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATAATTTTATAGATT
Found at i:61497457 original size:16 final size:18
Alignment explanation
Indices: 61497431--61497464 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
61497421 TTAAAATTGG
61497431 ATTGAGAAAATTA-TTTA
1 ATTGAGAAAATTAGTTTA
61497448 ATTG-GAAAATTAGTTTA
1 ATTGAGAAAATTAGTTTA
61497465 TCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (18 bp):
ATTGAGAAAATTAGTTTA
Found at i:61497873 original size:20 final size:19
Alignment explanation
Indices: 61497833--61497873 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
61497823 AAATAGTGAG
*
61497833 AAATTTATTTTCTAAGTAT
1 AAATTTATTTTCTAAGAAT
*
61497852 AAATTCTATTTTCTAGGAAT
1 AAATT-TATTTTCTAAGAAT
61497872 AA
1 AA
61497874 CAATTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (19 bp):
AAATTTATTTTCTAAGAAT
Found at i:61502600 original size:43 final size:43
Alignment explanation
Indices: 61502552--61502652 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
61502542 ACGAACTCGC
* * *
61502552 ACACTTAATGCCGATTAATTAGTTGAAACTATAATTGTATCGT
1 ACACTTAATGCCAATTAATTAGTCGAAACTACAATTGTATCGT
* ** *
61502595 ACACTTAGTGCCAATTAATTAGTCGAGGCTACAATTGTATCGC
1 ACACTTAATGCCAATTAATTAGTCGAAACTACAATTGTATCGT
* *
61502638 ACATTTAGTGCCAAT
1 ACACTTAATGCCAAT
61502653 ACATTAAACC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (43 bp):
ACACTTAATGCCAATTAATTAGTCGAAACTACAATTGTATCGT
Found at i:61507705 original size:27 final size:27
Alignment explanation
Indices: 61507675--61507852 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
61507665 ATATTGAGCC
* *
61507675 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
61507702 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
61507729 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
61507757 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
61507784 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
61507811 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
61507838 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61507853 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:61507787 original size:55 final size:54
Alignment explanation
Indices: 61507675--61507852 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
61507665 ATATTGAGCC
* * * * *
61507675 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
61507729 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
61507784 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
61507838 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61507853 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:61510344 original size:218 final size:218
Alignment explanation
Indices: 61509966--61510401 Score: 854
Period size: 218 Copynumber: 2.0 Consensus size: 218
61509956 ACCATAGATT
61509966 GCTCGTTCTCGAACGAGCAATTTATCACAGTCATTTATTGATAGTTGGATACAAGTCAGAAGTAT
1 GCTCGTTCTCGAACGAGCAATTTATCACAGTCATTTATTGATAGTTGGATACAAGTCAGAAGTAT
61510031 CACATTTCAAACTCATTCACTAGTAAAACTATCTGAGATTATTTTACATCTTAGTATTCCCCGAA
66 CACATTTCAAACTCATTCACTAGTAAAACTATCTGAGATTATTTTACATCTTAGTATTCCCCGAA
61510096 TGAACAGATAATTACTACTGTCAACTAGATATAACAATTGTTGTATGATCTCTGGATTTCTCGGT
131 TGAACAGATAATTACTACTGTCAACTAGATATAACAATTGTTGTATGATCTCTGGATTTCTCGGT
61510161 ACACAAACTCTTTCTCAAAATAA
196 ACACAAACTCTTTCTCAAAATAA
61510184 GCTCGTTCTCGAACGAGCAATTTATCACAGTCATTTATTGATAGTTGGATACAAGTCAGAAGTAT
1 GCTCGTTCTCGAACGAGCAATTTATCACAGTCATTTATTGATAGTTGGATACAAGTCAGAAGTAT
*
61510249 CACATTTCAAACTCATTCACTAGTAAAACTATCTGAGATTATTTTACATCTTAGTATTCCTCGAA
66 CACATTTCAAACTCATTCACTAGTAAAACTATCTGAGATTATTTTACATCTTAGTATTCCCCGAA
61510314 TGAACAGATAATTACTACTGTCAACTAGATATAACAATTGTTGTATGATCTCTGGATTTCTCGGT
131 TGAACAGATAATTACTACTGTCAACTAGATATAACAATTGTTGTATGATCTCTGGATTTCTCGGT
*
61510379 ACACGAACTCTTTCTCAAAATAA
196 ACACAAACTCTTTCTCAAAATAA
61510402 CAAATAATAA
Statistics
Matches: 216, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 216 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (218 bp):
GCTCGTTCTCGAACGAGCAATTTATCACAGTCATTTATTGATAGTTGGATACAAGTCAGAAGTAT
CACATTTCAAACTCATTCACTAGTAAAACTATCTGAGATTATTTTACATCTTAGTATTCCCCGAA
TGAACAGATAATTACTACTGTCAACTAGATATAACAATTGTTGTATGATCTCTGGATTTCTCGGT
ACACAAACTCTTTCTCAAAATAA
Found at i:61510419 original size:26 final size:26
Alignment explanation
Indices: 61510390--61510440 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
61510380 CACGAACTCT
*
61510390 TTCTCAAAATAACAAATAATAATCAA
1 TTCTCAAAACAACAAATAATAATCAA
*
61510416 TTCTCGAAACAACAAATAATAATCA
1 TTCTCAAAACAACAAATAATAATCA
61510441 TTTCCAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (26 bp):
TTCTCAAAACAACAAATAATAATCAA
Found at i:61515446 original size:46 final size:46
Alignment explanation
Indices: 61515396--61515571 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
61515386 TGGTTGAGCA
61515396 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
61515442 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
61515487 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
61515535 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
61515572 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:61515552 original size:93 final size:93
Alignment explanation
Indices: 61515393--61515564 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
61515383 GGATGGTTGA
* *
61515393 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
61515458 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
61515486 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
61515551 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
61515565 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:61523029 original size:46 final size:46
Alignment explanation
Indices: 61522979--61523151 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
61522969 TGGTTGAGCA
61522979 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
61523025 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
61523070 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
61523118 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
61523152 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:61523135 original size:93 final size:93
Alignment explanation
Indices: 61522976--61523147 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
61522966 GGATGGTTGA
* *
61522976 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
61523041 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
61523069 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
61523134 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
61523148 CTTAGGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:61526893 original size:27 final size:27
Alignment explanation
Indices: 61526863--61526918 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
61526853 TTTTTTTCAA
61526863 AAATCACTTTACAAAAACTATTAATCT
1 AAATCACTTTACAAAAACTATTAATCT
61526890 AAATCACTTTACAAAAACTATTAATCT
1 AAATCACTTTACAAAAACTATTAATCT
61526917 AA
1 AA
61526919 CATTAAACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATCACTTTACAAAAACTATTAATCT
Found at i:61536544 original size:14 final size:15
Alignment explanation
Indices: 61536522--61536598 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
61536512 CAATCAAACA
61536522 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
61536536 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
61536551 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
61536571 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
61536585 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
61536599 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:61536563 original size:20 final size:20
Alignment explanation
Indices: 61536538--61536577 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61536528 AATATTTTCC
*
61536538 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
61536558 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
61536578 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:61536583 original size:34 final size:35
Alignment explanation
Indices: 61536526--61536592 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
61536516 CAAACACCAG
*
61536526 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
61536561 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
61536593 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:61538573 original size:16 final size:17
Alignment explanation
Indices: 61538541--61538573 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
61538531 CATCAAGAAG
61538541 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
61538559 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
61538574 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:61546074 original size:20 final size:20
Alignment explanation
Indices: 61546045--61546088 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
61546035 TGTTTTATTG
61546045 TGGG-CCAACTGTATTAAAA
1 TGGGCCCAACTGTATTAAAA
* *
61546064 TGGGCCCAACTGTGTTAATA
1 TGGGCCCAACTGTATTAAAA
61546084 TGGGC
1 TGGGC
61546089 AAGACCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
TGGGCCCAACTGTATTAAAA
Done.