Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 194 of 198
Found at i:60425828 original size:3 final size:3
Alignment explanation
Indices: 60425802--60425848 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
60425792 TGTGAAAATA
* * *
60425802 TTC TGC TTC TTTC TTC GTC GTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
60425848 T
1 T
60425849 CTTGCCTGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.32, G:0.06, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:60428054 original size:32 final size:34
Alignment explanation
Indices: 60428004--60428066 Score: 96
Period size: 32 Copynumber: 1.9 Consensus size: 34
60427994 CCGAATATAA
60428004 TAAATATATATTTTTTA-TTTTTATTCTTTAATTT
1 TAAATATATATTTTTTATTTTTTATT-TTTAATTT
60428038 TAAA-ATAT-TTTTTTATTTTTTATTTTTAA
1 TAAATATATATTTTTTATTTTTTATTTTTAA
60428067 AATAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 12 0.43
33 12 0.43
34 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (34 bp):
TAAATATATATTTTTTATTTTTTATTTTTAATTT
Found at i:60428094 original size:25 final size:25
Alignment explanation
Indices: 60428019--60428092 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
60428009 ATATATTTTT
60428019 TATTTTTATTCTTTAATTTTAAAATA
1 TATTTTTATTCTTT-ATTTTAAAATA
* *
60428045 TTTTTTTATTTTTTATTTTTAAAATA
1 TATTTTTATTCTTTA-TTTTAAAATA
* *
60428071 -ATTTTTAATGTTTATTTTAAAA
1 TATTTTTATTCTTTATTTTAAAA
60428093 ATGGGCCGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 8 0.19
25 12 0.29
26 22 0.52
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (25 bp):
TATTTTTATTCTTTATTTTAAAATA
Found at i:60434833 original size:223 final size:223
Alignment explanation
Indices: 60434407--60434956 Score: 913
Period size: 223 Copynumber: 2.5 Consensus size: 223
60434397 AACATTTAGA
* *
60434407 TATGAAGAAGAAAATGAGAAATCATCATCATTGTCAAAGTCATCCAAAAATACAATAATTCAAGA
1 TATGAAGAAGAAAATGAGAAATCATCATCATCGTCAAAGTCCTCCAAAAATACAATAATTCAAGA
* * * * *
60434472 TGCACAATATCCAAATGAAATTGGTTCTTAAA-TCAAAAAATGGATTGAGTCCCTTTCTCAATCC
66 TGCACAACATCCAAATGAAATTGGTTCTCAAATTAAAAAAATGGACTGAGTCCCTCTCTCAATCC
* * * *
60434536 TCATAAGTAGCATTGGCCTTTTCACAAATGAAAGAGGAACCATCCAAAACCCAAATTTTCTCAAA
131 CCAAAAGTAGCATTGGCATTTTCACAAATGAAAGAGGAACCATCCAAAACCCAAATTTCCTCAAA
* * *
60434601 ACCAATTAAGTAATTGTATGAAATTTGC
196 ACAAATTAAGTAATGGTATAAAATTTGC
60434629 TATGAAGAAGAAAATGAGAAATCATCATCATCGTCAAAGTCCTCCAAAAATACAATAATTCAAGA
1 TATGAAGAAGAAAATGAGAAATCATCATCATCGTCAAAGTCCTCCAAAAATACAATAATTCAAGA
* *
60434694 TGCACAACATCCAAATGAAATTAGTTCTCAAATTAAAAAAATGGACTGAGTCCCTCTCTTAATCC
66 TGCACAACATCCAAATGAAATTGGTTCTCAAATTAAAAAAATGGACTGAGTCCCTCTCTCAATCC
60434759 CCAAAAGTAGCATTGGCATTTTCACAAATGAAAGAGGAACCATCCAAAACCCAAATTTCCTCAAA
131 CCAAAAGTAGCATTGGCATTTTCACAAATGAAAGAGGAACCATCCAAAACCCAAATTTCCTCAAA
*
60434824 ACAAATTAAGTCATGGTATAAAATTTGC
196 ACAAATTAAGTAATGGTATAAAATTTGC
*
60434852 CATGAAGAAGAAAATGAGAAATCATCATCATCGTCAAAGTCCTCCAAAAATACAATAATTCAAGA
1 TATGAAGAAGAAAATGAGAAATCATCATCATCGTCAAAGTCCTCCAAAAATACAATAATTCAAGA
* *
60434917 TGCACAAGATCCAAATGAAATTGGTTCTCAAATCAAAAAA
66 TGCACAACATCCAAATGAAATTGGTTCTCAAATTAAAAAA
60434957 TGGGATAAAA
Statistics
Matches: 306, Mismatches: 21, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
222 92 0.30
223 214 0.70
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (223 bp):
TATGAAGAAGAAAATGAGAAATCATCATCATCGTCAAAGTCCTCCAAAAATACAATAATTCAAGA
TGCACAACATCCAAATGAAATTGGTTCTCAAATTAAAAAAATGGACTGAGTCCCTCTCTCAATCC
CCAAAAGTAGCATTGGCATTTTCACAAATGAAAGAGGAACCATCCAAAACCCAAATTTCCTCAAA
ACAAATTAAGTAATGGTATAAAATTTGC
Found at i:60435609 original size:24 final size:24
Alignment explanation
Indices: 60435577--60435626 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
60435567 CTTAAGACAA
60435577 CTAAAATTGAGGTATTTTTAGTGG
1 CTAAAATTGAGGTATTTTTAGTGG
60435601 CTAAAATTGAGGTATTTTTAGTGG
1 CTAAAATTGAGGTATTTTTAGTGG
60435625 CT
1 CT
60435627 TCAACACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (24 bp):
CTAAAATTGAGGTATTTTTAGTGG
Found at i:60437782 original size:16 final size:16
Alignment explanation
Indices: 60437761--60437794 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
60437751 TAGTCTCTAT
60437761 ATTTTAATTTATCATA
1 ATTTTAATTTATCATA
60437777 ATTTTAATTTATCATA
1 ATTTTAATTTATCATA
60437793 AT
1 AT
60437795 AATAGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTAATTTATCATA
Found at i:60439854 original size:2 final size:2
Alignment explanation
Indices: 60439847--60439884 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
60439837 TCTAGGTCTT
* *
60439847 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60439885 ATGAAGACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:60450452 original size:31 final size:29
Alignment explanation
Indices: 60450406--60450507 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 29
60450396 TTAAAATTTT
* *
60450406 ATTTAAAAAAATTTGAGGGATCTAATTAAA
1 ATTTTAAAAATTTTGAGGGAT-TAATTAAA
** **
60450436 ATTTCTAAAAATTTTGAGAAAATTAATGGAA
1 ATTT-TAAAAATTTTGAG-GGATTAATTAAA
* * *
60450467 ATTTTGAAAATTTTAAAGGATTTAATTAAA
1 ATTTTAAAAATTTTGAGGGA-TTAATTAAA
60450497 ATTTTAAAAAT
1 ATTTTAAAAAT
60450508 ATAAAGAGCT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 1 0.02
30 31 0.56
31 21 0.38
32 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTTTAAAAATTTTGAGGGATTAATTAAA
Found at i:60464841 original size:1 final size:1
Alignment explanation
Indices: 60464835--60464861 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
60464825 TTGAAGGGTC
60464835 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
60464862 GAGCTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:60473865 original size:13 final size:13
Alignment explanation
Indices: 60473847--60473871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60473837 ATAAGTAACA
60473847 TTAATTAATTAAT
1 TTAATTAATTAAT
60473860 TTAATTAATTAA
1 TTAATTAATTAA
60473872 AATTTGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:60475508 original size:60 final size:60
Alignment explanation
Indices: 60475415--60475531 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
60475405 TATTTTTATA
*
60475415 ATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTGTG
1 ATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTGTG
60475475 ATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
1 ATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
60475532 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (60 bp):
ATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTGTG
Found at i:60475952 original size:102 final size:100
Alignment explanation
Indices: 60475726--60476013 Score: 388
Period size: 103 Copynumber: 2.8 Consensus size: 100
60475716 TTATAGTTAT
* *
60475726 TTATTTTATTAGTAATTTATGGGATTAGGT-TACAAATTGTTAGT-TTTTAGTATAGGGTTTTGT
1 TTATTTTGTTAGTAATTTAT--GATTAGGTATA-AAATTGTTAGTGTTTT-GTATAGTGTTTTGT
*
60475789 GGTTTTTTAGTAATGTAACTTTTTTTAAATAATTTTATAG
62 GATTTTTTAGTAATGTAA-TTTTTTTAAATAATTTTATAG
*
60475829 TTATTCTGTTAGTAATTTATGATTAGGTGATATAAATTGTTAGTGTTTTGTGAT-GTGTTTTGTG
1 TTATTTTGTTAGTAATTTATGATTAGGT-ATA-AAATTGTTAGTGTTTTGT-ATAGTGTTTTGTG
*
60475893 ATTTTTTAGTAATGTATTTTTTTTAAATAATTTTATAG
63 ATTTTTTAGTAATGTAATTTTTTTAAATAATTTTATAG
* * *
60475931 TTATTTTGTTAGTAATTTATGATTAGGTTATAAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGCT
1 TTATTTTGTTAGTAATTTATGATTAGG-TATAAAATTGTTAGTGTTTTGTATAGTGTTTTGTGAT
60475996 TTTTT--TAATGTAATTTTT
65 TTTTTAGTAATGTAATTTTT
60476014 ATATAATGTA
Statistics
Matches: 168, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
99 12 0.07
100 1 0.01
101 41 0.24
102 50 0.30
103 58 0.35
104 6 0.04
ACGTcount: A:0.25, C:0.01, G:0.17, T:0.56
Consensus pattern (100 bp):
TTATTTTGTTAGTAATTTATGATTAGGTATAAAATTGTTAGTGTTTTGTATAGTGTTTTGTGATT
TTTTAGTAATGTAATTTTTTTAAATAATTTTATAG
Found at i:60480877 original size:20 final size:20
Alignment explanation
Indices: 60480852--60480889 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
60480842 TTATAATATC
*
60480852 AACTCAATCCAATAACCCTA
1 AACTCAACCCAATAACCCTA
60480872 AACTCAACCCAATAACCC
1 AACTCAACCCAATAACCC
60480890 AATATCAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (20 bp):
AACTCAACCCAATAACCCTA
Found at i:60489342 original size:31 final size:31
Alignment explanation
Indices: 60489257--60489331 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
60489247 TACAATTTGA
* * * *
60489257 TCATTTAATTATTTGAATGTTTTTATTTAAG
1 TCATTGAACTATTTAAAAGTTTTTATTTAAG
60489288 TCATTGAACTATTTAAAAGTTTTTATTTAAG
1 TCATTGAACTATTTAAAAGTTTTTATTTAAG
60489319 TCATTTG-ACTATT
1 TCA-TTGAACTATT
60489332 AAGTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 36 0.92
32 3 0.08
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (31 bp):
TCATTGAACTATTTAAAAGTTTTTATTTAAG
Found at i:60490731 original size:29 final size:30
Alignment explanation
Indices: 60490698--60490767 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
60490688 TTAAAATTTT
* *
60490698 AGAATTTAGTTTATGTATTTTT-AT-TTTCA
1 AGAATTTAGTTT-TCTATTTTTCATATTACA
60490727 AGAATTTAGTCTTTCTATTTTTCATATTACA
1 AGAATTTAGT-TTTCTATTTTTCATATTACA
60490758 A-AATTTAGTT
1 AGAATTTAGTT
60490768 CCAATTGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 19 0.53
30 12 0.33
31 5 0.14
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (30 bp):
AGAATTTAGTTTTCTATTTTTCATATTACA
Found at i:60490967 original size:30 final size:30
Alignment explanation
Indices: 60490914--60490985 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
60490904 AATAACAGCC
* *
60490914 GGACTTAAATT-TTGAAATTTAAAAAGTA-GA
1 GGAC-TAAATTCTTGAAATAT-AAAAGTACAA
60490944 GAGACTAAATTCTTGAAA-ATAAAAGTACAA
1 G-GACTAAATTCTTGAAATATAAAAGTACAA
60490974 GGACTAAATTCT
1 GGACTAAATTCT
60490986 AAATTTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 18 0.49
30 10 0.27
31 9 0.24
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.29
Consensus pattern (30 bp):
GGACTAAATTCTTGAAATATAAAAGTACAA
Found at i:60492788 original size:20 final size:19
Alignment explanation
Indices: 60492759--60492812 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
60492749 AAATCTATAC
* *
60492759 AAATACATAAATATCTTAAA
1 AAATATATAAAAAT-TTAAA
*
60492779 ATATATATAATAAATTTAAA
1 AAATATATAA-AAATTTAAA
60492799 AAATATATAAAAAT
1 AAATATATAAAAAT
60492813 AATATTGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 4 0.14
20 22 0.76
21 3 0.10
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATATAAAAATTTAAA
Found at i:60500091 original size:3 final size:3
Alignment explanation
Indices: 60500083--60500119 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
60500073 TTAAAAACCG
60500083 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
60500120 TTTTCTTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:60501107 original size:2 final size:2
Alignment explanation
Indices: 60501100--60501124 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60501090 AGATTAATTC
60501100 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
60501125 GACACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60502782 original size:13 final size:13
Alignment explanation
Indices: 60502764--60502791 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60502754 ACATAAAAAT
60502764 AATAAAAGGGGTA
1 AATAAAAGGGGTA
60502777 AATAAAAGGGGTA
1 AATAAAAGGGGTA
60502790 AA
1 AA
60502792 AATATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (13 bp):
AATAAAAGGGGTA
Found at i:60503832 original size:12 final size:12
Alignment explanation
Indices: 60503817--60503841 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60503807 TATTACAGAA
60503817 TATTCATTTTTG
1 TATTCATTTTTG
60503829 TATTCATTTTTG
1 TATTCATTTTTG
60503841 T
1 T
60503842 TGTTTCTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTCATTTTTG
Found at i:60508206 original size:14 final size:15
Alignment explanation
Indices: 60508163--60508208 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
60508153 ATTATATTTG
*
60508163 ATTTTAATTTAAGTAA
1 ATTTTAATTT-ATTAA
*
60508179 A-TTTAATTTTTTAA
1 ATTTTAATTTATTAA
60508193 ATTTTAA-TTATTAA
1 ATTTTAATTTATTAA
60508207 AT
1 AT
60508209 CAAATCAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 12 0.46
15 13 0.50
16 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTTTAATTTATTAA
Found at i:60509715 original size:25 final size:25
Alignment explanation
Indices: 60509668--60509752 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
60509658 ATTTATTTAT
60509668 TTATTTATTTTAAA--CTT-TA-TA
1 TTATTTATTTTAAATTCTTCTATTA
*
60509689 TTATTTATTTTAAATTGTTCTATTA
1 TTATTTATTTTAAATTCTTCTATTA
* *
60509714 TTATTTATTTTAAGTTTTTC-ATATA
1 TTATTTATTTTAAATTCTTCTAT-TA
**
60509739 TTATCCATTTTAAA
1 TTATTTATTTTAAA
60509753 CTATTATATG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.26
23 2 0.04
24 4 0.08
25 33 0.62
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTTATTTTAAATTCTTCTATTA
Found at i:60511727 original size:21 final size:21
Alignment explanation
Indices: 60511702--60511747 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
60511692 CTTTTTAATT
60511702 AAAATTTA-TAAAAATTATACA
1 AAAATTTAGTAAAAATTATA-A
60511723 AAAATTTAGTTAAAAATTATAA
1 AAAATTTAG-TAAAAATTATAA
60511745 AAA
1 AAA
60511748 TAAAAAGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 11 0.48
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTTAGTAAAAATTATAA
Found at i:60513029 original size:14 final size:14
Alignment explanation
Indices: 60512993--60513026 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
60512983 TCATCATTTA
60512993 CCTATAACCAAAAC
1 CCTATAACCAAAAC
60513007 CCTATAACCAAAAC
1 CCTATAACCAAAAC
60513021 CC-ATAA
1 CCTATAA
60513027 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:60523781 original size:47 final size:45
Alignment explanation
Indices: 60523730--60523836 Score: 103
Period size: 49 Copynumber: 2.3 Consensus size: 45
60523720 ATTTAAATTT
*
60523730 TATTTTAATAATATTTTTA-AAT-AATATTCT-TTACATATTATTGAAAA
1 TATTTTAATAATATTTTAATAATAAATATT-TATTACA-ATTA-T--AAA
*
60523777 TATTTAATATTAATATTTTAATAATAAATATTTATTACAATTATAAA
1 TATTT--TAATAATATTTTAATAATAAATATTTATTACAATTATAAA
*
60523824 TATATTAATAATA
1 TATTTTAATAATA
60523837 AATGTTTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
45 7 0.14
47 12 0.24
49 13 0.25
50 8 0.16
51 11 0.22
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.50
Consensus pattern (45 bp):
TATTTTAATAATATTTTAATAATAAATATTTATTACAATTATAAA
Found at i:60523808 original size:15 final size:15
Alignment explanation
Indices: 60523774--60523844 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
60523764 ATATTATTGA
60523774 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
60523787 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
60523802 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
60523821 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
60523836 AAATGTTTT
1 AAATATTTT
60523845 GTAGTATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 18 0.40
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:60525089 original size:21 final size:20
Alignment explanation
Indices: 60525065--60525120 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
60525055 ATAAAGTCGT
60525065 AAGAAAGTTATAAAAAGTGTA
1 AAGAAA-TTATAAAAAGTGTA
**
60525086 AAGAAA-TATAAAATTTGTA
1 AAGAAATTATAAAAAGTGTA
*
60525105 TAAAAAATTATAAAAA
1 -AAGAAATTATAAAAA
60525121 CTATTGTACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (20 bp):
AAGAAATTATAAAAAGTGTA
Found at i:60525430 original size:19 final size:21
Alignment explanation
Indices: 60525389--60525438 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
60525379 TACATATTTC
*
60525389 TAATTTTTAATAAAATTTAAA
1 TAATTTTTATTAAAATTTAAA
60525410 T-ATTTTTATTAAAATTT-AA
1 TAATTTTTATTAAAATTTAAA
60525429 TAATTTTTAT
1 TAATTTTTAT
60525439 AACTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTTTATTAAAATTTAAA
Found at i:60525812 original size:4 final size:4
Alignment explanation
Indices: 60525805--60525830 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
60525795 GAAGGGAGGG
60525805 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
60525831 ACTTTGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:60534548 original size:45 final size:45
Alignment explanation
Indices: 60534497--60534639 Score: 207
Period size: 45 Copynumber: 3.2 Consensus size: 45
60534487 CAGTAATCAA
* *
60534497 TAACAGTAACAGTATTCAACACACAAAGTGCTGAACCTGTAACAG
1 TAACAGTAACAGTATTCGACACACAAAGTGCCGAACCTGTAACAG
** *
60534542 TAACAGTAACAGTATTCGACACACAAAGTGCCG-AGTTGGTAACGG
1 TAACAGTAACAGTATTCGACACACAAAGTGCCGAACCT-GTAACAG
* *
60534587 TAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAG
1 TAACAGTAACAGTATTCGACACACAAAGTGCCGAACCTGTAACAG
60534632 TAACAGTA
1 TAACAGTA
60534640 GTCGGCACAT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
44 2 0.02
45 84 0.97
46 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (45 bp):
TAACAGTAACAGTATTCGACACACAAAGTGCCGAACCTGTAACAG
Found at i:60534663 original size:38 final size:39
Alignment explanation
Indices: 60534491--60534666 Score: 131
Period size: 45 Copynumber: 4.2 Consensus size: 39
60534481 AGTATACAGT
* * * *
60534491 AATCAATAACAGTAACAGTATTCAACACACAAAGTGCTG
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
*
60534530 AACCTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AA----T--CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* * *
60534575 AGTTGGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 A------ATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
* *
60534620 AATCAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTG
1 AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCC-G
60534659 -ATCAGTAA
1 AATCAGTAA
60534667 GCCGGCAAAT
Statistics
Matches: 114, Mismatches: 10, Indels: 27
0.75 0.07 0.18
Matches are distributed among these distances:
38 15 0.13
39 27 0.24
43 1 0.01
45 70 0.61
51 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (39 bp):
AATCAGTAACAGTAACAGTAGTCGACACACAAAGTGCCG
Found at i:60545799 original size:31 final size:30
Alignment explanation
Indices: 60545764--60545862 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
60545754 TTAATATACC
*
60545764 ATTTGGTACCTGAGTTTGGCTTCAATATTCA
1 ATTTGGTACCTGAATTT-GCTTCAATATTCA
* * * *
60545795 ATTTGGTACATGAATTT--TT--TTGTCCCA
1 ATTTGGTACCTGAATTTGCTTCAATAT-TCA
*
60545822 ATTTAGTACCTGAATTTAGCTTCAATATTCA
1 ATTTGGTACCTGAATTT-GCTTCAATATTCA
60545853 ATTTGGTACC
1 ATTTGGTACC
60545863 CAGACTAAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
26 2 0.04
27 17 0.33
28 2 0.04
30 2 0.04
31 26 0.51
32 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (30 bp):
ATTTGGTACCTGAATTTGCTTCAATATTCA
Found at i:60552124 original size:28 final size:28
Alignment explanation
Indices: 60552070--60552154 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
60552060 ATTAAATGCA
*
60552070 TAAATTGGTATTTAAATTATATTTTTTT
1 TAAATTGATATTTAAATTATATTTTTTT
* *
60552098 TAAATTGATATTT-AATTTTTTTCTTTTT
1 TAAATTGATATTTAAATTATATT-TTTTT
*
60552126 TACATAAGTGATATTTAAATTAT-TTTTTT
1 T--A-AATTGATATTTAAATTATATTTTTT
60552155 CCTAAGTTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
27 7 0.15
28 18 0.38
30 5 0.11
31 12 0.26
32 5 0.11
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (28 bp):
TAAATTGATATTTAAATTATATTTTTTT
Found at i:60554338 original size:3 final size:3
Alignment explanation
Indices: 60554330--60554361 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
60554320 CATGTGATGT
*
60554330 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
60554362 GGTTGAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:60554677 original size:17 final size:17
Alignment explanation
Indices: 60554644--60554677 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60554634 TATAAGGACT
**
60554644 AATTTTTAACATTATGA
1 AATTTTTAACAAAATGA
60554661 AATTTTTAACAAAATGA
1 AATTTTTAACAAAATGA
60554678 CCCATTTAGT
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:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
AATTTTTAACAAAATGA
Found at i:60562103 original size:14 final size:16
Alignment explanation
Indices: 60562084--60562119 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
60562074 ATAACAAGGC
60562084 AATATATATGG-AA-A
1 AATATATATGGTAACA
60562098 AATATATATGGTAACA
1 AATATATATGGTAACA
60562114 AATATA
1 AATATA
60562120 GGGTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.55
15 2 0.10
16 7 0.35
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (16 bp):
AATATATATGGTAACA
Found at i:60562141 original size:17 final size:17
Alignment explanation
Indices: 60562115--60562149 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
60562105 ATGGTAACAA
*
60562115 ATATAGGGTAAAATATT
1 ATATAAGGTAAAATATT
*
60562132 ATATAAGGTAATATATT
1 ATATAAGGTAAAATATT
60562149 A
1 A
60562150 GAATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (17 bp):
ATATAAGGTAAAATATT
Found at i:60562168 original size:14 final size:14
Alignment explanation
Indices: 60562084--60562171 Score: 53
Period size: 14 Copynumber: 6.5 Consensus size: 14
60562074 ATAACAAGGC
60562084 AATATATATGGA-AA
1 AATATATAT-GATAA
*
60562098 AATATATATGGTAA
1 AATATATATGATAA
* *
60562112 CAA-ATATAGGGTAA
1 -AATATATATGATAA
60562126 AATAT-TAT-ATAA
1 AATATATATGATAA
** *
60562138 GGTA-ATAT-ATTAG
1 AATATATATGA-TAA
60562151 AATATATATGATAA
1 AATATATATGATAA
60562165 AATATAT
1 AATATAT
60562172 TTATCATTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
12 9 0.16
13 9 0.16
14 36 0.63
15 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.34
Consensus pattern (14 bp):
AATATATATGATAA
Found at i:60568613 original size:2 final size:2
Alignment explanation
Indices: 60568606--60568631 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60568596 ACAAAGGAAA
60568606 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
60568632 GAGAAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60573876 original size:4 final size:4
Alignment explanation
Indices: 60573867--60573892 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
60573857 TTTCAAGAGT
60573867 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
60573893 GTAGATCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:60580447 original size:31 final size:30
Alignment explanation
Indices: 60580399--60580470 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
60580389 AAATAGTTAT
* *
60580399 TGAACAATTTGAAAGTTTTCATTTAAATTAC
1 TGAACTATTAGAAAGTTTTCA-TTAAATTAC
* * * *
60580430 TGATCTATTAGAAAGTTTTTATTAAGTTAT
1 TGAACTATTAGAAAGTTTTCATTAAATTAC
60580460 TGAACTATTAG
1 TGAACTATTAG
60580471 GGTTTTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
TGAACTATTAGAAAGTTTTCATTAAATTAC
Found at i:60580470 original size:30 final size:31
Alignment explanation
Indices: 60580393--60580470 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
60580383 ATTACAAAAT
* *
60580393 AGTTATTGAACAATTTGAAAGTTTTCATTTA
1 AGTTATTGAACTATTAGAAAGTTTTCATTTA
* * * *
60580424 AATTACTGATCTATTAGAAAGTTTTTA-TTA
1 AGTTATTGAACTATTAGAAAGTTTTCATTTA
60580454 AGTTATTGAACTATTAG
1 AGTTATTGAACTATTAG
60580471 GGTTTTTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (31 bp):
AGTTATTGAACTATTAGAAAGTTTTCATTTA
Found at i:60596121 original size:18 final size:17
Alignment explanation
Indices: 60596098--60596142 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
60596088 TTTTATGTTC
60596098 TATAAATTACATAATATA
1 TATAAATTACATAAT-TA
*
60596116 TATAAATAACATAATTA
1 TATAAATTACATAATTA
*
60596133 -ATATATTACA
1 TATAAATTACA
60596143 AACTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 8 0.33
17 2 0.08
18 14 0.58
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAATTACATAATTA
Found at i:60600274 original size:16 final size:18
Alignment explanation
Indices: 60600253--60600288 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
60600243 ATGGGATGAG
60600253 AATAAATTT-A-TAATTA
1 AATAAATTTAATTAATTA
60600269 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
60600287 AA
1 AA
60600289 AATTTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:60601287 original size:29 final size:30
Alignment explanation
Indices: 60601246--60601319 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
60601236 ACAAAATAAT
* **
60601246 AACATAAGTGACTAAAACGTAACAT-TTCA
1 AACAAAAGTGACTAAAACGTAACATAGGCA
*
60601275 AACAAAAGTGACTAAAATGTAACATGAGGCA
1 AACAAAAGTGACTAAAACGTAACAT-AGGCA
60601306 AACAAAAGTGACTA
1 AACAAAAGTGACTA
60601320 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (30 bp):
AACAAAAGTGACTAAAACGTAACATAGGCA
Found at i:60603720 original size:18 final size:18
Alignment explanation
Indices: 60603697--60603736 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
60603687 GTTCAAGGTG
60603697 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
60603715 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
60603733 TAAT
1 TAAT
60603737 AAAAAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:60607700 original size:6 final size:6
Alignment explanation
Indices: 60607689--60607716 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
60607679 ATAAACAATT
60607689 CCTACC CCTACC CCTACC CCTACC CCTA
1 CCTACC CCTACC CCTACC CCTACC CCTA
60607717 TCCTTTTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.64, G:0.00, T:0.18
Consensus pattern (6 bp):
CCTACC
Found at i:60607742 original size:2 final size:2
Alignment explanation
Indices: 60607735--60607774 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
60607725 CCTTTACCAA
60607735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60607775 CGAAGTAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60609654 original size:159 final size:159
Alignment explanation
Indices: 60609365--60609686 Score: 626
Period size: 159 Copynumber: 2.0 Consensus size: 159
60609355 GCAACCGACA
*
60609365 TCTAAAATGATCTGTAGAAACCGAGCTTGCATAGGAGAGCAAAACTAGGAAAATAAATGTCTTAA
1 TCTAAAATGATCTGGAGAAACCGAGCTTGCATAGGAGAGCAAAACTAGGAAAATAAATGTCTTAA
60609430 ATGTAAGATTATGTCTCTATTACCCCATTAGCATTGCTAAAGTAAGCAAAACAGTCCCATTCTTC
66 ATGTAAGATTATGTCTCTATTACCCCATTAGCATTGCTAAAGTAAGCAAAACAGTCCCATTCTTC
60609495 TACACCTTTACTTGACAAGTCTCTCCAAC
131 TACACCTTTACTTGACAAGTCTCTCCAAC
*
60609524 TCTAAAATGATCTGGAGAAACCGAGCTTGCATAGGAGAGCAAAACTAGGAAAATAAATTTCTTAA
1 TCTAAAATGATCTGGAGAAACCGAGCTTGCATAGGAGAGCAAAACTAGGAAAATAAATGTCTTAA
60609589 ATGTAAGATTATGTCTCTATTACCCCATTAGCATTGCTAAAGTAAGCAAAACAGTCCCATTCTTC
66 ATGTAAGATTATGTCTCTATTACCCCATTAGCATTGCTAAAGTAAGCAAAACAGTCCCATTCTTC
60609654 TACACCTTTACTTGACAAGTCTCTCCAAC
131 TACACCTTTACTTGACAAGTCTCTCCAAC
60609683 TCTA
1 TCTA
60609687 GCAGTTTTGC
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 161 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (159 bp):
TCTAAAATGATCTGGAGAAACCGAGCTTGCATAGGAGAGCAAAACTAGGAAAATAAATGTCTTAA
ATGTAAGATTATGTCTCTATTACCCCATTAGCATTGCTAAAGTAAGCAAAACAGTCCCATTCTTC
TACACCTTTACTTGACAAGTCTCTCCAAC
Found at i:60610710 original size:39 final size:36
Alignment explanation
Indices: 60610629--60610713 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 36
60610619 TTTTAATGCC
* *
60610629 TGTGATAACTCAAAGCAAAAGAAATCAGAAGATTCA
1 TGTGATATCTCAAAGCAAAAAAAATCAGAAGATTCA
* * *
60610665 TCTGATATCTCAGAAGCAAAGCAAAAATTAGAAGATTCT
1 TGTGATATCTCA-AAGCAAA--AAAAATCAGAAGATTCA
60610704 TGTGATATCT
1 TGTGATATCT
60610714 TAGGGCCACA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 10 0.25
37 7 0.17
39 23 0.57
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (36 bp):
TGTGATATCTCAAAGCAAAAAAAATCAGAAGATTCA
Found at i:60614268 original size:21 final size:20
Alignment explanation
Indices: 60614225--60614265 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
60614215 TTTATATATA
60614225 TATTGATGGGGTTTTATTTT
1 TATTGATGGGGTTTTATTTT
* *
60614245 TATTGATGGGTTTTTCTTTT
1 TATTGATGGGGTTTTATTTT
60614265 T
1 T
60614266 TATCCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.02, G:0.22, T:0.63
Consensus pattern (20 bp):
TATTGATGGGGTTTTATTTT
Found at i:60621624 original size:2 final size:2
Alignment explanation
Indices: 60621617--60621641 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60621607 AATTAGACAA
60621617 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
60621642 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60625199 original size:42 final size:42
Alignment explanation
Indices: 60625145--60625298 Score: 139
Period size: 43 Copynumber: 3.6 Consensus size: 42
60625135 TTATTTTTAT
* * *
60625145 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TACAAAAA
1 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTC-AAAC
* * ** **
60625187 AAACGCCACTAAAGGTCAAGGTCTTTAATGGCGCATTTCTTAC
1 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGC-TTTCAAAC
* * * * **
60625230 AAACGCCGCTAAAGATCATGTTCTTTGGCGGCACTTTCTCCAC
1 AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTC-AAAC
60625273 AAACGCCACTAAAGGTCATGTTCTTT
1 AAACGCCACTAAAGGTCATGTTCTTT
60625299 TAGAGGCGTT
Statistics
Matches: 88, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
42 33 0.38
43 53 0.60
44 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (42 bp):
AAACGCCACTAAAGGTCATGTTCTTTAGCGGCGCTTTCAAAC
Found at i:60625329 original size:44 final size:43
Alignment explanation
Indices: 60625145--60625336 Score: 122
Period size: 43 Copynumber: 4.5 Consensus size: 43
60625135 TTATTTTTAT
* * * * *** *
60625145 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TACAAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGAGGCACTTTCTCCAC
* * * * * *
60625187 AAACGCCACTAAAGGTCAAGGTCTTTA-ATGGCGCATTTCT-TAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGA-GGCAC-TTTCTCCAC
* *
60625230 AAACGCCGCTAAAGATCATGTTCTTTGGCGGCACTTTCTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGAGGCACTTTCTCCAC
* * * *
60625273 AAACGCCACTAAAGGTCATGTTCTTTTAGAGGC-GTTTTTCCGAC
1 AAACGCCGCTAAAGATCATGTTC-TTTAGAGGCACTTTCTCC-AC
* *
60625317 AAACGTCGCTAAAGACCATG
1 AAACGCCGCTAAAGATCATG
60625337 ACTTTTAGCG
Statistics
Matches: 117, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
42 34 0.29
43 56 0.48
44 27 0.23
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGAGGCACTTTCTCCAC
Found at i:60627092 original size:9 final size:9
Alignment explanation
Indices: 60627078--60627702 Score: 154
Period size: 9 Copynumber: 71.9 Consensus size: 9
60627068 ATAATGTAAT
60627078 TAAGTTATG
1 TAAGTTATG
*
60627087 TAAGTTGTG
1 TAAGTTATG
60627096 T-A-TTAT-
1 TAAGTTATG
*
60627102 TAAAGTTAAG
1 T-AAGTTATG
60627112 T-A-TTATG
1 TAAGTTATG
*
60627119 TAAGTTATT
1 TAAGTTATG
60627128 TAAGTTATG
1 TAAGTTATG
**
60627137 TAAGTGGTG
1 TAAGTTATG
60627146 T-A-TTATG
1 TAAGTTATG
*
60627153 TAAGTTAAG
1 TAAGTTATG
60627162 TAAGTTATG
1 TAAGTTATG
* *
60627171 TAGGCTATG
1 TAAGTTATG
60627180 T-A-TTATG
1 TAAGTTATG
* *
60627187 CAAGTTATT
1 TAAGTTATG
* *
60627196 TATGTAAGTGG
1 TAAGTTA-T-G
* **
60627207 T--GTCAACA
1 TAAGT-TATG
*
60627215 TAAGTTATA
1 TAAGTTATG
60627224 TAAGTTATG
1 TAAGTTATG
* *
60627233 TAGGCTATG
1 TAAGTTATG
60627242 T-A-TTATG
1 TAAGTTATG
*
60627249 TAAGTGTATATA
1 TAA--GT-TATG
60627261 TAAGTTATG
1 TAAGTTATG
* *
60627270 ATATGAT-TG
1 -TAAGTTATG
*
60627279 ATAAATT-TG
1 -TAAGTTATG
*
60627288 --AGTTATT
1 TAAGTTATG
60627295 TAAGTTATG
1 TAAGTTATG
* *
60627304 ATATGATT-TA
1 -TAAG-TTATG
60627314 TAAGTTATG
1 TAAGTTATG
*
60627323 T-A-TAATG
1 TAAGTTATG
60627330 TAAGTTATG
1 TAAGTTATG
*
60627339 AAAGTTATG
1 TAAGTTATG
*
60627348 T-A-TTATA
1 TAAGTTATG
*
60627355 TAATTTATG
1 TAAGTTATG
*
60627364 TAAGTTGTG
1 TAAGTTATG
60627373 T-A-TTATG
1 TAAGTTATG
* *
60627380 CAAGTCATG
1 TAAGTTATG
* *
60627389 TAGGCTATG
1 TAAGTTATG
60627398 T-A-TTATG
1 TAAGTTATG
60627405 TAAGTTAT-
1 TAAGTTATG
*
60627413 TATGTTATTATG
1 TAAG---TTATG
60627425 TAAGTTATG
1 TAAGTTATG
* *
60627434 AAAGTTATATA
1 TAAG-T-TATG
60627445 TAAGTTAT-
1 TAAGTTATG
**
60627453 TAA-AAATG
1 TAAGTTATG
60627461 T-A-TTATG
1 TAAGTTATG
*
60627468 TAATTTATG
1 TAAGTTATG
*
60627477 TAAGTTGTG
1 TAAGTTATG
60627486 T-A-TTATG
1 TAAGTTATG
*
60627493 TAAGTCATG
1 TAAGTTATG
* *
60627502 TAGGCTATG
1 TAAGTTATG
60627511 T-A-TTATG
1 TAAGTTATG
60627518 TAAGTTATG
1 TAAGTTATG
* *
60627527 AAAGTTTTATA
1 TAAG--TTATG
*
60627538 TAAGTGAT-
1 TAAGTTATG
**
60627546 TAA-AAATG
1 TAAGTTATG
60627554 T-A-TTATG
1 TAAGTTATG
* *
60627561 TAATTTATT
1 TAAGTTATG
*
60627570 TAAATTATTATG
1 T-AA--GTTATG
60627582 TAAGTTATG
1 TAAGTTATG
*
60627591 AAAGTTATG
1 TAAGTTATG
60627600 T-A-TTATG
1 TAAGTTATG
* *
60627607 TAATTTATT
1 TAAGTTATG
60627616 TAAGTTATG
1 TAAGTTATG
*
60627625 TAAGTTGTG
1 TAAGTTATG
60627634 T-A-TTATG
1 TAAGTTATG
* *
60627641 CAAGTCATG
1 TAAGTTATG
* *
60627650 TAGGCTATG
1 TAAGTTATG
60627659 T-A-TTATG
1 TAAGTTATG
60627666 TAAGTTAT-
1 TAAGTTATG
*
60627674 TATGTTATTATG
1 TAAG---TTATG
60627686 TAAGTTATG
1 TAAGTTATG
*
60627695 AAAGTTAT
1 TAAGTTAT
60627703 ATATAAGTTA
Statistics
Matches: 440, Mismatches: 110, Indels: 132
0.65 0.16 0.19
Matches are distributed among these distances:
6 4 0.01
7 80 0.18
8 42 0.10
9 250 0.57
10 20 0.05
11 27 0.06
12 17 0.04
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:60627096 original size:29 final size:31
Alignment explanation
Indices: 60627054--60627124 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
60627044 TATTATGATA
*
60627054 TATGTATGTTGTGTATAATGT-AA-TTAAG-T
1 TATGTAAGTTGTGTATAAT-TAAAGTTAAGAT
*
60627083 TATGTAAGTTGTGTATTATTAAAGTTAAGTAT
1 TATGTAAGTTGTGTATAATTAAAGTTAAG-AT
60627115 TATGTAAGTT
1 TATGTAAGTT
60627125 ATTTAAGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 19 0.53
30 5 0.14
32 11 0.31
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (31 bp):
TATGTAAGTTGTGTATAATTAAAGTTAAGAT
Found at i:60627107 original size:25 final size:24
Alignment explanation
Indices: 60627076--60627172 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
60627066 GTATAATGTA
* *
60627076 ATTAAGTTATGTAAGTTGTGTATT
1 ATTAAGTTAAGTAAGTTATGTATT
60627100 ATTAAAGTTAAGT-A-TTATGTAAGTT
1 ATT-AAGTTAAGTAAGTTATGT-A-TT
* **
60627125 ATTTAAGTTATGTAAGTGGTGTATT
1 A-TTAAGTTAAGTAAGTTATGTATT
60627150 ATGTAAGTTAAGTAAGTTATGTA
1 AT-TAAGTTAAGTAAGTTATGTA
60627173 GGCTATGTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
23 5 0.09
24 6 0.10
25 39 0.67
26 4 0.07
27 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (24 bp):
ATTAAGTTAAGTAAGTTATGTATT
Found at i:60627154 original size:34 final size:34
Alignment explanation
Indices: 60627111--60627197 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
60627101 TTAAAGTTAA
*
60627111 GTATTATGTAAGTTATTTAAGTTATGTAAG-TGGT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGCT-AT
** *
60627145 GTATTATGTAAGTTAAGTAAGTTATGTAGGCTAT
1 GTATTATGTAAGTTATTTAAGTTATGTAAGCTAT
*
60627179 GTATTATGCAAGTTATTTA
1 GTATTATGTAAGTTATTTA
60627198 TGTAAGTGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 44 0.98
35 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (34 bp):
GTATTATGTAAGTTATTTAAGTTATGTAAGCTAT
Found at i:60627345 original size:25 final size:25
Alignment explanation
Indices: 60627315--60627702 Score: 202
Period size: 25 Copynumber: 16.3 Consensus size: 25
60627305 TATGATTTAT
*
60627315 AAGTTATGTATAATGTAAGTTATGA
1 AAGTTATGTATTATGTAAGTTATGA
* * *
60627340 AAGTTATGTATTATATAATTTATGT
1 AAGTTATGTATTATGTAAGTTATGA
* * * *
60627365 AAGTTGTGTATTATGCAAGTCATGT
1 AAGTTATGTATTATGTAAGTTATGA
* *
60627390 AGGCTATGTATTATGTAAG-T-T--
1 AAGTTATGTATTATGTAAGTTATGA
60627411 -A-TTATGTTATTATGTAAGTTATGA
1 AAGTTATG-TATTATGTAAGTTATGA
*
60627435 AAGTTA--TA-TA--TAAGTTATTA
1 AAGTTATGTATTATGTAAGTTATGA
* * *
60627455 AA--AATGTATTATGTAATTTATGT
1 AAGTTATGTATTATGTAAGTTATGA
* * *
60627478 AAGTTGTGTATTATGTAAGTCATGT
1 AAGTTATGTATTATGTAAGTTATGA
* *
60627503 AGGCTATGTATTATGTAAGTTATGA
1 AAGTTATGTATTATGTAAGTTATGA
* *
60627528 AAGTT-T-TA-TA--TAAGTGATTA
1 AAGTTATGTATTATGTAAGTTATGA
* * **
60627548 AA--AATGTATTATGTAATTTATTT
1 AAGTTATGTATTATGTAAGTTATGA
60627571 AA---AT-TATTATGTAAGTTATGA
1 AAGTTATGTATTATGTAAGTTATGA
* **
60627592 AAGTTATGTATTATGTAATTTATTT
1 AAGTTATGTATTATGTAAGTTATGA
* *
60627617 AAGTTATGTAAGTTGTGT-A-TTATGC
1 AAGTTATGT-A-TTATGTAAGTTATGA
* * *
60627642 AAGTCATGTAGGCTATGT-A-TTATGT
1 AAGTTATGTA--TTATGTAAGTTATGA
60627667 AAGTTATTATGTTATTATGTAAGTTATGA
1 AAG---TTATG-TATTATGTAAGTTATGA
60627696 AAGTTAT
1 AAGTTAT
60627703 ATATAAGTTA
Statistics
Matches: 277, Mismatches: 54, Indels: 63
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 36 0.13
21 21 0.08
22 7 0.03
23 23 0.08
24 4 0.01
25 146 0.53
26 9 0.03
27 10 0.04
28 5 0.02
29 10 0.04
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.46
Consensus pattern (25 bp):
AAGTTATGTATTATGTAAGTTATGA
Found at i:60627423 original size:20 final size:20
Alignment explanation
Indices: 60627394--60627454 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
60627384 TCATGTAGGC
60627394 TATG-TATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
60627413 TATGTTATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
* * *
60627433 GAAAGTTA-TATATAAGTTAT
1 -TATGTTATTATGTAAGTTAT
60627453 TA
1 TA
60627455 AAAATGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TATGTTATTATGTAAGTTAT
Found at i:60627539 original size:93 final size:89
Alignment explanation
Indices: 60627413--60627623 Score: 278
Period size: 93 Copynumber: 2.3 Consensus size: 89
60627403 TGTAAGTTAT
*
60627413 TATGTTATTATGTAAGTTATGAAAGTTATATATAAGTTATTAAAAATGTATTATGTAATTTATGT
1 TATG-TATTATGTAAGTTATGAAAGTTATATATAAGTGATTAAAAATGTATTATGTAATTTATGT
* * *
60627478 AAGTTGTGTATTATGTAAGTCATGTAGGC
65 AA---AT-TATTATGTAAGTCATGAAAGC
* *
60627507 TATGTATTATGTAAGTTATGAAAGTTTTATATAAGTGATTAAAAATGTATTATGTAATTTATTTA
1 TATGTATTATGTAAGTTATGAAAGTTATATATAAGTGATTAAAAATGTATTATGTAATTTATGTA
* *
60627572 AATTATTATGTAAGTTATGAAAGT
66 AATTATTATGTAAGTCATGAAAGC
* **
60627596 TATGTATTATGTAATTTATTTAAGTTAT
1 TATGTATTATGTAAGTTATGAAAGTTAT
60627624 GTAAGTTGTG
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
89 41 0.39
90 1 0.01
93 59 0.56
94 4 0.04
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (89 bp):
TATGTATTATGTAAGTTATGAAAGTTATATATAAGTGATTAAAAATGTATTATGTAATTTATGTA
AATTATTATGTAAGTCATGAAAGC
Found at i:60627542 original size:113 final size:115
Alignment explanation
Indices: 60627345--60627609 Score: 351
Period size: 113 Copynumber: 2.3 Consensus size: 115
60627335 TATGAAAGTT
* *
60627345 ATGTATTATATAATTTATGTAAGTTGTGTATTATGCAAGTCATGTAGGCTATGTATTATGTAAGT
1 ATGTATTATGTAATTTATGTAAGTTGTGTATTATGTAAGTCATGTAGGCTATGTATTATGTAAGT
* * * * * *
60627410 TATTATGTTATTATGTAAGTTA-TGAAAGT-TA-TATATAAGTTATTAAAA
66 TATAAAGTTATTATATAAGTGATTAAAAATGTATTATATAAGTTATT-AAA
60627458 ATGTATTATGTAATTTATGTAAGTTGTGTATTATGTAAGTCATGTAGGCTATGTATTATGTAAGT
1 ATGTATTATGTAATTTATGTAAGTTGTGTATTATGTAAGTCATGTAGGCTATGTATTATGTAAGT
* * *
60627523 TATGAAAGTT-TTATATAAGTGATTAAAAATGTATTATGTAATTTATTTAA
66 TAT-AAAGTTATTATATAAGTGATTAAAAATGTATTATATAAGTTATTAAA
* * *
60627573 AT-TATTATGTAAGTTATGAAAGTTATGTATTATGTAA
1 ATGTATTATGTAATTTATGTAAGTTGTGTATTATGTAA
60627610 TTTATTTAAG
Statistics
Matches: 134, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
113 76 0.57
114 41 0.31
115 6 0.04
116 11 0.08
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (115 bp):
ATGTATTATGTAATTTATGTAAGTTGTGTATTATGTAAGTCATGTAGGCTATGTATTATGTAAGT
TATAAAGTTATTATATAAGTGATTAAAAATGTATTATATAAGTTATTAAA
Found at i:60627684 original size:20 final size:20
Alignment explanation
Indices: 60627655--60627715 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
60627645 TCATGTAGGC
60627655 TATG-TATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
60627674 TATGTTATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
* * *
60627694 GAAAGTTA-TATATAAGTTAT
1 -TATGTTATTATGTAAGTTAT
60627714 TA
1 TA
60627716 AAAAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TATGTTATTATGTAAGTTAT
Found at i:60627773 original size:30 final size:28
Alignment explanation
Indices: 60627705--60627775 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
60627695 AAAGTTATAT
* *
60627705 ATAAGTTATTAAAAAATATATATTTTTA
1 ATAAGTTATTAAAAAATATATAATATTA
* *
60627733 ATATATTTATTAAAAATGTATATAAATATTA
1 ATA-AGTTATTAAAAA-ATATAT-AATATTA
60627764 ATAAGTTATTAA
1 ATAAGTTATTAA
60627776 GTTATATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.09
29 11 0.31
30 13 0.37
31 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (28 bp):
ATAAGTTATTAAAAAATATATAATATTA
Found at i:60627784 original size:23 final size:22
Alignment explanation
Indices: 60627758--60627802 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
60627748 ATGTATATAA
*
60627758 ATATTAATAAGTTATTAAGTTAT
1 ATATTAAAAAGTTA-TAAGTTAT
*
60627781 ATATTAAAAATTTATAAGTTAT
1 ATATTAAAAAGTTATAAGTTAT
60627803 GTAAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
ATATTAAAAAGTTATAAGTTAT
Found at i:60627798 original size:30 final size:30
Alignment explanation
Indices: 60627751--60627811 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
60627741 ATTAAAAATG
* *
60627751 TATATAAATATTAATAAGTTAT-TAAGTTA
1 TATATAAAAATTAATAAGTTATGTAAATTA
*
60627780 TATATTAAAAATTTATAAGTTATGTAAATTA
1 TATA-TAAAAATTAATAAGTTATGTAAATTA
60627811 T
1 T
60627812 GCAAGTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 16 0.59
31 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TATATAAAAATTAATAAGTTATGTAAATTA
Found at i:60629530 original size:22 final size:22
Alignment explanation
Indices: 60629505--60629554 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
60629495 AGTGCCTACA
*
60629505 CTAAAAAAGGTTCAAAGTTGCC
1 CTAAAAAAGGTTCAAAGTTGAC
60629527 CTAAAAAAGGTTCAAAGTTGAC
1 CTAAAAAAGGTTCAAAGTTGAC
60629549 CTAAAA
1 CTAAAA
60629555 TAAACTTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (22 bp):
CTAAAAAAGGTTCAAAGTTGAC
Found at i:60646660 original size:25 final size:22
Alignment explanation
Indices: 60646598--60646666 Score: 57
Period size: 25 Copynumber: 2.9 Consensus size: 22
60646588 AGCACTACTT
*
60646598 ATAATAAAAAAAATTAATACCA
1 ATAATAAAAAAATTTAATACCA
* *
60646620 ATATATATATATAATTTAAATACCAA
1 ATA-ATA-AAAAAATTT-AATACC-A
60646646 ATTAATAAAAAAATTTGAATA
1 A-TAATAAAAAAATTT-AATA
60646667 TCTAATCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
22 3 0.08
23 3 0.08
24 6 0.17
25 17 0.47
26 5 0.14
27 2 0.06
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.32
Consensus pattern (22 bp):
ATAATAAAAAAATTTAATACCA
Found at i:60648150 original size:2 final size:2
Alignment explanation
Indices: 60648138--60648189 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
60648128 TTTATAGGAG
*
60648138 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60648180 TA TA TA TA TA
1 TA TA TA TA TA
60648190 AAAGAAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:60648285 original size:6 final size:6
Alignment explanation
Indices: 60648274--60648300 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
60648264 ATCTCTTAAA
60648274 ATATTT ATATTT ATATTT ATATTT ATA
1 ATATTT ATATTT ATATTT ATATTT ATA
60648301 AATATATATA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:60649873 original size:21 final size:21
Alignment explanation
Indices: 60649835--60649877 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
60649825 AAGATTGTAA
*
60649835 AAAAAATTTTATTTAAAATAT
1 AAAAAATTTTATTAAAAATAT
60649856 AAAAAATTTTGA-TAAAAATAT
1 AAAAAATTTT-ATTAAAAATAT
60649877 A
1 A
60649878 TTGTTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAAATTTTATTAAAAATAT
Found at i:60650298 original size:31 final size:31
Alignment explanation
Indices: 60650257--60650315 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
60650247 TTATTCACTG
*
60650257 AAATATTCATTTAAGTCACTACACTATTCAA
1 AAATATTCATTTAAGTCACTAAACTATTCAA
* *
60650288 AAATTTTCATTTAAGTCATTAAACTATT
1 AAATATTCATTTAAGTCACTAAACTATT
60650316 TGAAAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (31 bp):
AAATATTCATTTAAGTCACTAAACTATTCAA
Found at i:60658330 original size:2 final size:2
Alignment explanation
Indices: 60658325--60658365 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
60658315 TTGTGGTGTG
*
60658325 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60658366 GTCGGTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60668215 original size:13 final size:13
Alignment explanation
Indices: 60668197--60668222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60668187 TTGTGGTTGA
60668197 AATCTAGCTTAGT
1 AATCTAGCTTAGT
60668210 AATCTAGCTTAGT
1 AATCTAGCTTAGT
60668223 TGAGTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
AATCTAGCTTAGT
Found at i:60672902 original size:23 final size:23
Alignment explanation
Indices: 60672859--60672905 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
60672849 CTTTGGGGCC
* *
60672859 AAAAAAATTTAAGTGTCAATTTG
1 AAAAAAATTTAAATATCAATTTG
*
60672882 AAAAAAA-TTAAATATCAAATTG
1 AAAAAAATTTAAATATCAATTTG
60672904 AA
1 AA
60672906 CATTAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (23 bp):
AAAAAAATTTAAATATCAATTTG
Found at i:60673562 original size:22 final size:20
Alignment explanation
Indices: 60673528--60673570 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
60673518 TAAATCCAAA
60673528 ATTAAATAAATTCATAATTAAC
1 ATTAAATAAATTC-T-ATTAAC
**
60673550 ATTAAATTTATTCTATTAAC
1 ATTAAATAAATTCTATTAAC
60673570 A
1 A
60673571 AAATAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 11 0.58
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAATAAATTCTATTAAC
Found at i:60675132 original size:2 final size:2
Alignment explanation
Indices: 60675125--60675153 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60675115 GTTATAATTC
60675125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60675154 AAGTAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60676388 original size:16 final size:16
Alignment explanation
Indices: 60676367--60676397 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60676357 AATAAAAAAA
60676367 TTCCATGAAGACAAAG
1 TTCCATGAAGACAAAG
*
60676383 TTCCATGCAGACAAA
1 TTCCATGAAGACAAA
60676398 AGTAATTTTT
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:0.23, G:0.16, T:0.19
Consensus pattern (16 bp):
TTCCATGAAGACAAAG
Found at i:60679705 original size:5 final size:6
Alignment explanation
Indices: 60679688--60679712 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
60679678 GTCTAAATTC
60679688 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
60679713 CGTGTCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:60682387 original size:18 final size:20
Alignment explanation
Indices: 60682350--60682389 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
60682340 AGGAAATTTT
*
60682350 TTTTATTTAAACTCTTTAAA
1 TTTTATTTAAAATCTTTAAA
60682370 TTTT-TTTAAAAT-TTTAAA
1 TTTTATTTAAAATCTTTAAA
60682388 TT
1 TT
60682390 AGTAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTTAAAATCTTTAAA
Found at i:60682720 original size:2 final size:2
Alignment explanation
Indices: 60682713--60682749 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60682703 ATCAATTCTT
60682713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60682750 TATTCATGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60683414 original size:3 final size:3
Alignment explanation
Indices: 60683406--60683435 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
60683396 TTGATCTTTG
60683406 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
60683436 TAAGAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:60687333 original size:29 final size:26
Alignment explanation
Indices: 60687265--60687322 Score: 102
Period size: 25 Copynumber: 2.3 Consensus size: 26
60687255 TGCTTTTTAA
60687265 ATAT-TATGTAAGCAATCTGGCCAAT
1 ATATATATGTAAGCAATCTGGCCAAT
60687290 ATATATAT-TAAGCAATCTGGCCAAT
1 ATATATATGTAAGCAATCTGGCCAAT
60687315 ATATATAT
1 ATATATAT
60687323 AATGTAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 29 0.91
26 3 0.09
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (26 bp):
ATATATATGTAAGCAATCTGGCCAAT
Found at i:60692634 original size:16 final size:15
Alignment explanation
Indices: 60692612--60692648 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
60692602 TATACATACA
60692612 AACATACACACAAAC
1 AACATACACACAAAC
*
60692627 ATACATACACACTAAC
1 A-ACATACACACAAAC
60692643 AACATA
1 AACATA
60692649 AAGGAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (15 bp):
AACATACACACAAAC
Found at i:60692928 original size:20 final size:20
Alignment explanation
Indices: 60692903--60692941 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
60692893 ACATACACAC
60692903 ACACACATAC-ACACATACAT
1 ACACACATACGA-ACATACAT
60692923 ACACACATACGAACATACA
1 ACACACATACGAACATACA
60692942 CAAACACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.51, C:0.33, G:0.03, T:0.13
Consensus pattern (20 bp):
ACACACATACGAACATACAT
Found at i:60692930 original size:12 final size:12
Alignment explanation
Indices: 60692899--60692932 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
60692889 TAATACATAC
*
60692899 ACACACACACAT
1 ACACACATACAT
60692911 ACACACATACAT
1 ACACACATACAT
60692923 ACACACATAC
1 ACACACATAC
60692933 GAACATACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (12 bp):
ACACACATACAT
Found at i:60692932 original size:8 final size:8
Alignment explanation
Indices: 60692882--60692921 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
60692872 AATACAAGAA
60692882 ACACACAT
1 ACACACAT
*
60692890 A-ATACAT
1 ACACACAT
60692897 ACACAC--
1 ACACACAT
60692903 ACACACAT
1 ACACACAT
60692911 ACACACAT
1 ACACACAT
60692919 ACA
1 ACA
60692922 TACACACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
6 6 0.22
7 6 0.22
8 15 0.56
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (8 bp):
ACACACAT
Found at i:60695332 original size:19 final size:19
Alignment explanation
Indices: 60695308--60695344 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60695298 ATACATATAT
*
60695308 TTTTATAATTTATAATTTA
1 TTTTATAATTTAAAATTTA
*
60695327 TTTTATATTTTAAAATTT
1 TTTTATAATTTAAAATTT
60695345 TATATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTAAAATTTA
Found at i:60709074 original size:39 final size:39
Alignment explanation
Indices: 60709020--60709098 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
60709010 TTGTATGCAT
60709020 ATTGTTTCTAGTGGAAAGTTGTCATCAGATTGCCTACCA
1 ATTGTTTCTAGTGGAAAGTTGTCATCAGATTGCCTACCA
*
60709059 ATTGTTTCTAGTGGAAAGTTGTCCTCAGATTGCCTACCA
1 ATTGTTTCTAGTGGAAAGTTGTCATCAGATTGCCTACCA
60709098 A
1 A
60709099 CTTACCACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (39 bp):
ATTGTTTCTAGTGGAAAGTTGTCATCAGATTGCCTACCA
Found at i:60717705 original size:2 final size:2
Alignment explanation
Indices: 60717698--60717727 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60717688 GAAAGTCGAC
60717698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60717728 TTGCTCACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60724499 original size:30 final size:29
Alignment explanation
Indices: 60724430--60724501 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
60724420 AATTGAATAA
* * * *
60724430 AAATTAAAATTTTATGTATATTTTAAACT
1 AAATTAAAATTTCATATACATATTAAACT
* *
60724459 ACAATAAAAATTTCATATACATAATTATACT
1 A-AATTAAAATTTCATATACAT-ATTAAACT
60724490 AAATTAAAATTT
1 AAATTAAAATTT
60724502 ATTTATCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 1 0.03
30 26 0.76
31 7 0.21
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (29 bp):
AAATTAAAATTTCATATACATATTAAACT
Found at i:60730305 original size:20 final size:21
Alignment explanation
Indices: 60730268--60730320 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
60730258 ATATATTGGT
*
60730268 AATA-ATATATAATTAATTTTA
1 AATATATATATAA-TAATTATA
60730289 AATATATATATAA-AATTATAA
1 AATATATATATAATAATTAT-A
*
60730310 AATAAATATAT
1 AATATATATAT
60730321 GTAAAGCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 15 0.54
22 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATATATATAATAATTATA
Found at i:60730941 original size:19 final size:18
Alignment explanation
Indices: 60730902--60730937 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
60730892 TTGAATTTTA
60730902 ATTTTTAATTTTTTAAAT
1 ATTTTTAATTTTTTAAAT
60730920 ATTTTATAA-TTTTTAAAT
1 ATTTT-TAATTTTTTAAAT
60730938 TATTGGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAATTTTTTAAAT
Found at i:60731334 original size:18 final size:18
Alignment explanation
Indices: 60731296--60731335 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
60731286 AAAATAAACC
*
60731296 ATTTAATAACAATTTGTT
1 ATTTAATAACAATTTATT
60731314 ATTTAAT-ACAATTTATAT
1 ATTTAATAACAATTTAT-T
60731332 ATTT
1 ATTT
60731336 TGGTACTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAATAACAATTTATT
Found at i:60736904 original size:15 final size:15
Alignment explanation
Indices: 60736884--60736915 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60736874 GGATGGAGAT
60736884 GGTGACGACGGTGGC
1 GGTGACGACGGTGGC
*
60736899 GGTGACGGCGGTGGC
1 GGTGACGACGGTGGC
60736914 GG
1 GG
60736916 AGGAGAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.19, G:0.59, T:0.12
Consensus pattern (15 bp):
GGTGACGACGGTGGC
Found at i:60744101 original size:22 final size:23
Alignment explanation
Indices: 60744070--60744112 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
60744060 GCTCCTTTTC
60744070 TTAAGTAATT-TTTTT-AGAAAA
1 TTAAGTAATTCTTTTTGAGAAAA
60744091 TTAAGATAATTCTTTTTGAGAA
1 TTAAG-TAATTCTTTTTGAGAA
60744113 GTCTATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 5 0.26
24 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (23 bp):
TTAAGTAATTCTTTTTGAGAAAA
Found at i:60745440 original size:8 final size:9
Alignment explanation
Indices: 60745417--60745443 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
60745407 TTTTGCTACT
60745417 TATTTTTAA
1 TATTTTTAA
60745426 TATTTTTAA
1 TATTTTTAA
60745435 TATTTTTAA
1 TATTTTTAA
60745444 AATTAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:60748642 original size:12 final size:12
Alignment explanation
Indices: 60748627--60748658 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
60748617 ATCACCACCC
60748627 CCACCACCGCCG
1 CCACCACCGCCG
*
60748639 CCACCACCGCTG
1 CCACCACCGCCG
60748651 CCACCACC
1 CCACCACC
60748659 ACCCATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.66, G:0.12, T:0.03
Consensus pattern (12 bp):
CCACCACCGCCG
Found at i:60756692 original size:6 final size:6
Alignment explanation
Indices: 60756681--60756706 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
60756671 TCGTGAAACG
60756681 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
60756707 CGAAAACGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:60757622 original size:44 final size:43
Alignment explanation
Indices: 60757414--60757622 Score: 185
Period size: 44 Copynumber: 4.9 Consensus size: 43
60757404 TGTAACTTTT
*
60757414 GGGAGATAGGATTGGTTTCTTTCGTCTGCTCCACTACTGCTTA
1 GGGAGATAAGATTGGTTTCTTTCGTCTGCTCCACTACTGCTTA
* * * * **
60757457 GGGAGATAAGACTAGATGCGAT--T-TGCTCCACTACTGCTTA
1 GGGAGATAAGATTGGTTTCTTTCGTCTGCTCCACTACTGCTTA
* * ** ** **
60757497 GGGAGATAATATCT-GTGGT-TTTAATCCACTCCACTACAACTTCA
1 GGGAGATAAGAT-TGGT-TTCTTTCGTCTGCTCCACTACTGCTT-A
* * *
60757541 GGGAGATAGGATTGATTTCTTTTGTCTGCTCCACTACTGCTTA
1 GGGAGATAAGATTGGTTTCTTTCGTCTGCTCCACTACTGCTTA
60757584 GGGAGATAAGATTTGGTTTCTTTCGTCTGCTCCACTACT
1 GGGAGATAAGA-TTGGTTTCTTTCGTCTGCTCCACTACT
60757623 ACTNNNNNNN
Statistics
Matches: 126, Mismatches: 31, Indels: 17
0.72 0.18 0.10
Matches are distributed among these distances:
40 29 0.23
41 2 0.02
42 1 0.01
43 40 0.32
44 54 0.43
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (43 bp):
GGGAGATAAGATTGGTTTCTTTCGTCTGCTCCACTACTGCTTA
Found at i:60757909 original size:87 final size:87
Alignment explanation
Indices: 60757762--60757968 Score: 299
Period size: 87 Copynumber: 2.4 Consensus size: 87
60757752 NNNNNNNNNN
* *
60757762 TCCACTGCAACCGATGGAGGCAAGGCTTTCTTTTCGATCTGCTCTGCTGTTAACGTAGGAAGGCA
1 TCCACCGCAACCGATGGAGGCAAGGCTTTCTTTTCGATCTGCTCTGCTGTTAACGCAGGAAGGCA
*
60757827 AGATCTGCTTTCTTTAACCAGC
66 AGATCTGCTATCTTTAACCAGC
* * * * * *
60757849 TCCACCGTAACCGATAGAGGCAAGGTTTTGTTTTCGATCTGCT-TCGCTGTTAATGCAGGAAGGT
1 TCCACCGCAACCGATGGAGGCAAGGCTTTCTTTTCGATCTGCTCT-GCTGTTAACGCAGGAAGGC
*
60757913 AAGATCTGCTATCTTTGACCAGC
65 AAGATCTGCTATCTTTAACCAGC
*
60757936 TCCACTGCAACCGATGGAGGCAAGGCTTTCTTT
1 TCCACCGCAACCGATGGAGGCAAGGCTTTCTTT
60757969 GATCTGTTCT
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 1 0.01
87 103 0.99
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (87 bp):
TCCACCGCAACCGATGGAGGCAAGGCTTTCTTTTCGATCTGCTCTGCTGTTAACGCAGGAAGGCA
AGATCTGCTATCTTTAACCAGC
Found at i:60758588 original size:108 final size:108
Alignment explanation
Indices: 60758399--60758594 Score: 304
Period size: 108 Copynumber: 1.8 Consensus size: 108
60758389 GAAAAATGCT
*
60758399 TGAAAAAGATTATCAAAATAGACAAAATGAAATTTTGTTGAGAGTAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATAGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
60758464 CAATCAAGACAGCAAATTTTGCTGAGGTACGAGATGTATAAGA
66 CAATCAAGACAGCAAATTTTGCTGAGGTACGAGATGTATAAGA
* * * * *
60758507 TGAAAAAGATTATCACAATGGATAAGATGGAAA-TTTGTTGAGAGCAAAGCTCTAAATAAACAAA
1 TGAAAAAGATTATCAAAATAGACAAAAT-GAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAA
* *
60758571 TTAATCAAGATAGCAAATTTTGCT
65 TCAATCAAGACAGCAAATTTTGCT
60758595 AGAATACAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 75 0.95
109 4 0.05
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATAGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
CAATCAAGACAGCAAATTTTGCTGAGGTACGAGATGTATAAGA
Found at i:60758658 original size:45 final size:44
Alignment explanation
Indices: 60758560--60758660 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 44
60758550 GCAAAGCTCT
* * *
60758560 AAATA-AACAAATTAATCAAGATAGCAAATTTTGCTAGAATACA
1 AAATAGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
* **
60758603 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACA
1 AAAT-AGAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATACA
60758649 AAA-ATGAATAAA
1 AAATA-GAATAAA
60758661 ATGGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
44 2 0.04
45 31 0.65
46 11 0.23
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (44 bp):
AAATAGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
Found at i:60758948 original size:13 final size:12
Alignment explanation
Indices: 60758930--60758983 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
60758920 TTGGCCTCTC
60758930 CTTTTTCTCTTTT
1 CTTTTTCT-TTTT
60758943 CTTTTTCGTTTTT
1 CTTTTTC-TTTTT
60758956 C-TTTTCTTTTTT
1 CTTTTTC-TTTTT
*
60758968 CTTTTTGTTTTT
1 CTTTTTCTTTTT
60758980 -TTTT
1 CTTTT
60758984 CTCAAGTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
11 4 0.11
12 16 0.43
13 16 0.43
14 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (12 bp):
CTTTTTCTTTTT
Found at i:60758960 original size:18 final size:17
Alignment explanation
Indices: 60758932--60758985 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
60758922 GGCCTCTCCT
60758932 TTTTCTCTTTTCTTTTTC
1 TTTT-TCTTTTCTTTTTC
60758950 GTTTTTCTTTTCTTTTTTC
1 -TTTTTCTTTTC-TTTTTC
*
60758969 TTTTTGTTTT-TTTTTC
1 TTTTTCTTTTCTTTTTC
60758985 T
1 T
60758986 CAAGTGAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 7 0.21
18 16 0.48
19 10 0.30
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTC
Found at i:60758961 original size:25 final size:23
Alignment explanation
Indices: 60758931--60758986 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 23
60758921 TGGCCTCTCC
60758931 TTTTTCTCTTTTCTTTTTCGTTTT
1 TTTTTCTCTTTTCTTTTT-GTTTT
*
60758955 TCTTTTCTTTTTTCTTTTTGTTTT
1 T-TTTTCTCTTTTCTTTTTGTTTT
60758979 TTTTTCTC
1 TTTTTCTC
60758987 AAGTGAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 7 0.24
25 16 0.55
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTTCTCTTTTCTTTTTGTTTT
Found at i:60760882 original size:62 final size:62
Alignment explanation
Indices: 60760703--60760885 Score: 321
Period size: 62 Copynumber: 3.0 Consensus size: 62
60760693 CTCAAAGCAC
* *
60760703 TTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTGATGCATGAACGCATAT
1 TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCATAT
* *
60760765 TTTTGGATTTTAAGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCGTAT
1 TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCATAT
*
60760827 TTTTGGATTTTAGGAAATTTGTTGCATGCAATGAAATGTAATGTTGATGCATGAATGCA
1 TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCA
60760886 AAAAAGAGAC
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 114 1.00
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.40
Consensus pattern (62 bp):
TTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATGCATAT
Found at i:60766415 original size:19 final size:20
Alignment explanation
Indices: 60766391--60766430 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
60766381 AGTCTGAGAG
60766391 AGTGAAACAG-ATCCAAGAA
1 AGTGAAACAGAATCCAAGAA
*
60766410 AGTGAATCAGAATCCAAGAA
1 AGTGAAACAGAATCCAAGAA
60766430 A
1 A
60766431 ATAGAGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.15, G:0.20, T:0.12
Consensus pattern (20 bp):
AGTGAAACAGAATCCAAGAA
Found at i:60766603 original size:3 final size:3
Alignment explanation
Indices: 60766595--60766625 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
60766585 CTTTTGTTTC
60766595 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
60766626 GGGTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:60766716 original size:29 final size:29
Alignment explanation
Indices: 60766675--60766732 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
60766665 TTATAAGGAT
*
60766675 TGGATTAAATTAGTCCATTTATTATTAAA
1 TGGATTAAATTAGTCCATATATTATTAAA
* *
60766704 TGGATTAATTTAGTCCATATGTTATTAAA
1 TGGATTAAATTAGTCCATATATTATTAAA
60766733 AAGAATCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (29 bp):
TGGATTAAATTAGTCCATATATTATTAAA
Found at i:60767400 original size:22 final size:21
Alignment explanation
Indices: 60767357--60767401 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
60767347 TAAACCCTCA
*
60767357 AAATTTTTAAAAATTATTATT
1 AAATTTTTAAAAATTATAATT
*
60767378 AAATTTCTTAAAAATTGTAATT
1 AAATTT-TTAAAAATTATAATT
60767400 AA
1 AA
60767402 GTCTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTTTTAAAAATTATAATT
Found at i:60780245 original size:15 final size:17
Alignment explanation
Indices: 60780227--60780258 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60780217 CAGAATAGAA
60780227 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
60780242 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
60780259 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:60780945 original size:3 final size:3
Alignment explanation
Indices: 60780925--60780977 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
60780915 GTGAGGTAAG
* *
60780925 TAT TAA TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
60780973 TAT TA
1 TAT TA
60780978 GTGAGAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:60782638 original size:29 final size:32
Alignment explanation
Indices: 60782595--60782678 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 32
60782585 AATAGTCTAT
*
60782595 ATTTTTATAATTTTTAAAAATTTAAA-T-CAA
1 ATTTTTATTATTTTTAAAAATTTAAAGTACAA
*
60782625 ATTTTTATTATTTTTAAAAA-CTAAAGTAC-A
1 ATTTTTATTATTTTTAAAAATTTAAAGTACAA
*
60782655 A-TTTTATTATTATTTAAAATTTTA
1 ATTTTTATTATT-TTTAAAAATTTA
60782679 TCAATTATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 14 0.30
30 29 0.63
31 3 0.07
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (32 bp):
ATTTTTATTATTTTTAAAAATTTAAAGTACAA
Found at i:60784079 original size:17 final size:15
Alignment explanation
Indices: 60784042--60784081 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
60784032 TTGTTCACTT
60784042 TTTTAATTTCATCCG
1 TTTTAATTTCATCCG
60784057 -TTTAATTTCATCCTAG
1 TTTTAATTTCATCC--G
60784073 TTTTAATTT
1 TTTTAATTT
60784082 AGCCCCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTTAATTTCATCCG
Found at i:60784545 original size:28 final size:29
Alignment explanation
Indices: 60784506--60784579 Score: 102
Period size: 28 Copynumber: 2.6 Consensus size: 29
60784496 AAAAATAAAA
60784506 ATTTACCAAAATATTATAAC-TTTTTT-TT
1 ATTTACCAAAATA-TATAACTTTTTTTATT
60784534 ATTTACCAAAATAT-T-ACTTTTTTTAATT
1 ATTTACCAAAATATATAACTTTTTTT-ATT
60784562 ATTTACCAAAATATATAA
1 ATTTACCAAAATATATAA
60784580 AAAAACACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.05
26 7 0.17
27 1 0.02
28 29 0.71
29 1 0.02
30 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTACCAAAATATATAACTTTTTTTATT
Found at i:60784666 original size:27 final size:27
Alignment explanation
Indices: 60784627--60784685 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
60784617 TCTGGGTTAG
*
60784627 GCCAATGGAATTGGCAGCACCAAAT-GT
1 GCCAATGCAATTGGCAGCACC-AATGGT
* *
60784654 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCAATTGGCAGCACCAATGGT
60784681 GCCAA
1 GCCAA
60784686 AGGACTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (27 bp):
GCCAATGCAATTGGCAGCACCAATGGT
Found at i:60784883 original size:19 final size:19
Alignment explanation
Indices: 60784859--60784994 Score: 161
Period size: 19 Copynumber: 7.3 Consensus size: 19
60784849 TCACTTTTGT
60784859 ATTTAATAACTCTATTTTA
1 ATTTAATAACTCTATTTTA
* * *
60784878 ATTTAATAA-ACTATTCTC
1 ATTTAATAACTCTATTTTA
*
60784896 ATTTAACAACTCTATTTTA
1 ATTTAATAACTCTATTTTA
* * *
60784915 ATTTAATAA-ACTATTCTC
1 ATTTAATAACTCTATTTTA
60784933 ATTTAATAACTCTATTTTA
1 ATTTAATAACTCTATTTTA
* * *
60784952 ATTTAATAA-ACTATTCTC
1 ATTTAATAACTCTATTTTA
60784970 ATTTAATAACTCTATTTTA
1 ATTTAATAACTCTATTTTA
60784989 ATTTAA
1 ATTTAA
60784995 AAAATTAAGT
Statistics
Matches: 94, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
18 44 0.47
19 50 0.53
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTAATAACTCTATTTTA
Found at i:60784907 original size:37 final size:37
Alignment explanation
Indices: 60784859--60784994 Score: 263
Period size: 37 Copynumber: 3.7 Consensus size: 37
60784849 TCACTTTTGT
60784859 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
*
60784896 ATTTAACAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
60784933 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
60784970 ATTTAATAACTCTATTTTAATTTAA
1 ATTTAATAACTCTATTTTAATTTAA
60784995 AAAATTAAGT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Done.