Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 73 of 345
Found at i:19895030 original size:25 final size:25
Alignment explanation
Indices: 19894980--19895078 Score: 119
Period size: 25 Copynumber: 4.0 Consensus size: 25
19894970 ATCGAATGCC
* *
19894980 CACACGGCCTAG-GACACGGACGTG
1 CACACGGCCTAGCCACACGGGCGTG
* *
19895004 CACACGGCCTAGCCATACGGGCATG
1 CACACGGCCTAGCCACACGGGCGTG
*
19895029 CACACGGCCTGGCCACACGGGCGTG
1 CACACGGCCTAGCCACACGGGCGTG
* * *
19895054 CACACAGCCTGGCCACACGAGCGTG
1 CACACGGCCTAGCCACACGGGCGTG
19895079 TGCCTCCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
24 12 0.18
25 53 0.82
ACGTcount: A:0.22, C:0.37, G:0.31, T:0.09
Consensus pattern (25 bp):
CACACGGCCTAGCCACACGGGCGTG
Found at i:19898107 original size:28 final size:29
Alignment explanation
Indices: 19898071--19898135 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
19898061 AAAGTGATTT
* *
19898071 TTGACAAAAATGTCAATT-AGGAATTAAA
1 TTGAGAAAAATGTAAATTGAGGAATTAAA
* **
19898099 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGAGAAAAATGTAAATTGAGGAATTAAA
*
19898128 TTGTGAAA
1 TTGAGAAA
19898136 TAAATGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (29 bp):
TTGAGAAAAATGTAAATTGAGGAATTAAA
Found at i:19914758 original size:55 final size:54
Alignment explanation
Indices: 19914640--19914760 Score: 147
Period size: 55 Copynumber: 2.2 Consensus size: 54
19914630 AACATGGCCC
* *
19914640 TGGTCGAACCTGCCAAACAACACGGGCGTGCGACACGCCCGTGTGGAAGAACCA
1 TGGTCGAACCTGCAAAACAACACGGGCGTGCGACACGCCCGTGTGCAAGAACCA
* * * *
19914694 TGGGT-GAACCTGCTAAAACTACACGGGCGTGCGACACGCCCGTGT-CTAGCACCCG
1 T-GGTCGAACCTGC-AAAACAACACGGGCGTGCGACACGCCCGTGTGCAAG-AACCA
19914749 TGGTCGAACCTG
1 TGGTCGAACCTG
19914761 TTAGATTGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
54 14 0.25
55 43 0.75
ACGTcount: A:0.24, C:0.31, G:0.30, T:0.15
Consensus pattern (54 bp):
TGGTCGAACCTGCAAAACAACACGGGCGTGCGACACGCCCGTGTGCAAGAACCA
Found at i:19930133 original size:28 final size:29
Alignment explanation
Indices: 19930097--19930161 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
19930087 AAAGTGATTT
* *
19930097 TTGACAAAAATGTCAATT-AGAGATTAAA
1 TTGAGAAAAATGTAAATTGAGAGATTAAA
* * *
19930125 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGAGAAAAATGTAAATTGAGAGATTAAA
*
19930154 TTGTGAAA
1 TTGAGAAA
19930162 TAAATGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (29 bp):
TTGAGAAAAATGTAAATTGAGAGATTAAA
Found at i:19930762 original size:47 final size:47
Alignment explanation
Indices: 19930708--19930831 Score: 149
Period size: 47 Copynumber: 2.6 Consensus size: 47
19930698 GAATAATACA
* ** *
19930708 TTGATTTGGCCACGGGCCATGGTATAGGTATTTTGAGAGGAGCTACC
1 TTGATTTGGCTACGGGCCATGGTATAGGTATTCCGAGAGAAGCTACC
* * * * *
19930755 TTGATTTGGCTATGGGCCATGGTACAGGTATTCCGGGATAAGTTACC
1 TTGATTTGGCTACGGGCCATGGTATAGGTATTCCGAGAGAAGCTACC
* *
19930802 TTGATTTGGGTACGGGCTATGGTATAGGTA
1 TTGATTTGGCTACGGGCCATGGTATAGGTA
19930832 CTTATTGATT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (47 bp):
TTGATTTGGCTACGGGCCATGGTATAGGTATTCCGAGAGAAGCTACC
Found at i:19936245 original size:21 final size:21
Alignment explanation
Indices: 19936221--19936273 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
19936211 TTGTTTAACC
*
19936221 CTTATGGGTTTCTATTTAGCA
1 CTTATGGGCTTCTATTTAGCA
*
19936242 CTTATGTGCTTCTATTTAGC-
1 CTTATGGGCTTCTATTTAGCA
*
19936262 CTT-TGGACTTCT
1 CTTATGGGCTTCT
19936274 GAAAATGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.25
20 3 0.11
21 18 0.64
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (21 bp):
CTTATGGGCTTCTATTTAGCA
Found at i:19937270 original size:20 final size:19
Alignment explanation
Indices: 19937225--19937262 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
19937215 GAGCAAAAGG
19937225 AACGAG-AAACGGGCCAAA
1 AACGAGAAAACGGGCCAAA
*
19937243 AACGGAGAAAATGGGCCAAA
1 AAC-GAGAAAACGGGCCAAA
19937263 GTACGAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 3 0.18
20 11 0.65
ACGTcount: A:0.50, C:0.18, G:0.29, T:0.03
Consensus pattern (19 bp):
AACGAGAAAACGGGCCAAA
Found at i:19944393 original size:39 final size:39
Alignment explanation
Indices: 19944340--19944533 Score: 275
Period size: 39 Copynumber: 5.0 Consensus size: 39
19944330 TGAGGTCCGC
* *
19944340 AGGC-TTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
1 AGGCATTTGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
* *
19944378 AGGCATTTGTACTGGTGTTATATCCGGGCTAAGTCCTGA
1 AGGCATTTGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
19944417 AGGCATTTGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
1 AGGCATTTGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
* *
19944456 AGGCATTTGTGCTAGTGTTATATCCGGGCTAAGTCCCGC
1 AGGCATTTGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
* * *
19944495 AGGC-TTTATGTTGGTATTATATCCGGGCTTAAAGTCCCG
1 AGGCATTTGTGCTGGTGTTATATCCGGGC-T-AAGTCCCG
19944534 CATGCTTTCT
Statistics
Matches: 141, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
38 24 0.17
39 109 0.77
40 8 0.06
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (39 bp):
AGGCATTTGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
Found at i:19944689 original size:18 final size:18
Alignment explanation
Indices: 19944666--19944701 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19944656 AAGTTGGTCA
19944666 GGTATGTATTATATACTT
1 GGTATGTATTATATACTT
19944684 GGTATGTATTATATACTT
1 GGTATGTATTATATACTT
19944702 TTATATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (18 bp):
GGTATGTATTATATACTT
Found at i:19950492 original size:40 final size:40
Alignment explanation
Indices: 19950427--19950641 Score: 322
Period size: 40 Copynumber: 5.4 Consensus size: 40
19950417 CGGATATCAC
* * * *
19950427 AACCAGCACGAATGCCTTCAGGACTTAACCCAGTTATAAT
1 AACCCGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
19950467 AACCCGCTCAAATGCCTTTGGGACTTAACCCGGTTATAAT
1 AACCCGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
*
19950507 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
19950547 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
19950587 AACCCGCACAAATGCCTTTGGGACTTAACCCGATTATAAT
1 AACCCGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
*
19950627 AACCCGCACGAATGC
1 AACCCGCACAAATGC
19950642 TATGCACATA
Statistics
Matches: 160, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 160 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (40 bp):
AACCCGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:19959013 original size:40 final size:40
Alignment explanation
Indices: 19958864--19959072 Score: 331
Period size: 40 Copynumber: 5.4 Consensus size: 40
19958854 TCGGATATAC
* *
19958864 AACCAGCACGAATGCCTTC-GGACTTAACCC-GTTATTAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
19958902 AACCCGCA--AATGCCTT-GGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
19958939 AACCCGCACGAATGCCTTC-GGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
19958978 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
19959018 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTTTAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
19959058 AACCCGCACGAATGC
1 AACCCGCACGAATGC
19959073 TATGCACATA
Statistics
Matches: 159, Mismatches: 6, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
36 19 0.12
37 15 0.09
38 7 0.04
39 46 0.29
40 72 0.45
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:19959022 original size:79 final size:78
Alignment explanation
Indices: 19958864--19959072 Score: 334
Period size: 79 Copynumber: 2.7 Consensus size: 78
19958854 TCGGATATAC
* *
19958864 AACCAGCACGAATGCCTTCGGACTTAACCC-GTTATTATAACCCGCA--AATGCCTTGGGACTTA
1 AACCCGCACGAATGCCTTCGGACTTAACCCGGTTATAATAACCCGCACGAATGCCTTGGGACTTA
19958926 ACCCGGTTATAAT
66 ACCCGGTTATAAT
*
19958939 AACCCGCACGAATGCCTTCGGACTTAACCCGGTTATAATAACCAGCACGAATGCCTTCGGGACTT
1 AACCCGCACGAATGCCTTCGGACTTAACCCGGTTATAATAACCCGCACGAATGCCTT-GGGACTT
19959004 AACCCGGTTATAAT
65 AACCCGGTTATAAT
* *
19959018 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTTTAATAACCCGCACGAATGC
1 AACCCGCACGAATGCCTTC-GGACTTAACCCGGTTATAATAACCCGCACGAATGC
19959073 TATGCACATA
Statistics
Matches: 123, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
75 29 0.24
76 14 0.11
78 8 0.07
79 40 0.33
80 32 0.26
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (78 bp):
AACCCGCACGAATGCCTTCGGACTTAACCCGGTTATAATAACCCGCACGAATGCCTTGGGACTTA
ACCCGGTTATAAT
Found at i:19967366 original size:40 final size:40
Alignment explanation
Indices: 19967264--19967475 Score: 322
Period size: 40 Copynumber: 5.4 Consensus size: 40
19967254 CTCGGATATC
* *
19967264 AACCAGCACGAATGCCTTC--GACTTAACCCAGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* * *
19967302 AA-CCGCTCAAATGCCTTTGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
19967341 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
19967381 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* * *
19967421 AACCCGCACAAATGCCTTTGGGACTTAACCCGATTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
19967461 AACCCGCACGAATGC
1 AACCCGCACGAATGC
19967476 TATGCACATA
Statistics
Matches: 157, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
37 12 0.08
38 2 0.01
39 20 0.13
40 123 0.78
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:19970937 original size:21 final size:20
Alignment explanation
Indices: 19970913--19970952 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19970903 ACTACTTTTT
*
19970913 ATTTTTTTAGAAGATTTTAGA
1 ATTTTATTAGAA-ATTTTAGA
*
19970934 ATTTTATTATAAATTTTAG
1 ATTTTATTAGAAATTTTAG
19970953 TTTTTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTTTATTAGAAATTTTAGA
Found at i:19972913 original size:13 final size:13
Alignment explanation
Indices: 19972895--19972935 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
19972885 TGAAGTAATT
*
19972895 TCACACGGGCGTG
1 TCACACGAGCGTG
19972908 TCACACGAGCGTG
1 TCACACGAGCGTG
19972921 TCACACGAGCGTG
1 TCACACGAGCGTG
19972934 TC
1 TC
19972936 CCTGCCGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.17
Consensus pattern (13 bp):
TCACACGAGCGTG
Found at i:19978090 original size:43 final size:44
Alignment explanation
Indices: 19978041--19978188 Score: 169
Period size: 43 Copynumber: 3.4 Consensus size: 44
19978031 GGTTACTGAG
* *
19978041 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
**
19978085 -TGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGT-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * * *
19978127 ATATGATTTCGTGTAAGACTC-TGTTTGGGACAGTGGCATCG-AT
1 ATGTGATTACATGTAAGAC-CATGTCTGGGACATTGGCATCGTAT
*
19978170 ATGTGATAACATGTAAGAC
1 ATGTGATTACATGTAAGAC
19978189 TATATCTGAG
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
42 1 0.01
43 86 0.98
44 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:19979959 original size:12 final size:12
Alignment explanation
Indices: 19979938--19979969 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19979928 TTAGTCATGG
19979938 ATATAAATAATA
1 ATATAAATAATA
*
19979950 ATATAGATAATA
1 ATATAAATAATA
19979962 ATATAAAT
1 ATATAAAT
19979970 TTTATTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:19980866 original size:25 final size:23
Alignment explanation
Indices: 19980837--19980901 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
19980827 AATAAAAAAC
*
19980837 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAAT-AAATACA
19980862 TTTAAAACATAAAAATAAAT--A
1 TTTAAAACATAAAAATAAATACA
19980883 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAATAAATA
19980902 AATAATAGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 1 0.03
23 4 0.11
24 4 0.11
25 11 0.29
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
TTTAAAACATAAAAATAAATACA
Found at i:19980894 original size:19 final size:20
Alignment explanation
Indices: 19980863--19980901 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
19980853 TCAAATACAT
19980863 TTAAAACATAAAAATAAATA
1 TTAAAACATAAAAATAAATA
19980883 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAATAAATA
19980902 AATAATAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (20 bp):
TTAAAACATAAAAATAAATA
Found at i:19981114 original size:32 final size:32
Alignment explanation
Indices: 19981077--19981138 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
19981067 AAAAGTAAAG
* *
19981077 TAAAAATACTAAAGTTATTTAAAATTAAAAAT
1 TAAAAATACTAAAATAATTTAAAATTAAAAAT
** *
19981109 TAAAAATTTTAAAATAATTTAATATTAAAA
1 TAAAAATACTAAAATAATTTAAAATTAAAA
19981139 TCGGGCCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (32 bp):
TAAAAATACTAAAATAATTTAAAATTAAAAAT
Found at i:19984397 original size:19 final size:19
Alignment explanation
Indices: 19984360--19984395 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19984350 GTTTGAGTTT
*
19984360 ATATTATTTTAGTAAAAAG
1 ATATTATTTTAATAAAAAG
19984379 ATATTA-TTTAATAAAAA
1 ATATTATTTTAATAAAAA
19984396 AGCAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (19 bp):
ATATTATTTTAATAAAAAG
Found at i:19985407 original size:178 final size:178
Alignment explanation
Indices: 19985108--19985464 Score: 669
Period size: 178 Copynumber: 2.0 Consensus size: 178
19985098 TTCCTGGTTG
* *
19985108 TTTTGAGTTTGCAAAATATTGGGAAGCTATGTTTTTCAGTCGAATAGAAGAATGAAAAAGGCTTC
1 TTTTGAGTTTGCAAAATATTGGGAAGCTATGTTTTTCAGTCGAATAAAAGAATGAAAAAGGCATC
19985173 TTCTTTTTGGGTCCCAAAAAGAATGTTGCGGTCCGAAAGATGCTTTTTCTCCCTTCTTCCATTTC
66 TTCTTTTTGGGTCCCAAAAAGAATGTTGCGGTCCGAAAGATGCTTTTTCTCCCTTCTTCCATTTC
*
19985238 ACAACAATTTCTTTGCTATTAATCAAGATGTTTATTTATGCCTGCTGA
131 ACAACAATTTCTTTGCTATTAATCAAGATGTTTAGTTATGCCTGCTGA
*
19985286 TTTTGAGTTTGCAAAATATTGGGAAGCTATGTTTTTCAGTCGAGTAAAAGAATGAAAAAGGCATC
1 TTTTGAGTTTGCAAAATATTGGGAAGCTATGTTTTTCAGTCGAATAAAAGAATGAAAAAGGCATC
*
19985351 TTCTTTTTGGGTCCCAAAAAGAATGTTGCGGTCCGAAAGATGTTTTTTCTCCCTTCTTCCATTTC
66 TTCTTTTTGGGTCCCAAAAAGAATGTTGCGGTCCGAAAGATGCTTTTTCTCCCTTCTTCCATTTC
19985416 ACAACAATTTCTTTGCTATTAATCAAGATGTTTAGTTATGCCTGCTGA
131 ACAACAATTTCTTTGCTATTAATCAAGATGTTTAGTTATGCCTGCTGA
19985464 T
1 T
19985465 GTCAGATCGT
Statistics
Matches: 174, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 174 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (178 bp):
TTTTGAGTTTGCAAAATATTGGGAAGCTATGTTTTTCAGTCGAATAAAAGAATGAAAAAGGCATC
TTCTTTTTGGGTCCCAAAAAGAATGTTGCGGTCCGAAAGATGCTTTTTCTCCCTTCTTCCATTTC
ACAACAATTTCTTTGCTATTAATCAAGATGTTTAGTTATGCCTGCTGA
Found at i:19990047 original size:7 final size:7
Alignment explanation
Indices: 19990031--19990064 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
19990021 AACATTATGC
19990031 TTTGCAG
1 TTTGCAG
*
19990038 TTTTCAG
1 TTTGCAG
19990045 TTTGCAG
1 TTTGCAG
19990052 TTTGCAG
1 TTTGCAG
*
19990059 TGTGCA
1 TTTGCA
19990065 ATATATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (7 bp):
TTTGCAG
Found at i:19992888 original size:47 final size:47
Alignment explanation
Indices: 19992818--19993347 Score: 817
Period size: 47 Copynumber: 11.3 Consensus size: 47
19992808 CCCTTCGAGA
* *
19992818 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
19992865 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
19992912 CTTGTCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
** *
19992959 CTTATCACATATATACACTTTCACATTCATCATGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
19993006 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * **
19993053 CTTGTCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
19993100 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
19993147 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
19993194 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
19993241 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACACGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
19993288 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
19993335 CTTATCACATATA
1 CTTATCACATATA
19993348 CATATCTTGT
Statistics
Matches: 433, Mismatches: 50, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 433 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:19997295 original size:487 final size:487
Alignment explanation
Indices: 19996382--19997358 Score: 1945
Period size: 487 Copynumber: 2.0 Consensus size: 487
19996372 TGAAACACTC
19996382 ATGAGGTGTGGTAAGTCTTCGTCTTTTCTAGATAAAGCATCTGCGGCCCTGTTCAACTTTCCTAC
1 ATGAGGTGTGGTAAGTCTTCGTCTTTTCTAGATAAAGCATCTGCGGCCCTGTTCAACTTTCCTAC
19996447 TTTATATTCCACTCGGAAATCAAACCCCATTAGCTTGCTGATCCAATGTTGTTGTGGGGATGTCG
66 TTTATATTCCACTCGGAAATCAAACCCCATTAGCTTGCTGATCCAATGTTGTTGTGGGGATGTCG
19996512 TAAGTTGTTGGTCTAACAAATACTTAAGACTGAATTGATCAGTACGGATGAGGAAGTGCCTTCCC
131 TAAGTTGTTGGTCTAACAAATACTTAAGACTGAATTGATCAGTACGGATGAGGAAGTGCCTTCCC
*
19996577 CAAAGATAGGGTCGCCAATGAGTCACTACCTTTGCCAAATCAATTAATTCACGTTCGTAGGCAGC
196 CAAAGATAGGGTCGCCAATGAGTCACTACCTTTGCCAAACCAATTAATTCACGTTCGTAGGCAGC
19996642 CAACTTAAGGTGTCGATCTGTAATCTTGCAACTGAAAAAGGAAATGAGGTGTCCCTTTTGTTGCA
261 CAACTTAAGGTGTCGATCTGTAATCTTGCAACTGAAAAAGGAAATGAGGTGTCCCTTTTGTTGCA
19996707 GTACGGCTCCAAACCCGCTGTCCGAAGCATCACATTCAACCACAAATTCCTCCGCAAAGTTGGGT
326 GTACGGCTCCAAACCCGCTGTCCGAAGCATCACATTCAACCACAAATTCCTCCGCAAAGTTGGGT
19996772 AATTGCAAAACTGGGGCTGCTGAAAGAGAAATTTTTAATTGGGTGAAAGCAACATCAGCTTCCTT
391 AATTGCAAAACTGGGGCTGCTGAAAGAGAAATTTTTAATTGGGTGAAAGCAACATCAGCTTCCTT
19996837 AGTCCAGTTGAAGACATTTTTCTTTAGAAGAG
456 AGTCCAGTTGAAGACATTTTTCTTTAGAAGAG
19996869 ATGAGGTGTGGTAAGTCTTCGTCTTTTCTAGATAAAGCATCTGCGGCCCTGTTCAACTTTCCTAC
1 ATGAGGTGTGGTAAGTCTTCGTCTTTTCTAGATAAAGCATCTGCGGCCCTGTTCAACTTTCCTAC
19996934 TTTATATTCCACTCGGAAATCAAACCCCATTAGCTTGCTGATCCAATGTTGTTGTGGGGATGTCG
66 TTTATATTCCACTCGGAAATCAAACCCCATTAGCTTGCTGATCCAATGTTGTTGTGGGGATGTCG
19996999 TAAGTTGTTGGTCTAACAAATACTTAAGACTGAATTGATCAGTACGGATGAGGAAGTGCCTTCCC
131 TAAGTTGTTGGTCTAACAAATACTTAAGACTGAATTGATCAGTACGGATGAGGAAGTGCCTTCCC
19997064 CAAAGATAGGGTCGCCAATGAGTCACTACCTTTGCCAAACCAATTAATTCACGTTCGTAGGCAGC
196 CAAAGATAGGGTCGCCAATGAGTCACTACCTTTGCCAAACCAATTAATTCACGTTCGTAGGCAGC
19997129 CAACTTAAGGTGTCGATCTGTAATCTTGCAACTGAAAAAGGAAATGAGGTGTCCCTTTTGTTGCA
261 CAACTTAAGGTGTCGATCTGTAATCTTGCAACTGAAAAAGGAAATGAGGTGTCCCTTTTGTTGCA
19997194 GTACGGCTCCAAACCCGCTGTCCGAAGCATCACATTCAACCACAAATTCCTCCGCAAAGTTGGGT
326 GTACGGCTCCAAACCCGCTGTCCGAAGCATCACATTCAACCACAAATTCCTCCGCAAAGTTGGGT
19997259 AATTGCAAAACTGGGGCTGCTGAAAGAGAAATTTTTAATTGGGTGAAAGCAACATCAGCTTCCTT
391 AATTGCAAAACTGGGGCTGCTGAAAGAGAAATTTTTAATTGGGTGAAAGCAACATCAGCTTCCTT
19997324 AGTCCAGTTGAAGACATTTTTCTTTAGAAGAG
456 AGTCCAGTTGAAGACATTTTTCTTTAGAAGAG
19997356 ATG
1 ATG
19997359 TTAAGGGTGC
Statistics
Matches: 489, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
487 489 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (487 bp):
ATGAGGTGTGGTAAGTCTTCGTCTTTTCTAGATAAAGCATCTGCGGCCCTGTTCAACTTTCCTAC
TTTATATTCCACTCGGAAATCAAACCCCATTAGCTTGCTGATCCAATGTTGTTGTGGGGATGTCG
TAAGTTGTTGGTCTAACAAATACTTAAGACTGAATTGATCAGTACGGATGAGGAAGTGCCTTCCC
CAAAGATAGGGTCGCCAATGAGTCACTACCTTTGCCAAACCAATTAATTCACGTTCGTAGGCAGC
CAACTTAAGGTGTCGATCTGTAATCTTGCAACTGAAAAAGGAAATGAGGTGTCCCTTTTGTTGCA
GTACGGCTCCAAACCCGCTGTCCGAAGCATCACATTCAACCACAAATTCCTCCGCAAAGTTGGGT
AATTGCAAAACTGGGGCTGCTGAAAGAGAAATTTTTAATTGGGTGAAAGCAACATCAGCTTCCTT
AGTCCAGTTGAAGACATTTTTCTTTAGAAGAG
Found at i:20005717 original size:3 final size:3
Alignment explanation
Indices: 20005709--20005746 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20005699 ATTTCAAGGT
20005709 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20005747 GTATAAACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20010689 original size:44 final size:44
Alignment explanation
Indices: 20010626--20010716 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
20010616 ATCGGTAGGG
20010626 CTAAAAAGACAATAAGTTTTACACAACTTTGAGATATTATTATT
1 CTAAAAAGACAATAAGTTTTACACAACTTTGAGATATTATTATT
20010670 CTAAAAAGACAATAAGTTTTACACAACTTTGAGATATTATTATT
1 CTAAAAAGACAATAAGTTTTACACAACTTTGAGATATTATTATT
20010714 CTA
1 CTA
20010717 CTCAAAATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (44 bp):
CTAAAAAGACAATAAGTTTTACACAACTTTGAGATATTATTATT
Found at i:20018271 original size:15 final size:15
Alignment explanation
Indices: 20018251--20018281 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20018241 GATGTTTTAG
20018251 AAACTAGACTCAAAT
1 AAACTAGACTCAAAT
20018266 AAACTAGACTCAAAT
1 AAACTAGACTCAAAT
20018281 A
1 A
20018282 TATTTCTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
AAACTAGACTCAAAT
Found at i:20022745 original size:4 final size:4
Alignment explanation
Indices: 20022732--20022774 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
20022722 TGGTTTCTCA
20022732 AATT -ATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
20022775 GAAGTTAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:20022798 original size:28 final size:27
Alignment explanation
Indices: 20022763--20022838 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 27
20022753 TTAATTAATT
20022763 AATT-AATTAATTGAAGT-TAGAAAATGA
1 AATTAAATTAATTG--GTATAGAAAATGA
20022790 AATTAAATTAATTGGTCATAGAAAATGA
1 AATTAAATTAATTGGT-ATAGAAAATGA
20022818 AATTAAATTAATTGGTGATAG
1 AATTAAATTAATTGGT-ATAG
20022839 TGAATCCGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 39 0.87
ACGTcount: A:0.49, C:0.01, G:0.16, T:0.34
Consensus pattern (27 bp):
AATTAAATTAATTGGTATAGAAAATGA
Found at i:20025881 original size:27 final size:27
Alignment explanation
Indices: 20025851--20025906 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
20025841 TATCGTTGTC
20025851 TCCAAACACTAGATTATGAGGATTTAT
1 TCCAAACACTAGATTATGAGGATTTAT
20025878 TCCAAACACTAGATTATGAGGATTTAT
1 TCCAAACACTAGATTATGAGGATTTAT
20025905 TC
1 TC
20025907 TTCATTTCAG
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:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (27 bp):
TCCAAACACTAGATTATGAGGATTTAT
Found at i:20035597 original size:199 final size:200
Alignment explanation
Indices: 20035253--20035617 Score: 531
Period size: 199 Copynumber: 1.8 Consensus size: 200
20035243 GGTTTACCTT
*
20035253 TTGTTTTGATCCAATCATGAACATCACCAATTATATCAATAAATAAGTGATTCTTACTAACTCTT
1 TTGTTTTGATCCAATCATGAACATCACCAAGTATATCAATAAATAAGTGATTCTTACTAACTCTT
* * *
20035318 TCTCAAGGTTAAAGTGGCCTATCATCATTAGACTGATCATTGACTAGATCAGTAACTTGAACATC
66 GCTAAAGGTTAAAGTGGCCTATCATCATTAGACTGATCATTGACTAGATCAATAACTTGAACATC
*
20035383 TTGACTTTTTGCTTCTAACT-TTTCTTTAAACTTAGCAATGCTAATGGGAGAGGGCACTTCCTTT
131 TTGACTTTCTGCTTCTAACTATTTCTTTAAACTTAGCAATGCTAATGGGAGAGGGCACTTCCTTT
20035447 GCCTC
196 GCCTC
* ** *
20035452 TTGTTTTGATCCTATCATGATA-ATCACCAAGTATATCAATAGGTGAGTGATTCTT-CTGAACTC
1 TTGTTTTGATCCAATCATGA-ACATCACCAAGTATATCAATAAATAAGTGATTCTTACT-AACTC
* * * *
20035515 TTGCTAAAGTTTGAAGTGG-CTCATCATCATTATACTGATCATTGACTAGATTAATAACTTGAAC
64 TTGCTAAAGGTTAAAGTGGCCT-ATCATCATTAGACTGATCATTGACTAGATCAATAACTTGAAC
* * *
20035579 ATCTTGACTTTCTGCTTCTAATTATTTTTTTAGACTTAG
128 ATCTTGACTTTCTGCTTCTAACTATTTCTTTAAACTTAG
20035618 TACTGCCAAG
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
198 4 0.03
199 128 0.88
200 14 0.10
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (200 bp):
TTGTTTTGATCCAATCATGAACATCACCAAGTATATCAATAAATAAGTGATTCTTACTAACTCTT
GCTAAAGGTTAAAGTGGCCTATCATCATTAGACTGATCATTGACTAGATCAATAACTTGAACATC
TTGACTTTCTGCTTCTAACTATTTCTTTAAACTTAGCAATGCTAATGGGAGAGGGCACTTCCTTT
GCCTC
Found at i:20042350 original size:47 final size:47
Alignment explanation
Indices: 20042241--20042351 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
20042231 CCGGGATAAG
*
20042241 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
20042288 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
20042335 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
20042352 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:20045082 original size:15 final size:15
Alignment explanation
Indices: 20045064--20045094 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20045054 ATATTTCCTC
20045064 AAATCATATAATTTT
1 AAATCATATAATTTT
20045079 AAATCATATAATTTT
1 AAATCATATAATTTT
20045094 A
1 A
20045095 TTAATAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATCATATAATTTT
Found at i:20045434 original size:3 final size:3
Alignment explanation
Indices: 20045426--20045462 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20045416 TAAATTACAA
20045426 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
20045463 GCACTGAATC
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:20046417 original size:75 final size:75
Alignment explanation
Indices: 20046294--20046445 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
20046284 TGTGATCAAA
*
20046294 TATAGTTTTATTTCATTAATATGATAAAAAGGTCATTGTAGTGATAGCTTTCTTCTTCTGCTTGC
1 TATAGTTTTATTTCAATAATATGATAAAAAGGTCATTGTAGTGATAGCTTTCTTCTTCTGCTTGC
20046359 ATTACATTAT
66 ATTACATTAT
*
20046369 TATAGTTTTATTTCAATAATATGATAAAATGGTCATTGTAGTGATAGCTTTCTTCTTCTGCTTGC
1 TATAGTTTTATTTCAATAATATGATAAAAAGGTCATTGTAGTGATAGCTTTCTTCTTCTGCTTGC
20046434 ATTACATTAT
66 ATTACATTAT
20046444 TA
1 TA
20046446 ATTCCATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (75 bp):
TATAGTTTTATTTCAATAATATGATAAAAAGGTCATTGTAGTGATAGCTTTCTTCTTCTGCTTGC
ATTACATTAT
Found at i:20065795 original size:20 final size:21
Alignment explanation
Indices: 20065760--20065800 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20065750 TAAAATTAGA
* *
20065760 TAATTAAATTAGC-TTTAATC
1 TAATTAAAATAACTTTTAATC
20065780 TAATTAAAATAACTTTTAATC
1 TAATTAAAATAACTTTTAATC
20065801 GATTCAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATTAAAATAACTTTTAATC
Found at i:20069596 original size:21 final size:21
Alignment explanation
Indices: 20069562--20069602 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20069552 AGACGAGCGA
* * *
20069562 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTAGAGTG
20069583 TACTCCAAAACAGGTAGAGT
1 TACTCCAAAACAGGTAGAGT
20069603 TTGAGCAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTAGAGTG
Found at i:20072174 original size:3 final size:3
Alignment explanation
Indices: 20072166--20072197 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20072156 TCTTCACCTC
20072166 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20072198 TTGATACCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20074543 original size:2 final size:2
Alignment explanation
Indices: 20074536--20074567 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20074526 GGATACACTA
20074536 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20074568 TTTGTTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20078111 original size:30 final size:28
Alignment explanation
Indices: 20078063--20078124 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 28
20078053 AAATTATTTT
20078063 ATTTTTAATTTTTTATTATTTTAAAGAC
1 ATTTTTAATTTTTTATTATTTTAAAGAC
*
20078091 ATTTGTTAATTTTGTTATTATTTTAGAGAC
1 ATTT-TTAATTTT-TTATTATTTTAAAGAC
20078121 ATTT
1 ATTT
20078125 ATTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 4 0.13
29 8 0.26
30 19 0.61
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (28 bp):
ATTTTTAATTTTTTATTATTTTAAAGAC
Found at i:20078229 original size:18 final size:18
Alignment explanation
Indices: 20078208--20078247 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
20078198 GAAATATTTA
*
20078208 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
20078226 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
20078244 TTTT
1 TTTT
20078248 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:20078270 original size:12 final size:12
Alignment explanation
Indices: 20078249--20078282 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20078239 TATATTTTTT
*
20078249 AAAATTATATAA
1 AAAATAATATAA
20078261 AAAATAATATAA
1 AAAATAATATAA
*
20078273 AAATTAATAT
1 AAAATAATAT
20078283 GGGCAGACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:20080524 original size:3 final size:3
Alignment explanation
Indices: 20080518--20080561 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
20080508 TTGTTAAACT
20080518 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20080562 TCATTTTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20081370 original size:21 final size:21
Alignment explanation
Indices: 20081323--20081371 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
20081313 CTAAAATAAT
* * *
20081323 AATAATAATAATAATTTAATA
1 AATAAAAATAAAAATTCAATA
20081344 AATAAAAATAAAAATTCAA-A
1 AATAAAAATAAAAATTCAATA
20081364 AACTAAAA
1 AA-TAAAA
20081372 CAAAAAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAAATAAAAATTCAATA
Found at i:20084209 original size:163 final size:163
Alignment explanation
Indices: 20083934--20084261 Score: 575
Period size: 163 Copynumber: 2.0 Consensus size: 163
20083924 TTCTGCCAAT
* * *
20083934 AACGTGGCTACATCAATAGATGAAGTAGAAATTTGTTCACTTTCATCAGAAATCTTTTTTTCCTT
1 AACGTGGCTACATCAATAAATAAAGTAGAAATTTGTTCACTTGCATCAGAAATCTTTTTTTCCTT
*
20083999 CTTTGAAAATGTGGAATCATCTTGGTTTCTAGATGGTTGCGGTTGTGTAGTTGAGAGATCCATCT
66 CTTTGAAAATGTGGAATCATCTTGGTTTCTAGATGGTTGCAGTTGTGTAGTTGAGAGATCCATCT
*
20084064 CATCTAAAGAAACATCAGCTTCGCATCCATGGA
131 CATCCAAAGAAACATCAGCTTCGCATCCATGGA
* *
20084097 AACGTGGCTGCATCAATAAATAAAGTAGAAATTTGTTCACTTGCATCAGAAATCTTTTTTTTCTT
1 AACGTGGCTACATCAATAAATAAAGTAGAAATTTGTTCACTTGCATCAGAAATCTTTTTTTCCTT
*
20084162 CTTTGAAAATGTGGAATCATCTTGGTTTCTAGATGGTTGTAGTTGTGTAGTTGAGAGATCCATCT
66 CTTTGAAAATGTGGAATCATCTTGGTTTCTAGATGGTTGCAGTTGTGTAGTTGAGAGATCCATCT
*
20084227 CATCCAAAGAAACATCAGCTTTGCATCCATGGA
131 CATCCAAAGAAACATCAGCTTCGCATCCATGGA
20084260 AA
1 AA
20084262 TCACTTCTTT
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
163 156 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (163 bp):
AACGTGGCTACATCAATAAATAAAGTAGAAATTTGTTCACTTGCATCAGAAATCTTTTTTTCCTT
CTTTGAAAATGTGGAATCATCTTGGTTTCTAGATGGTTGCAGTTGTGTAGTTGAGAGATCCATCT
CATCCAAAGAAACATCAGCTTCGCATCCATGGA
Found at i:20088102 original size:16 final size:16
Alignment explanation
Indices: 20088081--20088114 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20088071 CCAATATCCA
* *
20088081 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
20088097 ATTATCACATTTACAC
1 ATTATCACATTTACAC
20088113 AT
1 AT
20088115 ATATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:20088874 original size:17 final size:15
Alignment explanation
Indices: 20088856--20088897 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
20088846 TTCTCATTCT
20088856 TTTCTTCTTTCTTTTC
1 TTTCTTCTTT-TTTTC
*
20088872 TTTCTT-TCTTTTTC
1 TTTCTTCTTTTTTTC
20088886 TTTCTTCTTTTT
1 TTTCTTCTTTTT
20088898 ACTATACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.48
15 6 0.26
16 6 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTCTTTTTTTC
Found at i:20088878 original size:13 final size:13
Alignment explanation
Indices: 20088852--20088896 Score: 67
Period size: 12 Copynumber: 3.5 Consensus size: 13
20088842 TACATTCTCA
20088852 TTCTTTTC-TTCT
1 TTCTTTTCTTTCT
20088864 TTCTTTTCTTTCT
1 TTCTTTTCTTTCT
20088877 TTCTTTTTCTTTC-
1 TTC-TTTTCTTTCT
20088890 TTCTTTT
1 TTCTTTT
20088897 TACTATACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.39
13 10 0.32
14 9 0.29
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTCTTTCT
Found at i:20088897 original size:13 final size:13
Alignment explanation
Indices: 20088855--20088897 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
20088845 ATTCTCATTC
20088855 TTTTC-TTCTT-T
1 TTTTCTTTCTTCT
20088866 CTTTTCTTTCTTTCT
1 -TTTTCTTTC-TTCT
20088881 TTTTCTTTCTTCT
1 TTTTCTTTCTTCT
20088894 TTTT
1 TTTT
20088898 ACTATACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.18
13 11 0.39
14 11 0.39
15 1 0.04
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTCT
Found at i:20101831 original size:50 final size:50
Alignment explanation
Indices: 20101756--20101857 Score: 179
Period size: 50 Copynumber: 2.0 Consensus size: 50
20101746 CCAAGCTTCC
20101756 AACCTAACGAGTTTCCAAAGTACTATAAAATAG-AGAAAATAAAACAGAGT
1 AACCTAACGAGTTTCCAAAGTACTATAAAATAGAAG-AAATAAAACAGAGT
*
20101806 AACCTAACGAGTTTCCAAAGTACTATAAAATAGAAGAAATAAAATAGAGT
1 AACCTAACGAGTTTCCAAAGTACTATAAAATAGAAGAAATAAAACAGAGT
20101856 AA
1 AA
20101858 GCATTTAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 48 0.96
51 2 0.04
ACGTcount: A:0.53, C:0.13, G:0.14, T:0.21
Consensus pattern (50 bp):
AACCTAACGAGTTTCCAAAGTACTATAAAATAGAAGAAATAAAACAGAGT
Found at i:20102708 original size:24 final size:25
Alignment explanation
Indices: 20102614--20102708 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 25
20102604 AATACTCTAA
* *
20102614 AGAGCTAT-TAACGAGAAGCTCGCAG
1 AGAGCTATATAACGGGATGCTCG-AG
* * *
20102639 A-AACCATATAACGGGAAGCTCGAG
1 AGAGCTATATAACGGGATGCTCGAG
* * *
20102663 AGGGCTATATATCAGGATGCTC-ATG
1 AGAGCTATATAACGGGATGCTCGA-G
20102688 AGAGCTA-ATAACGGGATGCTC
1 AGAGCTATATAACGGGATGCTC
20102709 TTTCGAGCTG
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
24 20 0.36
25 35 0.64
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (25 bp):
AGAGCTATATAACGGGATGCTCGAG
Found at i:20103592 original size:13 final size:13
Alignment explanation
Indices: 20103574--20103601 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20103564 TTTTATTTTA
20103574 TTATTTATCATCT
1 TTATTTATCATCT
20103587 TTATTTATCATCT
1 TTATTTATCATCT
20103600 TT
1 TT
20103602 CTAATTTTAT
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:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:20112366 original size:23 final size:23
Alignment explanation
Indices: 20112336--20112400 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
20112326 CAACCCAATC
20112336 TTTCTTTTTATTTTTATTTATTT
1 TTTCTTTTTATTTTTATTTATTT
20112359 TTTC-TTTTATTATTTA-TTATTT
1 TTTCTTTTTATT-TTTATTTATTT
*
20112381 TCTT-TTTTTTTATTTTATTT
1 T-TTCTTTTTAT-TTTTATTT
20112401 TAGTTAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 14 0.39
23 19 0.53
24 3 0.08
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTCTTTTTATTTTTATTTATTT
Found at i:20112369 original size:22 final size:22
Alignment explanation
Indices: 20112336--20112401 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
20112326 CAACCCAATC
20112336 TTTCTTTTTATTTTTATTTATTT
1 TTTC-TTTTATTTTTATTTATTT
20112359 TTTCTTTTA---TTATTTATTAT
1 TTTCTTTTATTTTTATTTATT-T
20112379 TTTCTTTT-TTTTTATTTTATTT
1 TTTCTTTTATTTTTA-TTTATTT
20112401 T
1 T
20112402 AGTTAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 9 0.24
20 9 0.24
22 10 0.26
23 10 0.26
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTCTTTTATTTTTATTTATTT
Found at i:20112401 original size:15 final size:15
Alignment explanation
Indices: 20112340--20112401 Score: 70
Period size: 15 Copynumber: 4.0 Consensus size: 15
20112330 CCAATCTTTC
20112340 TTTTTATTTTTATTTAT
1 TTTTTA-TTTTATTT-T
* *
20112357 TTTTTCTTTTATTAT
1 TTTTTATTTTATTTT
* *
20112372 TTATTATTTTCTTTT
1 TTTTTATTTTATTTT
20112387 TTTTTATTTTATTTT
1 TTTTTATTTTATTTT
20112402 AGTTAAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
15 25 0.68
16 7 0.19
17 5 0.14
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTATTTT
Found at i:20112594 original size:43 final size:42
Alignment explanation
Indices: 20112511--20112601 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
20112501 TCCATGCTGT
* * * *
20112511 CAAACAGTTCTATTCCAGCCCAGAATGCCATATCTCTGCAGC
1 CAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCAGC
*
20112553 CAAACAGTCCTATTCCAGCCTTAGAATCCCCAAAAC-CTGCAGC
1 CAAACAGTCCTATTCCAGCC-CAGAAT-CCCAAAACTCTGCAGC
20112596 CAAACA
1 CAAACA
20112602 CCCCTTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 19 0.45
43 18 0.43
44 5 0.12
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (42 bp):
CAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCAGC
Found at i:20113607 original size:1 final size:1
Alignment explanation
Indices: 20113601--20113642 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
20113591 TAATAAAATT
* * *
20113601 AAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAGAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20113643 TAAGTACTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:20113626 original size:14 final size:14
Alignment explanation
Indices: 20113601--20113642 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
20113591 TAATAAAATT
20113601 AAAAAAA-AAAAAA
1 AAAAAAAGAAAAAA
20113614 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
*
20113628 AAAAGAAGAAAAAA
1 AAAAAAAGAAAAAA
20113642 A
1 A
20113643 TAAGTACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:20113631 original size:11 final size:11
Alignment explanation
Indices: 20113601--20113642 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
20113591 TAATAAAATT
20113601 AAAAAAAAAA-
1 AAAAAAAAAAG
20113611 AAAAAAAAAAG
1 AAAAAAAAAAG
20113622 AAAAAAAAAAG
1 AAAAAAAAAAG
20113633 AAGAAAAAAA
1 AA-AAAAAAA
20113643 TAAGTACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.33
11 13 0.43
12 7 0.23
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:20118656 original size:22 final size:23
Alignment explanation
Indices: 20118622--20118666 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20118612 GGGTTAAGGT
*
20118622 GGGTTAAGA-TTTTTATGGTTTA
1 GGGTTAAGATTTTTTAGGGTTTA
* *
20118644 GGGTTAGGGTTTTTTAGGGTTTA
1 GGGTTAAGATTTTTTAGGGTTTA
20118667 TAGTTTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (23 bp):
GGGTTAAGATTTTTTAGGGTTTA
Found at i:20118747 original size:16 final size:17
Alignment explanation
Indices: 20118708--20118748 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
20118698 AGGGTGTAAG
20118708 ATTAATTAATTAAATTAA
1 ATTAATTAATTAAA-TAA
20118726 A-T-ATTAATTAAA-AA
1 ATTAATTAATTAAATAA
20118740 ATTAATTAA
1 ATTAATTAA
20118749 ATTCGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.14
15 1 0.05
16 15 0.71
17 1 0.05
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATTAATTAAATAA
Found at i:20119234 original size:126 final size:126
Alignment explanation
Indices: 20118850--20119235 Score: 421
Period size: 126 Copynumber: 3.1 Consensus size: 126
20118840 TTTTTGGTTT
* * * *
20118850 TTTTTCTTCAGTAGTATCTGGAAAAAA-AATTTTAAGAAGA-AGTTTCT-AAAGAAATAGTATCC
1 TTTTTCTACAGTGGTATCT-GAAAAAATAATTTTAAGAAGACA-TTTCTGAAA-AAATAGTGTCA
* * * * *
20118912 AAAACGCTTCAAGCAGGATGTACTGTCAGTAAAATTACTGAAAATA---CTCACGTGGATGCT-
63 AAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTC
* * * *
20118972 TTTTTCTACAGTGGTATCT-AAGAAAATAATTTTGAGAAGACGTTTTTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTGGTATCTGAA-AAAATAATTTTAAGAAGACATTTCTGAAAAAATAGTGTCAAA
* * * * *
20119036 AACACTTTAAGCAGGATGCACTATCAGCAAAAGTACTAAAAAAAGCTC-CTACGTGGACGATC
65 AACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCTC-ACGTGGACGCTC
** * * *
20119098 TTTTGATACAGTGGTATCTGAAAAAATAATTGTAAGATGACATTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTGGTATCTGAAAAAATAATTTTAAGAAGACATTTCTGAAAAAATAGTGTCAAAA
* * * *
20119163 ACGCTTCATGCAGTATGCATTTTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTC
20119224 TTTTTCTACAGT
1 TTTTTCTACAGT
20119236 ACTTCCTATT
Statistics
Matches: 215, Mismatches: 38, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
120 2 0.01
121 4 0.02
122 79 0.37
123 3 0.01
124 1 0.00
125 10 0.05
126 113 0.53
127 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (126 bp):
TTTTTCTACAGTGGTATCTGAAAAAATAATTTTAAGAAGACATTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTC
Found at i:20123281 original size:49 final size:49
Alignment explanation
Indices: 20123209--20123751 Score: 942
Period size: 49 Copynumber: 11.1 Consensus size: 49
20123199 ACATAATAAT
* *
20123209 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAACTGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20123258 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20123307 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
20123356 ATATGTGACAAGGCCTAATGGCCGACGTGATGAATGTGAAACTGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20123405 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20123454 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
*
20123503 ATATGTGATAAGGCCTAATGGGCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
*
20123552 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAACTGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * * *
20123601 ATATGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAACTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * *
20123650 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTAAAAATGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * *
20123699 ATATGTGATAAGGCCTAATGGCCGACGCGATGAATGTGAAAGTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20123748 ATAT
1 ATAT
20123752 ATGTGGTAAA
Statistics
Matches: 475, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 475 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (49 bp):
ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
Found at i:20123875 original size:37 final size:36
Alignment explanation
Indices: 20123820--20123906 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 36
20123810 AACTTAGAAA
*
20123820 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTCTGGAGAT
20123858 TATGTCCGGGTACGACCCGATGACTACGTCTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTCTGGAGAT
20123895 TATGTCCGGGTA
1 TATGTCCGGGTA
20123907 AGACTTCGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.89
38 4 0.09
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTCTGGAGAT
Found at i:20125790 original size:40 final size:40
Alignment explanation
Indices: 20125735--20125966 Score: 419
Period size: 40 Copynumber: 5.8 Consensus size: 40
20125725 GAGAATTGAG
*
20125735 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
20125775 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
20125815 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATCCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
20125855 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
20125895 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* * *
20125935 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTTCCGAAGAGCA
20125967 ATCATGCTGG
Statistics
Matches: 186, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 186 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:20126812 original size:40 final size:40
Alignment explanation
Indices: 20126710--20126850 Score: 144
Period size: 40 Copynumber: 3.5 Consensus size: 40
20126700 TTCGAATGGT
* * * *
20126710 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAA
1 ATCCGGGCTAATTCCCGAAGGCATTTGTGC-GAGTCACTAA
* * *
20126751 ATCCGGG-TCAATCCCCAAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCT-AATTCCCGAAGGCATTTGTGCGAGTCACTAA
* *
20126791 ATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATA
1 ATCCGGGCTAATTCCCGAAGGCATTTGTGCGAGTCACTA-A
20126832 A-CCGGGCT-ATGTCCCGAAG
1 ATCCGGGCTAAT-TCCCGAAG
20126851 ACAATCGAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
39 2 0.02
40 56 0.66
41 27 0.32
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAATTCCCGAAGGCATTTGTGCGAGTCACTAA
Found at i:20126871 original size:40 final size:40
Alignment explanation
Indices: 20126793--20126871 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
20126783 GTTACTAAAT
* * *
20126793 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
* *
20126833 CCGGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATA
1 CCGGGCTAAT-TCCCGAAGACAATCGAGCGAATCACTATA
20126872 TTCGGTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
Found at i:20129231 original size:49 final size:49
Alignment explanation
Indices: 20129159--20129897 Score: 1307
Period size: 49 Copynumber: 15.1 Consensus size: 49
20129149 ACATAATAAT
* *
20129159 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAACTGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * *
20129208 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAACTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20129257 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
*
20129306 ATATGTGATAAGGCCTAATGGTCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20129355 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20129404 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
*
20129453 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAACTGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
20129502 ATATGTGATAAGGCCTAATGGTCGACGTGATGAATGTGAAACTGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
20129551 ATATGTGATAAGGCCTAATGGTCGACGTGATGAATGTGAAACTGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
*
20129600 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20129649 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20129698 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
20129747 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAACTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* * *
20129796 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTAAAAATGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
* *
20129845 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
20129894 ATAT
1 ATAT
20129898 ATGTGGTAAA
Statistics
Matches: 670, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 670 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (49 bp):
ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAATGTATAC
Found at i:20130025 original size:37 final size:37
Alignment explanation
Indices: 20129974--20130057 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 37
20129964 AATATGTTCT
* * *
20129974 GGGTGAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACTCGATGACTACGTCTGGAGATTATGTCC
*
20130011 GGGTACGACTCGATGACTACGTCTGGAGATTATGTCC
1 GGGTAAGACTCGATGACTACGTCTGGAGATTATGTCC
20130048 GGGTAAGACT
1 GGGTAAGACT
20130058 TCGTAATAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (37 bp):
GGGTAAGACTCGATGACTACGTCTGGAGATTATGTCC
Found at i:20132299 original size:29 final size:28
Alignment explanation
Indices: 20132267--20132371 Score: 78
Period size: 27 Copynumber: 3.8 Consensus size: 28
20132257 AAAACAACTT
20132267 TTATTCTATTACAAATATAAAAGAGTAAA
1 TTATT-TATTACAAATATAAAAGAGTAAA
* * *
20132296 TTA-TAATT-CAAATACTAAAA-A-CAACTT
1 TTATTTATTACAAATA-TAAAAGAGTAA--A
20132323 TTATTTTATTACAAATATAAAAGAGTAAA
1 TTA-TTTATTACAAATATAAAAGAGTAAA
*
20132352 TTA-TAATTA-AAATATTAAAA
1 TTATTTATTACAAATA-TAAAA
20132372 ACAACTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
25 2 0.03
26 12 0.20
27 21 0.35
28 1 0.02
29 15 0.25
30 7 0.12
31 2 0.03
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (28 bp):
TTATTTATTACAAATATAAAAGAGTAAA
Found at i:20132326 original size:27 final size:26
Alignment explanation
Indices: 20132296--20132382 Score: 61
Period size: 27 Copynumber: 3.2 Consensus size: 26
20132286 AAAGAGTAAA
20132296 TTATAATTCAAATACTAAAAACAACTT
1 TTATAATTCAAATA-TAAAAACAACTT
* * *
20132323 TTATTTTATTACAAATATAAAAGAGTAA--A
1 TTA--TAATT-CAAATATAAAA-A-CAACTT
*
20132352 TTATAATTAAAATATTAAAAACAACTT
1 TTATAATTCAAATA-TAAAAACAACTT
20132379 TTAT
1 TTAT
20132383 TTTATTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 2 0.04
26 6 0.13
27 16 0.36
29 12 0.27
30 7 0.16
31 2 0.04
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (26 bp):
TTATAATTCAAATATAAAAACAACTT
Found at i:20132406 original size:62 final size:56
Alignment explanation
Indices: 20132257--20132389 Score: 239
Period size: 56 Copynumber: 2.4 Consensus size: 56
20132247 TTCCTTATTC
* *
20132257 AAAACAACTTTTATTCTATTACAAATATAAAAGAGTAAATTATAATTCAAATACTA
1 AAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATACTA
*
20132313 AAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATATTA
1 AAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATACTA
20132369 AAAACAACTTTTATTTTATTA
1 AAAACAACTTTTATTTTATTA
20132390 AATCAAAGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (56 bp):
AAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATACTA
Found at i:20132932 original size:30 final size:30
Alignment explanation
Indices: 20132898--20132966 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
20132888 GTTGAAGTGT
*
20132898 TGGGCCCGGTGACTGTGTGGGCACTATTGA
1 TGGGCCCGGTGACTGTATGGGCACTATTGA
* * * * *
20132928 TGGGCCAGCTGATTGTATGGGCATTGTTGA
1 TGGGCCCGGTGACTGTATGGGCACTATTGA
20132958 TGGGCCCGG
1 TGGGCCCGG
20132967 GTCGTTATCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.13, C:0.19, G:0.41, T:0.28
Consensus pattern (30 bp):
TGGGCCCGGTGACTGTATGGGCACTATTGA
Found at i:20133472 original size:7 final size:7
Alignment explanation
Indices: 20133462--20133523 Score: 106
Period size: 7 Copynumber: 8.7 Consensus size: 7
20133452 TTGTATACAT
20133462 AATACTA
1 AATACTA
20133469 AATACTA
1 AATACTA
20133476 AATACTA
1 AATACTA
20133483 AATACTA
1 AATACTA
20133490 AATACTA
1 AATACTA
20133497 AATACTA
1 AATACTA
*
20133504 AATATTAA
1 AATACT-A
20133512 AATACTA
1 AATACTA
20133519 AATAC
1 AATAC
20133524 AAAACGATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
7 46 0.88
8 6 0.12
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
AATACTA
Found at i:20134501 original size:25 final size:26
Alignment explanation
Indices: 20134466--20134540 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
20134456 TTATAAAATT
20134466 AAAATTAAAATTGCATAAATGAAAAA
1 AAAATTAAAATTGCATAAATGAAAAA
*
20134492 AAAATT-AAATTG--T-ATTGAAAAA
1 AAAATTAAAATTGCATAAATGAAAAA
** *
20134514 TTAATTAAAATTGCATAAATTAAAAA
1 AAAATTAAAATTGCATAAATGAAAAA
20134540 A
1 A
20134541 TATTAAATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 12 0.31
23 7 0.18
25 7 0.18
26 13 0.33
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (26 bp):
AAAATTAAAATTGCATAAATGAAAAA
Found at i:20134557 original size:47 final size:48
Alignment explanation
Indices: 20134468--20134564 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 48
20134458 ATAAAATTAA
**
20134468 AATTAAAATTGCATAAATGAAAAAAAAATTAAATTGTATTGAAAAATT
1 AATTAAAATTGCATAAATGAAAAAAAAATTAAATACTATTGAAAAATT
* * *
20134516 AATTAAAATTGCATAAAT-TAAAAAATATTAAATACTATTGAAATATT
1 AATTAAAATTGCATAAATGAAAAAAAAATTAAATACTATTGAAAAATT
20134563 AA
1 AA
20134565 AATTATCACT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 26 0.59
48 18 0.41
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (48 bp):
AATTAAAATTGCATAAATGAAAAAAAAATTAAATACTATTGAAAAATT
Found at i:20134760 original size:32 final size:32
Alignment explanation
Indices: 20134715--20134791 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
20134705 TAAAGAGAGC
*
20134715 TTTGAGAAAATTTGCGAGAATATGAGAGAATT
1 TTTGAGAAAATTTGAGAGAATATGAGAGAATT
*
20134747 TTTG-GAATAATTTGAGAGAATTTGAGAGAA--
1 TTTGAGAA-AATTTGAGAGAATATGAGAGAATT
*
20134777 TTTGAGAGAATTTGA
1 TTTGAGAAAATTTGA
20134792 ATAGGAGGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 11 0.28
31 5 0.12
32 24 0.60
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (32 bp):
TTTGAGAAAATTTGAGAGAATATGAGAGAATT
Found at i:20134775 original size:12 final size:10
Alignment explanation
Indices: 20134715--20134791 Score: 84
Period size: 10 Copynumber: 7.5 Consensus size: 10
20134705 TAAAGAGAGC
*
20134715 TTTGAGAAAA
1 TTTGAGAGAA
*
20134725 TTTGCGAGAA
1 TTTGAGAGAA
*
20134735 TATGAGAGAA
1 TTTGAGAGAA
*
20134745 TTTTTG-GAATAA
1 --TTTGAG-AGAA
20134757 TTTGAGAGAA
1 TTTGAGAGAA
20134767 TTTGAGAGAA
1 TTTGAGAGAA
20134777 TTTGAGAGAA
1 TTTGAGAGAA
20134787 TTTGA
1 TTTGA
20134792 ATAGGAGGAC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
10 48 0.86
11 2 0.04
12 6 0.11
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:20142577 original size:22 final size:24
Alignment explanation
Indices: 20142533--20142661 Score: 73
Period size: 24 Copynumber: 5.2 Consensus size: 24
20142523 CAAGAGAATG
*
20142533 AAATAAATAACATAAAACTATTTA
1 AAATAAATAACATAAAACAATTTA
* *
20142557 AAATAAAT-AC-TGAAACAATTTT
1 AAATAAATAACATAAAACAATTTA
* *
20142579 AAATAAGTAATACATAAAAAATAGGTTTA
1 AAATAAAT-A-ACATAAAACA-A--TTTA
* * * *
20142608 AAATAGATATTATAGAAAATAATTTA
1 AAATA-A-ATAACATAAAACAATTTA
* * *
20142634 AAGTGAATAATATAAAACAATTTA
1 AAATAAATAACATAAAACAATTTA
20142658 AAAT
1 AAAT
20142662 CATTAATAAA
Statistics
Matches: 78, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
22 16 0.21
23 2 0.03
24 26 0.33
25 3 0.04
26 12 0.15
27 1 0.01
28 1 0.01
29 15 0.19
30 1 0.01
31 1 0.01
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATAAATAACATAAAACAATTTA
Found at i:20142668 original size:24 final size:24
Alignment explanation
Indices: 20142623--20142674 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
20142613 GATATTATAG
* * * *
20142623 AAAATAATTTAAAGTGAATAATAT
1 AAAACAATTTAAAATCAATAATAA
*
20142647 AAAACAATTTAAAATCATTAATAA
1 AAAACAATTTAAAATCAATAATAA
20142671 AAAA
1 AAAA
20142675 GTCTAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAACAATTTAAAATCAATAATAA
Found at i:20142947 original size:34 final size:34
Alignment explanation
Indices: 20142904--20142969 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
20142894 TATAAAAAAG
20142904 AAAAAAATCGAAATAATATGTATTAAAACAATGA
1 AAAAAAATCGAAATAATATGTATTAAAACAATGA
20142938 AAAAAAATCGAAATAATATGTATTAAAACAAT
1 AAAAAAATCGAAATAATATGTATTAAAACAAT
20142970 TTAATATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.24
Consensus pattern (34 bp):
AAAAAAATCGAAATAATATGTATTAAAACAATGA
Found at i:20142995 original size:24 final size:24
Alignment explanation
Indices: 20142967--20143015 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
20142957 GTATTAAAAC
* **
20142967 AATTTAATATGAATATTATATAGA
1 AATTTAAAATGAATAGCATATAGA
20142991 AATTTAAAATGAATAGCATATAGA
1 AATTTAAAATGAATAGCATATAGA
20143015 A
1 A
20143016 TAGTTAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (24 bp):
AATTTAAAATGAATAGCATATAGA
Found at i:20145612 original size:16 final size:16
Alignment explanation
Indices: 20145591--20145621 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20145581 ATTAAGTTGC
*
20145591 ATTATGTGATTAGATT
1 ATTATGTGATAAGATT
20145607 ATTATGTGATAAGAT
1 ATTATGTGATAAGAT
20145622 AACTTATATT
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:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (16 bp):
ATTATGTGATAAGATT
Found at i:20148164 original size:33 final size:33
Alignment explanation
Indices: 20148098--20148165 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
20148088 AATTTTTCAA
* *
20148098 TTTCTTTGGTATTTCTCAATTTGTATTTATCTT
1 TTTCTTTGGTATCTCTCAATTTGCATTTATCTT
20148131 TTTCTTTGGTATCTCT-ATGATTTGCATTT-TCTT
1 TTTCTTTGGTATCTCTCA--ATTTGCATTTATCTT
20148164 TT
1 TT
20148166 CAGTTCATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 1 0.03
33 21 0.68
34 9 0.29
ACGTcount: A:0.13, C:0.13, G:0.10, T:0.63
Consensus pattern (33 bp):
TTTCTTTGGTATCTCTCAATTTGCATTTATCTT
Found at i:20151727 original size:21 final size:21
Alignment explanation
Indices: 20151701--20151744 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20151691 TATAGTTGTT
20151701 AACAACATGTTGTCAAAAGAA
1 AACAACATGTTGTCAAAAGAA
20151722 AACAACATGTTGTCAAAAGAA
1 AACAACATGTTGTCAAAAGAA
20151743 AA
1 AA
20151745 TATTTTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (21 bp):
AACAACATGTTGTCAAAAGAA
Found at i:20156274 original size:21 final size:23
Alignment explanation
Indices: 20156240--20156287 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
20156230 ATTACAGTTC
*
20156240 AAAATATTGTTTTT-CATTTATT
1 AAAAGATTGTTTTTGCATTTATT
20156262 AAAAGATT-TTTTTGCATTTATT
1 AAAAGATTGTTTTTGCATTTATT
20156284 AAAA
1 AAAA
20156288 CTATGTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (23 bp):
AAAAGATTGTTTTTGCATTTATT
Found at i:20156697 original size:31 final size:31
Alignment explanation
Indices: 20156662--20156726 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
20156652 TATTTTTAAG
20156662 TACATGCCATCCTATTCAAAATTTTGAAACA
1 TACATGCCATCCTATTCAAAATTTTGAAACA
**
20156693 TACATGCCATTTTATTCAAAATTTTGAAACA
1 TACATGCCATCCTATTCAAAATTTTGAAACA
20156724 TAC
1 TAC
20156727 TCTCTTGGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (31 bp):
TACATGCCATCCTATTCAAAATTTTGAAACA
Found at i:20157073 original size:16 final size:15
Alignment explanation
Indices: 20157045--20157092 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
20157035 TCAATCATAC
20157045 AATACTCAATTCATG
1 AATACTCAATTCATG
*
20157060 AATACATCATTTCAT-
1 AATAC-TCAATTCATG
20157075 ACCATACTCAATTCATG
1 A--ATACTCAATTCATG
20157092 A
1 A
20157093 GTATATAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (15 bp):
AATACTCAATTCATG
Found at i:20157214 original size:53 final size:53
Alignment explanation
Indices: 20157142--20157249 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
20157132 CACATTCTAT
*
20157142 TTTCAATTCACTATATCACTTCTATTTCTCATACCATGCCATTTCAATATCAA
1 TTTCAATTCACTATATCACTTCCATTTCTCATACCATGCCATTTCAATATCAA
*
20157195 TTTCAATTCACTATTTCACTTCCATTTCTCATACCATGCCATTTCAATATCAA
1 TTTCAATTCACTATATCACTTCCATTTCTCATACCATGCCATTTCAATATCAA
20157248 TT
1 TT
20157250 ATAGAACTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.43
Consensus pattern (53 bp):
TTTCAATTCACTATATCACTTCCATTTCTCATACCATGCCATTTCAATATCAA
Found at i:20157475 original size:41 final size:41
Alignment explanation
Indices: 20157341--20157476 Score: 104
Period size: 41 Copynumber: 3.4 Consensus size: 41
20157331 ACCAGTTTGG
* * * * *
20157341 CACCCAGTGCCTCATCGAA-TAATTCGAAGTAATAATTTTA
1 CACCCAGTGTCTCATCGAATTAATCCGAAGTAGTAAATTGA
** * * * * *
20157381 CACATAGTGTCTTATTG-GTTAAACCG-A--AGTAAATTGG
1 CACCCAGTGTCTCATCGAATTAATCCGAAGTAGTAAATTGA
*
20157418 CACCCAGTG-CACCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGTC-TCATCGAATTAATCCGAAGTAGTAAATTGA
20157459 CACCCAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
20157477 CTCAAACTCG
Statistics
Matches: 68, Mismatches: 21, Indels: 13
0.67 0.21 0.13
Matches are distributed among these distances:
36 1 0.01
37 16 0.24
38 7 0.10
39 2 0.03
40 17 0.25
41 24 0.35
42 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGAATTAATCCGAAGTAGTAAATTGA
Found at i:20167683 original size:6 final size:6
Alignment explanation
Indices: 20167626--20167675 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
20167616 ATGGAATTTT
*
20167626 AAAT-A AAATAG AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
20167673 AAA
1 AAA
20167676 AAGTAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
5 4 0.10
6 38 0.90
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:20172419 original size:42 final size:42
Alignment explanation
Indices: 20172373--20172463 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
20172363 AGAAACCAAT
20172373 GAAGCAACATCGGAAAACAACATCCAGGTTCAGACAAAAAAG
1 GAAGCAACATCGGAAAACAACATCCAGGTTCAGACAAAAAAG
* * *
20172415 GAAGCAACTTGGGAAAACAACATCCAGGTTGAGACAAAAAAG
1 GAAGCAACATCGGAAAACAACATCCAGGTTCAGACAAAAAAG
20172457 GAAGCAA
1 GAAGCAA
20172464 TGTGGAAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.10
Consensus pattern (42 bp):
GAAGCAACATCGGAAAACAACATCCAGGTTCAGACAAAAAAG
Found at i:20174327 original size:27 final size:27
Alignment explanation
Indices: 20174290--20174342 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
20174280 CATGGTTCAC
*
20174290 CTTCTTAGGCACCTGATGAAACATTCT
1 CTTCTTAGGCACCTAATGAAACATTCT
20174317 CTTCTTAGGCACCTAATGAAACATTC
1 CTTCTTAGGCACCTAATGAAACATTC
20174343 CTATTTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (27 bp):
CTTCTTAGGCACCTAATGAAACATTCT
Found at i:20175603 original size:52 final size:52
Alignment explanation
Indices: 20175525--20175628 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
20175515 ATTTAGTAAA
20175525 ACTTTTTTAACAAATATAACATTTTGTTGTAAAATGAGTAACCGAAGAATAG
1 ACTTTTTTAACAAATATAACATTTTGTTGTAAAATGAGTAACCGAAGAATAG
20175577 ACTTTTTTAACAAATATAACATTTTGTTGTAAAATGAGTAACCGAAGAATAG
1 ACTTTTTTAACAAATATAACATTTTGTTGTAAAATGAGTAACCGAAGAATAG
20175629 TTTAAGTACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (52 bp):
ACTTTTTTAACAAATATAACATTTTGTTGTAAAATGAGTAACCGAAGAATAG
Found at i:20176652 original size:4 final size:4
Alignment explanation
Indices: 20176637--20176671 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
20176627 TAAAAAGAGC
* *
20176637 AAAT ATAT AAAT AAAT ACAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
20176672 AATTTCATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:20178383 original size:44 final size:44
Alignment explanation
Indices: 20178334--20178431 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
20178324 CTTTGGAGGT
* * * * **
20178334 ATAAGATTTGTTGCTTCAGTCTGCTCTACTGCAACTTCAATTAG
1 ATAAGATTTGTAGCTCCAATCTGCTCCACTGCAACTTCAAGGAG
* *
20178378 ATAAGATTTGTAGCTCCAATTTGCTCCACTGCAACTTCAGGGAG
1 ATAAGATTTGTAGCTCCAATCTGCTCCACTGCAACTTCAAGGAG
20178422 ATAAGATTTG
1 ATAAGATTTG
20178432 CTACAATGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (44 bp):
ATAAGATTTGTAGCTCCAATCTGCTCCACTGCAACTTCAAGGAG
Found at i:20179784 original size:46 final size:46
Alignment explanation
Indices: 20179701--20179912 Score: 180
Period size: 46 Copynumber: 4.6 Consensus size: 46
20179691 GTGTAATGCT
* * * *
20179701 GATGCCATGTCCCAGAAATGGTCTTACTCT-G-ACACATCTTGTAGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTTGAAGTC
* * * *
20179747 GATGCATGTCCCTGACATGTTTTACACTGGCTGACATCTCGAAG-C
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTTGAAGTC
* * * *
20179792 TGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTC-TCAATGTC
1 -GATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTTGAA-GTC
* * ** **
20179839 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTTGAAGTC
20179887 GATGCATGTCCCAGACATGTCTTACA
1 GATGCATGTCCCAGACATGTCTTACA
20179913 TTAGCACACA
Statistics
Matches: 134, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
44 8 0.06
45 16 0.12
46 58 0.43
47 27 0.20
48 24 0.18
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTTGAAGTC
Found at i:20179858 original size:47 final size:45
Alignment explanation
Indices: 20179793--20179917 Score: 146
Period size: 47 Copynumber: 2.7 Consensus size: 45
20179783 TCTCGAAGCT
*
20179793 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAA-T-GTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTC--AT-AAGTGGTC
* *
20179839 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAA-GTGGTC
*
20179887 GATGCATGTCCCAGACATGTCTTACATTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
20179918 ACACAATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
45 2 0.03
46 16 0.24
47 27 0.40
48 23 0.34
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAGTGGTC
Found at i:20196936 original size:20 final size:20
Alignment explanation
Indices: 20196911--20196955 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
20196901 TGCGAGTGAA
*
20196911 ATCCCATAGTTCTAACATAT
1 ATCCCATAGTTATAACATAT
*
20196931 ATCCCATAGTTATGACATAT
1 ATCCCATAGTTATAACATAT
20196951 ATCCC
1 ATCCC
20196956 TCCGTCAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (20 bp):
ATCCCATAGTTATAACATAT
Found at i:20203466 original size:33 final size:33
Alignment explanation
Indices: 20203424--20203487 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
20203414 TTAAGAATGC
20203424 ATCTATTTTATTGGTTTGGCTATTTTAATATGA
1 ATCTATTTTATTGGTTTGGCTATTTTAATATGA
*
20203457 ATCTATTTTATTGGTTTGTCTATTTTAATAT
1 ATCTATTTTATTGGTTTGGCTATTTTAATAT
20203488 TTGCTTGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.58
Consensus pattern (33 bp):
ATCTATTTTATTGGTTTGGCTATTTTAATATGA
Found at i:20203480 original size:17 final size:17
Alignment explanation
Indices: 20203425--20203483 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
20203415 TAAGAATGCA
20203425 TCTATTTTATTGGTTTG
1 TCTATTTTATTGGTTTG
* * * ***
20203442 GCTATTTTAAT-ATGAA
1 TCTATTTTATTGGTTTG
20203458 TCTATTTTATTGGTTTG
1 TCTATTTTATTGGTTTG
20203475 TCTATTTTA
1 TCTATTTTA
20203484 ATATTTGCTT
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59
Consensus pattern (17 bp):
TCTATTTTATTGGTTTG
Found at i:20204089 original size:17 final size:17
Alignment explanation
Indices: 20204067--20204101 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20204057 TCATTCGAAG
20204067 GTGACATCTCTTTCTCC
1 GTGACATCTCTTTCTCC
20204084 GTGACATCTCTTTCTCC
1 GTGACATCTCTTTCTCC
20204101 G
1 G
20204102 GCTCTACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.34, G:0.14, T:0.40
Consensus pattern (17 bp):
GTGACATCTCTTTCTCC
Found at i:20204793 original size:6 final size:6
Alignment explanation
Indices: 20204749--20204810 Score: 61
Period size: 6 Copynumber: 9.7 Consensus size: 6
20204739 TTGAGTCCGA
* *
20204749 TTATTT TTATGT TTATGT TTATTT TTATCTTCT TATATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTA--TT-T T-TATTT TTATTT TTATTT
*
20204801 TTCTTT TTAT
1 TTATTT TTAT
20204811 GTCTATTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
6 38 0.79
7 2 0.04
8 4 0.08
9 2 0.04
10 2 0.04
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:20215902 original size:46 final size:46
Alignment explanation
Indices: 20215835--20216062 Score: 332
Period size: 46 Copynumber: 5.0 Consensus size: 46
20215825 AGTGTGCTCT
20215835 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
20215881 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
20215927 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
20215973 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
20216019 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
20216063 TCATGTCAAA
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 165 0.99
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:20222026 original size:43 final size:44
Alignment explanation
Indices: 20221977--20222071 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 44
20221967 AGCCACTAAC
**
20221977 CTTATCTCTCTG-AGTTTGCA-GAGAGCAGGTTG-AAGATACAGGT
1 CTTATCTCTCTGAAG-TTGCAGGA-AGCAGACTGAAAGATACAGGT
* * *
20222020 CTTATCTTTCTGAAGTTGTAGGAAGCAGACTGAAAGTTACAGGT
1 CTTATCTCTCTGAAGTTGCAGGAAGCAGACTGAAAGATACAGGT
20222064 CTTATCTC
1 CTTATCTC
20222072 CATGTATCGG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 22 0.51
44 21 0.49
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (44 bp):
CTTATCTCTCTGAAGTTGCAGGAAGCAGACTGAAAGATACAGGT
Found at i:20222180 original size:176 final size:176
Alignment explanation
Indices: 20221886--20222742 Score: 1234
Period size: 176 Copynumber: 4.9 Consensus size: 176
20221876 TGAAAATTGA
** * *
20221886 GTCTTATCTCCATGTATCGACTATGGAGCAGATCGAAAATGGCGAGTCTTATCTTCATGTATCGA
1 GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAGATGGCGAGTCTTATCTCCATGTATCGA
*
20221951 CTATGGAGTAGATTTTAGCCACTAACCTTATCTCTCTGAGTTTGCAGAGAGCAGGTTGAAGATAC
66 CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTGAGTTTGCAGAGAGCAGGTTGAAGATAC
* * *
20222016 AGGTCTTATCTTTCTGAAGTTGTAGGAAGCAGACTGAAAGTTACAG
131 AAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
* * *
20222062 GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAAATGGTGAGTCTTATCTCCATGTATCGG
1 GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAGATGGCGAGTCTTATCTCCATGTATCGA
20222127 CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTGAGTTTGCAGAGAGCAGGTTGAAGATAC
66 CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTGAGTTTGCAGAGAGCAGGTTGAAGATAC
* * * *
20222192 AGGTCTTATCTTCCTGAAGTTGCAGGAAGTAGAATGAAAGTTAAAG
131 AAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
*
20222238 GTCTTATCTCCATGTATCGGTTATGGAGCAGATTGAAGATGGCGAGTCTTATCTCCATGTATCGA
1 GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAGATGGCGAGTCTTATCTCCATGTATCGA
*
20222303 CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTGAGTTTCCAGAGAGCAGGTTGAAGATAC
66 CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTGAGTTTGCAGAGAGCAGGTTGAAGATAC
*
20222368 AAGTCTTATCTTCTTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
131 AAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
* *
20222414 GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAGATGGAGAGTCTTATCTCCACGTATCGA
1 GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAGATGGCGAGTCTTATCTCCATGTATCGA
* * * *
20222479 CTATGGAGTAGATTTTAGCCACCAGCCTTATCTCTCTGAAG-TTGCAGTGGAGCAGGTTGAAGAT
66 CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTG-AGTTTGCAG-AGAGCAGGTTGAAGAT
* *
20222543 ACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAAATTACAG
129 ACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
* * * * * * * *
20222591 ATCTTAGCTCCATGTATTGGCTATGGAGCAGATTGAAGACGGCGAATCTTATCTCCATGTATCGG
1 GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAGATGGCGAGTCTTATCTCCATGTATCGA
* * * ** * * * *
20222656 CAATGGAGCAGATCTAAGTTATTAGCCTTATCTCCCTGAAG-TTGCAGTGGAGCAGGCTTGAA-A
66 CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTG-AGTTTGCAG-AGAGCAGG-TTGAAGA
* *
20222719 CTACAAGTGTTATCTCCCTGAAGT
128 -TACAAGTCTTATCTTCCTGAAGT
20222743 CGCAATAGGG
Statistics
Matches: 624, Mismatches: 53, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
176 433 0.69
177 165 0.26
178 26 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (176 bp):
GTCTTATCTCCATGTATCGGTTATGGAGCAGATCGAAGATGGCGAGTCTTATCTCCATGTATCGA
CTATGGAGCAGATTTTAGCCACTAACCTTATCTCTCTGAGTTTGCAGAGAGCAGGTTGAAGATAC
AAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAGTTACAG
Found at i:20226366 original size:3 final size:3
Alignment explanation
Indices: 20226360--20226387 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20226350 AGAAAAAGAA
20226360 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20226388 CATATATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20229056 original size:4 final size:4
Alignment explanation
Indices: 20229042--20229077 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
20229032 ATAAAAAGAG
* *
20229042 TAAA GAAA TAAA TAAA TATA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
20229078 ATTTCATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:20233894 original size:22 final size:23
Alignment explanation
Indices: 20233863--20233918 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
20233853 CTGAGCCGAT
* *
20233863 AAACGGTAAGCTCAATTGAGCTG
1 AAACGATAAGCTCAATAGAGCTG
**
20233886 -AACGATAAGCTCCGTAGAGCTG
1 AAACGATAAGCTCAATAGAGCTG
20233908 AAACGATAAGC
1 AAACGATAAGC
20233919 CCCTAAAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18
Consensus pattern (23 bp):
AAACGATAAGCTCAATAGAGCTG
Found at i:20233916 original size:23 final size:23
Alignment explanation
Indices: 20233880--20233943 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
20233870 AAGCTCAATT
*
20233880 GAGCTG-AACGATAAGCTCCGTA
1 GAGCTGAAACGATAAGCTCCCTA
20233902 GAGCTGAAACGATAAGC-CCCTA
1 GAGCTGAAACGATAAGCTCCCTA
*
20233924 AAGACTGAAAC-AGTAAGCTC
1 GAG-CTGAAACGA-TAAGCTC
20233944 ATACGAGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 13 0.36
23 22 0.61
24 1 0.03
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (23 bp):
GAGCTGAAACGATAAGCTCCCTA
Found at i:20242363 original size:20 final size:20
Alignment explanation
Indices: 20242338--20242377 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20242328 TCGAATGAAA
20242338 ACCTAGCCTTTAGCTTTCTT
1 ACCTAGCCTTTAGCTTTCTT
*
20242358 ACCTAGCCTTTGGCTTTCTT
1 ACCTAGCCTTTAGCTTTCTT
20242378 CTTTTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.30, G:0.12, T:0.45
Consensus pattern (20 bp):
ACCTAGCCTTTAGCTTTCTT
Found at i:20244464 original size:256 final size:256
Alignment explanation
Indices: 20244009--20244778 Score: 1360
Period size: 256 Copynumber: 3.0 Consensus size: 256
20243999 TTCCGGACCA
* ** * * *
20244009 CTAGTAATGCTGTTTCAGATCATTATAAATTTTTGTACTACCCGGATGCACACATAACCGACTAT
1 CTAGTAATGCTGTTTCAGATCATTATACATTTTCATACTACCCGGATACATAGATAACCGACTAT
* *
20244074 TGTAAGCTTTACTCAAAATCATCTGAATTAACTCTGAATTTCTCGAAACACAAATTCAATCTCGG
66 TGTGAGCTTTACTCAAAATCATCTGAATTAACTCTGAATTTCTCGAAACACAAATTCGATCTCGG
20244139 AATCTAAAACAATCATCTTTATCAACTCTGAATTCTGAATCAGACTCTACATCACACTAAGCTCT
131 AATCTAAAACAATCATCTTTATCAACTCTGAATTCTGAATCAGACTCTACATCACACTAAGCTCT
* * *
20244204 TTTAGCTAAAATCTCATTATCAATCTTCTGAGCTTCGATAATCTATTATAGGGACAAAAGT
196 TTTAGCTAAAATCTCATTATCAATCTTCTGAGCTTCGATAATCTGTTATAAGAACAAAAGT
*
20244265 CTAGTAATGTTGTTTCAGATCATTATACATTTTCATACTACCCGGATACATAGATAACCGACTAT
1 CTAGTAATGCTGTTTCAGATCATTATACATTTTCATACTACCCGGATACATAGATAACCGACTAT
* *
20244330 TGTGAGCTTTACTCAAAATCATCTGAATTAACTCTAAATTTCTCGAAACATAAATTCGATCTCGG
66 TGTGAGCTTTACTCAAAATCATCTGAATTAACTCTGAATTTCTCGAAACACAAATTCGATCTCGG
*
20244395 AATCTAAAACAATCATCTTTATCAACTCTGAATTCTGAATCAGACTCTACATCACACAAAGCTCT
131 AATCTAAAACAATCATCTTTATCAACTCTGAATTCTGAATCAGACTCTACATCACACTAAGCTCT
*
20244460 TTTAGCTAAAATCTCATTATCAATCTTCTGAGCTTCGATAATCTGTTGTAAGAACAAAAGT
196 TTTAGCTAAAATCTCATTATCAATCTTCTGAGCTTCGATAATCTGTTATAAGAACAAAAGT
* *
20244521 CTAGTAATGCTGTTTCAGATCATTATACGTTTTCATACTACCCAGATACATAGATAACCGACTAT
1 CTAGTAATGCTGTTTCAGATCATTATACATTTTCATACTACCCGGATACATAGATAACCGACTAT
*
20244586 TGTGAGCTTTACTCAAAATCATCTGAATTAACTCTGAATTTCTCGAAACACAAATTCGATCTCGA
66 TGTGAGCTTTACTCAAAATCATCTGAATTAACTCTGAATTTCTCGAAACACAAATTCGATCTCGG
20244651 AATCTAAAACAATCATCTTTATCAACTCTGAATTCTGAATCAGACTCTACATCACACTAAGCTCT
131 AATCTAAAACAATCATCTTTATCAACTCTGAATTCTGAATCAGACTCTACATCACACTAAGCTCT
*
20244716 TTTAGCTAAAATCTCATTATCAATCTTCTGAGCTTCGATAATCTGCTATAAGAACAAAAGT
196 TTTAGCTAAAATCTCATTATCAATCTTCTGAGCTTCGATAATCTGTTATAAGAACAAAAGT
20244777 CT
1 CT
20244779 TGCTTTCAAA
Statistics
Matches: 489, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
256 489 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (256 bp):
CTAGTAATGCTGTTTCAGATCATTATACATTTTCATACTACCCGGATACATAGATAACCGACTAT
TGTGAGCTTTACTCAAAATCATCTGAATTAACTCTGAATTTCTCGAAACACAAATTCGATCTCGG
AATCTAAAACAATCATCTTTATCAACTCTGAATTCTGAATCAGACTCTACATCACACTAAGCTCT
TTTAGCTAAAATCTCATTATCAATCTTCTGAGCTTCGATAATCTGTTATAAGAACAAAAGT
Found at i:20251546 original size:29 final size:28
Alignment explanation
Indices: 20251512--20251614 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
20251502 TACTCAATCA
*
20251512 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
20251541 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
20251570 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
20251599 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
20251615 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:20259590 original size:28 final size:27
Alignment explanation
Indices: 20259498--20259598 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 27
20259488 TGTGTAGAGT
* * *
20259498 TCGCACACATAGTGCTTAATACTCAATC
1 TCGCACACATAGTGCCT-ATATTCAAGC
* *
20259526 ACGCACACTTAGTGCCATATGATTCAAGC
1 TCGCACACATAGTGCC-TAT-ATTCAAGC
*
20259555 CCGCACACATAGTGCCTATATTACAAGC
1 TCGCACACATAGTGCCTATATT-CAAGC
20259583 TCGCACAC-TCAGTGCC
1 TCGCACACAT-AGTGCC
20259599 AATCTCGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
27 4 0.07
28 36 0.59
29 21 0.34
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.24
Consensus pattern (27 bp):
TCGCACACATAGTGCCTATATTCAAGC
Found at i:20267649 original size:11 final size:12
Alignment explanation
Indices: 20267633--20267662 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20267623 GGAAGCAGGG
20267633 AGAAAAA-GGAA
1 AGAAAAAGGGAA
20267644 AGAAAAAGGGAA
1 AGAAAAAGGGAA
20267656 AGAAAAA
1 AGAAAAA
20267663 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AGAAAAAGGGAA
Found at i:20270427 original size:16 final size:16
Alignment explanation
Indices: 20270406--20270440 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20270396 TGTACTCTTA
20270406 TAACATATAATTCATG
1 TAACATATAATTCATG
* *
20270422 TAACATGTATTTCATG
1 TAACATATAATTCATG
20270438 TAA
1 TAA
20270441 GGTATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (16 bp):
TAACATATAATTCATG
Found at i:20270661 original size:22 final size:22
Alignment explanation
Indices: 20270618--20270701 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
20270608 CCTGAGCTGA
* *
20270618 TAAACAGTAAGCTCA-ATTGAGC
1 TAAACGGTAAGCTCATA-AGAGC
* *
20270640 TAAACGGTAAGCTCCTAGGAGC
1 TAAACGGTAAGCTCATAAGAGC
* *
20270662 TGAACAGTAAGCTCATAAGAGCC
1 TAAACGGTAAGCTCATAAGAG-C
*
20270685 GAAACGGTAAGCTCATA
1 TAAACGGTAAGCTCATA
20270702 TGAGTTGTGG
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 34 0.68
23 16 0.32
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (22 bp):
TAAACGGTAAGCTCATAAGAGC
Found at i:20275235 original size:3 final size:3
Alignment explanation
Indices: 20275227--20275254 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20275217 GGAGAAAATA
20275227 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
20275255 GGAGTCGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:20281190 original size:2 final size:2
Alignment explanation
Indices: 20281183--20281210 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20281173 TGCAGCATGC
20281183 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
20281211 TCAGATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.