Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 126 of 325
Found at i:38014493 original size:71 final size:71
Alignment explanation
Indices: 38014411--38014550 Score: 244
Period size: 71 Copynumber: 2.0 Consensus size: 71
38014401 TTATAAGGAC
* *
38014411 TATTTTGTAAAAGATGTAAATGTGTGGTAGAAATGAGAAAATAATTGATAATGTGGGCTACCACA
1 TATTTTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
38014476 AGAAAA
66 AGAAAA
* *
38014482 TATTTTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTGCCATA
1 TATTTTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
38014547 AGAA
66 AGAA
38014551 GGAAAAGTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (71 bp):
TATTTTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
AGAAAA
Found at i:38028537 original size:12 final size:12
Alignment explanation
Indices: 38028522--38028548 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38028512 CTATTTTCAT
38028522 TTTCCATTTCCA
1 TTTCCATTTCCA
38028534 TTTCCATTTCCA
1 TTTCCATTTCCA
38028546 TTT
1 TTT
38028549 TGGAAACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTCCATTTCCA
Found at i:38030557 original size:55 final size:52
Alignment explanation
Indices: 38030476--38030631 Score: 199
Period size: 55 Copynumber: 2.9 Consensus size: 52
38030466 TGTGGTATCC
*
38030476 TTTCCTTAT-GAACTCACTAATGCCATGCCTTGGCATGGTCTTACATGGGACTT
1 TTTCCTTATAGAACTCATTAATGCCATGCCTTGGCATGGTCTTACAT-GGA-TT
* *
38030529 TTTCCTTATAGTAACTCATTAATGCCATGTCTTGACATGGTCTTACAT-GATT
1 TTTCCTTATAG-AACTCATTAATGCCATGCCTTGGCATGGTCTTACATGGATT
* *
38030581 TCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATG
1 T--TT-CCTTATAGAACTCATTAATGCCATGCCTTGGCATGGTCTTACATG
38030632 ATATCCTTAT
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
52 3 0.03
53 11 0.12
54 35 0.39
55 41 0.46
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (52 bp):
TTTCCTTATAGAACTCATTAATGCCATGCCTTGGCATGGTCTTACATGGATT
Found at i:38030630 original size:54 final size:52
Alignment explanation
Indices: 38030431--38030889 Score: 187
Period size: 54 Copynumber: 8.9 Consensus size: 52
38030421 TTTTCCTTTT
* * * * * ** * *
38030431 TGAACTTACCATTGCCTTGTCTTGACACGGTCTTATGTGGTATCCTTTCCTTA
1 TGAACTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCC-TTCCTTA
* *
38030484 TGAACTCA-CTAATGCCATGCCTTGGCATGGTCTTACATGGGACTTT--TTCCTTA
1 TGAACTTATC-AATGCCATGCCTTGACATGGTCTTACAT--GA-TTTCCTTCCTTA
* * *
38030537 TAGTAACTCATTAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA
1 T-G-AACTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCCTT-CCTTA
* *
38030592 TAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA--T--ATCCTTA
1 T-GAACTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCCTTCCTTA
* ** * * * *
38030641 T---CTTACCAAATGCCATGTTCC-AAACATGGTCTT-GATGGTATCCTTGTCTTA
1 TGAACTTATC-AATGCCATG--CCTTGACATGGTCTTACATGATTTCCTT-CCTTA
* *** * *
38030692 GTG--C----CAATGCCA-GATCTTGGTGTGGTCTTACATGGA-GTCC-T--TAA
1 -TGAACTTATCAATGCCATG-CCTTGACATGGTCTTACAT-GATTTCCTTCCTTA
* * * * **
38030736 TTAA--TGTCGATGCCATGTCTTGACATGGTCTTACATGA-GACCTTTTCCTTA
1 TGAACTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCC--TTCCTTA
* *
38030787 TAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA
1 T-G-AACTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCCTT-CCTTA
* *
38030842 TAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 T-GAACTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCCTT
38030890 ATCTTTCCAA
Statistics
Matches: 312, Mismatches: 54, Indels: 79
0.70 0.12 0.18
Matches are distributed among these distances:
43 1 0.00
44 2 0.01
45 5 0.02
46 18 0.06
47 41 0.13
48 16 0.05
49 9 0.03
50 2 0.01
51 7 0.02
52 6 0.02
53 41 0.13
54 80 0.26
55 80 0.26
56 4 0.01
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.37
Consensus pattern (52 bp):
TGAACTTATCAATGCCATGCCTTGACATGGTCTTACATGATTTCCTTCCTTA
Found at i:38030810 original size:55 final size:54
Alignment explanation
Indices: 38030745--38030883 Score: 199
Period size: 55 Copynumber: 2.6 Consensus size: 54
38030735 ATTAATGTCG
*
38030745 ATGCCATGTCTTGACATGGTCTTACATGA-GACCTTTTCCTTATAGTAACTCATCA
1 ATGCCATGTCTTGACATGGTCTTACATGATGACC-TTGCCTTATAG-AACTCATCA
** *
38030800 ATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCA
1 ATGCCATGTCTTGACATGGTCTTACATGATGACCTTGCCTTATAGAACTCATCA
* *
38030854 ATGCCATGCCTTGGCATGGTCTTACATGAT
1 ATGCCATGTCTTGACATGGTCTTACATGAT
38030884 ATCCTTATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
54 36 0.47
55 39 0.51
56 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (54 bp):
ATGCCATGTCTTGACATGGTCTTACATGATGACCTTGCCTTATAGAACTCATCA
Found at i:38030923 original size:47 final size:47
Alignment explanation
Indices: 38030868--38030989 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
38030858 CATGCCTTGG
* * *
38030868 CATGGTCTTACATGATATCCTTATCTTTCCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
38030915 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
* *
38030962 CATGTTCGTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
38030990 ATGCCAATGC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:38030976 original size:250 final size:248
Alignment explanation
Indices: 38030495--38030976 Score: 768
Period size: 250 Copynumber: 1.9 Consensus size: 248
38030485 GAACTCACTA
* * * *
38030495 ATGCCATGCCTTGGCATGGTCTTACATGGGACTTTTTCCTTATAGTAACTCATTAATGCCATGTC
1 ATGCCATGCCTTGACATGGTCTTACATGAGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
38030560 TTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
66 TTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
*
38030625 TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCTTGTCT
131 TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTCATGGTATCCTTGTCT
****** *
38030690 TAGTGCCAATGCCAGATCTTGGTGTGGTCTTACATGGAGTCCTTAATTAATGTCG
196 TA--GCCAATGCCAGATCCAAACATGGTCGTACATGGAGTCCTTAATTAATGTCG
*
38030745 ATGCCATGTCTTGACATGGTCTTACATGAGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
1 ATGCCATGCCTTGACATGGTCTTACATGAGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
38030810 TTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
66 TTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
*
38030875 TTACATGATATCCTTATCTTTCCAAATGCCATGTTCCAAACATGGTCTTACATGGTATCCTTGTC
131 TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTT-CATGGTATCCTTGTC
* *
38030940 TTA-CCAAATGCCATGTTCCAAACATGTTCGTACATGG
195 TTAGCC-AATGCCA-GATCCAAACATGGTCGTACATGG
38030977 TATCCTTGTC
Statistics
Matches: 213, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
248 2 0.01
249 7 0.03
250 187 0.88
251 17 0.08
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (248 bp):
ATGCCATGCCTTGACATGGTCTTACATGAGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
TTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTCATGGTATCCTTGTCT
TAGCCAATGCCAGATCCAAACATGGTCGTACATGGAGTCCTTAATTAATGTCG
Found at i:38031178 original size:44 final size:44
Alignment explanation
Indices: 38031129--38031212 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
38031119 TCCTTAACCG
* * *
38031129 TCAATTCCTCCTTAAATTCCATGTTATGAAC-ATGGACTTTTTCA
1 TCAATTCCTACTTAAATTCCATGGTA-CAACTATGGACTTTTTCA
* *
38031173 TCAATTCTTACTTAATTTCCATGGTACAACTATGGACTTT
1 TCAATTCCTACTTAAATTCCATGGTACAACTATGGACTTT
38031213 GAGATACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 3 0.09
44 31 0.91
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (44 bp):
TCAATTCCTACTTAAATTCCATGGTACAACTATGGACTTTTTCA
Found at i:38031302 original size:12 final size:12
Alignment explanation
Indices: 38031285--38031311 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38031275 CGCATAACTC
38031285 AATAATAACAAT
1 AATAATAACAAT
38031297 AATAATAACAAT
1 AATAATAACAAT
38031309 AAT
1 AAT
38031312 TGCATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATAACAAT
Found at i:38039819 original size:59 final size:59
Alignment explanation
Indices: 38039669--38039845 Score: 200
Period size: 59 Copynumber: 3.0 Consensus size: 59
38039659 CTGTAAAACT
* *
38039669 AGAAAACAGGGGACAAAACTGTAAAATTTAAAAAATAGGGG-ACAACTAT-AAATCTTAAAA
1 AGAAAA-AAGGGA-AAAACTGTAAAATTTAAAAAATAGGGGAAAAACTATAAAATC-TAAAA
* ** * * *
38039729 A-AATAAAGTCAAAATC-GTAAAATTTCAAAAATAGGGGAAAAACTATAAAATCTGAAA
1 AGAAAAAAGGGAAAAACTGTAAAATTTAAAAAATAGGGGAAAAACTATAAAATCTAAAA
* * *
38039786 AGAAAAAAGGGAAAAACTATAAAATCTAAAAAATGGGGGAAAAACTATAAAATCTAAAA
1 AGAAAAAAGGGAAAAACTGTAAAATTTAAAAAATAGGGGAAAAACTATAAAATCTAAAA
38039845 A
1 A
38039846 ATAAGGAACA
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
56 20 0.21
57 16 0.17
58 19 0.20
59 40 0.42
60 1 0.01
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (59 bp):
AGAAAAAAGGGAAAAACTGTAAAATTTAAAAAATAGGGGAAAAACTATAAAATCTAAAA
Found at i:38039847 original size:28 final size:28
Alignment explanation
Indices: 38039662--38039848 Score: 148
Period size: 28 Copynumber: 6.6 Consensus size: 28
38039652 GTCAATACTG
* * *
38039662 TAAAA-CTAGAAAACAGGGGACAAAACTG
1 TAAAATCTAAAAAATAGGGGA-AAAACTA
* *
38039690 TAAAATTTAAAAAATAGGGG-ACAACTA
1 TAAAATCTAAAAAATAGGGGAAAAACTA
** ** *
38039717 T-AAATCTTAAAAAAATAAAGTCAAAA-TCG
1 TAAAATC-T-AAAAAATAGGGGAAAAACT-A
* *
38039746 TAAAATTTCAAAAATAGGGGAAAAACTA
1 TAAAATCTAAAAAATAGGGGAAAAACTA
* *
38039774 TAAAATCTGAAAAGAAAAAAGGGAAAAACTA
1 TAAAATCT--AAA-AAATAGGGGAAAAACTA
*
38039805 TAAAATCTAAAAAATGGGGGAAAAACTA
1 TAAAATCTAAAAAATAGGGGAAAAACTA
38039833 TAAAATCTAAAAAATA
1 TAAAATCTAAAAAATA
38039849 AGGAACACAC
Statistics
Matches: 123, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
26 4 0.03
27 7 0.06
28 63 0.51
29 20 0.16
30 6 0.05
31 23 0.19
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.19
Consensus pattern (28 bp):
TAAAATCTAAAAAATAGGGGAAAAACTA
Found at i:38042021 original size:67 final size:67
Alignment explanation
Indices: 38041913--38042047 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
38041903 GGAGTATCTA
38041913 TATAATCATATATCAAGTATCAAAGCATTATTATATGTGGCATATAATATTCGTTTGTTAAATGT
1 TATAATCATATATCAAGTATCAAAGCATTATTATATGTGGCATATAATATTCGTTTGTTAAATGT
38041978 TG
66 TG
38041980 TATAATCATATATCAAGTATCAAAGCATTATTATATGTGGCATATAATATTCGTTTGTTAAATGT
1 TATAATCATATATCAAGTATCAAAGCATTATTATATGTGGCATATAATATTCGTTTGTTAAATGT
38042045 TG
66 TG
38042047 T
1 T
38042048 TTTAATTGAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (67 bp):
TATAATCATATATCAAGTATCAAAGCATTATTATATGTGGCATATAATATTCGTTTGTTAAATGT
TG
Found at i:38043519 original size:40 final size:40
Alignment explanation
Indices: 38043475--38043556 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
38043465 ATCAGCACGA
38043475 TTATCTTGTATTTTATAATATGGTTAGTCCAAATCTGTTG
1 TTATCTTGTATTTTATAATATGGTTAGTCCAAATCTGTTG
38043515 TTATCTTGTATTTTATAATATGGTTAGTCCAAATCTGTTG
1 TTATCTTGTATTTTATAATATGGTTAGTCCAAATCTGTTG
38043555 TT
1 TT
38043557 CAAGTTGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (40 bp):
TTATCTTGTATTTTATAATATGGTTAGTCCAAATCTGTTG
Found at i:38043739 original size:14 final size:14
Alignment explanation
Indices: 38043720--38043759 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
38043710 TCAGGTATAT
38043720 TTTATTATAATTTA
1 TTTATTATAATTTA
*
38043734 TTTATTAT-ATCATA
1 TTTATTATAAT-TTA
38043748 TTTATTATAATT
1 TTTATTATAATT
38043760 GGAGATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATTATAATTTA
Found at i:38050705 original size:25 final size:25
Alignment explanation
Indices: 38050677--38050724 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38050667 TTATACCATG
* * *
38050677 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38050702 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38050725 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38050827 original size:20 final size:20
Alignment explanation
Indices: 38050767--38050827 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
38050757 ATAAATATGG
*
38050767 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
38050787 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38050807 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38050827 T
1 T
38050828 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:38050904 original size:24 final size:24
Alignment explanation
Indices: 38050877--38051019 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
38050867 GAGGAAGTGA
38050877 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
38050901 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
38050925 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
38050948 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
38050972 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
38050996 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38051020 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:38050970 original size:47 final size:47
Alignment explanation
Indices: 38050877--38051019 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
38050867 GAGGAAGTGA
38050877 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
38050925 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
38050972 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
38051020 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:38050993 original size:71 final size:72
Alignment explanation
Indices: 38050877--38051020 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
38050867 GAGGAAGTGA
*
38050877 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
38050940 CCAGTTAT
65 CCAGTTAT
** * *
38050948 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
38051013 CAGTTAT
66 CAGTTAT
38051020 A
1 A
38051021 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:38051271 original size:30 final size:31
Alignment explanation
Indices: 38051211--38051273 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
38051201 CGTTTACAGT
38051211 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
38051242 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
38051272 AA
1 AA
38051274 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:38058897 original size:11 final size:11
Alignment explanation
Indices: 38058864--38058917 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
38058854 TATGGTATGT
38058864 ATGATATGCAC
1 ATGATATGCAC
*
38058875 ATGA-ATG--T
1 ATGATATGCAC
38058883 ATGATATGCAC
1 ATGATATGCAC
*
38058894 ATGATATG--T
1 ATGATATGCAC
38058903 ATGATATGCAC
1 ATGATATGCAC
38058914 ATGA
1 ATGA
38058918 GTAATCATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.12
9 11 0.32
10 3 0.09
11 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:38058904 original size:20 final size:20
Alignment explanation
Indices: 38058859--38058917 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
38058849 ATAAATATGG
38058859 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38058879 -ATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38058898 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38058918 GTAATCATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:38058994 original size:24 final size:24
Alignment explanation
Indices: 38058967--38059085 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
38058957 GAGGAAGTGA
*
38058967 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
38058991 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
38059014 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
38059038 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38059062 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38059086 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:38059036 original size:47 final size:48
Alignment explanation
Indices: 38058967--38059085 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
38058957 GAGGAAGTGA
38058967 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
38059014 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
38059062 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38059086 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:38059333 original size:28 final size:29
Alignment explanation
Indices: 38059274--38059334 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 29
38059264 CGTTTACAGT
38059274 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAG--ATATGAAATATGA
38059305 AAAGGCTTCGGCCCAG-TATGAAATATGA
1 AAAGGCTTCGGCCCAGATATGAAATATGA
38059333 AA
1 AA
38059335 TGAAAAGGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 14 0.47
31 16 0.53
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (29 bp):
AAAGGCTTCGGCCCAGATATGAAATATGA
Found at i:38059356 original size:34 final size:35
Alignment explanation
Indices: 38059291--38059357 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
38059281 TCGGCCCAGT
*
38059291 AATATGAAATATGAAAAGGCTTCGGCCCAGTATGA
1 AATATGAAATATGAAAAGGCTACGGCCCAGTATGA
38059326 AATATG-AA-ATGAAAAGGGCTACGGCCCAGTAT
1 AATATGAAATATGAAAA-GGCTACGGCCCAGTAT
38059358 ATGTTGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.23
34 17 0.57
35 6 0.20
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (35 bp):
AATATGAAATATGAAAAGGCTACGGCCCAGTATGA
Found at i:38066868 original size:25 final size:25
Alignment explanation
Indices: 38066839--38066886 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38066829 TTATACCATG
* * *
38066839 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38066864 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38066887 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38066989 original size:20 final size:20
Alignment explanation
Indices: 38066929--38066989 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
38066919 ATAAATATGG
*
38066929 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
38066949 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38066969 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
38066989 T
1 T
38066990 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:38067066 original size:24 final size:24
Alignment explanation
Indices: 38067039--38067157 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
38067029 GAGGAAGTGA
*
38067039 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
38067063 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
38067086 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
38067110 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38067134 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38067158 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:38067108 original size:47 final size:48
Alignment explanation
Indices: 38067039--38067157 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
38067029 GAGGAAGTGA
38067039 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
38067086 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
38067134 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38067158 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:38067384 original size:31 final size:31
Alignment explanation
Indices: 38067349--38067412 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
38067339 CGTTTACAGT
38067349 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
38067380 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
38067411 AA
1 AA
38067413 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:38078048 original size:18 final size:18
Alignment explanation
Indices: 38078013--38078064 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
38078003 TTGATATAAA
*
38078013 ATTATTTTACAT-TTTTT
1 ATTATTTTATATATTTTT
38078030 ATTATTTTATATATTTTT
1 ATTATTTTATATATTTTT
**
38078048 AAAATTTTATATATTTT
1 ATTATTTTATATATTTT
38078065 AAAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTATTTTATATATTTTT
Found at i:38078055 original size:26 final size:26
Alignment explanation
Indices: 38078026--38078078 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
38078016 ATTTTACATT
*
38078026 TTTTAT-TATTTTATATATTTTTAAAA
1 TTTTATATATTTTA-AAATTTTTAAAA
38078052 TTTTATATATTTTAAAATTTTTAAAA
1 TTTTATATATTTTAAAATTTTTAAAA
38078078 T
1 T
38078079 AATAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTATATATTTTAAAATTTTTAAAA
Found at i:38078065 original size:9 final size:9
Alignment explanation
Indices: 38078015--38078065 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
38078005 GATATAAAAT
*
38078015 TATTTTACA
1 TATTTTATA
*
38078024 TTTTTTAT-
1 TATTTTATA
38078032 TATTTTATA
1 TATTTTATA
38078041 TATTTT-TAA
1 TATTTTAT-A
*
38078050 AATTTTATA
1 TATTTTATA
38078059 TATTTTA
1 TATTTTA
38078066 AAATTTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 8 0.24
9 25 0.74
10 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTATA
Found at i:38078074 original size:18 final size:18
Alignment explanation
Indices: 38078033--38078072 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
38078023 ATTTTTTATT
38078033 ATTTTATATATTTTTAAA
1 ATTTTATATATTTTTAAA
38078051 ATTTTATATA-TTTTAAA
1 ATTTTATATATTTTTAAA
38078068 ATTTT
1 ATTTT
38078073 TAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATATATTTTTAAA
Found at i:38078086 original size:27 final size:27
Alignment explanation
Indices: 38078032--38078087 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
38078022 CATTTTTTAT
* * *
38078032 TATTTTATATATTTTTAAAATTTTATA
1 TATTTTATAAATTTTTAAAATATAATA
38078059 TATTTTA-AAATTTTTAAAATAATAATA
1 TATTTTATAAATTTTTAAAAT-ATAATA
38078086 TA
1 TA
38078088 AATAAATTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTTTATAAATTTTTAAAATATAATA
Found at i:38078667 original size:23 final size:23
Alignment explanation
Indices: 38078637--38078683 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
38078627 CTTTTTGACC
38078637 TAATTTCAAGTCCCTAGTCATTT
1 TAATTTCAAGTCCCTAGTCATTT
38078660 TAATTTCAAGTCCCTAGTCATTT
1 TAATTTCAAGTCCCTAGTCATTT
38078683 T
1 T
38078684 TCTTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (23 bp):
TAATTTCAAGTCCCTAGTCATTT
Found at i:38083966 original size:17 final size:18
Alignment explanation
Indices: 38083939--38083973 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
38083929 GATGTGAAAA
*
38083939 AATTATATATATTTTATT
1 AATTATATATATATTATT
38083957 AATT-TATATATATTATT
1 AATTATATATATATTATT
38083974 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTATATATATATTATT
Found at i:38084670 original size:19 final size:19
Alignment explanation
Indices: 38084646--38084693 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
38084636 AATAGTATTT
*
38084646 AAATTAAATTGAAATTGCG
1 AAATTAAATAGAAATTGCG
38084665 AAATTAAATAGAAATTGCG
1 AAATTAAATAGAAATTGCG
38084684 AAATTAAATA
1 AAATTAAATA
38084694 AATGACGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (19 bp):
AAATTAAATAGAAATTGCG
Found at i:38085488 original size:27 final size:26
Alignment explanation
Indices: 38085458--38085519 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
38085448 AGATAATTAA
38085458 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
38085485 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
38085512 AATAAAAT
1 AATAAAAT
38085520 GGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:38090867 original size:27 final size:26
Alignment explanation
Indices: 38090837--38090898 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
38090827 AGATAATTAA
38090837 AATAAAATCTTAAAATTAAATAATCCT
1 AATAAAATCTTAAAATT-AATAATCCT
* * *
38090864 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTTAAAATTAATAATCCT
38090891 AATAAAAT
1 AATAAAAT
38090899 GGAATCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.60
28 10 0.33
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAAAATCTTAAAATTAATAATCCT
Found at i:38092983 original size:28 final size:27
Alignment explanation
Indices: 38092946--38093042 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 27
38092936 AAAAATAGAA
38092946 GAAAA-CGAAAATAAGATATAATCCTT
1 GAAAATCGAAAATAAGATATAATCCTT
* * * ****
38092972 GATAAATTG-AAATATGA-AAAATAGAA
1 GA-AAATCGAAAATAAGATATAATCCTT
*
38092998 GAAAA-CAAAAATAAGATATAATCCTT
1 GAAAATCGAAAATAAGATATAATCCTT
38093024 GACAAATCGAAAATAAGAT
1 GA-AAATCGAAAATAAGAT
38093043 GGATGATGGA
Statistics
Matches: 49, Mismatches: 16, Indels: 10
0.65 0.21 0.13
Matches are distributed among these distances:
25 10 0.20
26 14 0.29
27 13 0.27
28 12 0.24
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.22
Consensus pattern (27 bp):
GAAAATCGAAAATAAGATATAATCCTT
Found at i:38092983 original size:52 final size:52
Alignment explanation
Indices: 38092905--38093035 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 52
38092895 ATCAACCATC
* * * *
38092905 TAAGAAATAATCATTGACACATTGAAAGATGAAAAATAGAAGAAAACGAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
* *
38092957 TAAGATATAATCCTTGATAAATTGAAATATGAAAAATAGAAGAAAACAAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
*
38093009 TAAGATATAATCCTTGACAAATCGAAA
1 TAAGATATAATCCTTGACAAATTGAAA
38093036 ATAAGATGGA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.21
Consensus pattern (52 bp):
TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
Found at i:38102817 original size:17 final size:18
Alignment explanation
Indices: 38102777--38102818 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
38102767 TATAAAATAC
*
38102777 AAATTATAAAAATATAAT
1 AAATAATAAAAATATAAT
* *
38102795 ATATAATAAAATTAT-AT
1 AAATAATAAAAATATAAT
38102812 AAATAAT
1 AAATAAT
38102819 TTAATATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAATAAAAATATAAT
Found at i:38102825 original size:29 final size:26
Alignment explanation
Indices: 38102765--38102816 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
38102755 CGTTAAAAAG
*
38102765 AATATAAAATACAAATTATAAAAATAT
1 AATATATAATA-AAATTATAAAAATAT
*
38102792 AATATATAATAAAATTATATAAATA
1 AATATATAATAAAATTATAAAAATA
38102817 ATTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATATATAATAAAATTATAAAAATAT
Found at i:38102835 original size:29 final size:28
Alignment explanation
Indices: 38102765--38102833 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
38102755 CGTTAAAAAG
*
38102765 AATATAAAATACAAA-T-TATAAAAATAT
1 AATATATAATA-AAATTATATAAAAATAT
*
38102792 AATATATAATAAAATTATATAAATAATTT
1 AATATATAATAAAATTATATAAA-AATAT
*
38102821 AATAT-TTATAAAA
1 AATATATAATAAAA
38102834 ATAATTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.08
27 11 0.31
28 13 0.36
29 9 0.25
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATATAATAAAATTATATAAAAATAT
Found at i:38115179 original size:27 final size:29
Alignment explanation
Indices: 38115144--38115198 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
38115134 TTATTACAGA
*
38115144 TAAATAATATTATAATTA-ATTATAAATT
1 TAAATAATATTATAATTATAATATAAATT
*
38115172 TAAA-AATATTTTAATTATAATATAAAT
1 TAAATAATATTATAATTATAATATAAAT
38115199 ATTATCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAATAATATTATAATTATAATATAAATT
Found at i:38115393 original size:2 final size:2
Alignment explanation
Indices: 38115386--38115422 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38115376 TAAATCTCAA
38115386 AT AT AT AT 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 AT AT AT AT A
38115423 AGATTTAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38115568 original size:27 final size:28
Alignment explanation
Indices: 38115512--38115565 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
38115502 TAAATTTTAA
* *
38115512 TTCAATTATATACATTTAAAAATAAAAT
1 TTCAATTATACACATTAAAAAATAAAAT
38115540 TTCAATTATACACATTAAAAAATAAA
1 TTCAATTATACACATTAAAAAATAAA
38115566 TTTATTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (28 bp):
TTCAATTATACACATTAAAAAATAAAAT
Found at i:38117406 original size:26 final size:28
Alignment explanation
Indices: 38117377--38117431 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
38117367 AAATATATTA
38117377 TGAACTT-AAAA-ATT-ATATATTAAATT
1 TGAACTTCAAAATATTAAT-TATTAAATT
38117403 TGAACTTCAAAATATTAATTATTAAATT
1 TGAACTTCAAAATATTAATTATTAAATT
38117431 T
1 T
38117432 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.27
27 4 0.15
28 13 0.50
29 2 0.08
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (28 bp):
TGAACTTCAAAATATTAATTATTAAATT
Found at i:38122740 original size:23 final size:23
Alignment explanation
Indices: 38122714--38122759 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
38122704 ACTATGTCCA
38122714 CAAATTAGGTTTAAATTATGATT
1 CAAATTAGGTTTAAATTATGATT
*
38122737 CAAATTAGGTTTAATTTATGATT
1 CAAATTAGGTTTAAATTATGATT
38122760 TGGCTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (23 bp):
CAAATTAGGTTTAAATTATGATT
Found at i:38122841 original size:41 final size:42
Alignment explanation
Indices: 38122792--38122881 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
38122782 TTTTTTTCAT
*
38122792 TTTGTTACTTA-AATTTTTTTTAGATTTAAAGTATTCATGTG
1 TTTGTTACTTACAATTTTTTTTAGATTTAAACTATTCATGTG
* * *
38122833 TTTGTTACTTACATTTTTTTTTGGATTTAACCTATTCATGTG
1 TTTGTTACTTACAATTTTTTTTAGATTTAAACTATTCATGTG
38122875 TTATGTT
1 TT-TGTT
38122882 TTGAGTCCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 11 0.26
42 28 0.65
43 4 0.09
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.58
Consensus pattern (42 bp):
TTTGTTACTTACAATTTTTTTTAGATTTAAACTATTCATGTG
Found at i:38123859 original size:15 final size:15
Alignment explanation
Indices: 38123839--38123888 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
38123829 AAAACAAACG
38123839 ATAAGATGAAAGAAA
1 ATAAGATGAAAGAAA
**
38123854 ATAAGA-GACAA-ATG
1 ATAAGATGA-AAGAAA
38123868 ATAAGATGAAAGAAA
1 ATAAGATGAAAGAAA
38123883 ATAAGA
1 ATAAGA
38123889 GACGAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.64, C:0.02, G:0.20, T:0.14
Consensus pattern (15 bp):
ATAAGATGAAAGAAA
Found at i:38123865 original size:29 final size:29
Alignment explanation
Indices: 38123832--38123891 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
38123822 TCATTCCAAA
38123832 ACAAACGATAAGATGAAAGAAAATAAGAG
1 ACAAACGATAAGATGAAAGAAAATAAGAG
*
38123861 ACAAATGATAAGATGAAAGAAAATAAGAG
1 ACAAACGATAAGATGAAAGAAAATAAGAG
38123890 AC
1 AC
38123892 GAGTTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.62, C:0.07, G:0.20, T:0.12
Consensus pattern (29 bp):
ACAAACGATAAGATGAAAGAAAATAAGAG
Found at i:38124052 original size:2 final size:2
Alignment explanation
Indices: 38124045--38124073 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38124035 AAAGAAAAAT
38124045 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 T
38124074 TTATTTTTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38124102 original size:16 final size:17
Alignment explanation
Indices: 38124076--38124113 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
38124066 ATATATATTT
38124076 ATTTTTCTATCCCTTCA
1 ATTTTTCTATCCCTTCA
**
38124093 ATTTTT-TATCTTTTCA
1 ATTTTTCTATCCCTTCA
38124109 ATTTT
1 ATTTT
38124114 CTTTCCACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTTCTATCCCTTCA
Found at i:38124354 original size:17 final size:17
Alignment explanation
Indices: 38124332--38124373 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
38124322 CAAATACCAA
38124332 TATATATTATAATTT-TT
1 TATATATT-TAATTTATT
38124349 TATATATTTAATTTATT
1 TATATATTTAATTTATT
38124366 TCATATAT
1 T-ATATAT
38124374 GTATTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 11 0.48
18 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTTAATTTATT
Found at i:38124462 original size:2 final size:2
Alignment explanation
Indices: 38124457--38124505 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38124447 TAATTTAAGG
38124457 TA TA TA 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
38124499 TA TA TA T
1 TA TA TA T
38124506 TTGATAAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38130027 original size:35 final size:35
Alignment explanation
Indices: 38129976--38130051 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
38129966 TATTGATATT
38129976 AGAATGGGTTTATCTATCAACTATAAAATGTTAAAA
1 AGAA-GGGTTTATCTATCAACTATAAAATGTTAAAA
*
38130012 AGAAGGGTTTATCTATCAGCTATAAAATGTTAAAA
1 AGAAGGGTTTATCTATCAACTATAAAATGTTAAAA
38130047 AGAAG
1 AGAAG
38130052 TGTAGGATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (35 bp):
AGAAGGGTTTATCTATCAACTATAAAATGTTAAAA
Found at i:38134649 original size:20 final size:20
Alignment explanation
Indices: 38134609--38134649 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38134599 CATGTCTGTA
* *
38134609 GGTATTGATATTGGCACTAG
1 GGTATTGATATTGACAATAG
*
38134629 GGTATTGATATTTACAATAG
1 GGTATTGATATTGACAATAG
38134649 G
1 G
38134650 TGGTATCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (20 bp):
GGTATTGATATTGACAATAG
Found at i:38135496 original size:2 final size:2
Alignment explanation
Indices: 38135485--38135533 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
38135475 AGGCATTTAT
* *
38135485 CA CA CA -A CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA TA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
38135526 CA CA CA CA
1 CA CA CA CA
38135534 TATAATACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.04
Consensus pattern (2 bp):
CA
Found at i:38144871 original size:42 final size:40
Alignment explanation
Indices: 38144788--38144932 Score: 116
Period size: 43 Copynumber: 3.5 Consensus size: 40
38144778 GTCCTGGACG
* * *
38144788 TGGTCTTACATGTAAT-TCAATGTCGATGCCTCTGTCTCAGACA
1 TGGTCTTACACG-AATATCAA--TCGATGCC-GTGTCCCAGACA
*
38144831 AGGTCTTACACGAA-ATCAGATACGATGCCGATGTCCCAGACA
1 TGGTCTTACACGAATATCA-AT-CGATGCCG-TGTCCCAGACA
* * *
38144873 TGGTCTTATACGTGAATCTCAATCGAGGCCTGTGTCCCAGACA
1 TGGTCTTACAC--GAATATCAATCGATGCC-GTGTCCCAGACA
38144916 TGGTCTTACACG-ATATC
1 TGGTCTTACACGAATATC
38144933 TTAGATAGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
40 4 0.05
41 2 0.02
42 31 0.37
43 38 0.45
44 6 0.07
45 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
TGGTCTTACACGAATATCAATCGATGCCGTGTCCCAGACA
Found at i:38147038 original size:13 final size:13
Alignment explanation
Indices: 38147020--38147053 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
38147010 TCGAATAAAG
38147020 GGCACACGGCCAA
1 GGCACACGGCCAA
38147033 GGCACACGGCCAA
1 GGCACACGGCCAA
38147046 GGCACACG
1 GGCACACG
38147054 CCCATGGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.38, G:0.32, T:0.00
Consensus pattern (13 bp):
GGCACACGGCCAA
Found at i:38148204 original size:48 final size:48
Alignment explanation
Indices: 38147988--38148355 Score: 244
Period size: 46 Copynumber: 7.8 Consensus size: 48
38147978 ATGCCGACGC
* *
38147988 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAT-AGCGAGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATATCA-TGAGGCCGATG
* * **
38148037 CCATGTCCCAGACATGTCTTACACTGGCTCTCATCT-ATCG-GTGTTGATG
1 -CATGTCCCAGACATGTCTTACACTAGCTCTCATATCAT-GAG-GCCGATG
* * * * * * *
38148086 CCATATCCCAGACAGGTCTTACACT-G-ACACACCA-CAT---GCTGACG
1 -CATGTCCCAGACATGTCTTACACTAGCTCTCA-TATCATGAGGCCGATG
* * *
38148130 CCATGTCCCAGACAGGTCTTACACTAGCT-TGTATATCACGAGGCCGATG
1 -CATGTCCCAGACATGTCTTACACTAGCTCT-CATATCATGAGGCCGATG
* * * *
38148179 CTTGTCCTAGACATGTCTTACACTAGCTCTCATCTCA--ATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATATCATGAGGCCGATG
* * * *
38148225 CATGTCCCAGACATGTCTTACACTGGCT-TAAATATCTTGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTCT-CATATCATGAGGCCGATG
* * * * * *
38148273 CATGTCCCAGACATGCCATACACTGGCTCTCATGT--TGTGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATATCATGAGGCCGATG
* * *
38148319 CATGTCCTAGACATGTCTTACACTAGCACACATATCA
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATATCA
38148356 CCTATTGTCA
Statistics
Matches: 252, Mismatches: 48, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
44 29 0.12
45 3 0.01
46 76 0.30
47 3 0.01
48 70 0.28
49 57 0.23
50 14 0.06
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATATCATGAGGCCGATG
Found at i:38148238 original size:46 final size:47
Alignment explanation
Indices: 38147978--38148342 Score: 230
Period size: 48 Copynumber: 7.7 Consensus size: 47
38147968 ATAGGTTAAG
* * *
38147978 ATGCCGACGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAGCG
1 ATGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATCT--CA
* *
38148028 AGGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTATCG
1 ATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATC--TCA
* ** * * * *
38148077 GTGTTGATGCCATATCCCAGACAGGTCTTACACT-G-ACACA-C-CA
1 ATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
* * * * * *
38148120 CATGCTGACGCCATGTCCCAGACAGGTCTTACACTAGCT-TGTATATCA
1 -ATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCA
* * * *
38148168 CGAGGCCGATG-CTTGTCCTAGACATGTCTTACACTAGCTCTCATCTCA
1 --ATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
* **
38148216 ATGCCGATG-CATGTCCCAGACATGTCTTACACTGGCT-TAAATATCTTG
1 ATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCT---CATCTCA
* * * * * *
38148264 AGGCCAATG-CATGTCCCAGACATGCCATACACTGGCTCTCATGT-T
1 ATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
* * *
38148309 GTGGCTGATG-CATGTCCTAGACATGTCTTACACT
1 AT-GCCGATGCCATGTCCCAGACATGTCTTACACT
38148343 AGCACACATA
Statistics
Matches: 250, Mismatches: 50, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.00
44 30 0.12
45 2 0.01
46 64 0.26
47 3 0.01
48 70 0.28
49 57 0.23
50 22 0.09
51 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
ATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
Found at i:38148354 original size:94 final size:94
Alignment explanation
Indices: 38148131--38148345 Score: 261
Period size: 94 Copynumber: 2.3 Consensus size: 94
38148121 ATGCTGACGC
* ** * * * *
38148131 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCACGAGGCCGATGCTTGTCCTAGACATGTC
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAGGCCAATGCATGTCCCAGACATGCC
*
38148196 TTACACTAGCTCTCATCTCAATGCCGATG
66 ATACACTAGCTCTCATCTCAATGCCGATG
* **
38148225 CATGTCCCAGACATGTCTTACACTGGCTTAAATATCTTGAGGCCAATGCATGTCCCAGACATGCC
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAGGCCAATGCATGTCCCAGACATGCC
* * ** *
38148290 ATACACTGGCTCTCATGT-TGTGGCTGATG
66 ATACACTAGCTCTCATCTCAAT-GCCGATG
*
38148319 CATGTCCTAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
38148346 ACACATATCA
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
93 1 0.01
94 101 0.99
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAGGCCAATGCATGTCCCAGACATGCC
ATACACTAGCTCTCATCTCAATGCCGATG
Found at i:38156797 original size:119 final size:119
Alignment explanation
Indices: 38156567--38156804 Score: 309
Period size: 119 Copynumber: 2.0 Consensus size: 119
38156557 GGTTAGCAAC
* * * * *
38156567 ATTGGCTAACTCAACCAAAAGACTAAGGATGGCTAGAGGAGGGAATGAAGAGAGTGATGGATGGT
1 ATTGGCGAACTCAACCAAAAGACTAAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGATGGT
* *
38156632 CAAGCGTGGGGAGTGTGGTATTGGGCACAAAATAAGGAATAGAAATTTCATCCT
66 CAAGCGAGGGGAGTGTGGTATTGGGCACAAAATAAGGAACAGAAATTTCATCCT
* * *
38156686 ATTGGCGAACTCAACTAGAAGACTGAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGA-GAG
1 ATTGGCGAACTCAACCAAAAGACTAAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGATG-G
* * ** *
38156750 TCAAGTGAGGGGATTGTGGTATTGGGCACAATCTGAA-GAACATAAATTTCATCCT
65 TCAAGCGAGGGGAGTGTGGTATTGGGCACAAAAT-AAGGAACAGAAATTTCATCCT
38156805 CTAGATGGAT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
118 1 0.01
119 99 0.97
120 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (119 bp):
ATTGGCGAACTCAACCAAAAGACTAAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGATGGT
CAAGCGAGGGGAGTGTGGTATTGGGCACAAAATAAGGAACAGAAATTTCATCCT
Found at i:38160716 original size:30 final size:32
Alignment explanation
Indices: 38160645--38160730 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 32
38160635 ATATAAGGAG
* *
38160645 AACAGCTACAAAGGCTTCCACATTTAACATAT
1 AACAACTACAAAGGCTTCCACATATAACATAT
** *
38160677 TTC-ACTACAAGGGC-T-CACATATAACATAT
1 AACAACTACAAAGGCTTCCACATATAACATAT
38160706 AACAACTACAAAGGCTTCCACATAT
1 AACAACTACAAAGGCTTCCACATAT
38160731 TAGAGAACGA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
29 14 0.33
30 11 0.26
31 10 0.23
32 8 0.19
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (32 bp):
AACAACTACAAAGGCTTCCACATATAACATAT
Found at i:38165822 original size:42 final size:43
Alignment explanation
Indices: 38165774--38165880 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
38165764 GTTGAGATTA
*
38165774 CGTGTAAGACCATATCTGGGATA-TGGAATCGATACGAGA-CTT
1 CGTGTAAGACCATATCTGGGATATTGGAATCGATACGAGATC-C
* * * * * *
38165816 TGTGTAAGATCATAGCTGGGCTATTGGCATCGATATGAGATCC
1 CGTGTAAGACCATATCTGGGATATTGGAATCGATACGAGATCC
*
38165859 CATGTAAGACCATATCTGGGAT
1 CGTGTAAGACCATATCTGGGAT
38165881 GTGGCATAGG
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 19 0.37
43 31 0.61
44 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCATATCTGGGATATTGGAATCGATACGAGATCC
Found at i:38169252 original size:14 final size:15
Alignment explanation
Indices: 38169223--38169252 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38169213 AATCATTTTC
38169223 ATGTTATTTATTAAT
1 ATGTTATTTATTAAT
38169238 ATGTTATTT-TTAAT
1 ATGTTATTTATTAAT
38169252 A
1 A
38169253 ATATAGTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
ATGTTATTTATTAAT
Found at i:38170346 original size:41 final size:41
Alignment explanation
Indices: 38170232--38170628 Score: 438
Period size: 41 Copynumber: 9.7 Consensus size: 41
38170222 ACTTAATTAT
* * *
38170232 CCCCTAAATTGCACATACATGGCCTTGTTTGTACTTCGGTA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* *
38170273 CCTCCAAAATTGCACATACGTGCCCCTATTTGTACTTCGGTA
1 CC-CCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* * * *
38170315 CCCCTGAATTACACATACGTGCCCTTGTTTGTACTTCGATA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* * * * * * *
38170356 -CCTTGAATTTCACATATGTTCCCCTATTTGCACTTCGGTA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* * *
38170396 CCCCTGAATTGCACATACATGCCCTTGTTTGTACTTCGGTA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* * * * * *
38170437 CCCCTAGATGGCACATACGTACCCCTATTTATAATTCGGTA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* * *
38170478 CCCCTAAATTGCATATACGTGCCCCAGTTTGTACTTTGGTA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
*
38170519 CCCCTAAATTGCACATACGTACCCCTGTTTGTACTTCGGTA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* * * *
38170560 CCCTTAAATTGTACATATGTGCCCCTGTTTGTACTTTGGTA
1 CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
* * * *
38170601 CCCTTGAATAGCACCTACGTG-CCCTGTT
1 CCCCTAAATTGCACATACGTGCCCCTGTT
38170629 AACACTCCGA
Statistics
Matches: 295, Mismatches: 59, Indels: 5
0.82 0.16 0.01
Matches are distributed among these distances:
40 39 0.13
41 220 0.75
42 36 0.12
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.34
Consensus pattern (41 bp):
CCCCTAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
Found at i:38170540 original size:21 final size:21
Alignment explanation
Indices: 38170434--38170544 Score: 66
Period size: 21 Copynumber: 5.4 Consensus size: 21
38170424 TTGTACTTCG
* *
38170434 GTACCCCTAGATGGCACATAC
1 GTACCCCTAAATTGCACATAC
* ** *
38170455 GTACCCCT-ATTTATA-ATTC
1 GTACCCCTAAATTGCACATAC
*
38170474 GGTACCCCTAAATTGCATATAC
1 -GTACCCCTAAATTGCACATAC
* ** * * **
38170496 GTGCCCC-AGTTTGTACTTTG
1 GTACCCCTAAATTGCACATAC
38170516 GTACCCCTAAATTGCACATAC
1 GTACCCCTAAATTGCACATAC
38170537 GTACCCCT
1 GTACCCCT
38170545 GTTTGTACTT
Statistics
Matches: 61, Mismatches: 25, Indels: 8
0.65 0.27 0.09
Matches are distributed among these distances:
19 3 0.05
20 22 0.36
21 33 0.54
22 3 0.05
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.30
Consensus pattern (21 bp):
GTACCCCTAAATTGCACATAC
Found at i:38170562 original size:20 final size:20
Alignment explanation
Indices: 38170499--38170603 Score: 57
Period size: 20 Copynumber: 5.2 Consensus size: 20
38170489 CATATACGTG
* *
38170499 CCCCAGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTAGGTA
** * * *
38170519 CCCCTAAATTGCACATACGTA
1 CCCCT-GTTTGTACTTAGGTA
*
38170540 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTAGGTA
* ** * * *
38170560 CCCTTAAATTGTACATATGTG
1 CCCCT-GTTTGTACTTAGGTA
*
38170581 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTAGGTA
38170601 CCC
1 CCC
38170604 TTGAATAGCA
Statistics
Matches: 56, Mismatches: 27, Indels: 4
0.64 0.31 0.05
Matches are distributed among these distances:
20 29 0.52
21 27 0.48
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (20 bp):
CCCCTGTTTGTACTTAGGTA
Found at i:38175119 original size:42 final size:42
Alignment explanation
Indices: 38175032--38175184 Score: 155
Period size: 42 Copynumber: 3.6 Consensus size: 42
38175022 AGATGCCAAT
* * * *
38175032 CCATGTCCCAGACATGGTCTTACATGCGATT-TCACATCGATG
1 CCATATCCCAGACATGGTCTTACATG-AATTCTCATATCGACG
* * *
38175074 CCATATCCCAGATATGGTCTTATATGAATTCTCATTTCGACG
1 CCATATCCCAGACATGGTCTTACATGAATTCTCATATCGACG
* * * * *
38175116 CCATGTCCTAGACATGGTCTTACACGAAATCTCATATCAACG
1 CCATATCCCAGACATGGTCTTACATGAATTCTCATATCGACG
* * *
38175158 CTATATCCCGGATATGGTCTTACATGA
1 CCATATCCCAGACATGGTCTTACATGA
38175185 TAACTCATAT
Statistics
Matches: 89, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 3 0.03
42 86 0.97
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (42 bp):
CCATATCCCAGACATGGTCTTACATGAATTCTCATATCGACG
Found at i:38175192 original size:84 final size:84
Alignment explanation
Indices: 38175032--38175192 Score: 198
Period size: 84 Copynumber: 1.9 Consensus size: 84
38175022 AGATGCCAAT
* ** * * * *
38175032 CCATGTCCCAGACATGGTCTTACATGCGATTTCACATCGATGCCATATCCCAGATATGGTCTTAT
1 CCATGTCCCAGACATGGTCTTACACGAAATCTCACATCAACGCCATATCCCAGATATGGTCTTAC
*
38175097 ATGAATTCTCATTTCGACG
66 ATGAATACTCATTTCGACG
* * * *
38175116 CCATGTCCTAGACATGGTCTTACACGAAATCTCATATCAACGCTATATCCCGGATATGGTCTTAC
1 CCATGTCCCAGACATGGTCTTACACGAAATCTCACATCAACGCCATATCCCAGATATGGTCTTAC
38175181 ATG-ATAACTCAT
66 ATGAAT-ACTCAT
38175193 ATTGATGTCG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
83 2 0.03
84 62 0.97
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (84 bp):
CCATGTCCCAGACATGGTCTTACACGAAATCTCACATCAACGCCATATCCCAGATATGGTCTTAC
ATGAATACTCATTTCGACG
Found at i:38179066 original size:68 final size:67
Alignment explanation
Indices: 38178994--38179143 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
38178984 CATCATGTGT
* * * *
38178994 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
38179056 ATGTAG
62 ATGTAG
** * *
38179062 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
38179127 AG
66 AG
38179129 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
38179144 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:38179099 original size:64 final size:64
Alignment explanation
Indices: 38179018--38179201 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
38179008 AGACATTATG
* *
38179018 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
38179082 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
38179147 AA
63 AA
* * * *
38179149 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
38179202 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:38180291 original size:2 final size:2
Alignment explanation
Indices: 38180284--38180314 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38180274 TCATGACATG
38180284 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38180315 GACTAGTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38184006 original size:40 final size:40
Alignment explanation
Indices: 38183961--38184127 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
38183951 CGGAATATAA
*
38183961 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
38184001 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
38184041 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
38184081 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38184120 CCGGATAT
1 CCGGATAT
38184128 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38189702 original size:40 final size:40
Alignment explanation
Indices: 38189657--38189822 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
38189647 CGGAATATAA
*
38189657 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
38189697 CCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
38189736 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
38189776 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38189815 CCGGATAT
1 CCGGATAT
38189823 CATTCAATTT
Statistics
Matches: 103, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
39 46 0.45
40 57 0.55
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38189742 original size:39 final size:39
Alignment explanation
Indices: 38189673--38189782 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 39
38189663 TTAATCACGT
* *
38189673 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAACAACTA
* * *
38189713 GCACGAATGCCTTCGGG-CTTAGCCCGGATATAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAACAACTA
*
38189752 GCACAATTGCCTTCGGGTCTTAACCCGGATA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATA
38189783 TAATTTCCAG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
38 2 0.03
39 31 0.51
40 28 0.46
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAACAACTA
Found at i:38195656 original size:55 final size:55
Alignment explanation
Indices: 38195572--38195714 Score: 135
Period size: 55 Copynumber: 2.6 Consensus size: 55
38195562 TGCAACATGG
* * * * * ** *
38195572 CCGTGGGCGAACCGACCAAAATAGCACGGGCGTACGACACGT-ACGTGCCTTGAAC
1 CCGTGGCCGAACCTATCAAATTAACACGGGCGTACGACAC-TCACGTGCCAAGAAA
* * * * *
38195627 CCGTGGCTGAACCTGTCAAATTAACACGGGCATGCGACACTCCCGTGCCAAGAAA
1 CCGTGGCCGAACCTATCAAATTAACACGGGCGTACGACACTCACGTGCCAAGAAA
* *
38195682 CCGTGGCCGAACCTATTAAATTAACATGGGCGT
1 CCGTGGCCGAACCTATCAAATTAACACGGGCGT
38195715 GGGCCTACAT
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
54 1 0.01
55 68 0.99
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (55 bp):
CCGTGGCCGAACCTATCAAATTAACACGGGCGTACGACACTCACGTGCCAAGAAA
Found at i:38198295 original size:36 final size:36
Alignment explanation
Indices: 38198255--38198329 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
38198245 TTCTTCTGAG
38198255 ATATTTTCCTTTTTAGTTATGAGCTAAATCCCCTAA
1 ATATTTTCCTTTTTAGTTATGAGCTAAATCCCCTAA
38198291 ATATTTTCCTTTTTAGTTATGAGCTAAATCCCCTAA
1 ATATTTTCCTTTTTAGTTATGAGCTAAATCCCCTAA
38198327 ATA
1 ATA
38198330 CTAAAGGGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (36 bp):
ATATTTTCCTTTTTAGTTATGAGCTAAATCCCCTAA
Found at i:38200241 original size:17 final size:18
Alignment explanation
Indices: 38200213--38200247 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
38200203 GGGCCAAATT
38200213 GGGCTGTGTGGGCCCCAC
1 GGGCTGTGTGGGCCCCAC
38200231 GGGCT-TGTGGGCCCCAC
1 GGGCTGTGTGGGCCCCAC
38200248 ACAGGTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.06, C:0.34, G:0.43, T:0.17
Consensus pattern (18 bp):
GGGCTGTGTGGGCCCCAC
Found at i:38200471 original size:27 final size:27
Alignment explanation
Indices: 38200431--38200492 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
38200421 TACCAAGACC
*
38200431 CCCTATATAGGGTAAAATGACTATTTTT
1 CCCT-TATAGGGTAAAATGACTATTTTA
* * *
38200459 CCCTTATATGGTAAGATGACTGTTTTA
1 CCCTTATAGGGTAAAATGACTATTTTA
38200486 CCCTTAT
1 CCCTTAT
38200493 GTGATGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (27 bp):
CCCTTATAGGGTAAAATGACTATTTTA
Found at i:38201173 original size:13 final size:13
Alignment explanation
Indices: 38201155--38201179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38201145 TAATAAGGCC
38201155 TCTTTGGATTTTA
1 TCTTTGGATTTTA
38201168 TCTTTGGATTTT
1 TCTTTGGATTTT
38201180 TAATTGCTTT
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:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (13 bp):
TCTTTGGATTTTA
Found at i:38201195 original size:16 final size:17
Alignment explanation
Indices: 38201169--38201203 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38201159 TGGATTTTAT
*
38201169 CTTTGGATTTTTAATTG
1 CTTTGGATTTTTAACTG
38201186 CTTT-GATTTTTAACTG
1 CTTTGGATTTTTAACTG
38201202 CT
1 CT
38201204 AGCAGTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.57
Consensus pattern (17 bp):
CTTTGGATTTTTAACTG
Found at i:38207925 original size:48 final size:49
Alignment explanation
Indices: 38207819--38208080 Score: 174
Period size: 48 Copynumber: 5.5 Consensus size: 49
38207809 AGATGCTGAA
38207819 GCCATGTCCCAGACATGGTCTTACACTGGCTTCCATATAGTAAGGCCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTTCCATATAGTAAGGCCGAT
* * * *
38207869 GCCATGTCCCATACAGGTCTTACACTGG-TTCTCATCTA-T-GGTGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTTC-CATATAGTAAG-GCCGAT
* * * * *
38207917 GCCATGTCCCAGACAGGTCTTACACTGAC--ACACA-A-CAA-GCCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTTCCATATAGTAAGGCCGAT
* * ** * * *
38207961 ACCATGTCCCAGACAGGTCTTACACTAGCTTGTATATCGTGAA-GACGGT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTTCCATATAGT-AAGGCCGAT
* * * ** *
38208010 G-CATGTCCCAGACATGTCTTACACTAGC-TCTCTTACGGT--GGCTGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTTC-CATATAGTAAGGCCGAT
*
38208056 G-CATGTCCCAGACATGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
38208081 AGAACACACA
Statistics
Matches: 167, Mismatches: 34, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
44 30 0.18
45 1 0.01
46 32 0.19
47 2 0.01
48 65 0.39
49 23 0.14
50 14 0.08
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTTCCATATAGTAAGGCCGAT
Found at i:38208076 original size:138 final size:144
Alignment explanation
Indices: 38207820--38208090 Score: 351
Period size: 140 Copynumber: 1.9 Consensus size: 144
38207810 GATGCTGAAG
* * *
38207820 CCATGTCCCAGACATGGTCTTACACTGGCTTCCATATAGTAAGGCCGATGCCATGTCCCATACAG
1 CCATGTCCCAGACATGGTCTTACACTAGCTTCCATATAGTAAGGACGATGCCATGTCCCAGACAG
* * * *
38207885 GTCTTACACTGGTTCTCATCTATGGTGTCGATGCCATGTCCCAGACAGGTCTTACACT-G-ACAC
66 GTCTTACACTAGCTCTCATCTACGGTGGCGATGCCATGTCCCAGACAGGTCTTACACTAGAACAC
38207948 ACAACAAGCCAATA
131 ACAACAAGCCAATA
** * *
38207962 CCATGTCCCAGACA-GGTCTTACACTAGCTTGTATATCGTGAA-GACGGTG-CATGTCCCAGACA
1 CCATGTCCCAGACATGGTCTTACACTAGCTTCCATATAGT-AAGGACGATGCCATGTCCCAGACA
* *
38208024 TGTCTTACACTAGCTCTC-T-TACGGTGGCTGATG-CATGTCCCAGACATGTCTTACACTAGAAC
65 GGTCTTACACTAGCTCTCATCTACGGTGGC-GATGCCATGTCCCAGACAGGTCTTACACTAGAAC
38208086 ACACA
129 ACACA
38208091 TCACCCATTA
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
138 30 0.27
139 6 0.05
140 34 0.30
141 26 0.23
142 16 0.14
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (144 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTTCCATATAGTAAGGACGATGCCATGTCCCAGACAG
GTCTTACACTAGCTCTCATCTACGGTGGCGATGCCATGTCCCAGACAGGTCTTACACTAGAACAC
ACAACAAGCCAATA
Found at i:38209339 original size:22 final size:22
Alignment explanation
Indices: 38209309--38209363 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
38209299 GTCCCAAGGT
38209309 CACACGGGCGTGTCCCTTGGAC
1 CACACGGGCGTGTCCCTTGGAC
*
38209331 CACATGGGCGTGTCCCTTGGAC
1 CACACGGGCGTGTCCCTTGGAC
*
38209353 CACCCGGGCGT
1 CACACGGGCGT
38209364 TTGACCCCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.13, C:0.36, G:0.33, T:0.18
Consensus pattern (22 bp):
CACACGGGCGTGTCCCTTGGAC
Found at i:38214669 original size:58 final size:59
Alignment explanation
Indices: 38214568--38214758 Score: 312
Period size: 58 Copynumber: 3.2 Consensus size: 59
38214558 GACAAGATTG
* * * * * *
38214568 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
38214628 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
38214686 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
38214745 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38214759 GATTCACTAT
Statistics
Matches: 124, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
58 55 0.44
59 54 0.44
60 15 0.12
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (59 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:38214728 original size:88 final size:87
Alignment explanation
Indices: 38214598--38214758 Score: 304
Period size: 88 Copynumber: 1.8 Consensus size: 87
38214588 AAAATTGTAC
38214598 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTA
1 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTA
38214663 AGTGTGCGAGCTGAAAATATAT
66 AGTGTGCGAGCTGAAAATATAT
*
38214685 AGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT
1 AGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT
38214750 AAGTGTGCG
65 AAGTGTGCG
38214759 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
87 23 0.32
88 49 0.68
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (87 bp):
AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACTA
AGTGTGCGAGCTGAAAATATAT
Found at i:38214770 original size:29 final size:29
Alignment explanation
Indices: 38214598--38214758 Score: 304
Period size: 29 Copynumber: 5.5 Consensus size: 29
38214588 AAAATTGTAC
*
38214598 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
38214627 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
38214656 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
38214685 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
38214715 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
38214744 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
38214759 GATTCACTAT
Statistics
Matches: 130, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
29 101 0.78
30 29 0.22
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:38216272 original size:48 final size:48
Alignment explanation
Indices: 38216172--38216393 Score: 182
Period size: 48 Copynumber: 4.6 Consensus size: 48
38216162 TCTCAATGCT
* * ***
38216172 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCTTATAAT-ATGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCA-AATCATGACC
* *
38216220 GATGCCATGTCCCAGACATGGTCTTACACTAGCGCACAAATCAAT-ACC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATC-ATGACC
** * * *
38216268 GATGCCATGTAACAGACATGGTCTTACACTGGCTCTC-ATTACATTACC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAAT-CATGACC
** * * * * * * *
38216316 GATTTCATGTTCCAAACATGGTCTTACACTGGCCCTCATATCCTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATCATGACC
*
38216364 GATGCCATATCCCA-ATCATGGTCTTACACT
1 GATGCCATGTCCCAGA-CATGGTCTTACACT
38216394 GGTATACATA
Statistics
Matches: 140, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
47 8 0.06
48 129 0.92
49 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATCATGACC
Found at i:38220740 original size:42 final size:42
Alignment explanation
Indices: 38220689--38220786 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
38220679 ATAGCCCATC
38220689 TATGGTCTTACACAAAATCTCAT-ATCGATGCCATATCCCAGA
1 TATGGTCTTACACAAAATCTCATAAT-GATGCCATATCCCAGA
* * *
38220731 TATGGTCTTACACGAAGTCTCATAATGATGTCATATCCCAGA
1 TATGGTCTTACACAAAATCTCATAATGATGCCATATCCCAGA
38220773 TATGGTCTTACACA
1 TATGGTCTTACACA
38220787 TAGCCTCGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (42 bp):
TATGGTCTTACACAAAATCTCATAATGATGCCATATCCCAGA
Found at i:38222654 original size:42 final size:42
Alignment explanation
Indices: 38222537--38222668 Score: 151
Period size: 42 Copynumber: 3.1 Consensus size: 42
38222527 ACACCAATGT
* * *
38222537 CATATCCCATATATGGTCTTACATG-GGATCTCGTATCGATGC
1 CATATCCCAGATATGGTCTTACATGAAG-TCTCATATCGATGC
* * * *
38222579 CAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCGATGC
1 C-ATATCCCAGATATGGTCTTACATGAAGTCTCATATCGATGC
*
38222622 CATATCCAAGATATGGTCTTACATGAAGTCTCATAAT-GATGC
1 CATATCCCAGATATGGTCTTACATGAAGTCTCAT-ATCGATGC
38222664 CATAT
1 CATAT
38222669 ACCCTAATGT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 39 0.52
43 36 0.48
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (42 bp):
CATATCCCAGATATGGTCTTACATGAAGTCTCATATCGATGC
Found at i:38224036 original size:119 final size:119
Alignment explanation
Indices: 38223856--38224075 Score: 431
Period size: 119 Copynumber: 1.8 Consensus size: 119
38223846 GTTACAACTG
38223856 TAACACCCCGTACCCGAGTCCGTTACCAGAATCGGACACAAGGTGCACACAGACTTAACTATTTT
1 TAACACCCCGTACCCGAGTCCGTTACCAGAATCGGACACAAGGTGCACACAGACTTAACTATTTT
38223921 CACAGTCCATTTAGAAATTTCCAGACTAGCTGGTCAGTGCGTCAAATAAAATTT
66 CACAGTCCATTTAGAAATTTCCAGACTAGCTGGTCAGTGCGTCAAATAAAATTT
*
38223975 TAACACCCCGTACCCGAGTCCGTTACCGGAATCGGACACAAGGTGCACACAGACTTAACTATTTT
1 TAACACCCCGTACCCGAGTCCGTTACCAGAATCGGACACAAGGTGCACACAGACTTAACTATTTT
38224040 CACAGTCCATTTAGAAATTTCCAGACTAGCTGGTCA
66 CACAGTCCATTTAGAAATTTCCAGACTAGCTGGTCA
38224076 CTGTGTCACT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 100 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (119 bp):
TAACACCCCGTACCCGAGTCCGTTACCAGAATCGGACACAAGGTGCACACAGACTTAACTATTTT
CACAGTCCATTTAGAAATTTCCAGACTAGCTGGTCAGTGCGTCAAATAAAATTT
Found at i:38225445 original size:79 final size:81
Alignment explanation
Indices: 38225344--38225528 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
38225334 ACGACTCGCT
** * *
38225344 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
38225407 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
38225424 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
38225488 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
38225504 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38225529 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:38225528 original size:40 final size:39
Alignment explanation
Indices: 38225337--38225528 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
38225327 GGATATAACG
* ** * *
38225337 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
38225377 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
38225417 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
38225456 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
38225496 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
38225529 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:38233585 original size:39 final size:39
Alignment explanation
Indices: 38233493--38233683 Score: 179
Period size: 39 Copynumber: 4.8 Consensus size: 39
38233483 GGATATAACG
* ** *
38233493 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGTG
1 ACTCGCACAAATGCCTTC-GGACTTAGCCCGGATT-TAGTA
* * *
38233533 ACTCGCACGAATGCCTTCGGACTTAACCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCCGGATTTAGTA
* * *
38233572 ACTTGCACAAATGCCTTCGGGCTTAGCCCGGATTTATTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCCGGATTTAGTA
* * * * *
38233611 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGA-CTTAGCCCGGATTTAGTA
*
38233651 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTC-GGACTTAGCCCGGA
38233684 CATCATTCGA
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
39 65 0.53
40 48 0.39
41 10 0.08
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGACTTAGCCCGGATTTAGTA
Found at i:38233592 original size:79 final size:81
Alignment explanation
Indices: 38233500--38233683 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 81
38233490 ACGACTCGCT
** * *
38233500 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTCGGATCCTAACCCG
* *
38233563 GGTTTAGTAACTT-GCA
65 GATATAGTAACTTAGCA
* **
38233579 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
38233643 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
38233659 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38233684 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
78 32 0.35
79 41 0.45
80 18 0.20
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:38243916 original size:40 final size:40
Alignment explanation
Indices: 38243857--38244025 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
38243847 CGGGACTTTA
* * *
38243857 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
38243897 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
38243937 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
38243977 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
38244017 CCCGGATAT
1 CCCGGATAT
38244026 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:38251909 original size:40 final size:40
Alignment explanation
Indices: 38251850--38252018 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
38251840 CGGGACTTTA
* * *
38251850 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
38251890 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
38251930 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
38251970 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
38252010 CCCGGATAT
1 CCCGGATAT
38252019 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:38257564 original size:28 final size:29
Alignment explanation
Indices: 38257523--38257578 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
38257513 CCGAGTTTTT
*
38257523 GGACACGGGTGTGT-CTAGGCCGTGTGAG
1 GGACACGGGCGTGTGCTAGGCCGTGTGAG
* *
38257551 GGACACTGGCGTGTGCTTGGCCGTGTGA
1 GGACACGGGCGTGTGCTAGGCCGTGTGA
38257579 AAACCCCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.12, C:0.20, G:0.45, T:0.23
Consensus pattern (29 bp):
GGACACGGGCGTGTGCTAGGCCGTGTGAG
Found at i:38257578 original size:29 final size:28
Alignment explanation
Indices: 38257523--38257578 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
38257513 CCGAGTTTTT
38257523 GGACACGGGTGTGTCTAGGCCGTGTGAG
1 GGACACGGGTGTGTCTAGGCCGTGTGAG
*
38257551 GGACACTGGCGTGTG-CTTGGCCGTGTGA
1 GGACAC-GG-GTGTGTCTAGGCCGTGTGA
38257579 AAACCCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 14 0.56
30 5 0.20
ACGTcount: A:0.12, C:0.20, G:0.45, T:0.23
Consensus pattern (28 bp):
GGACACGGGTGTGTCTAGGCCGTGTGAG
Found at i:38260983 original size:13 final size:13
Alignment explanation
Indices: 38260961--38260993 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
38260951 AAGGGTTTGT
38260961 TTAT-TAAACTAA
1 TTATCTAAACTAA
38260973 TTATCTAAACTAA
1 TTATCTAAACTAA
*
38260986 TTAACTAA
1 TTATCTAA
38260994 TTTAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:38264968 original size:14 final size:14
Alignment explanation
Indices: 38264951--38264981 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38264941 ATGTTTTATA
38264951 TTATAATATAACAT
1 TTATAATATAACAT
*
38264965 TTATAATATAATAT
1 TTATAATATAACAT
38264979 TTA
1 TTA
38264982 ATTTACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAATATAACAT
Found at i:38268399 original size:40 final size:40
Alignment explanation
Indices: 38268354--38268521 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
38268344 CGGAATATAA
*
38268354 CCGGATATAAGCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAAGCACT-AGCACAAATGCCTTCGGGTCTTAGC
* * *
38268394 CCGGATAGAATG-ACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-GCACTAGCACAAATGCCTTCGGGTCTTAGC
* *
38268434 CCGGATAT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAAG-CACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
38268474 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAAGCACTAGCACAAATGCCTTCGGGTCTTAGC
38268514 CCGGATAT
1 CCGGATAT
38268522 CATTCAATTT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 102 0.95
41 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAAGCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38268504 original size:80 final size:80
Alignment explanation
Indices: 38268370--38268521 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
38268360 ATAAGCATGT
* *
38268370 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
38268435 CGGATATAGCCACTA
66 CGGATATAGCCACTA
* * ** * *
38268450 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
38268513 CCCGGATAT
64 CCCGGATAT
38268522 CATTCAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.05
80 59 0.95
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATATAGCCACTA
Found at i:38270501 original size:6 final size:6
Alignment explanation
Indices: 38270490--38270571 Score: 69
Period size: 6 Copynumber: 13.7 Consensus size: 6
38270480 AAGAAAATTG
* * * * *
38270490 AAAAAT AAAAAT CAAAAG GAAAAT AAGAAT AAAATAA ATAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT
* *
38270540 AAAAAT AAGAAT --AAAT AACAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
38270572 TAGGAGGATT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
4 3 0.05
6 49 0.83
7 4 0.07
8 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:38270545 original size:32 final size:34
Alignment explanation
Indices: 38270475--38270571 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 34
38270465 TATGTCTTTC
* * * **
38270475 AAAATAAGAA-AATTGAAAAATAAAAATCAAAAGG
1 AAAATAAGAATAAAT-AACAATAAAAATAAAAATA
38270509 AAAATAAGAATAAA-ATA-AAT-AAAATAAAAATA
1 AAAATAAGAATAAATA-ACAATAAAAATAAAAATA
38270541 AAAATAAGAATAAATAACAATAAAAATAAAA
1 AAAATAAGAATAAATAACAATAAAAATAAAA
38270572 TAGGAGGATT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
32 24 0.44
33 8 0.15
34 20 0.37
35 2 0.04
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.16
Consensus pattern (34 bp):
AAAATAAGAATAAATAACAATAAAAATAAAAATA
Found at i:38270557 original size:10 final size:9
Alignment explanation
Indices: 38270517--38270564 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
38270507 GGAAAATAAG
38270517 AATAAAATA
1 AATAAAATA
38270526 AATAAAATA
1 AATAAAATA
38270535 AA-AATAA-A
1 AATAA-AATA
38270543 AATAAGAATA
1 AATAA-AATA
38270553 AATAACAATA
1 AATAA-AATA
38270563 AA
1 AA
38270565 AATAAAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 5 0.15
9 17 0.50
10 12 0.35
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:38270557 original size:16 final size:16
Alignment explanation
Indices: 38270509--38270570 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
38270499 AATCAAAAGG
38270509 AAAATAAGAATAAA-A
1 AAAATAAGAATAAATA
*
38270524 TAAATAA-AATAAAAATA
1 AAAATAAGAAT--AAATA
38270541 AAAATAAGAATAAATA
1 AAAATAAGAATAAATA
* *
38270557 ACAATAAAAATAAA
1 AAAATAAGAATAAA
38270571 ATAGGAGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.08
15 6 0.15
16 20 0.51
17 7 0.18
18 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAATAAGAATAAATA
Found at i:38270572 original size:27 final size:25
Alignment explanation
Indices: 38270509--38270573 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 25
38270499 AATCAAAAGG
38270509 AAAATAAGAATAAAATAAATAAAATA
1 AAAATAA-AATAAAATAAATAAAATA
38270535 AAAATAAAAATAAGAATAAATAACAATA
1 AAAAT-AAAATAA-AATAAATAA-AATA
38270563 AAAATAAAATA
1 AAAATAAAATA
38270574 GGAGGATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.28
27 17 0.47
28 9 0.25
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (25 bp):
AAAATAAAATAAAATAAATAAAATA
Found at i:38272520 original size:21 final size:21
Alignment explanation
Indices: 38272494--38272534 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38272484 CCCTTCTCCT
* *
38272494 ACGCCCGTGTGTTGTGGTACC
1 ACGCCCATGTATTGTGGTACC
*
38272515 ACGCCCATGTATTGTTGTAC
1 ACGCCCATGTATTGTGGTAC
38272535 ACGGTTGAAT
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:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (21 bp):
ACGCCCATGTATTGTGGTACC
Found at i:38288925 original size:25 final size:25
Alignment explanation
Indices: 38288896--38288943 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
38288886 TTATAATATG
* *
38288896 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38288921 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38288944 GTTTAGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38289027 original size:11 final size:11
Alignment explanation
Indices: 38288991--38289046 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
38288981 CATGGTATGT
38288991 ATGATATGCAC
1 ATGATATGCAC
* *
38289002 ATGACATG--T
1 ATGATATGCAC
38289011 ATGATATGCAC
1 ATGATATGCAC
*
38289022 ATGATATG--T
1 ATGATATGCAC
38289031 ATGATATGCAC
1 ATGATATGCAC
38289042 ATGAT
1 ATGAT
38289047 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:38289046 original size:20 final size:20
Alignment explanation
Indices: 38288980--38289046 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
38288970 ATTTTGATAA
*
38288980 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
38289000 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
38289020 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
38289040 ACATGAT
1 ACATGAT
38289047 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:38289123 original size:24 final size:24
Alignment explanation
Indices: 38289096--38289268 Score: 283
Period size: 24 Copynumber: 7.2 Consensus size: 24
38289086 GAGGAACTGC
38289096 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
38289120 AAAAAGGCTTATGCCCCAGTTGTC
1 AAAAGGGCTTATGCCCCAGTTATT
38289144 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38289168 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
38289192 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
38289216 AAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38289240 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
38289264 AAAAG
1 AAAAG
38289269 AGACTAGGCC
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 138 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:38290433 original size:49 final size:46
Alignment explanation
Indices: 38290363--38290483 Score: 127
Period size: 49 Copynumber: 2.6 Consensus size: 46
38290353 TGTCTTCGAC
** * * *
38290363 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATA-TATAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATA-A-A-ACT-GAT
* *
38290412 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCATAAAACTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATAAAACTGAT
*
38290458 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
38290484 CTGTCCTATC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
46 26 0.43
47 2 0.03
48 1 0.02
49 32 0.52
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATAAAACTGAT
Done.