Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 67 of 311
Found at i:20461507 original size:22 final size:22
Alignment explanation
Indices: 20461452--20461517 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
20461442 TAACATGTGT
20461452 CACATATA-TCATGAGCTCAGAC
1 CACATA-ACTCATGAGCTCAGAC
20461474 CACATTAACTCATGAGCTCAGAC
1 CACA-TAACTCATGAGCTCAGAC
20461497 CACATAACTCATGAGCTCAGA
1 CACATAACTCATGAGCTCAGA
20461518 TCACCACAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 22 0.52
23 20 0.48
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (22 bp):
CACATAACTCATGAGCTCAGAC
Found at i:20464999 original size:79 final size:81
Alignment explanation
Indices: 20464897--20465081 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
20464887 GCTCCTCGTT
* *
20464897 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
20464960 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
20464977 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
20465041 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
20465057 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20465082 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:20465081 original size:40 final size:40
Alignment explanation
Indices: 20464897--20465081 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
20464887 GCTCCTCGTT
* *
20464897 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20464937 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20464977 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
20465016 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
20465057 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20465082 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:20472836 original size:79 final size:81
Alignment explanation
Indices: 20472734--20472918 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 81
20472724 GCTCCTCGTT
* *
20472734 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
20472797 GGAT-TTAGTAAC-TCGCA
64 GGATATT-GTAACTTAGCA
* **
20472814 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
*
20472878 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
20472894 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20472919 CATCATTCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
78 3 0.03
79 54 0.58
80 36 0.39
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:20472918 original size:40 final size:41
Alignment explanation
Indices: 20472734--20472918 Score: 240
Period size: 40 Copynumber: 4.6 Consensus size: 41
20472724 GCTCCTCGTT
* *
20472734 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
*
20472774 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
*
20472814 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
* * *
20472853 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGTAAC-TCGCA
20472894 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20472919 CATCATTCAA
Statistics
Matches: 128, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 79 0.62
41 14 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
Found at i:20476586 original size:43 final size:44
Alignment explanation
Indices: 20476466--20476586 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 44
20476456 AGTTCGTACG
* *
20476466 ATGCCAAC-ATCCCAGACTTGGTCTTACATGT-AATCAAATATCA
1 ATGCC-ACTATCCCAGACATGGTCTTACACGTAAATCAAATATCA
* * * *
20476509 ATGCCACTATCCAATACAGGGTCTTACACG-AAATCAAATA-CG
1 ATGCCACTATCCCAGACATGGTCTTACACGTAAATCAAATATCA
* *
20476551 ATGTCGA-TGTCCCAGACATGGTCTTACACGTAAATC
1 ATG-CCACTATCCCAGACATGGTCTTACACGTAAATC
20476587 TCAAATTGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
42 25 0.40
43 38 0.60
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (44 bp):
ATGCCACTATCCCAGACATGGTCTTACACGTAAATCAAATATCA
Found at i:20478821 original size:25 final size:25
Alignment explanation
Indices: 20478783--20478849 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
20478773 CGATAAACGG
* *
20478783 TAAGCTCATTCGAGCTGA-ATATCGA
1 TAAGCTCGTACGAGCTGAGA-ATCGA
*
20478808 TAAGCTC-TCACGAGCTGAGAATCGG
1 TAAGCTCGT-ACGAGCTGAGAATCGA
20478833 TAAGCTCGTACGAGCTG
1 TAAGCTCGTACGAGCTG
20478850 CAGTAAGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 1 0.03
25 34 0.92
26 2 0.05
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (25 bp):
TAAGCTCGTACGAGCTGAGAATCGA
Found at i:20489710 original size:40 final size:39
Alignment explanation
Indices: 20489651--20489741 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 39
20489641 TCGGTATTGT
* *
20489651 ACACTTAGTGCCTCATATAGCCAAAGCTATTCCAATTTGC
1 ACACTTAGTG-CTCATATAGCCAAAGCTATTCCAAATCGC
* * *
20489691 ACACTTAGTGCTACTTATAGCCGAAGCTATTTCAAATCGC
1 ACACTTAGTGCT-CATATAGCCAAAGCTATTCCAAATCGC
20489731 ACACTTAGTGC
1 ACACTTAGTGC
20489742 CGAACATAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
39 2 0.04
40 43 0.96
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (39 bp):
ACACTTAGTGCTCATATAGCCAAAGCTATTCCAAATCGC
Found at i:20490618 original size:21 final size:21
Alignment explanation
Indices: 20490580--20490619 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20490570 ATTCATCACA
*
20490580 CATGCATGTCACAACATCAAT
1 CATGCATGGCACAACATCAAT
20490601 CATGCATGGC-CAACCATCA
1 CATGCATGGCACAA-CATCA
20490620 TGTTCACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (21 bp):
CATGCATGGCACAACATCAAT
Found at i:20494919 original size:46 final size:46
Alignment explanation
Indices: 20494869--20494997 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
20494859 TGGTTGAGCA
* *
20494869 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
20494915 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
20494961 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20494998 GCGGGTTACA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:20497930 original size:15 final size:15
Alignment explanation
Indices: 20497910--20497973 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
20497900 GTATCTTGGG
20497910 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
20497925 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
20497940 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
20497955 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
20497968 TTTCTT
1 TTTCTT
20497974 GTTATCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.13
14 4 0.09
15 33 0.73
16 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:20501968 original size:18 final size:18
Alignment explanation
Indices: 20501945--20501981 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20501935 TCTTGATCTA
20501945 TATGTATTCAAAATTAAC
1 TATGTATTCAAAATTAAC
20501963 TATGTATTCAAAATTAAC
1 TATGTATTCAAAATTAAC
20501981 T
1 T
20501982 CTTTTATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (18 bp):
TATGTATTCAAAATTAAC
Found at i:20508549 original size:50 final size:49
Alignment explanation
Indices: 20508431--20508614 Score: 201
Period size: 50 Copynumber: 3.7 Consensus size: 49
20508421 CTGCTACGCA
*
20508431 TAGTAGCCTGCACTTAGTACTACAC-TCATGACC-AATTATCCCGTACACG
1 TAGTAGCCTGCACTTAGTACTACACAT-GTGACCTAATTAT-CCGTACACG
** *
20508480 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAATTATCCG-TACACG
* * * * * * *
20508530 TAGTAGCCTGCACTTAGTACTACACACGTGATCATAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCTAATTATC-CGTACACG
*
20508581 TAGTAGCCTGCACTTAGTACTACACATGCGACCT
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT
20508615 CACAATAGAT
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
49 32 0.28
50 43 0.38
51 38 0.33
52 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAATTATCCGTACACG
Found at i:20508614 original size:101 final size:99
Alignment explanation
Indices: 20508431--20508614 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 99
20508421 CTGCTACGCA
* *
20508431 TAGTAGCCTGCACTTAGTACTACACTCATGACCAATTATCCCGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACATGACCAATTATCCCGTACACATAGTAGCCTGCACTTA
*
20508496 GTACTACACATGTGACCTAACCATCTGATACACG
66 GTACTACACATGCGACCTAACCATCTGATACACG
* * * ** *
20508530 TAGTAGCCTGCACTTAGTACTACACACGTGATCATAGTTTTCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACATGACCA-A-TTATCCCGTACACATAGTAGCCTGCACT
20508595 TAGTACTACACATGCGACCT
64 TAGTACTACACATGCGACCT
20508615 CACAATAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 31 0.42
100 1 0.01
101 42 0.57
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACATGACCAATTATCCCGTACACATAGTAGCCTGCACTTA
GTACTACACATGCGACCTAACCATCTGATACACG
Found at i:20510850 original size:7 final size:7
Alignment explanation
Indices: 20510840--20510876 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
20510830 AAGAGAGAAT
20510840 GATGAGG
1 GATGAGG
20510847 GATGAGG
1 GATGAGG
20510854 GATGAGG
1 GATGAGG
*
20510861 GATGATG
1 GATGAGG
*
20510868 AATGAGG
1 GATGAGG
20510875 GA
1 GA
20510877 ATGAAGGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.16
Consensus pattern (7 bp):
GATGAGG
Found at i:20514120 original size:55 final size:53
Alignment explanation
Indices: 20513938--20514192 Score: 218
Period size: 55 Copynumber: 4.8 Consensus size: 53
20513928 ACACGGGTAC
* * * * *
20513938 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA
* * *
20513987 CTTACCATTGCCATGTCTTGACATGGTCATACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
* * * *
20514040 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGTCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AA
* ***
20514095 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAGA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGA-A
* * * *
20514148 CCTTACCAATTGTCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
20514193 AAACCCTAAT
Statistics
Matches: 169, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 3 0.02
53 46 0.27
54 10 0.06
55 70 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
Found at i:20514129 original size:108 final size:110
Alignment explanation
Indices: 20513985--20514185 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
20513975 ATCCTTTTGA
* *
20513985 AACTTACCATTGCCATGTCTTGACATGGTCATACATGGTATCCTTGCCTTATGA-A-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCATACATGATATCCTTGCCTTA-GAGACCTCACCAA
20514048 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGTCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGTCTTATAGT
* * * *
20514093 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAGACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCATACATGATATCCTTGCCTTAGAGACCTCACCAAT
*
20514158 TGTCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
20514186 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 2 0.02
108 47 0.57
109 7 0.08
110 27 0.33
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCATACATGATATCCTTGCCTTAGAGACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGTCTTATAGT
Found at i:20522278 original size:54 final size:54
Alignment explanation
Indices: 20522196--20522304 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
20522186 AGCAAAGAGC
* *
20522196 TCCTTTTCAATTACCATATAATTGAGTTGGGCTCTAGTCAAAGTTCTACTTGCA
1 TCCTTTTCAATGACCATATAATTGAGTTGGGCTCCAGTCAAAGTTCTACTTGCA
20522250 TCCTTTTCAATGACCATATAATTGAGTTGGGCTCCAGTCAAAGTTCTACTTGCA
1 TCCTTTTCAATGACCATATAATTGAGTTGGGCTCCAGTCAAAGTTCTACTTGCA
20522304 T
1 T
20522305 AGTAAATAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (54 bp):
TCCTTTTCAATGACCATATAATTGAGTTGGGCTCCAGTCAAAGTTCTACTTGCA
Found at i:20523197 original size:13 final size:13
Alignment explanation
Indices: 20523179--20523207 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20523169 TCAACAATCG
20523179 TTTGATCACTTCC
1 TTTGATCACTTCC
20523192 TTTGATCACTTCC
1 TTTGATCACTTCC
20523205 TTT
1 TTT
20523208 CATAATAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.28, G:0.07, T:0.52
Consensus pattern (13 bp):
TTTGATCACTTCC
Found at i:20536358 original size:45 final size:45
Alignment explanation
Indices: 20536257--20536383 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 45
20536247 TTTTCTCAAA
* * *
20536257 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCTCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
*
20536299 TCACCGACATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
20536343 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
20536384 ATCAAGTCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
42 10 0.14
43 14 0.20
44 7 0.10
45 39 0.55
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:20536769 original size:43 final size:43
Alignment explanation
Indices: 20536713--20536909 Score: 304
Period size: 43 Copynumber: 4.6 Consensus size: 43
20536703 CAGTATTACA
* * *
20536713 CCTGCTACGCACGAAGGCTCGAATACACATCACCGGTACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
*
20536756 CCTGTTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
* * * *
20536799 CCTGCTAGGCACGAAGGCCCGGATATACATCACCAGCACTAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
*
20536842 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
*
20536885 CCTGCTAGGCATGAAGGCCCGAATA
1 CCTGCTAGGCACGAAGGCCCGAATA
20536910 TAATACCAGC
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 141 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.13
Consensus pattern (43 bp):
CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
Found at i:20536956 original size:38 final size:38
Alignment explanation
Indices: 20536902--20536985 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
20536892 GGCATGAAGG
* *
20536902 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAT
* *
20536940 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAT
*
20536978 ACCGAATA
1 CCCGAATA
20536986 CACATCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAT
Found at i:20541247 original size:43 final size:43
Alignment explanation
Indices: 20541199--20541460 Score: 379
Period size: 43 Copynumber: 6.1 Consensus size: 43
20541189 CCGGCATTAT
*
20541199 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
* *
20541242 GCCTGCTAGGCACGAAGGCCCGAATACAGATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
* *
20541285 GCCTGCTAGGCACGAAGGCTCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
20541328 GCCTGCTAGGCACGAAGG-CCGAAATACACATCACC-GACACTAA
1 GCCTGCTAGGCACGAAGGCCCG-AATACACATCACCAG-CACTAA
* * * *
20541371 GCCTGCTAGGCACGAAGGCCCTAATACACATCATCGGTACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
* *
20541414 GCCTGCTAGGCACGAAGGCCCGAATATA-AT-ACCAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
20541455 GCCTGC
1 GCCTGC
20541461 GGGATTTATC
Statistics
Matches: 200, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
41 13 0.06
42 5 0.03
43 179 0.89
44 3 0.01
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.13
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAA
Found at i:20543701 original size:20 final size:21
Alignment explanation
Indices: 20543676--20543741 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 21
20543666 GATATGATAG
20543676 ACATGAAT-TATATGATATAC
1 ACATGAATATATATGATATAC
* *
20543696 ACATG-ATATGTATGATATGC
1 ACATGAATATATATGATATAC
* * *
20543716 ACATG-ATATGTATGAAATGC
1 ACATGAATATATATGATATAC
20543736 ACATGA
1 ACATGA
20543742 TGTAATCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.05
20 39 0.95
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
ACATGAATATATATGATATAC
Found at i:20543742 original size:20 final size:20
Alignment explanation
Indices: 20543695--20543742 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
20543685 ATATGATATA
*
20543695 CACATGATATGTATGATATG
1 CACATGATATGTATGAAATG
20543715 CACATGATATGTATGAAATG
1 CACATGATATGTATGAAATG
20543735 CACATGAT
1 CACATGAT
20543743 GTAATCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
CACATGATATGTATGAAATG
Found at i:20543870 original size:53 final size:52
Alignment explanation
Indices: 20543792--20543928 Score: 219
Period size: 53 Copynumber: 2.7 Consensus size: 52
20543782 GAGGAAGTGC
*
20543792 AAAAGGAC-TATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
20543843 AAAAGGGCTTATGCCCTCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCC-CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
20543896 AAAAGGGCTT-TGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
20543929 AGGCCTCCAG
Statistics
Matches: 82, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
49 5 0.06
50 9 0.11
51 10 0.12
52 12 0.15
53 46 0.56
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:20543872 original size:27 final size:26
Alignment explanation
Indices: 20543792--20543928 Score: 183
Period size: 26 Copynumber: 5.3 Consensus size: 26
20543782 GAGGAAGTGC
*
20543792 AAAAGGAC-TATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
20543817 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
20543843 AAAAGGGCTTATGCCCTCAGTTTATTG
1 AAAAGGGCTTATGCCC-CAGTTTATTG
**
20543870 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
20543896 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
20543919 AAAAGAGGCT
1 AAAAG-GGCT
20543929 AGGCCTCCAG
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
23 5 0.05
24 7 0.07
25 15 0.15
26 49 0.49
27 24 0.24
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:20545459 original size:12 final size:12
Alignment explanation
Indices: 20545444--20545469 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20545434 CGAGGCCGCA
20545444 GACGTGGTCGCG
1 GACGTGGTCGCG
20545456 GACGTGGTCGCG
1 GACGTGGTCGCG
20545468 GA
1 GA
20545470 AGGGTGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.23, G:0.50, T:0.15
Consensus pattern (12 bp):
GACGTGGTCGCG
Found at i:20552008 original size:20 final size:20
Alignment explanation
Indices: 20551983--20552027 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
20551973 ATACGTGGGA
20551983 TATGATATACACATGATATG
1 TATGATATACACATGATATG
*
20552003 TATGATATGCACATGATATG
1 TATGATATACACATGATATG
20552023 TATGA
1 TATGA
20552028 AATGTACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (20 bp):
TATGATATACACATGATATG
Found at i:20552036 original size:20 final size:20
Alignment explanation
Indices: 20551992--20552039 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
20551982 ATATGATATA
*
20551992 CACATGATATGTATGATATG
1 CACATGATATGTATGAAATG
20552012 CACATGATATGTATGAAATG
1 CACATGATATGTATGAAATG
*
20552032 TACATGAT
1 CACATGAT
20552040 GTAATCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
CACATGATATGTATGAAATG
Found at i:20552138 original size:26 final size:25
Alignment explanation
Indices: 20552085--20552140 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
20552075 GATGAAGTGC
**
20552085 AAAAGGGCTATGCCCCAGTTTATTG
1 AAAAGGGCTATGCCCCAGTTTACCG
20552110 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGC-TATGCCCCAGTTTACCG
20552136 AAAAG
1 AAAAG
20552141 CCCCAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAAGGGCTATGCCCCAGTTTACCG
Found at i:20571954 original size:68 final size:68
Alignment explanation
Indices: 20571882--20572065 Score: 232
Period size: 68 Copynumber: 2.7 Consensus size: 68
20571872 CATCATGTGT
* * * *
20571882 ACAAGAAG-GCTAC-AAGATACTATATAGTAGCTAGGTCACATGTGTGTTACGGGATGTATCCCA
1 ACAAGAAGAGCTACGAAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGATACGAGATGTATCCCA
20571945 TGTAG
64 TGTAG
*
20571950 ACAAG-AGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGAGATGTATCCCAT
1 ACAAGAAGAGCTACG-AAGAGATAAATGTAGCTAGGTCACATGTGTGATACGAGATGTATCCCAT
20572014 GTAG
65 GTAG
* * *
20572018 ACAAG-AGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGAT
1 ACAAGAAGAGCTACG-AAGAGATAAATGTAGCTAGGTCACATGTGTGAT
20572066 TCCAAGTGAA
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
67 2 0.02
68 96 0.91
69 4 0.04
70 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.24
Consensus pattern (68 bp):
ACAAGAAGAGCTACGAAGAGATAAATGTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATG
TAG
Found at i:20572139 original size:66 final size:68
Alignment explanation
Indices: 20571942--20572139 Score: 201
Period size: 68 Copynumber: 2.9 Consensus size: 68
20571932 GGGATGTATC
* * *
20571942 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATA-C--GAGA
1 CCATGTAGACAAGAGAGCTAC-T-AGAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
* * **
20572004 TGTATC
63 AGGAGA
*
20572010 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC-T-AGAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
20572075 AGGAGA
63 AGGAGA
* *
20572081 CCATGTAGACAAGAGAGCTA-T-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACTAGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
20572140 TTCACCATGT
Statistics
Matches: 115, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
66 24 0.21
67 9 0.08
68 55 0.48
69 2 0.02
71 25 0.22
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.22
Consensus pattern (68 bp):
CCATGTAGACAAGAGAGCTACTAGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGG
AGA
Found at i:20573538 original size:46 final size:43
Alignment explanation
Indices: 20573452--20573574 Score: 140
Period size: 46 Copynumber: 2.7 Consensus size: 43
20573442 GGGGTAGAAT
20573452 GCCGATGCCATGTCCTAGACATGGTCTTACACTGACACATCTCGTA-
1 GCCGATG-CATGTCC-AGACAT-GTCTTACACTGACACATCTCG-AG
* *
20573498 GCCGATGCATGTCTCAGACATCTCTTACACTGGCTTACATCTCGAG
1 GCCGATGCATGTC-CAGACATGTCTTACACTGAC--ACATCTCGAG
*
20573544 GCTGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGT-CCAGACATGTCTTACACT
20573575 AGCTCTTGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
44 11 0.16
45 13 0.19
46 43 0.63
47 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (43 bp):
GCCGATGCATGTCCAGACATGTCTTACACTGACACATCTCGAG
Found at i:20591234 original size:46 final size:49
Alignment explanation
Indices: 20591128--20591249 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 49
20591118 TGTCTTCGAC
** * *
20591128 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCA-ATATATATATAAT
* * *
20591178 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATATAAT
*
20591224 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
20591250 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 27 0.43
47 1 0.02
48 5 0.08
50 30 0.48
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (49 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATATAAT
Found at i:20625078 original size:43 final size:43
Alignment explanation
Indices: 20624913--20625083 Score: 156
Period size: 43 Copynumber: 4.0 Consensus size: 43
20624903 ATATCGTACA
* * *
20624913 ATGCCAACGTCCCAGATGTGGTCTTACATGCAATTACATATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACACGCAATCACATATCG
**
20624956 ATGCCATTGTCCCAGACAG-GGTCTTACACG-AATCA-A-ATGCG
1 ATGCCAACGTCCCAGA-AGTGGTCTTACACGCAATCACATAT-CG
* * * *
20624997 ATACCGATGTCCCA-AAGCTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGAAG-TGGTCTTACACGCAATCACATATCG
* * *
20625040 ATGCCAACGTCCTAGATGTGGTCTTACACG-AGAACACATATCG
1 ATGCCAACGTCCCAGAAGTGGTCTTACACGCA-ATCACATATCG
20625083 A
1 A
20625084 AAATCCTATG
Statistics
Matches: 105, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 25 0.24
42 10 0.10
43 60 0.57
44 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGAAGTGGTCTTACACGCAATCACATATCG
Found at i:20626203 original size:14 final size:15
Alignment explanation
Indices: 20626186--20626214 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20626176 TCACGAAAAT
20626186 TTCACACAT-ATAAA
1 TTCACACATAATAAA
20626200 TTCACACATAATAAA
1 TTCACACATAATAAA
20626215 CATAGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:20628820 original size:42 final size:42
Alignment explanation
Indices: 20628678--20628825 Score: 160
Period size: 42 Copynumber: 3.5 Consensus size: 42
20628668 ACAATGCTAG
*
20628678 CGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCA
1 CGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCA
* * *
20628720 CTATCCTAGACAG-GGTCTTACACG-AACTCATATAT-GATGCCGA
1 C-GTCCCAGAC-GTGGTCTTACACGTAA-TCACATATCGATGCC-A
* *
20628763 TGTCCCAGACATGGTCTTACACGTAATCACA-ATCGATGCCAA
1 CGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCC-A
*
20628805 CGTCCCAGATGTGGTCTTACA
1 CGTCCCAGACGTGGTCTTACA
20628826 TGAGTCACAT
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 56 0.65
43 27 0.31
44 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (42 bp):
CGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCA
Found at i:20631670 original size:27 final size:27
Alignment explanation
Indices: 20631640--20631691 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
20631630 AAACCTGGCA
*
20631640 AGCTGGTATCCGCTAGTAGGCTTGGTG
1 AGCTGGTATCCGCCAGTAGGCTTGGTG
**
20631667 AGCTGGTATTTGCCAGTAGGCTTGG
1 AGCTGGTATCCGCCAGTAGGCTTGG
20631692 CGAGTTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.37, T:0.31
Consensus pattern (27 bp):
AGCTGGTATCCGCCAGTAGGCTTGGTG
Found at i:20631705 original size:27 final size:27
Alignment explanation
Indices: 20631654--20631735 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
20631644 GGTATCCGCT
* *
20631654 AGTAGGCTTGGTGAGCTGGTATTTGCC
1 AGTAGGCTTGGCGAGCTGATATTTGCC
* *
20631681 AGTAGGCTTGGCGAGTTGATTTTTGCC
1 AGTAGGCTTGGCGAGCTGATATTTGCC
** * * * *
20631708 AACAGGCCTGGAGAGCTGAAATTCGCC
1 AGTAGGCTTGGCGAGCTGATATTTGCC
20631735 A
1 A
20631736 AGGCCTGACA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (27 bp):
AGTAGGCTTGGCGAGCTGATATTTGCC
Found at i:20634963 original size:41 final size:41
Alignment explanation
Indices: 20634914--20635127 Score: 238
Period size: 41 Copynumber: 5.3 Consensus size: 41
20634904 ACAAAAGTGT
*
20634914 ATTCAGGGGTATCGAAGTACAAATAGGGGCACGTATGTGCA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACGTATGTGCA
* **
20634955 ATTCAGGGGTA-CTGAAGTACAAACAGGAGCACACATGTGCA
1 ATTCAGGGGTATC-GAAGTACAAACAGGGGCACGTATGTGCA
** * *
20634996 ATTCAAAGGTATCAAAGTACAAATAGGGGCACGTATGTGCA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACGTATGTGCA
* * * *
20635037 AGTCAAGGGTATC-AAGTACAAACGGGGGCATGTATGTGCA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACGTATGTGCA
* * *
20635077 ATTCAGGGGTACCGACA-TACAAACAGAGGCAC-TAAGTGCA
1 ATTCAGGGGTATCGA-AGTACAAACAGGGGCACGTATGTGCA
*
20635117 ATTCAGAGGTA
1 ATTCAGGGGTA
20635128 CGGAAATAGA
Statistics
Matches: 145, Mismatches: 24, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
40 52 0.36
41 91 0.63
42 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.20
Consensus pattern (41 bp):
ATTCAGGGGTATCGAAGTACAAACAGGGGCACGTATGTGCA
Found at i:20640475 original size:41 final size:41
Alignment explanation
Indices: 20640416--20640557 Score: 230
Period size: 41 Copynumber: 3.5 Consensus size: 41
20640406 AGTGAGAAAA
* *
20640416 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
1 CGTGTAAGACCCTGTCTGGGACACTGGCATCGTATATGATT
* * *
20640457 CGTGTAAGACCCTATCTGGGATAGTGGCATCGTATATGATT
1 CGTGTAAGACCCTGTCTGGGACACTGGCATCGTATATGATT
*
20640498 CATGTAAGACCCTGTCTGGGACACTGGCATCGTATATGATT
1 CGTGTAAGACCCTGTCTGGGACACTGGCATCGTATATGATT
20640539 CGTGTAAGACCCTGTCTGG
1 CGTGTAAGACCCTGTCTGG
20640558 TATGGTAATG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (41 bp):
CGTGTAAGACCCTGTCTGGGACACTGGCATCGTATATGATT
Found at i:20644069 original size:34 final size:34
Alignment explanation
Indices: 20644031--20644137 Score: 94
Period size: 34 Copynumber: 3.1 Consensus size: 34
20644021 CATTATGAGT
20644031 TTCTAGTTATGCCTTTCGGATTAACGAATGCACC
1 TTCTAGTTATGCCTTTCGGATTAACGAATGCACC
* ** ** * **
20644065 TTCTATTTTTATG--GATCTAATGAATCGAATG-AGT
1 TTCTA--GTTATGCCTTTCGGATTAA-CGAATGCACC
20644099 TTCTAGTTATGCCTTTCGGATTAACGAATGCACC
1 TTCTAGTTATGCCTTTCGGATTAACGAATGCACC
20644133 TTCTA
1 TTCTA
20644138 TTTTTATGGA
Statistics
Matches: 51, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
32 5 0.10
33 6 0.12
34 29 0.57
35 6 0.12
36 5 0.10
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (34 bp):
TTCTAGTTATGCCTTTCGGATTAACGAATGCACC
Found at i:20644134 original size:68 final size:68
Alignment explanation
Indices: 20644025--20644159 Score: 270
Period size: 68 Copynumber: 2.0 Consensus size: 68
20644015 TATTAACATT
20644025 ATGAGTTTCTAGTTATGCCTTTCGGATTAACGAATGCACCTTCTATTTTTATGGATCTAATGAAT
1 ATGAGTTTCTAGTTATGCCTTTCGGATTAACGAATGCACCTTCTATTTTTATGGATCTAATGAAT
20644090 CGA
66 CGA
20644093 ATGAGTTTCTAGTTATGCCTTTCGGATTAACGAATGCACCTTCTATTTTTATGGATCTAATGAAT
1 ATGAGTTTCTAGTTATGCCTTTCGGATTAACGAATGCACCTTCTATTTTTATGGATCTAATGAAT
20644158 CG
66 CG
20644160 GATCTTCAGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (68 bp):
ATGAGTTTCTAGTTATGCCTTTCGGATTAACGAATGCACCTTCTATTTTTATGGATCTAATGAAT
CGA
Found at i:20645883 original size:43 final size:43
Alignment explanation
Indices: 20645836--20645938 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 43
20645826 CCTCAATTGA
* **
20645836 GATTTACATATAAGACCATGTCTGGAACATCGGCATCG-TATCT
1 GATTTACATGTAAGACCATGTCTGGAACAGAGGCATCGATAT-T
* * *
20645879 GATTT-CGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATT
1 GATTTACATGTAAGACCATGTCTGGAACAGAGGCATCGATATT
*
20645921 GAATTACATGTAAGACCA
1 GATTTACATGTAAGACCA
20645939 CGTCCAGGAC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 31 0.63
43 18 0.37
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
GATTTACATGTAAGACCATGTCTGGAACAGAGGCATCGATATT
Found at i:20657422 original size:27 final size:26
Alignment explanation
Indices: 20657375--20657425 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
20657365 CGAGGCTGCC
*
20657375 AGATATTGTGACGAAGTCACTAGAAT
1 AGATATTGTGACGAAGCCACTAGAAT
* *
20657401 AGATATATGTGGCGAGGCCACTAGA
1 AGATAT-TGTGACGAAGCCACTAGA
20657426 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACTAGAAT
Found at i:20658105 original size:27 final size:27
Alignment explanation
Indices: 20658075--20658140 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
20658065 AGGGGCAAAA
*
20658075 TGGTAATTTTACCCTACAAGGGTATCT
1 TGGTAATTCTACCCTACAAGGGTATCT
* * *
20658102 TGGTAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATCT
*
20658129 TAGTAATTCTAC
1 TGGTAATTCTAC
20658141 AACTTATCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (27 bp):
TGGTAATTCTACCCTACAAGGGTATCT
Found at i:20664795 original size:27 final size:26
Alignment explanation
Indices: 20664747--20664806 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
20664737 GCGAGGCTGC
*
20664747 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
20664774 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
20664800 CAGATAT
1 CAGATAT
20664807 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:20675418 original size:27 final size:27
Alignment explanation
Indices: 20675366--20675424 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
20675356 CAGAAATAGT
*
20675366 ATCAGGTGGCCTTAGCCCATTAACAGA
1 ATCAGGTGGCCTTAGCCCAATAACAGA
20675393 ATCAGGTGGGCCTTAGCCCAAT-ACAGA
1 ATCAGGT-GGCCTTAGCCCAATAACAGA
20675420 ATCAG
1 ATCAG
20675425 TATTAGATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (27 bp):
ATCAGGTGGCCTTAGCCCAATAACAGA
Found at i:20679582 original size:11 final size:11
Alignment explanation
Indices: 20679566--20679590 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20679556 TTATATATAC
20679566 TAATAAAATAA
1 TAATAAAATAA
20679577 TAATAAAATAA
1 TAATAAAATAA
20679588 TAA
1 TAA
20679591 AATATCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:20684070 original size:58 final size:58
Alignment explanation
Indices: 20683980--20684095 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
20683970 TGGCATTTGT
*
20683980 GTGAATATGCATTATTTTTAATGGTAAATTAGTAATAAGACAAATAAAGGTTAATAAA
1 GTGAATAAGCATTATTTTTAATGGTAAATTAGTAATAAGACAAATAAAGGTTAATAAA
20684038 GTGAATAAGCATTATTTTTAATGGTAAATTAGTAATAAGACAAATAAAGGTTAATAAA
1 GTGAATAAGCATTATTTTTAATGGTAAATTAGTAATAAGACAAATAAAGGTTAATAAA
20684096 ATTAAAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (58 bp):
GTGAATAAGCATTATTTTTAATGGTAAATTAGTAATAAGACAAATAAAGGTTAATAAA
Found at i:20684904 original size:21 final size:22
Alignment explanation
Indices: 20684869--20684919 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
20684859 TTGTTGGACC
*
20684869 ATGATTTGAAAATGATTCTACA
1 ATGATTTGAAAATGATTCGACA
*
20684891 ATGATTTG-AAATGATTCGACT
1 ATGATTTGAAAATGATTCGACA
20684912 ATGATTTG
1 ATGATTTG
20684920 GTATTGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
ATGATTTGAAAATGATTCGACA
Found at i:20685125 original size:47 final size:47
Alignment explanation
Indices: 20685009--20685139 Score: 154
Period size: 47 Copynumber: 2.8 Consensus size: 47
20684999 GTGCGAGTTA
* ** * *
20685009 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTTGGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTA-CTCCGAGAGAAAT
* * * *
20685057 TACCTTAATTTGGCTAGGGGCCATAGTATAGGTACTCCGAGATAAAT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGAGAGAAAT
* *
20685104 TACCTTGATTTGGTTATGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
20685140 TATCGACTGA
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
47 39 0.56
48 31 0.44
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGAGAGAAAT
Found at i:20687830 original size:42 final size:42
Alignment explanation
Indices: 20687715--20687853 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
20687705 GTATGTGTTA
* * * *
20687715 TCATGTAAAACCATATCTGAGATATGGC-GCTGATATGAGATT
1 TCATGTAAGACCATATCTAAGATATGGCATC-GAAATGAGATT
* * * *
20687757 TCGTGTAAGACCACATC-AAGGACATGTCATCGAAATGAGATT
1 TCATGTAAGACCATATCTAA-GATATGGCATCGAAATGAGATT
* * ** *
20687799 TCATATAAGACCATATCTTAGATATGGCATCGATGTGAGATC
1 TCATGTAAGACCATATCTAAGATATGGCATCGAAATGAGATT
*
20687841 CCATGTAAGACCA
1 TCATGTAAGACCA
20687854 CGTCTGGGAC
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
41 1 0.01
42 72 0.96
43 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (42 bp):
TCATGTAAGACCATATCTAAGATATGGCATCGAAATGAGATT
Found at i:20690258 original size:21 final size:22
Alignment explanation
Indices: 20690218--20690258 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20690208 CCTCTGAGTT
*
20690218 TGGTTTTGACTATGTTTGGTTA
1 TGGTTTTAACTATGTTTGGTTA
*
20690240 TGGTTTTAACTGT-TTTGGT
1 TGGTTTTAACTATGTTTGGT
20690259 GATGATGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.12, C:0.05, G:0.27, T:0.56
Consensus pattern (22 bp):
TGGTTTTAACTATGTTTGGTTA
Found at i:20696070 original size:43 final size:43
Alignment explanation
Indices: 20695946--20696105 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
20695936 TGATGTGTTC
* *
20695946 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT-TATGATT
1 TCGTGTAAGACCATGTCTGGGACGTTGGCATCGA-TATTTGATT
* * * *
20695989 TACGTGTAAGACCATGTCTGGGACATCGACATTG-TATTTGATT
1 T-CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATT
* * * *
20696032 TCGTTTAAGACCCTGTTTGGGACAG-TGGCATCGATATTTAATT
1 TCGTGTAAGACCATGTCTGGGAC-GTTGGCATCGATATTTGATT
*
20696075 ACGTGTAAGACCATGTCTGGGACGTTGGCAT
1 TCGTGTAAGACCATGTCTGGGACGTTGGCAT
20696106 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 26 0.28
43 41 0.44
44 27 0.29
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATT
Found at i:20702711 original size:27 final size:27
Alignment explanation
Indices: 20702687--20702973 Score: 313
Period size: 27 Copynumber: 10.6 Consensus size: 27
20702677 TTAGTTTACC
20702687 AAATTACCAAAATACCCCTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
20702714 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* ***
20702741 AAATCACCAAAATACCCCTGGTTCGCA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
20702768 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
20702795 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * *
20702822 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* * *
20702849 AAATTACCAAAATACCTCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
20702876 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * * * *
20702903 AAATCATCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* ** * *
20702930 AAATTACCAAAATAGCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGGTTTATA
*
20702957 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
20702974 TCGACCTGTA
Statistics
Matches: 223, Mismatches: 37, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 223 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTATA
Found at i:20702824 original size:81 final size:81
Alignment explanation
Indices: 20702687--20703045 Score: 348
Period size: 81 Copynumber: 4.4 Consensus size: 81
20702677 TTAGTTTACC
* * * * *
20702687 AAATTACCAAAATACCCCTGGTTTATAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATCACCAAA
* * * *
20702752 ATACCCCTGGTTCGCA
66 ATACCCTTAGTTTGTA
* * *
20702768 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATCACCAAA
* *
20702833 ATACCCTTTGTTTATA
66 ATACCCTTAGTTTGTA
* * *
20702849 AAATTACCAAAATA-CCTCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATCATCAA
1 AAATTACCAAAATACCCT-TGGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATCACCAA
20702913 AATACCCTTAGTTTGTA
65 AATACCCTTAGTTTGTA
** * * * * ** * ***
20702930 AAATTACCAAAATAGCCC-TAATTTGTGAAATTACTAAAATA-CCCTCGACCTGTAAAATTATTG
1 AAATTACCAAAATA-CCCTTGGTTTATAAAATTACCAAAATACCCCTAG-TTTGTAAAATCACCA
* *
20702993 AAATACCC-TCGACTTGTA
64 AAATACCCTTAG-TTTGTA
* * *
20703011 AAATTACCAAAGTACCCTTGATTTATAGAATTACC
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACC
20703046 GTTTTACCCT
Statistics
Matches: 234, Mismatches: 38, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
80 13 0.06
81 219 0.94
83 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (81 bp):
AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATCACCAAA
ATACCCTTAGTTTGTA
Found at i:20702974 original size:54 final size:54
Alignment explanation
Indices: 20702677--20702973 Score: 362
Period size: 54 Copynumber: 5.5 Consensus size: 54
20702667 TTAGAATACT
** * * *
20702677 TTAGTTTACCAAATTACCAAAATACCCCTGGTTTATAAAATTACTAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC
* * * * *
20702731 TTGGTTTATAAAATCACCAAAATACCCCTGGTTCGCAAAATTACCAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC
* * *
20702785 TTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC
* *
20702839 TTTGTTTATAAAATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC
* * * * *
20702893 CTAGTTTGTAAAATCATCAAAATACCCTTAGTTTGTAAAATTACCAAAATAGCCC
1 TTAGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATA-CCC
* * * *
20702948 -TAATTTGTGAAATTACTAAAATACCC
1 TTAGTTTATAAAATTACCAAAATACCC
20702974 TCGACCTGTA
Statistics
Matches: 212, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 209 0.99
55 3 0.01
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (54 bp):
TTAGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC
Found at i:20703042 original size:27 final size:27
Alignment explanation
Indices: 20702687--20703045 Score: 307
Period size: 27 Copynumber: 13.3 Consensus size: 27
20702677 TTAGTTTACC
* * *
20702687 AAATTACCAAAATACCCCTGGTTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
* * *
20702714 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
* * * * *
20702741 AAATCACCAAAATACCCCTGGTTCGCA
1 AAATTACCAAAATACCCTTGATTTGTA
* **
20702768 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGATTTGTA
*
20702795 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* *
20702822 AAATTACTAAAATACCCTTTG-TTTATA
1 AAATTACCAAAATACCC-TTGATTTGTA
*
20702849 AAATTACCAAAATACCTCTAG-TTTGTA
1 AAATTACCAAAATACC-CTTGATTTGTA
*
20702876 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* *
20702903 AAATCATCAAAATACCCTT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* *
20702930 AAATTACCAAAATAGCCC-TAATTTGTG
1 AAATTACCAAAATA-CCCTTGATTTGTA
* * **
20702957 AAATTACTAAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
*** * *
20702984 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
20703011 AAATTACCAAAGTACCCTTGATTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
*
20703038 GAATTACC
1 AAATTACC
20703046 GTTTTACCCT
Statistics
Matches: 276, Mismatches: 47, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.01
27 266 0.96
28 6 0.02
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGATTTGTA
Found at i:20703080 original size:27 final size:27
Alignment explanation
Indices: 20702767--20703081 Score: 99
Period size: 27 Copynumber: 11.7 Consensus size: 27
20702757 CCTGGTTCGC
* * * * *
20702767 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTATCGAAATACCCTCGATTTAT
* * * *
20702794 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTATCGAAATACCCTCGA-TTTAT
* *
20702821 AAAATTA-CTAAAATACCCTTTG-TTTAT
1 AAAATTATC-GAAATACCC-TCGATTTAT
* * * *
20702848 AAAATTACCAAAATA-CCTCTAGTTTGT
1 AAAATTATCGAAATACCCTCGA-TTTAT
* * * *
20702875 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTATCGAAATACCCTCGA-TTTAT
* * * *
20702902 AAAATCATCAAAATACCCT-TAGTTTGT
1 AAAATTATCGAAATACCCTCGA-TTTAT
* * * *
20702929 AAAATTACCAAAATAGCCCT-AATTTGT
1 AAAATTATCGAAATA-CCCTCGATTTAT
* * ** *
20702956 GAAATTA-CTAAAATACCCTCGACCTGT
1 AAAATTATC-GAAATACCCTCGATTTAT
* * *
20702983 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTATCGAAATACCCTCGATTTAT
* *
20703010 AAAATTA-CCAAAGTACCCTTGATTTAT
1 AAAATTATCGAAA-TACCCTCGATTTAT
* * *** *
20703037 AGAATTACCGTTTTACCCTCGATTTAC
1 AAAATTATCGAAATACCCTCGATTTAT
20703064 AAAATTATCGAAATACCC
1 AAAATTATCGAAATACCC
20703082 CTGTAAGGTA
Statistics
Matches: 232, Mismatches: 41, Indels: 30
0.77 0.14 0.10
Matches are distributed among these distances:
25 1 0.00
26 11 0.05
27 211 0.91
28 9 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCGATTTAT
Found at i:20703096 original size:27 final size:27
Alignment explanation
Indices: 20703066--20703260 Score: 221
Period size: 27 Copynumber: 7.3 Consensus size: 27
20703056 CGATTTACAA
* *
20703066 AATTATCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* **
20703093 AATTACCGGAATACCCCTACAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
20703120 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
20703147 AATTATTGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
20703174 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * * *
20703201 AATTACTAAAATAACCTTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
20703228 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
20703254 AATTACC
1 AATTACC
20703261 ATTTTGCCCC
Statistics
Matches: 141, Mismatches: 27, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
26 17 0.12
27 124 0.88
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:20703223 original size:81 final size:81
Alignment explanation
Indices: 20703066--20703242 Score: 246
Period size: 81 Copynumber: 2.2 Consensus size: 81
20703056 CGATTTACAA
*
20703066 AATTATCGAAATACCCCTGTAAGGTAGAATTACCGGAATACCCCTACAGGGTAGAATTACCAAAA
1 AATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTACAGGGTAGAATTACCAAAA
*
20703131 TACCCCTGTAGGGTAG
66 TAACCCTGTAGGGTAG
* * * ** *
20703147 AATTATTGCAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAA
1 AATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTACAGGGTAGAATTACCAAAA
* *
20703212 TAACCTTGTAGGGTGG
66 TAACCCTGTAGGGTAG
* *
20703228 AATTACCGAGATACC
1 AATTATCGAAATACC
20703243 TTGTGGGGTA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (81 bp):
AATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTACAGGGTAGAATTACCAAAA
TAACCCTGTAGGGTAG
Found at i:20703729 original size:22 final size:22
Alignment explanation
Indices: 20703686--20703750 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
20703676 TTAAAGCCTT
* * * *
20703686 CTGATTATGGCTTTCTGTCAAC
1 CTGAATATGGCTCTGTGCCAAC
20703708 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-ATATGGCTCTGTGCCAAC
* *
20703730 CTGATTATGGCTGTGTGCCAA
1 CTGAATATGGCTCTGTGCCAA
20703751 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGAATATGGCTCTGTGCCAAC
Found at i:20703941 original size:27 final size:27
Alignment explanation
Indices: 20703911--20704010 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
20703901 TCTGTTAAGC
* *
20703911 GGCTTTGCCACATTATCTGTTTCTGGT
1 GGCTCTGCCACAATATCTGTTTCTGGT
*
20703938 GGCTATGCCACAAATATCTG-TTCTGGT
1 GGCTCTGCCAC-AATATCTGTTTCTGGT
*
20703965 GGCTCTGCCACAATATCTGTATCTGGT
1 GGCTCTGCCACAATATCTGTTTCTGGT
* *
20703992 GACTCTGTCACAATATCTG
1 GGCTCTGCCACAATATCTG
20704011 ATAACTGAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 8 0.12
27 50 0.77
28 7 0.11
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
GGCTCTGCCACAATATCTGTTTCTGGT
Found at i:20704187 original size:6 final size:6
Alignment explanation
Indices: 20704176--20704272 Score: 74
Period size: 6 Copynumber: 15.8 Consensus size: 6
20704166 TTACCTAATA
* * *
20704176 CTGATT CTGATT TTGATT TTG-TT ACTTGATA CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT -C-TGATT CTGATT CTGATT CTGATT
* * *
20704225 CTGATT CTG-TCAC CTAATT TTGATT CTGATT CTGATT CT-AGTT CTGAT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
20704273 AATGTTTCTT
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
5 4 0.05
6 61 0.84
7 6 0.08
8 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (6 bp):
CTGATT
Found at i:20704193 original size:31 final size:31
Alignment explanation
Indices: 20704155--20704227 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
20704145 ACATTCTAAT
20704155 TTTTGATTCTGTTACCTAATACTGATTCTGA
1 TTTTGATTCTGTTACCTAATACTGATTCTGA
* * *
20704186 TTTTGATTTTGTTACTTGATACTGATTCTGA
1 TTTTGATTCTGTTACCTAATACTGATTCTGA
*
20704217 TTCTGATTCTG
1 TTTTGATTCTG
20704228 ATTCTGTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.19, C:0.14, G:0.15, T:0.52
Consensus pattern (31 bp):
TTTTGATTCTGTTACCTAATACTGATTCTGA
Found at i:20704217 original size:37 final size:37
Alignment explanation
Indices: 20704176--20704263 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
20704166 TTACCTAATA
* * * * *
20704176 CTGATTCTGATTTTGATTTTGTTACTTGATACTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATACTGATT
**
20704213 CTGATTCTGATTCTGATTCTGTCACCTAATTTTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATACTGATT
20704250 CTGATTCTGATTCT
1 CTGATTCTGATTCT
20704264 AGTTCTGATA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.18, C:0.16, G:0.15, T:0.51
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTCACCTAATACTGATT
Found at i:20715588 original size:42 final size:41
Alignment explanation
Indices: 20715480--20715607 Score: 148
Period size: 42 Copynumber: 3.0 Consensus size: 41
20715470 TTCCAGTATG
* * * * *
20715480 TGATTTCGTGTAAGACCATATCTGGGACGTTGGCATTGATT
1 TGATTTTGTGTAAGACCATGTCTGGGACATTGGCATCGATA
*
20715521 TGAGATTTATGTGTAAGACCATGTCTAGGACATTGGCATCGTATA
1 T--GATTT-TGTGTAAGACCATGTCTGGGACATTGGCATCG-ATA
* *
20715566 TGATTTTGTGTAAGACCTTGTCTGGGACAGTGGCATCGATA
1 TGATTTTGTGTAAGACCATGTCTGGGACATTGGCATCGATA
20715607 T
1 T
20715608 TCAATTACAT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
41 5 0.07
42 29 0.39
43 10 0.14
44 27 0.36
45 3 0.04
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (41 bp):
TGATTTTGTGTAAGACCATGTCTGGGACATTGGCATCGATA
Found at i:20718018 original size:42 final size:42
Alignment explanation
Indices: 20717911--20718020 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 42
20717901 ATATGTGTTC
* *
20717911 TCGTGTAAGACCACATCTGGGACGTCGGCATCAACTTATGATT
1 TCGTGTAAGACC-CATCTGGGACATCAGCATCAACTTATGATT
* *
20717954 TATGTGTAAGA-CCATGCTTGGGATATCAGCATCATA-TT-TGATT
1 T-CGTGTAAGACCCAT-C-TGGGACATCAGCATCA-ACTTATGATT
20717997 TCGTGTAAGACCCTATCTGGGACA
1 TCGTGTAAGACCC-ATCTGGGACA
20718021 GTGGCATCGA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
42 17 0.31
43 12 0.22
44 25 0.45
45 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (42 bp):
TCGTGTAAGACCCATCTGGGACATCAGCATCAACTTATGATT
Found at i:20718028 original size:42 final size:41
Alignment explanation
Indices: 20717911--20718069 Score: 121
Period size: 42 Copynumber: 3.7 Consensus size: 41
20717901 ATATGTGTTC
20717911 TCGTGTAAGACCACATCTGGGACGTCGGCATCA-ACTTATGATT
1 TCGTGTAAGACC-CATCTGGGACGTCGGCATCATA-TT-TGATT
* ** *
20717954 TATGTGTAAGA-CCATGCTTGGGATATCAGCATCATATTTGATT
1 T-CGTGTAAGACCCAT-C-TGGGACGTCGGCATCATATTTGATT
20717997 TCGTGTAAGACCCTATCTGGGACAGT-GGCATCGATATTT-ATT
1 TCGTGTAAGACCC-ATCTGGGAC-GTCGGCATC-ATATTTGATT
* * *
20718039 ACATGTAAGA-CCATGTCTGGGACGTTGGCAT
1 TCGTGTAAGACCCA--TCTGGGACGTCGGCAT
20718070 GGTACAAGCT
Statistics
Matches: 95, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
40 1 0.01
41 4 0.04
42 45 0.47
43 19 0.20
44 25 0.26
45 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (41 bp):
TCGTGTAAGACCCATCTGGGACGTCGGCATCATATTTGATT
Found at i:20728638 original size:92 final size:92
Alignment explanation
Indices: 20728481--20728666 Score: 336
Period size: 92 Copynumber: 2.0 Consensus size: 92
20728471 ATTGTAGGTT
* * *
20728481 TGACAAGCTGGCTTGAGAATCGAGATAGGTCGAAGGCTCGTTCACACTATCCAAAGACCTAAATT
1 TGACAAGCCGGCCTGAGAATCGAGATAGGTCAAAGGCTCGTTCACACTATCCAAAGACCTAAATT
20728546 GGTAAAATGGCTTGTATATTTTGAATG
66 GGTAAAATGGCTTGTATATTTTGAATG
*
20728573 TGACAAGCCGGCCTGAGAATCGGGATAGGTCAAAGGCTCGTTCACACTATCCAAAGACCTAAATT
1 TGACAAGCCGGCCTGAGAATCGAGATAGGTCAAAGGCTCGTTCACACTATCCAAAGACCTAAATT
20728638 GGTAAAATGGCTTGTATATTTTGAATG
66 GGTAAAATGGCTTGTATATTTTGAATG
20728665 TG
1 TG
20728667 GCATGTATAG
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (92 bp):
TGACAAGCCGGCCTGAGAATCGAGATAGGTCAAAGGCTCGTTCACACTATCCAAAGACCTAAATT
GGTAAAATGGCTTGTATATTTTGAATG
Found at i:20738259 original size:25 final size:23
Alignment explanation
Indices: 20738223--20738280 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 23
20738213 TTTACCTTAC
20738223 TTTTA-TATTATACATTATAAGATTA
1 TTTTATTA-TATACATTAT--GATTA
* *
20738248 TTTTATTATATATATTATTATTA
1 TTTTATTATATACATTATGATTA
20738271 -TTTATTATAT
1 TTTTATTATAT
20738281 CTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 10 0.33
23 4 0.13
25 14 0.47
26 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATTATATACATTATGATTA
Found at i:20738261 original size:20 final size:22
Alignment explanation
Indices: 20738238--20738280 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20738228 TATTATACAT
20738238 TATAAGATTA-T-TTTATTATA
1 TATAAGATTATTATTTATTATA
**
20738258 TATATTATTATTATTTATTATA
1 TATAAGATTATTATTTATTATA
20738280 T
1 T
20738281 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATAAGATTATTATTTATTATA
Found at i:20738266 original size:3 final size:3
Alignment explanation
Indices: 20738244--20738342 Score: 59
Period size: 3 Copynumber: 33.7 Consensus size: 3
20738234 ACATTATAAG
*
20738244 ATT ATT -TT ATT A-T ATAT ATT ATT ATT ATTT ATT ATAT CTT ATT -TT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT A-TT ATT AT-T ATT ATT ATT
** * *
20738289 -TT CACAA ATT ATT ATT ATT ATT ATT -TT A-C ATT ATT ATT TTT A-T
1 ATT -A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20738332 ATT ATT ATT AT
1 ATT ATT ATT AT
20738343 ATCTTACTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
2 13 0.17
3 53 0.71
4 9 0.12
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:20738285 original size:20 final size:17
Alignment explanation
Indices: 20738244--20738384 Score: 64
Period size: 19 Copynumber: 8.2 Consensus size: 17
20738234 ACATTATAAG
20738244 ATTATTTTATTATATAT
1 ATTATTTTATTATATAT
20738261 ATTATTATTATTTATTATAT
1 ATTATT-TTA-TTA-TATAT
* *
20738281 CTTATTTT-TTCACA-A-
1 ATTATTTTATT-ATATAT
20738296 ATTATTATTATTAT-TAT
1 ATTATT-TTATTATATAT
* **
20738313 TTTACATTATTAT-T-T
1 ATTATTTTATTATATAT
*
20738328 -TTATATTATTATTATAT
1 ATTATTTTATTA-TATAT
* *
20738345 CTTACTTGTATTATATAT
1 ATTA-TTTTATTATATAT
20738363 -TTATTAATTATTTATATAT
1 ATTATT--TTA-TTATATAT
20738382 ATT
1 ATT
20738385 GTTCTTACAT
Statistics
Matches: 96, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
14 10 0.10
15 7 0.07
16 16 0.17
17 18 0.19
18 14 0.15
19 19 0.20
20 12 0.12
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (17 bp):
ATTATTTTATTATATAT
Found at i:20738315 original size:25 final size:25
Alignment explanation
Indices: 20738272--20738337 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
20738262 TTATTATTAT
*
20738272 TTATTATATCTTATT-TTTTCACA-AA
1 TTATTAT-TATTATTATTTT-ACATAA
*
20738297 TTATTATTATTATTATTTTACATTA
1 TTATTATTATTATTATTTTACATAA
*
20738322 TTATTTTTA-TATTATT
1 TTATTATTATTATTATT
20738338 ATTATATCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATTATTATTATTATTTTACATAA
Found at i:20738335 original size:14 final size:14
Alignment explanation
Indices: 20738304--20738340 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20738294 AAATTATTAT
20738304 TATTATTA-TTTTA
1 TATTATTATTTTTA
*
20738317 CATTATTATTTTTA
1 TATTATTATTTTTA
20738331 TATTATTATT
1 TATTATTATT
20738341 ATATCTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTATTTTTA
Found at i:20738368 original size:33 final size:31
Alignment explanation
Indices: 20738297--20738379 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 31
20738287 TTTTCACAAA
* *
20738297 TTATTATTATTATTATTTTACATTATTATTTT
1 TTATTATTATTA-TATCTTACATTATTATTAT
*
20738329 TATATTATTATTATATCTTACTTGTATTATATAT
1 T-TATTATTATTATATCTTACAT-TATTAT-TAT
20738363 TTATTAATTATTTATAT
1 TTATT-ATTA-TTATAT
20738380 ATATTGTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 9 0.21
33 21 0.49
34 7 0.16
35 6 0.14
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (31 bp):
TTATTATTATTATATCTTACATTATTATTAT
Found at i:20738928 original size:13 final size:12
Alignment explanation
Indices: 20738874--20738931 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 12
20738864 CATTTCATTT
20738874 TTTTATATATATA
1 TTTTATATAT-TA
** *
20738887 TTGCATATATCA
1 TTTTATATATTA
20738899 TGTGTTATATATTA
1 T-T-TTATATATTA
20738913 TTTTATATATTTA
1 TTTTATATA-TTA
20738926 TTTTAT
1 TTTTAT
20738932 GAATATGTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
12 9 0.25
13 19 0.53
14 8 0.22
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.60
Consensus pattern (12 bp):
TTTTATATATTA
Found at i:20750897 original size:210 final size:211
Alignment explanation
Indices: 20750622--20751174 Score: 746
Period size: 210 Copynumber: 2.6 Consensus size: 211
20750612 TCATCAGGGC
* * *
20750622 AGATCCAAGATGACAGATCTTATCTCTCTATATTCGGCGGGGAGCAAATCGAAGATATAGCTGAT
1 AGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAAATCGAAGACATAGCTGAT
*
20750687 TTGGCTTTCACGTGTTTACGATGAAGCAAATTTAAGATGATTTGTCATCTCTGTATTGTCAGAGA
66 TTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGA
* *
20750752 ACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAACAGACACATAGCAGATCTCACCTTCAGA
131 ACAAATCGAAGTCTGGAATCTCCACTTCAATGGAGAACAGACACACAGCAGATCTCACCTTCAGA
* * * *
20750817 TGTTTACG-TTGAAG-T
196 CGATTA-GACTGAAGCA
* * *
20750832 AGATCCAAGAGGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAGATCGAAAACATAGCTGAT
1 AGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAAATCGAAGACATAGCTGAT
*
20750897 TTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTTTATTGTCAGAGA
66 TTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGA
* * *
20750962 ACAAATCGAAGTCTGGAATCTCCACTTCAATGGAGAGCAGATACACAGCAGATCTGACCTTCAGA
131 ACAAATCGAAGTCTGGAATCTCCACTTCAATGGAGAACAGACACACAGCAGATCTCACCTTCAGA
*
20751027 CGATTAGACTGAGGCA
196 CGATTAGACTGAAGCA
** * * * * *
20751043 AGATCCAAGATGATTTG-GC--ATC-CT-TGTGCTT--ACAAGGAACAAATCGAAGACATAGCTG
1 AGATCCAAGATGA-CAGATCTTATCTCTCTGT-ATTCGGCAGGGAGCAAATCGAAGACATAGCTG
* * * * *
20751101 ATTTGGCTTTCACGTGCTTACGATGAAGAAAATCTAAGATAATTTGGCATCTCTGTATTATCAGA
64 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
20751166 GAACAAATC
129 GAACAAATC
20751175 AAAGAAGCAG
Statistics
Matches: 305, Mismatches: 34, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
206 90 0.30
207 3 0.01
208 4 0.01
209 4 0.01
210 190 0.62
211 13 0.04
212 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (211 bp):
AGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCAGGGAGCAAATCGAAGACATAGCTGAT
TTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGA
ACAAATCGAAGTCTGGAATCTCCACTTCAATGGAGAACAGACACACAGCAGATCTCACCTTCAGA
CGATTAGACTGAAGCA
Found at i:20752799 original size:25 final size:23
Alignment explanation
Indices: 20752763--20752820 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 23
20752753 TTTACCTTAC
20752763 TTTTA-TATTATACATTATAAGATTA
1 TTTTATTA-TATACATTAT--GATTA
* *
20752788 TTTTATTATATATATTATTATTA
1 TTTTATTATATACATTATGATTA
20752811 -TTTATTATAT
1 TTTTATTATAT
20752821 CTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 10 0.33
23 4 0.13
25 14 0.47
26 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATTATATACATTATGATTA
Found at i:20752801 original size:20 final size:22
Alignment explanation
Indices: 20752778--20752820 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20752768 TATTATACAT
20752778 TATAAGATTA-T-TTTATTATA
1 TATAAGATTATTATTTATTATA
**
20752798 TATATTATTATTATTTATTATA
1 TATAAGATTATTATTTATTATA
20752820 T
1 T
20752821 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATAAGATTATTATTTATTATA
Found at i:20752825 original size:20 final size:17
Alignment explanation
Indices: 20752784--20752927 Score: 59
Period size: 19 Copynumber: 8.2 Consensus size: 17
20752774 ACATTATAAG
20752784 ATTATTTTATTATATAT
1 ATTATTTTATTATATAT
20752801 ATTATTATTATTTATTATAT
1 ATTATT-TTA-TTA-TATAT
* *
20752821 CTTATTTT-TTCGCAAAT-T
1 ATTATTTTATT---ATATAT
20752839 ATTATTATTATTAT-TAT
1 ATTATT-TTATTATATAT
* **
20752856 TTTACATTATTAT-T-T
1 ATTATTTTATTATATAT
*
20752871 -TTATATTATTATTATAT
1 ATTATTTTATTA-TATAT
* *
20752888 CTTACTTGTATTATATAT
1 ATTA-TTTTATTATATAT
20752906 -TTATTAATTATTTATATAT
1 ATTATT--TTA-TTATATAT
20752925 ATT
1 ATT
20752928 GTTCTTACAT
Statistics
Matches: 98, Mismatches: 11, Indels: 33
0.69 0.08 0.23
Matches are distributed among these distances:
14 10 0.10
15 2 0.02
16 12 0.12
17 17 0.17
18 19 0.19
19 23 0.23
20 15 0.15
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (17 bp):
ATTATTTTATTATATAT
Found at i:20752844 original size:3 final size:3
Alignment explanation
Indices: 20752836--20752885 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
20752826 TTTTTCGCAA
* *
20752836 ATT ATT ATT ATT ATT ATT ATT -TT A-C ATT ATT ATT TTT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20752881 ATT AT
1 ATT AT
20752886 ATCTTACTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 5 0.12
3 35 0.88
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20752911 original size:33 final size:31
Alignment explanation
Indices: 20752801--20752922 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 31
20752791 TATTATATAT
* * * *
20752801 ATTATTATTATTTATTATATCTTATTTTTTCGC
1 ATTATTATTATTTATTAT-TATTATATCTT-AC
*
20752834 A-AATTATTA-TTATTATTATTAT-T-TTAC
1 ATTATTATTATTTATTATTATTATATCTTAC
*
20752861 ATTATTATTTTTATATTATTATTATATCTTAC
1 ATTATTATTATT-TATTATTATTATATCTTAC
*
20752893 TTGTATTATATATTTATTAATTATTTATAT
1 AT-TATTAT-TATTTATT-ATTA-TTATAT
20752923 ATATTGTTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
27 2 0.03
28 8 0.11
29 2 0.03
30 17 0.23
31 8 0.11
32 12 0.16
33 11 0.15
34 7 0.10
35 6 0.08
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (31 bp):
ATTATTATTATTTATTATTATTATATCTTAC
Found at i:20755531 original size:13 final size:13
Alignment explanation
Indices: 20755513--20755539 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20755503 AAAATAATCA
20755513 CACACGGGCGTGT
1 CACACGGGCGTGT
20755526 CACACGGGCGTGT
1 CACACGGGCGTGT
20755539 C
1 C
20755540 CCGTCTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:20757497 original size:20 final size:19
Alignment explanation
Indices: 20757454--20757497 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
20757444 CAGCTTTTTT
* *
20757454 GAGTTGTAGTAGTTTTTTC
1 GAGTTGTAGTAGTATCTTC
20757473 GAGTTGTAGTTAGTATCTTC
1 GAGTTGTAG-TAGTATCTTC
*
20757493 TAGTT
1 GAGTT
20757498 AACTTAGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (19 bp):
GAGTTGTAGTAGTATCTTC
Found at i:20761240 original size:50 final size:50
Alignment explanation
Indices: 20761160--20761357 Score: 209
Period size: 50 Copynumber: 4.0 Consensus size: 50
20761150 GACCTTGTAT
* * * *
20761160 ATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTGGATTTTGA
1 ATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTTGA
* * *
20761210 ATATTTGGCCATGA-AGGTATGCACAAATGTGATATTATATTTGATTTTGT
1 ATATTCGGCCAT-ATAGGTATGCACATATGTGATATTATATTTGATTTTGA
* * * ** * * * * *
20761260 ATATTCAGCCATATAAGTAAGTTCATATTTGATGTTAAATTTGATCTTGC
1 ATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTTGA
* *
20761310 ATATTCGGCCATATATGTATGCACATATGTGATATTATATTCGATTTT
1 ATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTT
20761358 CTCTAATTGA
Statistics
Matches: 117, Mismatches: 29, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
49 1 0.01
50 115 0.98
51 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (50 bp):
ATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTTGA
Found at i:20761332 original size:100 final size:100
Alignment explanation
Indices: 20761159--20761357 Score: 256
Period size: 100 Copynumber: 2.0 Consensus size: 100
20761149 TGACCTTGTA
* * * * * *
20761159 TATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTGGATTTTGAATATTTGGCCATGA
1 TATATTCAGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
*
20761224 AGGTATGCACAAATGTGATATTATATTTGATTTTG
66 AGGTATGCACAAATGTGATATTATATTCGATTTTG
* * * * *
20761259 TATATTCAGCCATATAAGTAAGTTCATATTTGATGTTAAATTTGATCTTGCATATTCGGCCAT-A
1 TATATTCAGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
* *
20761323 TATGTATGCACATATGTGATATTATATTCGATTTT
66 -AGGTATGCACAAATGTGATATTATATTCGATTTT
20761358 CTCTAATTGA
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 83 0.99
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (100 bp):
TATATTCAGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
AGGTATGCACAAATGTGATATTATATTCGATTTTG
Found at i:20779220 original size:50 final size:50
Alignment explanation
Indices: 20779140--20779337 Score: 227
Period size: 50 Copynumber: 4.0 Consensus size: 50
20779130 GACCTTGTAT
* * * * *
20779140 ATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTGGATTTTGA
1 ATATTTGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTTGA
* *
20779190 ATATTTGGCCATGA-AGGTATGCACAAATGTGATATTATATTTGAATTTGA
1 ATATTTGGCCAT-ATAGGTATGCACATATGTGATATTATATTTGATTTTGA
* * * * * * * * *
20779240 ATATTCGGCCATATAAGTAAGTACATATTTGATGTTAAATTTGATCTTGC
1 ATATTTGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTTGA
*
20779290 ATATTTGACCATATAGGTATGCACATATGTGATATTATATTTGATTTT
1 ATATTTGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTT
20779338 CTATCGACCA
Statistics
Matches: 119, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
49 1 0.01
50 117 0.98
51 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (50 bp):
ATATTTGGCCATATAGGTATGCACATATGTGATATTATATTTGATTTTGA
Found at i:20779313 original size:100 final size:100
Alignment explanation
Indices: 20779140--20779333 Score: 282
Period size: 100 Copynumber: 1.9 Consensus size: 100
20779130 GACCTTGTAT
* * * * *
20779140 ATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTGGATTTTGAATATTTGGCCATGAA
1 ATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTTGACCATGAA
20779205 GGTATGCACAAATGTGATATTATATTTGAATTTGA
66 GGTATGCACAAATGTGATATTATATTTGAATTTGA
* * * *
20779240 ATATTCGGCCATATAAGTAAGTACATATTTGATGTTAAATTTGATCTTGCATATTTGACCAT-AT
1 ATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTTGACCATGA-
*
20779304 AGGTATGCACATATGTGATATTATATTTGA
65 AGGTATGCACAAATGTGATATTATATTTGA
20779334 TTTTCTATCG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 1 0.01
100 82 0.99
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (100 bp):
ATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTTGACCATGAA
GGTATGCACAAATGTGATATTATATTTGAATTTGA
Found at i:20791977 original size:3 final size:3
Alignment explanation
Indices: 20791969--20792014 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
20791959 TATGTTAACT
20791969 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20792015 AGCATCTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20798365 original size:27 final size:26
Alignment explanation
Indices: 20798335--20798396 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
20798325 AGATAATTAA
20798335 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
20798362 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
20798389 AATAAAAT
1 AATAAAAT
20798397 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:20809778 original size:20 final size:20
Alignment explanation
Indices: 20809753--20809793 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20809743 TGTTATGCTC
20809753 TTGCTTTTCGCATATTAAGT
1 TTGCTTTTCGCATATTAAGT
*
20809773 TTGCTTTTTGCATATTAAGT
1 TTGCTTTTCGCATATTAAGT
20809793 T
1 T
20809794 CAGCAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.54
Consensus pattern (20 bp):
TTGCTTTTCGCATATTAAGT
Found at i:20812958 original size:84 final size:84
Alignment explanation
Indices: 20812865--20813034 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
20812855 AATCAACATG
*
20812865 TACCGATTTTTTGGTCAATCGATTCAATATCCTCTTCTGAACTAATATCTCGACTTGCCCTTAGT
1 TACCGATTTTTGGGTCAATCGATTCAATATCCTCTTCTGAACTAATATCTCGACTTGCCCTTAGT
*
20812930 CCAACCGATCGATTCAACC
66 CCAACCGACCGATTCAACC
20812949 TACCGATTTTTGGGTCAATCGATTCAATATCCTCTTCTGAACTAATATCTCGACTTGCCCTTAGT
1 TACCGATTTTTGGGTCAATCGATTCAATATCCTCTTCTGAACTAATATCTCGACTTGCCCTTAGT
20813014 CCAACCGACCGATTCAACC
66 CCAACCGACCGATTCAACC
20813033 TA
1 TA
20813035 ACTCAAATAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (84 bp):
TACCGATTTTTGGGTCAATCGATTCAATATCCTCTTCTGAACTAATATCTCGACTTGCCCTTAGT
CCAACCGACCGATTCAACC
Found at i:20813123 original size:21 final size:21
Alignment explanation
Indices: 20813099--20813167 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
20813089 AATGTATTTA
20813099 AATAAAACAAACACATGTTAG
1 AATAAAACAAACACATGTTAG
**
20813120 AATAACAAGGAA-A-ATGTATTTA-
1 AATAA-AACAAACACATG---TTAG
20813142 AATAAAACAAACACATGTTAG
1 AATAAAACAAACACATGTTAG
20813163 AATAA
1 AATAA
20813168 CAAGGGACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
20 6 0.16
21 15 0.41
22 10 0.27
23 6 0.16
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.22
Consensus pattern (21 bp):
AATAAAACAAACACATGTTAG
Found at i:20813131 original size:43 final size:43
Alignment explanation
Indices: 20813084--20813172 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
20813074 CAACCTTAAG
20813084 AGGAAAATGTATTTAAATAAAACAAACACATGTTAGAATAACA
1 AGGAAAATGTATTTAAATAAAACAAACACATGTTAGAATAACA
20813127 AGGAAAATGTATTTAAATAAAACAAACACATGTTAGAATAACA
1 AGGAAAATGTATTTAAATAAAACAAACACATGTTAGAATAACA
20813170 AGG
1 AGG
20813173 GACACCAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.22
Consensus pattern (43 bp):
AGGAAAATGTATTTAAATAAAACAAACACATGTTAGAATAACA
Found at i:20816599 original size:27 final size:27
Alignment explanation
Indices: 20816465--20816599 Score: 121
Period size: 27 Copynumber: 5.0 Consensus size: 27
20816455 CACGAAAATG
* * * *
20816465 TTCCTTTTCAGAGATAGTCATAAAGAC
1 TTCCTTTACAGAGATTGTCACAAAGGC
* *
20816492 TTCCTTTAACAGAGATCGCCACAAAGGC
1 TTCCTTT-ACAGAGATTGTCACAAAGGC
* * *
20816520 ATCCTTTATAGAGATTGTCACAAAGAC
1 TTCCTTTACAGAGATTGTCACAAAGGC
* * *
20816547 TCCCCTTT-TAGATATTGTCACAAAGGC
1 T-TCCTTTACAGAGATTGTCACAAAGGC
20816574 TTCCTTTACAGAGATT-TCCACAAAGG
1 TTCCTTTACAGAGATTGT-CACAAAGG
20816600 AGTTTCTTCC
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
26 6 0.07
27 55 0.63
28 26 0.30
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (27 bp):
TTCCTTTACAGAGATTGTCACAAAGGC
Found at i:20823929 original size:129 final size:129
Alignment explanation
Indices: 20823699--20823957 Score: 518
Period size: 129 Copynumber: 2.0 Consensus size: 129
20823689 AATACGAACC
20823699 ATGCAATAATATTAAAATAAATTTTCTTTTTAGCTCAAATTTGTGGTCCCGAAACCACTATTCCG
1 ATGCAATAATATTAAAATAAATTTTCTTTTTAGCTCAAATTTGTGGTCCCGAAACCACTATTCCG
20823764 ATTTCATTGAAAATGGGCTGTTACTTGTCCAATCAAGCATTTGCACTTGGTAATGAATATTCTA
66 ATTTCATTGAAAATGGGCTGTTACTTGTCCAATCAAGCATTTGCACTTGGTAATGAATATTCTA
20823828 ATGCAATAATATTAAAATAAATTTTCTTTTTAGCTCAAATTTGTGGTCCCGAAACCACTATTCCG
1 ATGCAATAATATTAAAATAAATTTTCTTTTTAGCTCAAATTTGTGGTCCCGAAACCACTATTCCG
20823893 ATTTCATTGAAAATGGGCTGTTACTTGTCCAATCAAGCATTTGCACTTGGTAATGAATATTCTA
66 ATTTCATTGAAAATGGGCTGTTACTTGTCCAATCAAGCATTTGCACTTGGTAATGAATATTCTA
20823957 A
1 A
20823958 CTCAAAATTG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (129 bp):
ATGCAATAATATTAAAATAAATTTTCTTTTTAGCTCAAATTTGTGGTCCCGAAACCACTATTCCG
ATTTCATTGAAAATGGGCTGTTACTTGTCCAATCAAGCATTTGCACTTGGTAATGAATATTCTA
Found at i:20824877 original size:36 final size:36
Alignment explanation
Indices: 20824830--20824900 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
20824820 GGCATTAGCC
* *
20824830 ATCTTGAAAAGAAAAGAAGAGTTGTTATTAAAATTA
1 ATCTTAAAAAGAAAAGAAAAGTTGTTATTAAAATTA
*
20824866 ATCTTAAAAAGAAAGGAAAAGTTGTTATTAAAATT
1 ATCTTAAAAAGAAAAGAAAAGTTGTTATTAAAATT
20824901 CCAACGGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (36 bp):
ATCTTAAAAAGAAAAGAAAAGTTGTTATTAAAATTA
Found at i:20839684 original size:17 final size:17
Alignment explanation
Indices: 20839658--20839698 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
20839648 AGAGATGGAA
*
20839658 TCAAGAAATGTTATTTT
1 TCAAGGAATGTTATTTT
20839675 TCAAGGAATGTTATTTT
1 TCAAGGAATGTTATTTT
20839692 TCAAGGA
1 TCAAGGA
20839699 TTCTTATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (17 bp):
TCAAGGAATGTTATTTT
Found at i:20839705 original size:17 final size:17
Alignment explanation
Indices: 20839658--20839705 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
20839648 AGAGATGGAA
* *
20839658 TCAAGAAATGTTATTTT
1 TCAAGGAATCTTATTTT
*
20839675 TCAAGGAATGTTATTTT
1 TCAAGGAATCTTATTTT
*
20839692 TCAAGGATTCTTAT
1 TCAAGGAATCTTAT
20839706 GTGATCTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (17 bp):
TCAAGGAATCTTATTTT
Found at i:20850962 original size:13 final size:12
Alignment explanation
Indices: 20850931--20850968 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
20850921 TAATTATCAC
20850931 TTAATTAA-TAT
1 TTAATTAATTAT
20850942 TATAATTAATTAT
1 T-TAATTAATTAT
20850955 GTTAATTAATTAT
1 -TTAATTAATTAT
20850968 T
1 T
20850969 ATTTTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.04
12 8 0.33
13 14 0.58
14 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
TTAATTAATTAT
Found at i:20853543 original size:17 final size:17
Alignment explanation
Indices: 20853510--20853548 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
20853500 TAAGCTTTTG
20853510 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
20853527 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
20853544 ATTTT
1 ATTTT
20853549 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:20854314 original size:15 final size:15
Alignment explanation
Indices: 20854290--20854319 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20854280 TGGAGATCGA
*
20854290 GGAAATGGTCGTGGT
1 GGAAAAGGTCGTGGT
20854305 GGAAAAGGTCGTGGT
1 GGAAAAGGTCGTGGT
20854320 CAAGAAGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (15 bp):
GGAAAAGGTCGTGGT
Found at i:20857662 original size:15 final size:15
Alignment explanation
Indices: 20857642--20857672 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20857632 GTCATGTAAG
20857642 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
20857657 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
20857672 T
1 T
20857673 ATATTGTTTT
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:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:20857862 original size:17 final size:17
Alignment explanation
Indices: 20857829--20857867 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
20857819 TAAGCTTTTG
20857829 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
20857846 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
20857863 ATTTT
1 ATTTT
20857868 CCACAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:20860634 original size:21 final size:21
Alignment explanation
Indices: 20860606--20860658 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
20860596 CATAACTTGT
20860606 ATAA-CTATCATTAAACATTC
1 ATAATCTATCATTAAACATTC
20860626 ATAATCTATCATTAAACATTC
1 ATAATCTATCATTAAACATTC
*
20860647 ACAATCTATCAT
1 ATAATCTATCAT
20860659 CAATCATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAATCTATCATTAAACATTC
Found at i:20863322 original size:25 final size:25
Alignment explanation
Indices: 20863294--20863348 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
20863284 TATATTTTTT
*
20863294 ATTTAT-ATATTTTAAATTAAATATA
1 ATTTATGAAATTTTAAATT-AATATA
*
20863319 ATTT-TGAAATTTTAAATTTATATA
1 ATTTATGAAATTTTAAATTAATATA
20863343 ATTTAT
1 ATTTAT
20863349 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTTATGAAATTTTAAATTAATATA
Found at i:20866276 original size:25 final size:25
Alignment explanation
Indices: 20866187--20866282 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
20866177 CAACTCTTAT
*
20866187 GAGCATCCCGATA-TTAGGCTCTCAC
1 GAGCTTCCCGATATTTA-GCTCTCAC
* * * *
20866212 GAGCTTCCTGATACTTGGTTCTCAC
1 GAGCTTCCCGATATTTAGCTCTCAC
* *
20866237 GAGCTTCCCGTTATTTAGCTCTCAT
1 GAGCTTCCCGATATTTAGCTCTCAC
* *
20866262 GAGCTTCCCAATATTTGGCTC
1 GAGCTTCCCGATATTTAGCTC
20866283 GTAAGAGCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 55 0.96
26 2 0.04
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGATATTTAGCTCTCAC
Found at i:20866291 original size:50 final size:50
Alignment explanation
Indices: 20866237--20866352 Score: 144
Period size: 50 Copynumber: 2.3 Consensus size: 50
20866227 TGGTTCTCAC
** * * * *
20866237 GAGCTTCCCGTTATTTAGCTCTCATGAGCTTCCCAATATTTGGCTCGTAA
1 GAGCTTCCCGTTATACAACTCACATGAGCTTCCCAATATATGGCTCGGAA
* **
20866287 GAGCTTCTCGTTATACAACTCACATGAGCTTCCCGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATACAACTCACATGAGCTTCCCAATATATGGCTCGGAA
20866337 GAGCTTCCCGTT-TACA
1 GAGCTTCCCGTTATACA
20866353 TGTTTGTATA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 4 0.07
50 52 0.93
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (50 bp):
GAGCTTCCCGTTATACAACTCACATGAGCTTCCCAATATATGGCTCGGAA
Found at i:20866340 original size:25 final size:25
Alignment explanation
Indices: 20866237--20866348 Score: 89
Period size: 25 Copynumber: 4.5 Consensus size: 25
20866227 TGGTTCTCAC
* * *
20866237 GAGCTTCCCGTTATTTAGCTCTCAT
1 GAGCTTCCCGTTATATAGCTCGCAA
** * * *
20866262 GAGCTTCCCAATATTTGGCTCGTAA
1 GAGCTTCCCGTTATATAGCTCGCAA
* * * * *
20866287 GAGCTTCTCGTTATACAACTCACAT
1 GAGCTTCCCGTTATATAGCTCGCAA
* *
20866312 GAGCTTCCCGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATATAGCTCGCAA
20866337 GAGCTTCCCGTT
1 GAGCTTCCCGTT
20866349 TACATGTTTG
Statistics
Matches: 64, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCGCAA
Found at i:20886140 original size:13 final size:13
Alignment explanation
Indices: 20886110--20886134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20886100 TCAACCGAGA
20886110 ATGTGTATTCGGT
1 ATGTGTATTCGGT
20886123 ATGTGTATTCGG
1 ATGTGTATTCGG
20886135 CTTGTGAATG
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:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (13 bp):
ATGTGTATTCGGT
Found at i:20893328 original size:14 final size:14
Alignment explanation
Indices: 20893309--20893335 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20893299 ATATTTGACT
20893309 TGTTCTTAATTCTA
1 TGTTCTTAATTCTA
20893323 TGTTCTTAATTCT
1 TGTTCTTAATTCT
20893336 TATTTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (14 bp):
TGTTCTTAATTCTA
Found at i:20919668 original size:25 final size:25
Alignment explanation
Indices: 20919640--20919758 Score: 134
Period size: 25 Copynumber: 4.8 Consensus size: 25
20919630 CAACTCTTAT
*
20919640 GAGCGTCCCGATATTTGGCTCTCAC
1 GAGCTTCCCGATATTTGGCTCTCAC
*
20919665 GAGCTTCCCGATACTTGGCTCTCAC
1 GAGCTTCCCGATATTTGGCTCTCAC
* * * *
20919690 GAGCTTCTCGTTATTTAGCTCTCAT
1 GAGCTTCCCGATATTTGGCTCTCAC
* *
20919715 GAGCTTCCCGAT-TAATGGCTCTC-T
1 GAGCTTCCCGATAT-TTGGCTCTCAC
*
20919739 TAGCTTCCCGATATTTGGCT
1 GAGCTTCCCGATATTTGGCT
20919759 TGCAAGAGCT
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
24 18 0.23
25 61 0.77
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGATATTTGGCTCTCAC
Found at i:20926173 original size:21 final size:20
Alignment explanation
Indices: 20926148--20926197 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
20926138 TTTAATTTTG
*
20926148 TATTAAATAAAAAATTAAAA
1 TATTAAAGAAAAAATTAAAA
* *
20926168 TAATTATAAGACAAATTTAAAA
1 T-ATTA-AAGAAAAAATTAAAA
20926190 TATTAAAG
1 TATTAAAG
20926198 GAATAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
22 13 0.52
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (20 bp):
TATTAAAGAAAAAATTAAAA
Found at i:20932004 original size:5 final size:5
Alignment explanation
Indices: 20931994--20932025 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
20931984 AAGATATTAT
20931994 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
20932026 ATTAAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:20932628 original size:17 final size:16
Alignment explanation
Indices: 20932608--20932653 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
20932598 TATTTATCTA
20932608 ATTATATTTCTATTATT
1 ATTATATTTCTATT-TT
20932625 ATTATATTTCTA-TTT
1 ATTATATTTCTATTTT
*
20932640 ATTGTATTTCTATT
1 ATTATATTTCTATT
20932654 CCTATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 12 0.44
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTATATTTCTATTTT
Found at i:20932929 original size:26 final size:25
Alignment explanation
Indices: 20932900--20932958 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
20932890 ATATTATTTA
*
20932900 TTTTTATCGTTTTACCTATTTTAAAC
1 TTTTTATC-TATTACCTATTTTAAAC
* * *
20932926 TTTTATATCTATTACTTGTTTTAAAG
1 TTTT-TATCTATTACCTATTTTAAAC
20932952 TTTTTAT
1 TTTTTAT
20932959 ATTGTTTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.11
26 21 0.75
27 4 0.14
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (25 bp):
TTTTTATCTATTACCTATTTTAAAC
Done.