Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 101 of 144
Found at i:30946876 original size:46 final size:45
Alignment explanation
Indices: 30946813--30946928 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 45
30946803 AACAATTAAG
* *
30946813 TAACTAAAATGAATTTAATAAAAATAAAGTCCAACAACTCAATTAT
1 TAACTAAGATGAGTTT-ATAAAAATAAAGTCCAACAACTCAATTAT
* *
30946859 TAACTAAGATGAG-TT-T---AATAAAGTCCAGCAACTTAATTAT
1 TAACTAAGATGAGTTTATAAAAATAAAGTCCAACAACTCAATTAT
*
30946899 TAACTAAGATGAGTTTACTAAAATTAAAGT
1 TAACTAAGATGAGTTTA-TAAAAATAAAGT
30946929 TCAGCTTGCA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
40 35 0.59
41 2 0.03
43 2 0.03
45 2 0.03
46 18 0.31
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.31
Consensus pattern (45 bp):
TAACTAAGATGAGTTTATAAAAATAAAGTCCAACAACTCAATTAT
Found at i:30946882 original size:40 final size:40
Alignment explanation
Indices: 30946835--30946920 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
30946825 ATTTAATAAA
30946835 AATAAAGTCCAACAACTCAATTATTAACTAAGATGAGTTT
1 AATAAAGTCCAACAACTCAATTATTAACTAAGATGAGTTT
* *
30946875 AATAAAGTCCAGCAACTTAATTATTAACTAAGATGAGTTT
1 AATAAAGTCCAACAACTCAATTATTAACTAAGATGAGTTT
*
30946915 ACTAAA
1 AATAAA
30946921 ATTAAAGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.30
Consensus pattern (40 bp):
AATAAAGTCCAACAACTCAATTATTAACTAAGATGAGTTT
Found at i:30949096 original size:26 final size:26
Alignment explanation
Indices: 30949047--30949111 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
30949037 TGCAATCTCA
*
30949047 ATTTCTTCAATCT--CACTTGTTTTT
1 ATTTCTTCAATCTCACACTTATTTTT
30949071 ATTTCTTCAATCTCACACTTATTTTT
1 ATTTCTTCAATCTCACACTTATTTTT
30949097 ATTTCTTCAATCTCA
1 ATTTCTTCAATCTCA
30949112 ATTTCTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 13 0.34
26 25 0.66
ACGTcount: A:0.22, C:0.23, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTCTTCAATCTCACACTTATTTTT
Found at i:30954108 original size:16 final size:17
Alignment explanation
Indices: 30954087--30954121 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30954077 TTTCTTAAAC
*
30954087 AAATTTT-GTGTTTTAA
1 AAATTTTCGTGTTTCAA
30954103 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
30954120 AA
1 AA
30954122 GTAAAATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:30954140 original size:21 final size:19
Alignment explanation
Indices: 30954108--30954162 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
30954098 TTTAAAAATT
*
30954108 TTCGTGTTTCAAAAGTAAAA
1 TTCGTGTTTCAAAA-AAAAA
30954128 TTCGTGTTTTCAAAAAAAAA
1 TTCGTG-TTTCAAAAAAAAA
30954148 TCTCGTGTTTCAAAA
1 T-TCGTGTTTCAAAA
30954163 TTTTTGTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (19 bp):
TTCGTGTTTCAAAAAAAAA
Found at i:30954172 original size:37 final size:36
Alignment explanation
Indices: 30954131--30954200 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
30954121 AGTAAAATTC
30954131 GTGTTTTCAAAAAAAAATCTCGTGTTTC-AAAATTTTT
1 GTGTTTTCAAAAAAAAAT-T-GTGTTTCTAAAATTTTT
*
30954168 GTGTTTTTAAAAAAAAATTGTGTTTCTAAAATT
1 GTGTTTTCAAAAAAAAATTGTGTTTCTAAAATT
30954201 CTTATATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 7 0.23
36 7 0.23
37 17 0.55
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (36 bp):
GTGTTTTCAAAAAAAAATTGTGTTTCTAAAATTTTT
Found at i:30959025 original size:19 final size:20
Alignment explanation
Indices: 30958989--30959027 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
30958979 CAAGTAGAAT
*
30958989 TAAGCTCAGAATCAGCTCAA
1 TAAGCTCAGAACCAGCTCAA
30959009 TAAGCTCA-AACCAGCTCAA
1 TAAGCTCAGAACCAGCTCAA
30959028 CTTAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (20 bp):
TAAGCTCAGAACCAGCTCAA
Found at i:30963993 original size:7 final size:7
Alignment explanation
Indices: 30963981--30964006 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
30963971 ATTGCATATT
30963981 TGAGATA
1 TGAGATA
30963988 TGAGATA
1 TGAGATA
30963995 TGAGATA
1 TGAGATA
30964002 TGAGA
1 TGAGA
30964007 ATGTCTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (7 bp):
TGAGATA
Found at i:30965426 original size:22 final size:22
Alignment explanation
Indices: 30965394--30965437 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30965384 TTTTGAACCA
30965394 TTACCAATTCGTACCAAATCCC
1 TTACCAATTCGTACCAAATCCC
* *
30965416 TTACCATTTCGTACCAATTCCC
1 TTACCAATTCGTACCAAATCCC
30965438 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (22 bp):
TTACCAATTCGTACCAAATCCC
Found at i:30972217 original size:10 final size:10
Alignment explanation
Indices: 30972204--30972259 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
30972194 TGCTCACTCG
30972204 AGCTCAATTC
1 AGCTCAATTC
30972214 AGCTC-ATTC
1 AGCTCAATTC
*
30972223 GAGCTCAAGTC
1 -AGCTCAATTC
30972234 AGCTCACA--C
1 AGCTCA-ATTC
30972243 GAGCTCAATTC
1 -AGCTCAATTC
30972254 AGCTCA
1 AGCTCA
30972260 TTGAGCTCGC
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 6 0.15
10 28 0.72
11 5 0.13
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:30972224 original size:20 final size:20
Alignment explanation
Indices: 30972195--30972259 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
30972185 ATGCGGTTCT
30972195 GCTCACTCGAGCTCAATTCA
1 GCTCACTCGAGCTCAATTCA
* *
30972215 GCTCATTCGAGCTCAAGTCA
1 GCTCACTCGAGCTCAATTCA
*
30972235 GCTCACACGAGCTCAATTCA
1 GCTCACTCGAGCTCAATTCA
30972255 GCTCA
1 GCTCA
30972260 TTGAGCTCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (20 bp):
GCTCACTCGAGCTCAATTCA
Found at i:30978035 original size:23 final size:22
Alignment explanation
Indices: 30977984--30978035 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
30977974 CCTCGTCTTT
30977984 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTGTTTCTTTTTCTAAC
*
30978006 -TCATTTTCTTTTCTTTCTTC-AAC
1 TTC-TTTT-GTTTCTTT-TTCTAAC
30978029 TTCTTTT
1 TTCTTTT
30978036 TCGATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 4 0.16
23 14 0.56
24 5 0.20
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCTTTTGTTTCTTTTTCTAAC
Found at i:30978095 original size:17 final size:18
Alignment explanation
Indices: 30978051--30978084 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30978041 TTTATCTTTT
30978051 TCAATTTCTTTCTCAATC
1 TCAATTTCTTTCTCAATC
30978069 TCAATTTCTTT-TCAAT
1 TCAATTTCTTTCTCAAT
30978085 TCTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:30978781 original size:22 final size:22
Alignment explanation
Indices: 30978756--30978807 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
30978746 ATCTCACGTT
*
30978756 TCACTTTCAAAGAAGAATTCAC
1 TCACTCTCAAAGAAGAATTCAC
30978778 TCACTCTCAAAGAAGAATTCAC
1 TCACTCTCAAAGAAGAATTCAC
30978800 TCACTCTC
1 TCACTCTC
30978808 GTGTTTGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.27
Consensus pattern (22 bp):
TCACTCTCAAAGAAGAATTCAC
Found at i:30981359 original size:6 final size:6
Alignment explanation
Indices: 30981289--30981341 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
30981279 AGCGAAGAGG
** * * *
30981289 AAGAAA AAG-AA AAGAAA GTGAAA AGGAAA TAGAAA ACGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
30981336 AAGAAA
1 AAGAAA
30981342 GTGCAAGTGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:30981377 original size:36 final size:36
Alignment explanation
Indices: 30981291--30981368 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
30981281 CGAAGAGGAA
*
30981291 GAAAAAG-AAAAGAAAGTGAAAAGGAAATAGAAAAC
1 GAAAAAGAAAAAGAAAGTGAAAAGGAAAAAGAAAAC
* *
30981326 GAAAAAGAAAAAGAAAGTG-CAAGTGAAAAAGAAATC
1 GAAAAAGAAAAAGAAAGTGAAAAG-GAAAAAGAAAAC
30981362 GAAAAAG
1 GAAAAAG
30981369 TGAGAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 10 0.26
36 28 0.74
ACGTcount: A:0.67, C:0.04, G:0.23, T:0.06
Consensus pattern (36 bp):
GAAAAAGAAAAAGAAAGTGAAAAGGAAAAAGAAAAC
Found at i:30986066 original size:15 final size:15
Alignment explanation
Indices: 30986046--30986086 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
30986036 TATACGAAAT
30986046 TTTAAAAAAAAGTGA
1 TTTAAAAAAAAGTGA
**
30986061 TTTAAAAAATTTGTGA
1 TTTAAAAAA-AAGTGA
30986077 TTTAAAAAAA
1 TTTAAAAAAA
30986087 CAAAAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
TTTAAAAAAAAGTGA
Found at i:30989599 original size:16 final size:16
Alignment explanation
Indices: 30989575--30989623 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
30989565 TTCGCTGTAT
30989575 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
30989591 TGGAGTAGAGGTGTAA
1 TGGAATAGAGGCGTAA
*
30989607 TGAAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
30989623 T
1 T
30989624 AGCAAATCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:30989874 original size:16 final size:16
Alignment explanation
Indices: 30989837--30989878 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
30989827 TTAATCATAT
*
30989837 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
30989853 TT-AAATATATTATAA
1 TTAAAATATATTATAA
30989868 TTAAAATATAT
1 TTAAAATATAT
30989879 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:30989885 original size:14 final size:15
Alignment explanation
Indices: 30989846--30989887 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30989836 TTTAAACATA
*
30989846 ATTATTATTAAATAT
1 ATTATAATTAAATAT
30989861 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
30989875 A-TATAATTTAATA
1 ATTATAATTAAATA
30989888 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:30989937 original size:61 final size:61
Alignment explanation
Indices: 30989872--30990059 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
30989862 TTATAATTAA
30989872 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * *
30989933 AATATATGATACT-ATAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTCA-AATCA
*
30989991 A
61 T
*
30989992 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
30990053 AATATAT
1 AATATAT
30990060 GATACTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
58 3 0.03
59 33 0.34
60 17 0.18
61 40 0.42
62 3 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:30989996 original size:16 final size:16
Alignment explanation
Indices: 30989952--30989998 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
30989942 TACTATAAAA
*
30989952 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
30989968 TATTATT-AAATATAT
1 TATAATTAAAATATAT
30989983 TATAATTAAAATATAT
1 TATAATTAAAATATAT
30989999 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:30990053 original size:120 final size:120
Alignment explanation
Indices: 30989835--30990081 Score: 467
Period size: 120 Copynumber: 2.0 Consensus size: 120
30989825 ATTTAATCAT
30989835 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
30989900 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
30989956 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
30990021 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
30990076 ATTTAA
1 ATTTAA
30990082 TTTTCTTATA
Statistics
Matches: 124, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
120 120 0.97
121 4 0.03
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:30990096 original size:57 final size:57
Alignment explanation
Indices: 30989903--30990099 Score: 184
Period size: 59 Copynumber: 3.4 Consensus size: 57
30989893 CTTAATAATC
*
30989903 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
1 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAACATAATTT
* * * * * * * * *
30989960 AACATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TTAATAAAATTCTTAATAAT
1 -A-AT-ATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAA--CATAAT--T
30990022 T
57 T
*
30990023 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
1 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAACATAATTT
*
30990080 AATTTTCTTATATGAATTTA
1 AATATTCTTATATGAATTTA
30990100 TACAATTTAA
Statistics
Matches: 107, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
57 21 0.20
58 4 0.04
59 31 0.29
60 14 0.13
61 31 0.29
62 4 0.04
63 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.44
Consensus pattern (57 bp):
AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAACATAATTT
Found at i:30993484 original size:24 final size:24
Alignment explanation
Indices: 30993457--30993511 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
30993447 AAATTGAGAA
*
30993457 AAAAAGATAAA-AAAGTTACAAAAG
1 AAAAAGA-AAAGAAAGTGACAAAAG
* * *
30993481 AAAATGAAAAGAAAGTGAGAAAAT
1 AAAAAGAAAAGAAAGTGACAAAAG
30993505 AAAAAGA
1 AAAAAGA
30993512 CGAAAAGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.11
Consensus pattern (24 bp):
AAAAAGAAAAGAAAGTGACAAAAG
Found at i:31001294 original size:18 final size:18
Alignment explanation
Indices: 31001268--31001331 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
31001258 GAACGAATCC
*
31001268 AAAATGAAATTGAGAAAA
1 AAAAAGAAATTGAGAAAA
*
31001286 AAAAAGAAATGAGAGAAAA
1 AAAAAGAAAT-TGAGAAAA
*
31001305 AGGAAAAGACATTGA-AAAA
1 A--AAAAGAAATTGAGAAAA
31001324 CAAAAAGA
1 -AAAAAGA
31001332 GAGTGAGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 15 0.39
19 12 0.32
20 3 0.08
21 8 0.21
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAAGAAATTGAGAAAA
Found at i:31003328 original size:25 final size:25
Alignment explanation
Indices: 31003294--31003345 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
31003284 TCATCTTAGT
* *
31003294 TTTAATTAATAAGTGTTTTTTTTAA
1 TTTAATTAATAAGTGTTGTTCTTAA
*
31003319 TTTATTTAATAAGTGTTGTTCTTAA
1 TTTAATTAATAAGTGTTGTTCTTAA
31003344 TT
1 TT
31003346 AATCTAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (25 bp):
TTTAATTAATAAGTGTTGTTCTTAA
Found at i:31004191 original size:43 final size:45
Alignment explanation
Indices: 31004141--31004234 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 45
31004131 TATCACTTTC
*
31004141 ATAGTGTG-G-CGTTCATCATATACCAAGGTTCTTATC-GTCATTG
1 ATAGTGTGTGACGTTCATCATATACCAAGGTTCCTATCAGTC-TTG
* *
31004184 ATAGTGTGTGAGGTTCATCATATACCAAGGTTCCTATCATTCTTG
1 ATAGTGTGTGACGTTCATCATATACCAAGGTTCCTATCAGTCTTG
31004229 ATAGTG
1 ATAGTG
31004235 GGTCGAGGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
43 8 0.18
44 1 0.02
45 34 0.76
46 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (45 bp):
ATAGTGTGTGACGTTCATCATATACCAAGGTTCCTATCAGTCTTG
Found at i:31004200 original size:45 final size:46
Alignment explanation
Indices: 31004151--31004243 Score: 136
Period size: 45 Copynumber: 2.0 Consensus size: 46
31004141 ATAGTGTGGC
* *
31004151 GTTCATCATATACCAAGGTTCTTATC-GTCATTGATAGTGTGT-GAG
1 GTTCATCATATACCAAGGTTCCTATCAGTC-TTGATAGTGGGTCGAG
*
31004196 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCAGTCTTGATAGTGGGTCGAG
31004242 GT
1 GT
31004244 CTTTTCTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 36 0.84
46 7 0.16
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCAGTCTTGATAGTGGGTCGAG
Found at i:31008966 original size:18 final size:19
Alignment explanation
Indices: 31008945--31009003 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
31008935 TTCCAAAAAC
31008945 AAAAGAGAGTG-AAAAGAA
1 AAAAGAGAGTGAAAAAGAA
*
31008963 AAAAGAGATTGAAAAAGAA
1 AAAAGAGAGTGAAAAAGAA
31008982 ATTGAAAGAGAG-GAAAAAGAA
1 A---AAAGAGAGTGAAAAAGAA
31009003 A
1 A
31009004 TAGTGGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 10 0.29
19 8 0.23
21 10 0.29
22 7 0.20
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.08
Consensus pattern (19 bp):
AAAAGAGAGTGAAAAAGAA
Found at i:31008999 original size:21 final size:22
Alignment explanation
Indices: 31008964--31009004 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31008954 TGAAAAGAAA
*
31008964 AAAGAGATTGAAAAAGAAATTG
1 AAAGAGATGGAAAAAGAAATTG
31008986 AAAGAGA-GGAAAAAGAAAT
1 AAAGAGATGGAAAAAGAAAT
31009005 AGTGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.12
Consensus pattern (22 bp):
AAAGAGATGGAAAAAGAAATTG
Found at i:31028029 original size:20 final size:22
Alignment explanation
Indices: 31027984--31028029 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
31027974 AGCTAGTGTT
*
31027984 TTTAATTTGTCTTAGCATATTA
1 TTTAATTTGTCTTAGCATACTA
*
31028006 TTTAATTTGTC-TA-CATGCTA
1 TTTAATTTGTCTTAGCATACTA
31028026 TTTA
1 TTTA
31028030 GTCCATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (22 bp):
TTTAATTTGTCTTAGCATACTA
Found at i:31031550 original size:26 final size:26
Alignment explanation
Indices: 31031521--31031615 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 26
31031511 TTTCACACTC
31031521 TTTTTCTTTTTCTTTTGTCACTCTTG
1 TTTTTCTTTTTCTTTTGTCACTCTTG
* * ** * *
31031547 TTTTTATCTCACTTTCGTCAGTCTT-
1 TTTTTCTTTTTCTTTTGTCACTCTTG
31031572 TTCTTTCTTTTTC-TTT-TCACTCTTTTTG
1 TT-TTTCTTTTTCTTTTGTCACTC---TTG
*
31031600 TTTCTCTTTTTCTTTT
1 TTTTTCTTTTTCTTTT
31031616 TCTTGCTCAA
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
24 5 0.10
25 4 0.08
26 25 0.50
27 11 0.22
28 5 0.10
ACGTcount: A:0.05, C:0.21, G:0.05, T:0.68
Consensus pattern (26 bp):
TTTTTCTTTTTCTTTTGTCACTCTTG
Found at i:31031588 original size:15 final size:15
Alignment explanation
Indices: 31031568--31031619 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
31031558 CTTTCGTCAG
31031568 TCTTTTCTTTCTTTT
1 TCTTTTCTTTCTTTT
**
31031583 TCTTTTCACTCTTTT
1 TCTTTTCTTTCTTTT
*
31031598 TGTTTCTCTTTTTCTTTT
1 TCTTT-TC--TTTCTTTT
31031616 TCTT
1 TCTT
31031620 GCTCAATGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 17 0.61
16 2 0.07
18 9 0.32
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (15 bp):
TCTTTTCTTTCTTTT
Found at i:31037479 original size:42 final size:42
Alignment explanation
Indices: 31037420--31037522 Score: 179
Period size: 42 Copynumber: 2.5 Consensus size: 42
31037410 GGAAATTGGT
*
31037420 CTACTCACACGAGCTGTGGGTCAGAATGTAAGCTATACGATG
1 CTACTCATACGAGCTGTGGGTCAGAATGTAAGCTATACGATG
31037462 CTACTCATACGAGCTGTGGGTCAGAATGTAAGCTATACGATG
1 CTACTCATACGAGCTGTGGGTCAGAATGTAAGCTATACGATG
* *
31037504 CTGCTCATACAAGCTGTGG
1 CTACTCATACGAGCTGTGG
31037523 AGTATTCATA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (42 bp):
CTACTCATACGAGCTGTGGGTCAGAATGTAAGCTATACGATG
Found at i:31044949 original size:20 final size:20
Alignment explanation
Indices: 31044924--31044968 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
31044914 CCAAATTAAT
*
31044924 TGTGTCTTAAC-TTAAATAAA
1 TGTGTCTAAACATT-AATAAA
*
31044944 TGTGTCTAAACATTAATTAA
1 TGTGTCTAAACATTAATAAA
31044964 TGTGT
1 TGTGT
31044969 TTTACTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTGTCTAAACATTAATAAA
Found at i:31047203 original size:11 final size:12
Alignment explanation
Indices: 31047173--31047205 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
31047163 TTCATCTTGT
31047173 AAAGAAAAATTG
1 AAAGAAAAATTG
31047185 AGAAGAAAAA-TG
1 A-AAGAAAAATTG
31047197 AAAGAAAAA
1 AAAGAAAAA
31047206 GAACAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 4 0.20
13 8 0.40
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (12 bp):
AAAGAAAAATTG
Found at i:31047298 original size:14 final size:15
Alignment explanation
Indices: 31047281--31047310 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31047271 AAAAAAATTG
31047281 AGAGT-GAAAAAGAA
1 AGAGTGGAAAAAGAA
31047295 AGAGTGGAAAAAGAA
1 AGAGTGGAAAAAGAA
31047310 A
1 A
31047311 AAGAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.63, C:0.00, G:0.30, T:0.07
Consensus pattern (15 bp):
AGAGTGGAAAAAGAA
Found at i:31053908 original size:20 final size:20
Alignment explanation
Indices: 31053856--31053909 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
31053846 TAAATCTTAT
* *
31053856 TTTAAGTGAAATATAATGTTA
1 TTTAAGT-AACTAAAATGTTA
** *
31053877 TTTACTTTACTAAAATGTTA
1 TTTAAGTAACTAAAATGTTA
31053897 TTTAAGTAACTAA
1 TTTAAGTAACTAA
31053910 TTTTTTAGTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (20 bp):
TTTAAGTAACTAAAATGTTA
Found at i:31059732 original size:36 final size:35
Alignment explanation
Indices: 31059685--31059756 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
31059675 CAACTCCGGA
31059685 GCTTGGCAAATAAGGAAA-GAGATCTTTTGAAGATAT
1 GCTTGGCAAAT-AGGAAAGGAGATCTTTT-AAGATAT
* * *
31059721 GCTTGGTAAATATGAAAGGTGATCTTTTAAGATAT
1 GCTTGGCAAATAGGAAAGGAGATCTTTTAAGATAT
31059756 G
1 G
31059757 TGATCCTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (35 bp):
GCTTGGCAAATAGGAAAGGAGATCTTTTAAGATAT
Found at i:31060129 original size:48 final size:48
Alignment explanation
Indices: 31060054--31060147 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
31060044 TAAGGGAATT
** *
31060054 CTGTTGAATCCTTTATTGTTGAGAGTTAAGCTGACTTAGGCATTTTTA
1 CTGTTGAATCCTTTATTACTGAGAGTTAAGCTAACTTAGGCATTTTTA
* *
31060102 CTGTTGAATCCTTTATTACTGCA-AGTTAGGCTAACTTAGGCGTTTT
1 CTGTTGAATCCTTTATTACTG-AGAGTTAAGCTAACTTAGGCATTTT
31060148 GAGCAAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (48 bp):
CTGTTGAATCCTTTATTACTGAGAGTTAAGCTAACTTAGGCATTTTTA
Found at i:31078936 original size:40 final size:40
Alignment explanation
Indices: 31078885--31079114 Score: 327
Period size: 40 Copynumber: 5.8 Consensus size: 40
31078875 ATTTGAATTT
* * *
31078885 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAG-TGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGA-TA
*
31078925 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATA
* *
31078965 TATCCGGGCTAAGACCTGAAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATA
* *
31079005 TATCCGGGCTAAGACCTGAAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATA
* *
31079045 TATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATA
* * *
31079085 TGTCCGGGTTAAGACCCGAAGGCAAATGTG
1 TATCCGGGCTAAGACCCGAAGGCAATTGTG
31079115 TTTGCGGCTA
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 173 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATA
Found at i:31083344 original size:17 final size:17
Alignment explanation
Indices: 31083322--31083360 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
31083312 ACCAACTCAA
31083322 GCTCAAGAACGTGATAG
1 GCTCAAGAACGTGATAG
*
31083339 GCTCAAGAACGTGATGG
1 GCTCAAGAACGTGATAG
31083356 GCTCA
1 GCTCA
31083361 TATTACCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.18
Consensus pattern (17 bp):
GCTCAAGAACGTGATAG
Found at i:31084031 original size:12 final size:12
Alignment explanation
Indices: 31084014--31084042 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31084004 TTACACTGAA
31084014 TTCTCTTTGAGT
1 TTCTCTTTGAGT
31084026 TTCTCTTTGAGT
1 TTCTCTTTGAGT
31084038 TTCTC
1 TTCTC
31084043 CAAGAATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.21, G:0.14, T:0.59
Consensus pattern (12 bp):
TTCTCTTTGAGT
Found at i:31085274 original size:201 final size:201
Alignment explanation
Indices: 31084929--31085330 Score: 804
Period size: 201 Copynumber: 2.0 Consensus size: 201
31084919 GAAAAAGTCA
31084929 TAAAAATATAAAAATATGAAATTAAATAAAAATTAAAAAAATATTTAGCGGGTTGAGTTTAGTGC
1 TAAAAATATAAAAATATGAAATTAAATAAAAATTAAAAAAATATTTAGCGGGTTGAGTTTAGTGC
31084994 CGAAACTTTCCAGATCAAATATACAATATTTAAGGACATTCCAATTTAAATTCGAATGAGGGAAG
66 CGAAACTTTCCAGATCAAATATACAATATTTAAGGACATTCCAATTTAAATTCGAATGAGGGAAG
31085059 GGGATGAATGGAAAACAGCCTTTAAAACAAAATTTGGATTATATGAATGGTTAGTTATGCCTTTC
131 GGGATGAATGGAAAACAGCCTTTAAAACAAAATTTGGATTATATGAATGGTTAGTTATGCCTTTC
31085124 GGCCTT
196 GGCCTT
31085130 TAAAAATATAAAAATATGAAATTAAATAAAAATTAAAAAAATATTTAGCGGGTTGAGTTTAGTGC
1 TAAAAATATAAAAATATGAAATTAAATAAAAATTAAAAAAATATTTAGCGGGTTGAGTTTAGTGC
31085195 CGAAACTTTCCAGATCAAATATACAATATTTAAGGACATTCCAATTTAAATTCGAATGAGGGAAG
66 CGAAACTTTCCAGATCAAATATACAATATTTAAGGACATTCCAATTTAAATTCGAATGAGGGAAG
31085260 GGGATGAATGGAAAACAGCCTTTAAAACAAAATTTGGATTATATGAATGGTTAGTTATGCCTTTC
131 GGGATGAATGGAAAACAGCCTTTAAAACAAAATTTGGATTATATGAATGGTTAGTTATGCCTTTC
31085325 GGCCTT
196 GGCCTT
31085331 ACTAATGCAC
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 201 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (201 bp):
TAAAAATATAAAAATATGAAATTAAATAAAAATTAAAAAAATATTTAGCGGGTTGAGTTTAGTGC
CGAAACTTTCCAGATCAAATATACAATATTTAAGGACATTCCAATTTAAATTCGAATGAGGGAAG
GGGATGAATGGAAAACAGCCTTTAAAACAAAATTTGGATTATATGAATGGTTAGTTATGCCTTTC
GGCCTT
Found at i:31090674 original size:28 final size:27
Alignment explanation
Indices: 31090611--31090762 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
31090601 ATATTAAGTC
* *
31090611 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
31090638 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
31090666 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
31090693 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
31090721 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
31090748 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31090763 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31090695 original size:55 final size:55
Alignment explanation
Indices: 31090611--31090787 Score: 264
Period size: 55 Copynumber: 3.2 Consensus size: 55
31090601 ATATTAAGTC
* * *
31090611 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
31090666 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
31090721 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT
31090777 CGCACACTTAG
1 CGCACACTTAG
31090788 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 95 0.86
56 16 0.14
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:31098460 original size:27 final size:27
Alignment explanation
Indices: 31098430--31098607 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31098420 ATATTGAGTC
* * * *
31098430 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31098457 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31098484 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31098512 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31098539 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31098566 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31098593 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31098608 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:31098569 original size:82 final size:81
Alignment explanation
Indices: 31098451--31098606 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31098441 TGCTATATAA
* *
31098451 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31098516 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31098533 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31098597 CACTTAGTGC
65 CACTTAGTGC
31098607 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31100321 original size:19 final size:21
Alignment explanation
Indices: 31100291--31100334 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 21
31100281 CAACTCATTT
31100291 ATTAATCTAAGATGA-AATTA
1 ATTAATCTAAGATGAGAATTA
31100311 ATTAA-CTAAGATGAGTAATTA
1 ATTAATCTAAGATGAG-AATTA
31100332 ATT
1 ATT
31100335 CAAGCAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 5 0.23
21 8 0.36
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (21 bp):
ATTAATCTAAGATGAGAATTA
Found at i:31112736 original size:30 final size:31
Alignment explanation
Indices: 31112650--31112737 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 31
31112640 TTCTAGTTGA
* * *
31112650 TCAGCTCAATCCTAGCTTATTGAGCT-TGAT
1 TCAGCTCAATCTTAGCTCATTGAGCTCAGAT
* *
31112680 TCAGCTCGAAT-TTCAGTTCCTTGAGCTCAG-T
1 TCAGCTC-AATCTT-AGCTCATTGAGCTCAGAT
31112711 TCAGCTCAATCTTAGCTCATTGAGCTC
1 TCAGCTCAATCTTAGCTCATTGAGCTC
31112738 GATGCTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
30 23 0.49
31 23 0.49
32 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (31 bp):
TCAGCTCAATCTTAGCTCATTGAGCTCAGAT
Found at i:31114067 original size:24 final size:26
Alignment explanation
Indices: 31114030--31114096 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 26
31114020 TTCAAAACCT
31114030 TAGCCAAATTTCCATCCTCA-TTCACC
1 TAGCC-AATTTCCATCCTCATTTCACC
* *
31114056 TAGCC-ATTTCCATCATCATTTCACT
1 TAGCCAATTTCCATCCTCATTTCACC
31114081 TAGCCAATTT-CATCCT
1 TAGCCAATTTCCATCCT
31114097 TTCTTATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.33
25 15 0.42
26 9 0.25
ACGTcount: A:0.25, C:0.34, G:0.04, T:0.36
Consensus pattern (26 bp):
TAGCCAATTTCCATCCTCATTTCACC
Found at i:31114094 original size:25 final size:25
Alignment explanation
Indices: 31114028--31114091 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 25
31114018 TCTTCAAAAC
*
31114028 CTTAGCCAAATTTCCATCCTCATTCA
1 CTTAGCC-AATTTCCATCATCATTCA
*
31114054 CCTAGCC-ATTTCCATCATCATTTCA
1 CTTAGCCAATTTCCATCATCA-TTCA
31114079 CTTAGCCAATTTC
1 CTTAGCCAATTTC
31114092 ATCCTTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 12 0.36
25 10 0.30
26 11 0.33
ACGTcount: A:0.25, C:0.34, G:0.05, T:0.36
Consensus pattern (25 bp):
CTTAGCCAATTTCCATCATCATTCA
Found at i:31119494 original size:21 final size:21
Alignment explanation
Indices: 31119468--31119510 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
31119458 AAACGGTTTC
31119468 TAAAGCTTCTACTGTAAACAA
1 TAAAGCTTCTACTGTAAACAA
31119489 TAAAGCTTCTACTGTAAACAA
1 TAAAGCTTCTACTGTAAACAA
31119510 T
1 T
31119511 GTTTTGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (21 bp):
TAAAGCTTCTACTGTAAACAA
Found at i:31130116 original size:56 final size:51
Alignment explanation
Indices: 31130046--31130243 Score: 211
Period size: 50 Copynumber: 3.8 Consensus size: 51
31130036 ATATGAGTAA
* * *
31130046 AGAGATCCCATGTAAGACCATGTCTGGCACATGGCATTGGCATCATTGATATTATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCATC---G-TA-TATG
* * *
31130102 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCG-AGATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGTATATG
* * * *
31130152 AGAGGTTCCATGTAAGACCATGTCTGGGATATGGCGTTGGCATC-TATATG
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGTATATG
** * *
31130202 AGAACTCCTATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
31130244 GCACAAGAAA
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
50 83 0.67
51 1 0.01
53 1 0.01
56 39 0.31
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (51 bp):
AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGTATATG
Found at i:31130242 original size:100 final size:102
Alignment explanation
Indices: 31130053--31130243 Score: 260
Period size: 100 Copynumber: 1.9 Consensus size: 102
31130043 TAAAGAGATC
**
31130053 CCATGTAAGACCATGTCTGGCACATGGCATTGGCATCATTGATATTATGAGAGGTCCCATGTAAG
1 CCATGTAAGACCATGTCTGGCACATGGCATTGGCATC----ATATTATGAGAACTCCCATGTAAG
*
31130118 ACCATATCTGGGACATGGCGTTGGCACCGAGATGAGAGGTT
62 ACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTT
* * * *
31130159 CCATGTAAGACCATGTCTGGGATATGGCGTTGGCATC-TA-TATGAGAACTCCTATGTAAGACCA
1 CCATGTAAGACCATGTCTGGCACATGGCATTGGCATCATATTATGAGAACTCCCATGTAAGACCA
*
31130222 TATCTGGGATATGGCATTGGCA
66 TATCTGGGACATGGCATTGGCA
31130244 GCACAAGAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
100 41 0.53
101 2 0.03
106 34 0.44
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (102 bp):
CCATGTAAGACCATGTCTGGCACATGGCATTGGCATCATATTATGAGAACTCCCATGTAAGACCA
TATCTGGGACATGGCATTGGCACCGAGATGAGAGGTT
Found at i:31130300 original size:100 final size:100
Alignment explanation
Indices: 31130050--31130293 Score: 247
Period size: 100 Copynumber: 2.4 Consensus size: 100
31130040 GAGTAAAGAG
* * * ** *
31130050 ATCCCATGTAAGACCATGTCTGGCACATGGCATTGGCATCATTGATATTATGAGAGGTCCCATGT
1 ATCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCATC-----TA-TATGAGAACTCCTATGT
* * * * *
31130115 AAGACCATATCTGGGACATGGCGTTGGCACCGAGATGAGAG
60 AAGACCATATCTGGGACATGGCATTGGCACCGACAAGAAAC
* * * *
31130156 GTTCCATGTAAGACCATGTCTGGGATATGGCGTTGGCATCTATATGAGAACTCCTATGTAAGACC
1 ATCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCATCTATATGAGAACTCCTATGTAAGACC
* *
31130221 ATATCTGGGATATGGCATTGGCAGC-ACAAGAAAC
66 ATATCTGGGACATGGCATTGGCACCGACAAGAAAC
** *
31130255 ATCCCATGTAAGATTATGTCTGGGACATAGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCAT
31130294 GTTATATTCA
Statistics
Matches: 116, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
99 37 0.32
100 42 0.36
101 2 0.02
106 35 0.30
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (100 bp):
ATCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCATCTATATGAGAACTCCTATGTAAGACC
ATATCTGGGACATGGCATTGGCACCGACAAGAAAC
Found at i:31132955 original size:50 final size:50
Alignment explanation
Indices: 31132831--31133121 Score: 314
Period size: 50 Copynumber: 5.8 Consensus size: 50
31132821 AAATATAACA
* * * * ** * * * *
31132831 TGCCAAAGCTATGTCCCAGACATAGTCTTACTTGGGATGTTTCTTGT-GC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * ** * *
31132880 TGCCAATGACATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
31132930 TGCCCATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
31132980 TGCCAACGCCATGTCCTAGTCATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
31133030 TGCCACCACCATGTCTCAGACATGGTTTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
31133080 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31133122 TTACCCAAAT
Statistics
Matches: 203, Mismatches: 38, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
49 34 0.17
50 169 0.83
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31138512 original size:50 final size:50
Alignment explanation
Indices: 31138444--31138735 Score: 406
Period size: 50 Copynumber: 5.8 Consensus size: 50
31138434 TTTCTTGTAC
* * * * * ** * *
31138444 TGCCAATGCCATATCCCAGATATGGTATTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
31138494 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
31138544 TGCCAACGCCATGT-CCAGCACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAG-ACATGGTCTTACATGGGACCTCTCATCTCGG
*
31138594 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
31138644 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTATCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
31138694 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31138736 TTGCCCAAAT
Statistics
Matches: 216, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
49 4 0.02
50 209 0.97
51 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31138569 original size:100 final size:100
Alignment explanation
Indices: 31138395--31138735 Score: 402
Period size: 100 Copynumber: 3.4 Consensus size: 100
31138385 GAATATAACA
* * * ** * * * * *
31138395 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTAC--TGCCAATGCCATAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTGCCAACGCCATGT
* * * * ** *
31138458 CCCAGATATGGTATTACATGAGAGTTCTCATATAGG
65 CTCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * **
31138494 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* *
31138559 -CAGCACATGGTCTTACATGGGACCTCTTATCTCGG
66 TCAG-ACATGGTCTTACATGGGACCTCTCATCTAGG
*
31138594 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
*
31138659 TCAGACATGGTCTTACATGGGACCTATCATCTCA-G
66 TCAGACATGGTCTTACATGGGACCTCTCATCT-AGG
31138694 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31138736 TTGCCCAAAT
Statistics
Matches: 207, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
98 1 0.00
99 39 0.19
100 164 0.79
101 3 0.01
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (100 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
TCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:31138638 original size:150 final size:150
Alignment explanation
Indices: 31138395--31138736 Score: 422
Period size: 150 Copynumber: 2.3 Consensus size: 150
31138385 GAATATAACA
* * * * * * *
31138395 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGA--TGTT-TCTTGTACTGCCAATGCCATA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG--GTGCCAACGCCATA
* ** * *
31138457 TCCCAGATATGGTATTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTCCCAGACATGGTCT
64 TCCCAGACATGGTATTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCT
* * *
31138522 TACGGGGGACCTCTCATCTCGG
129 TACAGGGGACCTATCATCTCAG
*
31138544 TGCCAACGCCATGT-CCAGCACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGT
1 TGCCAACGCCATGTCCCAG-ACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATAT
* * * * * *
31138608 CCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCTCAGACATGGTCTT
65 CCCAGACATGGTATTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCTT
*
31138673 ACATGGGACCTATCATCTCAG
130 ACAGGGGACCTATCATCTCAG
31138694 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
31138737 TGCCCAAATG
Statistics
Matches: 165, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
148 4 0.02
149 29 0.18
150 121 0.73
151 7 0.04
152 4 0.02
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (150 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATATC
CCAGACATGGTATTACATGAGACCTCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCTTA
CAGGGGACCTATCATCTCAG
Found at i:31139551 original size:30 final size:31
Alignment explanation
Indices: 31139517--31139578 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
31139507 ACCCTAGCCA
31139517 TGGTTTCCCCTTGTGAAATTCAGCCAT-GGG
1 TGGTTTCCCCTTGTGAAATTCAGCCATAGGG
* *
31139547 TGGTTTCCCGTTGTGAAATTCGGCCATAGGG
1 TGGTTTCCCCTTGTGAAATTCAGCCATAGGG
31139578 T
1 T
31139579 TGAAGATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (31 bp):
TGGTTTCCCCTTGTGAAATTCAGCCATAGGG
Found at i:31142024 original size:17 final size:18
Alignment explanation
Indices: 31141991--31142038 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
31141981 TAAAAATAAT
31141991 TTAAATATTAAATAAATA
1 TTAAATATTAAATAAATA
31142009 TTAAAT-TT-AATAAAATA
1 TTAAATATTAAAT-AAATA
*
31142026 TTTAATA-TAAATA
1 TTAAATATTAAATA
31142039 TGTATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.12
17 14 0.54
18 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATATTAAATAAATA
Found at i:31142879 original size:19 final size:19
Alignment explanation
Indices: 31142848--31142901 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
31142838 AAAAGGACAT
31142848 AAAATATA-A-AATATTTA
1 AAAATATATATAATATTTA
31142865 AAAATATATATAATATTTA
1 AAAATATATATAATATTTA
31142884 AAAATATATATAA-ATTTA
1 AAAATATATATAATATTTA
31142902 TATAAAGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.23
18 6 0.17
19 21 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATATATATAATATTTA
Found at i:31142898 original size:10 final size:10
Alignment explanation
Indices: 31142846--31142907 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 10
31142836 ATAAAAGGAC
31142846 ATAAA-ATAT
1 ATAAATATAT
*
31142855 A-AAATATTT
1 ATAAATATAT
*
31142864 AAAAATATAT
1 ATAAATATAT
*
31142874 AT-AATATTT
1 ATAAATATAT
*
31142883 AAAAATATAT
1 ATAAATATAT
*
31142893 ATAAATTTAT
1 ATAAATATAT
31142903 ATAAA
1 ATAAA
31142908 GGTATAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
8 3 0.07
9 12 0.29
10 27 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAAATATAT
Found at i:31147363 original size:26 final size:25
Alignment explanation
Indices: 31147328--31147385 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
31147318 AAAAGTATTC
31147328 AAAAAT-TATAAACAATA-AAATTTT
1 AAAAATATATAAA-AATATAAATTTT
31147352 AAAGAATATATAAAAATATTAAATTTT
1 AAA-AATATATAAAAATA-TAAATTTT
31147379 AAAAATA
1 AAAAATA
31147386 AAAATTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 3 0.10
25 7 0.23
26 10 0.33
27 10 0.33
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAAATATATAAAAATATAAATTTT
Found at i:31147668 original size:10 final size:10
Alignment explanation
Indices: 31147645--31147713 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
31147635 TGGTCTCTCT
*
31147645 AAAAAAATTAC
1 AAAATAATT-C
31147656 AAAATAATTC
1 AAAATAATTC
*
31147666 AAAATAATTTT
1 AAAATAA-TTC
31147677 AAAA-AATTC
1 AAAATAATTC
*
31147686 AAAATAATTT
1 AAAATAATTC
*
31147696 TAAA-AATTC
1 AAAATAATTC
31147705 AAAATAATT
1 AAAATAATT
31147714 ATATAAATTC
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
9 13 0.27
10 21 0.44
11 14 0.29
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATAATTC
Found at i:31147702 original size:19 final size:19
Alignment explanation
Indices: 31147661--31147763 Score: 109
Period size: 19 Copynumber: 5.1 Consensus size: 19
31147651 ATTACAAAAT
31147661 AATTCAAAATAATTTTAAAA
1 AATTCAAAATAATTTT-AAA
31147681 AATTCAAAATAATTTTAAA
1 AATTCAAAATAATTTTAAA
* *
31147700 AATTCAAAATAATTATATA
1 AATTCAAAATAATTTTAAA
31147719 AATTCAAAAATTTATATTTTTAAA
1 AATTC-AAAA--TA-A-TTTTAAA
*
31147743 AAATCATAAA-AATTTTAAA
1 AATTCA-AAATAATTTTAAA
31147762 AA
1 AA
31147764 AATATAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
19 34 0.47
20 21 0.29
21 1 0.01
22 2 0.03
23 2 0.03
24 12 0.17
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:31147775 original size:20 final size:20
Alignment explanation
Indices: 31147734--31147773 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31147724 AAAAATTTAT
*
31147734 ATTTTTAAAAAATCATAAAA
1 ATTTTAAAAAAATCATAAAA
31147754 ATTTTAAAAAAAT-ATAAAA
1 ATTTTAAAAAAATCATAAAA
31147773 A
1 A
31147774 ATATTTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTTAAAAAAATCATAAAA
Found at i:31153808 original size:15 final size:15
Alignment explanation
Indices: 31153784--31153828 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
31153774 AATACATCAT
*
31153784 TTTTCT-TTTTGCTC
1 TTTTCTATTTTTCTC
*
31153798 TTTTCTATTTTTTTC
1 TTTTCTATTTTTCTC
*
31153813 TTTTTTATTTTTCTC
1 TTTTCTATTTTTCTC
31153828 T
1 T
31153829 CAATTTCTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTCTATTTTTCTC
Found at i:31154430 original size:50 final size:49
Alignment explanation
Indices: 31154348--31154583 Score: 181
Period size: 50 Copynumber: 4.7 Consensus size: 49
31154338 ATAACTTTGA
* * *
31154348 TGTCAGGGAAGCAAGATTCGCTGCTGTGGCTTTAATCTGTTCCACTGCAC
1 TGTCTGGGAAGCAAGATTCGCTGATGTAGCTTTAATCT-TTCCACTGCAC
* * * * * * *
31154398 TATCTGGGAAGTAAGATTCGCTGTTGTAGCTTTAATATTCTCAACTACAA
1 TGTCTGGGAAGCAAGATTCGCTGATGTAGCTTTAATCTT-TCCACTGCAC
* * *
31154448 TGTC-GAGGAAGCAAGATTCACCGATGTGGCTTTAATCTACTT-CACTGCAC
1 TGTCTG-GGAAGCAAGATTCGCTGATGTAGCTTTAATCT--TTCCACTGCAC
* * ** * *
31154498 TGCCT-GGAAGGTAAGATTCGCTGATGTAGCTTTAATCTTTTGAAATGCAA
1 TGTCTGGGAA-GCAAGATTCGCTGATGTAGCTTTAATC-TTTCCACTGCAC
* * * *
31154548 TGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAAT
1 TGTCTGGGAAGCAAGATTCGCTGATGTAGCTTTAAT
31154584 TTTGTGACAG
Statistics
Matches: 144, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
49 8 0.06
50 129 0.90
51 6 0.04
52 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (49 bp):
TGTCTGGGAAGCAAGATTCGCTGATGTAGCTTTAATCTTTCCACTGCAC
Found at i:31154520 original size:100 final size:100
Alignment explanation
Indices: 31154347--31154583 Score: 318
Period size: 100 Copynumber: 2.4 Consensus size: 100
31154337 CATAACTTTG
* * * * *
31154347 ATGTCAGGGAAGCAAGATTCGCTGCTGTGGCTTTAATCTGTTCCACTGCACTATCTGGGAAGTAA
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAATCTCTTCCACTGCACTACCTGGGAAGTAA
* *
31154412 GATTCGCTGTTGTAGCTTTAATATTCTCAACTACA
66 GATTCGCTGATGTAGCTTTAATATTCTCAAATACA
*
31154447 ATGTC-GAGGAAGCAAGATTCACCGATGTGGCTTTAATCTACTT-CACTGCACTGCCT-GGAAGG
1 ATGTCAG-GGAAGCAAGATTCACCGATGTGGCTTTAATCT-CTTCCACTGCACTACCTGGGAA-G
* * * *
31154509 TAAGATTCGCTGATGTAGCTTTAATCTTTTGAAATGCA
63 TAAGATTCGCTGATGTAGCTTTAATATTCTCAAATACA
31154547 ATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAAT
1 ATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAAT
31154584 TTTGTGACAG
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
99 5 0.04
100 113 0.93
101 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (100 bp):
ATGTCAGGGAAGCAAGATTCACCGATGTGGCTTTAATCTCTTCCACTGCACTACCTGGGAAGTAA
GATTCGCTGATGTAGCTTTAATATTCTCAAATACA
Found at i:31156152 original size:40 final size:39
Alignment explanation
Indices: 31156121--31156330 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
31156111 GGACTAAGAT
* *
31156121 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
31156161 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
31156201 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
31156241 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
31156281 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
31156320 CCGAAGGCATT
1 CCGAAGGCATT
31156331 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:31156284 original size:120 final size:120
Alignment explanation
Indices: 31156068--31156330 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
31156058 TTGAATGCTG
* *
31156068 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
31156132 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
31156188 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
31156251 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
31156307 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
31156331 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:31156350 original size:79 final size:80
Alignment explanation
Indices: 31156069--31156365 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
31156059 TGAATGCTGT
* ** * * * **
31156069 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
31156132 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
31156149 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
31156213 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
31156229 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
31156293 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
31156308 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
31156366 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:31164102 original size:40 final size:39
Alignment explanation
Indices: 31164071--31164280 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
31164061 GGACTAAGAT
* *
31164071 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
31164111 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
31164151 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
31164191 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
31164231 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
31164270 CCGAAGGCATT
1 CCGAAGGCATT
31164281 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:31164234 original size:120 final size:120
Alignment explanation
Indices: 31164018--31164280 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
31164008 TTGAATGCTG
* *
31164018 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
31164082 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
31164138 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
31164201 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
31164257 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
31164281 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:31164300 original size:79 final size:80
Alignment explanation
Indices: 31164019--31164315 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
31164009 TGAATGCTGT
* ** * * * **
31164019 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
31164082 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
31164099 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
31164163 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
31164179 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
31164243 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
31164258 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
31164316 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:31165761 original size:50 final size:49
Alignment explanation
Indices: 31165702--31165965 Score: 237
Period size: 50 Copynumber: 5.3 Consensus size: 49
31165692 AGATTTGCTA
*
31165702 ATGTAGCTTTAATCTTTTGAACTGTAATGTCAGGGAAGCAAGATTCACTG
1 ATGTAGCTTTAATCTTTTGAACTG-AATGTCAGGGAAGCAAGATTCACCG
* * * ** * * *
31165752 ATGTGGCTTTAATATGTTCCACTGCATCGCCTA--GAAGGTAAGATTC-CCG
1 ATGTAGCTTTAATCTTTTGAACTGAAT-GTC-AGGGAA-GCAAGATTCACCG
31165801 ATGTAGCTTTAATCTTTTGAACTGCAATGTCAGGGAAGCAAGATTCACCG
1 ATGTAGCTTTAATCTTTTGAACTG-AATGTCAGGGAAGCAAGATTCACCG
* * * ** * ** ** * *
31165851 ACGTGGCTTTAATCTGTTCCACTGCATCACCTGGAAGGTAAGATTCACTG
1 ATGTAGCTTTAATCTTTTGAACTGAATGTCAGGGAA-GCAAGATTCACCG
*
31165901 ATGTAGCTTTAATCTTTTGAACTGGAATGTCAGGGAAGCATGATTCACCG
1 ATGTAGCTTTAATCTTTTGAACT-GAATGTCAGGGAAGCAAGATTCACCG
*
31165951 ATGTGGCTTTAATCT
1 ATGTAGCTTTAATCT
31165966 GTTCCACTGC
Statistics
Matches: 162, Mismatches: 43, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
48 1 0.01
49 43 0.27
50 109 0.67
51 9 0.06
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (49 bp):
ATGTAGCTTTAATCTTTTGAACTGAATGTCAGGGAAGCAAGATTCACCG
Found at i:31165947 original size:100 final size:99
Alignment explanation
Indices: 31165666--31165976 Score: 505
Period size: 100 Copynumber: 3.1 Consensus size: 99
31165656 GTTACAAATT
* * *
31165666 TGTTCCACTGCATCGCCTGGAAGGTAAGATTTGCTAATGTAGCTTTAATCTTTTGAACTGTAATG
1 TGTTCCACTGCATCGCCTGGAAGGTAAGA-TTCCTGATGTAGCTTTAATCTTTTGAACTGCAATG
* *
31165731 TCAGGGAAGCAAGATTCACTGATGTGGCTTTAATA
65 TCAGGGAAGCAAGATTCACCGATGTGGCTTTAATC
* *
31165766 TGTTCCACTGCATCGCCTAGAAGGTAAGATTCCCGATGTAGCTTTAATCTTTTGAACTGCAATGT
1 TGTTCCACTGCATCGCCTGGAAGGTAAGATTCCTGATGTAGCTTTAATCTTTTGAACTGCAATGT
*
31165831 CAGGGAAGCAAGATTCACCGACGTGGCTTTAATC
66 CAGGGAAGCAAGATTCACCGATGTGGCTTTAATC
* *
31165865 TGTTCCACTGCATCACCTGGAAGGTAAGATTCACTGATGTAGCTTTAATCTTTTGAACTGGAATG
1 TGTTCCACTGCATCGCCTGGAAGGTAAGATTC-CTGATGTAGCTTTAATCTTTTGAACTGCAATG
*
31165930 TCAGGGAAGCATGATTCACCGATGTGGCTTTAATC
65 TCAGGGAAGCAAGATTCACCGATGTGGCTTTAATC
31165965 TGTTCCACTGCA
1 TGTTCCACTGCA
31165977 ACCTTAGGGA
Statistics
Matches: 196, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
99 93 0.47
100 103 0.53
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (99 bp):
TGTTCCACTGCATCGCCTGGAAGGTAAGATTCCTGATGTAGCTTTAATCTTTTGAACTGCAATGT
CAGGGAAGCAAGATTCACCGATGTGGCTTTAATC
Found at i:31166080 original size:43 final size:43
Alignment explanation
Indices: 31166031--31166296 Score: 433
Period size: 43 Copynumber: 6.2 Consensus size: 43
31166021 ACCTCAGGGG
* *
31166031 GATAAGACTCGTGGCTTGGATCTGTTTCCCTACTCCTGGGGAA
1 GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCCTGGGGAA
*
31166074 GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCTTGGGGAA
1 GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCCTGGGGAA
* * *
31166117 GATAAGATTCGTAGCTTGGATATGTTTCCCTACTCTTTGGGAA
1 GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCCTGGGGAA
* *
31166160 GATAAGATTCATAGCTTGGATCTGTTTCCCTACTCTTGGGGAA
1 GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCCTGGGGAA
*
31166203 GATAAGATTCGTAGCTTGGATCTATTTCCCTACTCCTGGGGAA
1 GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCCTGGGGAA
* *
31166246 GATAAGATTCGTAGCTTAGATCTGTTTCCCTACTCCTAGGGAA
1 GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCCTGGGGAA
31166289 GATAAGAT
1 GATAAGAT
31166297 CTGCAATCTT
Statistics
Matches: 209, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 209 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (43 bp):
GATAAGATTCGTAGCTTGGATCTGTTTCCCTACTCCTGGGGAA
Found at i:31168612 original size:14 final size:14
Alignment explanation
Indices: 31168593--31168619 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31168583 AGATTTTAAC
31168593 AAATTAATTAACTT
1 AAATTAATTAACTT
31168607 AAATTAATTAACT
1 AAATTAATTAACT
31168620 AATTTAACTA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTAATTAACTT
Found at i:31169039 original size:24 final size:24
Alignment explanation
Indices: 31169007--31169053 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
31168997 AGATTCAAAT
31169007 CACTGTCTCTAACACCACTAAAAC
1 CACTGTCTCTAACACCACTAAAAC
31169031 CACTGTCTCTAACACCACTAAAA
1 CACTGTCTCTAACACCACTAAAA
31169054 AATAGGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.36, G:0.04, T:0.21
Consensus pattern (24 bp):
CACTGTCTCTAACACCACTAAAAC
Found at i:31171916 original size:13 final size:15
Alignment explanation
Indices: 31171893--31171925 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
31171883 CTAAGCATGA
31171893 TTAATCTAATTAAT-
1 TTAATCTAATTAATC
31171907 TTAA-CTAATTAATC
1 TTAATCTAATTAATC
31171921 TTAAT
1 TTAAT
31171926 ATATAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATCTAATTAATC
Found at i:31176696 original size:12 final size:12
Alignment explanation
Indices: 31176679--31176703 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31176669 CACATGCCCC
31176679 TGCTAGGCTGTG
1 TGCTAGGCTGTG
31176691 TGCTAGGCTGTG
1 TGCTAGGCTGTG
31176703 T
1 T
31176704 CGTATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.40, T:0.36
Consensus pattern (12 bp):
TGCTAGGCTGTG
Found at i:31177914 original size:42 final size:42
Alignment explanation
Indices: 31177855--31177956 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
31177845 TGTGGATACT
* * *
31177855 CCACAGCTTGTTTGAGCAGTATCGTGTAGCTTACATTTCGAC
1 CCACAGCTCGTGTGAGCAGTATCGTATAGCTTACATTTCGAC
*
31177897 CCACAGCTCGTGTGAGCAGTATCGTATAGCTTACATTTTGAC
1 CCACAGCTCGTGTGAGCAGTATCGTATAGCTTACATTTCGAC
*
31177939 CCACAGCTCGTGTAAGCA
1 CCACAGCTCGTGTGAGCA
31177957 AGCCCATTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (42 bp):
CCACAGCTCGTGTGAGCAGTATCGTATAGCTTACATTTCGAC
Found at i:31181971 original size:25 final size:25
Alignment explanation
Indices: 31181937--31181993 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
31181927 TAATTAAGGT
*
31181937 TACCGATTTATAGCTCGTGAGAGCA
1 TACCAATTTATAGCTCGTGAGAGCA
31181962 TACCAATTTATAGCTCGTGAGAGCA
1 TACCAATTTATAGCTCGTGAGAGCA
*
31181987 CACCAAT
1 TACCAAT
31181994 CTTCAGCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (25 bp):
TACCAATTTATAGCTCGTGAGAGCA
Found at i:31182001 original size:25 final size:25
Alignment explanation
Indices: 31181942--31182002 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
31181932 AAGGTTACCG
* *
31181942 ATTTATAGCTCGTGAGAGCATACCA
1 ATTTACAGCTCGTGAGAGCACACCA
*
31181967 ATTTATAGCTCGTGAGAGCACACCA
1 ATTTACAGCTCGTGAGAGCACACCA
31181992 ATCTT-CAGCTC
1 AT-TTACAGCTC
31182003 AAATGAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 31 0.94
26 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (25 bp):
ATTTACAGCTCGTGAGAGCACACCA
Found at i:31183239 original size:12 final size:12
Alignment explanation
Indices: 31183222--31183263 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
31183212 TCAGGCTATT
31183222 ACATGGCCTGGC
1 ACATGGCCTGGC
31183234 ACATGGCCTGGC
1 ACATGGCCTGGC
31183246 ACATGGCCTGGC
1 ACATGGCCTGGC
31183258 ACATGG
1 ACATGG
31183264 GCGTGTGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (12 bp):
ACATGGCCTGGC
Found at i:31187143 original size:42 final size:42
Alignment explanation
Indices: 31187079--31187158 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
31187069 TTAAAGGTTG
31187079 CATTTCAAAAGTTACATGGCCTAGCACACAGGCGTGTGAGGC
1 CATTTCAAAAGTTACATGGCCTAGCACACAGGCGTGTGAGGC
* * * *
31187121 CATTTCGAAGGTTACACT-GCCTAGCACACGGGTGTGTG
1 CATTTCAAAAGTTACA-TGGCCTAGCACACAGGCGTGTG
31187159 GCTTGGCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (42 bp):
CATTTCAAAAGTTACATGGCCTAGCACACAGGCGTGTGAGGC
Found at i:31188750 original size:25 final size:25
Alignment explanation
Indices: 31188722--31188770 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
31188712 AGGGTTATCA
* *
31188722 ATACTCAGCTATTATGAGCTTACCG
1 ATACTCAACTAGTATGAGCTTACCG
*
31188747 ATACTCAACTCGTATGAGCTTACC
1 ATACTCAACTAGTATGAGCTTACC
31188771 TTTATTTAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (25 bp):
ATACTCAACTAGTATGAGCTTACCG
Found at i:31188783 original size:25 final size:25
Alignment explanation
Indices: 31188762--31188850 Score: 99
Period size: 25 Copynumber: 3.5 Consensus size: 25
31188752 CAACTCGTAT
* *
31188762 GAGCTTACCTTTATTTAGCTCGAAA
1 GAGCTTACCTTTATTCAGCTCGAAG
*
31188787 GAGCTTA-CTGTTATTCAGCTCGGAG
1 GAGCTTACCT-TTATTCAGCTCGAAG
* * *
31188812 GAGTTTACCGTTATTCAGGTCGAAG
1 GAGCTTACCTTTATTCAGCTCGAAG
31188837 GAGCTTACCGTTTA
1 GAGCTTACC-TTTA
31188851 CAGCTTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
24 2 0.04
25 46 0.88
26 4 0.08
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (25 bp):
GAGCTTACCTTTATTCAGCTCGAAG
Found at i:31191820 original size:13 final size:13
Alignment explanation
Indices: 31191798--31191830 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
31191788 GGTGTGACGA
*
31191798 AAGATTCTACTGC
1 AAGATCCTACTGC
31191811 AAGATCCTACTGC
1 AAGATCCTACTGC
31191824 AAGATCC
1 AAGATCC
31191831 GAGGCACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (13 bp):
AAGATCCTACTGC
Found at i:31196526 original size:25 final size:25
Alignment explanation
Indices: 31196484--31196570 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
31196474 AATGGGTTAT
* *
31196484 CGATACTCAACTCCTATGAGCTTAC
1 CGATACTCAGCTCGTATGAGCTTAC
31196509 CGATACTCAGCTCGTATGAGCTTAC
1 CGATACTCAGCTCGTATGAGCTTAC
* * *
31196534 C-ATTATTCAGCTCGGAGGAGCTTAC
1 CGA-TACTCAGCTCGTATGAGCTTAC
* *
31196559 CGTTATTCAGCT
1 CGATACTCAGCT
31196571 TGGAGGAGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
24 1 0.02
25 53 0.98
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (25 bp):
CGATACTCAGCTCGTATGAGCTTAC
Found at i:31196575 original size:25 final size:25
Alignment explanation
Indices: 31196501--31196595 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
31196491 CAACTCCTAT
* * * *
31196501 GAGCTTACCGATACTCAGCTCGTAT
1 GAGCTTACCGTTATTCAGCTCGGAG
*
31196526 GAGCTTACCATTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
*
31196551 GAGCTTACCGTTATTCAGCTTGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
* *
31196576 GAGTTTACCGTT-TACAGCTC
1 GAGCTTACCGTTATTCAGCTC
31196596 ATATGAGCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
24 6 0.10
25 54 0.90
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGGAG
Found at i:31198926 original size:17 final size:18
Alignment explanation
Indices: 31198899--31198937 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
31198889 TATTTTTAAT
31198899 TTTTAAAATTA-TTAAGTA
1 TTTTAAAATTATTTAAG-A
31198917 TTTT-AAATTATTTAAGA
1 TTTTAAAATTATTTAAGA
31198934 TTTT
1 TTTT
31198938 TTATCAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTTAAAATTATTTAAGA
Found at i:31198938 original size:18 final size:18
Alignment explanation
Indices: 31198897--31198938 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
31198887 TTTATTTTTA
31198897 ATTTTTAAAATTATTAAG
1 ATTTTTAAAATTATTAAG
31198915 -TATTTT-AAATTATTTAAG
1 AT-TTTTAAAATTA-TTAAG
31198933 ATTTTT
1 ATTTTT
31198939 TATCAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
17 7 0.33
18 13 0.62
19 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
ATTTTTAAAATTATTAAG
Found at i:31203914 original size:11 final size:11
Alignment explanation
Indices: 31203898--31203922 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31203888 TGACTGCTTT
31203898 CAATAATGATC
1 CAATAATGATC
31203909 CAATAATGATC
1 CAATAATGATC
31203920 CAA
1 CAA
31203923 AATAACAAAG
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (11 bp):
CAATAATGATC
Found at i:31205961 original size:11 final size:11
Alignment explanation
Indices: 31205945--31205971 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31205935 ACGAATTTTC
31205945 TTTTTTGAATT
1 TTTTTTGAATT
31205956 TTTTTTGAATT
1 TTTTTTGAATT
31205967 TTTTT
1 TTTTT
31205972 CACTAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTGAATT
Found at i:31207505 original size:9 final size:9
Alignment explanation
Indices: 31207491--31207516 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31207481 TAAAAACACA
31207491 AACTAAAAT
1 AACTAAAAT
31207500 AACTAAAAT
1 AACTAAAAT
31207509 AACTAAAA
1 AACTAAAA
31207517 ATTAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:31209084 original size:40 final size:40
Alignment explanation
Indices: 31209033--31209112 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
31209023 TGCACCTTCT
*
31209033 TATGTTTCGACCTCCATTCAGTTGGCTGACATTTTTACAA
1 TATGTTCCGACCTCCATTCAGTTGGCTGACATTTTTACAA
31209073 TATGTTCCGACCTCCATTCAGTTGGCTGACATTTTTACAA
1 TATGTTCCGACCTCCATTCAGTTGGCTGACATTTTTACAA
31209113 AGGTTCTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (40 bp):
TATGTTCCGACCTCCATTCAGTTGGCTGACATTTTTACAA
Found at i:31216323 original size:42 final size:41
Alignment explanation
Indices: 31216227--31216358 Score: 147
Period size: 42 Copynumber: 3.1 Consensus size: 41
31216217 AAACACATAT
* * * **
31216227 ATCACATACAATGCCATATCCCAGATATGATCTTACATGTT
1 ATCACATACGATGCCATGTCCCAGATATGGTCTTACATGAA
* *
31216268 ATCACATATCGATGCCACTGTCCCAGATAGGGTCTTATATGAA
1 ATCACATA-CGATGCCA-TGTCCCAGATATGGTCTTACATGAA
* * *
31216311 ATCATATACGATGCCAATGTCCCAGACATGGTCTTACACGAA
1 ATCACATACGATGCC-ATGTCCCAGATATGGTCTTACATGAA
31216353 ATCACA
1 ATCACA
31216359 CCTCAGGAGT
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
41 8 0.11
42 40 0.53
43 27 0.36
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (41 bp):
ATCACATACGATGCCATGTCCCAGATATGGTCTTACATGAA
Found at i:31218783 original size:44 final size:42
Alignment explanation
Indices: 31218719--31218873 Score: 126
Period size: 44 Copynumber: 3.7 Consensus size: 42
31218709 TATGTGTTAT
* * *
31218719 CGTGTAAGATCACGTATGGGACGTTGGCGTCGATTTGAGATTTA
1 CGTGTAAGACCA-GTCTGGGACGTTGGCATCGATTT-AGATTTA
* *
31218763 CGTGTAAGACCATGTCTGGGACATTGGCATCG-TATACGATTT-
1 CGTGTAAGACCA-GTCTGGGACGTTGGCATCGATTTA-GATTTA
* *
31218805 CGTGTAAGACC---CTAGGACAG-TGGCATCGATATTTGA-TTA
1 CGTGTAAGACCAGTCTGGGAC-GTTGGCATCGAT-TTAGATTTA
*
31218844 CATGTAAGACCAAGTCTGGGACGTTGGCAT
1 CGTGTAAGACC-AGTCTGGGACGTTGGCAT
31218874 TTTAAGAGCT
Statistics
Matches: 89, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
38 16 0.18
39 13 0.15
40 1 0.01
42 13 0.15
43 19 0.21
44 27 0.30
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCAGTCTGGGACGTTGGCATCGATTTAGATTTA
Found at i:31229197 original size:101 final size:101
Alignment explanation
Indices: 31229017--31229207 Score: 260
Period size: 101 Copynumber: 1.9 Consensus size: 101
31229007 AGTTACGATT
* * * * * *
31229017 TTGCGGTAATGCTTTATAATCTTTTTCTGGCAATGGAGGAGGGTTAGGGATGATACATCTAGTGG
1 TTGCAGTAATGCTTTATAATCCTATTCTAGCAACGGAGAAGGGTTAGGGATGATACATCTAGTGG
*
31229082 TATCAAAGCTACAATTTAGTTGATTCTCGAACTGAA
66 TATCAAAGCTACAATTTAGTCGATTCTCGAACTGAA
* * *
31229118 TTGCAGTAATGCTTTATAATCCTATTCTAGCGACGGA-AACGGGTTAGAGG-TGTTACATTTAGT
1 TTGCAGTAATGCTTTATAATCCTATTCTAGCAACGGAGAA-GGGTTAG-GGATGATACATCTAGT
31229181 GGTATCAAAGCTACAATTTAGTCGATT
64 GGTATCAAAGCTACAATTTAGTCGATT
31229208 ATATAACCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
100 1 0.01
101 75 0.96
102 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (101 bp):
TTGCAGTAATGCTTTATAATCCTATTCTAGCAACGGAGAAGGGTTAGGGATGATACATCTAGTGG
TATCAAAGCTACAATTTAGTCGATTCTCGAACTGAA
Found at i:31235682 original size:16 final size:16
Alignment explanation
Indices: 31235657--31235690 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31235647 ATGAATATGT
* *
31235657 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
31235673 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
31235689 AT
1 AT
31235691 TGGATACTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:31239508 original size:16 final size:16
Alignment explanation
Indices: 31239487--31239518 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31239477 GTTTTGTTGC
*
31239487 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
31239503 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
31239519 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:31239804 original size:51 final size:51
Alignment explanation
Indices: 31239742--31239883 Score: 171
Period size: 51 Copynumber: 2.8 Consensus size: 51
31239732 GATACCAGTT
* *
31239742 CACATAGTAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCAATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT-AGCTATCCAATA
* * ***
31239793 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAGCTATCCAATA
* *
31239844 CGCATAGTAGCCTGCACATAGTACTACACAGGTGACCATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATA
31239884 ACTTTCACTT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 3 0.04
51 72 0.94
52 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAGCTATCCAATA
Found at i:31239901 original size:51 final size:50
Alignment explanation
Indices: 31239742--31239912 Score: 164
Period size: 51 Copynumber: 3.4 Consensus size: 50
31239732 GATACCAGTT
* *
31239742 CACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCAATA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCATAACTATCC-ATA
* * * * **
31239793 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCTGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGA-CCATAACTATC-CATA
* * * * * *
31239844 CGCATAGTAGCCTGCACATAGTACTACACAGGTGACCATAACTTTCACTTT
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCATAACTATC-CATA
*
31239895 CACATAGTGGCCTACACA
1 CACATAGTAGCCTACACA
31239913 CAGTCCATGC
Statistics
Matches: 96, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
50 2 0.02
51 92 0.96
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTACACATAGTACTACACACGTGACCATAACTATCCATA
Found at i:31239937 original size:47 final size:48
Alignment explanation
Indices: 31239884--31239977 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
31239874 GGTGACCATA
31239884 ACTTTCACTTTCACAT-AGTGGCCTACACACAGTCCATGCCACACATC
1 ACTTTCACTTTCACATAAGTGGCCTACACACAGTCCATGCCACACATC
31239931 ACTTTCACTTTCACATAAGTGGCCTACACACAGTCCATGCCACACAT
1 ACTTTCACTTTCACATAAGTGGCCTACACACAGTCCATGCCACACAT
31239978 GTGATCATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 16 0.35
48 30 0.65
ACGTcount: A:0.29, C:0.35, G:0.11, T:0.26
Consensus pattern (48 bp):
ACTTTCACTTTCACATAAGTGGCCTACACACAGTCCATGCCACACATC
Found at i:31240181 original size:15 final size:16
Alignment explanation
Indices: 31240152--31240183 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31240142 AATCCAGTCC
31240152 AAAAATCACATTTTTG
1 AAAAATCACATTTTTG
*
31240168 AAAAATTACATTTTTG
1 AAAAATCACATTTTTG
31240184 CCCCTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
AAAAATCACATTTTTG
Found at i:31255214 original size:99 final size:103
Alignment explanation
Indices: 31255111--31255352 Score: 305
Period size: 99 Copynumber: 2.4 Consensus size: 103
31255101 TATCATGTAC
* * * ***
31255111 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGTGTTCTCATATCGGTGTCC-ATGCCATGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CCAATGCCATGT
*
31255175 CCCAGACATGGTCTTAC-GGGGACCTCTC-ATCTC-GG-
65 CCCAAACATGGTCTTACAGGGGACCTCTCAATCTCAGGA
* * * *
31255210 TGCCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCGTCTCGGTGCCAATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCCATGTC
*
31255275 CCAAACATGGTCTTACATGGGACCTCTCATGATCTCAAGGA
66 CCAAACATGGTCTTACAGGGGACCTCTCA--ATCTC-AGGA
31255316 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
31255353 TCCCTTTACC
Statistics
Matches: 121, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
98 2 0.02
99 67 0.55
100 10 0.08
103 5 0.04
105 2 0.02
106 35 0.29
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (103 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCCATGTC
CCAAACATGGTCTTACAGGGGACCTCTCAATCTCAGGA
Found at i:31255222 original size:49 final size:50
Alignment explanation
Indices: 31255062--31255352 Score: 311
Period size: 50 Copynumber: 5.7 Consensus size: 50
31255052 GATAATAACA
* * * ** * *
31255062 TGCCAAAGCCATGTCCTAGACACGGTCTTACATGGGATATATCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * *** *
31255111 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGTGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
31255161 TGTCC-ATGCCATGTCCCAGACATGGTCTTAC-GGGGACCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
31255210 TGCCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
31255260 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
31255315 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
31255353 TCCCTTTACC
Statistics
Matches: 203, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
48 3 0.01
49 76 0.37
50 80 0.39
51 2 0.01
53 4 0.02
55 2 0.01
56 36 0.18
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31255375 original size:106 final size:98
Alignment explanation
Indices: 31255164--31255352 Score: 243
Period size: 106 Copynumber: 1.8 Consensus size: 98
31255154 ATATCGGTGT
*
31255164 CCATGCCATGTCCCAGACATGGTCTTACGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAG
1 CCATGCCATGTCCCAAACATGGTCTTACGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAG
* * **
31255229 ACATGGTCTTACATTGGACCTCTCGTCTCGGTG
66 ACATGGTCTTACATGGGACCTCTCGTCCCAATG
* *
31255262 CCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATGCCA
1 CC-ATGCCATGTCCCAAACATGGTCTTAC-GGGGACCTCTC---ATCTC--GG-TGCCAACGCCA
31255327 TGTCCCAGACATGGTCTTACATGGGA
58 TGTCCCAGACATGGTCTTACATGGGA
31255353 TCCCTTTACC
Statistics
Matches: 79, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
98 2 0.03
99 25 0.32
100 10 0.13
103 5 0.06
105 2 0.03
106 35 0.44
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (98 bp):
CCATGCCATGTCCCAAACATGGTCTTACGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAG
ACATGGTCTTACATGGGACCTCTCGTCCCAATG
Found at i:31265936 original size:25 final size:23
Alignment explanation
Indices: 31265908--31265971 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
31265898 TTACCGATTC
31265908 TCAGCTCG-AGAGAGCTTACTGATAT
1 TCAGCTCGTA-AGAGCTTACT-AT-T
*
31265933 TCAGCTCGTATGAGCTTACTATT
1 TCAGCTCGTAAGAGCTTACTATT
31265956 TACAGCTCGTAAGAGC
1 T-CAGCTCGTAAGAGC
31265972 ATACCGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 2 0.06
24 15 0.43
25 17 0.49
26 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
TCAGCTCGTAAGAGCTTACTATT
Found at i:31265966 original size:24 final size:24
Alignment explanation
Indices: 31265919--31265996 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
31265909 CAGCTCGAGA
31265919 GAGCTTACTGATATT-CAGCTCGTAT
1 GAGCTTACT-AT-TTACAGCTCGTAT
*
31265944 GAGCTTACTATTTACAGCTCGTAA
1 GAGCTTACTATTTACAGCTCGTAT
* * * *
31265968 GAGCATACCGATTTAGAACTCGTAT
1 GAGCTTA-CTATTTACAGCTCGTAT
31265993 GAGC
1 GAGC
31265997 ATACATGTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.04
24 17 0.38
25 26 0.58
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (24 bp):
GAGCTTACTATTTACAGCTCGTAT
Found at i:31267362 original size:25 final size:25
Alignment explanation
Indices: 31267333--31267380 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31267323 TGAGCTTACT
*
31267333 ATTTACAGCTCGTAAGAGCATACCG
1 ATTTACAACTCGTAAGAGCATACCG
* *
31267358 ATTTAGAACTCGTATGAGCATAC
1 ATTTACAACTCGTAAGAGCATAC
31267381 ATGTACAGGA
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:0.21, G:0.19, T:0.27
Consensus pattern (25 bp):
ATTTACAACTCGTAAGAGCATACCG
Found at i:31277117 original size:39 final size:39
Alignment explanation
Indices: 31277074--31277211 Score: 163
Period size: 39 Copynumber: 3.5 Consensus size: 39
31277064 ATGTTTGTCA
*
31277074 ATATTGTGATATATGCTTAAATGTTATGTGATTATACGT
1 ATATTGTGATATATGCTTAAATGTTATGTGATTATATGT
* *
31277113 ATATTATGATATATGCTTGAATGTTATGTGATTATATG-
1 ATATTGTGATATATGCTTAAATGTTATGTGATTATATGT
* * * *
31277151 AGTATTGTGATTTATGCTTGAATGTTAGGTGGTTATATGT
1 A-TATTGTGATATATGCTTAAATGTTATGTGATTATATGT
* *
31277191 GTAATAG-GATATATGCTTAAA
1 AT-ATTGTGATATATGCTTAAA
31277212 AGTGAATATG
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 1 0.01
39 81 0.95
40 3 0.04
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (39 bp):
ATATTGTGATATATGCTTAAATGTTATGTGATTATATGT
Found at i:31280607 original size:20 final size:20
Alignment explanation
Indices: 31280582--31280620 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31280572 GTTTTTACAT
31280582 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
31280602 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
31280621 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:31281926 original size:66 final size:66
Alignment explanation
Indices: 31281820--31281949 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
31281810 ACATTGGCCC
* *
31281820 CAAAGATGTTCCCTTGTATATTCATTTGATAGTAAGTTGTGTGATTTATCAAAAACAAAAGTAAT
1 CAAAGATGCTCCCTTGTATATTCATTTGATAGTAAGTTGTGTGATTTATCAAAAAAAAAAGTAAT
31281885 A
66 A
31281886 CAAAGATGCTCCCTTGTATATTCATTTGATAGTAAGTTGTGTGATTTATCAAAAAAAAAAGTAA
1 CAAAGATGCTCCCTTGTATATTCATTTGATAGTAAGTTGTGTGATTTATCAAAAAAAAAAGTAA
31281950 GTTGTGTGAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (66 bp):
CAAAGATGCTCCCTTGTATATTCATTTGATAGTAAGTTGTGTGATTTATCAAAAAAAAAAGTAAT
A
Found at i:31282207 original size:11 final size:11
Alignment explanation
Indices: 31282191--31282216 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31282181 AACCATCTGT
31282191 ATATAACCAAA
1 ATATAACCAAA
31282202 ATATAACCAAA
1 ATATAACCAAA
31282213 ATAT
1 ATAT
31282217 CATCCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Done.