Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 42 of 328
Found at i:12212341 original size:24 final size:24
Alignment explanation
Indices: 12212314--12212359 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
12212304 TGCAGCTACG
*
12212314 TTTACAGCTGGTCTTGCATTTCCT
1 TTTACAGCTGGTCTAGCATTTCCT
* * *
12212338 TTTAGATCTGTTCTAGCATTTC
1 TTTACAGCTGGTCTAGCATTTC
12212360 TAACCTTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (24 bp):
TTTACAGCTGGTCTAGCATTTCCT
Found at i:12216345 original size:52 final size:54
Alignment explanation
Indices: 12216246--12216348 Score: 124
Period size: 52 Copynumber: 1.9 Consensus size: 54
12216236 AAATGAAAGG
*
12216246 AAAACATAAGTAATATCGAATTTAAATATATATAAAAATAATAAATAAATAGGC
1 AAAACATAAGTAATATCAAATTTAAATATATATAAAAATAATAAATAAATAGGC
* * *
12216300 AAAACA-AA-TAATATTAAATTTAAGTAT-T-TAAAAAGTAAATGAATAAATA
1 AAAACATAAGTAATATCAAATTTAAATATATATAAAAA-T-AATAAATAAATA
12216349 AAATAAGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
50 6 0.14
51 2 0.05
52 27 0.63
53 2 0.05
54 6 0.14
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (54 bp):
AAAACATAAGTAATATCAAATTTAAATATATATAAAAATAATAAATAAATAGGC
Found at i:12216481 original size:11 final size:11
Alignment explanation
Indices: 12216461--12216502 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
12216451 TTAACATATG
*
12216461 AGAAAGAATAA
1 AGAAATAATAA
12216472 AGAAATAATAA
1 AGAAATAATAA
12216483 AGAAATAAATAA
1 AGAAAT-AATAA
12216495 AGAAATAA
1 AGAAATAA
12216503 ATAAGTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (11 bp):
AGAAATAATAA
Found at i:12216494 original size:4 final size:4
Alignment explanation
Indices: 12216467--12216517 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
12216457 TATGAGAAAG
* * * *
12216467 AATA AAGA AAT- AATA AAGA AATA AATA AAGA AATA AATA AGTA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
12216514 AATA
1 AATA
12216518 TAAAAGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:12216495 original size:12 final size:12
Alignment explanation
Indices: 12216467--12216517 Score: 79
Period size: 12 Copynumber: 4.3 Consensus size: 12
12216457 TATGAGAAAG
12216467 AATAAAGAAAT-
1 AATAAAGAAATA
12216478 AATAAAGAAATA
1 AATAAAGAAATA
12216490 AATAAAGAAATA
1 AATAAAGAAATA
12216502 AAT-AAGTAAATA
1 AATAAAG-AAATA
12216514 AATA
1 AATA
12216518 TAAAAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 14 0.38
12 23 0.62
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.20
Consensus pattern (12 bp):
AATAAAGAAATA
Found at i:12219258 original size:18 final size:18
Alignment explanation
Indices: 12219235--12219272 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12219225 ATCAAAGGGC
12219235 TCATGCTGGTTAGTTCAA
1 TCATGCTGGTTAGTTCAA
12219253 TCATGCTGGTTAGTTCAA
1 TCATGCTGGTTAGTTCAA
12219271 TC
1 TC
12219273 TTCTTCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (18 bp):
TCATGCTGGTTAGTTCAA
Found at i:12225113 original size:177 final size:177
Alignment explanation
Indices: 12224815--12225168 Score: 537
Period size: 177 Copynumber: 2.0 Consensus size: 177
12224805 TCCAAGTTTC
* * * *
12224815 ATGGTAGGTTGACTCTTTTTCGTTACCTCCTTTTTAAATTGGTAACTCTAGATATTCTAATATCT
1 ATGGTAGGTTGACTCTTTTTCGCTACCTCCTCTTTAAATTGGTAACTCTAAATACTCTAATATCT
* * **
12224880 ACTTAAAGTTAAGACTTTTATGGGATGACATTCGTTCTTTGATACAGTAGGTACATATCAAAACT
66 ACTAAAAGTTAAGACTTTTATAGGATGACATTCGTTCTTTGATACAACAGGTACATATCAAAACT
* * *
12224945 CAACATGGACACCATTAGATGGACCACTTCATTTGTAGAGCGGCGTT
131 CAACATGGACACCATCAAATGGACCACTTCATTTGGAGAGCGGCGTT
* *
12224992 ATGGTAGGTTGACTCTTTTTCGCTACCTTCTCTTTAAATTGGTAACTCTAAATACTCTAATATTT
1 ATGGTAGGTTGACTCTTTTTCGCTACCTCCTCTTTAAATTGGTAACTCTAAATACTCTAATATCT
* * * * **
12225057 ACTAAAAGTTAAGATTTTTATAGGATGACATTTGTTCTTTGTTACAACATGTACATATCAGTACT
66 ACTAAAAGTTAAGACTTTTATAGGATGACATTCGTTCTTTGATACAACAGGTACATATCAAAACT
12225122 CAACATGGACACCATCAAATGGACCACTTCATTTGGAGAGCGGCGTT
131 CAACATGGACACCATCAAATGGACCACTTCATTTGGAGAGCGGCGTT
12225169 GTTCATGTTT
Statistics
Matches: 158, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
177 158 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (177 bp):
ATGGTAGGTTGACTCTTTTTCGCTACCTCCTCTTTAAATTGGTAACTCTAAATACTCTAATATCT
ACTAAAAGTTAAGACTTTTATAGGATGACATTCGTTCTTTGATACAACAGGTACATATCAAAACT
CAACATGGACACCATCAAATGGACCACTTCATTTGGAGAGCGGCGTT
Found at i:12227130 original size:33 final size:33
Alignment explanation
Indices: 12227092--12227158 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12227082 TGAGATGTCT
12227092 TTAAGATTATATATGAAAATGGGTCATTGAAAG
1 TTAAGATTATATATGAAAATGGGTCATTGAAAG
12227125 TTAAGATTATATATGAAAATGGGTCATTGAAAG
1 TTAAGATTATATATGAAAATGGGTCATTGAAAG
12227158 T
1 T
12227159 GATGGAGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (33 bp):
TTAAGATTATATATGAAAATGGGTCATTGAAAG
Found at i:12227353 original size:22 final size:21
Alignment explanation
Indices: 12227321--12227365 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
12227311 CCGCTCATTC
12227321 CTCTGCACCGACGAGACTCCT
1 CTCTGCACCGACGAGACTCCT
* *
12227342 CTCTGCCACCGACGGGACTGCT
1 CTCTG-CACCGACGAGACTCCT
12227364 CT
1 CT
12227366 GAGCTATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (21 bp):
CTCTGCACCGACGAGACTCCT
Found at i:12227530 original size:6 final size:6
Alignment explanation
Indices: 12227519--12227549 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12227509 TGAGGGAAGA
*
12227519 AAAAAG AAAAAG AAAAAG AGAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
12227550 GAAGGAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12227550 original size:12 final size:12
Alignment explanation
Indices: 12227519--12227552 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12227509 TGAGGGAAGA
*
12227519 AAAAAGAAAAAG
1 AAAAAGAGAAAG
12227531 AAAAAGAGAAAG
1 AAAAAGAGAAAG
12227543 AAAAAGAGAA
1 AAAAAGAGAA
12227553 GGAGGAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:12228009 original size:13 final size:13
Alignment explanation
Indices: 12228000--12228025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12227990 AGCTTAATAG
12228000 TATATTTTAAAAA
1 TATATTTTAAAAA
12228013 TATATTTTAAAAA
1 TATATTTTAAAAA
12228026 ATCCAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATTTTAAAAA
Found at i:12228188 original size:12 final size:13
Alignment explanation
Indices: 12228160--12228193 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
12228150 GTATTTTTTG
*
12228160 AAAAATAAAATCC
1 AAAAATAAAATCA
12228173 AAAAATAAAAT-A
1 AAAAATAAAATCA
12228185 AAAAATAAA
1 AAAAATAAA
12228194 CGGCCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAATCA
Found at i:12228317 original size:147 final size:144
Alignment explanation
Indices: 12228023--12229348 Score: 1752
Period size: 143 Copynumber: 9.1 Consensus size: 144
12228013 TATATTTTAA
* * *
12228023 AAAATCCAAAAATAAAAT-TAAAAAAA-GGCCAAAATTAGAGTTTTTTACTAAATTAATATAAAT
1 AAAATCCGAAAATAAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAA-
*
12228086 ATACTAAAATAATACATATGAAACATTATGTACTAAAATAATA-AAAAAATAAAATACGAAAATA
65 AAACTAAAATAATACAT-TGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
* *
12228150 GTATTTTTTGAAAAAT
129 GTATATTTTAAAAAAT
* * *
12228166 AAAATCCAAAAATAAAATAAAAAATAAACGGCCAAAATCAGAATTTTTTACTAAATAAATATAAA
1 AAAATCCGAAAATAAAATAAAAAA-AAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAA
* *
12228231 AAATTAAAATAACACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAAT
65 AAACTAAAATAATACA-TTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAAT
*
12228296 AGTACATTTTAAAAAAT
128 AGTATATTTTAAAAAAT
* ** * *
12228313 AAAATCCGAAAACAAAATTAAAAAAAAAAAGCCAAAATCACAGATTTTTACTAAATTAATATAAA
1 AAAATCCGAAAATAAAA-TAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AA
*
12228378 AAAACTAAAATAATACA-TGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACAAAAAT
64 AAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAAT
* **
12228442 AATATATCCTAAAAAAT
128 AGTATATTTTAAAAAAT
* * * *
12228459 AAAATCCGAAAAT-AAA-AATAAAAAAGGGCCAAAGTCAGAGTTTTTTTTTTCTAAATTAATATA
1 AAAATCCGAAAATAAAATAAAAAAAAACGGCCAAAATCAGAG---TTTTTTACTAAATTAATATA
* *
12228522 AAAAACTAAAATAATACA-TGAAACATTATGTACTAAAATAATATAAAAAA-CAAATACAAAAAT
63 AAAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAAT
* *
12228585 AATAAATTTTAAAAAAT
128 AGTATATTTTAAAAAAT
* * * *
12228602 AAAATTCGAAAAT-AAA-AATAAAAAA-GGCCAAAATCATAGTTTTTTTCTAAATTAATATAAAA
1 AAAATCCGAAAATAAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAA
*
12228664 AACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAGAATAAAATACGAAAAGA
66 AACTAAAATAATACA-TTGAAACATTATGTACTAAAATAATATAAAA-AATAAAATACGAAAATA
12228729 GTATATTTTAAAAAAT
129 GTATATTTTAAAAAAT
** * * * * *
12228745 AAAATATGAAAACAAAAT-AAATAAAACGCCCAAAATCACAGATTTTTACTAAATTAATATAAAA
1 AAAATCCGAAAATAAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT--AA
12228809 AAAACTAAAATAATACA-TGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
64 AAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
12228873 GTATATTTTAAAAAAT
129 GTATATTTTAAAAAAT
* * * *
12228889 AAAATCCTAAAAT-AAA-AAATAAAAAGGGCCAAAATCAGAGTTTTTTTTCTAAATTAATATAAA
1 AAAATCCGAAAATAAAATAAAAAAAAACGGCCAAAATCAGAG-TTTTTTACTAAATTAATAT-AA
* **
12228952 AAAACTAAAATAATACA-TGAAACATTATGTACTAAAATAATATAAAAAACAAAATATAAAAATA
64 AAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
12229016 GTATATTTTAAAAAAT
129 GTATATTTTAAAAAAT
* * *
12229032 AAAATTCGAAAATAAAATAAAAAATAAATGGCCAAAATCAGAGTTTTTTATTAAATTAATATAAA
1 AAAATCCGAAAATAAAATAAAAAA-AAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AA
12229097 AAAACTAAAATAATACATTTCG-AACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAA
64 AAAACTAAAATAATACA-TT-GAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAA
*
12229161 TAGTATATTTTAAAAAGT
127 TAGTATATTTTAAAAAAT
* * *
12229179 AAAATCCGAAAATAAAATAAAAAAACAAACAGTCAAAATCAGAGTTTTTTATTAAATTAATATAA
1 AAAATCCGAAAATAAAAT-AAAAAA-AAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT--
* *
12229244 AAAAATACAAAAATAATACATTTGAAACATTATGTACTAAAATAATAT-AAAAATAAAAAACGAA
62 AAAAA-ACTAAAATAATACA-TTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAA
*
12229308 AATAATATATTTTAAAAAAT
125 AATAGTATATTTTAAAAAAT
*
12229328 AAAATCCAAAAATAAAATAAA
1 AAAATCCGAAAATAAAATAAA
12229349 TACCAAAATA
Statistics
Matches: 1062, Mismatches: 89, Indels: 59
0.88 0.07 0.05
Matches are distributed among these distances:
139 38 0.04
141 30 0.03
142 14 0.01
143 234 0.22
144 80 0.08
145 190 0.18
146 139 0.13
147 173 0.16
148 68 0.06
149 57 0.05
150 39 0.04
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (144 bp):
AAAATCCGAAAATAAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAA
AACTAAAATAATACATTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGT
ATATTTTAAAAAAT
Found at i:12228429 original size:13 final size:13
Alignment explanation
Indices: 12228411--12228447 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
12228401 ATTATGTACT
12228411 AAAATAATATAAA
1 AAAATAATATAAA
* *
12228424 AAAATAAAATACA
1 AAAATAATATAAA
12228437 AAAATAATATA
1 AAAATAATATA
12228448 TCCTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAATATAAA
Found at i:12235947 original size:28 final size:28
Alignment explanation
Indices: 12235878--12235978 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
12235868 GACAAGATTG
* * * *
12235878 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
12235908 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
12235936 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
12235965 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
12235979 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:12238953 original size:22 final size:22
Alignment explanation
Indices: 12238927--12238968 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12238917 AAAATTACCT
12238927 TTTCTTTTCTTTAT-TCTTCTCC
1 TTTC-TTTCTTTATATCTTCTCC
*
12238949 TTTCTTTCTTTCTATCTTCT
1 TTTCTTTCTTTATATCTTCT
12238969 TCTTCTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTCTTTATATCTTCTCC
Found at i:12239089 original size:27 final size:27
Alignment explanation
Indices: 12239059--12239116 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
12239049 GAGAAAGGCA
12239059 CCACTGGTGCCGCCTGTGGGGTACCCT
1 CCACTGGTGCCGCCTGTGGGGTACCCT
*
12239086 CCACTGTTGCCGCCTGTGGGGTACCCT
1 CCACTGGTGCCGCCTGTGGGGTACCCT
12239113 CCAC
1 CCAC
12239117 CCTTATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.09, C:0.40, G:0.29, T:0.22
Consensus pattern (27 bp):
CCACTGGTGCCGCCTGTGGGGTACCCT
Found at i:12239940 original size:2 final size:2
Alignment explanation
Indices: 12239933--12239963 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12239923 CACGTTTAAA
12239933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12239964 ATTGTAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12240099 original size:30 final size:31
Alignment explanation
Indices: 12240043--12240102 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
12240033 TTACAAATGG
* *
12240043 TCATTGAATTATTTGAGAGTTTTTATTTAAA
1 TCATTGAACTATTTGAAAGTTTTTATTTAAA
12240074 TCATTGAACTATTTGAAAG-TTTTATTTAA
1 TCATTGAACTATTTGAAAGTTTTTATTTAA
12240103 GTAATTGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (31 bp):
TCATTGAACTATTTGAAAGTTTTTATTTAAA
Found at i:12254032 original size:12 final size:12
Alignment explanation
Indices: 12254015--12254050 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
12254005 ATTATCATAA
12254015 TAAATTTAATAT
1 TAAATTTAATAT
12254027 TAAATTTAATAT
1 TAAATTTAATAT
12254039 TAAATTTAATAT
1 TAAATTTAATAT
12254051 AATATTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATTTAATAT
Found at i:12254057 original size:12 final size:11
Alignment explanation
Indices: 12254014--12254058 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 11
12254004 TATTATCATA
12254014 ATAAATTTAAT
1 ATAAATTTAAT
12254025 ATTAAATTTAAT
1 A-TAAATTTAAT
12254037 ATTAAATTTAAT
1 A-TAAATTTAAT
12254049 ATAATATTTA
1 ATAA-ATTTA
12254059 TCTTTATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATAAATTTAAT
Found at i:12257144 original size:28 final size:28
Alignment explanation
Indices: 12257112--12257167 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
12257102 GCAGCACAAA
*
12257112 ATCATTCTATTGTTCTTCGTTTCATTAC
1 ATCATTCTATTGTTCTTCCTTTCATTAC
12257140 ATCATTCTATTGTTCTTCCTTTCATTAC
1 ATCATTCTATTGTTCTTCCTTTCATTAC
12257168 TGGTTTTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (28 bp):
ATCATTCTATTGTTCTTCCTTTCATTAC
Found at i:12265008 original size:2 final size:2
Alignment explanation
Indices: 12265001--12265032 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12264991 CGTAAATACC
12265001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12265033 TTGAAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12267104 original size:19 final size:19
Alignment explanation
Indices: 12267080--12267119 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12267070 TTTTAAAAAA
* *
12267080 TAAAAATCATTAAAATTATT
1 TAAAAA-CATAAAAAATATT
12267100 TAAAAACATAAAAAATATT
1 TAAAAACATAAAAAATATT
12267119 T
1 T
12267120 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAACATAAAAAATATT
Found at i:12269785 original size:34 final size:35
Alignment explanation
Indices: 12269747--12269812 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
12269737 GGATGTTTAA
*
12269747 TTTTTCAATT-AAGGAATCTTATTGACTTGTTTCT
1 TTTTTCAATTGAAGAAATCTTATTGACTTGTTTCT
**
12269781 TTTTTCTTTTGAAGAAATCTTATTGACTTGTT
1 TTTTTCAATTGAAGAAATCTTATTGACTTGTT
12269813 ATTTGCACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.23, C:0.11, G:0.12, T:0.55
Consensus pattern (35 bp):
TTTTTCAATTGAAGAAATCTTATTGACTTGTTTCT
Found at i:12272031 original size:2 final size:2
Alignment explanation
Indices: 12272024--12272055 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12272014 TTCCTTCCAC
12272024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12272056 CCTTCTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12278409 original size:17 final size:17
Alignment explanation
Indices: 12278349--12278409 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
12278339 TGTTATAATG
12278349 ACAGTTCACACATTGAC
1 ACAGTTCACACATTGAC
* *
12278366 ACA-TCTCGCACATTTAC
1 ACAGT-TCACACATTGAC
*
12278383 ACAGTCCACACATTGAC
1 ACAGTTCACACATTGAC
*
12278400 ATAGTTCACA
1 ACAGTTCACA
12278410 TATAAACACA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
16 1 0.03
17 33 0.94
18 1 0.03
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (17 bp):
ACAGTTCACACATTGAC
Found at i:12278445 original size:17 final size:17
Alignment explanation
Indices: 12278398--12278470 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
12278388 CCACACATTG
* *
12278398 ACATAGTTCACATATAA
1 ACATAGCTCTCATATAA
* *
12278415 ACACAACT-TGCATATAA
1 ACATAGCTCT-CATATAA
12278432 ACATAGCTCTCATATAA
1 ACATAGCTCTCATATAA
* * **
12278449 ATATAGTTAGCATATAA
1 ACATAGCTCTCATATAA
12278466 ACATA
1 ACATA
12278471 ACTCAGATTG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
17 42 0.98
18 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.29
Consensus pattern (17 bp):
ACATAGCTCTCATATAA
Found at i:12278573 original size:16 final size:16
Alignment explanation
Indices: 12278552--12278583 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12278542 ACAATGATAG
12278552 TTTGCATATTCAAGTA
1 TTTGCATATTCAAGTA
12278568 TTTGCATATTCAAGTA
1 TTTGCATATTCAAGTA
12278584 ATCACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
TTTGCATATTCAAGTA
Found at i:12279875 original size:26 final size:26
Alignment explanation
Indices: 12279843--12279894 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
12279833 CGAACAACTG
12279843 AATTGGCATACCAATTGTATCCTATC
1 AATTGGCATACCAATTGTATCCTATC
*
12279869 AATTGGCATACCACTTGTATCCTATC
1 AATTGGCATACCAATTGTATCCTATC
12279895 TTTTCTTACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.35
Consensus pattern (26 bp):
AATTGGCATACCAATTGTATCCTATC
Found at i:12286121 original size:28 final size:28
Alignment explanation
Indices: 12286057--12286121 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
12286047 TTATCGAGCT
12286057 TTGTCTCTACGCAGACCACTGTTACTAA
1 TTGTCTCTACGCAGACCACTGTTACTAA
* * *
12286085 TTTTCTCTACGGAGACCACTGTTACTGA
1 TTGTCTCTACGCAGACCACTGTTACTAA
*
12286113 TTGTGTCTA
1 TTGTCTCTA
12286122 TAGAGACCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (28 bp):
TTGTCTCTACGCAGACCACTGTTACTAA
Found at i:12286127 original size:28 final size:28
Alignment explanation
Indices: 12286057--12286129 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
12286047 TTATCGAGCT
12286057 TTGTCTCTAC-GCAGACCACTGTTACTAA
1 TTGTCTCTACAG-AGACCACTGTTACTAA
* * *
12286085 TTTTCTCTACGGAGACCACTGTTACTGA
1 TTGTCTCTACAGAGACCACTGTTACTAA
* *
12286113 TTGTGTCTATAGAGACC
1 TTGTCTCTACAGAGACC
12286130 TTGGTGTGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (28 bp):
TTGTCTCTACAGAGACCACTGTTACTAA
Found at i:12293673 original size:156 final size:156
Alignment explanation
Indices: 12293389--12293701 Score: 590
Period size: 156 Copynumber: 2.0 Consensus size: 156
12293379 TGCTCCACGC
12293389 ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
1 ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
*
12293454 TTTTAGATTATCCCTTAATCCGTCCTCAAATTAGACACACCTCTCATACTCAGTCGTAACCATGC
66 TTTTAGATTATCCCTTAATCCGTCCTCAAATTAGACACACCTCTCATACTCAGTCGCAACCATGC
12293519 CTCGAGTGTAGCGACTCAGCCTCAAA
131 CTCGAGTGTAGCGACTCAGCCTCAAA
12293545 ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
1 ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
* * *
12293610 TTTTAGATTATCCTTTAATCCGTCCTCAAATTGGGCACACCTCTCATACTCAGTCGCAACCATGC
66 TTTTAGATTATCCCTTAATCCGTCCTCAAATTAGACACACCTCTCATACTCAGTCGCAACCATGC
12293675 CTCGAGTGTAGCGACTCAGCCTCAAA
131 CTCGAGTGTAGCGACTCAGCCTCAAA
12293701 A
1 A
12293702 ACTCGACCTT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (156 bp):
ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
TTTTAGATTATCCCTTAATCCGTCCTCAAATTAGACACACCTCTCATACTCAGTCGCAACCATGC
CTCGAGTGTAGCGACTCAGCCTCAAA
Found at i:12299216 original size:26 final size:26
Alignment explanation
Indices: 12299187--12299244 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
12299177 GATAAAAAGC
12299187 ATATTTGATAAGGTATATCAAAATGA
1 ATATTTGATAAGGTATATCAAAATGA
*
12299213 ATATTTGATAAGGTATATTAAAATGA
1 ATATTTGATAAGGTATATCAAAATGA
12299239 ATATTT
1 ATATTT
12299245 AAGTTTTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.40
Consensus pattern (26 bp):
ATATTTGATAAGGTATATCAAAATGA
Found at i:12300343 original size:41 final size:41
Alignment explanation
Indices: 12300265--12300345 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
12300255 TACATCTTCA
*
12300265 ACTGAATTATATGTAGAGAACAACGAATCATCACCCTTGTC
1 ACTGAATTATATGTAGAGAACAACAAATCATCACCCTTGTC
* * *
12300306 ACTGAATTATATGTAGAGAACAATAAATTATCGCCCTTGT
1 ACTGAATTATATGTAGAGAACAACAAATCATCACCCTTGT
12300346 TATTGGCCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (41 bp):
ACTGAATTATATGTAGAGAACAACAAATCATCACCCTTGTC
Found at i:12301773 original size:23 final size:22
Alignment explanation
Indices: 12301745--12301792 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
12301735 ACATTCAATC
12301745 AAAGGGAAAACAAAGGGACAACA
1 AAAGGG-AAACAAAGGGACAACA
**
12301768 AAAGGGAAATGAAGGGACAACA
1 AAAGGGAAACAAAGGGACAACA
12301790 AAA
1 AAA
12301793 CTGCTCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.60, C:0.10, G:0.27, T:0.02
Consensus pattern (22 bp):
AAAGGGAAACAAAGGGACAACA
Found at i:12301884 original size:37 final size:37
Alignment explanation
Indices: 12301830--12301925 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
12301820 CATCAAGTAT
* * * *
12301830 AGAGACATGACTATTCAAATATATA-TGGACTAAGTGA
1 AGAGACATGACTTTTCAAATATACACAGAAC-AAGTGA
* * *
12301867 AGAGACATGGCTTTTCAACTACACACAGAACAAGTGA
1 AGAGACATGACTTTTCAAATATACACAGAACAAGTGA
*
12301904 AGAGACATGACCTTTCAAATAT
1 AGAGACATGACTTTTCAAATAT
12301926 CTTCCATTAG
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
37 44 0.94
38 3 0.06
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.24
Consensus pattern (37 bp):
AGAGACATGACTTTTCAAATATACACAGAACAAGTGA
Found at i:12310846 original size:21 final size:22
Alignment explanation
Indices: 12310811--12310851 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12310801 TTATGTTTGT
12310811 TAAACATCACTTAATTAGTTAG
1 TAAACATCACTTAATTAGTTAG
*
12310833 TAAAC-TCAGTTAATTAGTT
1 TAAACATCACTTAATTAGTT
12310852 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
TAAACATCACTTAATTAGTTAG
Found at i:12315044 original size:24 final size:25
Alignment explanation
Indices: 12315008--12315054 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
12314998 TATTTATGGA
*
12315008 TAGAACGTCCACAATCTTTAATTGGT
1 TAGAACGTCCAC-ACCTTTAATTGGT
12315034 TAGAAC-T-CACACCTTTAATTG
1 TAGAACGTCCACACCTTTAATTG
12315055 CAAATCCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 1 0.05
26 6 0.30
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (25 bp):
TAGAACGTCCACACCTTTAATTGGT
Found at i:12319050 original size:2 final size:2
Alignment explanation
Indices: 12319043--12319077 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12319033 CTCATCAAGG
12319043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12319078 TAATTGGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12322085 original size:30 final size:31
Alignment explanation
Indices: 12322047--12322120 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
12322037 AAAAAAACTT
* *
12322047 AATAGTTCAGTGACTCAAA-TAAAACTTTCA
1 AATAGTTCAATGACTCAAACGAAAACTTTCA
* *
12322077 ACTAGTTCAATGACTTAAACGAAAACTTTCA
1 AATAGTTCAATGACTCAAACGAAAACTTTCA
12322108 AATAGTTCAATGA
1 AATAGTTCAATGA
12322121 TCATTTTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (31 bp):
AATAGTTCAATGACTCAAACGAAAACTTTCA
Found at i:12326172 original size:34 final size:33
Alignment explanation
Indices: 12326112--12326191 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 33
12326102 CCATCTTAGT
* *
12326112 ACAGTATCAATTATGCAGTAGGGCCTTAGCCCATC
1 ACAGTATC-AGTATGCAGTAGAGCCTTAGCCCA-C
* *
12326147 ATAGTATCAGTATGCATTAGAGCCTTAGCCCAC
1 ACAGTATCAGTATGCAGTAGAGCCTTAGCCCAC
12326180 ACAGTATCAGTA
1 ACAGTATCAGTA
12326192 GTAGTCATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 12 0.30
34 21 0.52
35 7 0.17
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (33 bp):
ACAGTATCAGTATGCAGTAGAGCCTTAGCCCAC
Found at i:12341011 original size:24 final size:24
Alignment explanation
Indices: 12340979--12341027 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12340969 TTAGGGTTAG
12340979 CCACCTAGAGCCTTCCCTTTCATT
1 CCACCTAGAGCCTTCCCTTTCATT
12341003 CCACCTAGAGCCTTCCCTTTCATT
1 CCACCTAGAGCCTTCCCTTTCATT
12341027 C
1 C
12341028 TATTCTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.33
Consensus pattern (24 bp):
CCACCTAGAGCCTTCCCTTTCATT
Found at i:12342737 original size:60 final size:61
Alignment explanation
Indices: 12342673--12342787 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 61
12342663 AGTTGTAATA
* *
12342673 GGGCTACGGCCCAGATTGATACTGATATGGGCT-AGGCCCAG-TATACTCTGATTTTGTAAG
1 GGGCTACGGCCCAGATTAATACTGATATGGGATAAGGCCCAGTTA-ACTCTGATTTTGTAAG
* *
12342733 GGGCTATGGCCCAGATTAATATTGATATGGGATAAGGCCCAGTTAACTCTGATTT
1 GGGCTACGGCCCAGATTAATACTGATATGGGATAAGGCCCAGTTAACTCTGATTT
12342788 CTGAATAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 29 0.59
61 18 0.37
62 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (61 bp):
GGGCTACGGCCCAGATTAATACTGATATGGGATAAGGCCCAGTTAACTCTGATTTTGTAAG
Found at i:12344268 original size:24 final size:26
Alignment explanation
Indices: 12344241--12344289 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
12344231 TAAGAACTAA
12344241 TTCAA-TTAGAAAAATAAAA-ATATC
1 TTCAATTTAGAAAAATAAAATATATC
*
12344265 TTCAATTTATAAAAATAAAATATAT
1 TTCAATTTAGAAAAATAAAATATAT
12344290 TATTTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (26 bp):
TTCAATTTAGAAAAATAAAATATATC
Found at i:12345113 original size:19 final size:19
Alignment explanation
Indices: 12345091--12345127 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12345081 CATTTTGTTT
12345091 TTATTATTAATAAAAATTA
1 TTATTATTAATAAAAATTA
*
12345110 TTATTTTTAATAAAAATT
1 TTATTATTAATAAAAATT
12345128 TCATCCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTATTAATAAAAATTA
Found at i:12345800 original size:20 final size:19
Alignment explanation
Indices: 12345781--12345833 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
12345771 AATTTAAAAT
12345781 TTATTAAAAATTAT-TGAAA
1 TTATTAAAAATTATAT-AAA
*
12345800 TTATAAAAAATTAATATAAA
1 TTATTAAAAATT-ATATAAA
12345820 TTATTTAAAAATTA
1 TTA-TTAAAAATTA
12345834 ATCTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 11 0.38
20 9 0.31
21 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TTATTAAAAATTATATAAA
Found at i:12345833 original size:11 final size:10
Alignment explanation
Indices: 12345774--12345833 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
12345764 AGAAAATAAT
*
12345774 TTAAAATTTA
1 TTAAAAATTA
12345784 TTAAAAATTA
1 TTAAAAATTA
*
12345794 TT-GAAATTA
1 TTAAAAATTA
*
12345803 TAAAAAATTA
1 TTAAAAATTA
* *
12345813 ATATAAATTA
1 TTAAAAATTA
12345823 TTTAAAAATTA
1 -TTAAAAATTA
12345834 ATCTTAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.18
10 24 0.62
11 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:12346218 original size:18 final size:20
Alignment explanation
Indices: 12346189--12346226 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
12346179 TGTATAATTA
12346189 ATTTTAAATTTTAA-TATTT
1 ATTTTAAATTTTAACTATTT
12346208 ATTTT-AATTTTAACTATTT
1 ATTTTAAATTTTAACTATTT
12346227 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTAAATTTTAACTATTT
Found at i:12348815 original size:27 final size:26
Alignment explanation
Indices: 12348785--12348839 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
12348775 TTTCCAACAG
12348785 TAAACCCTA-AACCTAAACCCCAAACTA
1 TAAA-CCTATAACCTAAACCCCAAA-TA
* *
12348812 TAAACCTATATCCTAAACCCTAAATA
1 TAAACCTATAACCTAAACCCCAAATA
12348838 TA
1 TA
12348840 TATATTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (26 bp):
TAAACCTATAACCTAAACCCCAAATA
Found at i:12348835 original size:20 final size:20
Alignment explanation
Indices: 12348785--12348835 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12348775 TTTCCAACAG
12348785 TAAACCCTAAACCTAAACCC
1 TAAACCCTAAACCTAAACCC
* ** * *
12348805 CAAACTATAAACCTATATCC
1 TAAACCCTAAACCTAAACCC
12348825 TAAACCCTAAA
1 TAAACCCTAAA
12348836 TATATATATT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAACCCTAAACCTAAACCC
Found at i:12349027 original size:14 final size:14
Alignment explanation
Indices: 12349010--12349041 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12349000 AAAAAGCCAC
*
12349010 AAACTCTAAACCAT
1 AAACTCTAAACCAA
12349024 AAACTCTAAACCAA
1 AAACTCTAAACCAA
12349038 AAAC
1 AAAC
12349042 AATAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (14 bp):
AAACTCTAAACCAA
Found at i:12349175 original size:7 final size:7
Alignment explanation
Indices: 12349165--12349198 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
12349155 CCCTAAACTC
12349165 TAAACCA
1 TAAACCA
12349172 TAAACCA
1 TAAACCA
*
12349179 TAAAACA
1 TAAACCA
12349186 TAAACCA
1 TAAACCA
12349193 TAAACC
1 TAAACC
12349199 CTTAACCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCA
Found at i:12349793 original size:41 final size:41
Alignment explanation
Indices: 12349748--12349937 Score: 263
Period size: 41 Copynumber: 4.6 Consensus size: 41
12349738 TTACTTTTTT
* * *
12349748 GCGGCGTTTTTTCAAAAGCGCCGCTAAAACCTTGATTTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
*
12349789 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCAATCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
* * *
12349830 ACTGCGTTTTTCCAAAAGCGCCGCTAAAACATCGATCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
* * * *
12349871 GTGGCGTTTTTCCAAAAGTGCCACTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
* *
12349912 GTGGCGTTTTTCCGAAAGCGCCGCTA
1 GCGGCGTTTTTCCAAAAGCGCCGCTA
12349938 TTGTTCTGTT
Statistics
Matches: 131, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 131 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (41 bp):
GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
Found at i:12350006 original size:51 final size:52
Alignment explanation
Indices: 12349950--12350053 Score: 167
Period size: 51 Copynumber: 2.0 Consensus size: 52
12349940 GTTCTGTTTG
*
12349950 GTCAAAACGCCGCTATTGCTCAGTTTTTTGTG-G-CATTTTATTGCAAACGCC
1 GTCAAAACGCCGCCATTGCTCAGTTTTTT-TGCGACATTTTATTGCAAACGCC
*
12350001 GTCAAAACGCCGCCATTGCTTAGTTTTTTTGCGACATTTTATTGCAAACGCC
1 GTCAAAACGCCGCCATTGCTCAGTTTTTTTGCGACATTTTATTGCAAACGCC
12350053 G
1 G
12350054 CTAATGTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
50 2 0.04
51 28 0.57
52 19 0.39
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (52 bp):
GTCAAAACGCCGCCATTGCTCAGTTTTTTTGCGACATTTTATTGCAAACGCC
Found at i:12350786 original size:21 final size:22
Alignment explanation
Indices: 12350762--12350802 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12350752 GTTTAATCCT
*
12350762 TTAAAATATATAAA-TTATAAA
1 TTAAAACATATAAACTTATAAA
*
12350783 TTAATACATATAAACTTATA
1 TTAAAACATATAAACTTATA
12350803 TTTTGATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAACATATAAACTTATAAA
Found at i:12354051 original size:14 final size:14
Alignment explanation
Indices: 12354032--12354061 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12354022 GAAAGCAAAT
12354032 AAATAAACAAAAGA
1 AAATAAACAAAAGA
*
12354046 AAATAAACAAATGA
1 AAATAAACAAAAGA
12354060 AA
1 AA
12354062 GAAGGGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (14 bp):
AAATAAACAAAAGA
Found at i:12354062 original size:18 final size:18
Alignment explanation
Indices: 12354022--12354064 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
12354012 CGCATAAAAG
* *
12354022 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
* *
12354040 AAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
12354058 GAAAGAA
1 GAAAGAA
12354065 GGGGGAAGGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.07, G:0.12, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:12380511 original size:209 final size:209
Alignment explanation
Indices: 12380151--12380569 Score: 811
Period size: 209 Copynumber: 2.0 Consensus size: 209
12380141 TCTTTAAAAC
12380151 CTGTCTCGAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCAAGCATAAAAAATGA
1 CTGTCTCGAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCAAGCATAAAAAATGA
12380216 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
66 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
12380281 ACAAAAATTAACTAAATAGAGGATTTAATTAAAATTTTAAAAAAACTAGGGATATAAATTGCAAA
131 ACAAAAATTAACTAAATAGAGGATTTAATTAAAATTTTAAAAAAACTAGGGATATAAATTGCAAA
12380346 TAATAAAAAGTAGG
196 TAATAAAAAGTAGG
*
12380360 CTGTCTCGAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCGAGCATAAAAAATGA
1 CTGTCTCGAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCAAGCATAAAAAATGA
12380425 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
66 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
* *
12380490 ACAGAAATTAACTAAATAGAGGATTTAATTAAAATTTTAAAAAAACTAGGGGTATAAATTGCAAA
131 ACAAAAATTAACTAAATAGAGGATTTAATTAAAATTTTAAAAAAACTAGGGATATAAATTGCAAA
12380555 TAATAAAAAGTAGG
196 TAATAAAAAGTAGG
12380569 C
1 C
12380570 CAATAAGGGT
Statistics
Matches: 207, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
209 207 1.00
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (209 bp):
CTGTCTCGAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCAAGCATAAAAAATGA
TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
ACAAAAATTAACTAAATAGAGGATTTAATTAAAATTTTAAAAAAACTAGGGATATAAATTGCAAA
TAATAAAAAGTAGG
Found at i:12382909 original size:2 final size:2
Alignment explanation
Indices: 12382898--12382938 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
12382888 ACCATCAATC
12382898 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12382939 TTCTTTGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12383159 original size:38 final size:39
Alignment explanation
Indices: 12383116--12383209 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
12383106 TGAAACCAAT
*
12383116 TACCAGCAC-AAGCCTGTGGGAATTTAAACCCGG-TATAA
1 TACCAGCACAAAGCCTGTGGGAATTT-AACCCGGACATAA
* * * * * *
12383154 TACCAGCTCGAAGCCTATGGGACTTTAGCCCGGACATAT
1 TACCAGCACAAAGCCTGTGGGAATTTAACCCGGACATAA
12383193 TACCAGCACAAAGCCTG
1 TACCAGCACAAAGCCTG
12383210 CGGACCCTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
38 14 0.31
39 31 0.69
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (39 bp):
TACCAGCACAAAGCCTGTGGGAATTTAACCCGGACATAA
Found at i:12383226 original size:39 final size:39
Alignment explanation
Indices: 12383197--12383306 Score: 184
Period size: 39 Copynumber: 2.8 Consensus size: 39
12383187 ACATATTACC
*
12383197 AGCACAAAGCCTGCGGACCCTAAGTCCGGATATAATTCT
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCT
*
12383236 AGCACATAGCCTGCGAACCCTAAGTCCGGATATAATTCT
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCT
* *
12383275 AGCATATAGCCTGCGGACCCTAAGTCTGGATA
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATA
12383307 AACATCACTG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (39 bp):
AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCT
Found at i:12389430 original size:51 final size:49
Alignment explanation
Indices: 12389346--12389471 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 49
12389336 AATCTGCTTT
* * * *
12389346 ACTGCAACTTCAGGGAGATAAGATTAATGGCTTGTAGCTTTAGTCTATTCC
1 ACTGCAACTTCAGGGAAATAAGATTTATAGCTTGTAGCTTTAATC--TTCC
* * *
12389397 ACTGCAACTTCAAGAAAATAAGATTTTTAGCTTGTAGCTTTAATCTTCC
1 ACTGCAACTTCAGGGAAATAAGATTTATAGCTTGTAGCTTTAATCTTCC
*
12389446 ACTACAACTTCAGGGAAATAAGATTT
1 ACTGCAACTTCAGGGAAATAAGATTT
12389472 GCTATCTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 27 0.42
51 38 0.58
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (49 bp):
ACTGCAACTTCAGGGAAATAAGATTTATAGCTTGTAGCTTTAATCTTCC
Found at i:12389657 original size:44 final size:44
Alignment explanation
Indices: 12389590--12389855 Score: 244
Period size: 44 Copynumber: 5.9 Consensus size: 44
12389580 ATCTGCTATT
** *
12389590 TTCAATCTGTTCCACTACAACTTCAGGGAGATAAGATTAGTAGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
* * * *
12389634 TTCAATCTACTCCATTGCGACTTCAGGAAGATAAGATTTGTAACTTGTAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGA--T-T-A---GTAGC
* ** * * * *
12389685 TTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTTGCTATC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGC
* * * * *
12389730 TTCAATCTACTCCACTACAACTTCAGGGAGATGAGATTTGTGGT
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
* * *
12389774 TTTAATCTACTCCACTGCAACTTTAGGGAGATAAGATTAGTGGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
* *
12389818 TTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATT
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
12389856 CGCCATAATG
Statistics
Matches: 177, Mismatches: 37, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
44 104 0.59
45 36 0.20
46 1 0.01
47 1 0.01
48 2 0.01
49 1 0.01
51 32 0.18
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTAGC
Found at i:12389737 original size:140 final size:140
Alignment explanation
Indices: 12389544--12389811 Score: 360
Period size: 140 Copynumber: 1.9 Consensus size: 140
12389534 AGGTTTATAG
* * * **
12389544 CTTTAATCTGCTTTACTGTAACTTCAGAAAGATAGGATCTGCTATTTTCAATCTGTTCCACTACA
1 CTTTAATCTGCTTCACTGTAACTTCAGAAAGATAAGATCTGCTATCTTCAATCTACTCCACTACA
* *
12389609 ACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCATTGCGACTTCAGGAAGATAAGATTTG
66 ACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTTG
12389674 TAACTTGTAA
131 TAACTTGTAA
* *
12389684 CTTTAATCTG-TTCCACTGTAACTTCAGGGAA-ATAAGATTTGCTATCTTCAATCTACTCCACTA
1 CTTTAATCTGCTT-CACTGTAACTTCA-GAAAGATAAGATCTGCTATCTTCAATCTACTCCACTA
* * * * * * *
12389747 CAACTTCAGGGAGATGAGATTTGTGGTTTTAATCTACTCCACTGCAACTTTAGGGAGATAAGATT
64 CAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATT
12389812 AGTGGCTTCA
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
139 2 0.02
140 105 0.95
141 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (140 bp):
CTTTAATCTGCTTCACTGTAACTTCAGAAAGATAAGATCTGCTATCTTCAATCTACTCCACTACA
ACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTTG
TAACTTGTAA
Found at i:12397235 original size:47 final size:47
Alignment explanation
Indices: 12397103--12397396 Score: 491
Period size: 47 Copynumber: 6.3 Consensus size: 47
12397093 ATAAGATATG
* * *
12397103 TATATGTGGTAAAGCCGAATGGCCAATGTGATGAATGTGAATATGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
12397150 TATATGTGATAAGGCC-AATGGCCAATGTGATGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12397196 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12397243 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12397290 TATATGTGATACGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
* * *
12397337 TATATGTGATAAGGCCAAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12397384 TAAATGTGATAAG
1 TATATGTGATAAG
12397397 TCCCGAAGGG
Statistics
Matches: 235, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
46 45 0.19
47 190 0.81
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
Found at i:12399852 original size:40 final size:40
Alignment explanation
Indices: 12399797--12400096 Score: 483
Period size: 40 Copynumber: 7.5 Consensus size: 40
12399787 GTATGAGACT
12399797 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
**
12399837 TAGTGATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
*
12399877 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTTGTGC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
** *
12399917 TAGTGATGTATCCGGGCTAAGCCCCGAAGGGCATTCGTGC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
12399957 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
* ** *
12399997 TAGTGATATATCCGGGCTAAGCCCCGAAGGGCATTCGTGC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
*
12400037 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGTATTCGTGC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
* *
12400077 TAGTGATATATCCGTGCTAA
1 TAGTGATGTATCCGGGCTAA
12400097 ACCCCGAAGA
Statistics
Matches: 237, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 237 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.27
Consensus pattern (40 bp):
TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGC
Found at i:12399930 original size:80 final size:80
Alignment explanation
Indices: 12399797--12400109 Score: 554
Period size: 80 Copynumber: 3.9 Consensus size: 80
12399787 GTATGAGACT
*
12399797 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGCCCC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGCCCC
12399862 GAAGAGCATTCGTGC
66 GAAGAGCATTCGTGC
* *
12399877 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTTGTGCTAGTGATGTATCCGGGCTAAGCCCC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGCCCC
*
12399942 GAAGGGCATTCGTGC
66 GAAGAGCATTCGTGC
12399957 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGCCCC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGCCCC
*
12400022 GAAGGGCATTCGTGC
66 GAAGAGCATTCGTGC
* * *
12400037 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGTATTCGTGCTAGTGATATATCCGTGCTAAACCCC
1 TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGCCCC
12400102 GAAGAGCA
66 GAAGAGCA
12400110 ATCATGCTGG
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 225 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (80 bp):
TAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGCCCC
GAAGAGCATTCGTGC
Found at i:12400326 original size:25 final size:25
Alignment explanation
Indices: 12400285--12400336 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
12400275 TGTGTAATAA
12400285 TGAATGAATAAGAGCACTATGTGTG
1 TGAATGAATAAGAGCACTATGTGTG
* *
12400310 TGAATG-ATTAGAGGCACTGTGTGTG
1 TGAATGAATAAGA-GCACTATGTGTG
12400335 TG
1 TG
12400337 CGAATTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
TGAATGAATAAGAGCACTATGTGTG
Found at i:12402672 original size:47 final size:47
Alignment explanation
Indices: 12402622--12402869 Score: 397
Period size: 47 Copynumber: 5.3 Consensus size: 47
12402612 ATAAGATATG
* * * *
12402622 TATATGTGGTAAAGCCGAATGGCCAATGTGATGAATGTGAATATGTG
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12402669 TATATGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12402716 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12402763 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
* * *
12402810 TATATGTGATAAGGCCAAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
*
12402857 TAAATGTGATAAG
1 TATATGTGATAAG
12402870 TCCCGAAGGG
Statistics
Matches: 189, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 189 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
Found at i:12402675 original size:25 final size:25
Alignment explanation
Indices: 12402647--12402725 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
12402637 CGAATGGCCA
12402647 ATGTGATGAATGTGAATATGTGTAT
1 ATGTGATGAATGTGAATATGTGTAT
* ** *
12402672 ATGTGAT-AAGGCCAA-ATG-GCCA-
1 ATGTGATGAATGTGAATATGTG-TAT
* *
12402694 ATGTGATGAATGTGAATGTGTATAT
1 ATGTGATGAATGTGAATATGTGTAT
12402719 ATGTGAT
1 ATGTGAT
12402726 AAGGCCGAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 8 0.21
23 9 0.23
24 8 0.21
25 14 0.36
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (25 bp):
ATGTGATGAATGTGAATATGTGTAT
Found at i:12402735 original size:25 final size:25
Alignment explanation
Indices: 12402707--12402830 Score: 75
Period size: 25 Copynumber: 5.2 Consensus size: 25
12402697 TGATGAATGT
12402707 GAATGTGTATATATGTGATAAGGCC
1 GAATGTGTATATATGTGATAAGGCC
** * * *
12402732 GAATG-G-CCA-ATGTGACGAATG-T
1 GAATGTGTATATATGTGA-TAAGGCC
12402754 GAATGTGTATATATGTGATAAGGCC
1 GAATGTGTATATATGTGATAAGGCC
** * * *
12402779 GAATG-G-CCA-ATGTGACGAATG-T
1 GAATGTGTATATATGTGA-TAAGGCC
12402801 GAATGTGTATATATGTGATAAGGCC
1 GAATGTGTATATATGTGATAAGGCC
*
12402826 AAATG
1 GAATG
12402831 GCCAATGTGA
Statistics
Matches: 68, Mismatches: 21, Indels: 20
0.62 0.19 0.18
Matches are distributed among these distances:
22 22 0.32
23 10 0.15
24 10 0.15
25 26 0.38
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (25 bp):
GAATGTGTATATATGTGATAAGGCC
Found at i:12418152 original size:324 final size:324
Alignment explanation
Indices: 12417563--12418210 Score: 1170
Period size: 324 Copynumber: 2.0 Consensus size: 324
12417553 TATCCTTTGC
*
12417563 AGTTGGTGGTGACGTACAGAGCCTTTGTAGATCCCATGGCCCCTGGTAGTATTTCATCATCATTA
1 AGTTGGTGGTGACGTACAGAGCCTTTGTAGATCCCATGCCCCCTGGTAGTATTTCATCATCATTA
*
12417628 AAGAAGATGAAGCTATCTGCACTTATACTGTTAACTAGGCGGTCCAGATTGTTTATCGAGATATC
66 AAGAAGATGAAGCTATCTACACTTATACTGTTAACTAGGCGGTCCAGATTGTTTATCGAGATATC
* * *
12417693 GTTGGTGACATAAGTTTCATTTAGCACTTTCATCAATGCGCTACAACGTGTCTTCGAACTTAAGA
131 ATTGGTGACATAAGTTTCATTTAGCACTTTCATCAATGCGCTACAACGTGTCTCCAAACTTAAGA
12417758 GTAAAGCTAGCACTGATATGCAAGCTGGTTGTTTATGTAGCTGTTCTACAACACTATACTCGCTA
196 GTAAAGCTAGCACTGATATGCAAGCTGGTTGTTTATGTAGCTGTTCTACAACACTATACTCGCTA
*
12417823 TGCTTTAATAATTTCAAGAATTCTTTAGCCTCTTTCTCAATTACCGGCTTATTAACCGGTGATT
261 TGCTTTAATAATTTCAAGAATTCTTTAGCCTCTTTCTCAATTACCAGCTTATTAACCGGTGATT
* * *
12417887 AGTTGGTGGTGATGTGCAGAGCCTTTGTAGATCTCATGCCCCCTGGTAGTATTTCATCATCATTA
1 AGTTGGTGGTGACGTACAGAGCCTTTGTAGATCCCATGCCCCCTGGTAGTATTTCATCATCATTA
* *
12417952 AAGAAGATGAAGCTATCTACACTTATATTGTTAACTAGGCGGTCCAGCTTGTTTATCGAGATATC
66 AAGAAGATGAAGCTATCTACACTTATACTGTTAACTAGGCGGTCCAGATTGTTTATCGAGATATC
* *
12418017 ATTGGTGATATAAGTTTCATTTAGCACTTTCATCAATGCGCTACAATGTGTCTCCAAACTTAAGA
131 ATTGGTGACATAAGTTTCATTTAGCACTTTCATCAATGCGCTACAACGTGTCTCCAAACTTAAGA
12418082 GTAAAGCTAGCACTGATATGCAAGCTGGTTGTTTATGTAGCTGTTCTACAACACTATACTCGCTA
196 GTAAAGCTAGCACTGATATGCAAGCTGGTTGTTTATGTAGCTGTTCTACAACACTATACTCGCTA
*
12418147 TGCTTTAATAATTTCAAGAATTCTTTAGCCTCTTTCTCAGTTACCAGCTTATTAACCGGTGATT
261 TGCTTTAATAATTTCAAGAATTCTTTAGCCTCTTTCTCAATTACCAGCTTATTAACCGGTGATT
12418211 CAAGCCTGGC
Statistics
Matches: 310, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
324 310 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (324 bp):
AGTTGGTGGTGACGTACAGAGCCTTTGTAGATCCCATGCCCCCTGGTAGTATTTCATCATCATTA
AAGAAGATGAAGCTATCTACACTTATACTGTTAACTAGGCGGTCCAGATTGTTTATCGAGATATC
ATTGGTGACATAAGTTTCATTTAGCACTTTCATCAATGCGCTACAACGTGTCTCCAAACTTAAGA
GTAAAGCTAGCACTGATATGCAAGCTGGTTGTTTATGTAGCTGTTCTACAACACTATACTCGCTA
TGCTTTAATAATTTCAAGAATTCTTTAGCCTCTTTCTCAATTACCAGCTTATTAACCGGTGATT
Found at i:12425686 original size:31 final size:31
Alignment explanation
Indices: 12425651--12425713 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
12425641 ATATTCATAG
12425651 TTAGAATATTAAAATACTCATGCTTTTTTAA
1 TTAGAATATTAAAATACTCATGCTTTTTTAA
12425682 TTAGAATATTAAAATACTCATGCTTTTTTAA
1 TTAGAATATTAAAATACTCATGCTTTTTTAA
12425713 T
1 T
12425714 AAACATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAGAATATTAAAATACTCATGCTTTTTTAA
Found at i:12433456 original size:7 final size:8
Alignment explanation
Indices: 12433444--12433477 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
12433434 ATAATAAAAT
12433444 ATAT-AAA
1 ATATCAAA
12433451 ATAT-AAA
1 ATATCAAA
12433458 ATATCAAA
1 ATATCAAA
12433466 ATATCAAA
1 ATATCAAA
12433474 ATAT
1 ATAT
12433478 TAGAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATCAAA
Found at i:12433459 original size:24 final size:24
Alignment explanation
Indices: 12433432--12433488 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
12433422 ATAATGATGC
*
12433432 AAATAATAAAATATATAAAATA-TA
1 AAATAATAAAATAT-CAAAATATTA
12433456 AAAT-ATCAAAATATCAAAATATTA
1 AAATAAT-AAAATATCAAAATATTA
*
12433480 GAATAATAA
1 AAATAATAA
12433489 TAAATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 8 0.29
24 18 0.64
25 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATAATAAAATATCAAAATATTA
Found at i:12433484 original size:16 final size:15
Alignment explanation
Indices: 12433432--12433484 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
12433422 ATAATGATGC
12433432 AAATAATAAAATATATA
1 AAAT-ATAAAATAT-TA
*
12433449 AAATATAAAATATCA
1 AAATATAAAATATTA
12433464 AAATATCAAAATATTA
1 AAATAT-AAAATATTA
*
12433480 GAATA
1 AAATA
12433485 ATAATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 7 0.22
16 21 0.66
17 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATATAAAATATTA
Found at i:12433657 original size:20 final size:20
Alignment explanation
Indices: 12433632--12433698 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
12433622 TAAATACATA
12433632 ATAATATTAAAAGTATGTAC
1 ATAATATTAAAAGTATGTAC
* **
12433652 ATAATA-T-AATGTTAAAAATAC
1 ATAATATTAAAAG-T--ATGTAC
12433673 A-AATATTAAAAGTATGTAC
1 ATAATATTAAAAGTATGTAC
12433692 ATAATAT
1 ATAATAT
12433699 AATGTTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 3 0.09
19 7 0.20
20 15 0.43
21 7 0.20
22 3 0.09
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.34
Consensus pattern (20 bp):
ATAATATTAAAAGTATGTAC
Found at i:12433689 original size:40 final size:40
Alignment explanation
Indices: 12433634--12433713 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12433624 AATACATAAT
12433634 AATATTAAAAGTATGTACATAATATAATGTTAAAAATACA
1 AATATTAAAAGTATGTACATAATATAATGTTAAAAATACA
12433674 AATATTAAAAGTATGTACATAATATAATGTTAAAAATACA
1 AATATTAAAAGTATGTACATAATATAATGTTAAAAATACA
12433714 TACATAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (40 bp):
AATATTAAAAGTATGTACATAATATAATGTTAAAAATACA
Found at i:12433697 original size:26 final size:26
Alignment explanation
Indices: 12433668--12433747 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 26
12433658 TAATGTTAAA
* **
12433668 AATACAAATATTAAAAGTATGTACAT
1 AATACAAATATTAAAAATACATACAT
* *
12433694 AATA-TAATGTTAAAAATACATACAT
1 AATACAAATATTAAAAATACATACAT
** *
12433719 AATACAGTTATTAAAAAATATATACAT
1 AATACAAATATT-AAAAATACATACAT
12433746 AA
1 AA
12433748 GATAATATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
25 20 0.48
26 7 0.17
27 15 0.36
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (26 bp):
AATACAAATATTAAAAATACATACAT
Found at i:12433761 original size:23 final size:22
Alignment explanation
Indices: 12433598--12433829 Score: 92
Period size: 23 Copynumber: 10.1 Consensus size: 22
12433588 AATACTACAT
* * *
12433598 AAATATGTACATATATATTA-A
1 AAATATATACATAAATAATATA
*
12433619 AAATAAATACAT-AATAATATTA
1 AAATATATACATAAATAATA-TA
* * *
12433641 AAAGTATGTACATAATATAATGTT
1 AAA-TATATACATAA-ATAATATA
12433665 AAA-A-ATAC--AAAT-AT-TA
1 AAATATATACATAAATAATATA
* *
12433681 AAAGTATGTACATAATATAATGTTAA
1 AAA-TATATACATAA-ATAAT-AT-A
*
12433707 AAATACATACAT-AATACAGTTATTAAA
1 AAATATATACATAAATA-A--TA-T--A
12433734 AAATATATACATAAGATAATATA
1 AAATATATACATAA-ATAATATA
*
12433757 AAATATATACATGAAATAGTATAAA
1 AAATATATACAT-AAATA--ATATA
12433782 AAATATATA-ACT-AATAATATTAA
1 AAATATATACA-TAAATAATA-T-A
12433805 AAATATATACAT-AATATATATA
1 AAATATATACATAAATA-ATATA
12433827 AAA
1 AAA
12433830 ACAATTACGA
Statistics
Matches: 164, Mismatches: 17, Indels: 59
0.68 0.07 0.25
Matches are distributed among these distances:
16 4 0.02
17 2 0.01
18 3 0.02
19 5 0.03
20 5 0.03
21 18 0.11
22 11 0.07
23 48 0.29
24 14 0.09
25 28 0.17
26 8 0.05
27 13 0.08
28 2 0.01
29 3 0.02
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (22 bp):
AAATATATACATAAATAATATA
Found at i:12433830 original size:23 final size:23
Alignment explanation
Indices: 12433732--12433830 Score: 107
Period size: 23 Copynumber: 4.2 Consensus size: 23
12433722 ACAGTTATTA
*
12433732 AAAAATATATACATAAGATA-AT
1 AAAAATATATACATAATATATAT
12433754 ATAAAATATATACATGAA-ATAGTAT
1 A-AAAATATATACAT-AATATA-TAT
12433779 AAAAAATATATA-ACTAATA-ATATT
1 -AAAAATATATACA-TAATATATA-T
12433803 AAAAATATATACATAATATATAT
1 AAAAATATATACATAATATATAT
12433826 AAAAA
1 AAAAA
12433831 CAATTACGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 19
0.78 0.00 0.22
Matches are distributed among these distances:
22 1 0.01
23 40 0.60
24 11 0.16
25 14 0.21
26 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (23 bp):
AAAAATATATACATAATATATAT
Found at i:12433970 original size:3 final size:3
Alignment explanation
Indices: 12433955--12433996 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
12433945 ATACTAGTAC
*
12433955 TAA TAA TAT TAA TAA TAA -ATA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
12433997 ATATATATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12435899 original size:29 final size:29
Alignment explanation
Indices: 12435857--12435914 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
12435847 CAATCTTTAT
* * *
12435857 CCTCAGTGTGTGACCCGAGGCTCAACTCA
1 CCTCAGCGTATGACCCGAAGCTCAACTCA
*
12435886 CCTCAGCGTATGACCTGAAGCTCAACTCA
1 CCTCAGCGTATGACCCGAAGCTCAACTCA
12435915 TCTCTCGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (29 bp):
CCTCAGCGTATGACCCGAAGCTCAACTCA
Found at i:12435960 original size:14 final size:14
Alignment explanation
Indices: 12435943--12435972 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12435933 GATTTGTTTG
12435943 AAACATAAATTGAA
1 AAACATAAATTGAA
12435957 AAACATAAATTGAA
1 AAACATAAATTGAA
12435971 AA
1 AA
12435973 TATCTCGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (14 bp):
AAACATAAATTGAA
Found at i:12436047 original size:89 final size:89
Alignment explanation
Indices: 12435896--12436091 Score: 293
Period size: 89 Copynumber: 2.2 Consensus size: 89
12435886 CCTCAGCGTA
* * *
12435896 TGACCTGAAGCTCAACTCATCTCTCGCAATTTGAGTTGATTTGTTTGAAACATAAATTGAAAAAC
1 TGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTGTTTGAAACATAAATTGAAAAAA
* * * *
12435961 ATAAATTGAAAATATCTCGGCGCG
66 AGAAATTGAAAATACCTCAGCACG
* * *
12435985 TGACCTGAGGCTCAACTCATCTCTTGTAATATGAGTTGATTTTTTTGAAACATAAATTGAAAAAA
1 TGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTGTTTGAAACATAAATTGAAAAAA
*
12436050 AGAAATTGAAAATACCTCAGCATG
66 AGAAATTGAAAATACCTCAGCACG
12436074 TGACCTGAGGCTCAACTC
1 TGACCTGAGGCTCAACTC
12436092 GCCTCTAGCA
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 96 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (89 bp):
TGACCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTGTTTGAAACATAAATTGAAAAAA
AGAAATTGAAAATACCTCAGCACG
Found at i:12436242 original size:164 final size:164
Alignment explanation
Indices: 12435955--12436431 Score: 687
Period size: 163 Copynumber: 2.9 Consensus size: 164
12435945 ACATAAATTG
* * * * *
12435955 AAAAACATA-AATTGAAAATATCTCGGCGCGTGACCTGAGGCTCAACTCATCTCTTGTAATATGA
1 AAAAACA-AGAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTTGCAATATGA
* *
12436019 GTTGATTTTTTTGAAACATAAATTGAAAAAAAGAAATTGAAAATACCTCAGCATGTGACCTGAGG
65 GTTGATTTTTTTGAAACATAAATTGAAAAACAGAAATTGAAAATACCTAAGCATGTGACCTGAGG
12436084 CTCAACTCGCCTCTAGCAATACGAGCTGACTTTTA
130 CTCAACTCGCCTCTAGCAATACGAGCTGACTTTTA
12436119 AAAAA-AAGAATTGAAAATACCTCAGCGTGT-AGCCTGAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAAGAATTGAAAATACCTCAGCGTGTGA-CCTGAGGCTCAACTCACCTCTTGCAATATGA
* *
12436182 GTTGATTTTTTTTGAAACATAAATTGAAAAACAGAAATTAAAAATACC-AAGGCGTGTGACCTGA
65 GTTGA-TTTTTTTGAAACATAAATTGAAAAACAGAAATTGAAAATACCTAA-GCATGTGACCTGA
* *
12436246 GGCTCAACTCGCCTCTTGCAATACGAGTTGACTTTTA
128 GGCTCAACTCGCCTCTAGCAATACGAGCTGACTTTTA
* *
12436283 AAAAACAGGAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAAGAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTTGCAATATGAG
* * * * *
12436348 TTGATTTTTTT-AAACAGAAATTGAAAAACAGAAATTGAAAATACCT-CGACATGTAACCCGAGC
66 TTGATTTTTTTGAAACATAAATTGAAAAACAGAAATTGAAAATACCTAAG-CATGTGACCTGAGG
* *
12436411 CTCAACTCACCTCTCGCAATA
130 CTCAACTCGCCTCTAGCAATA
12436432 TGAGTTGATT
Statistics
Matches: 283, Mismatches: 22, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
162 3 0.01
163 116 0.41
164 104 0.37
165 59 0.21
166 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (164 bp):
AAAAACAAGAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTTGCAATATGAG
TTGATTTTTTTGAAACATAAATTGAAAAACAGAAATTGAAAATACCTAAGCATGTGACCTGAGGC
TCAACTCGCCTCTAGCAATACGAGCTGACTTTTA
Found at i:12436336 original size:75 final size:74
Alignment explanation
Indices: 12436208--12436374 Score: 228
Period size: 75 Copynumber: 2.2 Consensus size: 74
12436198 ACATAAATTG
* * *
12436208 AAAAACAGAAATTAAAAATACCAAGGCGTGTGACCTGAGGCTCAACTCGCCTCTTGCAATACGAG
1 AAAAACAGAAATTGAAAATACCAAGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAG
12436273 TTGACTTTTA
66 TTGA-TTTTA
* * *
12436283 AAAAACAGGAATTGAAAATACCTCA-GCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACC-AAGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGA
*
12436347 GTTGATTTTT
65 GTTGATTTTA
**
12436357 TTAAACAGAAATTGAAAA
1 AAAAACAGAAATTGAAAA
12436375 ACAGAAATTG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 19 0.23
75 61 0.75
76 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (74 bp):
AAAAACAGAAATTGAAAATACCAAGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAG
TTGATTTTA
Found at i:12436378 original size:14 final size:14
Alignment explanation
Indices: 12436359--12436388 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12436349 TGATTTTTTT
12436359 AAACAGAAATTGAA
1 AAACAGAAATTGAA
12436373 AAACAGAAATTGAA
1 AAACAGAAATTGAA
12436387 AA
1 AA
12436389 TACCTCGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (14 bp):
AAACAGAAATTGAA
Found at i:12436463 original size:14 final size:14
Alignment explanation
Indices: 12436444--12436479 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12436434 AGTTGATTTT
*
12436444 TTTGAAAAATAGAA
1 TTTGAAAAACAGAA
12436458 TTTGAAAAACAGAA
1 TTTGAAAAACAGAA
12436472 TTTGAAAA
1 TTTGAAAA
12436480 TACCTCGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.28
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:12436495 original size:91 final size:90
Alignment explanation
Indices: 12436283--12436554 Score: 394
Period size: 91 Copynumber: 3.0 Consensus size: 90
12436273 TTGACTTTTA
* * *
12436283 AAAAACAGGAATTGAAAATACCTC-AGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACA-GAATTGAAAATACCTCGA-CATGTAACCCGAGGCTCAACTCACCTCTCGCAATATGA
12436347 GTTGATTTTTTT---AAACAGAAATTG
64 GTTGATTTTTTTGAAAAACAGAAATTG
*
12436371 AAAAACAGAAATTGAAAATACCTCGACATGTAACCCGAGCCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAG-AATTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACCTCTCGCAATATGAG
* *
12436436 TTGATTTTTTTGAAAAATAGAATTTG
65 TTGATTTTTTTGAAAAACAGAAATTG
* *
12436462 AAAAACAGAATTTGAAAATACCTCGACATGTAACTCGAGGCTCAATTCACCTCTCGCAATATGAG
1 AAAAACAGAA-TTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACCTCTCGCAATATGAG
12436527 TTGA--TTTTTGAAAAACAGAAATTG
65 TTGATTTTTTTGAAAAACAGAAATTG
12436551 AAAA
1 AAAA
12436555 TACCTCAGAA
Statistics
Matches: 167, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
87 1 0.01
88 68 0.41
89 23 0.14
90 2 0.01
91 73 0.44
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (90 bp):
AAAAACAGAATTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTGAAAAACAGAAATTG
Found at i:12436579 original size:254 final size:252
Alignment explanation
Indices: 12436119--12436628 Score: 713
Period size: 254 Copynumber: 2.0 Consensus size: 252
12436109 CTGACTTTTA
* * * * *
12436119 AAAAAAAGAATTGAAAATACCTCAGCGTGTAGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAAAAAGAATTGAAAATACCTCAGCATGTAACCCGAGCCTCAACTCACCTCTCGCAATATGAGT
* * * *
12436184 TGATTTTTTTTGAAACATAAATTGAAAAACAGAAATTAAAAATACCAAGGCGTGTGACCTGAGGC
66 TGATTTTTTTTGAAAAATAAATTGAAAAACAGAAATTAAAAATACCAAGACATGTAACCTGAGGC
* * * **
12436249 TCAACTCGCCTCTTGCAATACGAGTTGACTTTTAAAAAACAGGAATTGAAAATACCTCAGCGTGT
131 TCAACTCACCTCTCGCAATACGAGTTGACTTTTAAAAAACAGAAATTGAAAATACCTCAGAATGT
* *
12436314 GACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-TAAACAGAAATT
196 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATT
*
12436370 GAAAAACAGAAATTGAAAATACCTC-GACATGTAACCCGAGCCTCAACTCACCTCTCGCAATATG
1 -AAAAAAAG-AATTGAAAATACCTCAG-CATGTAACCCGAGCCTCAACTCACCTCTCGCAATATG
* * **
12436434 AGTTGA-TTTTTTTGAAAAATAGAATTTGAAAAACAGAATTTGAAAATACCTCGACATGTAA-CT
63 AGTTGATTTTTTTTGAAAAATA-AA-TTGAAAAACAGAAATTAAAAATACCAAGACATGTAACCT
* * * *
12436497 CGAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCA
126 -GAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTAAAAAACAGAAATTGAAAATACCTCA
12436562 GAATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATT
190 GAATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATT
12436625 AAAA
1 AAAA
12436629 CATCAGAGTA
Statistics
Matches: 227, Mismatches: 25, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
252 22 0.10
253 57 0.25
254 137 0.60
255 11 0.05
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (252 bp):
AAAAAAAGAATTGAAAATACCTCAGCATGTAACCCGAGCCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTTGAAAAATAAATTGAAAAACAGAAATTAAAAATACCAAGACATGTAACCTGAGGC
TCAACTCACCTCTCGCAATACGAGTTGACTTTTAAAAAACAGAAATTGAAAATACCTCAGAATGT
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATT
Found at i:12436581 original size:75 final size:75
Alignment explanation
Indices: 12436458--12436628 Score: 274
Period size: 75 Copynumber: 2.3 Consensus size: 75
12436448 AAAAATAGAA
* * *
12436458 TTTGAAAAACAGAATTTGAAAATACCTCGACATGTAACTCGAGGCTCAATTCACCTCTCGCAATA
1 TTTGAAAAACAGAAATTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACCTCTCGCAATA
12436523 TGAGTTGATT
66 TGAGTTGATT
*
12436533 TTTGAAAAACAGAAATTGAAAATACCTCAGA-ATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAATACCTC-GACATGTAACCCGAGGCTCAACTCACCTCTCGCAAT
12436597 ATGAGTTGATT
65 ATGAGTTGATT
*
12436608 TTTTAAAAACAGAAATT-AAAA
1 TTTGAAAAACAGAAATTGAAAA
12436629 CATCAGAGTA
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
74 4 0.04
75 84 0.93
76 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (75 bp):
TTTGAAAAACAGAAATTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATT
Found at i:12441112 original size:45 final size:45
Alignment explanation
Indices: 12441046--12441145 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
12441036 AGTTAATGAG
*
12441046 AATGA-AAAGACCATGAAAAAATGCATCTTCATTAATGTTCATTT
1 AATGATAAAGACCATGAAAAAATGCATCTTCATTAATGTTCATCT
*
12441090 AATGATAAAGACCATGACAAAATGCATCTTCATTAATGTTCATCT
1 AATGATAAAGACCATGAAAAAATGCATCTTCATTAATGTTCATCT
12441135 AATGATAAAGA
1 AATGATAAAGA
12441146 GCAAATCATA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
44 5 0.09
45 48 0.91
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (45 bp):
AATGATAAAGACCATGAAAAAATGCATCTTCATTAATGTTCATCT
Found at i:12448609 original size:14 final size:14
Alignment explanation
Indices: 12448581--12448628 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
12448571 TGATGCAAAT
12448581 AATA-AAATATATAA
1 AATATAAATAT-TAA
12448595 AATATAAATATTAA
1 AATATAAATATTAA
*
12448609 AATATCAAAATATTAG
1 AATAT--AAATATTAA
12448625 AATA
1 AATA
12448629 ATAATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 12 0.40
15 6 0.20
16 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AATATAAATATTAA
Found at i:12448609 original size:23 final size:22
Alignment explanation
Indices: 12448577--12448632 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
12448567 ATAATGATGC
*
12448577 AAATAATAAAATATATAAAATAT
1 AAATAATAAAATAT-CAAAATAT
*
12448600 AAATATTAAAATATCAAAATATT
1 AAATAATAAAATATCAAAATA-T
12448623 AGAATAATAA
1 A-AATAATAA
12448633 TAAATAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.21
23 15 0.54
24 7 0.25
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATAATAAAATATCAAAATAT
Found at i:12448613 original size:8 final size:8
Alignment explanation
Indices: 12448577--12448628 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
12448567 ATAATGATGC
*
12448577 AAATAATA
1 AAATATTA
12448585 AAATATATA
1 AAATAT-TA
12448594 AAATA-T-
1 AAATATTA
12448600 AAATATTA
1 AAATATTA
*
12448608 AAATATCA
1 AAATATTA
12448616 AAATATTA
1 AAATATTA
*
12448624 GAATA
1 AAATA
12448629 ATAATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 5 0.14
7 2 0.05
8 23 0.62
9 7 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AAATATTA
Found at i:12448619 original size:16 final size:15
Alignment explanation
Indices: 12448577--12448628 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
12448567 ATAATGATGC
12448577 AAATAATAAAATATATA
1 AAAT-ATAAAATAT-TA
12448594 AAATAT-AAATATTA
1 AAATATAAAATATTA
12448608 AAATATCAAAATATTA
1 AAATAT-AAAATATTA
*
12448624 GAATA
1 AAATA
12448629 ATAATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 8 0.25
15 6 0.19
16 14 0.44
17 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AAATATAAAATATTA
Found at i:12448793 original size:23 final size:23
Alignment explanation
Indices: 12448749--12448940 Score: 180
Period size: 25 Copynumber: 8.1 Consensus size: 23
12448739 AATACTACAT
*
12448749 AAATATGTACAT-AT-ATATTAA
1 AAATATATACATAATAATATTAA
*
12448770 AAATAAATACATAATAATATTAA
1 AAATATATACATAATAATATTAA
* *
12448793 AAGTATGTACATAATATAGTATTAA
1 AAATATATACATAATA-A-TATTAA
*
12448818 AAATACATACATAATATAGTTATTAAA
1 AAATATATACATAATA-A--TATT-AA
12448845 AAATATATACATAAGATAATA-TAA
1 AAATATATACAT-A-ATAATATTAA
* *
12448869 AAATATATACATGAAATAGTATAAA
1 AAATATATACAT--AATAATATTAA
12448894 AAATATA-AC-TAATAATATTAA
1 AAATATATACATAATAATATTAA
12448915 AAATATATACATAAT-ATATATAA
1 AAATATATACATAATAATAT-TAA
12448938 AAA
1 AAA
12448941 CAATTACGAT
Statistics
Matches: 144, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
21 26 0.18
22 8 0.06
23 31 0.22
24 22 0.15
25 33 0.23
26 6 0.04
27 13 0.09
28 2 0.01
29 3 0.02
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATATATACATAATAATATTAA
Found at i:12449114 original size:22 final size:18
Alignment explanation
Indices: 12449063--12449101 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12449053 ACTAGTACTA
*
12449063 ATAATATTAATAATAAAT
1 ATAATAATAATAATAAAT
12449081 ATAATAATAATAATAAAT
1 ATAATAATAATAATAAAT
12449099 ATA
1 ATA
12449102 TATGCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATAATAATAAAT
Found at i:12449210 original size:15 final size:15
Alignment explanation
Indices: 12449163--12449212 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
12449153 TAATATAAGA
*
12449163 ATAATAATAATA-AT
1 ATAACAATAATATAT
* *
12449177 ATAAAAATAATAGT-G
1 ATAACAATAATA-TAT
12449192 ATAACAATAATATAT
1 ATAACAATAATATAT
12449207 ATAACA
1 ATAACA
12449213 TGAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (15 bp):
ATAACAATAATATAT
Found at i:12449909 original size:18 final size:18
Alignment explanation
Indices: 12449886--12449952 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
12449876 ATATGTATAT
*
12449886 AAAAAGAGAGAAA-AAACA
1 AAAAAGAAAGAAAGAAA-A
12449904 AAAAAGAAAGAAAGAAAA
1 AAAAAGAAAGAAAGAAAA
*
12449922 AAAATTCGAAAG-AAGAAAA
1 AAAA--AGAAAGAAAGAAAA
12449941 AAAAAG-AAGAAA
1 AAAAAGAAAGAAA
12449953 AGGATGCTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
16 3 0.07
17 3 0.07
18 17 0.40
19 14 0.33
20 5 0.12
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAGAAAGAAAA
Found at i:12449951 original size:16 final size:17
Alignment explanation
Indices: 12449886--12449948 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 17
12449876 ATATGTATAT
* *
12449886 AAAAAGAGAGAAAAAACA
1 AAAAAGAAAGAAGAAA-A
12449904 AAAAAGAAAGAAAGAAAA
1 AAAAAGAAAG-AAGAAAA
*
12449922 AAAATTCGAAAGAAGAAAA
1 AAAA--AGAAAGAAGAAAA
12449941 AAAAAGAA
1 AAAAAGAA
12449949 GAAAAGGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.08
18 14 0.37
19 16 0.42
20 5 0.13
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAGAAGAAAA
Found at i:12449952 original size:20 final size:20
Alignment explanation
Indices: 12449888--12449952 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
12449878 ATGTATATAA
12449888 AAAGAGAGAAAAAACAAAAAAG
1 AAAGA-AGAAAAAA-AAAAAAG
***
12449910 AAAGAA-AGAAAAAAAATTCG
1 AAAGAAGA-AAAAAAAAAAAG
*
12449930 AAAGAAGAAAAAAAAAGAAG
1 AAAGAAGAAAAAAAAAAAAG
12449950 AAA
1 AAA
12449953 AGGATGCTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 23 0.66
21 7 0.20
22 5 0.14
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAGAAGAAAAAAAAAAAAG
Found at i:12451386 original size:8 final size:8
Alignment explanation
Indices: 12451373--12451415 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
12451363 ATAATATAAC
12451373 AAAAAAAT
1 AAAAAAAT
12451381 AAAAAAAT
1 AAAAAAAT
12451389 AAAAGAAAT
1 AAAA-AAAT
*
12451398 AGAAAAAT
1 AAAAAAAT
* *
12451406 GAAATAAT
1 AAAAAAAT
12451414 AA
1 AA
12451416 TGACAATAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12451403 original size:17 final size:16
Alignment explanation
Indices: 12451373--12451415 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
12451363 ATAATATAAC
12451373 AAAAAAATAAAAAAAT
1 AAAAAAATAAAAAAAT
*
12451389 AAAAGAAATAGAAAAAT
1 AAAA-AAATAAAAAAAT
* *
12451406 GAAATAATAA
1 AAAAAAATAA
12451416 TGACAATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:12452562 original size:15 final size:15
Alignment explanation
Indices: 12452539--12452568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12452529 GCTTTCATTT
*
12452539 CTGCTATTGTTTCTG
1 CTGCCATTGTTTCTG
12452554 CTGCCATTGTTTCTG
1 CTGCCATTGTTTCTG
12452569 TCCTTCTTTC
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:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (15 bp):
CTGCCATTGTTTCTG
Found at i:12454867 original size:12 final size:12
Alignment explanation
Indices: 12454852--12454876 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12454842 TACATCTCTG
12454852 CTATAATCTTCA
1 CTATAATCTTCA
12454864 CTATAATCTTCA
1 CTATAATCTTCA
12454876 C
1 C
12454877 AGCATAAAGA
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:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (12 bp):
CTATAATCTTCA
Found at i:12458885 original size:28 final size:29
Alignment explanation
Indices: 12458848--12458977 Score: 106
Period size: 28 Copynumber: 4.4 Consensus size: 29
12458838 TAAAATATGC
* *
12458848 TATCAAAATCAAGC-ATATATGTGATCTA
1 TATCACAATCAACCAATATATGTGATCTA
12458876 TATCACAATC-ACCAATATATGTGATCAAAATA
1 TATCACAATCAACCAATATATGTGATC----TA
* * *
12458908 TGCTATCAAAATCAAGC-ATATATGTGATCCA
1 ---TATCACAATCAACCAATATATGTGATCTA
*
12458939 TATCACAATC-ACCAATATATGTGATCAA
1 TATCACAATCAACCAATATATGTGATCTA
*
12458967 AATCACAATCA
1 TATCACAATCA
12458978 CAATCACCAA
Statistics
Matches: 82, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
27 4 0.05
28 52 0.63
31 1 0.01
32 2 0.02
35 21 0.26
36 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (29 bp):
TATCACAATCAACCAATATATGTGATCTA
Found at i:12458912 original size:63 final size:63
Alignment explanation
Indices: 12458834--12458969 Score: 254
Period size: 63 Copynumber: 2.1 Consensus size: 63
12458824 ACATACATGG
*
12458834 GATCTAAAATATGCTATCAAAATCAAGCATATATGTGATCTATATCACAATCACCAATATATGT
1 GATC-AAAATATGCTATCAAAATCAAGCATATATGTGATCCATATCACAATCACCAATATATGT
12458898 GATCAAAATATGCTATCAAAATCAAGCATATATGTGATCCATATCACAATCACCAATATATGT
1 GATCAAAATATGCTATCAAAATCAAGCATATATGTGATCCATATCACAATCACCAATATATGT
12458961 GATCAAAAT
1 GATCAAAAT
12458970 CACAATCACA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 67 0.94
64 4 0.06
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (63 bp):
GATCAAAATATGCTATCAAAATCAAGCATATATGTGATCCATATCACAATCACCAATATATGT
Found at i:12462130 original size:19 final size:19
Alignment explanation
Indices: 12462099--12462140 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
12462089 GCGCGACCCT
12462099 TTTTTTAATAATATAATTTA
1 TTTTTTAATAATATAA-TTA
*
12462119 TTTTTTAA-AATATTATTA
1 TTTTTTAATAATATAATTA
12462137 TTTT
1 TTTT
12462141 ATTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTAATAATATAATTA
Found at i:12462392 original size:3 final size:3
Alignment explanation
Indices: 12462377--12462451 Score: 89
Period size: 3 Copynumber: 24.7 Consensus size: 3
12462367 TGCAGCAGCA
*
12462377 AAG AGAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
12462422 AAG AAG AAG GAG AAG GAG GAG AAAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG -AAG AAG AA
12462452 AAATGTTAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 56 0.89
4 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12465343 original size:33 final size:32
Alignment explanation
Indices: 12465301--12465384 Score: 105
Period size: 33 Copynumber: 2.6 Consensus size: 32
12465291 CCACATCTGC
12465301 ACTCTACTCCTCCCGGCTCATATCCACCACCAT
1 ACTCTACTCCTCCCGGCTCATATCCA-CACCAT
* * * *
12465334 ACTCTACTCCTCCTGGCCCATATCCACGCCGT
1 ACTCTACTCCTCCCGGCTCATATCCACACCAT
* *
12465366 TCTCTACTCCACCCGGCTC
1 ACTCTACTCCTCCCGGCTC
12465385 GAGTTCATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 19 0.44
33 24 0.56
ACGTcount: A:0.17, C:0.49, G:0.10, T:0.25
Consensus pattern (32 bp):
ACTCTACTCCTCCCGGCTCATATCCACACCAT
Found at i:12469305 original size:15 final size:14
Alignment explanation
Indices: 12469253--12469319 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
12469243 GTTTGCAGGT
* *
12469253 AAAATGTTTTCCGG
1 AAAATGATTTCTGG
*
12469267 AAAATGATTTCTGA
1 AAAATGATTTCTGG
*
12469281 AAAATAATTTCTTGG
1 AAAATGATTTC-TGG
12469296 AAAATGATTTCTGG
1 AAAATGATTTCTGG
12469310 AAAATGATTT
1 AAAATGATTT
12469320 ACTTTTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 34 0.74
15 12 0.26
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:12469474 original size:2 final size:2
Alignment explanation
Indices: 12469467--12469503 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12469457 AGTTTACTTT
12469467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12469504 TAATAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12470383 original size:27 final size:27
Alignment explanation
Indices: 12470345--12470404 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
12470335 AGGGGAGTCG
12470345 CGCCTCTGCAGCAGAAGCGACTGGTCA
1 CGCCTCTGCAGCAGAAGCGACTGGTCA
* *
12470372 CGCCTCTGCAGCAGGAGCGACTGGTCG
1 CGCCTCTGCAGCAGAAGCGACTGGTCA
12470399 CGCCTC
1 CGCCTC
12470405 CGGGTCTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.37, G:0.32, T:0.15
Consensus pattern (27 bp):
CGCCTCTGCAGCAGAAGCGACTGGTCA
Found at i:12470503 original size:18 final size:17
Alignment explanation
Indices: 12470472--12470513 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
12470462 AAAATATAAT
12470472 AAAATAATAATATTTAAA
1 AAAATAATAATA-TTAAA
* *
12470490 AAAATTATATTATTAAA
1 AAAATAATAATATTAAA
12470507 AAAATAA
1 AAAATAA
12470514 GTCGCGCCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATAATATTAAA
Found at i:12478038 original size:11 final size:11
Alignment explanation
Indices: 12478024--12478066 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
12478014 AGTTAAAAAT
12478024 TATTTTATTAA
1 TATTTTATTAA
12478035 TATTTTACTT-A
1 TATTTTA-TTAA
*
12478046 TATATTTATTAT
1 TAT-TTTATTAA
12478058 TATTTTATT
1 TATTTTATT
12478067 TAGGAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:12478873 original size:17 final size:18
Alignment explanation
Indices: 12478838--12478875 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
12478828 TTGATATGAT
12478838 ATTAAAATTATTAAAAAA
1 ATTAAAATTATTAAAAAA
12478856 ATTAAAA-TATATAAAAAA
1 ATTAAAATTAT-TAAAAAA
12478874 AT
1 AT
12478876 CAGGGAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAAATTATTAAAAAA
Done.