Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 54 of 79
Found at i:18159376 original size:152 final size:154
Alignment explanation
Indices: 18158701--18159522 Score: 1035
Period size: 158 Copynumber: 5.3 Consensus size: 154
18158691 AAATATTAAA
* **
18158701 ATATTGTATCAACGGATACATATCGATACATACATATATAAATCGATATTGATAAAAACATATCA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
* * *
18158766 ATAAATATATATCTCGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCACCATTTTTTTTA
66 ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCA--TTTTTTA
*
18158831 TTTTGAAAGATATTTCGCATCATTTT
129 TTTTGAAAGATGTTTCGCATCATTTT
* *
18158857 ATATTGTATCAATGGATACAGATCGATACATA-C---------CGATATTGATCAAAACATA-CT
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATC-
* * *
18158911 AATAAATATATATCTTGAGATACGAGAATGATTTTTGTTCCCTGCATTTTCTCATGATTTTTTTT
65 AATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCA---TTTTT
18158976 TAATTTTGAAAGATGTTTCGCATCATTTT
127 T-ATTTTGAAAGATGTTTCGCATCATTTT
** * *
18159005 ATATTGTATCAACGGATACAGATAAATACATACCGATATAAATCGATATTGATCAAAACATATAA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
* * *
18159070 ATAAATACATATCTCGAGATATGAGAATGATTTTTGTTCCCCGCATTTTCTCTTCATTTTTTTTT
66 ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCA----TTTTT
*
18159135 TATTTTGAAAGATGTTTCGCATGATTTT
127 TATTTTGAAAGATGTTTCGCATCATTTT
* *
18159163 ATATTGTATCAATGGATACAGATC-AGTACATACCGATATAAATCGATATTGATAAACACATATC
1 ATATTGTATCAACGGATACAGATCGA-TACATACCGATATAAATCGATATTGATAAAAACATATC
*
18159227 AATAAATACATATCTTGAGATACGAGAATGAGTTTTGTTCCCCGCATTTTCTCATCA-TTTTT-T
65 AATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCATTTTTTAT
* *
18159290 TTTGAAAGATGTTTCGCATGATTTC
130 TTTGAAAGATGTTTCGCATCATTTT
* *
18159315 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATTGATATTGATAAAAACATATTA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
* * * *
18159380 ATAAATACATATCTTAAGATACGAGAATAATTTTTGTTCCCTGCATTTTTCTTATCAATTTTTTT
66 ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCA-TTTTCTCATC-A----TTT
* *
18159445 TTTATTTTAAAAGATGTTCCGCATCATTTT
125 TTTATTTTGAAAGATGTTTCGCATCATTTT
* * * *
18159475 ATATTATATCAA-GAGATACAGATCGATGCATACCAATATAAAACGATA
1 ATATTGTATCAACG-GATACAGATCGATACATACCGATATAAATCGATA
18159523 AATACATATA
Statistics
Matches: 592, Mismatches: 48, Indels: 48
0.86 0.07 0.07
Matches are distributed among these distances:
145 1 0.00
146 71 0.12
147 8 0.01
148 55 0.09
149 1 0.00
152 125 0.21
153 15 0.03
154 1 0.00
156 30 0.05
157 1 0.00
158 206 0.35
159 15 0.03
160 63 0.11
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (154 bp):
ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCATTTTTTATT
TTGAAAGATGTTTCGCATCATTTT
Found at i:18172520 original size:13 final size:13
Alignment explanation
Indices: 18172502--18172526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18172492 GAATTAATAT
18172502 GTGTGAAAATTTC
1 GTGTGAAAATTTC
18172515 GTGTGAAAATTT
1 GTGTGAAAATTT
18172527 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:18177588 original size:14 final size:14
Alignment explanation
Indices: 18177569--18177596 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18177559 TTCCATGCCT
18177569 AATTCCTATTTGTC
1 AATTCCTATTTGTC
18177583 AATTCCTATTTGTC
1 AATTCCTATTTGTC
18177597 TAGCATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
AATTCCTATTTGTC
Found at i:18178502 original size:14 final size:13
Alignment explanation
Indices: 18178483--18178525 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
18178473 GAAGCTGAAC
18178483 CTAACTTAGCTAG
1 CTAACTTAGCTAG
18178496 TCTAACTTAGCTAG
1 -CTAACTTAGCTAG
*
18178510 CTAACTCAGCT-G
1 CTAACTTAGCTAG
18178522 CTAA
1 CTAA
18178526 GACATTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 13 0.46
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (13 bp):
CTAACTTAGCTAG
Found at i:18179030 original size:3 final size:3
Alignment explanation
Indices: 18178960--18179014 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
18178950 GTGTTTGATG
*
18178960 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18179008 TTA TTA T
1 TTA TTA T
18179015 GTTCCCCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18179246 original size:19 final size:18
Alignment explanation
Indices: 18179222--18179257 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18179212 ATTGTTTATG
*
18179222 GTTATTATTATTTATCGTC
1 GTTATTAATATTT-TCGTC
18179241 GTTATTAATATTTTCGT
1 GTTATTAATATTTTCGT
18179258 TTCTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.58
Consensus pattern (18 bp):
GTTATTAATATTTTCGTC
Found at i:18181717 original size:16 final size:17
Alignment explanation
Indices: 18181685--18181717 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18181675 AAAAGTTTTC
18181685 TTTTTTCTAAAAGTTCA
1 TTTTTTCTAAAAGTTCA
18181702 TTTTTTCTAAAA-TTCA
1 TTTTTTCTAAAAGTTCA
18181718 AAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTTTCTAAAAGTTCA
Found at i:18182777 original size:67 final size:67
Alignment explanation
Indices: 18182669--18182813 Score: 254
Period size: 67 Copynumber: 2.2 Consensus size: 67
18182659 TTTAACTTAG
* *
18182669 TAATTTAACGGTTGGTGACCAAAAAGCATAAAATCAAATAGTTAGTTAACTATTTTAAAACTTTT
1 TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTGAAAACTTTT
18182734 CA
66 CA
* *
18182736 TAATTTAACGGTTGGTGACTAAAAAACATAAAATTAAATAGTTAGTTAACTATTTGAAAACTTTT
1 TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTGAAAACTTTT
18182801 CA
66 CA
18182803 TAATTTAACGG
1 TAATTTAACGG
18182814 AAAAAGAAGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (67 bp):
TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTGAAAACTTTT
CA
Found at i:18185781 original size:27 final size:29
Alignment explanation
Indices: 18185737--18185805 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
18185727 AATAAACACC
*
18185737 AAAAATTTATTTTCAAAA-TAAAAAAATA
1 AAAAAATTATTTTCAAAATTAAAAAAATA
*
18185765 AAAAAATTATTTT-AAAATTAAAAAATTA
1 AAAAAATTATTTTCAAAATTAAAAAAATA
18185793 AAAAAATATATTT
1 AAAAAAT-TATTT
18185806 ATTATATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 4 0.11
28 28 0.76
29 5 0.14
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAAATTATTTTCAAAATTAAAAAAATA
Found at i:18197293 original size:18 final size:20
Alignment explanation
Indices: 18197267--18197306 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
18197257 CCCCTTTTAC
18197267 ATATATTA-TTATA-TAAAT
1 ATATATTATTTATATTAAAT
*
18197285 ATATCTTATTTATATTAAAT
1 ATATATTATTTATATTAAAT
18197305 AT
1 AT
18197307 TTCATTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATTTATATTAAAT
Found at i:18206173 original size:25 final size:24
Alignment explanation
Indices: 18206136--18206224 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 24
18206126 CAGATTCAAT
* *
18206136 AAAAAATATAAAAAAAGAGAAAAA
1 AAAAAAAAGAAAAAAAGAGAAAAA
*
18206160 AATAAAAAAGAAAAAAGAAAGAAAAA
1 AA-AAAAAAGAAAAAA-AGAGAAAAA
18206186 GAAAAAAAAGAAAGAAGAAGAG-AAAA
1 -AAAAAAAAGAAA-AA-AAGAGAAAAA
*
18206212 TAAAAAAAGAAAA
1 AAAAAAAAGAAAA
18206225 GGAGAGGCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 3 0.05
25 22 0.40
26 22 0.40
27 7 0.13
28 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAGAGAAAAA
Found at i:18206174 original size:26 final size:25
Alignment explanation
Indices: 18206136--18206224 Score: 92
Period size: 26 Copynumber: 3.4 Consensus size: 25
18206126 CAGATTCAAT
*
18206136 AAAAAATATAAAAAAAGAGAAAAAAA
1 AAAAAAGA-AAAAAAAGAGAAAAAAA
18206162 TAAAAAAGAAAAAAGAA-AGAAAAAGAA
1 -AAAAAAGAAAAAA-AAGAGAAAAA-AA
* *
18206189 AAAAAAGAAAGAAGAAGAG-AAAATA
1 AAAAAAGAAA-AAAAAGAGAAAAAAA
18206214 AAAAAAGAAAA
1 AAAAAAGAAAA
18206225 GGAGAGGCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
24 1 0.02
25 11 0.20
26 28 0.51
27 15 0.27
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (25 bp):
AAAAAAGAAAAAAAAGAGAAAAAAA
Found at i:18206176 original size:7 final size:7
Alignment explanation
Indices: 18206156--18206224 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
18206146 AAAAAAGAGA
*
18206156 AAAAAAT
1 AAAAAAG
18206163 AAAAAAG
1 AAAAAAG
18206170 AAAAAAG
1 AAAAAAG
18206177 AAAGAAAAAG
1 --A-AAAAAG
18206187 AAAAAA-
1 AAAAAAG
*
18206193 AAGAAAG
1 AAAAAAG
*
18206200 AAGAAGAG
1 AA-AAAAG
*
18206208 AAAATA-
1 AAAAAAG
18206214 AAAAAAG
1 AAAAAAG
18206221 AAAA
1 AAAA
18206225 GGAGAGGCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
6 10 0.20
7 27 0.54
8 6 0.12
9 1 0.02
10 6 0.12
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:18206185 original size:19 final size:19
Alignment explanation
Indices: 18206145--18206211 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
18206135 TAAAAAATAT
*
18206145 AAAAAAAGAGAAAA-AAA-
1 AAAAAAAGAAAAAAGAAAG
*
18206162 TAAAAAAGAAAAAAGAAAG
1 AAAAAAAGAAAAAAGAAAG
18206181 AAAAAGAA-AAAAAAGAAAG
1 AAAAA-AAGAAAAAAGAAAG
* *
18206200 AAGAAGAGAAAA
1 AAAAAAAGAAAA
18206212 TAAAAAAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
17 12 0.29
18 4 0.10
19 23 0.56
20 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (19 bp):
AAAAAAAGAAAAAAGAAAG
Found at i:18206225 original size:26 final size:25
Alignment explanation
Indices: 18206148--18206225 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 25
18206138 AAAATATAAA
18206148 AAAAG-AGAAA-AAAAT-AAAAAAG
1 AAAAGAAGAAAGAAAATAAAAAAAG
*
18206170 AAAA-AAGAAAGAAAA-AGAAAAAAA
1 AAAAGAAGAAAGAAAATA-AAAAAAG
18206194 AGAAAGAAGAAGAGAAAATAAAAAAAG
1 A-AAAGAAGAA-AGAAAATAAAAAAAG
18206221 AAAAG
1 AAAAG
18206226 GAGAGGCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
22 9 0.20
23 4 0.09
24 7 0.15
25 3 0.07
26 9 0.20
27 13 0.28
28 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (25 bp):
AAAAGAAGAAAGAAAATAAAAAAAG
Found at i:18207199 original size:24 final size:24
Alignment explanation
Indices: 18207165--18207216 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
18207155 ATGTCCCAAA
*
18207165 ATTACAGTGGACTT-AACCTTGAAG
1 ATTACAATGGA-TTGAACCTTGAAG
**
18207189 ATTACAATGGATTGAAGTTTGAAG
1 ATTACAATGGATTGAACCTTGAAG
18207213 ATTA
1 ATTA
18207217 TAGTGGGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (24 bp):
ATTACAATGGATTGAACCTTGAAG
Found at i:18207678 original size:90 final size:89
Alignment explanation
Indices: 18207491--18208060 Score: 284
Period size: 89 Copynumber: 6.5 Consensus size: 89
18207481 CAATGAAGTT
* * * *
18207491 GCAGATCTTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTATAC
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
* *
18207556 TGACAGCGGAGCAGATTGAAGATA
66 TGACAGCGAAGCAGATCGAAGATA
* * * * * * * * * *
18207580 ACATATCTTGTCTTCCTGTATTTGCAGCAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCAATA
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAG-CCTTGCCTTCCAATA
* * *
18207645 TTGGCAGCGAAGTAGATCGAAGATA
65 CTGACAGCGAAGCAGATCGAAGATA
* ** * * * **
18207670 GCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGATACCATAG-TTTGCAGT--AA-
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACC--AGCCTTGCCTTCCAAT
* * * * *
18207731 AGT-AGA-CTAA--AGATAGCAGAT-
64 ACTGACAGCGAAGCAGATCGAAGATA
* * * ** * * * **
18207752 -CTTG-CCTT-CCTGTACTG-ACAACGAAGC-AA----ATCGAAGACACCAGCCTTACCTTCCTG
1 GC-AGATCTTGCCT-TCCTGTAC-TGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAA
* *
18207808 TACTGACAACGGAGCAGA-CTGAAGATA
63 TACTGACAGCGAAGCAGATC-GAAGATA
* * * * **
18207835 GCAGATCTTGCCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTAC
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
* *
18207900 TGACAGCGGAGCCGA-CTGAAGATA
66 TGACAGCGAAGCAGATC-GAAGATA
* * * ** * ***
18207924 GCAGATCATACCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCTTGTAC
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
*
18207989 TGACAG-AATAGCAGA-CTGAAGATA
66 TGACAGCGA-AGCAGATC-GAAGATA
* * ** * *
18208013 GCAGATCTTGCATTCCTGTACTGACAGTGAAGTAGATCGAAGACACCA
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCA
18208061 TAATTTGCAG
Statistics
Matches: 368, Mismatches: 87, Indels: 52
0.73 0.17 0.10
Matches are distributed among these distances:
74 2 0.01
75 4 0.01
76 11 0.03
78 2 0.01
79 2 0.01
80 9 0.02
81 10 0.03
82 9 0.02
83 10 0.03
84 12 0.03
85 10 0.03
86 1 0.00
87 2 0.01
88 2 0.01
89 208 0.57
90 72 0.20
92 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (89 bp):
GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
TGACAGCGAAGCAGATCGAAGATA
Found at i:18207707 original size:45 final size:45
Alignment explanation
Indices: 18207491--18207714 Score: 236
Period size: 45 Copynumber: 5.0 Consensus size: 45
18207481 CAATGAAGTT
* *
18207491 GCAGATCTTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGACA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
* * * *
18207536 CCAG-CCTTGCCTTCCTATACTGACAGCGGAGCAGATTGAAGATA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
* * * * * * * *
18207580 ACATATCTTGTCTTCCTGTATTTG-CAGCAAAGTAGATCAAAGATA
1 GCAGATCTTGCCTTCCTATA-CTGACAGCGAAGCAGATCGAAGATA
* * * * *
18207625 GCAGATCTTGTCTTCCAATATTGGCAGCGAAGTAGATCGAAGATA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
* *
18207670 GCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGATA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
18207715 CCATAGTTTG
Statistics
Matches: 146, Mismatches: 30, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
44 40 0.27
45 104 0.71
46 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (45 bp):
GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
Found at i:18207832 original size:44 final size:46
Alignment explanation
Indices: 18207747--18208060 Score: 249
Period size: 45 Copynumber: 7.0 Consensus size: 46
18207737 CTAAAGATAG
* *
18207747 CAGATCTTGCCTTCCTGTACTGACAACGAAGCA-AATCGAAGACAC
1 CAGACCTTGCCTTCCTGTACTGACAACGAAGCAGACTCGAAGACAC
* * * *
18207792 CAG-CCTTACCTTCCTGTACTGACAACGGAGCAGACT-GAAGATAG
1 CAGACCTTGCCTTCCTGTACTGACAACGAAGCAGACTCGAAGACAC
* *
18207836 CAGATCTTGCCTTCCTGTACT-AGCAGCGAAGCAGA-TCGAAGACAC
1 CAGACCTTGCCTTCCTGTACTGA-CAACGAAGCAGACTCGAAGACAC
* * * * * *
18207881 TAG-CCTTGCCTTCCTGTACTGACAGCGGAGCCGACT-GAAGATAG
1 CAGACCTTGCCTTCCTGTACTGACAACGAAGCAGACTCGAAGACAC
* * * * * **
18207925 CAGATCATACCTTCCTGTACCGGCAGTGAAGCAGA-TCGAAGACAC
1 CAGACCTTGCCTTCCTGTACTGACAACGAAGCAGACTCGAAGACAC
* * *
18207970 CAG-CCTTGCCTTCTTGTACTGAC-A-GAATAGCAGACT-GAAGATAG
1 CAGACCTTGCCTTCCTGTACTGACAACG-A-AGCAGACTCGAAGACAC
* * ** *
18208014 CAGATCTTGCATTCCTGTACTGACAGTGAAGTAGA-TCGAAGACAC
1 CAGACCTTGCCTTCCTGTACTGACAACGAAGCAGACTCGAAGACAC
18208059 CA
1 CA
18208061 TAATTTGCAG
Statistics
Matches: 209, Mismatches: 45, Indels: 30
0.74 0.16 0.11
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 102 0.49
45 103 0.49
46 1 0.00
47 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (46 bp):
CAGACCTTGCCTTCCTGTACTGACAACGAAGCAGACTCGAAGACAC
Found at i:18207886 original size:89 final size:89
Alignment explanation
Indices: 18207734--18208060 Score: 460
Period size: 89 Copynumber: 3.7 Consensus size: 89
18207724 GCAGTAAAGT
* * *
18207734 AGACTAAAGATAGCAGATCTTGCCTTCCTGTACTGACAACGAAGCAAATCGAAGACACCAGCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTT
*
18207799 ACCTTCCTGTACTGACAACGGAGC
66 GCCTTCCTGTACTGACAACGGAGC
*
18207823 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACT-AGCAGCGAAGCAGATCGAAGACACTAGCCT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACACCAGCCT
*
18207887 TGCCTTCCTGTACTGACAGCGGAGC
65 TGCCTTCCTGTACTGACAACGGAGC
* * * * * *
18207912 CGACTGAAGATAGCAGATCATACCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACACCAGCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTT
* **
18207977 GCCTTCTTGTACTGACAGA-ATAGC
66 GCCTTCCTGTACTGACA-ACGGAGC
* * *
18208001 AGACTGAAGATAGCAGATCTTGCATTCCTGTACTGACAGTGAAGTAGATCGAAGACACCA
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
18208061 TAATTTGCAG
Statistics
Matches: 211, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
88 1 0.00
89 210 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (89 bp):
AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTT
GCCTTCCTGTACTGACAACGGAGC
Found at i:18208317 original size:44 final size:43
Alignment explanation
Indices: 18208260--18208639 Score: 175
Period size: 44 Copynumber: 8.7 Consensus size: 43
18208250 GATCGCATCC
* *
18208260 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACT
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGC-ACT
* * ** * *
18208304 AGTCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCAC-
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATT-GAAGCACT
* * * * *
18208347 ATATCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-T-CA-CATCC
1 A-ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCA-CT
* * * *
18208389 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAT
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCACT
* * *
18208432 CAATCCTATCTTCCTAAAGTTGCAGTGAAGC-GAATTAAAATG-AC-
1 -AATCCTATCTCCCTAAAGTTGCAGTGGAGCAG-ATT-GAA-GCACT
* * * * * * *
18208476 AGATCTTATCTCTCTAAAGTTGCAGTAGAGCGGA-TCACACCATGAT
1 A-ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGA-AGCA--CT
* * * * **
18208522 AAGTCTTATCTCCCTAAGGTTACAGTGGAGCAGACTGGAGATAAC-
1 AA-TCCTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTGA-AGCACT
* * * * *
18208567 AAACCTTATCTCCCTGAAGTTGAAATGGAGCAAATTGAAGCTACT
1 AATCC-TATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGC-ACT
* * *
18208612 AATCCTATCTCCTTGAAGTTGCAATGGA
1 AATCCTATCTCCCTAAAGTTGCAGTGGA
18208640 ACGGATTAAA
Statistics
Matches: 252, Mismatches: 60, Indels: 48
0.70 0.17 0.13
Matches are distributed among these distances:
40 2 0.01
41 31 0.12
42 3 0.01
43 9 0.04
44 140 0.56
45 36 0.14
46 28 0.11
48 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCACT
Found at i:18208368 original size:129 final size:129
Alignment explanation
Indices: 18208216--18208588 Score: 437
Period size: 129 Copynumber: 2.8 Consensus size: 129
18208206 ATCGAAGATG
* * *
18208216 ACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCAATCTTATCTCCCTAAAGTTG
1 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTG
* ** * * * * *
18208281 CAGTGGAGTAGATTGAAGCTA-CTAGTCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACC
66 CAGTGGAGCAGATTGAAGAAATC-AATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACC
* *
18208345 ACATATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTG
* **
18208410 CAGTGGAGCAGATTGAAGAAATCAATCCTATCTTCCTAAAGTTGCAGTGAAGCGAATTAAAATG
66 CAGTGGAGCAGATTGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACC
*
18208474 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCGGATCACA-CCATGATAAGTCTTATCTCCCTA
1 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCC-----AA-TCTTATCTCCCTA
* * * * * *
18208538 AGGTTACAGTGGAGCAGACTGGAGATAA-CAAACCTTATCTCCCTGAAGTTG
60 AAGTTGCAGTGGAGCAGATTGAAGA-AATCAATCC-TATCTCCCTAAAGTTG
18208589 AAATGGAGCA
Statistics
Matches: 209, Mismatches: 26, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
128 2 0.01
129 150 0.72
130 1 0.00
133 2 0.01
134 38 0.18
135 16 0.08
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (129 bp):
ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTG
CAGTGGAGCAGATTGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACC
Found at i:18209307 original size:11 final size:11
Alignment explanation
Indices: 18209291--18209315 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18209281 TTCGGTATAA
18209291 AAACCGATTGT
1 AAACCGATTGT
18209302 AAACCGATTGT
1 AAACCGATTGT
18209313 AAA
1 AAA
18209316 GGGGAAAGCG
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (11 bp):
AAACCGATTGT
Found at i:18211332 original size:16 final size:17
Alignment explanation
Indices: 18211311--18211343 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18211301 GACATTAACT
18211311 AATCAA-TAGGTACCAA
1 AATCAACTAGGTACCAA
18211327 AATCAACTAGGTACCAA
1 AATCAACTAGGTACCAA
18211344 TTTTTTGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.18
Consensus pattern (17 bp):
AATCAACTAGGTACCAA
Found at i:18213290 original size:14 final size:14
Alignment explanation
Indices: 18213271--18213298 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18213261 CTGATAGCGA
18213271 CAGCAAGACTCCGG
1 CAGCAAGACTCCGG
18213285 CAGCAAGACTCCGG
1 CAGCAAGACTCCGG
18213299 TATTCAGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (14 bp):
CAGCAAGACTCCGG
Found at i:18215086 original size:3 final size:3
Alignment explanation
Indices: 18215080--18215149 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
18215070 ATAATAATAA
* * * *
18215080 TAT TAT TAC TAT TAT TAT CGTAT TAG TAT TAG TAT TAG TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
18215127 TAA TAT TAC TGT TAT TAT CAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
18215150 CATTTCCATT
Statistics
Matches: 49, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
3 46 0.94
5 3 0.06
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (3 bp):
TAT
Found at i:18215141 original size:18 final size:18
Alignment explanation
Indices: 18215061--18215144 Score: 60
Period size: 18 Copynumber: 4.5 Consensus size: 18
18215051 TTGGTTTTTT
* * *
18215061 TATTAATTAATAATAATAA
1 TATT-ATTATTAATATTAC
* *
18215080 TATTATTACTATTATTATC
1 TATTATTATTAATATTA-C
* * *
18215099 GTATTAGTATTAGTATTAG
1 -TATTATTATTAATATTAC
18215118 TATTATTATTAATATTAC
1 TATTATTATTAATATTAC
*
18215136 TGTTATTAT
1 TATTATTAT
18215145 CATTACATTT
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
18 33 0.65
19 4 0.08
20 14 0.27
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (18 bp):
TATTATTATTAATATTAC
Found at i:18216091 original size:73 final size:72
Alignment explanation
Indices: 18215981--18216122 Score: 216
Period size: 73 Copynumber: 2.0 Consensus size: 72
18215971 TCTTTTCAAA
* *
18215981 CTCAAGTTTTAAACGATCTCGGGAAGTAAGAAGAGATCGTGTCCTAACTTACT-GCGCATGATCC
1 CTCAAGTTTTAAACGATCTCGGAAAGTAAGAAGAGATCGTGTCCTAACTTACTAG-GAATGATCC
18216045 CTTTTTTC
65 CTTTTTTC
*
18216053 CTCAAGTTTTTAAACGATCTCGGAAATTAAGGAA-AGATCGTGTCCTAACTTACTAGGAATGATC
1 CTCAAG-TTTTAAACGATCTCGGAAAGTAA-GAAGAGATCGTGTCCTAACTTACTAGGAATGATC
18216117 CCTTTT
64 CCTTTT
18216123 CTAAACCCGA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
72 6 0.09
73 54 0.84
74 4 0.06
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCTCGGAAAGTAAGAAGAGATCGTGTCCTAACTTACTAGGAATGATCCC
TTTTTTC
Found at i:18222296 original size:2 final size:2
Alignment explanation
Indices: 18222289--18222319 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18222279 TCAATTATCA
18222289 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
18222320 CATTTATATC
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:18225549 original size:22 final size:22
Alignment explanation
Indices: 18225522--18225564 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18225512 TACTTTTTAA
18225522 TTTAATTT-TTAATAGAATAATT
1 TTTAATTTATT-ATAGAATAATT
*
18225544 TTTAATTTATTATATAATAAT
1 TTTAATTTATTATAGAATAAT
18225565 ATTATTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATTTATTATAGAATAATT
Found at i:18226064 original size:12 final size:13
Alignment explanation
Indices: 18226047--18226076 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18226037 GACTAAAAAA
18226047 TTCTTCTT-CTTT
1 TTCTTCTTCCTTT
18226059 TTCTTCTTCCTTT
1 TTCTTCTTCCTTT
18226072 TTCTT
1 TTCTT
18226077 TTTATGGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCTTCTTCCTTT
Found at i:18228988 original size:33 final size:33
Alignment explanation
Indices: 18228944--18229029 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
18228934 ATTTTTTAAT
*
18228944 AATTTTAAAATTTTAAAAATAGTTTTCTTTT-TA
1 AATTTTTAAATTTTAAAAATAGTTTT-TTTTCTA
*
18228977 AATTTTTAAATTTTAAAAATAGTTTTTTTTCTG
1 AATTTTTAAATTTTAAAAATAGTTTTTTTTCTA
18229010 AATTTTTAAATTTTAAAAAT
1 AATTTTTAAATTTTAAAAAT
18229030 TAATTAAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 4 0.08
33 46 0.92
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (33 bp):
AATTTTTAAATTTTAAAAATAGTTTTTTTTCTA
Found at i:18231100 original size:22 final size:22
Alignment explanation
Indices: 18231070--18231112 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18231060 ACAGCAGAAC
* *
18231070 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
18231092 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
18231113 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:18231265 original size:42 final size:42
Alignment explanation
Indices: 18231184--18231355 Score: 251
Period size: 42 Copynumber: 4.1 Consensus size: 42
18231174 ACGTCACTAA
*
18231184 CTTTTGCGGCGCTTACGTAAAAAAACGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTA-G-AAAAAAACGCCGCTAAAGATCATGCT
*
18231228 CTTTAGCGGCGCTTAGAAAACAAACGCC-CTAAAGATCACGCT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGCT
*
18231270 CTTTAGCGGCGCTTAG--AAAAACGCCACTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCT
* *
18231310 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCT
18231352 CTTT
1 CTTT
18231356 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
39 7 0.06
40 30 0.25
42 59 0.50
43 8 0.07
44 14 0.12
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCT
Found at i:18245205 original size:13 final size:12
Alignment explanation
Indices: 18245166--18245218 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
18245156 AGTTCTTCAT
18245166 TGCTTTTAAAAAG
1 TGCTTTT-AAAAG
**
18245179 TGCTGTGGAAAAG
1 TGCT-TTTAAAAG
18245192 TGCTTTTAAGAAG
1 TGCTTTTAA-AAG
18245205 TGCTTTTGAAAAG
1 TGCTTTT-AAAAG
18245218 T
1 T
18245219 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 3 0.09
13 27 0.82
14 3 0.09
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
TGCTTTTAAAAG
Found at i:18245205 original size:26 final size:26
Alignment explanation
Indices: 18245166--18245218 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
18245156 AGTTCTTCAT
18245166 TGCTTTTAAAAAGTGCTGTGGAAAAG
1 TGCTTTTAAAAAGTGCTGTGGAAAAG
* * *
18245192 TGCTTTTAAGAAGTGCTTTTGAAAAG
1 TGCTTTTAAAAAGTGCTGTGGAAAAG
18245218 T
1 T
18245219 TTGGTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGCTTTTAAAAAGTGCTGTGGAAAAG
Found at i:18254514 original size:50 final size:50
Alignment explanation
Indices: 18254409--18254587 Score: 160
Period size: 50 Copynumber: 3.5 Consensus size: 50
18254399 GAGATGAGAC
* ***
18254409 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTAAGGTTATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGC---ACCGA-G--ATGAGAGGT
* * **
18254465 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGTGCCGAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGT
** * * **
18254515 CCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGT
* *
18254565 CTCATGTAAGACCATATCTGGGA
1 CCCATGTAAGACCATGTCTGGGA
18254588 TATGNNNNNN
Statistics
Matches: 102, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 67 0.66
52 1 0.01
53 1 0.01
56 33 0.32
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGT
Found at i:18257034 original size:64 final size:64
Alignment explanation
Indices: 18256950--18257108 Score: 219
Period size: 64 Copynumber: 2.5 Consensus size: 64
18256940 CACACTGCTC
* * * * *
18256950 GACACACGCCCGTGTCTCTTGCCCGTGTGACTCCAAAACTTAACTCAGTGAGTTACATGGCCTA
1 GACACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAGGGAGTTACACGACCTA
* * **
18257014 GACACACGCCAGTGTGTCTTGCCCATGTAACTCCAAGTCTTAACTCAGGGAGTTACACGACCTA
1 GACACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAGGGAGTTACACGACCTA
* *
18257078 GACAAACGCCTGTGTGTCTTGCCCGTGTGAC
1 GACACACGCCAGTGTGTCTTGCCCGTGTGAC
18257109 CCCTACACCT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 82 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (64 bp):
GACACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAGGGAGTTACACGACCTA
Found at i:18266770 original size:11 final size:11
Alignment explanation
Indices: 18266754--18266778 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18266744 AATCACTTGG
18266754 TTCTATCGCAT
1 TTCTATCGCAT
18266765 TTCTATCGCAT
1 TTCTATCGCAT
18266776 TTC
1 TTC
18266779 ACTTTGACGT
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:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (11 bp):
TTCTATCGCAT
Found at i:18275156 original size:20 final size:20
Alignment explanation
Indices: 18275131--18275168 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18275121 GTATGTAACA
18275131 TATATATA-TCATGACATACT
1 TATATATAGTCAT-ACATACT
18275151 TATATATAGTCATACATA
1 TATATATAGTCATACATA
18275169 ACATAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (20 bp):
TATATATAGTCATACATACT
Found at i:18278752 original size:24 final size:24
Alignment explanation
Indices: 18278724--18278776 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
18278714 ATTCGCAAGT
* *
18278724 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTATACTAATAAATAC
*
18278748 TAAATATATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
18278772 TAAAT
1 TAAAT
18278777 TTTTTAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:18281022 original size:40 final size:36
Alignment explanation
Indices: 18280962--18281047 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
18280952 AAATTAGTAT
* * *
18280962 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
18280998 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
18281038 TATTATTATT
1 TATTATTATT
18281048 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:18284529 original size:160 final size:155
Alignment explanation
Indices: 18284110--18284554 Score: 463
Period size: 160 Copynumber: 2.8 Consensus size: 155
18284100 GCAAGTTGAA
*
18284110 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
**
18284175 ACTTTAAAAAATCATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGTATTATGTTATT
66 ACTTTAAAAAAT-ATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTATT
** **
18284240 TCTTTATTAATTTAGTGTGTTTTTTT
130 TCTTTATTAATTTAGTCCGAATTTTT
** * * * * *
18284266 AAATTAATTTAGTGTAAAAAAAACAACCCTTATTCTTAC--CC-TTTGCTCGTATTATTTTCCCG
1 AAA--AA---AGT-T-AGTAAAAC-ACTCTT-TACTT-CGGCCATTTGTTCGTATTTTTTTCTCG
* * * * *
18284328 A-ATTTTATTACTTCCAAAAAATAT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCATTA
56 ACATTTTATTACTT-TAAAAAATATCA-TAATTTC-TAATTTTATAATTTTACATTATTTCAGTA
* **
18284390 CATTTTGTTTAAAATTT-TTGTATTAATTTTTTCCGAATTTTT
118 CATTATG-TT---ATTTCTT-TATTAATTTAGTCCGAATTTTT
18284432 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
18284497 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTA
66 ACTTT-AAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTA
18284555 CTTCGGCCTT
Statistics
Matches: 229, Mismatches: 35, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
156 4 0.02
157 4 0.02
158 9 0.04
159 26 0.11
160 56 0.24
161 8 0.03
162 49 0.21
163 34 0.15
164 9 0.04
165 6 0.03
166 24 0.10
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.50
Consensus pattern (155 bp):
AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATT
ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTATGTTATTT
CTTTATTAATTTAGTCCGAATTTTT
Found at i:18284580 original size:97 final size:99
Alignment explanation
Indices: 18284454--18284651 Score: 271
Period size: 98 Copynumber: 2.0 Consensus size: 99
18284444 AAAACACTCT
* * * *
18284454 TTACTTCGGCCATTTGTTCGTATTTTTTTCTCGACATTTTATTACTTT-AA-AAAAATATCA-TA
1 TTACTTCGGCCATTTGCTCGTATTATTTTC-CCAAATTTTATTACTTTCAATAAAAATAT-ATTA
18284516 ATTTC-TAATTTTATAATTTTACATTATTTCAGTACA
64 ATTTCGT-ATTTTATAATTTTACATTATTTCAGTACA
*
18284552 TTACTTCGGCC-TTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTATT
1 TTACTTCGGCCATTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTAAT
* *
18284616 TTCGTATTTTATTATTTTATATTATTTCAGTACA
66 TTCGTATTTTATAATTTTACATTATTTCAGTACA
18284650 TT
1 TT
18284652 TTGTGAGAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
96 15 0.17
97 19 0.21
98 54 0.61
99 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (99 bp):
TTACTTCGGCCATTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTAAT
TTCGTATTTTATAATTTTACATTATTTCAGTACA
Found at i:18285894 original size:3 final size:3
Alignment explanation
Indices: 18285822--18285876 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
18285812 TGTAGCATTT
* *
18285822 TTA TTA TT- TTG TTCA TTA TT- CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18285866 TTA TTA TTA TT
1 TTA TTA TTA TT
18285877 TAATGTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.07
3 41 0.89
4 2 0.04
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18285894 original size:9 final size:9
Alignment explanation
Indices: 18285818--18285894 Score: 57
Period size: 9 Copynumber: 8.2 Consensus size: 9
18285808 CCTTTGTAGC
18285818 ATTTTTATT
1 ATTTTTATT
18285827 ATTTTGTTCATT
1 A-TTT-TT-ATT
*
18285839 A-TTCTATT
1 ATTTTTATT
*
18285847 ATTATTATT
1 ATTTTTATT
*
18285856 ATTATTATT
1 ATTTTTATT
*
18285865 ATTATTATT
1 ATTTTTATT
* *
18285874 ATTTAATGTT
1 ATTT-TTATT
18285884 ATTTTTATT
1 ATTTTTATT
18285893 AT
1 AT
18285895 CATCGCATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
8 4 0.07
9 33 0.60
10 12 0.22
11 2 0.04
12 4 0.07
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (9 bp):
ATTTTTATT
Found at i:18286263 original size:23 final size:22
Alignment explanation
Indices: 18286210--18286263 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
18286200 TATATATACC
* *
18286210 TATATATATACTTTTTATATTA
1 TATACATATACTTTTTATATGA
*
18286232 TATATATATACTTTTT-TATGA
1 TATACATATACTTTTTATATGA
18286253 TAGTTACATAT
1 TA--TACATAT
18286264 GTATAGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 16 0.57
23 6 0.21
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (22 bp):
TATACATATACTTTTTATATGA
Found at i:18287874 original size:14 final size:14
Alignment explanation
Indices: 18287855--18287898 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
18287845 CCTTTCCTTG
18287855 TCTTTCCTTCTTTT
1 TCTTTCCTTCTTTT
18287869 TCTTT-C--C-TTT
1 TCTTTCCTTCTTTT
18287879 TCTTTCCTTCTTTT
1 TCTTTCCTTCTTTT
18287893 TCTTTC
1 TCTTTC
18287899 TTTCCTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
13 2 0.08
14 14 0.54
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TCTTTCCTTCTTTT
Found at i:18287884 original size:4 final size:4
Alignment explanation
Indices: 18287855--18287959 Score: 55
Period size: 4 Copynumber: 26.5 Consensus size: 4
18287845 CCTTTCCTTG
* *
18287855 TCTT TCCT TC-T T-TT TCTT TCCTTT TCTT TCCT TC-T T-TT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT T-C-TT TCTT TCTT TCTT TCTT TCTT TCTT
* *
18287901 TCCTC TCATCT CCTT TCCTTT TCTT TC-T T-TT TCTT TCTT TCTT TCTT
1 T-CTT TC-T-T TCTT T-C-TT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
18287948 TC-T TC-T TCTT TC
1 TCTT TCTT TCTT TC
18287960 CATCTCCTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 28
0.70 0.05 0.24
Matches are distributed among these distances:
3 18 0.22
4 47 0.58
5 9 0.11
6 7 0.09
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:18287917 original size:57 final size:58
Alignment explanation
Indices: 18287856--18287965 Score: 147
Period size: 57 Copynumber: 1.9 Consensus size: 58
18287846 CTTTCCTTGT
18287856 CTTTCCTTCTT-TTTCTTTC-CTTTTCTTTCCTTCTTT-TTCTTTCTTTCC-TCTCATCTC
1 CTTTCCTT-TTCTTTCTTTCTC-TTTCTTTCCTTCTTTCTTC-TTCTTTCCATCTCATCTC
* *
18287913 CTTTCCTTTTCTTTCTTTTTCTTTCTTTCTTTCTTTCTTCTTCTTTCCATCTC
1 CTTTCCTTTTCTTTCTTTCTCTTTCTTTCCTTCTTTCTTCTTCTTTCCATCTC
18287966 CTTCTCTTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
56 2 0.04
57 37 0.79
58 8 0.17
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (58 bp):
CTTTCCTTTTCTTTCTTTCTCTTTCTTTCCTTCTTTCTTCTTCTTTCCATCTCATCTC
Found at i:18287921 original size:24 final size:24
Alignment explanation
Indices: 18287839--18287960 Score: 97
Period size: 24 Copynumber: 5.5 Consensus size: 24
18287829 TTTTTTGTTC
*
18287839 TCTTCTCCTTTCCTTGTCTTTCCT
1 TCTTCTCCTTTCCTTTTCTTTCCT
* *
18287863 TCTTTTTCTTTCCTTTTCTTTCCT
1 TCTTCTCCTTTCCTTTTCTTTCCT
18287887 TC-T-T--TTT-C-TTTCTTTCCT
1 TCTTCTCCTTTCCTTTTCTTTCCT
*
18287905 CTCATCTCCTTTCCTTTTCTTT-CT
1 -TCTTCTCCTTTCCTTTTCTTTCCT
*
18287929 T-TT-T-CTTT-C-TTTCTTTCTT
1 TCTTCTCCTTTCCTTTTCTTTCCT
*
18287948 TCTTCTTCTTTCC
1 TCTTCTCCTTTCC
18287961 ATCTCCTTCT
Statistics
Matches: 81, Mismatches: 5, Indels: 25
0.73 0.05 0.23
Matches are distributed among these distances:
18 17 0.21
19 6 0.07
20 10 0.12
21 3 0.04
22 6 0.07
23 6 0.07
24 26 0.32
25 7 0.09
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.66
Consensus pattern (24 bp):
TCTTCTCCTTTCCTTTTCTTTCCT
Found at i:18287926 original size:10 final size:10
Alignment explanation
Indices: 18287866--18287960 Score: 63
Period size: 10 Copynumber: 9.0 Consensus size: 10
18287856 CTTTCCTTCT
18287866 TTTTCTTTCC
1 TTTTCTTTCC
18287876 TTTTCTTTCC
1 TTTTCTTTCC
18287886 TTCTT-TTT-C
1 TT-TTCTTTCC
18287895 -TTTCTTTCC
1 TTTTCTTTCC
18287904 TCTCATCTCCTTTCC
1 T-T--T-T-CTTTCC
*
18287919 TTTTCTTTCT
1 TTTTCTTTCC
*
18287929 TTTTCTTTCTT
1 TTTTCTTTC-C
18287940 TCTTTCTTT-C
1 T-TTTCTTTCC
18287950 TTCTTCTTTCC
1 TT-TTCTTTCC
18287961 ATCTCCTTCT
Statistics
Matches: 70, Mismatches: 2, Indels: 25
0.72 0.02 0.26
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 3 0.04
10 36 0.51
11 7 0.10
12 8 0.11
13 1 0.01
14 2 0.03
15 7 0.10
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTCTTTCC
Found at i:18287937 original size:14 final size:14
Alignment explanation
Indices: 18287913--18287959 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
18287903 CTCTCATCTC
*
18287913 CTTTCCTTTTCTTT
1 CTTTCTTTTTCTTT
18287927 CTTT-TTCTTTCTTT
1 CTTTCTT-TTTCTTT
18287941 CTTTCTTTCTTC-TT
1 CTTTCTTT-TTCTTT
18287955 CTTTC
1 CTTTC
18287960 CATCTCCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 1 0.03
14 23 0.79
15 5 0.17
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
CTTTCTTTTTCTTT
Found at i:18294859 original size:25 final size:25
Alignment explanation
Indices: 18294806--18294859 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
18294796 CGGCCCGTTT
* * *
18294806 TTAATTAAAATTAAAATTAGTTTTT
1 TTAATTAAAATTAAAACTAATTTTA
18294831 TTAA-TAAAATTAAAACTAATTGTTA
1 TTAATTAAAATTAAAACTAATT-TTA
18294856 TTAA
1 TTAA
18294860 AATTAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAATTAAAATTAAAACTAATTTTA
Found at i:18294878 original size:16 final size:16
Alignment explanation
Indices: 18294841--18294880 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
18294831 TTAATAAAAT
* *
18294841 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
18294857 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
18294873 TAAAATTA
1 TAAAATTA
18294881 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:18294950 original size:66 final size:59
Alignment explanation
Indices: 18294883--18295002 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
18294873 TAAAATTATC
* * *
18294883 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
18294941 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
18295000 AAA
1 AAA
18295003 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:18295096 original size:23 final size:22
Alignment explanation
Indices: 18295068--18295110 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
18295058 AAATAAACTT
*
18295068 AAAATAAAAACTATTATATTTTA
1 AAAATAAAAAATA-TATATTTTA
18295091 AAAATAAAAAATATATATTT
1 AAAATAAAAAATATATATTT
18295111 AATATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAAAAAATATATATTTTA
Found at i:18295210 original size:31 final size:33
Alignment explanation
Indices: 18295174--18295244 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
18295164 ATTTTTTAAA
*
18295174 CGGGCCTAAAATTTTGCCC-AAG-CCCATATTT
1 CGGGCCTAAAATTTTACCCAAAGCCCCATATTT
* *
18295205 CGGGCCTATATTTTTACCCAAAGCCTCCCATATTT
1 CGGGCCTAAAATTTTACCCAAAG-C-CCCATATTT
18295240 CGGGC
1 CGGGC
18295245 GGGCCGTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.48
32 3 0.09
35 14 0.42
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.30
Consensus pattern (33 bp):
CGGGCCTAAAATTTTACCCAAAGCCCCATATTT
Found at i:18296385 original size:44 final size:44
Alignment explanation
Indices: 18296249--18296387 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 44
18296239 AGTTGCAGAT
* *
18296249 CTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAGAC-TCAAAC
1 CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACAT-AAAC
* * * * * * * * * *
18296293 CTTGCC-TCTCT-CGGTTG-TGGTGGAGCTGGTTGAAGACAGCATAT
1 CTTGCCTTC-CTGC-ATTGACGGCGAAGCAGATCGAAGACA-TAAAC
18296337 CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAAC
1 CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAAC
18296381 CTTGCCT
1 CTTGCCT
18296388 CTCTCGGTTG
Statistics
Matches: 66, Mismatches: 22, Indels: 14
0.65 0.22 0.14
Matches are distributed among these distances:
43 15 0.23
44 33 0.50
45 18 0.27
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAAC
Found at i:18296985 original size:88 final size:88
Alignment explanation
Indices: 18296245--18296963 Score: 1077
Period size: 88 Copynumber: 8.2 Consensus size: 88
18296235 ATGAAGTTGC
* * *
18296245 AGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAGACTCAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* **
18296310 TGGTGGAGCTGGTTGAAGACAGC
66 TGATGGAGCTGGTTGAAGACAAA
* * * *
18296333 ATATCTTGCCTTCCTGCATTGACGGCGAAGCAGATCGAAGACATAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
18296398 TGATAGAGCCGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
18296421 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAG--ACAAACCTTCCCTCTCTCTGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
18296484 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
18296507 AGATCTTGCCTTCCTGCATTGTCAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
18296572 TGATGGAGCTGGTTGAAGATAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * **
18296595 AGATCTTGCTTTCCTGCATTGACAACGAAAAAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
18296660 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
18296683 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTTGAAGACACAAACCTTGCCTCTCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
18296748 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
18296771 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* *
18296836 T-AGTGCAGCTGGTTGAAGACAAC
66 TGA-TGGAGCTGGTTGAAGACAAA
* * * *
18296859 AGATCTTGCCTTCCTGCATTGACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* * * * *
18296924 -CAGTAGAGCTGGTTAAAGATAAC
66 TGA-TGGAGCTGGTTGAAGACAAA
18296947 AGATCTTGCCTTCCTGC
1 AGATCTTGCCTTCCTGC
18296964 GTTAACAACG
Statistics
Matches: 579, Mismatches: 48, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
86 80 0.14
87 1 0.00
88 498 0.86
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:18297495 original size:20 final size:21
Alignment explanation
Indices: 18297472--18297510 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18297462 TGCCCAATAC
18297472 ACCT-AAACAAACCCAAATTG
1 ACCTAAAACAAACCCAAATTG
*
18297492 ACCTAAAACTAACCCAAAT
1 ACCTAAAACAAACCCAAAT
18297511 GCAGCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.51, C:0.31, G:0.03, T:0.15
Consensus pattern (21 bp):
ACCTAAAACAAACCCAAATTG
Found at i:18299426 original size:112 final size:110
Alignment explanation
Indices: 18299292--18299497 Score: 315
Period size: 112 Copynumber: 1.8 Consensus size: 110
18299282 TCAAAAAAGG
* *
18299292 AAAATATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCT-AAGGTGC
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTC-A-AAAA-ATGCCCTAAAGGTGC
*
18299356 TGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAA
63 TGGGTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAA
*
18299404 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAATGCCCTAAGAAGGTGCT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAAAAATGCCCT-A-AAGGTGCT
*
18299469 GGGTGTCGATTTTTCTCATTTAACCAAAT
64 GGGTGTCGATTTTTCTCATTCAACCAAAT
18299498 TGCTAAAACA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
109 7 0.08
110 3 0.03
111 1 0.01
112 75 0.87
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (110 bp):
AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAAAAATGCCCTAAAGGTGCTGG
GTGTCGATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAA
Found at i:18300311 original size:21 final size:21
Alignment explanation
Indices: 18300285--18300372 Score: 74
Period size: 21 Copynumber: 4.1 Consensus size: 21
18300275 AAATATATTT
*
18300285 TTTCTTTCCCTGTTCTCCTTC
1 TTTCTTTCCTTGTTCTCCTTC
**
18300306 TTTCTTTTTTTGTTCT-CTTC
1 TTTCTTTCCTTGTTCTCCTTC
* *
18300326 -TCCTTTCCTTGTCTTTCCTTC
1 TTTCTTTCCTTGT-TCTCCTTC
18300347 TTTTCTTTCCTT-TTCTTTCCTTC
1 -TTTCTTTCCTTGTTC--TCCTTC
18300370 TTT
1 TTT
18300373 TTCTTTCTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
19 9 0.17
20 6 0.12
21 18 0.35
22 4 0.08
23 15 0.29
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTCTTTCCTTGTTCTCCTTC
Found at i:18300343 original size:10 final size:10
Alignment explanation
Indices: 18300328--18300385 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
18300318 TTCTCTTCTC
*
18300328 CTTTCCTTGT
1 CTTTCCTTTT
18300338 CTTTCCTTCTTTT
1 CTTTCC---TTTT
18300351 CTTTCCTTTT
1 CTTTCCTTTT
18300361 CTTTCCTTCTT
1 CTTTCCTT-TT
18300372 -TTT-C-TTT
1 CTTTCCTTTT
18300379 CTTTCCT
1 CTTTCCT
18300386 CTCATCTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 2 0.05
10 21 0.52
11 2 0.05
13 9 0.22
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:18300354 original size:23 final size:24
Alignment explanation
Indices: 18300328--18300379 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
18300318 TTCTCTTCTC
18300328 CTTTCCTTGTCTTTCCTTC-TTTT
1 CTTTCCTTGTCTTTCCTTCTTTTT
*
18300351 CTTTCCTTTTCTTTCCTTCTTTTT
1 CTTTCCTTGTCTTTCCTTCTTTTT
18300375 CTTTC
1 CTTTC
18300380 TTTCCTCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (24 bp):
CTTTCCTTGTCTTTCCTTCTTTTT
Found at i:18301544 original size:40 final size:36
Alignment explanation
Indices: 18301484--18301569 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
18301474 AAATTAGTAT
* * *
18301484 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
18301520 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
18301560 TATTATTATT
1 TATTATTATT
18301570 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:18307220 original size:16 final size:15
Alignment explanation
Indices: 18307199--18307228 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18307189 CAAAAAAATA
18307199 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
18307215 TATTATTTTATATT
1 TATTATTTTATATT
18307229 ATTTCATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:18307232 original size:165 final size:162
Alignment explanation
Indices: 18307040--18307559 Score: 544
Period size: 165 Copynumber: 3.2 Consensus size: 162
18307030 ATTATCATAA
*
18307040 TTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTCTTTATTAATTTAGTGTGT
1 TTTCT-ATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTCTTTATTAATTTAGTATGT
18307105 TTTTTAAGTTAATTTAGTGTAAAAAAAATTTCAACCTTTATTCTTGCCCTTTGCTCGTATTATTT
65 TTTTTAA-TTAATTTAGTGTAAAAAAAA-TTCAACCTTTATTCTTGCCCTTTGCTCGTATTATTT
18307170 TCCCGAATTTTATTACTTCCAAAAAAATATATTAT
128 TCCCGAATTTTATTACTTCCAAAAAAATATATTAT
* * * * * *
18307205 TTTCATATTTTATTATTTTATATTATTTCATTACATTTTGTTTGAAATTT-TTGTATTAATTT-T
1 TTTC-TATTTTATAATTTTACATTATTTCAGTGCATTATG-TT---ATTTCTT-TATTAATTTAG
* ** ** * * * * *
18307268 TTTCAAATTTTTAAAAAATTTA--GT-AAAACACTT-----TTTACTTC-GGCCATTTGTTCGTA
60 TAT--GTTTTTTAATTAATTTAGTGTAAAAAAAATTCAACCTTTA-TTCTTGCCCTTTGCTCGTA
* * * * *
18307324 TTTTTTTCTCGGCATTTTATTACTT-TAAAAAAATATCA-TAA
122 TTATTTTC-CCGAATTTTATTACTTCCAAAAAAATAT-ATTAT
*
18307365 TTTCTAATTTTGTAATTTTACATTATTTCAGTGCATTATGTTATTTCTTTATTAATTTAGTATGT
1 TTTCT-ATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTCTTTATTAATTTAGTATGT
* *
18307430 TTTTTAAAATTAATTTAGTGTAAAAAAAATACAACCCTTATTCTTGCCCTTTGCTCGTATTATTT
65 TTTTT--AATTAATTTAGTGTAAAAAAAATTCAACCTTTATTCTTGCCCTTTGCTCGTATTATTT
18307495 TCCCGAATTTTATTACTTCCAAAAAAATATATTAT
128 TCCCGAATTTTATTACTTCCAAAAAAATATATTAT
* *
18307530 TTTCGTATTTTATTATTTTATATTATTTCA
1 TTTC-TATTTTATAATTTTACATTATTTCA
18307560 TTACATTTTT
Statistics
Matches: 279, Mismatches: 48, Indels: 56
0.73 0.13 0.15
Matches are distributed among these distances:
155 5 0.02
156 13 0.05
157 12 0.04
159 5 0.02
160 73 0.26
161 18 0.06
164 18 0.06
165 94 0.34
166 9 0.03
167 2 0.01
168 4 0.01
169 19 0.07
170 7 0.03
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (162 bp):
TTTCTATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTCTTTATTAATTTAGTATGTT
TTTTAATTAATTTAGTGTAAAAAAAATTCAACCTTTATTCTTGCCCTTTGCTCGTATTATTTTCC
CGAATTTTATTACTTCCAAAAAAATATATTAT
Found at i:18307279 original size:23 final size:25
Alignment explanation
Indices: 18307234--18307279 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
18307224 ATATTATTTC
*
18307234 ATTACATTTTGTTTGAAATTTTTGT
1 ATTACATTTTGTTTCAAATTTTTGT
18307259 ATTA-ATTTT-TTTCAAATTTTT
1 ATTACATTTTGTTTCAAATTTTT
18307280 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 5 0.25
25 4 0.20
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (25 bp):
ATTACATTTTGTTTCAAATTTTTGT
Found at i:18307607 original size:325 final size:325
Alignment explanation
Indices: 18307017--18307608 Score: 1069
Period size: 325 Copynumber: 1.8 Consensus size: 325
18307007 TACTTCGGCC
*
18307017 ATTACTTTAAAAAATTATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
1 ATTACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
* * * *
18307082 ATTTCTTTATTAATTTAGTGTGTTTTTTAAGTTAATTTAGTGTAAAAAAAATTTCAACCTTTATT
66 ATTTCTTTATTAATTTAGTATGTTTTTTAAATTAATTTAGTGTAAAAAAAATTACAACCCTTATT
18307147 CTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCATA
131 CTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCATA
* *
18307212 TTTTATTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCAAATT
196 TTTTATTATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCAAATT
18307277 TTTAAAAAATTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
261 TTTAAAAAATTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
*
18307342 ATTACTTTAAAAAAATATCATAATTTCTAATTTTGTAATTTTACATTATTTCAGTGCATTATGTT
1 ATTACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
18307407 ATTTCTTTATTAATTTAGTATGTTTTTTAAAATTAATTTAGTGTAAAAAAAA-TACAACCCTTAT
66 ATTTCTTTATTAATTTAGTATGTTTTTT-AAATTAATTTAGTGTAAAAAAAATTACAACCCTTAT
*
18307471 TCTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGT
130 TCTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCAT
* *
18307536 ATTTTATTATTTTATATTATTTCATTACATTTTTTTTAAAATTTTTGTATTAATTTTTTCCGAAT
195 ATTTTATTATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCAAAT
18307601 TTTTAAAA
260 TTTTAAAA
18307609 GAACACTTAT
Statistics
Matches: 255, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
325 233 0.91
326 22 0.09
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (325 bp):
ATTACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
ATTTCTTTATTAATTTAGTATGTTTTTTAAATTAATTTAGTGTAAAAAAAATTACAACCCTTATT
CTTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCATA
TTTTATTATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCAAATT
TTTAAAAAATTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTT
Found at i:18309683 original size:16 final size:15
Alignment explanation
Indices: 18309640--18309696 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
18309630 TTTACATACG
* *
18309640 TTTTATATTTTTTTA
1 TTTTATATATTTTAA
* *
18309655 TTTTATCTCTTTTAA
1 TTTTATATATTTTAA
18309670 CTTTTATATATTTTATA
1 -TTTTATATATTTTA-A
*
18309687 TTATATATAT
1 TTTTATATAT
18309697 ATATATACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.35
16 21 0.62
17 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTATATATTTTAA
Found at i:18310266 original size:19 final size:20
Alignment explanation
Indices: 18310229--18310266 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
18310219 ACCAAAATCA
* *
18310229 TTTTTTTCTTGATTTAAAGG
1 TTTTTTTCTTGAATAAAAGG
18310249 TTTTTTT-TTGAATAAAAG
1 TTTTTTTCTTGAATAAAAG
18310267 CATTATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTTTTTCTTGAATAAAAGG
Found at i:18311744 original size:19 final size:19
Alignment explanation
Indices: 18311704--18311745 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
18311694 GTCTCTTTTC
* *
18311704 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
18311723 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
18311742 GCAT
1 GCAT
18311746 CAAACACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:18313654 original size:20 final size:20
Alignment explanation
Indices: 18313629--18313669 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
18313619 GCAAATGTTC
18313629 TTTCATTCTTT-ACGATTTTT
1 TTTCATTCTTTCA-GATTTTT
18313649 TTTCATTCTTTCAGATTTTT
1 TTTCATTCTTTCAGATTTTT
18313669 T
1 T
18313670 CTGCCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTCATTCTTTCAGATTTTT
Found at i:18314613 original size:7 final size:7
Alignment explanation
Indices: 18314589--18314630 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
18314579 AGTGATGTGA
18314589 AAAAATG
1 AAAAATG
18314596 AAAAGAT-
1 AAAA-ATG
18314603 AAAAATG
1 AAAAATG
18314610 AAAAATG
1 AAAAATG
18314617 AAAAA-G
1 AAAAATG
18314623 TAAAAATG
1 -AAAAATG
18314631 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:18314615 original size:21 final size:21
Alignment explanation
Indices: 18314589--18314630 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18314579 AGTGATGTGA
18314589 AAAAATG-AAAAGATAAAAATG
1 AAAAATGAAAAAG-TAAAAATG
18314610 AAAAATGAAAAAGTAAAAATG
1 AAAAATGAAAAAGTAAAAATG
18314631 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAAGTAAAAATG
Found at i:18315980 original size:44 final size:44
Alignment explanation
Indices: 18315930--18316420 Score: 453
Period size: 44 Copynumber: 11.1 Consensus size: 44
18315920 GCAGATTTTA
* *
18315930 TCTTCATGTATTGACATGAAGTAGATCGAAAATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
* * *
18315974 TCTTCATGTATTGACATGAAGTAGATC-AGAGATAGTAAATCTTA
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
* *
18316018 TCTTCATGTATTGACATTAAGTAGATCGAAGATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
* * **
18316062 TCTTCATGTATTGACATGAAATAGATC-AGGGATAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
*** * ***
18316106 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATAGATCTTG
1 TCTTCATGTA-TTGACATGAAGTAGATCGAAGATAATAGATCTTG
***
18316151 TCTTCATGTATTGACATGAAGTAGATC-AGAGATGGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAATAGATCTTG
** * * * *
18316195 TCTTCCCATAGTGGTG--GTGAAGTAGATCGAAGATAATGGGTCTTA
1 TCTT--CAT-GTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
* ** *
18316240 TCCTCATG-ATTTG-CATTGAAGTAGATC-AGAGATAGCAGATCTTA
1 TCTTCATGTA-TTGACA-TGAAGTAGATCGA-AGATAATAGATCTTG
* *
18316284 TCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
*
18316328 TCTTCATGTATTGACATGAAGTAGATC-AGAGA-AAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGA-AGATAA-TAGATCTTG
* * * **
18316372 TCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
18316416 TCTTC
1 TCTTC
18316421 CCATACTGGT
Statistics
Matches: 360, Mismatches: 66, Indels: 42
0.77 0.14 0.09
Matches are distributed among these distances:
42 3 0.01
43 10 0.03
44 277 0.77
45 61 0.17
46 5 0.01
47 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (44 bp):
TCTTCATGTATTGACATGAAGTAGATCGAAGATAATAGATCTTG
Found at i:18316076 original size:88 final size:88
Alignment explanation
Indices: 18315919--18316420 Score: 625
Period size: 88 Copynumber: 5.7 Consensus size: 88
18315909 GTTGAAAAGC
* *
18315919 AGCAGATTTTATCTTCATGTATTGACATGAAGTAGATCGAAAATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
18315984 TTGACATGAAGTAGATCAGAGAT
66 TTGACATGAAGTAGATCAGAGAT
* * *
18316007 AGTAAATCTTATCTTCATGTATTGACATTAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
* *
18316072 TTGACATGAAATAGATCAGGGAT
66 TTGACATGAAGTAGATCAGAGAT
* *** * *** *
18316095 AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATAGATCTTGTCTTCATGT
1 AGCAGATCTTATCTTCATGTA-TTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
18316160 ATTGACATGAAGTAGATCAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
* * ** * * * *
18316184 GGCAGATCTTGTCTTCCCATAGTGGTG--GTGAAGTAGATCGAAGATAATGGGTCTTATCCTCAT
1 AGCAGATCTTATCTT--CAT-GTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCAT
18316247 G-ATTTG-CATTGAAGTAGATCAGAGAT
63 GTA-TTGACA-TGAAGTAGATCAGAGAT
*
18316273 AGCAGATCTTATCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
*
18316338 TTGACATGAAGTAGATCAGAGAA
66 TTGACATGAAGTAGATCAGAGAT
* * * * ***
18316361 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTC
1 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTC
18316421 CCATACTGGT
Statistics
Matches: 354, Mismatches: 50, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
86 4 0.01
87 3 0.01
88 202 0.57
89 142 0.40
91 2 0.01
92 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (88 bp):
AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
TTGACATGAAGTAGATCAGAGAT
Found at i:18316167 original size:133 final size:132
Alignment explanation
Indices: 18315930--18316420 Score: 467
Period size: 133 Copynumber: 3.7 Consensus size: 132
18315920 GCAGATTTTA
* *** ** *
18315930 TCTTCATGTATTGACATGAAGTAGATC-GAAAATAATGGATCTTGTCTTCATGTATT-GACATGA
1 TCTTCATGTATTGACATGAAGTAGATCAG-AGATAGCAGATCTTGTCTTCACATATTGGA-GTGA
* * *
18315993 AGTAGATCAGAGATAGTAAATCTTATCTTCATGTATTGACATTAAGTAGATCGAAGATAATGGAT
64 AGTAGATCAGAGATAGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGAT
18316058 CTTG
129 CTTG
* * * * *
18316062 TCTTCATGTATTGACATGAAATAGATCAGGGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAA
1 TCTTCATGTATTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCACATATTGG-AGTGAA
** * ****
18316127 GTAGATC-GAAGATAATAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATGGCAGA
65 GTAGATCAG-AGATAGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGA-AGATAATGGA
18316190 TCTTG
128 TCTTG
** * *** * * * * * *
18316195 TCTTCCCATAGTGGTG--GTGAAGTAGATC-GAAGATAATGGGTCTTATCCTCATGAT-TTGCAT
1 TCTT--CAT-GTATTGACATGAAGTAGATCAG-AGATAGCAGATCTTGTCTTCA-CATATTGGAG
*
18316256 TGAAGTAGATCAGAGATAGCAGATCTTATCTTCATGTATTGACATGAAGTTGATCGAAGATAATG
61 TGAAGTAGATCAGAGATAGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
18316321 GATCTTG
126 GATCTTG
* ** *
18316328 TCTTCATGTATTGACATGAAGTAGATCAGAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TCTTCATGTATTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCACATATTGGAGTGAAG
* *
18316393 TAGATCAAAGATAGCAGATCTTGTCTTC
66 TAGATCAGAGATAGCAGATCTTATCTTC
18316421 CCATACTGGT
Statistics
Matches: 281, Mismatches: 62, Indels: 32
0.75 0.17 0.09
Matches are distributed among these distances:
130 4 0.01
131 4 0.01
132 105 0.37
133 132 0.47
134 27 0.10
135 5 0.02
136 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (132 bp):
TCTTCATGTATTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCACATATTGGAGTGAAG
TAGATCAGAGATAGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCT
TG
Found at i:18316313 original size:177 final size:176
Alignment explanation
Indices: 18315919--18316405 Score: 606
Period size: 177 Copynumber: 2.8 Consensus size: 176
18315909 GTTGAAAAGC
* *
18315919 AGCAGATTTTATCTTCATGTATTGACATGAAGTAGATCGAAAATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
* * * * *
18315984 TTGACATGAAGTAGATCAGAGATAGTAAATCTTATCTT-CATGTATTGACATTAAGTAGATCGAA
66 TTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCATGTAGTGA-ATGAAGTAGATCGAA
* * *
18316048 GATAATGGATCTTGTCTTCATGTATTGACATGAAATAGATCAGGGAT
130 GATAATGGATCTTATCCTCATGTATTGACATGAAATAGATCAGAGAT
* *** * *** *
18316095 AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATAGATCTTGTCTTCATGT
1 AGCAGATCTTATCTTCATGTA-TTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
* * *
18316160 ATTGACATGAAGTAGATCAGAGATGGCAGATCTTGTCTTCCCATAGTGGTG-GTGAAGTAGATCG
65 ATTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTT-CCAT-GTAGTGAATGAAGTAGATCG
* *
18316224 AAGATAATGGGTCTTATCCTCATG-ATTTG-CATTGAAGTAGATCAGAGAT
128 AAGATAATGGATCTTATCCTCATGTA-TTGACA-TGAAATAGATCAGAGAT
*
18316273 AGCAGATCTTATCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
* * ** *
18316338 TTGACATGAAGTAGATCAGAGAAAGCAGATCTTGTCTT-CATGTATTGGCGTGAAGTAGATCAAA
66 TTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCATGTAGT-GAATGAAGTAGATCGAA
18316402 GATA
130 GATA
18316406 GCAGATCTTG
Statistics
Matches: 264, Mismatches: 39, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
174 3 0.01
175 4 0.02
176 34 0.13
177 149 0.56
178 67 0.25
179 3 0.01
180 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (176 bp):
AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
TTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCATGTAGTGAATGAAGTAGATCGAAG
ATAATGGATCTTATCCTCATGTATTGACATGAAATAGATCAGAGAT
Found at i:18316494 original size:45 final size:45
Alignment explanation
Indices: 18316439--18316566 Score: 122
Period size: 45 Copynumber: 2.9 Consensus size: 45
18316429 GTGGCGAAGT
* *
18316439 AGATCGAAGATAACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGC
1 AGATTGAAGATAACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGC
** *
18316484 AGATTGAAGATAGTGAA-TCTTATCTCCCTGAAGTTGCAGTGGAGC
1 AGATTGAAGATA-ACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGC
* *
18316529 -GAATT-AA-A-ACCACAGATCTTATCCCTCTGAAGTTGCAG
1 AG-ATTGAAGATAACA-AG-TCTTATCCCCCTGAAGTTGCAG
18316567 GAGAAAGCAG
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 1 0.01
44 23 0.33
45 40 0.58
46 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (45 bp):
AGATTGAAGATAACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGC
Found at i:18316495 original size:266 final size:265
Alignment explanation
Indices: 18315946--18316466 Score: 642
Period size: 266 Copynumber: 2.0 Consensus size: 265
18315936 TGTATTGACA
* * * * *
18315946 TGAAGTAGATCGAAAATAATGGATCTTGTCTTCATG-TATTGACA-TGAAGTAGATCAGAGATAG
1 TGAAGCAGATCGAAGATAATGGGTCTTATCCTCATGAT-TTG-CATTGAAGTAGATCAGAGATAG
* *
18316009 TAAATCTTATCTTCATGTATTGACATTAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATT
64 CAAATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATT
* * * * *
18316074 GACATGAAATAGATCAGGGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
129 GACATGAAATAGATCAGAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAGA
* * * ** * *
18316139 TAATAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATGGCAGATCTTGTCTTCCCAT
194 TAACAGATCTTGTCTTCATCTAGTGACA-GAAGTAGATCAGAGATAACAGATCTTATCTCCCCAT
**
18316204 AGTGGTGG
258 AGTGGCAG
*
18316212 TGAAGTAGATCGAAGATAATGGGTCTTATCCTCATGATTTGCATTGAAGTAGATCAGAGATAGCA
1 TGAAGCAGATCGAAGATAATGGGTCTTATCCTCATGATTTGCATTGAAGTAGATCAGAGATAGCA
* *
18316277 GATCTTATCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTGTCTTCATGTATTGA
66 AATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGA
* ** *
18316342 CATGAAGTAGATCAGAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATA
131 CATGAAATAGATCAGAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAGATA
* * *
18316406 GCAGATCTTGTCTTCCCATACTGGTGGC-GAAGTAGATC-GAAGATAACA-AGTCTTATC-CCCC
196 ACAGATCTTGTCTT--CAT-CTAGTGACAGAAGTAGATCAG-AGATAACAGA-TCTTATCTCCCC
18316467 TGAAGTTGCA
Statistics
Matches: 221, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
265 37 0.17
266 176 0.80
267 4 0.02
268 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (265 bp):
TGAAGCAGATCGAAGATAATGGGTCTTATCCTCATGATTTGCATTGAAGTAGATCAGAGATAGCA
AATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGA
CATGAAATAGATCAGAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAGATA
ACAGATCTTGTCTTCATCTAGTGACAGAAGTAGATCAGAGATAACAGATCTTATCTCCCCATAGT
GGCAG
Found at i:18316563 original size:44 final size:45
Alignment explanation
Indices: 18316500--18316655 Score: 132
Period size: 44 Copynumber: 3.6 Consensus size: 45
18316490 AAGATAGTGA
18316500 ATCTTATCTCC-CTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
1 ATCTTATCTCCTCTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
* * *
18316544 ATCTTATC-CCTCTGAAGTTGCAG-GAGAAAGC-AGA-TCATATC-CAG
1 ATCTTATCTCCTCTGAAGTTGCAGTG-G--AGCGA-ATTAAAACCACAG
* * *
18316588 -TCTTATCTTCCT-TGAAGTTGCAATGGAGTGGATTAAAACCACAG
1 ATCTTATC-TCCTCTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
* *
18316632 ATCTCATCT-ATCTGAAGTTGCAGT
1 ATCTTATCTCCTCTGAAGTTGCAGT
18316656 AGAGTAGATC
Statistics
Matches: 87, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
42 3 0.03
43 15 0.17
44 50 0.57
45 15 0.17
46 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
ATCTTATCTCCTCTGAAGTTGCAGTGGAGCGAATTAAAACCACAG
Found at i:18319822 original size:163 final size:161
Alignment explanation
Indices: 18319605--18320146 Score: 542
Period size: 163 Copynumber: 3.4 Consensus size: 161
18319595 TTTTCTCGGC
*
18319605 ATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTA
1 ATTTTATTACTTCAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTA
18319670 TGTTATTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAAATCCAACCCT
66 TGTTATTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGT-AAAAAAAAT-CAACCCT
18319735 TATTCTTGCCCTTTGCTTGTATTATTTTCCCGA
129 TATTCTTGCCCTTTGCTTGTATTATTTTCCCGA
* * * * *
18319768 ATTTT-TTACTTCCAAAAAATAT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCATTACA
1 ATTTTATTACTT-CAAAAAATATCA-TAATTTC-TAATTTTATAATTTTACATTATTTCAGTGCA
* ** * * **
18319830 TTTTGTTTGAAATTT-TTGTATTAATTTTTTTTGAATTTTTAAA--AA---AGT-T-AGTAAAA-
63 TTATG-TT---ATTTCTT-TATTAATTTAGTGTG-TTTTTTAAATTAATTTAGTGTAAAAAAAAT
* * * * * *
18319886 C-ACTCTTTACTTC-GGCCATTTG-TTCGTATTTTTTTCTCGGC
122 CAAC-CCTTA-TTCTTGCCCTTTGCTT-GTATTATTTTC-CCGA
* * * *
18319927 ATTTTATTACTTTAAAAAATATCATAATTTCTAATCTTGTAATTTTACATTATTTCAGTGAATTA
1 ATTTTATTACTTCAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTA
*
18319992 TGTTATTTCTTTATTAATTTAGTGTGTGTTTTAAATTAATTTAGTGTAAAAAAAATACAACCCTT
66 TGTTATTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAAT-CAACCCTT
*
18320057 ATTCTTGCCCTTTGCTCGTATTATTTTCCCGA
130 ATTCTTGCCCTTTGCTTGTATTATTTTCCCGA
* * *
18320089 ATTTTATTACTTCCAAAAAATAT-ATTATTT-TCATATTTTATTATTTTATATTATTTCA
1 ATTTTATTACTT-CAAAAAATATCATAATTTCT-A-ATTTTATAATTTTACATTATTTCA
18320147 TTACATTTTG
Statistics
Matches: 298, Mismatches: 49, Indels: 64
0.73 0.12 0.16
Matches are distributed among these distances:
154 7 0.02
155 16 0.05
156 4 0.01
157 4 0.01
158 25 0.08
159 54 0.18
160 13 0.04
161 6 0.02
162 32 0.11
163 103 0.35
164 6 0.02
166 4 0.01
167 16 0.05
168 8 0.03
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.51
Consensus pattern (161 bp):
ATTTTATTACTTCAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTA
TGTTATTTCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAATCAACCCTTA
TTCTTGCCCTTTGCTTGTATTATTTTCCCGA
Found at i:18319856 original size:24 final size:24
Alignment explanation
Indices: 18319824--18319869 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
18319814 ATATTATTTC
18319824 ATTACATTTTGTTTGAAATTTTTGT
1 ATTACATTTTGTTTG-AATTTTTGT
*
18319849 ATTA-ATTTTTTTTGAATTTTT
1 ATTACATTTTGTTTGAATTTTT
18319870 AAAAAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.65
Consensus pattern (24 bp):
ATTACATTTTGTTTGAATTTTTGT
Found at i:18320132 original size:16 final size:15
Alignment explanation
Indices: 18320111--18320140 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18320101 CCAAAAAATA
18320111 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
18320127 TATTATTTTATATT
1 TATTATTTTATATT
18320141 ATTTCATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:18320133 original size:322 final size:322
Alignment explanation
Indices: 18319548--18320306 Score: 1380
Period size: 322 Copynumber: 2.4 Consensus size: 322
18319538 GCAAGTTGAA
18319548 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
*
18319613 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTT
66 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGAATTATGTTATTT
* *
18319678 CTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAAATCCAACCCTTATTCTTG
131 CTTTATTAATTTAGTGTGTGTTTTAAATTAATTTAGTGTAAAAAAAAATACAACCCTTATTCTTG
* *
18319743 CCCTTTGCTTGTATTATTTTCCCGAATTTTTTACTTCCAAAAAATATATTATTTTCGTATTTTAT
196 CCCTTTGCTCGTATTATTTTCCCGAATTTTTTACTTCCAAAAAATATATTATTTTCATATTTTAT
* **
18319808 TATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTTGAATTTTT
261 TATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCGAATTTTT
18319870 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
* *
18319935 ACTTTAAAAAATATCATAATTTCTAATCTTGTAATTTTACATTATTTCAGTGAATTATGTTATTT
66 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGAATTATGTTATTT
18320000 CTTTATTAATTTAGTGTGTGTTTTAAATTAATTTAGTGT-AAAAAAAATACAACCCTTATTCTTG
131 CTTTATTAATTTAGTGTGTGTTTTAAATTAATTTAGTGTAAAAAAAAATACAACCCTTATTCTTG
18320064 CCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCATATTTTA
196 CCCTTTGCTCGTATTATTTTCCCGAATTTT-TTACTTCCAAAAAATATATTATTTTCATATTTTA
18320129 TTATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCGAATTTTT
260 TTATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCGAATTTTT
*
18320192 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTTGTA-TTTTTT-TCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
18320255 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGT
66 ACTTT-AAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGT
18320307 ACATTACTTC
Statistics
Matches: 422, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
320 18 0.04
321 103 0.24
322 301 0.71
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (322 bp):
AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGAATTATGTTATTT
CTTTATTAATTTAGTGTGTGTTTTAAATTAATTTAGTGTAAAAAAAAATACAACCCTTATTCTTG
CCCTTTGCTCGTATTATTTTCCCGAATTTTTTACTTCCAAAAAATATATTATTTTCATATTTTAT
TATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCGAATTTTT
Found at i:18320438 original size:247 final size:251
Alignment explanation
Indices: 18320065--18320559 Score: 736
Period size: 247 Copynumber: 2.0 Consensus size: 251
18320055 TTATTCTTGC
*
18320065 CCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCATATTTTAT
1 CCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTCCAAAAAATATATTA--TT-ATATTTTAT
* * *
18320130 TATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCGAATTTTTAAA
63 TATTTTATATTATTTCAGTACATTTTGTTTAAAATATTTGTATTAATTATTTCCGAATTTTTAAA
* **
18320195 AAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTTGTA-TTTTTT-TCGGCATTTTATTACT
128 AAAGTTAGTAAAACACTC-TTACTTCGGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTACT
*
18320258 TTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGG
192 TT-AAAAAATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGG
* * *
18320319 CCTTTGTTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAA-ATA-TA-T-TATTTTCTTA
1 CCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTCCAA-AAAATATATTATTATATTTTATTA
**
18320380 TTTTATATTATTT-AGTACATTTT-TTTAGAAATATTTGTATTAATTATTTGTGAATTTTTAAAA
65 TTTTATATTATTTCAGTACATTTTGTTTA-AAATATTTGTATTAATTATTTCCGAATTTTTAAAA
*
18320443 AAGTTAGTAAAACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTACTTT
129 AAGTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTACTTT
*
18320508 AAAAAATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTGCATTA
194 AAAAAATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTA
18320560 TGTTNNNNNN
Statistics
Matches: 222, Mismatches: 15, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
246 24 0.11
247 113 0.51
248 38 0.17
250 1 0.00
253 2 0.01
254 40 0.18
255 4 0.02
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (251 bp):
CCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTCCAAAAAATATATTATTATATTTTATTAT
TTTATATTATTTCAGTACATTTTGTTTAAAATATTTGTATTAATTATTTCCGAATTTTTAAAAAA
GTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTACTTTAA
AAAATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGG
Found at i:18321464 original size:9 final size:8
Alignment explanation
Indices: 18321443--18321612 Score: 57
Period size: 8 Copynumber: 22.0 Consensus size: 8
18321433 ATACTTTTTT
18321443 TTCTTTCC
1 TTCTTTCC
*
18321451 CTCTTCTCC
1 TTCTT-TCC
18321460 TTCTTT-C
1 TTCTTTCC
*
18321467 TT-TTT-T
1 TTCTTTCC
18321473 TTCTCTT-C
1 TTCT-TTCC
*
18321481 TCCTTTCC
1 TTCTTTCC
18321489 TTTTCTTTCC
1 --TTCTTTCC
*
18321499 TTATTT--
1 TTCTTTCC
18321505 TTCTTT-C
1 TTCTTTCC
**
18321512 TT-TTTTT
1 TTCTTTCC
18321519 TTC-TT-C
1 TTCTTTCC
18321525 TTCTTTCC
1 TTCTTTCC
18321533 TTTTCTTTCC
1 --TTCTTTCC
18321543 TTCTTT--
1 TTCTTTCC
*
18321549 TTCTTTCT
1 TTCTTTCC
18321557 TTCTTTCC
1 TTCTTTCC
18321565 TCTCCTTTCC
1 T-T-CTTTCC
*
18321575 -T-TTTCT
1 TTCTTTCC
18321581 TTCTTT--
1 TTCTTTCC
*
18321587 TTCTTTCT
1 TTCTTTCC
18321595 TTCTTTCTTC
1 TTCTTTC--C
18321605 TTCTTTCC
1 TTCTTTCC
18321613 CTCTCCTTCT
Statistics
Matches: 126, Mismatches: 13, Indels: 46
0.68 0.07 0.25
Matches are distributed among these distances:
6 32 0.25
7 15 0.12
8 43 0.34
9 8 0.06
10 28 0.22
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (8 bp):
TTCTTTCC
Found at i:18321467 original size:4 final size:4
Alignment explanation
Indices: 18321460--18321611 Score: 76
Period size: 4 Copynumber: 37.8 Consensus size: 4
18321450 CCTCTTCTCC
*
18321460 TTCT TTCT TT-T TT-T TCTCT TCTCCT TTCCTT TTCT TTCCT TATTT TTCT
1 TTCT TTCT TTCT TTCT T-TCT T-T-CT TT-C-T TTCT TT-CT T-TCT TTCT
*
18321509 TTCT TT-T TT-T TTC- TTC- TTCT TTCCTT TTCT TTCC TTC- TT-T TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT
*
18321553 TTCT TTCT TTCCT CTCCT TTCCTT TTCT TTC- TT-T TTCT TTCT TTCT
1 TTCT TTCT TT-CT -TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT
18321599 TTC- TTC- TTCT TTC
1 TTCT TTCT TTCT TTC
18321612 CCTCTCCTTC
Statistics
Matches: 124, Mismatches: 5, Indels: 38
0.74 0.03 0.23
Matches are distributed among these distances:
3 31 0.25
4 58 0.47
5 21 0.17
6 14 0.11
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:18321498 original size:10 final size:10
Alignment explanation
Indices: 18321460--18321612 Score: 93
Period size: 10 Copynumber: 14.8 Consensus size: 10
18321450 CCTCTTCTCC
18321460 TTCTTT-CTT
1 TTCTTTCCTT
*
18321469 TTTTTTCTCTT
1 TTCTTTC-CTT
*
18321480 CTCCTTTCCTT
1 -TTCTTTCCTT
18321491 TTCTTTCCTT
1 TTCTTTCCTT
18321501 ATT-TTTCTTTCTT
1 -TTCTTTC---CTT
* *
18321514 TTTTTTTCTT
1 TTCTTTCCTT
18321524 CTTCTTTCCTT
1 -TTCTTTCCTT
18321535 TTCTTTCCTT
1 TTCTTTCCTT
*
18321545 CTT-TTTCTTTCT
1 -TTCTTTC-CT-T
*
18321557 TTCTTTCCTC
1 TTCTTTCCTT
*
18321567 TCCTTTCCTT
1 TTCTTTCCTT
*
18321577 TTCTTTCTTT
1 TTCTTTCCTT
18321587 TTCTTT-C-T
1 TTCTTTCCTT
18321595 TTCTTT-CTT
1 TTCTTTCCTT
18321604 CTTCTTTCC
1 -TTCTTTCC
18321613 CTCTCCTTCT
Statistics
Matches: 113, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
8 8 0.07
9 6 0.05
10 58 0.51
11 23 0.20
12 12 0.11
13 6 0.05
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (10 bp):
TTCTTTCCTT
Found at i:18321508 original size:14 final size:13
Alignment explanation
Indices: 18321469--18321612 Score: 85
Period size: 14 Copynumber: 10.0 Consensus size: 13
18321459 CTTCTTTCTT
18321469 TTTTTTCTCTTCTCC
1 TTTTTT-TCTT-TCC
18321484 TTTCCTTTTCTTTCC
1 TTT--TTTTCTTTCC
*
18321499 TTATTTTTCTTTCTT
1 TT-TTTTTCTTTC-C
*
18321514 TTTTTTTCTTCTTC
1 TTTTTTTCTT-TCC
18321528 TTTCCTTTTCTTTCC
1 TTT--TTTTCTTTCC
18321543 TTCTTTTTCTTT-C
1 TT-TTTTTCTTTCC
* *
18321556 TTTCTTTCCTCTCC
1 TTT-TTTTCTTTCC
*
18321570 TTTCCTTTTCTTTCT
1 TTT--TTTTCTTTCC
18321585 TTTTCTTTCTTT-C
1 TTTT-TTTCTTTCC
18321598 TTTCTTCTTCTTTCC
1 TTT-TT-TTCTTTCC
18321613 CTCTCCTTCT
Statistics
Matches: 104, Mismatches: 10, Indels: 30
0.72 0.07 0.21
Matches are distributed among these distances:
12 1 0.01
13 14 0.13
14 46 0.44
15 27 0.26
16 13 0.12
17 3 0.03
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTCTTTCC
Found at i:18321529 original size:34 final size:34
Alignment explanation
Indices: 18321460--18321603 Score: 134
Period size: 34 Copynumber: 4.1 Consensus size: 34
18321450 CCTCTTCTCC
* * * *
18321460 TTCTTT-CTTTTTTT-TCTCTTCTCCTTTCCT-T
1 TTCTTTCCTTTTTTTCTTTCTTTTTCTTTCTTCT
*
18321491 TTCTTTCCTTATTTTTCTTTCTTTTTTTTTCTTC-
1 TTCTTTCCTT-TTTTTCTTTCTTTTTCTTTCTTCT
*
18321525 TTCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCT
1 TTCTTTCCTTTT-TTTCTTTCTTTTTCTTTC-TTCT
*
18321561 TTCCTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTTCT
1 TT-CTTTCCTTT--TTTTCTTTCTTTTTCTTTC-TTCT
18321599 TTCTT
1 TTCTT
18321604 CTTCTTTCCC
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
31 6 0.06
32 3 0.03
33 7 0.08
34 37 0.40
35 3 0.03
36 2 0.02
37 10 0.11
38 24 0.26
39 1 0.01
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (34 bp):
TTCTTTCCTTTTTTTCTTTCTTTTTCTTTCTTCT
Found at i:18321560 original size:38 final size:38
Alignment explanation
Indices: 18321464--18321612 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 38
18321454 TTCTCCTTCT
*
18321464 TTCTTTTT-TTTC--TCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTCTTTCTTCTTCTTTCCTTTTCTTTCC
*
18321499 TTATTTTTCTTTCTTTTTTTTTCTTCTTCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTC------TTTCTTCTTCTTTCCTTTTCTTTCC
18321543 TTCTTTTTCTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTT-C
1 TTCTTTTTCTTTCTTTC-TT-CT-T-CTTTCCTTTTCTTTCC
*
18321584 TTTTTCTTTCTTTCTTTCTTCTTCTTTCC
1 TTCTT-TTTCTTTCTTTCTTCTTCTTTCC
18321613 CTCTCCTTCT
Statistics
Matches: 96, Mismatches: 4, Indels: 25
0.77 0.03 0.20
Matches are distributed among these distances:
35 7 0.07
36 4 0.04
38 10 0.10
39 3 0.03
40 4 0.04
41 8 0.08
42 26 0.27
44 34 0.35
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (38 bp):
TTCTTTTTCTTTCTTTCTTCTTCTTTCCTTTTCTTTCC
Found at i:18335690 original size:12 final size:12
Alignment explanation
Indices: 18335673--18335700 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18335663 CGTTACATTC
18335673 GATCACCGAAGT
1 GATCACCGAAGT
18335685 GATCACCGAAGT
1 GATCACCGAAGT
18335697 GATC
1 GATC
18335701 TTGTAAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (12 bp):
GATCACCGAAGT
Found at i:18336874 original size:60 final size:59
Alignment explanation
Indices: 18336799--18336983 Score: 254
Period size: 60 Copynumber: 3.2 Consensus size: 59
18336789 AGTGGTTTCG
* *
18336799 CATGTAATAATGTGACTCGCATGTAATAACATATTATTGACTCGCATAAGCAATGATTCA
1 CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCATAA-CAATGGTTCA
* *
18336859 CATGTAATAATGTGACTTGCATGTAATAACATATCATTGACTCGCATAAACAGTGGTTCA
1 CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCAT-AACAATGGTTCA
* *
18336919 CATGTAATAATGTGACTCACATG---T--CATATCATTGACTTGCATGAACAATGGTTCA
1 CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCAT-AACAATGGTTCA
18336974 CATGTAATAA
1 CATGTAATAA
18336984 CATATACTTG
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
55 38 0.33
57 1 0.01
60 74 0.64
61 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (59 bp):
CATGTAATAATGTGACTCGCATGTAATAACATATCATTGACTCGCATAACAATGGTTCA
Found at i:18339462 original size:114 final size:113
Alignment explanation
Indices: 18339261--18339609 Score: 501
Period size: 114 Copynumber: 3.1 Consensus size: 113
18339251 CCTTTTTGAA
* * *
18339261 TTTTTTTTAAACTTTTTTCGTATACTAGTGCCGACCATTGACATGAAAAAAGTAAAAAAAAAATT
1 TTTTTTTT-AACTTTTTTCGTATACTGGTGCTG-CCATTGACACGAAAAAAGT-AAAAAAAAATT
*
18339326 CCAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
63 CCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
18339377 TTTTTTTTAACTTTTTTCGTATACTGGTGCTTGCCATTGACACGAAAAAAGT-AAAAAAAATTCT
1 TTTTTTTTAACTTTTTTCGTATACTGGTGC-TGCCATTGACACGAAAAAAGTAAAAAAAAATTC-
*
18339441 CATAAAGGTGGTGCCGACCATTGGCAGGCCACCACCAAATTTTTTTTT--
64 CATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
*
18339489 TTACTTTTTTAACTTTTTTCGTATAATGGTGCCTGCCATTGACAC-AAAAAAGTAAAAAAAAAAT
1 TT--TTTTTTAACTTTTTTCGTATACTGGTG-CTGCCATTGACACGAAAAAAGT-AAAAAAAAAT
* **
18339553 CCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CAAATTTTTTTAAAC
62 TCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
18339604 TTTTTT
1 TTTTTT
18339610 CGTATATTGG
Statistics
Matches: 214, Mismatches: 10, Indels: 21
0.87 0.04 0.09
Matches are distributed among these distances:
112 2 0.01
113 34 0.16
114 117 0.55
115 52 0.24
116 9 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (113 bp):
TTTTTTTTAACTTTTTTCGTATACTGGTGCTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCA
TAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTAC
Found at i:18339486 original size:102 final size:101
Alignment explanation
Indices: 18339377--18339652 Score: 320
Period size: 114 Copynumber: 2.6 Consensus size: 101
18339367 TTTTTTTTAC
* * *
18339377 TTTTTTTTAACTTTTTTCGTATACTGGTGCTTGCCATTGACACGAAAAAAGTAAAAAAAATTCTC
1 TTTTTTTTAACTTTTTTCGTATAATGGTGC-TGCCATTGACACGAAAAAAGTAAAAAAAAATCCC
18339442 ATAAAGGTGGTGCCGACCATTGGCAGGCCACCACCAAA
65 ATAAAGGTGGTGCCGACCATTGGCAGGCCACCA-CAAA
18339480 TTTTTTTTTTTACTTTTTTAACTTTTTTCGTATAATGGTGCCTGCCATTGACAC-AAAAAAGTAA
1 ---------TT--TTTTTTAACTTTTTTCGTATAATGGTG-CTGCCATTGACACGAAAAAAGT-A
*
18339544 AAAAAAAATCCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAA
53 AAAAAAAATCCCATAAAGGTGGTGCCGACCATTGGCAGGCCACCACAAA
* * * *
18339593 TTTTTTTAAACTTTTTTCGTATATTGGTGCCGACCATTGACAAGAAAAAAAGTAAAAAAA
1 TTTTTTTTAACTTTTTTCGTATAATGGTGCTG-CCATTGACACG-AAAAAAGTAAAAAAA
18339653 CAAGTTTTCT
Statistics
Matches: 149, Mismatches: 8, Indels: 23
0.83 0.04 0.13
Matches are distributed among these distances:
101 2 0.01
102 34 0.23
103 7 0.05
104 10 0.07
112 2 0.01
113 12 0.08
114 81 0.54
115 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (101 bp):
TTTTTTTTAACTTTTTTCGTATAATGGTGCTGCCATTGACACGAAAAAAGTAAAAAAAAATCCCA
TAAAGGTGGTGCCGACCATTGGCAGGCCACCACAAA
Found at i:18343843 original size:35 final size:35
Alignment explanation
Indices: 18343794--18343860 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
18343784 GAGAAATCCA
*
18343794 ACGGTAAACGTTGTGGATTATGTAGGTTAAGTCCG
1 ACGGTAAACATTGTGGATTATGTAGGTTAAGTCCG
*
18343829 ACGGTAAGCATTGTGGATTATGTAGGTTAAGT
1 ACGGTAAACATTGTGGATTATGTAGGTTAAGT
18343861 GGTCATAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.33
Consensus pattern (35 bp):
ACGGTAAACATTGTGGATTATGTAGGTTAAGTCCG
Found at i:18347431 original size:51 final size:48
Alignment explanation
Indices: 18347353--18347451 Score: 171
Period size: 51 Copynumber: 2.0 Consensus size: 48
18347343 TAGTCTCCGG
18347353 GTGAATTTAATTTTTTTAGGGGTTAAAATTAAATTGTAATTTTTACGA
1 GTGAATTTAATTTTTTTAGGGGTTAAAATTAAATTGTAATTTTTACGA
18347401 GTGAATTTAAATTTTTTTTAGGGGGTTAAAATTAAATTGTAATTTTTACGA
1 GTGAATTT-AA-TTTTTTTA-GGGGTTAAAATTAAATTGTAATTTTTACGA
18347452 TAGTAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
48 8 0.17
49 2 0.04
50 8 0.17
51 30 0.62
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.47
Consensus pattern (48 bp):
GTGAATTTAATTTTTTTAGGGGTTAAAATTAAATTGTAATTTTTACGA
Found at i:18367238 original size:1 final size:1
Alignment explanation
Indices: 18367232--18367342 Score: 60
Period size: 1 Copynumber: 111.0 Consensus size: 1
18367222 TACTTTTCTT
* * * * * * * * * *
18367232 AAAAAAAAAGAAAAGAAAAGAAAAAAAGAAAAAATAAAAATAAAATAAAATAAAAAAGAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
18367297 GAAAAGAAAAAGAAAAAAAAGAAAGAAAGAAAAGAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18367343 GGAAAAGGAG
Statistics
Matches: 74, Mismatches: 36, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.04
Consensus pattern (1 bp):
A
Found at i:18367245 original size:5 final size:5
Alignment explanation
Indices: 18367232--18367349 Score: 92
Period size: 5 Copynumber: 25.0 Consensus size: 5
18367222 TACTTTTCTT
* * * *
18367232 AAAAA AAAAG AAAAG AAAAG -AAA- AAAAG AAAA- AATA- AAAAT AAAAT
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
18367278 AAAAT AAAAA AGAAAG -AAAG AAAAG AAAAAG AAAA- AAAAG -AAAG -AAAG
1 AAAAG AAAAG A-AAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
*
18367326 AAAAG AAAAG AAAA- AAAGG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
18367350 GAGAGGCCAA
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
4 31 0.32
5 58 0.60
6 8 0.08
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:18367258 original size:13 final size:13
Alignment explanation
Indices: 18367242--18367348 Score: 94
Period size: 13 Copynumber: 8.1 Consensus size: 13
18367232 AAAAAAAAAG
18367242 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
18367255 AAAAGAAAA-AATA
1 AAAAGAAAAGAA-A
* *
18367268 AAAATAAAATAAA
1 AAAAGAAAAGAAA
*
18367281 ATAA-AAAAGAAA
1 AAAAGAAAAGAAA
*
18367293 GAAAGAAAAGAAAA
1 AAAAGAAAAG-AAA
*
18367307 AGAAAAAAAAGAAA
1 A-AAAGAAAAGAAA
*
18367321 GAAAGAAAAGAAA
1 AAAAGAAAAGAAA
18367334 AGAAA-AAAAGGAAA
1 A-AAAGAAAA-GAAA
18367348 A
1 A
18367349 GGAGAGGCCA
Statistics
Matches: 77, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
12 11 0.14
13 42 0.55
14 16 0.21
15 8 0.10
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:18367263 original size:28 final size:27
Alignment explanation
Indices: 18367232--18367342 Score: 125
Period size: 27 Copynumber: 4.0 Consensus size: 27
18367222 TACTTTTCTT
18367232 AAAAAAAAAGAAAAGAAAAGAAAAAAA
1 AAAAAAAAAGAAAAGAAAAGAAAAAAA
* * * *
18367259 GAAAAAATA-AAAATAAAATAAAATAAA
1 AAAAAAAAAGAAAAGAAAAGAAAA-AAA
18367286 AAAGAAAGAAAGAAAAGAAAAAGAAAAAAA
1 AAA-AAA-AAAGAAAAG-AAAAGAAAAAAA
* *
18367316 AGAAAGAAAGAAAAGAAAAGAAAAAAA
1 AAAAAAAAAGAAAAGAAAAGAAAAAAA
18367343 GGAAAAGGAG
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
26 12 0.17
27 24 0.35
28 12 0.17
29 4 0.06
30 9 0.13
31 8 0.12
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.04
Consensus pattern (27 bp):
AAAAAAAAAGAAAAGAAAAGAAAAAAA
Found at i:18367349 original size:28 final size:28
Alignment explanation
Indices: 18367233--18367349 Score: 125
Period size: 28 Copynumber: 4.2 Consensus size: 28
18367223 ACTTTTCTTA
*
18367233 AAAAAAAAGAAAAGAAAAGAAAA-AAAG
1 AAAAGAAAGAAAAGAAAAGAAAAAAAAG
* * *
18367260 AAAA-AATA-AAAATAAAATAAAATAAAAA
1 AAAAGAA-AGAAAAGAAAAGAAAA-AAAAG
18367288 AGAAAGAAAGAAAAGAAAAAGAAAAAAAAG
1 A-AAAGAAAGAAAAG-AAAAGAAAAAAAAG
*
18367318 -AAAGAAAGAAAAGAAAAGAAAAAAAGG
1 AAAAGAAAGAAAAGAAAAGAAAAAAAAG
18367345 AAAAG
1 AAAAG
18367350 GAGAGGCCAA
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
26 14 0.19
27 18 0.24
28 21 0.28
29 4 0.05
30 10 0.13
31 8 0.11
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (28 bp):
AAAAGAAAGAAAAGAAAAGAAAAAAAAG
Found at i:18368653 original size:87 final size:87
Alignment explanation
Indices: 18368507--18369051 Score: 582
Period size: 87 Copynumber: 6.4 Consensus size: 87
18368497 GGTGAAACAG
18368507 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
18368572 GTGGAGAGGATTAACATTCAGA
66 GTGGAGAGGATTAACATTCAGA
18368594 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
*
18368659 GTGGAGCGGATTAACATTCAGA
66 GTGGAGAGGATTAACATTCAGA
* * * *
18368681 TCTTATCTCCCTGAAGTTGTAGTGGAACAGACAGAAGAAATCAATCCTATTTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* *
18368746 GTGGAGCGGATTAACATCCAGA
66 GTGGAGAGGATTAACATTCAGA
** * * * * *
18368768 TCTTATCTTTCTGAGGTTGCA---GAG-AG-CAGATCG-CATCCAGTCTTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-CAATCCTATCTCCCTGAAGTTG
* * ** * *
18368827 CAGGGGAGTAGACAGAAAAAATCA-A
64 CAGTGGAG-AG-GATTAACATTCAGA
* ** * ** *
18368852 TCCTATCTCCCTGAAGTTGCAGTGGAGC-G---GATTAACATCCAGATCTTATCTTTCTGAGGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CA-ATCCTATCTCCCTGAAGTT
* *
18368913 GCAG-AGAGCA-GA-TCACATTCAG-
63 GCAGTGGAG-AGGATTAACATTCAGA
*
18368935 TCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* *
18369000 GTGGAGCGGATTAACATCCAGA
66 GTGGAGAGGATTAACATTCAGA
** * *
18369022 TCTTATCTTTCTGAGGTTGCAG-AGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
18369052 TCACATCCAG
Statistics
Matches: 379, Mismatches: 59, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
82 6 0.02
83 59 0.16
84 42 0.11
85 15 0.04
86 26 0.07
87 231 0.61
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
GTGGAGAGGATTAACATTCAGA
Found at i:18368827 original size:40 final size:40
Alignment explanation
Indices: 18368504--18369092 Score: 271
Period size: 44 Copynumber: 13.8 Consensus size: 40
18368494 ACCGGTGAAA
*
18368504 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-
1 CAGTCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATA-ACATC
* * * *
18368548 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGATTAACATT
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCA-GA-TAACATC
*
18368590 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-
1 CAG-TCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATA-ACATC
* * * * *
18368635 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATT
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
* * *
18368677 CAGATCTTATCTCCCTGAAGTTGTAGTGGAACAGACAGA-AGAAAT-
1 CAG-TCTTATCTCCCTGAAGTTGCA---G-AGAG-CAGATA-ACATC
* * * * * *
18368722 CAATCCTATTTCCCTGAAGTTGTAGTGGAGCGGATTAACATC
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
** * **
18368764 CAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATC
1 CAG-TCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
* *
18368805 CAGTCTTATCTCCCTGAAGTTGCAGGGGAGTAGACAGAAAAAAT-
1 CAGTCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATAACATC
* * * *
18368849 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATC
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
** * * *
18368891 CAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCACATT
1 CAG-TCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
*
18368932 CAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGA-AGAAAT-
1 CAGTCTTATCTCCCTGAAGTTGCA---GAG-AG-CAGATA-ACATC
* * * *
18368976 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATC
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TAACATC
** * *
18369018 CAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCACATC
1 CAG-TCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
* *
18369059 CAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 CAGTCTTATCTCCCTGAAGTTGCAG-AGAGCAGA
18369093 CAGAAGAAAT
Statistics
Matches: 412, Mismatches: 85, Indels: 99
0.69 0.14 0.17
Matches are distributed among these distances:
39 1 0.00
40 68 0.17
41 63 0.15
42 36 0.09
43 97 0.24
44 109 0.26
45 20 0.05
46 12 0.03
47 5 0.01
48 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (40 bp):
CAGTCTTATCTCCCTGAAGTTGCAGAGAGCAGATAACATC
Found at i:18368840 original size:127 final size:127
Alignment explanation
Indices: 18368672--18369154 Score: 840
Period size: 127 Copynumber: 3.8 Consensus size: 127
18368662 GAGCGGATTA
* * * * *
18368672 ACATTCAGATCTTATCTCCCTGAAGTTGTAGTGGAACAGACAGAAGAAATCAATCCTATTTCCCT
1 ACATCCAG-TCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCT
*
18368737 GAAGTTGTAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
65 GAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
* * *
18368800 GCATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGTAGACAGAAAAAATCAATCCTATCTCCCTG
1 ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
18368865 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
*
18368927 ACATTCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
18368992 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
* *
18369054 ACATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
*
18369119 AAGTTGCAGTGGAGCGGATTAACATCTAGATCTTAT
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTAT
18369155 GAGAGCAGAT
Statistics
Matches: 338, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
127 332 0.98
128 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (127 bp):
ACATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
Found at i:18369028 original size:214 final size:216
Alignment explanation
Indices: 18368500--18369051 Score: 669
Period size: 214 Copynumber: 2.6 Consensus size: 216
18368490 ACAAACCGGT
18368500 GAAA-CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
* * *
18368564 AAGTTGCAGTGGAGAGGATTAACATTCAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGA
* *
18368629 AGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATTCAGATCTTATCTCCCTG
131 AAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTG
* *
18368694 AAGTTGTAGTGGAACAGACAGAA
196 AAGTTGCAGTAGAACAGAC--AA
* * * * ** * **
18368717 GAAATCAATCCTATTTCCCTGAAGTTGTAGTGGAGC-G---GATTAACATCCAGATCTTATCTTT
1 GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CA-ATCCTATCTCC
* * * ** *
18368778 CTGAGGTTGCAG-AGAGCAGA-TCGCATCCAG-TCTTATCTCCCTGAAGTTGCAGGGGAGTAGAC
63 CTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGAC
**
18368840 AGAAAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTT
128 AGAAAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCC
* *
18368905 CTGAGGTTGCAG-AGAGCAGATC-A
193 CTGAAGTTGCAGTAGAACAGA-CAA
* * *
18368928 -CATTCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
1 GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
** * *
18368992 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCA-GAGAGCAGA
66 AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGA
18369052 TCACATCCAG
Statistics
Matches: 275, Mismatches: 48, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
210 28 0.10
211 21 0.08
212 8 0.03
213 23 0.08
214 128 0.47
215 9 0.03
216 7 0.03
217 24 0.09
218 27 0.10
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (216 bp):
GAAATCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTG
AAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGA
AAAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTCCCTG
AAGTTGCAGTAGAACAGACAA
Found at i:18377838 original size:42 final size:43
Alignment explanation
Indices: 18377735--18377999 Score: 211
Period size: 43 Copynumber: 6.3 Consensus size: 43
18377725 TTATGTGGAA
* * * *
18377735 AAACGCCGCTATAGAACATGACCTTTTGCTGCG-TTTT--TA-
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
** * * * *
18377774 TGACGCCGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
18377817 AAACGCCACTAAAGAA-ATGACCTTTAACGGCACTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
18377859 AAACGGCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
18377902 AAACGCCGCTATAA-AACATGATC-TTAGCGGTGCTTTCCCCAC
1 AAACGCCGCTA-AAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * ** * * *
18377944 AAATGCTGCTAAAGAACAGGACTTTTAGTTGCGCTTTTACTAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
18377987 AAACGCCACTAAA
1 AAACGCCGCTAAA
18378000 TGTCATGTTC
Statistics
Matches: 175, Mismatches: 43, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
39 27 0.15
40 4 0.02
41 2 0.01
42 67 0.38
43 74 0.42
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:18377896 original size:43 final size:43
Alignment explanation
Indices: 18377735--18377981 Score: 227
Period size: 42 Copynumber: 5.9 Consensus size: 43
18377725 TTATGTGGAA
* * *
18377735 AAACGCCGCTATAGAACATGACCTTTTGCTGCG-TTTT--TA-
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
** * * *
18377774 TGACGCCGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
18377817 AAACGCCACTAAAGAA-ATGACCTTTAACGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
18377859 AAACGGCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
18377902 AAACGCCGCTATAAAACATGATC-TTAGCGGTGCTTTCCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * **
18377944 AAATGCTGCTAAAGAACAGGACTTTTAGTTGCGCTTTT
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTT
18377982 ACTAAAAACG
Statistics
Matches: 163, Mismatches: 39, Indels: 8
0.78 0.19 0.04
Matches are distributed among these distances:
39 27 0.17
40 4 0.02
42 68 0.42
43 64 0.39
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:18377943 original size:85 final size:84
Alignment explanation
Indices: 18377780--18377999 Score: 228
Period size: 85 Copynumber: 2.6 Consensus size: 84
18377770 TTTATGACGC
* * * *
18377780 CGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCACAAACGCCACTAAAGAAATGACCTTTAAC
1 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAAATGACCTTTAAC
*
18377845 GGCACTTTTCCCACAAACGG
66 GGCACTTTCCCCACAAA-GG
* *
18377865 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCGCTATAA-AACATGATC-TTA
1 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTA-AAGAA-ATGACCTTTA
* ** *
18377928 GCGGTGCTTTCCCCACAAATG
64 ACGGCACTTTCCCCACAAAGG
* * * * * * *
18377949 CTGCTAAAGAACAGGACTTTTAGTTGCGCTTTTACTAAAAACGCCACTAAA
1 C-GCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAA
18378000 TGTCATGTTC
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
84 4 0.04
85 102 0.90
86 7 0.06
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (84 bp):
CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAAATGACCTTTAAC
GGCACTTTCCCCACAAAGG
Found at i:18383089 original size:40 final size:40
Alignment explanation
Indices: 18383034--18383113 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
18383024 ATATATTCTG
18383034 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
1 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
18383074 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
1 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
18383114 AGGCTGTTGG
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:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (40 bp):
TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
Found at i:18383325 original size:15 final size:15
Alignment explanation
Indices: 18383301--18383330 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18383291 TCCGATCCAC
*
18383301 CCTCCTAAACATTTT
1 CCTCCCAAACATTTT
18383316 CCTCCCAAACATTTT
1 CCTCCCAAACATTTT
18383331 AAGTGAAAAA
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:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (15 bp):
CCTCCCAAACATTTT
Found at i:18383856 original size:20 final size:20
Alignment explanation
Indices: 18383831--18383871 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18383821 GAAAAATTTG
18383831 TACTCCATTTCGATAGTCAT
1 TACTCCATTTCGATAGTCAT
18383851 TACTCCATTTCGATAGTCAT
1 TACTCCATTTCGATAGTCAT
18383871 T
1 T
18383872 GCTTACCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (20 bp):
TACTCCATTTCGATAGTCAT
Found at i:18384093 original size:9 final size:9
Alignment explanation
Indices: 18384079--18384191 Score: 97
Period size: 9 Copynumber: 12.6 Consensus size: 9
18384069 TATTTATGTA
18384079 TTATGTAAG
1 TTATGTAAG
18384088 TTATGTAAG
1 TTATGTAAG
*
18384097 TTATGATATG
1 TTATG-TAAG
* * *
18384107 ATATAT-AT
1 TTATGTAAG
18384115 TTATGTAAG
1 TTATGTAAG
*
18384124 TTATGTAAA
1 TTATGTAAG
*
18384133 TTATGCAAG
1 TTATGTAAG
18384142 TTATGTAAG
1 TTATGTAAG
*
18384151 TTATGATATG
1 TTATG-TAAG
* *
18384161 ATATAT-A-
1 TTATGTAAG
18384168 TTAATGTAAG
1 TT-ATGTAAG
18384178 TTATGTAAG
1 TTATGTAAG
18384187 TTATG
1 TTATG
18384192 ATTATCATCT
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
7 1 0.01
8 7 0.09
9 58 0.73
10 14 0.17
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:18384119 original size:27 final size:27
Alignment explanation
Indices: 18384088--18384182 Score: 120
Period size: 27 Copynumber: 3.5 Consensus size: 27
18384078 ATTATGTAAG
18384088 TTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGATATGATATATAT
* * ** *
18384115 TTATGTAAGTTATGTAAATTATGCA-AG
1 TTATGTAAGTTATG-ATATGATATATAT
18384142 TTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGATATGATATATAT
*
18384169 TAATGTAAGTTATG
1 TTATGTAAGTTATG
18384183 TAAGTTATGA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
26 6 0.11
27 43 0.78
28 6 0.11
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (27 bp):
TTATGTAAGTTATGATATGATATATAT
Found at i:18384143 original size:54 final size:54
Alignment explanation
Indices: 18384078--18384191 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 54
18384068 ATATTTATGT
* *
18384078 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
1 ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
18384132 ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
1 ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
*
18384186 GTTATG
1 ATTATG
18384192 ATTATCATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.37, C:0.01, G:0.18, T:0.45
Consensus pattern (54 bp):
ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
Found at i:18384220 original size:13 final size:13
Alignment explanation
Indices: 18384202--18384226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18384192 ATTATCATCT
18384202 TTAAATTTTAACA
1 TTAAATTTTAACA
18384215 TTAAATTTTAAC
1 TTAAATTTTAAC
18384227 CCTTTAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTTTAACA
Found at i:18384493 original size:17 final size:17
Alignment explanation
Indices: 18384471--18384503 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18384461 ACTAACCTTA
18384471 CATGATAAATGAAATTG
1 CATGATAAATGAAATTG
18384488 CATGATAAATGAAATT
1 CATGATAAATGAAATT
18384504 ATATTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (17 bp):
CATGATAAATGAAATTG
Done.