Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 105 of 120
Found at i:30689500 original size:2 final size:2
Alignment explanation
Indices: 30689493--30689520 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30689483 AAAATCATAA
30689493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30689521 GATTGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30692894 original size:3 final size:3
Alignment explanation
Indices: 30692881--30692910 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30692871 TATACCTACA
*
30692881 TAT TCT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30692911 ATTGGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30696299 original size:21 final size:21
Alignment explanation
Indices: 30696275--30696337 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
30696265 TTAATAAATT
30696275 CTCTATTTCTTTTACTTTCAA
1 CTCTATTTCTTTTACTTTCAA
* ***
30696296 CTCTA-TTATGCCA-TTTCAA
1 CTCTATTTCTTTTACTTTCAA
30696315 CTCT-TTTCCTTTTACTTTCAA
1 CTCTATTT-CTTTTACTTTCAA
30696336 CT
1 CT
30696338 TTTTGATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
19 12 0.39
20 6 0.19
21 13 0.42
ACGTcount: A:0.19, C:0.27, G:0.02, T:0.52
Consensus pattern (21 bp):
CTCTATTTCTTTTACTTTCAA
Found at i:30705073 original size:21 final size:21
Alignment explanation
Indices: 30705035--30705090 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
30705025 TTTTAAATTT
*
30705035 TAAAAATTATTTAAAAAA-TCA
1 TAAAAATTA-TAAAAAAATTCA
*
30705056 TAAAAATTATAAACAAAATTTA
1 TAAAAATTATAAA-AAAATTCA
*
30705078 TAAAAATTTTAAA
1 TAAAAATTATAAA
30705091 TTTATAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 13 0.43
22 14 0.47
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAATTATAAAAAAATTCA
Found at i:30721685 original size:27 final size:26
Alignment explanation
Indices: 30721655--30721807 Score: 146
Period size: 27 Copynumber: 5.7 Consensus size: 26
30721645 AACTTTTAAC
*
30721655 TTTTAATATACTATTATAAATATACTT-
1 TTTTAATATACTATT-TTAATATA-TTG
*
30721682 TTTTAATATATTATTTTAATATATTG
1 TTTTAATATACTATTTTAATATATTG
* * *
30721708 TTATAAATATACTATTTTAATATACTA
1 TT-TTAATATACTATTTTAATATATTG
* *
30721735 TTATAAATATACTTTTTTAATATATTG
1 TT-TTAATATACTATTTTAATATATTG
* * *
30721762 TTTTAATATATTGTTATAAATATATTG
1 TTTTAATATACTATT-TTAATATATTG
* *
30721789 TTTTAATATAATGTTTTAA
1 TTTTAATATACTATTTTAA
30721808 CTTTTAATAT
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
25 2 0.02
26 22 0.20
27 84 0.78
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTTAATATACTATTTTAATATATTG
Found at i:30721698 original size:15 final size:13
Alignment explanation
Indices: 30721655--30721798 Score: 121
Period size: 13 Copynumber: 10.8 Consensus size: 13
30721645 AACTTTTAAC
*
30721655 TTTTAATATACTA
1 TTTTAATATATTA
*
30721668 TTATAAATATACTT-
1 TT-TTAATATA-TTA
30721682 TTTTAATATATTA
1 TTTTAATATATTA
*
30721695 TTTTAATATATTG
1 TTTTAATATATTA
* *
30721708 TTATAAATATACTA
1 TT-TTAATATATTA
*
30721722 TTTTAATATACTA
1 TTTTAATATATTA
*
30721735 TTATAAATATACTT-
1 TT-TTAATATA-TTA
*
30721749 TTTTAATATATTG
1 TTTTAATATATTA
*
30721762 TTTTAATATATTG
1 TTTTAATATATTA
* *
30721775 TTATAAATATATTG
1 TT-TTAATATATTA
30721789 TTTTAATATA
1 TTTTAATATA
30721799 ATGTTTTAAC
Statistics
Matches: 110, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.04
13 64 0.58
14 40 0.36
15 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (13 bp):
TTTTAATATATTA
Found at i:30721712 original size:40 final size:40
Alignment explanation
Indices: 30721671--30721807 Score: 154
Period size: 40 Copynumber: 3.4 Consensus size: 40
30721661 TATACTATTA
*
30721671 TAAATATACTTTTTTAATATATTATT-TTAATATATTGTT
1 TAAATATACTTTTTTAATATATTATTATAAATATATTGTT
* *
30721710 ATAAATATACTATTTTAATATACTATTATAAATATACTT-TT
1 -TAAATATACTTTTTTAATATATTATTATAAATATA-TTGTT
* *
30721751 TTAATATA-TTGTTTTAATATATTGTTATAAATATATTGTT
1 TAAATATACTT-TTTTAATATATTATTATAAATATATTGTT
* * *
30721791 TTAATATAATGTTTTAA
1 TAAATATACTTTTTTAA
30721808 CTTTTAATAT
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
39 3 0.04
40 69 0.82
41 10 0.12
42 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (40 bp):
TAAATATACTTTTTTAATATATTATTATAAATATATTGTT
Found at i:30721726 original size:67 final size:67
Alignment explanation
Indices: 30721655--30721798 Score: 261
Period size: 67 Copynumber: 2.1 Consensus size: 67
30721645 AACTTTTAAC
30721655 TTTTAATATACTATTATAAATATACTTTTTTAATATATTATTTTAATATATTGTTATAAATATAC
1 TTTTAATATACTATTATAAATATACTTTTTTAATATATTATTTTAATATATTGTTATAAATATAC
30721720 TA
66 TA
* *
30721722 TTTTAATATACTATTATAAATATACTTTTTTAATATATTGTTTTAATATATTGTTATAAATATAT
1 TTTTAATATACTATTATAAATATACTTTTTTAATATATTATTTTAATATATTGTTATAAATATAC
*
30721787 TG
66 TA
30721789 TTTTAATATA
1 TTTTAATATA
30721799 ATGTTTTAAC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (67 bp):
TTTTAATATACTATTATAAATATACTTTTTTAATATATTATTTTAATATATTGTTATAAATATAC
TA
Found at i:30724227 original size:9 final size:9
Alignment explanation
Indices: 30724221--30724252 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
30724211 GAACGATGAC
*
30724221 GACGATGAT
1 GACGACGAT
30724230 GACGACGAT
1 GACGACGAT
30724239 GACGACGAT
1 GACGACGAT
30724248 GACGA
1 GACGA
30724253 TGAATATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.12
Consensus pattern (9 bp):
GACGACGAT
Found at i:30724232 original size:12 final size:12
Alignment explanation
Indices: 30724215--30724246 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30724205 CAAAAAGAAC
30724215 GATGACGACGAT
1 GATGACGACGAT
30724227 GATGACGACGAT
1 GATGACGACGAT
*
30724239 GACGACGA
1 GATGACGA
30724247 TGACGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.12
Consensus pattern (12 bp):
GATGACGACGAT
Found at i:30724497 original size:30 final size:30
Alignment explanation
Indices: 30724461--30724552 Score: 166
Period size: 30 Copynumber: 3.1 Consensus size: 30
30724451 AAAGATAGTT
*
30724461 TGAAGCAAAATTAGAGATTGGGATTTTCAA
1 TGAAGCAAAATTACAGATTGGGATTTTCAA
*
30724491 TGAAGCAAAATTACAGATTGGGATTTTCAG
1 TGAAGCAAAATTACAGATTGGGATTTTCAA
30724521 TGAAGCAAAATTACAGATTGGGATTTTCAA
1 TGAAGCAAAATTACAGATTGGGATTTTCAA
30724551 TG
1 TG
30724553 CTTGATTTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (30 bp):
TGAAGCAAAATTACAGATTGGGATTTTCAA
Found at i:30730656 original size:32 final size:32
Alignment explanation
Indices: 30730620--30730686 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
30730610 TATATAGCCT
*
30730620 CTTATTCAAGCAGAACTTATCTCTCCTTGATC
1 CTTATTCAAGCAAAACTTATCTCTCCTTGATC
*
30730652 CTTATTCAAGCAAAACTTATCTCTCTTTGATC
1 CTTATTCAAGCAAAACTTATCTCTCCTTGATC
30730684 CTT
1 CTT
30730687 CCTCTATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.40
Consensus pattern (32 bp):
CTTATTCAAGCAAAACTTATCTCTCCTTGATC
Found at i:30732171 original size:16 final size:17
Alignment explanation
Indices: 30732150--30732182 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30732140 AGTGTAGTTG
*
30732150 CCTTTATGT-TGTTTTT
1 CCTTTAGGTGTGTTTTT
30732166 CCTTTAGGTGTGTTTTT
1 CCTTTAGGTGTGTTTTT
30732183 TATTTGGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.06, C:0.12, G:0.18, T:0.64
Consensus pattern (17 bp):
CCTTTAGGTGTGTTTTT
Found at i:30734523 original size:8 final size:7
Alignment explanation
Indices: 30734503--30734535 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
30734493 TTAACAAGTC
30734503 TTAAAAA
1 TTAAAAA
30734510 TTAAAAA
1 TTAAAAA
30734517 TTAAAAA
1 TTAAAAA
30734524 TTACAAAA
1 TTA-AAAA
30734532 TTAA
1 TTAA
30734536 TTAGCCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:30736774 original size:69 final size:69
Alignment explanation
Indices: 30736693--30736830 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
30736683 ACGATAAATG
30736693 TACTCTCTTACTAAGTTTTTGATGTTCTAGAAAGTTATAGATCCAAAATATAAGAATGAAACATA
1 TACTCTCTTACTAAGTTTTTGATGTTCTAGAAAGTTATAGATCCAAAATATAAGAATGAAACATA
30736758 TCTA
66 TCTA
30736762 TACTCTCTTACTAAGTTTTTGATGTTCTAGAAAGTTATAGATCCAAAATATAAGAATGAAACATA
1 TACTCTCTTACTAAGTTTTTGATGTTCTAGAAAGTTATAGATCCAAAATATAAGAATGAAACATA
30736827 TCTA
66 TCTA
30736831 AATTAATGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (69 bp):
TACTCTCTTACTAAGTTTTTGATGTTCTAGAAAGTTATAGATCCAAAATATAAGAATGAAACATA
TCTA
Found at i:30744698 original size:20 final size:20
Alignment explanation
Indices: 30744660--30744698 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30744650 CAATTCTGAC
*
30744660 AAAAAAATTGATGATCTTGA
1 AAAAAAATTGATGACCTTGA
30744680 AAAAAAATT-ATGTACCTTG
1 AAAAAAATTGATG-ACCTTG
30744699 TCATGTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.31
Consensus pattern (20 bp):
AAAAAAATTGATGACCTTGA
Found at i:30746686 original size:14 final size:15
Alignment explanation
Indices: 30746667--30746700 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30746657 TCAATATGTC
30746667 TAAAAAAT-TATAAA
1 TAAAAAATATATAAA
*
30746681 TAAAAAATATTTAAA
1 TAAAAAATATATAAA
30746696 TAAAA
1 TAAAA
30746701 GTACGGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAAATATATAAA
Found at i:30747060 original size:24 final size:24
Alignment explanation
Indices: 30747033--30747084 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
30747023 TTTCCAGAAG
* *
30747033 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGCATAATAT
30747057 ATTTAGAATTTATTAGCATAATAT
1 ATTTAGAATTTATTAGCATAATAT
30747081 ATTT
1 ATTT
30747085 GACTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCATAATAT
Found at i:30753188 original size:20 final size:19
Alignment explanation
Indices: 30753150--30753188 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30753140 CAATTCTGAC
*
30753150 AAAAAAATTGATGATCTTG
1 AAAAAAATTGATGACCTTG
*
30753169 AAAAAAATTTATGTACCTTG
1 AAAAAAATTGATG-ACCTTG
30753189 TCATATGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (19 bp):
AAAAAAATTGATGACCTTG
Found at i:30756586 original size:3 final size:3
Alignment explanation
Indices: 30756578--30756659 Score: 110
Period size: 3 Copynumber: 27.3 Consensus size: 3
30756568 TTTAGCAATT
* * *
30756578 TTA TTA TTA TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
30756626 TTA TTG TTA TTA TTA TTA TTA TAA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30756660 GCATATACGT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:30756777 original size:22 final size:22
Alignment explanation
Indices: 30756752--30756794 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30756742 TAAAACATGT
30756752 ATAT-TATATATATTATTATTTC
1 ATATCTATATAT-TTATTATTTC
*
30756774 ATATCTATATATTTTTTATTT
1 ATATCTATATATTTATTATTT
30756795 TTTAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATCTATATATTTATTATTTC
Found at i:30766666 original size:44 final size:44
Alignment explanation
Indices: 30766596--30767112 Score: 266
Period size: 44 Copynumber: 11.9 Consensus size: 44
30766586 AGAATTTCAG
** *
30766596 ATCTTATCTCCCTGAGATTATTGCGGAACAGATTGAAGAT-AGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAAG-A
* ** * *
30766640 ATCCTATCTCCCTGAGATTACAGCGGAGTGGATT-AAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT-AAGA
* ** * * * *
30766684 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG-TG-TCAG-
1 ATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGATAAGA
*
30766725 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAAG-A
* * * * *
30766769 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATGAAGG
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT-AAGA
* * * * * *
30766813 ATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-TG-TCAG-
1 ATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGATAAGA
* * * * ** *
30766854 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAG-
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-A--TAAGA
* *
30766900 ATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCT-AGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAAG-A
* * * * *
30766944 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATGAAGG
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT-AAGA
* * * * * *
30766988 ATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-CG-TCAG-
1 ATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGATAAGA
* * * ** *
30767029 GTCTTATTTCCCTGAGATTACAGTGG-GACAGACCGAAGAATTTCAG-
1 ATCTTATCTCCCTGAGATTACAGCGGAG-CAGATTGAAG-A--TAAGA
30767075 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
30767113 CCAGTAATTC
Statistics
Matches: 354, Mismatches: 86, Indels: 64
0.70 0.17 0.13
Matches are distributed among these distances:
40 1 0.00
41 77 0.22
42 16 0.05
43 18 0.05
44 165 0.47
45 6 0.02
46 70 0.20
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAAGA
Found at i:30766802 original size:129 final size:129
Alignment explanation
Indices: 30766592--30766933 Score: 497
Period size: 129 Copynumber: 2.6 Consensus size: 129
30766582 CCGAAGAATT
**
30766592 TCAGATCTTATCTCCCTGAGATTATTGCGGAACAGATTGAAGATAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGATAGTAATCCTATCTCCCTGAGA
* *
30766657 TTACAGCGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
66 TTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTG
* *
30766721 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGATAGTAATCCTATCTCCCTGAGA
* *
30766786 TTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTG
66 TTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTG
* * * ** * *
30766850 TCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGA-ATTTCAGATCTTATCTCCCTG
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGATA-GT-A-ATCCTATCTCCCTG
* *
30766914 AGATTACAGCAGAGCAGATT
63 AGATTACAGCGGAGCGGATT
30766934 GAAGCTAGTA
Statistics
Matches: 190, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.01
129 158 0.83
130 1 0.01
131 30 0.16
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (129 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGATAGTAATCCTATCTCCCTGAGA
TTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTG
Found at i:30766872 original size:85 final size:85
Alignment explanation
Indices: 30766777--30767054 Score: 337
Period size: 85 Copynumber: 3.2 Consensus size: 85
30766767 TAATCCTATC
30766777 TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGT
1 TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGT
*
30766842 AGATCGTGTCAGGTCTTATT
66 AGATCGAGTCAGGTCTTATT
* * ** ** *
30766862 TCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCA-GATCTTATCTCCCTG-AGATTACAGCA
1 TCCCTGAGATTACAGTGGAGCGGA-TTAA-AA-TGAAGGATCTTATCTCTCTGAAG-TTACAGCA
* * * * *
30766925 GAGCAGATTGAAG-CTAGTAATCCTATC
62 GAGTAGATCG-AGTC-AG--GTCTTATT
30766952 TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGT
1 TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGT
*
30767017 AGATCGCGTCAGGTCTTATT
66 AGATCGAGTCAGGTCTTATT
30767037 TCCCTGAGATTACAGTGG
1 TCCCTGAGATTACAGTGG
30767055 GACAGACCGA
Statistics
Matches: 156, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
85 45 0.29
86 4 0.03
87 38 0.24
88 38 0.24
89 4 0.03
90 27 0.17
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (85 bp):
TCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGT
AGATCGAGTCAGGTCTTATT
Found at i:30766909 original size:175 final size:175
Alignment explanation
Indices: 30766721--30767128 Score: 771
Period size: 175 Copynumber: 2.3 Consensus size: 175
30766711 GTAGATCGTG
30766721 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
30766786 TTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTGT
66 TTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
30766851 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATT
131 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATT
*
30766896 TCAGATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
30766961 TTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
66 TTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
*
30767026 CAGGTCTTATTTCCCTGAGATTACAGTGGGACAGACCGAAGAATT
131 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATT
* *
30767071 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATTCTATCTC
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTC
30767129 TCCGACGTTG
Statistics
Matches: 227, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 227 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (175 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATT
Found at i:30767012 original size:88 final size:88
Alignment explanation
Indices: 30766724--30767128 Score: 359
Period size: 87 Copynumber: 4.6 Consensus size: 88
30766714 GATCGTGTCA
*
30766724 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
30766789 CAGTGGAGCGGATTAAAATGAAG
66 CAGTGGAGCGGATTAAAATGAAG
* * * * * * *
30766812 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-TG-TCAG--GTCTTATTTCCCTGAGAT
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGCAGATTGAAGCT-AGTAATCCTATCTCCCTGAGAT
* * ** **
30766872 TACAGTGGAACAGACCGAAGAATTTCA-
64 TACAGTGGAGCGGA-TTAA-AA-TGAAG
30766899 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
30766964 CAGTGGAGCGGATTAAAATGAAG
66 CAGTGGAGCGGATTAAAATGAAG
* * * * * * *
30766987 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-CG-TCAG--GTCTTATTTCCCTGAGAT
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGCAGATTGAAGCT-AGTAATCCTATCTCCCTGAGAT
* ** **
30767047 TACAGTGG-GACAGACCGAAGAATTTCA-
64 TACAGTGGAG-CGGA-TTAA-AA-TGAAG
* * *
30767074 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATTCTATCTC
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTC
30767129 TCCGACGTTG
Statistics
Matches: 246, Mismatches: 49, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
84 1 0.00
85 53 0.22
86 6 0.02
87 75 0.30
88 75 0.30
89 3 0.01
90 33 0.13
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (88 bp):
GATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
CAGTGGAGCGGATTAAAATGAAG
Found at i:30768651 original size:3 final size:3
Alignment explanation
Indices: 30768643--30768703 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
30768633 TTTAGCAATT
* *
30768643 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30768691 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
30768704 AATTGTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:30773392 original size:81 final size:81
Alignment explanation
Indices: 30773280--30773742 Score: 551
Period size: 81 Copynumber: 5.7 Consensus size: 81
30773270 GGGGTATAAT
* * *
30773280 AGTCATTTTACCCTATGGGGGTATTTTGATCATTCTACCCTACGAGGGTATTTTGGTCATTCTAC
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGAGGGTATTTCGGTCATTCTAC
*
30773345 CCTATGGGGGTATTTT
66 CCTATGGGGGTATTTC
* * * * *
30773361 GGTCATTTTACCCTATGGGGGTATTTCGATCAATT-TACCCTATGGGGGTATTACAGTCATTTTA
1 AGTCATTTTACCCTATGGGGGTATTTCGATC-ATTCTACCCTATGAGGGTATTTCGGTCATTCTA
*
30773425 CCTTATGGGGGTATTTC
65 CCCTATGGGGGTATTTC
* * * * * *
30773442 GGTCA-TATACCCTGTGGGGGTACTTCGGTCATTCTACCCTAT-AGGGGTATCTCGGTCATGT-T
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGA-GGGTATTTCGGTCAT-TCT
30773504 ACCCTATGGGGGTATTTC
64 ACCCTATGGGGGTATTTC
* * * * *
30773522 AATCATTTTACCCTACGGGGGTA-TTGGATAATTCTACCTTATGAGGGTATTTCGGTCATTCTAC
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGAGGGTATTTCGGTCATTCTAC
* *
30773586 CTTATAGGGGTATTTC
66 CCTATGGGGGTATTTC
* * * * * *
30773602 AGTCATTTTATCCTATGGGGGTATTTTGGTTAGTT-TACCCTATGGGGGTATTTCGGTCATTTTA
1 AGTCATTTTACCCTATGGGGGTATTTCGATCA-TTCTACCCTATGAGGGTATTTCGGTCATTCTA
*
30773666 CCCTATAGGGGTATTTC
65 CCCTATGGGGGTATTTC
* * *
30773683 AGTCATTTTACCCTATAGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCGATCAT
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGAGGGTATTTCGGTCAT
30773743 AACAGTGTAA
Statistics
Matches: 325, Mismatches: 47, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
79 4 0.01
80 130 0.40
81 186 0.57
82 5 0.02
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (81 bp):
AGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGAGGGTATTTCGGTCATTCTAC
CCTATGGGGGTATTTC
Found at i:30773736 original size:27 final size:27
Alignment explanation
Indices: 30773282--30773742 Score: 482
Period size: 27 Copynumber: 17.1 Consensus size: 27
30773272 GGTATAATAG
*
30773282 TCATTTTACCCTATGGGGGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * * * *
30773309 TCATTCTACCCTACGAGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
30773336 TCATTCTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGA
30773363 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
30773390 TCAATTTACCCTATGGGGGTATTAC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
30773416 GTCATTTTACCTTATGGGGGTATTTCGG
1 -TCATTTTACCCTATGGGGGTATTTCGA
* * * *
30773444 TCA-TATACCCTGTGGGGGTACTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* * * *
30773470 TCATTCTACCCTATAGGGGTATCTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
30773497 TCATGTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
30773524 TCATTTTACCCTACGGGGGTA-TTGGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * * * *
30773550 TAATTCTACCTTATGAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
30773577 TCATTCTACCTTATAGGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
30773603 GTCATTTTATCCTATGGGGGTATTTTGG
1 -TCATTTTACCCTATGGGGGTATTTCGA
* * *
30773631 TTAGTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
*
30773658 TCATTTTACCCTATAGGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
*
30773684 GTCATTTTACCCTATAGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTCGA
*
30773712 TCATTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
30773739 TCAT
1 TCAT
30773743 AACAGTGTAA
Statistics
Matches: 365, Mismatches: 61, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
26 42 0.12
27 322 0.88
28 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:30781579 original size:2 final size:2
Alignment explanation
Indices: 30781574--30781612 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
30781564 GAGGGAGGGG
* *
30781574 GA GA GA GA GC GA GT GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30781613 TGTGTGTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.03, G:0.51, T:0.03
Consensus pattern (2 bp):
GA
Found at i:30781617 original size:2 final size:2
Alignment explanation
Indices: 30781612--30781652 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
30781602 GAGAGAGAGA
*
30781612 GT GT GT GT GT GT GT GT GT GT GT AT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
30781653 AGTGAGTGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
GT
Found at i:30784566 original size:33 final size:34
Alignment explanation
Indices: 30784523--30784592 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
30784513 TATACAACAG
* * *
30784523 ACAGTGACAGTCTGGGCCTGAGCCCTATTCAGTA
1 ACAGTGACAGTATGGGCCTGAGCCCAATACAGTA
*
30784557 ACAGT-ACAGTATGGGCCTTAGCCCAATACAGTA
1 ACAGTGACAGTATGGGCCTGAGCCCAATACAGTA
30784590 ACA
1 ACA
30784593 ATGTGGGCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (34 bp):
ACAGTGACAGTATGGGCCTGAGCCCAATACAGTA
Found at i:30784601 original size:28 final size:28
Alignment explanation
Indices: 30784568--30784645 Score: 147
Period size: 28 Copynumber: 2.8 Consensus size: 28
30784558 CAGTACAGTA
30784568 TGGGCCTTAGCCCAATACAGTAACAATG
1 TGGGCCTTAGCCCAATACAGTAACAATG
30784596 TGGGCCTTAGCCCAATACAGTAACAATG
1 TGGGCCTTAGCCCAATACAGTAACAATG
*
30784624 TGGGCCTTAGCCCAATATAGTA
1 TGGGCCTTAGCCCAATACAGTA
30784646 TAGGTACAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATACAGTAACAATG
Found at i:30785022 original size:14 final size:13
Alignment explanation
Indices: 30784991--30785032 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
30784981 AAAAATCATA
30784991 AAATTTGAATTAC
1 AAATTTGAATTAC
30785004 AAATTT-AATTAGCC
1 AAATTTGAATTA--C
30785018 AAATTTGAATTAC
1 AAATTTGAATTAC
30785031 AA
1 AA
30785033 GTTTTAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 7 0.27
15 5 0.19
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (13 bp):
AAATTTGAATTAC
Found at i:30789143 original size:20 final size:20
Alignment explanation
Indices: 30789118--30789155 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30789108 CAATTCTGAC
30789118 AAAAATTTGATG-ATGTTGAA
1 AAAAATTT-ATGTATGTTGAA
30789138 AAAAATTTATGTATGTTG
1 AAAAATTTATGTATGTTG
30789156 TCACGTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (20 bp):
AAAAATTTATGTATGTTGAA
Found at i:30791489 original size:24 final size:24
Alignment explanation
Indices: 30791462--30791513 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
30791452 TTTCTAGAAG
* *
30791462 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGCATAATAT
30791486 ATTTAGAATTTATTAGCATAATAT
1 ATTTAGAATTTATTAGCATAATAT
30791510 ATTT
1 ATTT
30791514 GACTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCATAATAT
Found at i:30797583 original size:59 final size:59
Alignment explanation
Indices: 30797508--30797621 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
30797498 AAGCCCTATC
* *
30797508 TTTGGTTAGTTGGCTTTTAAGTAAAAGTTGGCAAATAATTAACAGAATGGGCCTGCTAG
1 TTTGGTCAGTAGGCTTTTAAGTAAAAGTTGGCAAATAATTAACAGAATGGGCCTGCTAG
*
30797567 TTTGGTCAGTAGGCTTTTAAGTAAAAGTTGGCATATAATTAACAGAATGGGCCTG
1 TTTGGTCAGTAGGCTTTTAAGTAAAAGTTGGCAAATAATTAACAGAATGGGCCTG
30797622 TTGGTCTGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (59 bp):
TTTGGTCAGTAGGCTTTTAAGTAAAAGTTGGCAAATAATTAACAGAATGGGCCTGCTAG
Found at i:30804778 original size:27 final size:28
Alignment explanation
Indices: 30804747--30804800 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
30804737 CTATTCAGTA
*
30804747 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
30804774 ACAGTAACAATGTGGGCCTTAGCCCAA
1 ACAGTAACAATGTGGGCCTTAGCCCAA
30804801 AATTCCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:30806009 original size:2 final size:2
Alignment explanation
Indices: 30806004--30806042 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
30805994 GAGGGAGGGG
* *
30806004 GA GA GA GA GC GA GT GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30806043 TGTGTGTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.03, G:0.51, T:0.03
Consensus pattern (2 bp):
GA
Found at i:30806047 original size:2 final size:2
Alignment explanation
Indices: 30806042--30806082 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30806032 GAGAGAGAGA
30806042 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
30806083 AGTGAGTGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:30809021 original size:33 final size:33
Alignment explanation
Indices: 30808953--30809049 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 33
30808943 ATACAACAGG
* * * *
30808953 CAGTGACAGTCTGGGCC-TGAGCCCTATTCAGTAA
1 CAGT-ACAGTGTGGGCCTTG-GCCCAATACAATAA
30808987 CAGTACAGTGTGGGCCTTGGCCCAATACAATAA
1 CAGTACAGTGTGGGCCTTGGCCCAATACAATAA
*
30809020 C---A-A-TGTGGGCCTTAGCCCAATACAATAA
1 CAGTACAGTGTGGGCCTTGGCCCAATACAATAA
30809048 CA
1 CA
30809050 ATGTGGGCCT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 25 0.45
29 1 0.02
30 1 0.02
33 23 0.41
34 6 0.11
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (33 bp):
CAGTACAGTGTGGGCCTTGGCCCAATACAATAA
Found at i:30809037 original size:28 final size:28
Alignment explanation
Indices: 30808995--30809068 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
30808985 AACAGTACAG
*
30808995 TGTGGGCCTTGGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAATAACAA
30809023 TGTGGGCCTTAGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAATAACAA
30809051 TGTGGGCCTTAGCCCAAT
1 TGTGGGCCTTAGCCCAAT
30809069 TTCCGTAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.23
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAATAACAA
Found at i:30815917 original size:14 final size:15
Alignment explanation
Indices: 30815898--30815931 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30815888 TCAATATGTC
30815898 TAAAAAAT-TATAAA
1 TAAAAAATATATAAA
*
30815912 TAAAAAATATTTAAA
1 TAAAAAATATATAAA
30815927 TAAAA
1 TAAAA
30815932 GTACGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAAATATATAAA
Found at i:30816295 original size:24 final size:24
Alignment explanation
Indices: 30816267--30816318 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
30816257 TTTCTATAAG
* *
30816267 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGCATAATAT
30816291 ATTTAGAATTTATTAGCATAATAT
1 ATTTAGAATTTATTAGCATAATAT
30816315 ATTT
1 ATTT
30816319 GACTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCATAATAT
Found at i:30820225 original size:47 final size:49
Alignment explanation
Indices: 30820172--30820298 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 49
30820162 ATTATGAAAT
*
30820172 TTCCGTGTAAGACCATATCTGGAATATGGCATC-AT-TGTGATATGTCA
1 TTCCGTGTAAGACCATATCTGGACTATGGCATCGATATGTGATATGTCA
* * * * *
30820219 TTCCGTGTAAGACTATAGCTGGGCTATGGCATCGGTATGTGATATGTGA
1 TTCCGTGTAAGACCATATCTGGACTATGGCATCGATATGTGATATGTCA
* *
30820268 TTACATGTAAGACCATAGT-TGGACTATGGCA
1 TTCCGTGTAAGACCATA-TCTGGACTATGGCA
30820299 ATGTGAAAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 29 0.44
48 1 0.02
49 36 0.55
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (49 bp):
TTCCGTGTAAGACCATATCTGGACTATGGCATCGATATGTGATATGTCA
Found at i:30822966 original size:101 final size:101
Alignment explanation
Indices: 30822851--30823136 Score: 475
Period size: 101 Copynumber: 2.8 Consensus size: 101
30822841 AAAGTGATGG
*
30822851 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTGC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
30822916 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* *
30822952 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGTACCAGAATGATAGGTCGTATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
30823017 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
30823053 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
*
30823117 ACTATGTGCATGCTACTATG
64 ACTATGTGCAGGCTACTATG
30823137 TGAATCCGCA
Statistics
Matches: 173, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 136 0.79
102 33 0.19
103 4 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:30822971 original size:51 final size:50
Alignment explanation
Indices: 30822851--30823134 Score: 274
Period size: 51 Copynumber: 5.6 Consensus size: 50
30822841 AAAGTGATGG
* * * * *
30822851 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GTTCGA
* * * * *
30822901 TCGCATGTGTAGTGCTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TTCGA
* * *
30822952 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGTACCAGAATGATAGGTCG-
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-G---GATAGTTCGA
* *
30823005 T-A--TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TTCGA
* *
30823053 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT--TCGA
* *
30823104 TCACATGTGTAGTACTATGTGCATGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
30823135 TGTGAATCCG
Statistics
Matches: 192, Mismatches: 29, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
46 5 0.03
47 3 0.02
48 1 0.01
49 2 0.01
50 67 0.35
51 102 0.53
52 3 0.02
53 1 0.01
54 3 0.02
55 5 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTCGA
Found at i:30823138 original size:26 final size:26
Alignment explanation
Indices: 30823058--30823138 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
30823048 TTCGATCACG
*
30823058 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
30823084 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
30823109 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
30823135 TGTG
1 TGTG
30823139 AATCCGCATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:30824237 original size:33 final size:33
Alignment explanation
Indices: 30824200--30824268 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
30824190 ATGATAATAA
30824200 TGATATATGGATGATTATATCATTGAGTTGCAT
1 TGATATATGGATGATTATATCATTGAGTTGCAT
30824233 TGATATATGGATGATTATATCATTGAGTTGCAT
1 TGATATATGGATGATTATATCATTGAGTTGCAT
30824266 TGA
1 TGA
30824269 CCAAAAAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.42
Consensus pattern (33 bp):
TGATATATGGATGATTATATCATTGAGTTGCAT
Found at i:30825175 original size:3 final size:3
Alignment explanation
Indices: 30825167--30825307 Score: 124
Period size: 3 Copynumber: 47.3 Consensus size: 3
30825157 ACACCTATTT
***
30825167 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GCG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * * * **
30825215 ATC AT- GTC ATG GTT ATC ATC ATA ATA TTA A-C ATGA ACG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
30825259 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30825307 A
1 A
30825308 CATTACGGGT
Statistics
Matches: 112, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
2 2 0.02
3 109 0.97
4 1 0.01
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30827365 original size:52 final size:52
Alignment explanation
Indices: 30827287--30827390 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
30827277 AACAACAATT
30827287 CCAGATCCTAAATACAGTAACCAACTTATCGAGTTAGCAAATAAACATGAGA
1 CCAGATCCTAAATACAGTAACCAACTTATCGAGTTAGCAAATAAACATGAGA
*
30827339 CCAGATCCTACATACAGTAACCAACTTATCGAGTTAGCAAATAAACATGAGA
1 CCAGATCCTAAATACAGTAACCAACTTATCGAGTTAGCAAATAAACATGAGA
30827391 ATTGACCCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.21
Consensus pattern (52 bp):
CCAGATCCTAAATACAGTAACCAACTTATCGAGTTAGCAAATAAACATGAGA
Found at i:30831396 original size:144 final size:143
Alignment explanation
Indices: 30831102--30831364 Score: 382
Period size: 144 Copynumber: 1.8 Consensus size: 143
30831092 GAGTTTATTT
* **
30831102 ACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTGGTAGACCTAAACCAGACTTTCTAATT
1 ACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTGGTAGACCTAAACCAGACTTTATAAAA
* **
30831167 AAAAAAGGCAATTCCACTAATCACAACATTCATTACCAACTCAAGTGCCACATAGGAGCATCAAT
66 AAAAAAGGCAATTCCACTAATCACAACATTCATCACCAACTCAAGTGCCACATA-GAAAATCAAT
** ** *
30831232 TCTTGAGTTTATTT
130 TAGTGAGTAAATTG
* *
30831246 CCTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTGGTAGACCTAAACTAGACTTTATAAAA
1 ACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTGGTAGACCTAAACCAGACTTTAT-AAA
*
30831311 AAAAAAAGGCAATTCCACTAATCACAACATTCATCACCAACTCAAGTGTCACAT
65 AAAAAAAGGCAATTCCACTAATCACAACATTCATCACCAACTCAAGTGCCACAT
30831365 TAAAAATTCG
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
144 58 0.52
145 53 0.48
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (143 bp):
ACTTACTTTAATATCTCAATTTGGTTCTTCTATCACTTGGTAGACCTAAACCAGACTTTATAAAA
AAAAAAGGCAATTCCACTAATCACAACATTCATCACCAACTCAAGTGCCACATAGAAAATCAATT
AGTGAGTAAATTG
Found at i:30833609 original size:13 final size:13
Alignment explanation
Indices: 30833591--30833618 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30833581 GTGTTGTTAG
30833591 GAAAAGGTCGTGA
1 GAAAAGGTCGTGA
30833604 GAAAAGGTCGTGA
1 GAAAAGGTCGTGA
30833617 GA
1 GA
30833619 TGTTCGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.39, T:0.14
Consensus pattern (13 bp):
GAAAAGGTCGTGA
Found at i:30835781 original size:23 final size:23
Alignment explanation
Indices: 30835748--30835791 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30835738 TGGGTAGGAA
*
30835748 GTTTTCTAAAAAATCTGCATTAT
1 GTTTTCCAAAAAATCTGCATTAT
* *
30835771 GTTTTCCAAAAATTTTGCATT
1 GTTTTCCAAAAAATCTGCATT
30835792 TACATAACCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (23 bp):
GTTTTCCAAAAAATCTGCATTAT
Found at i:30839562 original size:16 final size:15
Alignment explanation
Indices: 30839537--30839567 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
30839527 TTGAGGAGAG
30839537 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
30839552 AAAAATAAAAATAAAT
1 AAAAAT-AAAATAAAT
30839568 TAAACTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:30839563 original size:21 final size:22
Alignment explanation
Indices: 30839537--30839585 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
30839527 TTGAGGAGAG
30839537 AAAAATAAAATAAA-TAAAAAT
1 AAAAATAAAATAAACTAAAAAT
* * *
30839558 AAAAATAAATTAAACTCAAACT
1 AAAAATAAAATAAACTAAAAAT
30839580 AAAAAT
1 AAAAAT
30839586 CCCATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAATAAAATAAACTAAAAAT
Found at i:30854482 original size:44 final size:44
Alignment explanation
Indices: 30854407--30854828 Score: 339
Period size: 44 Copynumber: 9.5 Consensus size: 44
30854397 GTGGTGAATT
* * ** *
30854407 TTATCTCCATGAAAGTTGCAGTGGAGTAGATTAAAGCCAAAAATC
1 TTATCTCCCT-AAAGTTGCAGTGGAGCAGATTAAAGATACAAATC
* * *
30854452 TTGTCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATA-CAAATC
* * * * * * *
30854497 TTATCTCTCTAAAGTTACAGTAGAGAAAATTAAAGCTACAAACC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATC
* * * * *
30854541 TTATCCCCCTAAAGTTGCAATAGAGCAGATTAAAAATATTAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATA-CAAATC
* * * * * *
30854586 TTATCTCCCTGAAGCT-CTAGTGGAGTAGATTGAAGTTACAAAAC
1 TTATCTCCCTAAAGTTGC-AGTGGAGCAGATTAAAGATACAAATC
* * * *
30854630 TTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTTACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATC
* ** * *
30854674 TCATCTCCCTAAAGTTGCAGTGGAATAGATTGAAA-ATACGAGTC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AAAGATACAAATC
* * *
30854718 TCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATC
* * * * *
30854762 TAATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCA-ACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAG-ATACAAATC
* * *
30854806 CTATAC-CTCTAAAGTTGTAGTGG
1 TTAT-CTCCCTAAAGTTGCAGTGG
30854829 GTTAGAATGA
Statistics
Matches: 300, Mismatches: 69, Indels: 17
0.78 0.18 0.04
Matches are distributed among these distances:
43 3 0.01
44 221 0.74
45 76 0.25
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGATACAAATC
Found at i:30854697 original size:88 final size:89
Alignment explanation
Indices: 30854407--30854803 Score: 379
Period size: 89 Copynumber: 4.5 Consensus size: 89
30854397 GTGGTGAATT
* * * * * *
30854407 TTATCTCCATGAAAGTTGCAGTGGAGTAGATTAAAGCCA-AAAATCTTGTCTTCCTAAAGTTGCA
1 TTATCTCCCT-AAAGTTACAGTGGAGTAGATTGAAGCTACAAAA-CTTATCTCCCTAAAGTTGCA
*
30854471 GTGGAGCAGATTGAAGATAGCAAATC
64 GTGGAGCAGATTAAAGATAGCAAATC
* * * * * * * *
30854497 TTATCTCTCTAAAGTTACAGTAGAGAAAATTAAAGCTACAAACCTTATCCCCCTAAAGTTGCAAT
1 TTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGCTACAAAACTTATCTCCCTAAAGTTGCAGT
* * **
30854562 AGAGCAGATTAAAAATATTAAATC
66 GGAGCAGATTAAAGATAGCAAATC
* * * *
30854586 TTATCTCCCTGAAGCT-CTAGTGGAGTAGATTGAAGTTACAAAACTTATCTCCCTGAAGTTGCAG
1 TTATCTCCCTAAAGTTAC-AGTGGAGTAGATTGAAGCTACAAAACTTATCTCCCTAAAGTTGCAG
* * *
30854650 TGGAGCGGATTGAAGTTA-CAAATC
65 TGGAGCAGATTAAAGATAGCAAATC
* * * ** * ** *
30854674 TCATCTCCCTAAAGTTGCAGTGGAATAGATTGAAAATACGAGTCTCATCTCCCTAAAGTTGCAGT
1 TTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGCTACAAAACTTATCTCCCTAAAGTTGCAGT
* *
30854739 GGAGCAGATTAAAGCTA-CAAGTC
66 GGAGCAGATTAAAGATAGCAAATC
* * *
30854762 TAATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCAACAAA
1 TTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGCTACAAA
30854804 TCCTATACCT
Statistics
Matches: 245, Mismatches: 59, Indels: 8
0.79 0.19 0.03
Matches are distributed among these distances:
88 110 0.45
89 124 0.51
90 11 0.04
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (89 bp):
TTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGCTACAAAACTTATCTCCCTAAAGTTGCAGT
GGAGCAGATTAAAGATAGCAAATC
Found at i:30856402 original size:15 final size:12
Alignment explanation
Indices: 30856371--30856395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30856361 GTTCCTTTAT
30856371 TTTATTTTATTA
1 TTTATTTTATTA
30856383 TTTATTTTATTA
1 TTTATTTTATTA
30856395 T
1 T
30856396 GACTTATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:30856614 original size:28 final size:28
Alignment explanation
Indices: 30856582--30856639 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
30856572 ATTTATGTTG
30856582 TTCATATTTGTACATTTTTCGCTCATTA
1 TTCATATTTGTACATTTTTCGCTCATTA
*
30856610 TTCATATTTGTACATTTTTTGCTCATTA
1 TTCATATTTGTACATTTTTCGCTCATTA
30856638 TT
1 TT
30856640 TATTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (28 bp):
TTCATATTTGTACATTTTTCGCTCATTA
Found at i:30859027 original size:12 final size:11
Alignment explanation
Indices: 30858981--30859029 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
30858971 GTTCAATTGA
30858981 TTTTTAAT-AT
1 TTTTTAATAAT
*
30858991 TTTTT-CT-AT
1 TTTTTAATAAT
30859000 TTTTT-ATAAT
1 TTTTTAATAAT
30859010 TTTTTAATAAT
1 TTTTTAATAAT
30859021 TTATTTAAT
1 TT-TTTAAT
30859030 TGAATTGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 9 0.26
10 12 0.35
11 7 0.21
12 6 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:30862035 original size:46 final size:47
Alignment explanation
Indices: 30861923--30862037 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 47
30861913 CTGCACTATC
* * * *
30861923 TAGTGGTTTAACCACAT-T-TCTGTTCTGGCAGCTTGACTACATTTA
1 TAGTGGCTTCACCACATATATCTGTTATGGCAGCTTGACTACATATA
* * *
30861968 TGGTGGC-TCGACCACAGATATCTGTTATGGCAGCTT-AGCTGCA-ATA
1 TAGTGGCTTC-ACCACATATATCTGTTATGGCAGCTTGA-CTACATATA
30862014 TAGTGGCTTCACCACATATATCTG
1 TAGTGGCTTCACCACATATATCTG
30862038 ATCTAGCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
44 1 0.02
45 11 0.20
46 23 0.41
47 21 0.38
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (47 bp):
TAGTGGCTTCACCACATATATCTGTTATGGCAGCTTGACTACATATA
Found at i:30862183 original size:23 final size:23
Alignment explanation
Indices: 30862151--30862194 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
30862141 TGGGTAGGAA
30862151 GTTTTCTGAAAA-ATCTGCATTTT
1 GTTTTCTGAAAATAT-TGCATTTT
*
30862174 GTTTTTTGAAAATATTGCATT
1 GTTTTCTGAAAATATTGCATT
30862195 CACGTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (23 bp):
GTTTTCTGAAAATATTGCATTTT
Found at i:30865405 original size:21 final size:21
Alignment explanation
Indices: 30865381--30865423 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
30865371 TTTTATGGAT
30865381 TTTTGAAAATTATTTA-ATAAA
1 TTTT-AAAATTATTTACATAAA
* *
30865402 TTTTCAAATTTTTTACATAAA
1 TTTTAAAATTATTTACATAAA
30865423 T
1 T
30865424 ATTTCTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTAAAATTATTTACATAAA
Found at i:30867906 original size:5 final size:5
Alignment explanation
Indices: 30867896--30867926 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
30867886 TGTTAGTCTC
30867896 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
30867927 TTGAGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:30870132 original size:60 final size:59
Alignment explanation
Indices: 30870058--30870189 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 59
30870048 CAATCTCAAT
* * * * *
30870058 TAGTTGAGTGACCAAATTTAATAAATTGATAGTTAGGTGACCAAAAGAGAAAAGGGGCAA
1 TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAA-GGACAA
* *
30870118 TAGTTGGGTGACCAAATTAAAAAAATTGGTAGTTGGGTGACCAAAAAAGAAAAGGACAA
1 TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAAGGACAA
*
30870177 TAGTTGGCTGACC
1 TAGTTGGGTGACC
30870190 TATGTTGTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 17 0.27
60 47 0.73
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (59 bp):
TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAAGGACAA
Found at i:30876531 original size:61 final size:61
Alignment explanation
Indices: 30876452--30876585 Score: 191
Period size: 61 Copynumber: 2.2 Consensus size: 61
30876442 GTCACTCTTA
** *
30876452 TTTTTTGGTCATCCAACTATGAAAAGTTACAAAATGGTCAC-CTAATTATGTTTTTTTTTTC
1 TTTTTTGGTCATCCAACTATGAAAAGTTACAAAATAATCACTC-AACTATGTTTTTTTTTTC
*
30876513 TTTTTTGGTTA-CCAAACTATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
1 TTTTTTGGTCATCC-AACTATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
*
30876574 TTTTTTGATCAT
1 TTTTTTGGTCAT
30876586 GAGTGTGTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
60 2 0.03
61 61 0.95
62 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (61 bp):
TTTTTTGGTCATCCAACTATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
Found at i:30883184 original size:14 final size:15
Alignment explanation
Indices: 30883165--30883197 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30883155 ATATAATTAC
*
30883165 TTAATT-AATTTATT
1 TTAATTAAACTTATT
30883179 TTAATTAAACTTATT
1 TTAATTAAACTTATT
30883194 TTAA
1 TTAA
30883198 ATTTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAAACTTATT
Found at i:30887520 original size:23 final size:24
Alignment explanation
Indices: 30887476--30887519 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
30887466 TTAGCTAGAA
*
30887476 GAAAACAAAAAATGGTTTAAAAGG
1 GAAAACAAAAAATGCTTTAAAAGG
30887500 GAAAA-AAAAAA-GCTTTAAAA
1 GAAAACAAAAAATGCTTTAAAA
30887520 AAGGCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.16, T:0.16
Consensus pattern (24 bp):
GAAAACAAAAAATGCTTTAAAAGG
Found at i:30902011 original size:20 final size:20
Alignment explanation
Indices: 30901986--30902025 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30901976 AATATTTTCC
*
30901986 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
30902006 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
30902026 TCATTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:30904966 original size:2 final size:2
Alignment explanation
Indices: 30904959--30904988 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30904949 TAAATAACAA
30904959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30904989 TTAAACATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30911658 original size:22 final size:23
Alignment explanation
Indices: 30911623--30911666 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
30911613 ATTTTTTAAT
30911623 ATTTAAATTATTATATACTATAG
1 ATTTAAATTATTATATACTATAG
* *
30911646 ATTT-AATTTTTATATATTATA
1 ATTTAAATTATTATATACTATA
30911667 AATTACGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATTATTATATACTATAG
Found at i:30912214 original size:136 final size:135
Alignment explanation
Indices: 30911969--30912241 Score: 476
Period size: 136 Copynumber: 2.0 Consensus size: 135
30911959 AGATAGCCCA
* *
30911969 ACTCATTTTCAGAATAGTCAAGTACTCTATTACTATTTGATACCAATAATCCTATACTTAAAATG
1 ACTCATTTTCAGAATAGTCAAGGACTCTATTACTATTTGATACCAATAATCCTAGACTTAAAATG
30912034 AAAAAAAAAAAAAAGCAAAAGTGATGACTGTTCAGAGTTCTTTCTCACTCGTCAGAAACCCAGAA
66 AAAAAAAAAAAAAAGCAAAAGTGATGACTGTTCAGAGTTCTTTCTCACTCGTCAGAAACCCAGAA
30912099 CCAGC
131 CCAGC
*
30912104 ACTCATTTTCAGAATAGTCAAGGACTCAATGTTACTATTTGATACCAATAATCCTAGACTTAAAA
1 ACTCATTTTCAGAATAGTCAAGGACTC--TATTACTATTTGATACCAATAATCCTAGACTTAAAA
* *
30912169 TG-AAAAAAAATAAAAGCAAAAGTGATGACTGTTCAGAGTTCTTTCTCACTGGTCAGAAACCCAG
64 TGAAAAAAAAAAAAAAGCAAAAGTGATGACTGTTCAGAGTTCTTTCTCACTCGTCAGAAACCCAG
30912233 AACCAGC
129 AACCAGC
30912240 AC
1 AC
30912242 AACAGGCTCG
Statistics
Matches: 131, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
135 26 0.20
136 69 0.53
137 36 0.27
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (135 bp):
ACTCATTTTCAGAATAGTCAAGGACTCTATTACTATTTGATACCAATAATCCTAGACTTAAAATG
AAAAAAAAAAAAAAGCAAAAGTGATGACTGTTCAGAGTTCTTTCTCACTCGTCAGAAACCCAGAA
CCAGC
Found at i:30915468 original size:18 final size:18
Alignment explanation
Indices: 30915445--30915479 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30915435 GAAACTTGTC
* *
30915445 CAACAGGGTTAGAGTTTT
1 CAACAGAGTCAGAGTTTT
30915463 CAACAGAGTCAGAGTTT
1 CAACAGAGTCAGAGTTT
30915480 CGAATGGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (18 bp):
CAACAGAGTCAGAGTTTT
Found at i:30917583 original size:3 final size:3
Alignment explanation
Indices: 30917575--30917604 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30917565 CAGTACCATT
30917575 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
30917605 CAAATTCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:30922193 original size:22 final size:20
Alignment explanation
Indices: 30922155--30922203 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
30922145 ATGATTTGTA
* *
30922155 TATTTTTTCTAGATTATTTTT
1 TATTTTTTATAGATTA-TTTC
*
30922176 TATTTTTTATATATTTATTTC
1 TATTTTTTATAGA-TTATTTC
30922197 TATTTTT
1 TATTTTT
30922204 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTTTATAGATTATTTC
Found at i:30923997 original size:6 final size:6
Alignment explanation
Indices: 30923986--30924011 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30923976 CATCAATTGA
30923986 TTTTAG TTTTAG TTTTAG TTTTAG TT
1 TTTTAG TTTTAG TTTTAG TTTTAG TT
30924012 ATTATGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTTAG
Found at i:30928382 original size:30 final size:33
Alignment explanation
Indices: 30928314--30928392 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
30928304 TTGGCCCATT
*
30928314 AAAGAATAGATACTAATTTTCTTAAAAAAAAGA
1 AAAGAATAGATACTAAATTTCTTAAAAAAAAGA
*
30928347 AAAGAATAGATACTAAATTTC-T-CAAAAAA-A
1 AAAGAATAGATACTAAATTTCTTAAAAAAAAGA
*
30928377 CAAGAATAGATACTAA
1 AAAGAATAGATACTAA
30928393 TATTGAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.37
31 6 0.14
32 1 0.02
33 20 0.47
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (33 bp):
AAAGAATAGATACTAAATTTCTTAAAAAAAAGA
Found at i:30934235 original size:6 final size:6
Alignment explanation
Indices: 30934225--30934270 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
30934215 AAATTTTTTT
*
30934225 AAAAAT AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
30934271 GGTTCCAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:30936870 original size:30 final size:30
Alignment explanation
Indices: 30936831--30936887 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
30936821 TTTTATAAAT
30936831 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
30936861 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
30936888 AATAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:30937085 original size:13 final size:13
Alignment explanation
Indices: 30937067--30937115 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
30937057 TAAACTAAAC
30937067 TTTTCAAAAATAT
1 TTTTCAAAAATAT
*
30937080 TTTTCAAAAATCAC
1 TTTTCAAAAAT-AT
* *
30937094 TTTTCCAAACTAT
1 TTTTCAAAAATAT
*
30937107 TTCTCAAAA
1 TTTTCAAAA
30937116 GAAATGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAATAT
Found at i:30937716 original size:21 final size:20
Alignment explanation
Indices: 30937691--30937780 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 20
30937681 GTTTCTTTTG
30937691 AATCGATTGTTTATATGTTTA
1 AATCGATTGTTT-TATGTTTA
* *
30937712 AATCGATTG--TTATGGTGA
1 AATCGATTGTTTTATGTTTA
* * * *
30937730 AATACTGCTTCTTCTT-TTTTTG
1 AAT-C-GATTGTT-TTATGTTTA
30937752 AATCGATTGTTTATATGTTTA
1 AATCGATTGTTT-TATGTTTA
30937773 AATCGATT
1 AATCGATT
30937781 ATTAGCTTGA
Statistics
Matches: 50, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
18 9 0.18
19 3 0.06
20 9 0.18
21 22 0.44
22 5 0.10
23 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.50
Consensus pattern (20 bp):
AATCGATTGTTTTATGTTTA
Found at i:30937775 original size:61 final size:61
Alignment explanation
Indices: 30937686--30937803 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 61
30937676 GTACTGTTTC
*
30937686 TTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATG-GTGAAATACTGCTTCTTCTTT
1 TTTTGAATCGATTGTTTATATGTTTAAATCGATTATTA-GCGTGAAATACTGCTTCTTCTTT
* *
30937747 TTTTGAATCGATTGTTTATATGTTTAAATCGATTATTAGCTTGAAATATTGCTTCTT
1 TTTTGAATCGATTGTTTATATGTTTAAATCGATTATTAGCGTGAAATACTGCTTCTT
30937804 TTAAATCAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
60 1 0.02
61 52 0.98
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (61 bp):
TTTTGAATCGATTGTTTATATGTTTAAATCGATTATTAGCGTGAAATACTGCTTCTTCTTT
Found at i:30942042 original size:18 final size:19
Alignment explanation
Indices: 30942019--30942054 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30942009 AAACCAATGT
30942019 ATAAAAAATGAA-TAATAA
1 ATAAAAAATGAACTAATAA
*
30942037 ATAAAATATGAACTAATA
1 ATAAAAAATGAACTAATA
30942055 TAAGTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (19 bp):
ATAAAAAATGAACTAATAA
Found at i:30944134 original size:12 final size:12
Alignment explanation
Indices: 30944117--30944141 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30944107 TCCTGCTTTA
30944117 GTAGAGGAAAGT
1 GTAGAGGAAAGT
30944129 GTAGAGGAAAGT
1 GTAGAGGAAAGT
30944141 G
1 G
30944142 ATGATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
GTAGAGGAAAGT
Found at i:30949935 original size:16 final size:16
Alignment explanation
Indices: 30949914--30949950 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
30949904 TTGATTCACT
*
30949914 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
30949930 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
30949946 GTAAT
1 GTAAT
30949951 AGGTAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:30950019 original size:44 final size:46
Alignment explanation
Indices: 30949932--30950024 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
30949922 ATAGATGCGT
*
30949932 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
30949978 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
30950022 AAT
1 AAT
30950025 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:30950020 original size:39 final size:42
Alignment explanation
Indices: 30949932--30950040 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 42
30949922 ATAGATGCGT
*
30949932 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTT--ATGG
30949978 AATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTATGG
* *
30950017 AATGGAATAGAGGTGTAATAGTAT
1 AATGGAATAGAGGCGTAATGGTAT
30950041 AAGGAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
39 23 0.38
40 1 0.02
43 1 0.02
44 13 0.22
45 3 0.05
46 19 0.32
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (42 bp):
AATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTATGG
Found at i:30955665 original size:39 final size:40
Alignment explanation
Indices: 30955593--30955740 Score: 194
Period size: 39 Copynumber: 3.6 Consensus size: 40
30955583 ACCAAAAATT
30955593 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
30955637 TATTTTAAAATTAAAAAAATT-AAAAAAGTATTTT-AAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
* * *
30955675 CATTTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
30955716 TATTTTAAAATTAAAATAA-TAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAA
30955741 TAATAAAAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
38 13 0.14
39 29 0.31
40 27 0.28
41 14 0.15
43 6 0.06
44 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:30955695 original size:9 final size:9
Alignment explanation
Indices: 30955629--30955702 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
30955619 AAAAAAGTAT
30955629 TTTAAAAATA
1 TTTAAAAA-A
*
30955639 TTT-TAAAA
1 TTTAAAAAA
*
30955647 TTAAAAAAA
1 TTTAAAAAA
*
30955656 TTAAAAAAGTA
1 TTTAAAAA--A
*
30955667 TTTTAAAACA
1 -TTTAAAAAA
*
30955677 TTT-TAAAA
1 TTTAAAAAA
30955685 TTTAAAAAA
1 TTTAAAAAA
30955694 TTTAAAAAA
1 TTTAAAAAA
30955703 AGTATTTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
8 9 0.18
9 31 0.61
10 4 0.08
11 1 0.02
12 6 0.12
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:30960238 original size:2 final size:2
Alignment explanation
Indices: 30960231--30960261 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30960221 ATAATGGTTA
30960231 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
30960262 ACGCATCCTA
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:30960360 original size:2 final size:2
Alignment explanation
Indices: 30960305--30960345 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
30960295 AAGCAAATCA
*
30960305 AT AT AT CAT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30960346 TCGGAATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30960455 original size:6 final size:6
Alignment explanation
Indices: 30960402--30960465 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
30960392 AAAAATGTTT
* * * *
30960402 AATATA AATAAA ACGTAAA AGTAAA AGTAAA AAT-AA AAT-AA AAT-AA
1 AATAAA AATAAA A-ATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
30960448 AATAAAA AATAAA AATAA
1 AAT-AAA AATAAA AATAA
30960466 TAGTAATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
5 15 0.29
6 27 0.52
7 10 0.19
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:30960461 original size:5 final size:5
Alignment explanation
Indices: 30960402--30960454 Score: 52
Period size: 5 Copynumber: 9.4 Consensus size: 5
30960392 AAAAATGTTT
30960402 AATATA AATAA AACGTAA AAGTAA AAGTAAA AATAA AATAA AATAA AATAA
1 AATA-A AATAA AA--TAA AA-TAA AA-T-AA AATAA AATAA AATAA AATAA
30960453 AA
1 AA
30960455 AATAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
5 22 0.50
6 13 0.30
7 9 0.20
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:30962280 original size:130 final size:131
Alignment explanation
Indices: 30962042--30962356 Score: 478
Period size: 130 Copynumber: 2.4 Consensus size: 131
30962032 TGGATGTGAT
* *
30962042 CTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTGCTCTTCACTCTATTCCACTGTTGCCCAGG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTGCTCTTCACTCTATTCCACTGTTGCCCAGA
30962106 GAGATAGAACTACCAGCTTCAATGTACTCCACCGTAATCAGGGAGGTAAAATCCGCCATCTTCGA
66 GAGATAGAACTACCAGCTTCAATGTACTCCACCGTAATCAGGGAGGTAAAATCCGCCATCTTCGA
30962171 C
131 C
* *
30962172 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGGT-TTCTTTC-GTCTATTCCACTGTTGCCCAG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTGCTC-TTCACTCTATTCCACTGTTGCCCAG
** * * *
30962235 AGAGATAGAACTA-TTGACTTTAATGTACTCCACCGTAATCGGGGAGGTAAAATCCGCCATCTTT
65 AGAGATAGAACTACCAG-CTTCAATGTACTCCACCGTAATCAGGGAGGTAAAATCCGCCATCTTC
30962299 GAC
129 GAC
**
30962302 CTGCTCCACTATTGCTTAGGGAGATAAGATCT-GTAATCTTCACTCTATTCCACTG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTGCTCTTCACTCTATTCCACTG
30962357 CCAAATACAG
Statistics
Matches: 169, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
129 6 0.04
130 158 0.93
131 5 0.03
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (131 bp):
CTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTGCTCTTCACTCTATTCCACTGTTGCCCAGA
GAGATAGAACTACCAGCTTCAATGTACTCCACCGTAATCAGGGAGGTAAAATCCGCCATCTTCGA
C
Found at i:30962492 original size:46 final size:46
Alignment explanation
Indices: 30962442--30962635 Score: 130
Period size: 46 Copynumber: 4.3 Consensus size: 46
30962432 ATCTACTTTG
30962442 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
* ** * * ** * *
30962488 CTGCCAAATACAGGGAGATAGAGTTAT-C-GGCTTCAATGTACTCCA
1 CTGCCAAATACAGGAAGGCA-AGATCTGCAATCTTCAATCTATTCCA
* * * * * * * * * * *
30962533 CTG--TAGT-CAGGGAGGTAAAATTTACCATCTTCGATCTGCTT-CG
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT-ATTCCA
* *
30962576 TTGCCAAATACAGGAAGGCAAGATCTGTAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
30962622 CTGCCAAATACAGG
1 CTGCCAAATACAGG
30962636 GAGATAGAGT
Statistics
Matches: 104, Mismatches: 36, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
41 3 0.03
42 10 0.10
43 12 0.12
44 1 0.01
45 20 0.19
46 54 0.52
47 4 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
Found at i:30962501 original size:134 final size:134
Alignment explanation
Indices: 30962327--30962708 Score: 665
Period size: 134 Copynumber: 2.9 Consensus size: 134
30962317 TTAGGGAGAT
*
30962327 AAGATCTGTAATCTTCACTCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
1 AAGATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
* * *
30962392 TACTCCTCTGTGGTCAGGGAGGTAAAATCTGCCATCTTCTATCTACTTTGCTGCCAAATACAGGA
66 TACTCCTCTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTTCGCTGCCAAATACAGGA
30962457 AGGC
131 AGGC
*
30962461 AAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
1 AAGATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
* * * * *
30962526 TACTCCACTGTAGTCAGGGAGGTAAAATTTACCATCTTCGATCTGCTTCGTTGCCAAATACAGGA
66 TACTCCTCTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTTCGCTGCCAAATACAGGA
30962591 AGGC
131 AGGC
30962595 AAGATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
1 AAGATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
*
30962660 TACTCCTCTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTC
66 TACTCCTCTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTTC
30962709 NNNNNNNNNN
Statistics
Matches: 234, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 234 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (134 bp):
AAGATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATG
TACTCCTCTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTTCGCTGCCAAATACAGGA
AGGC
Found at i:30962535 original size:45 final size:45
Alignment explanation
Indices: 30962473--30962665 Score: 117
Period size: 45 Copynumber: 4.3 Consensus size: 45
30962463 GATCTGCAAT
* *
30962473 CTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCAG
* * * * * * * *
30962518 CTTCAATGTACTCCACTG--TAGT-CAGGGAGGTAAAATTTACCAT
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGAT-AGAGTTATCAG
* * * ** * * * *
30962561 CTTCGATCTGCTTCGTTGCCAAATACAGGAAGGCA-AGA-TCTGTAAT
1 CTTCAATCTACTCCACTGCCAAATACAGGGA-G-ATAGAGT-TATCAG
* *
30962607 CTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCAG
*
30962652 CTTCAATGTACTCC
1 CTTCAATCTACTCC
30962666 TCTGTAGTCA
Statistics
Matches: 102, Mismatches: 37, Indels: 18
0.65 0.24 0.11
Matches are distributed among these distances:
42 8 0.08
43 20 0.20
44 1 0.01
45 37 0.36
46 35 0.34
47 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (45 bp):
CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCAG
Found at i:30963028 original size:46 final size:46
Alignment explanation
Indices: 30962942--30963037 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
30962932 CCTCTGTAGT
* * * * *
30962942 CAGGGAGGTAAAATCTGCCATCTACGATCTGCTTCCCTGCCAAATA
1 CAGGAAGGCAAAATCTGCAATCTACAATCTGATTCCCTGCCAAATA
*
30962988 CAGGAAGGCAAAATCTGCAATCTTCAATCT-ATTCCACTGCCAAATA
1 CAGGAAGGCAAAATCTGCAATCTACAATCTGATTCC-CTGCCAAATA
30963034 CAGG
1 CAGG
30963038 GAGATAGAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 4 0.09
46 39 0.91
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (46 bp):
CAGGAAGGCAAAATCTGCAATCTACAATCTGATTCCCTGCCAAATA
Found at i:30963151 original size:42 final size:42
Alignment explanation
Indices: 30963104--30963282 Score: 292
Period size: 42 Copynumber: 4.3 Consensus size: 42
30963094 CATCTTCGAC
30963104 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGT
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGT
* *
30963146 CTGCTCCACTATTGCTTAGGGAGATAAGA-CT-TGATGC-GAT
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTG-T
*
30963186 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGT
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGT
30963228 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGT
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGT
*
30963270 CTGCTCCAATATT
1 CTGCTCCACTATT
30963283 TTTAAAATAC
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
39 1 0.01
40 33 0.26
41 4 0.03
42 87 0.69
43 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (42 bp):
CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGT
Found at i:30963202 original size:82 final size:82
Alignment explanation
Indices: 30963104--30963256 Score: 297
Period size: 82 Copynumber: 1.9 Consensus size: 82
30963094 CATCTTCGAC
*
30963104 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTAGGGAG
30963169 ATAAGACTTGATGCGAT
66 ATAAGACTTGATGCGAT
30963186 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTAGGGAG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTAGGGAG
30963251 ATAAGA
66 ATAAGA
30963257 TCTGTGGTTC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (82 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTAGGGAG
ATAAGACTTGATGCGAT
Found at i:30963784 original size:31 final size:31
Alignment explanation
Indices: 30963749--30963852 Score: 95
Period size: 31 Copynumber: 3.2 Consensus size: 31
30963739 AAACTTCAAT
30963749 TTTGATCCCTCTATTATGCTTAAATTTTATA
1 TTTGATCCCTCTATTATGCTTAAATTTTATA
* *
30963780 TTTGACCACTACCCTTTAGATT-TGCCTAAATTTTA-A
1 TTTG---A-T-CCCTCT--ATTATGCTTAAATTTTATA
*
30963816 TTTTGATCTCTCTATTATGCTTAAATTTTATA
1 -TTTGATCCCTCTATTATGCTTAAATTTTATA
30963848 TTTGA
1 TTTGA
30963853 CCACTACCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
30 3 0.05
31 21 0.36
32 5 0.09
33 1 0.02
34 2 0.03
35 1 0.02
36 6 0.10
37 16 0.28
38 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (31 bp):
TTTGATCCCTCTATTATGCTTAAATTTTATA
Found at i:30974711 original size:80 final size:81
Alignment explanation
Indices: 30974611--30974891 Score: 411
Period size: 84 Copynumber: 3.4 Consensus size: 81
30974601 CTGAGATGTG
*
30974611 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-CGAAAAAAATGAGAT
1 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATGAGAT
**
30974675 GTTTTTTTTTTTATTT
66 GTTTTTAATTTTATTT
*
30974691 TTTTATTTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCCAAAAAAAAATGAG
1 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-CC-AAAAAAAATGAG
30974756 ATGTGTTTTAATTTTATTT
64 ATGT-TTTTAATTTTATTT
* * * *
30974775 TTTTATTTTTTAAATATTAATTAGAATATTTTTCGGGCTTTAAATTCCTCCAAAAAAAACTGAGA
1 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAA-TGAGA
*
30974840 TGTGTTTAATTTTATTT
65 TGTTTTTAATTTTATTT
* *
30974857 TTTAAAAATTTTAAATATTAATTAGAATATTTGTC
1 TTT-TAATTTTTAAATATTAATTAGAATATTTGTC
30974892 CGGTCTAAAA
Statistics
Matches: 183, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
80 48 0.26
82 25 0.14
83 52 0.28
84 58 0.32
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (81 bp):
TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATGAGAT
GTTTTTAATTTTATTT
Found at i:30974828 original size:83 final size:83
Alignment explanation
Indices: 30974611--30974891 Score: 417
Period size: 83 Copynumber: 3.4 Consensus size: 83
30974601 CTGAGATGTG
*
30974611 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-C-GAAAAAAATGAGA
1 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAAATGAGA
**
30974674 TGT-TTTTTTTTTTATTT
66 TGTGTTTTAATTTTATTT
*
30974691 TTTTATTTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCCAAAAAAAAATGAG
1 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-CCAAAAAAAAATGAG
30974756 ATGTGTTTTAATTTTATTT
65 ATGTGTTTTAATTTTATTT
* * * * *
30974775 TTTTATTTTTTAAATATTAATTAGAATATTTTTCGGGCTTTAAATTCCTCCAAAAAAAACTGAGA
1 TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAAATGAGA
30974840 TGTG-TTTAATTTTATTT
66 TGTGTTTTAATTTTATTT
* *
30974857 TTTAAAAATTTTAAATATTAATTAGAATATTTGTC
1 TTT-TAATTTTTAAATATTAATTAGAATATTTGTC
30974892 CGGTCTAAAA
Statistics
Matches: 184, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
80 48 0.26
82 17 0.09
83 61 0.33
84 58 0.32
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (83 bp):
TTTTAATTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAAATGAGA
TGTGTTTTAATTTTATTT
Found at i:30984465 original size:19 final size:19
Alignment explanation
Indices: 30984443--30984479 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30984433 TTTAAAATAC
*
30984443 TTTTAAAATATTTTTTTAT
1 TTTTAAAATAATTTTTTAT
30984462 TTTTAAAATAATTTTTTA
1 TTTTAAAATAATTTTTTA
30984480 ATGTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAAAATAATTTTTTAT
Found at i:30984486 original size:20 final size:19
Alignment explanation
Indices: 30984444--30984486 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
30984434 TTAAAATACT
* *
30984444 TTTAAAATATTTTTTTATT
1 TTTAAAATATTTTTTAATG
30984463 TTTAAAATAATTTTTTAATG
1 TTTAAAAT-ATTTTTTAATG
30984483 TTTA
1 TTTA
30984487 TTTAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTAAAATATTTTTTAATG
Found at i:30995300 original size:9 final size:9
Alignment explanation
Indices: 30995283--30995452 Score: 64
Period size: 9 Copynumber: 18.2 Consensus size: 9
30995273 TTTTGGTACG
*
30995283 ATAACTTTT
1 ATAATTTTT
30995292 ATAATTTTT
1 ATAATTTTT
*
30995301 -TACGAATTTT
1 ATA--ATTTTT
*
30995311 ATATTTCTTT
1 ATAATT-TTT
*
30995321 ATATTTTTT
1 ATAATTTTT
30995330 ATAATTTTAT
1 ATAATTTT-T
*
30995340 AAAATTTTCCT
1 ATAATTTT--T
* *
30995351 GT-ATTTCT
1 ATAATTTTT
30995359 AT-ATATTTT
1 ATAAT-TTTT
30995368 AT-ATTTTT
1 ATAATTTTT
* *
30995376 CTAATTCTTA
1 ATAATT-TTT
*
30995386 ATAAATTTT
1 ATAATTTTT
*
30995395 A-ATTTTTT
1 ATAATTTTT
30995403 CAT-ATTTTT
1 -ATAATTTTT
** *
30995412 ATTGAAAATTA
1 A-T-AATTTTT
30995423 ATAATTTTT
1 ATAATTTTT
30995432 ATAATTTTT
1 ATAATTTTT
30995441 ATTAATTTTT
1 A-TAATTTTT
30995451 AT
1 AT
30995453 TATCTTTTTT
Statistics
Matches: 120, Mismatches: 26, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
8 17 0.14
9 54 0.45
10 42 0.35
11 7 0.06
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:30995446 original size:10 final size:10
Alignment explanation
Indices: 30995424--30995454 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
30995414 TGAAAATTAA
30995424 TAATTTTTA-
1 TAATTTTTAT
30995433 TAATTTTTAT
1 TAATTTTTAT
30995443 TAATTTTTAT
1 TAATTTTTAT
30995453 TA
1 TA
30995455 TCTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TAATTTTTAT
Found at i:30996063 original size:88 final size:87
Alignment explanation
Indices: 30995875--30996188 Score: 350
Period size: 88 Copynumber: 3.6 Consensus size: 87
30995865 CCGACTCTGG
* * *
30995875 CTTTTTTGATGCATTTTGACAATTCAAGTACCCAATTGAGTG-AAAAAAAGCATAGGC-T-ATTT
1 CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTGAAAAAAAAGCATAGGCTTAATTT
*
30995937 TTTTTTTTTTAAGTTTGAGGGT
66 TTTTTTTTTTAAGTTTGAAGGT
* * *
30995959 CTTTTTTTATATATTTTGACAGTTCAAGTGCCCAATTAAGTGAAAAAAAAGCATAGGCTTAATTG
1 CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTGAAAAAAAAGCATAGGCTTAATT-
* *
30996024 TTTTTTTTTTTTAGTTTGAAGGC
65 TTTTTTTTTTTAAGTTTGAAGGT
* * * * * *
30996047 CTTTTTTTATACATTTTGGCAGTTAAAGTGCCCAATTAAGTGAGAGAAAAAAAACA-AGGGTTTA
1 CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGT--GA-AAAAAAAGCATA-GGCTTA
*
30996111 ATTTTATTTTATTTTTAAGTTTGAAAGT
62 ATTTT-TTTT-TTTTTAAGTTTGAAGGT
* * *
30996139 C-TTTTTGATACATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAA
1 CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTG-AAAAAAAA
30996189 TAAGGGCTTA
Statistics
Matches: 195, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
84 36 0.18
85 15 0.08
86 1 0.01
87 3 0.02
88 58 0.30
89 8 0.04
90 6 0.03
91 53 0.27
92 15 0.08
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (87 bp):
CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTGAAAAAAAAGCATAGGCTTAATTT
TTTTTTTTTTAAGTTTGAAGGT
Found at i:30996150 original size:91 final size:87
Alignment explanation
Indices: 30995875--30996224 Score: 327
Period size: 88 Copynumber: 4.0 Consensus size: 87
30995865 CCGACTCTGG
* * * * * * *
30995875 CTTTTTTGATGCATTTTGACAATTCAAGTACCCAATTGAGTG-AAAAAAAGCATAGGC-T-ATTT
1 CTTTTTTTATACATTTTGACAGTTAAAGTGCCCAATTAAGTGAAAAAAAAACATAGGCTTAATTT
*
30995937 TTTTTTTTTTAAGTTTGAGGGT
66 TTTTTTTTTTAAGTTTGAAGGT
* * *
30995959 CTTTTTTTATATATTTTGACAGTTCAAGTGCCCAATTAAGTGAAAAAAAAGCATAGGCTTAATTG
1 CTTTTTTTATACATTTTGACAGTTAAAGTGCCCAATTAAGTGAAAAAAAAACATAGGCTTAATT-
* *
30996024 TTTTTTTTTTTTAGTTTGAAGGC
65 TTTTTTTTTTTAAGTTTGAAGGT
* *
30996047 CTTTTTTTATACATTTTGGCAGTTAAAGTGCCCAATTAAGTGAGAGAAAAAAAACA-AGGGTTTA
1 CTTTTTTTATACATTTTGACAGTTAAAGTGCCCAATTAAGT--GA-AAAAAAAACATA-GGCTTA
*
30996111 ATTTTATTTTATTTTTAAGTTTGAAAGT
62 ATTTT-TTTT-TTTTTAAGTTTGAAGGT
* * * * * *
30996139 C-TTTTTGATACATTTTGAAAGTTCAAA-TACCCAATTGAGTGCAAAAAAAATA-AGGGCTTAAT
1 CTTTTTTTATACATTTTGACAGTT-AAAGTGCCCAATTAAGTGAAAAAAAAACATA-GGCTTAAT
*
30996201 TGCTTCTTCTTTTTTAAAGTTTGA
64 T--TT-TT-TTTTTTTAAGTTTGA
30996225 GAGCTTTTCA
Statistics
Matches: 225, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
84 36 0.16
85 15 0.07
86 1 0.00
87 3 0.01
88 77 0.34
89 1 0.00
90 21 0.09
91 53 0.24
92 18 0.08
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (87 bp):
CTTTTTTTATACATTTTGACAGTTAAAGTGCCCAATTAAGTGAAAAAAAAACATAGGCTTAATTT
TTTTTTTTTTAAGTTTGAAGGT
Found at i:30996398 original size:11 final size:12
Alignment explanation
Indices: 30996367--30996399 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30996357 TTTCCCTCAA
30996367 TTTCATTCTTTT
1 TTTCATTCTTTT
*
30996379 TTTCCTTCTTTT
1 TTTCATTCTTTT
30996391 TTT-ATTCTT
1 TTTCATTCTT
30996400 CCATTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCATTCTTTT
Found at i:30996917 original size:21 final size:21
Alignment explanation
Indices: 30996876--30996915 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
30996866 CGAATATAAT
30996876 AAATATATTTTCTTATTTTTA
1 AAATATATTTTCTTATTTTTA
*
30996897 AAATAT-TTTTTTTATTTTT
1 AAATATATTTTCTTATTTTT
30996916 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
AAATATATTTTCTTATTTTTA
Found at i:30996934 original size:28 final size:28
Alignment explanation
Indices: 30996881--30996935 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
30996871 ATAATAAATA
*
30996881 TATTTTCTTATTTTTAAAATATTTTTTT
1 TATTTTCTTATTTTTAAAATAATTTTTT
*
30996909 TATTTT-TTATTTTTAAAATAAATTTTT
1 TATTTTCTTATTTTTAAAATAATTTTTT
30996936 GGTGTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (28 bp):
TATTTTCTTATTTTTAAAATAATTTTTT
Found at i:30997478 original size:23 final size:22
Alignment explanation
Indices: 30997440--30997499 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
30997430 TAATTTTAAA
30997440 AATATATTTTAT-ATT-AATATT
1 AATATATTTTATAATTAAAT-TT
30997461 AATATATTTTTATAATTAAATTT
1 AATATA-TTTTATAATTAAATTT
30997484 AA-ATAATTTT-TAATTA
1 AATAT-ATTTTATAATTA
30997500 TTTAATTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.34
22 12 0.34
23 8 0.23
24 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTTTATAATTAAATTT
Found at i:30997506 original size:24 final size:23
Alignment explanation
Indices: 30997440--30997507 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
30997430 TAATTTTAAA
30997440 AATATA-TTTTA-TA-TTAATATT
1 AATATATTTTTATTATTTAAT-TT
* *
30997461 AATATATTTTTATAATTAAATTT
1 AATATATTTTTATTATTTAATTT
30997484 AA-ATAATTTTTAATTATTTAATTT
1 AATAT-ATTTTT-ATTATTTAATTT
30997508 GAATTGAGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.16
22 7 0.18
23 11 0.29
24 14 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATATTTTTATTATTTAATTT
Found at i:30999330 original size:14 final size:14
Alignment explanation
Indices: 30999311--30999348 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
30999301 CTTATAGGTA
30999311 AAATCATAAAATAT
1 AAATCATAAAATAT
30999325 AAATCATAAAATAT
1 AAATCATAAAATAT
30999339 AAATCATAAA
1 AAATCATAAA
30999349 TAATATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATCATAAAATAT
Found at i:30999657 original size:27 final size:27
Alignment explanation
Indices: 30999611--30999662 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
30999601 CTTACAAATT
* * *
30999611 ATTATAACCTATTAAGATAACACGATG
1 ATTATAACATATAAAAATAACACGATG
*
30999638 ATTATAACATATAAAAATAATACGA
1 ATTATAACATATAAAAATAACACGA
30999663 ATACGATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.29
Consensus pattern (27 bp):
ATTATAACATATAAAAATAACACGATG
Found at i:31007396 original size:104 final size:103
Alignment explanation
Indices: 31007120--31007399 Score: 515
Period size: 103 Copynumber: 2.7 Consensus size: 103
31007110 AAGGAGGCTT
31007120 ATAGGTAGAAATGCTCAAAAGTATTGAGAGTGGTAACTTCGATTTGAATACAATCTAATTTCACT
1 ATAGGTAGAAATGCTCAAAAGTATTGAGAGTGGTAACTTCGATTTGAATACAATCTAATTTCACT
* *
31007185 CCTCACTCGATGTAATGATATCCTTTATCGGAAGCTCA
66 CCCCACTCGATGTAATGATATCCTTTATCAGAAGCTCA
*
31007223 ATAGGTAGAAATGCTCAGAAGTATTGAGAGTGGTAACTTCGATTTGAATACAATCTAATTTCACT
1 ATAGGTAGAAATGCTCAAAAGTATTGAGAGTGGTAACTTCGATTTGAATACAATCTAATTTCACT
31007288 CCCCACTCGATGTAATGATATCCTTTATCAGAAGCTCA
66 CCCCACTCGATGTAATGATATCCTTTATCAGAAGCTCA
*
31007326 ATAGGTAGAAATGCTCAAAAAGTATTGAGAGTGGTAACTTCGATTTGAATACAATTTAATTTCAC
1 ATAGGTAGAAATGCTC-AAAAGTATTGAGAGTGGTAACTTCGATTTGAATACAATCTAATTTCAC
31007391 TCCCCACTC
65 TCCCCACTC
31007400 AAGAGGAATC
Statistics
Matches: 171, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
103 116 0.68
104 55 0.32
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (103 bp):
ATAGGTAGAAATGCTCAAAAGTATTGAGAGTGGTAACTTCGATTTGAATACAATCTAATTTCACT
CCCCACTCGATGTAATGATATCCTTTATCAGAAGCTCA
Found at i:31016529 original size:88 final size:88
Alignment explanation
Indices: 31016349--31016554 Score: 258
Period size: 88 Copynumber: 2.4 Consensus size: 88
31016339 TTTGTACTTG
* * * * * *
31016349 GGTATTTGAACTTTC-AAATGCATCAAAAAGGCCTCAAGCATTTTCAAAAATAGCAATTAAGCTC
1 GGTACTTGAACTTTCAAAATGCATAAAAAAAGCCTCAAACATTTTCAAAAATAACAATTAAGATC
31016413 CTATTTTTTTTTACACTTAATTT
66 CTATTTTTTTTTACACTTAATTT
*
31016436 GGTACTTGAACTTTCAAAATGCATAAAAAAAGCTCTCAAACTTTTTCAAGAAA-AACAATTAAGA
1 GGTACTTGAACTTTCAAAATGCATAAAAAAAGC-CTCAAACATTTTCAA-AAATAACAATTAAGA
*
31016500 TTCT-TTTTTTTTTACACTTAA-TT
64 TCCTATTTTTTTTTACACTTAATTT
** *
31016523 GAGTACTTGAACTGCCAATATGCATAAAAAAA
1 G-GTACTTGAACTTTCAAAATGCATAAAAAAA
31016555 TGTCCTTTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
87 17 0.16
88 59 0.57
89 25 0.24
90 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (88 bp):
GGTACTTGAACTTTCAAAATGCATAAAAAAAGCCTCAAACATTTTCAAAAATAACAATTAAGATC
CTATTTTTTTTTACACTTAATTT
Found at i:31016735 original size:9 final size:9
Alignment explanation
Indices: 31016698--31016797 Score: 52
Period size: 9 Copynumber: 11.2 Consensus size: 9
31016688 TTAAATTTTA
31016698 ATAAAAA-T
1 ATAAAAATT
*
31016706 ATAGAAATGT
1 ATAAAAAT-T
*
31016716 AGAAAAATT
1 ATAAAAATT
*
31016725 ATAAAATTT
1 ATAAAAATT
*
31016734 AT-AAAGTCGT
1 ATAAAAAT--T
31016744 A-AAAAATT
1 ATAAAAATT
31016752 A-AAAAATGT
1 ATAAAAAT-T
31016761 A-AAGAAA-T
1 ATAA-AAATT
31016769 AT-AAAATT
1 ATAAAAATT
*
31016777 CATAAAAAAT
1 -ATAAAAATT
31016787 ATAAAAATT
1 ATAAAAATT
31016796 AT
1 AT
31016798 TGTACCAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
7 3 0.04
8 22 0.31
9 26 0.36
10 21 0.29
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (9 bp):
ATAAAAATT
Done.