Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 135 of 190
Found at i:39865200 original size:48 final size:48
Alignment explanation
Indices: 39865144--39865243 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
39865134 CTTCGGGGGA
39865144 ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
1 ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
* * *
39865192 ATGGGCGGCATGGGTGACATGATGGGTGGCATGGGCGGCATGGGTGGC
1 ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
39865240 ATGG
1 ATGG
39865244 ATGAATTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.15, C:0.17, G:0.52, T:0.16
Consensus pattern (48 bp):
ATGGGCGGCATGGGCGACATGATGGGCGGCATGGGCGGCATGGGCGGC
Found at i:39865217 original size:30 final size:30
Alignment explanation
Indices: 39865183--39865242 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
39865173 CATGGGCGGC
39865183 ATGGGCGGCATGGGCGGCATGGGTGACATG
1 ATGGGCGGCATGGGCGGCATGGGTGACATG
* *
39865213 ATGGGTGGCATGGGCGGCATGGGTGGCATG
1 ATGGGCGGCATGGGCGGCATGGGTGACATG
39865243 GATGAATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.18
Consensus pattern (30 bp):
ATGGGCGGCATGGGCGGCATGGGTGACATG
Found at i:39866155 original size:60 final size:60
Alignment explanation
Indices: 39866081--39866202 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
39866071 TTTGTCTCAT
*
39866081 GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTGTTTTTACACTAACTGCAG
1 GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTATTTTTACACTAACTGCAG
* *
39866141 GTTACAGTATTATTACAGTATTTAATTTTACAATTATTGTTATTTTTACACTAATTGCAG
1 GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTATTTTTACACTAACTGCAG
39866201 GT
1 GT
39866203 AAATATACCG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (60 bp):
GTTACAGTATTATTACAGTATTTAATTTTACAATTATCGTTATTTTTACACTAACTGCAG
Found at i:39866693 original size:20 final size:20
Alignment explanation
Indices: 39866660--39866712 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
39866650 TTTTATACAG
39866660 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
39866679 ATTTTGAATTTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
39866699 ATTTTGTAATTTTT
1 ATTTTG-AATTTTT
39866713 GTTGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:39866857 original size:23 final size:23
Alignment explanation
Indices: 39866827--39866870 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
39866817 CAACTCGAAC
39866827 TTATTCAAGTTGGCTT-GAATTGT
1 TTATTCAAGTTGG-TTCGAATTGT
39866850 TTATTCAAGTTGGTTCGAATT
1 TTATTCAAGTTGGTTCGAATT
39866871 ATTCGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.48
Consensus pattern (23 bp):
TTATTCAAGTTGGTTCGAATTGT
Found at i:39874098 original size:13 final size:14
Alignment explanation
Indices: 39874076--39874107 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39874066 TTATGTGTTC
39874076 TATTTATTTTTAAT
1 TATTTATTTTTAAT
39874090 TATTT-TTTTTAAT
1 TATTTATTTTTAAT
39874103 T-TTTA
1 TATTTA
39874108 AATCCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTTATTTTTAAT
Found at i:39876573 original size:46 final size:46
Alignment explanation
Indices: 39876470--39876630 Score: 267
Period size: 46 Copynumber: 3.6 Consensus size: 46
39876460 TACGTATGAT
* *
39876470 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
39876513 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
39876559 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
39876605 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
39876631 AGTACTAAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
43 10 0.09
44 5 0.04
45 28 0.25
46 69 0.62
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:39884701 original size:25 final size:25
Alignment explanation
Indices: 39884653--39884701 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
39884643 CGTTAGTTCA
* * *
39884653 ATTTTTTTTCCAAATTTATGTTTTT
1 ATTTTTTTTCCAAACTCATATTTTT
*
39884678 ATTTTTTTTTCAAACTCATATTTT
1 ATTTTTTTTCCAAACTCATATTTT
39884702 GACATATACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTTTTTCCAAACTCATATTTTT
Found at i:39892601 original size:51 final size:51
Alignment explanation
Indices: 39892545--39892653 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
39892535 AAATGGGTTG
* * *
39892545 TTTTTTTTAATGGAGCCTATCTGAGAGGTGCCAATGAATATTTTATATTAA
1 TTTTTTTTAATGGAGCCTATCTGACAGGCGCCAATCAATATTTTATATTAA
*
39892596 TTTTTTTTAATGGCGCCTATCTGACAGGCGCCAATCAATATTTTATATTAA
1 TTTTTTTTAATGGAGCCTATCTGACAGGCGCCAATCAATATTTTATATTAA
*
39892647 ATTTTTT
1 TTTTTTT
39892654 AATAAAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (51 bp):
TTTTTTTTAATGGAGCCTATCTGACAGGCGCCAATCAATATTTTATATTAA
Found at i:39894800 original size:16 final size:16
Alignment explanation
Indices: 39894781--39894819 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
39894771 AAAATCAAAT
39894781 AAAATTACATTATATA
1 AAAATTACATTATATA
39894797 AAAATTACATTATATA
1 AAAATTACATTATATA
39894813 AAAATTA
1 AAAATTA
39894820 AATGAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTACATTATATA
Found at i:39895027 original size:60 final size:60
Alignment explanation
Indices: 39894934--39895053 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
39894924 AATACTAAAC
* *
39894934 TAAACACAATAATTTATAACTAAATCCCAAATTACTAATAAATTAATTTTAAAATAATTA
1 TAAACACAAAAATTTATAACTAAATCCCAAATTACTAACAAATTAATTTTAAAATAATTA
*
39894994 TAAACACAAAAATTTATAAC-ATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 TAAACACAAAAATTTATAACTA-AATCCCAAATTACTAACAAATTAATTTTAAAATAATTA
39895054 AAAAAAGCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (60 bp):
TAAACACAAAAATTTATAACTAAATCCCAAATTACTAACAAATTAATTTTAAAATAATTA
Found at i:39895175 original size:14 final size:13
Alignment explanation
Indices: 39895150--39895205 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
39895140 TTACCTTTTA
39895150 TTTTTCTTTCTTC
1 TTTTTCTTTCTTC
39895163 TTTTTCTTATCTTC
1 TTTTTCTT-TCTTC
* *
39895177 TTCTCCTTTC-TC
1 TTTTTCTTTCTTC
39895189 TCTTTTCTTTCTCTC
1 T-TTTTCTTTCT-TC
39895204 TT
1 TT
39895206 CCGTTCATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
12 3 0.09
13 17 0.49
14 12 0.34
15 3 0.09
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTCTTTCTTC
Found at i:39895194 original size:27 final size:27
Alignment explanation
Indices: 39895155--39895206 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
39895145 TTTTATTTTT
39895155 CTTTCTTCTTTTTCTTATCT-TCTTCTC
1 CTTTCTTCTTTTTCTT-TCTCTCTTCTC
39895182 CTTTC-TCTCTTTTCTTTCTCTCTTC
1 CTTTCTTCT-TTTTCTTTCTCTCTTC
39895207 CGTTCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (27 bp):
CTTTCTTCTTTTTCTTTCTCTCTTCTC
Found at i:39896207 original size:13 final size:13
Alignment explanation
Indices: 39896189--39896213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39896179 TCTTCTTCAC
39896189 TAGATTTAAATGG
1 TAGATTTAAATGG
39896202 TAGATTTAAATG
1 TAGATTTAAATG
39896214 TATGGTAAAA
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
TAGATTTAAATGG
Found at i:39902600 original size:8 final size:8
Alignment explanation
Indices: 39902584--39902619 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
39902574 CACGACCTAC
*
39902584 AAAATAAT
1 AAAAAAAT
39902592 AAAAAAAT
1 AAAAAAAT
39902600 AAAAAAAT
1 AAAAAAAT
39902608 -AAAAAAT
1 AAAAAAAT
39902615 AAAAA
1 AAAAA
39902620 CAAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:39902624 original size:12 final size:11
Alignment explanation
Indices: 39902584--39902630 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
39902574 CACGACCTAC
*
39902584 AAAATAATAAA
1 AAAAAAATAAA
39902595 AAAATAAA-AAA
1 AAAA-AAATAAA
39902606 ATAAAAAATAAA
1 A-AAAAAATAAA
39902618 AACAAAAATAAA
1 AA-AAAAATAAA
39902630 A
1 A
39902631 GGTAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 12 0.39
12 19 0.61
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:39902638 original size:19 final size:19
Alignment explanation
Indices: 39902584--39902630 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
39902574 CACGACCTAC
39902584 AAAATAATAAAA-AAATAA-A
1 AAAATAA-AAAATAAA-AACA
39902603 AAAATAAAAAATAAAAACA
1 AAAATAAAAAATAAAAACA
39902622 AAAATAAAA
1 AAAATAAAA
39902631 GGTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAATAAAAAATAAAAACA
Found at i:39903571 original size:16 final size:16
Alignment explanation
Indices: 39903530--39903575 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
39903520 AGTAAGAGGA
39903530 TTTGGATAAAAAT-A-
1 TTTGGATAAAAATAAG
*
39903544 TAT-GATTAAAAATAAG
1 TTTGGA-TAAAAATAAG
39903560 TTTGGATAAAAATAAG
1 TTTGGATAAAAATAAG
39903576 ACCCGTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.35
15 1 0.04
16 12 0.46
17 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (16 bp):
TTTGGATAAAAATAAG
Found at i:39907397 original size:16 final size:18
Alignment explanation
Indices: 39907365--39907398 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
39907355 GGCTATTGAG
39907365 TATACTATTTGTTAAATT
1 TATACTATTTGTTAAATT
39907383 TATACT-TTT-TTAAATT
1 TATACTATTTGTTAAATT
39907399 GTACTATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TATACTATTTGTTAAATT
Found at i:39921661 original size:5 final size:6
Alignment explanation
Indices: 39921645--39921669 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39921635 TAAATCTTTT
39921645 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
39921670 TATTATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:39929040 original size:238 final size:238
Alignment explanation
Indices: 39928622--39929070 Score: 686
Period size: 238 Copynumber: 1.9 Consensus size: 238
39928612 TGACATCGTA
*
39928622 ATGAGGAATCTTCCCACGTCACAACAACGCAACGATGGCAGGCCAAAATGGGGTTGACTCCTTGG
1 ATGAGGAATCTTCCCACGTCACAACAACGCAACGATGGCAGGCCAAAATAGGGTTGACTCCTTGG
* * *
39928687 ACAACACTCTTGGGGTATTTCTATATTTAGACCCTGGCAATTTAAAAGTATCTTGTATTAAATAA
66 ACAACACTCTTGGGATATTTCCATATTTAGACCCTAGCAATTTAAAAGTATCTTGTATTAAATAA
* * *
39928752 TATCTTAATGTATCTAGGGTTAAATGGTCAACAAGTAGCCCATAGCCTATATAAGTAATCTTA-A
131 TATCTAAATGTATCTAGGGTTAAATGGTCAACAAGTAACCCATAGCCTATATAAGTAACCTTAGA
39928816 GGTCACCGAAATTGGGGGAAGAGTTTCATGGTGGCAACATCATT
196 -GTCACCGAAATTGGGGGAAGAGTTTCATGGTGGCAACATCATT
* * * *
39928860 ATGAGGAATCTTCCCACGTCACGACGACGCGACGATGGCAGGCCAAAATAGGGTTGATTCCTTGG
1 ATGAGGAATCTTCCCACGTCACAACAACGCAACGATGGCAGGCCAAAATAGGGTTGACTCCTTGG
* * * * * *
39928925 ATGAA-ACTCTTGGGATATTTCCATTTTTAGACCCTAGCAATTTAAGAGTATTTTGTATTAATTG
66 A-CAACACTCTTGGGATATTTCCATATTTAGACCCTAGCAATTTAAAAGTATCTTGTATTAAATA
* *
39928989 ATATCTAAATGTATCTAGGGTTGAATGGTCACCAAGTAACCCATAGCCTATATAAGTAACCTTAG
130 ATATCTAAATGTATCTAGGGTTAAATGGTCAACAAGTAACCCATAGCCTATATAAGTAACCTTAG
*
39929054 AGTCACCGGAATTGGGG
195 AGTCACCGAAATTGGGG
39929071 TGCAAACATA
Statistics
Matches: 189, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
238 186 0.98
239 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (238 bp):
ATGAGGAATCTTCCCACGTCACAACAACGCAACGATGGCAGGCCAAAATAGGGTTGACTCCTTGG
ACAACACTCTTGGGATATTTCCATATTTAGACCCTAGCAATTTAAAAGTATCTTGTATTAAATAA
TATCTAAATGTATCTAGGGTTAAATGGTCAACAAGTAACCCATAGCCTATATAAGTAACCTTAGA
GTCACCGAAATTGGGGGAAGAGTTTCATGGTGGCAACATCATT
Found at i:39929744 original size:13 final size:14
Alignment explanation
Indices: 39929721--39929750 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39929711 TTTAGGCTAA
39929721 TTAATTTAATAAGT
1 TTAATTTAATAAGT
39929735 TTAA-TTAATAAGT
1 TTAATTTAATAAGT
39929748 TTA
1 TTA
39929751 TTTGGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAATTTAATAAGT
Found at i:39938808 original size:26 final size:26
Alignment explanation
Indices: 39938640--39938798 Score: 120
Period size: 26 Copynumber: 6.4 Consensus size: 26
39938630 TGGTTATCCG
* *
39938640 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAATGGCTCTTTGT
* ****
39938665 GAGCTTCTTGATTAAAATTTCTTTGT
1 GAGCTTCCTGATTAATGGCTCTTTGT
* *
39938691 GAACTTCCTGATT-ATGGCTC-TTAT
1 GAGCTTCCTGATTAATGGCTCTTTGT
* *
39938715 GAGCTTCCTG-TTATATAGCTC--GGAT
1 GAGCTTCCTGATTA-ATGGCTCTTTG-T
*
39938740 AAGCTTCCTGA-T-A-GGCTCTTTGT
1 GAGCTTCCTGATTAATGGCTCTTTGT
39938763 GAGCTTCCTGATTAATGGCTCTTTGT
1 GAGCTTCCTGATTAATGGCTCTTTGT
*
39938789 GAGTTTCCTG
1 GAGCTTCCTG
39938799 CTATATGGCT
Statistics
Matches: 103, Mismatches: 21, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
22 4 0.04
23 14 0.14
24 14 0.14
25 25 0.24
26 46 0.45
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (26 bp):
GAGCTTCCTGATTAATGGCTCTTTGT
Found at i:39944331 original size:26 final size:26
Alignment explanation
Indices: 39944268--39944342 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
39944258 CCATAAACCC
*
39944268 AACCCTAAACCCT-AAA-C-ACTA-A
1 AACCTTAAACCCTAAAACCAACTATA
* * *
39944290 AATCTTGAACCATAAAACCAACTATA
1 AACCTTAAACCCTAAAACCAACTATA
* *
39944316 AACCTTAAACCCTAAACCCAACCATA
1 AACCTTAAACCCTAAAACCAACTATA
39944342 A
1 A
39944343 CAATAAAACC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 9 0.22
23 3 0.08
24 1 0.03
25 4 0.10
26 23 0.57
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.17
Consensus pattern (26 bp):
AACCTTAAACCCTAAAACCAACTATA
Found at i:39944607 original size:14 final size:14
Alignment explanation
Indices: 39944539--39944724 Score: 77
Period size: 14 Copynumber: 13.7 Consensus size: 14
39944529 AACCCCAACA
*
39944539 CTAAACCATAGACC
1 CTAAACCATAAACC
* *
39944553 CTAAAATCTTAAACC
1 CT-AAACCATAAACC
* * *
39944568 ATAAACC--CAACA
1 CTAAACCATAAACC
* *
39944580 CTAGACCTTAAACC
1 CTAAACCATAAACC
39944594 CTAAACCATAAACC
1 CTAAACCATAAACC
* *
39944608 C--AAGCAT-AACA
1 CTAAACCATAAACC
*
39944619 CTAAAACCCT-AACC
1 CT-AAACCATAAACC
*
39944633 CT-AACCTTAAACC
1 CTAAACCATAAACC
* **
39944646 ATAAAAAATAAACC
1 CTAAACCATAAACC
* *
39944660 AT-AACTATAAACC
1 CTAAACCATAAACC
*
39944673 ATAAACCATAAACC
1 CTAAACCATAAACC
* *
39944687 ATAAACCTTAAACTC
1 CTAAACCATAAAC-C
39944702 C-AAACCAT-AACC
1 CTAAACCATAAACC
*
39944714 TTTAAACCATA
1 -CTAAACCATA
39944725 GACCATAACC
Statistics
Matches: 129, Mismatches: 30, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
11 4 0.03
12 19 0.15
13 19 0.15
14 76 0.59
15 11 0.09
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:39944626 original size:33 final size:33
Alignment explanation
Indices: 39944547--39944630 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
39944537 CACTAAACCA
* *
39944547 TAGACCCTAAAATCTTAAACCATAAACCCAACAC
1 TAGA-CCTAAAACCCTAAACCATAAACCCAACAC
*
39944581 TAGACCTTAAACCCTAAACCATAAACCCAAGCA-
1 TAGACCTAAAACCCTAAACCATAAACCCAA-CAC
39944614 TA-ACACTAAAACCCTAA
1 TAGAC-CTAAAACCCTAA
39944631 CCCTAACCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
32 2 0.05
33 36 0.82
34 6 0.14
ACGTcount: A:0.48, C:0.32, G:0.04, T:0.17
Consensus pattern (33 bp):
TAGACCTAAAACCCTAAACCATAAACCCAACAC
Found at i:39944650 original size:7 final size:7
Alignment explanation
Indices: 39944635--39944732 Score: 85
Period size: 7 Copynumber: 14.1 Consensus size: 7
39944625 CCCTAACCCT
*
39944635 AACCTTA
1 AACCATA
39944642 AACCATA
1 AACCATA
**
39944649 AAAAATA
1 AACCATA
39944656 AACCAT-
1 AACCATA
*
39944662 AACTATA
1 AACCATA
39944669 AACCATA
1 AACCATA
39944676 AACCATA
1 AACCATA
39944683 AACCATA
1 AACCATA
*
39944690 AACCTTA
1 AACCATA
*
39944697 AACTC-CA
1 AAC-CATA
39944704 AACCAT-
1 AACCATA
*
39944710 AACCTTTA
1 AACC-ATA
39944718 AACCATA
1 AACCATA
*
39944725 GACCATA
1 AACCATA
39944732 A
1 A
39944733 CCCTAACCTC
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
6 10 0.14
7 57 0.79
8 5 0.07
ACGTcount: A:0.53, C:0.27, G:0.01, T:0.19
Consensus pattern (7 bp):
AACCATA
Found at i:39944659 original size:27 final size:27
Alignment explanation
Indices: 39944629--39944699 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
39944619 CTAAAACCCT
*
39944629 AACCCTAACCTTAAACCATAAAAAATA
1 AACCATAACCTTAAACCATAAAAAATA
**
39944656 AACCATAA-CTATAAACCATAAACCATA
1 AACCATAACCT-TAAACCATAAAAAATA
39944683 AACCATAAACCTTAAAC
1 AACCAT-AACCTTAAAC
39944700 TCCAAACCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 2 0.05
27 27 0.71
28 7 0.18
29 2 0.05
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (27 bp):
AACCATAACCTTAAACCATAAAAAATA
Found at i:39944733 original size:21 final size:19
Alignment explanation
Indices: 39944612--39944734 Score: 78
Period size: 21 Copynumber: 6.4 Consensus size: 19
39944602 TAAACCCAAG
* *
39944612 CATAACACTAAAACCCTAAC
1 CATAAC-CTTAAACCATAAC
*
39944632 CCTAACCTTAAACCATAA-
1 CATAACCTTAAACCATAAC
*
39944650 -A-AA--ATAAACCATAAC
1 CATAACCTTAAACCATAAC
* *
39944665 TATAAACCATAAACCATAAAC
1 CAT-AACCTTAAACCAT-AAC
39944686 CATAAACCTTAAACTCCA-AAC
1 CAT-AACCTTAAA--CCATAAC
39944707 CATAACCTTTAAACCATAGAC
1 CATAACC-TTAAACCATA-AC
39944728 CATAACC
1 CATAACC
39944735 CTAACCTCTA
Statistics
Matches: 84, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
18 2 0.02
19 13 0.15
20 19 0.23
21 34 0.40
23 3 0.04
ACGTcount: A:0.50, C:0.30, G:0.01, T:0.19
Consensus pattern (19 bp):
CATAACCTTAAACCATAAC
Found at i:39945235 original size:19 final size:20
Alignment explanation
Indices: 39945184--39945226 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
39945174 AAGTATGTGT
39945184 CCCTAAACCCTAACACTAAC
1 CCCTAAACCCTAACACTAAC
39945204 CCC-AAACCCTAACA-TAAC
1 CCCTAAACCCTAACACTAAC
39945222 CCCTA
1 CCCTA
39945227 GACCTTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 12 0.55
20 3 0.14
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.14
Consensus pattern (20 bp):
CCCTAAACCCTAACACTAAC
Found at i:39945278 original size:14 final size:15
Alignment explanation
Indices: 39945259--39945291 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39945249 CCCTGAACAT
*
39945259 AACCTT-AAATCCTA
1 AACCTTAAAATCATA
39945273 AACCTTAAAATCATA
1 AACCTTAAAATCATA
39945288 AACC
1 AACC
39945292 AAAGCCCAAC
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:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
AACCTTAAAATCATA
Found at i:39951103 original size:3 final size:3
Alignment explanation
Indices: 39951097--39951184 Score: 126
Period size: 3 Copynumber: 29.0 Consensus size: 3
39951087 TTTTTTTACT
39951097 TTA TTA TTA TTA TTA TTA TTA TT- TATA TT- TATA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA -TTA TTA TTA TTA
*
39951143 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39951185 AGGTTTGTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
2 2 0.03
3 72 0.92
4 3 0.04
5 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39956108 original size:6 final size:6
Alignment explanation
Indices: 39956097--39956136 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
39956087 TTCAATCAAA
39956097 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
39956137 AAGAAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:39958474 original size:100 final size:100
Alignment explanation
Indices: 39958344--39958734 Score: 566
Period size: 100 Copynumber: 3.9 Consensus size: 100
39958334 AATACCAATT
* *
39958344 TTACTCCCCAGGCAATGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGTTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGCTTCCCCGACAT
*
39958409 TGCAGTTAAAAAGATCAAAGCTACAACAATGAATC
66 TGCAGTTAAAAAGATCAAAGCTACAACAGTGAATC
* * *
39958444 TTACTTCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGCTTCCCCGACAT
* *
39958509 TACAGTTAAAAAGATTAAAGCTACAACAGTGAATC
66 TGCAGTTAAAAAGATCAAAGCTACAACAGTGAATC
* * * *
39958544 TCACTCCCCAGGCGATACAGTGGAACAGATTAAAGCCACATCGATGAATCTTACTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGCTTCCCCGACAT
* *
39958609 TGCAGTTAAAAAGATCAAAGCTACAACGGCGAATC
66 TGCAGTTAAAAAGATCAAAGCTACAACAGTGAATC
* * * * ****
39958644 TTACTTCCCAGGCGGTGCAGTGGAATAGATTAAAGCCACAACGGCAAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGCTTCCCCGACAT
**
39958709 TGCAGTTAAAAAGATTGAAGCTACAA
66 TGCAGTTAAAAAGATCAAAGCTACAA
39958735 TGGCGAATCT
Statistics
Matches: 260, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 260 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (100 bp):
TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGCTTCCCCGACAT
TGCAGTTAAAAAGATCAAAGCTACAACAGTGAATC
Found at i:39958696 original size:200 final size:200
Alignment explanation
Indices: 39958346--39958734 Score: 625
Period size: 200 Copynumber: 1.9 Consensus size: 200
39958336 TACCAATTTT
* **
39958346 ACTCCCCAGGCAATGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGTTTCCCCGACATTG
1 ACTCCCCAGGCAATACAGTGGAACAGATTAAAGCCACATCAATGAATCTTACTTCCCCGACATTG
*
39958411 CAGTTAAAAAGATCAAAGCTACAACAATGAATCTTACTTCCCAGACGATGCAGTGGAACAGATTA
66 CAGTTAAAAAGATCAAAGCTACAACAACGAATCTTACTTCCCAGACGATGCAGTGGAACAGATTA
* **
39958476 AAGCCACATCAGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAACAGTGA
131 AAGCCACAACAGCAAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAACAGTGA
39958541 ATCTC
196 ATCTC
* *
39958546 ACTCCCCAGGCGATACAGTGGAACAGATTAAAGCCACATCGATGAATCTTACTTCCCCGACATTG
1 ACTCCCCAGGCAATACAGTGGAACAGATTAAAGCCACATCAATGAATCTTACTTCCCCGACATTG
** * * *
39958611 CAGTTAAAAAGATCAAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAATAGATTA
66 CAGTTAAAAAGATCAAAGCTACAACAACGAATCTTACTTCCCAGACGATGCAGTGGAACAGATTA
* * *
39958676 AAGCCACAACGGCAAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTGAAGCTACAA
131 AAGCCACAACAGCAAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAA
39958735 TGGCGAATCT
Statistics
Matches: 172, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
200 172 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (200 bp):
ACTCCCCAGGCAATACAGTGGAACAGATTAAAGCCACATCAATGAATCTTACTTCCCCGACATTG
CAGTTAAAAAGATCAAAGCTACAACAACGAATCTTACTTCCCAGACGATGCAGTGGAACAGATTA
AAGCCACAACAGCAAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAACAGTGA
ATCTC
Found at i:39958744 original size:50 final size:50
Alignment explanation
Indices: 39958370--39958746 Score: 310
Period size: 50 Copynumber: 7.5 Consensus size: 50
39958360 GCAGTGGAAC
* * ** **
39958370 AGATTAAAGCCACATCAATGAATCTTGTTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* ** * ** *
39958420 AGATCAAAGCTACAACAATGAATCTTACTTCCCAGACGA-TGCAGTGGAAC
1 AGATTAAAGCTACAACGGTGAATCTTACTTCCCCGAC-ATTGCAGTTAAAA
* * * * *
39958470 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTACAGTTAAAA
1 AGATTAAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * ** *
39958520 AGATTAAAGCTACAACAGTGAATCTCAC-TCCCCAGGCGA-TACAGTGGAAC
1 AGATTAAAGCTACAACGGTGAATCTTACTTCCCC-GAC-ATTGCAGTTAAAA
* * *
39958570 AGATTAAAGCCACATCGATGAATCTTACTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * ** ** *
39958620 AGATCAAAGCTACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAAT
1 AGATTAAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* ** *
39958670 AGATTAAAGCCACAACGGCAAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * *
39958720 AGATTGAAGCTACAATGGCGAATCTTA
1 AGATTAAAGCTACAACGGTGAATCTTA
39958747 TTTTCCAAAA
Statistics
Matches: 256, Mismatches: 65, Indels: 12
0.77 0.20 0.04
Matches are distributed among these distances:
49 7 0.03
50 242 0.95
51 7 0.03
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCTACAACGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:39960210 original size:3 final size:3
Alignment explanation
Indices: 39960204--39960272 Score: 113
Period size: 3 Copynumber: 23.0 Consensus size: 3
39960194 TTTTTTTACT
*
39960204 TTA TTA TTA TTA TTA TTA TCA TTA TTTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
39960249 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
39960273 AGGTTTGTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39971550 original size:50 final size:50
Alignment explanation
Indices: 39971475--39971572 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
39971465 TTACTAACAT
* * * * *
39971475 TTAAATATATATGATACTAGTTTTCGTGAATATCTCTTTTAATAACGTCA
1 TTAAATATATATAATACTAATTTTCGTGAATACCTCATTAAATAACGTCA
* *
39971525 TTAAATATATATAATATTAATTTTCGTGATTACCTCATTAAATAACGT
1 TTAAATATATATAATACTAATTTTCGTGAATACCTCATTAAATAACGT
39971573 TATATTCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (50 bp):
TTAAATATATATAATACTAATTTTCGTGAATACCTCATTAAATAACGTCA
Found at i:39971767 original size:21 final size:20
Alignment explanation
Indices: 39971728--39971768 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39971718 GAATATATTG
**
39971728 TAATTAAAGTGTGACTTTAT
1 TAATTAAAGTGAAACTTTAT
39971748 TAATTAAAGTGAAAACTTTAT
1 TAATTAAAGTG-AAACTTTAT
39971769 GTTCTCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (20 bp):
TAATTAAAGTGAAACTTTAT
Found at i:39990120 original size:21 final size:21
Alignment explanation
Indices: 39990094--39990160 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
39990084 TTTGGTTGAA
* *
39990094 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACAAGCTTCTAT
*
39990115 TCAGCTCTTATAAGCTTCTAT
1 TCAGCTCTTACAAGCTTCTAT
39990136 TCAGCTCTTACAAGCTTCTAT
1 TCAGCTCTTACAAGCTTCTAT
39990157 TCAG
1 TCAG
39990161 ATTTCGAGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (21 bp):
TCAGCTCTTACAAGCTTCTAT
Found at i:39990375 original size:21 final size:20
Alignment explanation
Indices: 39990349--39990397 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
39990339 AATAGAAGTT
39990349 GTGAATGACAA-GAAATTGAC
1 GTGAATGACAATG-AATTGAC
*
39990369 GGTGAATTACAATGAATTGAC
1 -GTGAATGACAATGAATTGAC
*
39990390 ATGAATGA
1 GTGAATGA
39990398 TTTTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 17 0.71
22 1 0.04
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (20 bp):
GTGAATGACAATGAATTGAC
Found at i:39990736 original size:4 final size:4
Alignment explanation
Indices: 39990727--39990808 Score: 164
Period size: 4 Copynumber: 20.5 Consensus size: 4
39990717 AATATGAGTG
39990727 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39990775 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
39990809 TTGAATTATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 78 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:39995950 original size:10 final size:10
Alignment explanation
Indices: 39995935--39995975 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
39995925 TAATAAATAT
39995935 ATTTTTTAAA
1 ATTTTTTAAA
*
39995945 ATTTTTTTAA
1 ATTTTTTAAA
39995955 A--TTTTAAA
1 ATTTTTTAAA
39995963 ATATTTTTAAA
1 AT-TTTTTAAA
39995974 AT
1 AT
39995976 ACTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.27
10 10 0.38
11 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:39995961 original size:18 final size:18
Alignment explanation
Indices: 39995938--39996054 Score: 65
Period size: 18 Copynumber: 6.0 Consensus size: 18
39995928 TAAATATATT
*
39995938 TTTTAAAATTTTTTTAAA
1 TTTTAAAATATTTTTAAA
39995956 TTTTAAAATATTTTTAAAATA
1 TTTTAAAATATTTTT--AA-A
** *
39995977 CTTTTTTTATTACTTTTT-AA
1 --TTTTAAAATA-TTTTTAAA
39995997 TTTTAAAATATTTTTAAAATA
1 TTTTAAAATATTTTT--AA-A
* * *
39996018 CTTTTTAAATTTTTTTTAA
1 -TTTTAAAATATTTTTAAA
*
39996037 TCTTAAAATATTTTTAAA
1 TTTTAAAATATTTTTAAA
39996055 ATACTTTTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
17 5 0.07
18 35 0.47
19 1 0.01
20 5 0.07
21 3 0.04
22 13 0.18
23 7 0.09
24 5 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAAAATATTTTTAAA
Found at i:39995976 original size:11 final size:11
Alignment explanation
Indices: 39995937--39996063 Score: 57
Period size: 11 Copynumber: 12.5 Consensus size: 11
39995927 ATAAATATAT
39995937 TTTTTAAAAT-
1 TTTTTAAAATA
*
39995947 TTTTT-TAA-A
1 TTTTTAAAATA
39995956 -TTTTAAAATA
1 TTTTTAAAATA
39995966 TTTTTAAAATA
1 TTTTTAAAATA
** *
39995977 CTTTTTTTATTA
1 -TTTTTAAAATA
39995989 CTTTTT---A-A
1 -TTTTTAAAATA
39995997 -TTTTAAAATA
1 TTTTTAAAATA
39996007 TTTTTAAAATA
1 TTTTTAAAATA
39996018 CTTTTT-AAAT-
1 -TTTTTAAAATA
*
39996028 TTTTT---TTA
1 TTTTTAAAATA
* *
39996036 ATCTTAAAATA
1 TTTTTAAAATA
39996047 TTTTTAAAATA
1 TTTTTAAAATA
39996058 CTTTTT
1 -TTTTT
39996064 TTAATTTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
8 8 0.09
9 10 0.11
10 7 0.08
11 35 0.39
12 24 0.27
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:39995999 original size:41 final size:40
Alignment explanation
Indices: 39995948--39996066 Score: 184
Period size: 40 Copynumber: 2.9 Consensus size: 40
39995938 TTTTAAAATT
39995948 TTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTATTAC
1 TTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTATT-C
** *
39995990 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAATTT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTC
*
39996030 TTTTTAATCTTAAAATATTTTTAAAATACTTTTTTTA
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
39996067 ATTTTTAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
40 34 0.48
41 32 0.45
42 5 0.07
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (40 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTC
Found at i:39996001 original size:30 final size:30
Alignment explanation
Indices: 39995967--39996030 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
39995957 TTTAAAATAT
** *
39995967 TTTTAAAATACTTTTTTTATTACTTTTT-AA
1 TTTTAAAATA-TTTTTAAAATACTTTTTAAA
39995997 TTTTAAAATATTTTTAAAATACTTTTTAAA
1 TTTTAAAATATTTTTAAAATACTTTTTAAA
39996027 TTTT
1 TTTT
39996031 TTTTAATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTAAAATATTTTTAAAATACTTTTTAAA
Found at i:39996034 original size:40 final size:40
Alignment explanation
Indices: 39995928--39996072 Score: 191
Period size: 41 Copynumber: 3.5 Consensus size: 40
39995918 TCCGATATAA
* *
39995928 TAAATATATTTTTTAAAATTTTTTTAAATTTTAAAATATTTT
1 TAAA-ATACTTTTT-AAATTTTTTTTAATTTTAAAATATTTT
** *
39995970 TAAAATACTTTTTTTATTACTTTTTAATTTTAAAATATTTT
1 TAAAATACTTTTTAAATT-TTTTTTAATTTTAAAATATTTT
*
39996011 TAAAATACTTTTTAAATTTTTTTTAATCTTAAAATATTTT
1 TAAAATACTTTTTAAATTTTTTTTAATTTTAAAATATTTT
*
39996051 TAAAATACTTTTTTTAATTTTT
1 TAAAATAC-TTTTTAAATTTTT
39996073 AAAATAAATT
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
40 31 0.34
41 56 0.62
42 4 0.04
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (40 bp):
TAAAATACTTTTTAAATTTTTTTTAATTTTAAAATATTTT
Found at i:39996084 original size:21 final size:21
Alignment explanation
Indices: 39996046--39996085 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39996036 ATCTTAAAAT
**
39996046 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
39996067 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
39996086 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:39996092 original size:22 final size:21
Alignment explanation
Indices: 39996045--39996103 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
39996035 AATCTTAAAA
* *
39996045 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
39996065 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
39996088 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
39996104 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:40001309 original size:18 final size:19
Alignment explanation
Indices: 40001281--40001318 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40001271 AGCTGGTCAT
40001281 CCCTCCTTTTT-TTCTTTCC
1 CCCTCCTTTTTGTT-TTTCC
40001300 CCCT-CTTTTTGTTTTTCC
1 CCCTCCTTTTTGTTTTTCC
40001318 C
1 C
40001319 TTCTCTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.00, C:0.39, G:0.03, T:0.58
Consensus pattern (19 bp):
CCCTCCTTTTTGTTTTTCC
Found at i:40004053 original size:22 final size:22
Alignment explanation
Indices: 40004022--40004064 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40004012 TAAATATTTA
*
40004022 CTAAACAGTTAAAATTTTTAAC
1 CTAAACAGTTAAAAATTTTAAC
*
40004044 CTAAATAGTTAAAAATTTTAA
1 CTAAACAGTTAAAAATTTTAA
40004065 ATATACGTTA
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:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (22 bp):
CTAAACAGTTAAAAATTTTAAC
Found at i:40004791 original size:12 final size:12
Alignment explanation
Indices: 40004762--40004791 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40004752 ATGCTTCTTG
40004762 TTTTTTCTTTTT
1 TTTTTTCTTTTT
*
40004774 CTTTTTCTTTTT
1 TTTTTTCTTTTT
40004786 TTTTTT
1 TTTTTT
40004792 TGCAGATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:40010326 original size:41 final size:39
Alignment explanation
Indices: 40010281--40010357 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 39
40010271 CCTTTATTGA
40010281 AATTCTTTTGA-TTGTAATTTCTATTTTTCATATAAACTCTT
1 AATTCTTTTGACTT-T-ATTT-TATTTTTCATATAAACTCTT
*
40010322 AATTCTTTTTACTTTATTTTATTTTTCATATAAACT
1 AATTCTTTTGACTTTATTTTATTTTTCATATAAACT
40010358 TTGTTTATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
39 17 0.50
40 4 0.12
41 11 0.32
42 2 0.06
ACGTcount: A:0.27, C:0.12, G:0.03, T:0.58
Consensus pattern (39 bp):
AATTCTTTTGACTTTATTTTATTTTTCATATAAACTCTT
Found at i:40019598 original size:15 final size:14
Alignment explanation
Indices: 40019573--40019603 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
40019563 TAGATTTGGC
40019573 ATATATATACATAT
1 ATATATATACATAT
40019587 ATATATTATACATAT
1 ATATA-TATACATAT
40019602 AT
1 AT
40019604 TCTCATGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:40035113 original size:51 final size:51
Alignment explanation
Indices: 40035037--40035276 Score: 275
Period size: 51 Copynumber: 4.9 Consensus size: 51
40035027 NNNNAAGCTT
*
40035037 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGA
* * * * *
40035088 TGGTCACATGTGTAGTACTAAGTGAAGGCTAC-A-ATG--T-G-T-ACT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGA
*
40035131 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGA
* * * * *
40035182 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAA-GCTT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATG--A
*
40035233 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
40035277 ATGATAAAAG
Statistics
Matches: 158, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
43 29 0.18
44 3 0.02
45 3 0.02
46 1 0.01
47 2 0.01
48 1 0.01
49 4 0.03
50 6 0.04
51 109 0.69
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGA
Found at i:40035136 original size:43 final size:44
Alignment explanation
Indices: 40035083--40035221 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 44
40035073 TGAATCGATA
40035083 AATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGT
1 AATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGT
* * * ** *
40035127 ACT-TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGAT
1 AATGATGGTCACATGTGTAGTACTAAGTGAAGGCTAC-A-ATG--T-G-T
*
40035176 AAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGT
1 -AATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGT
40035221 A
1 A
40035222 TCGAAAAGCT
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
43 29 0.39
44 4 0.05
45 3 0.04
46 1 0.01
47 2 0.03
48 1 0.01
49 3 0.04
50 2 0.03
51 29 0.39
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (44 bp):
AATGATGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGT
Found at i:40035195 original size:94 final size:97
Alignment explanation
Indices: 40035031--40035276 Score: 399
Period size: 94 Copynumber: 2.5 Consensus size: 97
40035021 NNNNNNNNNN
40035031 AAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 AAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
40035096 TGTGTAGTACTAAGTGAAGGCTACAATGTG-T
66 TGTGTAGTACTAAGTGAAGGCTACAATGTGAT
40035127 -A-CTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 AAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
*
40035190 TGTGTAGTACTAAGTGAAGGCTACTATGTGTAT
66 TGTGTAGTACTAAGTGAAGGCTACAATGTG-AT
* *
40035223 CGAAAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 ----AAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA
40035277 ATGATAAAAG
Statistics
Matches: 139, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
94 91 0.65
95 1 0.01
96 1 0.01
101 1 0.01
102 45 0.32
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (97 bp):
AAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
TGTGTAGTACTAAGTGAAGGCTACAATGTGAT
Found at i:40035299 original size:51 final size:50
Alignment explanation
Indices: 40035131--40035309 Score: 180
Period size: 51 Copynumber: 3.5 Consensus size: 50
40035121 ATGTGTACTT
* * * *
40035131 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCG-ATAAATGA
1 TGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAT-GAT-A
* * * * *
40035182 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGAAAAGCTT
1 TGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCG-AATGATA
*
40035233 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAA
1 TGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGAT-A
** * * *
40035284 AAGTAACATGGGTAGTACTGTGTGAA
1 TGGTCACATGTGTAGTACTATGTGAA
40035310 AAACCCCAAA
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 4 0.04
51 98 0.94
52 1 0.01
53 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (50 bp):
TGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATA
Found at i:40035537 original size:37 final size:38
Alignment explanation
Indices: 40035468--40035540 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
40035458 ATGTGTGGAA
* **
40035468 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
*
40035506 TTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAA
40035541 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:40040405 original size:19 final size:19
Alignment explanation
Indices: 40040381--40040420 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
40040371 TTTATAAGAG
40040381 TCCCTAAGAAATTCAGCTA
1 TCCCTAAGAAATTCAGCTA
40040400 TCCCTAAGAAATTCAGCTA
1 TCCCTAAGAAATTCAGCTA
40040419 TC
1 TC
40040421 TTGTATGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (19 bp):
TCCCTAAGAAATTCAGCTA
Found at i:40044555 original size:5 final size:5
Alignment explanation
Indices: 40044547--40044574 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40044537 TAAAAACCCC
40044547 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
40044575 GAATAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:40045236 original size:30 final size:31
Alignment explanation
Indices: 40045186--40045249 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
40045176 ATTTCTTATG
* *
40045186 CCAATATCTCGATACTCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATATTTGACTTT
*
40045217 CCAATAT-TTGATACCCATATATTTGACTTT
1 CCAATATCTCGATACCCATATATTTGACTTT
40045247 CCA
1 CCA
40045250 TAAATATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (31 bp):
CCAATATCTCGATACCCATATATTTGACTTT
Found at i:40049867 original size:30 final size:30
Alignment explanation
Indices: 40049821--40049909 Score: 125
Period size: 25 Copynumber: 3.1 Consensus size: 30
40049811 ATTTCTTATG
*
40049821 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
40049852 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
40049881 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
40049907 CCA
1 CCA
40049910 TAAATATGGA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
25 23 0.43
26 2 0.04
29 2 0.04
30 19 0.36
31 7 0.13
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:40049876 original size:15 final size:15
Alignment explanation
Indices: 40049831--40049877 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
40049821 CCAATATCTC
40049831 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
40049846 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
40049861 GATACCCATATCTTT
1 GATACCCATATCTTT
40049876 GA
1 GA
40049878 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:40052405 original size:2 final size:2
Alignment explanation
Indices: 40052398--40052424 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40052388 TGGCATTTCT
40052398 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
40052425 TTTATCTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:40061854 original size:14 final size:15
Alignment explanation
Indices: 40061829--40061858 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
40061819 CTTTCAAACA
40061829 AAATATTAAAAAAAT
1 AAATATTAAAAAAAT
40061844 AAATA-TAAAAAAAT
1 AAATATTAAAAAAAT
40061858 A
1 A
40061859 CAGGACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATATTAAAAAAAT
Found at i:40068654 original size:18 final size:18
Alignment explanation
Indices: 40068629--40068665 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40068619 ATGTATTTTA
40068629 AAATTAAAAAATAT-ATT
1 AAATTAAAAAATATGATT
40068646 AAATGTAAAAAATATGATT
1 AAAT-TAAAAAATATGATT
40068665 A
1 A
40068666 TTTTAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AAATTAAAAAATATGATT
Found at i:40070087 original size:31 final size:31
Alignment explanation
Indices: 40070052--40070113 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
40070042 CTCAAAACTT
40070052 GTAAGGTTTAATGTAACTTTTTATCAACTAA
1 GTAAGGTTTAATGTAACTTTTTATCAACTAA
*
40070083 GTAAGGTTTAATGTAGCTTTTTATCAACTAA
1 GTAAGGTTTAATGTAACTTTTTATCAACTAA
40070114 CTTGTCAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (31 bp):
GTAAGGTTTAATGTAACTTTTTATCAACTAA
Found at i:40072939 original size:17 final size:17
Alignment explanation
Indices: 40072917--40072957 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
40072907 AGAACACAAG
40072917 TTTCTTTCTGTT-TTTTT
1 TTTCTTTCT-TTCTTTTT
40072934 TTTCTTTCTTTCTTTTT
1 TTTCTTTCTTTCTTTTT
*
40072951 CTTCTTT
1 TTTCTTT
40072958 AAGATACAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTCTTTCTTTCTTTTT
Found at i:40078927 original size:20 final size:20
Alignment explanation
Indices: 40078897--40078945 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
40078887 TATTTAAAAA
40078897 ATATGAAAAATGTAAATAGAT
1 ATAT-AAAAATGTAAATAGAT
* *
40078918 ATATAAAAATTTAAATATAT
1 ATATAAAAATGTAAATAGAT
40078938 ATATAAAA
1 ATATAAAA
40078946 TCTAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
ATATAAAAATGTAAATAGAT
Found at i:40078939 original size:18 final size:18
Alignment explanation
Indices: 40078888--40078946 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
40078878 TGATAGTTTT
*
40078888 ATTTAAA-AAATATGAAAA
1 ATTTAAATATATAT-AAAA
*
40078906 ATGTAAATAGATATATAAAA
1 ATTTAAAT--ATATATAAAA
40078926 ATTTAAATATATATATAAA
1 ATTTAAATATATATA-AAA
40078945 AT
1 AT
40078947 CTAGAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 13 0.38
19 5 0.15
20 11 0.32
21 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
ATTTAAATATATATAAAA
Found at i:40078967 original size:11 final size:11
Alignment explanation
Indices: 40078951--40078980 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
40078941 TAAAATCTAG
40078951 AAAAATAATAT
1 AAAAATAATAT
40078962 AAAAATAATAT
1 AAAAATAATAT
40078973 AAAAATAA
1 AAAAATAA
40078981 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:40080317 original size:40 final size:40
Alignment explanation
Indices: 40080273--40080352 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
40080263 ACATCTATTT
40080273 GGCTTGTGCTATGGTTATAAGGATTTGGTGGTGGGGATGA
1 GGCTTGTGCTATGGTTATAAGGATTTGGTGGTGGGGATGA
40080313 GGCTTGTGCTATGGTTATAAGGATTTGGTGGTGGGGATGA
1 GGCTTGTGCTATGGTTATAAGGATTTGGTGGTGGGGATGA
40080353 AGTGAAGTGC
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:0.17, C:0.05, G:0.42, T:0.35
Consensus pattern (40 bp):
GGCTTGTGCTATGGTTATAAGGATTTGGTGGTGGGGATGA
Found at i:40084674 original size:8 final size:8
Alignment explanation
Indices: 40084661--40084688 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40084651 TGCTTGTCTT
40084661 AATTATAA
1 AATTATAA
40084669 AATTATAA
1 AATTATAA
40084677 AATTATAA
1 AATTATAA
40084685 AATT
1 AATT
40084689 TTGGGAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATTATAA
Found at i:40086653 original size:26 final size:26
Alignment explanation
Indices: 40086624--40086680 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
40086614 TCCAAAACCC
40086624 CAAACGACATACTTGAGAAACTACTT
1 CAAACGACATACTTGAGAAACTACTT
*
40086650 CAAACGACATACTTGATAAACTACTT
1 CAAACGACATACTTGAGAAACTACTT
40086676 CAAAC
1 CAAAC
40086681 TTCAAGAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.23
Consensus pattern (26 bp):
CAAACGACATACTTGAGAAACTACTT
Found at i:40087707 original size:16 final size:16
Alignment explanation
Indices: 40087682--40087723 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
40087672 GTTAGAAAGT
*
40087682 TATAAATATATTTAAA
1 TATAATTATATTTAAA
*
40087698 TATAATTATAATTAAA
1 TATAATTATATTTAAA
*
40087714 -ATAATAATAT
1 TATAATTATAT
40087724 AAACATGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATTATATTTAAA
Found at i:40088526 original size:2 final size:2
Alignment explanation
Indices: 40088521--40088548 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40088511 AATAGAAGTG
40088521 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40088549 AAATTGAGAA
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):
TA
Found at i:40094633 original size:46 final size:46
Alignment explanation
Indices: 40094552--40094996 Score: 434
Period size: 46 Copynumber: 10.6 Consensus size: 46
40094542 TACGTATGAT
* * *
40094552 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
* *
40094596 CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
*
40094642 CACTTATCATTTTGTCACTTGATCAGAT-AA-GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
* *
40094678 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
*
40094724 CACTTATCACTTTGTCTCTTGATCAGAT-AA-GT-G-T--AG-T--
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
* *
40094761 -ACTTATCACTTTGTCACTTGATCAGATAAGTGTGGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
*
40094806 CACTTATCACTTTGTCTCTTGATCAGAT-AA-GT-G-T--AG-T--
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
* *
40094843 -ACTTATCACTTTGTCACTTGATCAGATAAGTGTGGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
*
40094888 CACTTATCACTTTGTCTCTTGATCAGAT-AA-GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
*
40094924 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
* *
40094970 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
40094997 AGTACTCAAA
Statistics
Matches: 334, Mismatches: 25, Indels: 82
0.76 0.06 0.19
Matches are distributed among these distances:
36 105 0.31
37 4 0.01
38 8 0.02
39 6 0.02
40 12 0.04
42 12 0.04
43 6 0.02
44 17 0.05
45 10 0.03
46 154 0.46
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTAAAGCTAC
Found at i:40094682 original size:36 final size:36
Alignment explanation
Indices: 40094642--40094960 Score: 305
Period size: 36 Copynumber: 8.0 Consensus size: 36
40094632 CTAAAGCTAA
*
40094642 CACTTATCATTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
40094678 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG
*
40094720 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
40094760 TACTTATCACTTTGTCACTTGATCAGATAAGTGTGGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG
*
40094802 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
40094842 TACTTATCACTTTGTCACTTGATCAGATAAGTGTGGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG
*
40094884 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
40094924 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
40094960 C
1 C
40094961 TAAAGCTACC
Statistics
Matches: 240, Mismatches: 13, Indels: 60
0.77 0.04 0.19
Matches are distributed among these distances:
36 120 0.50
38 6 0.03
39 3 0.01
40 9 0.04
42 9 0.04
43 3 0.01
44 6 0.03
46 84 0.35
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:40094738 original size:82 final size:82
Alignment explanation
Indices: 40094596--40094996 Score: 703
Period size: 82 Copynumber: 4.9 Consensus size: 82
40094586 CTAAGGCTAC
* * * * *
40094596 CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAACACTTATCATTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
40094661 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
*
40094678 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
40094743 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
* *
40094760 TACTTATCACTTTGTCACTTGATCAGATAAGTGTGGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
40094825 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
* *
40094842 TACTTATCACTTTGTCACTTGATCAGATAAGTGTGGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
40094907 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
*
40094924 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
40094989 TGATCAGA
66 TGATCAGA
40094997 AGTACTCAAA
Statistics
Matches: 307, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 307 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTGTAG
Found at i:40100925 original size:27 final size:28
Alignment explanation
Indices: 40100876--40100928 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
40100866 CTCATTACAA
**
40100876 TAATTAAAAATACAATATTTATAAAAAC
1 TAATTAAAAATACAATACGTATAAAAAC
*
40100904 TAATTAAAAATTCAA-ACGTATAAAA
1 TAATTAAAAATACAATACGTATAAAA
40100929 TCACATAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (28 bp):
TAATTAAAAATACAATACGTATAAAAAC
Found at i:40102408 original size:44 final size:42
Alignment explanation
Indices: 40102357--40102484 Score: 211
Period size: 44 Copynumber: 3.0 Consensus size: 42
40102347 CAGCATTTAC
40102357 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT--A
*
40102401 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTA
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
*
40102443 AAAAAAGCACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 AAAAAA-AACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
40102485 TCATCACGAA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
42 7 0.09
43 33 0.41
44 40 0.50
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
Found at i:40102447 original size:43 final size:43
Alignment explanation
Indices: 40102352--40102546 Score: 214
Period size: 43 Copynumber: 4.5 Consensus size: 43
40102342 TTTTGCAGCA
*
40102352 TTTACAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
1 TTTA-AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGC
*
40102396 TTCGAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGC
1 TT-TAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGC
* *
40102440 -TTAAAAAAAGCACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
1 TTTAAAAAAA-AACGCCGCTAAAGATCATGTTCTTTAGCGACGC
* ** ** * *
40102483 TTTCATCACGAACGCCGCGAAA-AGTAATGTTCTTTAGCGACGC
1 TTTAAAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGACGC
* * *
40102526 TTTTATAAAAAACGCCACTAA
1 TTTAAAAAAAAACGCCGCTAA
40102547 TTTTTGGATT
Statistics
Matches: 127, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
42 8 0.06
43 74 0.58
44 44 0.35
45 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (43 bp):
TTTAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGC
Found at i:40102957 original size:21 final size:21
Alignment explanation
Indices: 40102933--40102998 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
40102923 TCTCTCGCTG
* *
40102933 CTTCTCGCGCTGCAGCCTCTA
1 CTTCTCTCGTTGCAGCCTCTA
* *
40102954 CTTCTCTCATTGCAGCCTCTG
1 CTTCTCTCGTTGCAGCCTCTA
*
40102975 CTTCTCTCGTTGCCGCCTCTA
1 CTTCTCTCGTTGCAGCCTCTA
40102996 CTT
1 CTT
40102999 TAAGTTGTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.08, C:0.41, G:0.15, T:0.36
Consensus pattern (21 bp):
CTTCTCTCGTTGCAGCCTCTA
Found at i:40107813 original size:9 final size:9
Alignment explanation
Indices: 40107797--40107874 Score: 65
Period size: 9 Copynumber: 9.1 Consensus size: 9
40107787 CTAACAGCGT
40107797 TGTAAGTTA
1 TGTAAGTTA
*
40107806 TTTAAGTTA
1 TGTAAGTTA
**
40107815 TGTAAGTGG
1 TGTAAGTTA
40107824 TGT-A-TTA
1 TGTAAGTTA
40107831 TGTAAGTTA
1 TGTAAGTTA
*
40107840 AGTAAGTTA
1 TGTAAGTTA
* *
40107849 TGTAGGCTA
1 TGTAAGTTA
40107858 TGT-A-TTA
1 TGTAAGTTA
*
40107865 TGCAAGTTA
1 TGTAAGTTA
40107874 T
1 T
40107875 TTAACCTATG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
7 8 0.15
8 3 0.06
9 41 0.79
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.44
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:40107852 original size:25 final size:25
Alignment explanation
Indices: 40107803--40107852 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
40107793 GCGTTGTAAG
* * *
40107803 TTATTTAAGTTATGTAAGTGGTGTA
1 TTATGTAAGTTAAGTAAGTGATGTA
*
40107828 TTATGTAAGTTAAGTAAGTTATGTA
1 TTATGTAAGTTAAGTAAGTGATGTA
40107853 GGCTATGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (25 bp):
TTATGTAAGTTAAGTAAGTGATGTA
Found at i:40107862 original size:34 final size:34
Alignment explanation
Indices: 40107797--40107873 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
40107787 CTAACAGCGT
** *
40107797 TGTAAGTTATTTAAGTTATGTAAGTGGTGTATTA
1 TGTAAGTTAAGTAAGTTATGTAAGTGATGTATTA
*
40107831 TGTAAGTTAAGTAAGTTATGTAGGCT-ATGTATTA
1 TGTAAGTTAAGTAAGTTATGTAAG-TGATGTATTA
*
40107865 TGCAAGTTA
1 TGTAAGTTA
40107874 TTTAACCTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (34 bp):
TGTAAGTTAAGTAAGTTATGTAAGTGATGTATTA
Found at i:40110823 original size:15 final size:15
Alignment explanation
Indices: 40110803--40110834 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40110793 TCTAACATCT
40110803 AACCCCTAAACCCTA
1 AACCCCTAAACCCTA
*
40110818 AACCCCTAAACCTTA
1 AACCCCTAAACCCTA
40110833 AA
1 AA
40110835 TCTTGGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.16
Consensus pattern (15 bp):
AACCCCTAAACCCTA
Found at i:40111119 original size:15 final size:15
Alignment explanation
Indices: 40111099--40111132 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40111089 CCTAGCACGT
40111099 CTAA-CCTCTAAACCC
1 CTAACCCTCT-AACCC
40111114 CTAACCCTCTAACCC
1 CTAACCCTCTAACCC
40111129 CTAA
1 CTAA
40111133 ACATAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (15 bp):
CTAACCCTCTAACCC
Found at i:40111704 original size:114 final size:114
Alignment explanation
Indices: 40111468--40112232 Score: 964
Period size: 114 Copynumber: 6.7 Consensus size: 114
40111458 ATTTTTGGCT
* ** *
40111468 GCTAAATGCCCTGAAAGCT-AAGAAAACGGCGTCGTTATGCTTAGGTTTTTTTGCGGCGCTTCCT
1 GCTAAAT-CCCCGAAAGCTCAA-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
* * * *
40111532 CAAAAATGCCGCTAAAGCCCTGAGCGTTAGCGGCACTTTCTTAGAAACGCC
64 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * *
40111583 GCTAAATCCCCCGAAAGCTCAAAAAACGACATCGTTGTGCTTAGGTTTTTTTGCGACGCTTTCTC
1 GCTAAAT-CCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTC
* * *
40111648 -AAAATGCCGTTAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
65 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * * *
40111697 GCTAAATCCCCGAAAGCTCACAAAACGACGTCGCTGGGCTTAGGTTTTCTTGCGGCGCTTCCTCA
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
* * *
40111762 AAAACGTCGCTAAAGCCCTGAGCTTTAGCGGCGCTTTCTTAGAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * *
40111811 GCTAAATCTCCCGAAAGCTCAGAAAATGGCGTCGTTGTGTTTAGGTTTTTTT-CTGGCGCTTTCT
1 GCTAAATC-CCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC-GGCGCTTTCT
* * *
40111875 CAGAAACGCCACTAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCC
64 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * *
40111926 GCTAGATCCCCGAAAGCTTAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
* *
40111991 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGC-ATTTACCTAAAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTT-CTTAAAAACGCC
* * * * *
40112040 GCTAAATCCCTGAAAGCTCACAAAATGGCGTCGTTGGGCATATG-TTTTTTGCGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
* ** *
40112104 GAATTGCCGCTAAAGCCCTGAGAATTAGCGGCGCTTTCTTAAAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * * * * *
40112153 GCAAAATCCCCAAAAGCTCAAAAAACAGTGTCGTTGGGCTTATGTTTTTTTTGCGGCTCTTTCTT
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTA-GGTTTTTTTGCGGCGCTTTCTC
*
40112218 AAAAACGTCGCTAAA
65 AAAAACGCCGCTAAA
40112233 TCCCCAAAAG
Statistics
Matches: 563, Mismatches: 78, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
113 146 0.26
114 234 0.42
115 181 0.32
116 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (114 bp):
GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
Found at i:40112252 original size:74 final size:74
Alignment explanation
Indices: 40112131--40112296 Score: 221
Period size: 74 Copynumber: 2.3 Consensus size: 74
40112121 CTGAGAATTA
* *
40112131 GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGTGTCGTTGGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTGGGCTTAG
40112196 GTTTTTTTT
66 GTTTTTTTT
* * * ** *
40112205 GCGGCTCTTTCTTAAAAACGTCGCTAAATCCCCAAAAGCTCGTAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTGGGCTTAG
40112270 G---TTTTT
66 GTTTTTTTT
**
40112276 GCGGCGCTTTCTGGAAAACGC
1 GCGGCGCTTTCTTAAAAACGC
40112297 TGCTAATGCT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
71 22 0.28
74 58 0.73
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (74 bp):
GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTGGGCTTAG
GTTTTTTTT
Found at i:40113971 original size:9 final size:9
Alignment explanation
Indices: 40113886--40113970 Score: 109
Period size: 9 Copynumber: 9.4 Consensus size: 9
40113876 GTAGTGATTC
*
40113886 AATTTGGTT
1 AATTCGGTT
*
40113895 AATTCGATT
1 AATTCGGTT
*
40113904 AATTCGGGT
1 AATTCGGTT
40113913 AATTCGGTT
1 AATTCGGTT
40113922 AATTCGAG-T
1 AATTCG-GTT
*
40113931 AATTCGGAT
1 AATTCGGTT
40113940 AATTCGGTT
1 AATTCGGTT
40113949 AATTCGGTT
1 AATTCGGTT
*
40113958 AATTTGGTT
1 AATTCGGTT
40113967 AATT
1 AATT
40113971 TTTAACCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
8 1 0.01
9 65 0.97
10 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:40115285 original size:16 final size:16
Alignment explanation
Indices: 40115266--40115296 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40115256 TTGAAAAAGT
40115266 TTTCAAATCTATATGG
1 TTTCAAATCTATATGG
*
40115282 TTTCAAATTTATATG
1 TTTCAAATCTATATG
40115297 CTCTGACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATCTATATGG
Found at i:40122523 original size:26 final size:26
Alignment explanation
Indices: 40122494--40122549 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
40122484 CCATTTTTTT
* * *
40122494 AATAAACACCAAAAAATTATTTTAAA
1 AATAAAAAACAAAAAAGTATTTTAAA
*
40122520 AATAAAAAATAAAAAAGTATTTTAAA
1 AATAAAAAACAAAAAAGTATTTTAAA
40122546 AATA
1 AATA
40122550 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (26 bp):
AATAAAAAACAAAAAAGTATTTTAAA
Found at i:40122551 original size:11 final size:11
Alignment explanation
Indices: 40122531--40122560 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
40122521 ATAAAAAATA
40122531 AAAAAGTATTTT
1 AAAAA-TATTTT
40122543 AAAAATATTTT
1 AAAAATATTTT
40122554 AAAAATA
1 AAAAATA
40122561 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40124750 original size:6 final size:6
Alignment explanation
Indices: 40124739--40124770 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40124729 AATTAAAGGT
40124739 GGTGGG GGTGGG GGTGGG GGTGGG GGTGGG GG
1 GGTGGG GGTGGG GGTGGG GGTGGG GGTGGG GG
40124771 AGGGAGCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.84, T:0.16
Consensus pattern (6 bp):
GGTGGG
Found at i:40137074 original size:20 final size:19
Alignment explanation
Indices: 40137035--40137076 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40137025 GTTCAATTAA
* *
40137035 ATAAAAAAATTTATTTTTT
1 ATAAAAAAATTTACTATTT
40137054 ATAAAAAAATGTTACTATTT
1 ATAAAAAAAT-TTACTATTT
40137074 ATA
1 ATA
40137077 TTTTGTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAAAAAAATTTACTATTT
Found at i:40137128 original size:17 final size:17
Alignment explanation
Indices: 40137106--40137139 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40137096 TATTTTTATT
*
40137106 AGTGAATAATATTCAAA
1 AGTGAATAAAATTCAAA
40137123 AGTGAATAAAATTCAAA
1 AGTGAATAAAATTCAAA
40137140 CCACTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (17 bp):
AGTGAATAAAATTCAAA
Found at i:40138020 original size:7 final size:7
Alignment explanation
Indices: 40138008--40138032 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40137998 TGAGAAAAAG
40138008 TAAATTT
1 TAAATTT
40138015 TAAATTT
1 TAAATTT
40138022 TAAATTT
1 TAAATTT
40138029 TAAA
1 TAAA
40138033 AAGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:40138039 original size:14 final size:14
Alignment explanation
Indices: 40138002--40138040 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
40137992 GGTTGATGAG
40138002 AAAAAGTAAATTTT
1 AAAAAGTAAATTTT
***
40138016 AAATTTTAAATTTT
1 AAAAAGTAAATTTT
40138030 AAAAAGTAAAT
1 AAAAAGTAAAT
40138041 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAAAGTAAATTTT
Found at i:40146488 original size:16 final size:18
Alignment explanation
Indices: 40146467--40146504 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40146457 TTCTATATGG
40146467 ATTTTACT-TT-TATTTT
1 ATTTTACTATTGTATTTT
40146483 ATTTTACTATTGTATTTT
1 ATTTTACTATTGTATTTT
40146501 ATTT
1 ATTT
40146505 AAATAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTTACTATTGTATTTT
Found at i:40146728 original size:27 final size:27
Alignment explanation
Indices: 40146698--40146754 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
40146688 GAAGCGACTT
40146698 AGTCATCAAATCTATAGGATTTTCATG
1 AGTCATCAAATCTATAGGATTTTCATG
40146725 AGTCATCAAATCTATAGGATTTTCATG
1 AGTCATCAAATCTATAGGATTTTCATG
40146752 AGT
1 AGT
40146755 ACTAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (27 bp):
AGTCATCAAATCTATAGGATTTTCATG
Found at i:40151213 original size:17 final size:18
Alignment explanation
Indices: 40151191--40151228 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
40151181 GATTTGACAA
40151191 AAAAAAGTT-TAAAACTT
1 AAAAAAGTTGTAAAACTT
40151208 AAAAAAGTTGTAAAACTT
1 AAAAAAGTTGTAAAACTT
40151226 AAA
1 AAA
40151229 GGCCTCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (18 bp):
AAAAAAGTTGTAAAACTT
Found at i:40151213 original size:18 final size:19
Alignment explanation
Indices: 40151190--40151228 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
40151180 TGATTTGACA
40151190 AAAAAAAGTT-TAAAACTT
1 AAAAAAAGTTGTAAAACTT
40151208 -AAAAAAGTTGTAAAACTT
1 AAAAAAAGTTGTAAAACTT
40151226 AAA
1 AAA
40151229 GGCCTCTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 8 0.42
19 2 0.11
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (19 bp):
AAAAAAAGTTGTAAAACTT
Found at i:40156889 original size:9 final size:9
Alignment explanation
Indices: 40156872--40156910 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
40156862 GTTAAATTTT
40156872 ATAATTCGA
1 ATAATTCGA
*
40156881 ATAACTCGA
1 ATAATTCGA
*
40156890 ATAATTTGA
1 ATAATTCGA
40156899 ATAATTCGA
1 ATAATTCGA
40156908 ATA
1 ATA
40156911 GCAGATTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (9 bp):
ATAATTCGA
Found at i:40158891 original size:25 final size:25
Alignment explanation
Indices: 40158854--40158904 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
40158844 TCACTTAATT
40158854 GCCAACTCATTTGGGTTCGATCCTC
1 GCCAACTCATTTGGGTTCGATCCTC
40158879 GCCAACTTC-TTTGGGTTCGATCCTC
1 GCCAAC-TCATTTGGGTTCGATCCTC
40158904 G
1 G
40158905 GAGTACTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (25 bp):
GCCAACTCATTTGGGTTCGATCCTC
Found at i:40159638 original size:13 final size:15
Alignment explanation
Indices: 40159609--40159640 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
40159599 TATGTTATTG
40159609 TTAATATAATATTTA
1 TTAATATAATATTTA
40159624 TTAAT-TAAT-TTTA
1 TTAATATAATATTTA
40159637 TTAA
1 TTAA
40159641 AGGCAATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATATAATATTTA
Found at i:40173794 original size:21 final size:21
Alignment explanation
Indices: 40173756--40173799 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40173746 ATTTATCATA
*
40173756 TTTATTAAATTTAGAAATTAT
1 TTTATTAAATTTAGAAATGAT
*
40173777 TTTATTATAATTT-TAAATGAT
1 TTTATTA-AATTTAGAAATGAT
40173798 TT
1 TT
40173800 ATTTACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTATTAAATTTAGAAATGAT
Found at i:40174252 original size:19 final size:19
Alignment explanation
Indices: 40174230--40174267 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40174220 AGCCATTGTC
*
40174230 ACCCACTGTAATCAAATTT
1 ACCCACCGTAATCAAATTT
40174249 ACCCACCGTAATCAAATTT
1 ACCCACCGTAATCAAATTT
40174268 GTTATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (19 bp):
ACCCACCGTAATCAAATTT
Found at i:40178185 original size:76 final size:77
Alignment explanation
Indices: 40178045--40178221 Score: 252
Period size: 76 Copynumber: 2.3 Consensus size: 77
40178035 CAACCCCTTG
* * * *
40178045 GGGGAATCAGTACTTAGCAACCCCCTTCACATTTCAAAGATATGGTGGAATCAGCACTTAGCAAC
1 GGGGAATTAGCACTTAGCAACCCCCTTCACATTTCAAAAATACGGTGGAATCAGCACTTAGCAAC
40178110 CACCAAT-GAATA
66 CACCAATAG-ATA
* *
40178122 GGGGAATTAGCATTTAGCAACCCCCTTTCACA-TT-AAAAATACGGTGGGATCAGCACTTAGCAA
1 GGGGAATTAGCACTTAGCAACCCCC-TTCACATTTCAAAAATACGGTGGAATCAGCACTTAGCAA
*
40178185 CCACCAATAGGTA
65 CCACCAATAGATA
40178198 GGGGAATTAGCACTTAGCAACCCC
1 GGGGAATTAGCACTTAGCAACCCC
40178222 TCGGGGGAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
76 59 0.66
77 25 0.28
78 6 0.07
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (77 bp):
GGGGAATTAGCACTTAGCAACCCCCTTCACATTTCAAAAATACGGTGGAATCAGCACTTAGCAAC
CACCAATAGATA
Found at i:40178305 original size:103 final size:103
Alignment explanation
Indices: 40178122--40178325 Score: 311
Period size: 103 Copynumber: 2.0 Consensus size: 103
40178112 CCAATGAATA
* *
40178122 GGGGAATTAGCATTTAGCAACCCCCTTTCACATTAAAAATACGGTGGGATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTAAAAATACGGTGGGATCAGCACTTAGCAACC
* * **
40178187 ACCAATAGGTAGGGGAATTAGCACTTAGCAACCCCTCG
66 ACCAATAGATAGGGGAATCAGCACACAGCAACCCCTCG
*
40178225 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGGATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTAAAAATACGGTGGGATCAGCACTTAGCAACC
* *
40178290 ACC-ATTGAATCGGGGAATCAGCACACAGCAACCCCT
66 ACCAATAG-ATAGGGGAATCAGCACACAGCAACCCCT
40178326 TTATATGCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 3 0.03
103 88 0.97
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTCACATTAAAAATACGGTGGGATCAGCACTTAGCAACC
ACCAATAGATAGGGGAATCAGCACACAGCAACCCCTCG
Found at i:40181833 original size:23 final size:26
Alignment explanation
Indices: 40181793--40181839 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
40181783 ATATTTATGT
*
40181793 TCAATATAGGAAGTAATT-CTAATAA
1 TCAATATAGGAAGAAATTACTAATAA
40181818 TCAAT-TA-GAAGAAATTACTAAT
1 TCAATATAGGAAGAAATTACTAAT
40181840 TCTAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
TCAATATAGGAAGAAATTACTAATAA
Found at i:40193090 original size:210 final size:211
Alignment explanation
Indices: 40192727--40193150 Score: 683
Period size: 210 Copynumber: 2.0 Consensus size: 211
40192717 CAAGAAGTTT
* * *
40192727 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTTGGGGTCAAGAAATAACATTTTGAGAGA
1 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
* *
40192792 TGAGGGTGGTGCATATGATTCTTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
66 CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
* * *
40192857 CGATATTGGAACTAACGAATTTTCATATGATGTCCTAGTTTACTAAATACAGAAGAGTAGGTTTA
131 CGATATTGGAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
40192922 ATATGGTTCAACTTCC
196 ATATGGTTCAACTTCC
* *
40192938 ATAGTCTTGATTGCTGGTTCAGTTTTCC-GATATTGGTAGGGCTCAAGAAATAACATTGT-AGAG
1 ATAGTCTTGATTGCTGGTTCAG-TTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAG
* *
40193001 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGGTGAAATT
65 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAAT
* *
40193066 TTGATATTGTG-ACTAAAGAATTTTCATATGATGCCCTCGTTTACTAAAGACAGAAGAGTAGGTT
130 TCGATATTG-GAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTT
40193130 TAATATGGTTCAACTTCC
194 TAATATGGTTCAACTTCC
40193148 ATA
1 ATA
40193151 AAGAAGCCTG
Statistics
Matches: 197, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
210 143 0.73
211 49 0.25
212 5 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (211 bp):
ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
CGATATTGGAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
ATATGGTTCAACTTCC
Found at i:40196384 original size:18 final size:18
Alignment explanation
Indices: 40196358--40196393 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40196348 ATTGAATCGA
*
40196358 TTGTTATGTTGAAATATT
1 TTGTCATGTTGAAATATT
*
40196376 TTGTCATGTTGGAATATT
1 TTGTCATGTTGAAATATT
40196394 ACTTCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (18 bp):
TTGTCATGTTGAAATATT
Found at i:40196543 original size:55 final size:54
Alignment explanation
Indices: 40196387--40196715 Score: 164
Period size: 55 Copynumber: 5.9 Consensus size: 54
40196377 TGTCATGTTG
* ** * * *
40196387 GAATATTACTTCTTTTGAATCGGTTGTTTATATGTTTAAAAT-AATTGTTATGTAG
1 GAATACTACTTCTTTTGAAT-AATTGTTTATATGGTT-AAATCGATTGTTATGTAA
* * * * *
40196442 GAATACTA-TT-TTTTTAATTGACTGTTTACAT-GTGTAAATGGATTGTTATGTAA
1 GAATACTACTTCTTTTGAA-TAATTGTTTATATGGT-TAAATCGATTGTTATGTAA
* * *
40196495 TAATACTACTTCTTTTGAATCAATTGTTTATACGGTTAAATCGATTGTTCTGGTGAA
1 GAATACTACTTCTTTTGAAT-AATTGTTTATATGGTTAAATCGATTGTTAT-GT-AA
* * * * **
40196552 -ATATTGCTTCTTCTTCTTTGGAATAGATTGTTTATATGTTTAAATCGATTATTATGTTG
1 GA-A-TACTACTTC-T-TTT-GAATA-ATTGTTTATATGGTTAAATCGATTGTTATGTAA
* * ** ** * **
40196611 GAATATTGCTTCTTTTGAATAGATTGTTTATATATTTAAATTAATTGTTATATCG
1 GAATACTACTTCTTTTGAATA-ATTGTTTATATGGTTAAATCGATTGTTATGTAA
* * * * * **
40196666 GAATATTACTTCTTTTGAGTTCATCGTTTATATGTTTAAATTAATTGTTA
1 GAATACTACTTCTTTTGA-ATAATTGTTTATATGGTTAAATCGATTGTTA
40196716 AAAAACACGT
Statistics
Matches: 219, Mismatches: 38, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
52 5 0.02
53 34 0.16
54 6 0.03
55 110 0.50
56 9 0.04
57 4 0.02
58 13 0.06
59 2 0.01
60 7 0.03
61 29 0.13
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (54 bp):
GAATACTACTTCTTTTGAATAATTGTTTATATGGTTAAATCGATTGTTATGTAA
Found at i:40196598 original size:61 final size:57
Alignment explanation
Indices: 40196503--40196651 Score: 160
Period size: 61 Copynumber: 2.6 Consensus size: 57
40196493 AATAATACTA
* * * *
40196503 CTTCTTTTGAATCA-ATTGTTTATACGGTTAAATCGATTGTTCTGGTGAAATATTGCTTCTT
1 CTTC-TTTGAAT-AGATTGTTTATATGTTTAAATCGATTATTATGGTGAAATATTG---CTT
* *
40196564 CTTCTTTGGAATAGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATATTGCTT
1 CTTCTTT-GAATAGATTGTTTATATGTTTAAATCGATTATTATGGTGAAATATTGCTT
*
40196622 C-T-TTTGAATAGATTGTTTATATATTTAAAT
1 CTTCTTTGAATAGATTGTTTATATGTTTAAAT
40196652 TAATTGTTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
55 24 0.30
56 3 0.04
57 1 0.01
58 4 0.05
60 4 0.05
61 43 0.54
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (57 bp):
CTTCTTTGAATAGATTGTTTATATGTTTAAATCGATTATTATGGTGAAATATTGCTT
Found at i:40202181 original size:10 final size:10
Alignment explanation
Indices: 40202132--40202179 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
40202122 TAAACTCTCA
40202132 AAAGATAAAT
1 AAAGATAAAT
* ** *
40202142 ACATTTAATT
1 AAAGATAAAT
40202152 AAAGATAAAT
1 AAAGATAAAT
40202162 AAAGATAAAT
1 AAAGATAAAT
40202172 AAA-ATAAA
1 AAAGATAAA
40202180 ATCCTAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40203157 original size:27 final size:26
Alignment explanation
Indices: 40203127--40203193 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
40203117 GCACATAATT
*
40203127 GGGAAGCCTTCTCTCAAGCCATATAAC
1 GGGAAGCCTTATCT-AAGCCATATAAC
* * *
40203154 GGGAAG-CTTATGTGAGCCATGTAAC
1 GGGAAGCCTTATCTAAGCCATATAAC
*
40203179 GGGAAGCTTTATCTA
1 GGGAAGCCTTATCTA
40203194 GGCTGTAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 16 0.50
26 10 0.31
27 6 0.19
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (26 bp):
GGGAAGCCTTATCTAAGCCATATAAC
Found at i:40203374 original size:26 final size:26
Alignment explanation
Indices: 40203345--40203395 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40203335 CGGAGAGTTA
40203345 TTAATC-AGGAAGCTCAAAAAGAGCCT
1 TTAATCGA-GAAGCTCAAAAAGAGCCT
**
40203371 TTAATCGAGAAGCTCACGAAGAGCC
1 TTAATCGAGAAGCTCAAAAAGAGCC
40203396 ATATAACGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
TTAATCGAGAAGCTCAAAAAGAGCCT
Done.