Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 11 of 170
Found at i:3213639 original size:11 final size:12
Alignment explanation
Indices: 3213623--3213651 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3213613 TTGGCCTCTC
3213623 CTTTTTCTT-TT
1 CTTTTTCTTCTT
3213634 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3213646 CTTTTT
1 CTTTTT
3213652 TTTAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3216824 original size:11 final size:11
Alignment explanation
Indices: 3216804--3216865 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 11
3216794 AGAAAATTAA
3216804 AAAAAGTATTTT
1 AAAAA-TATTTT
3216816 AAAAATATTTT
1 AAAAATATTTT
**
3216827 AAAAATA--AA
1 AAAAATATTTT
3216836 AAAAAGTATTTT
1 AAAAA-TATTTT
3216848 -AAAATATTTTT
1 AAAAATA-TTTT
3216859 AAAAATA
1 AAAAATA
3216866 AAAAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 21 0.51
12 11 0.27
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:3216887 original size:32 final size:32
Alignment explanation
Indices: 3216791--3216870 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
3216781 CAAAAAAAAA
*
3216791 TTTAGAAAATTAAAAAAAGTATTTTAAAA-ATAT
1 TTTA-AAAATAAAAAAAAGTATTTTAAAATAT-T
3216824 TTTAAAAATAAAAAAAAGTATTTTAAAATATT
1 TTTAAAAATAAAAAAAAGTATTTTAAAATATT
3216856 TTTAAAAATAAAAAA
1 TTTAAAAATAAAAAA
3216871 TATATATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 39 0.87
33 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (32 bp):
TTTAAAAATAAAAAAAAGTATTTTAAAATATT
Found at i:3218912 original size:16 final size:17
Alignment explanation
Indices: 3218874--3218912 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3218864 AATAAGATAC
*
3218874 ATAAATAAATAGTAATA
1 ATAAATAAATAGCAATA
3218891 AT-AATAAATA-CAATA
1 ATAAATAAATAGCAATA
3218906 ATAAATA
1 ATAAATA
3218913 TGGTACAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 12 0.60
17 2 0.10
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
ATAAATAAATAGCAATA
Found at i:3221125 original size:2 final size:2
Alignment explanation
Indices: 3221118--3221144 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3221108 TCTAAAAAGT
3221118 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3221145 CTTTGCCATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3221286 original size:14 final size:14
Alignment explanation
Indices: 3221263--3221296 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3221253 ATTTTACCCC
3221263 AAAA-AAAAAGAAA
1 AAAAGAAAAAGAAA
*
3221276 GAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
3221290 AAAAGAA
1 AAAAGAA
3221297 CTTAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:3223533 original size:17 final size:17
Alignment explanation
Indices: 3223502--3223535 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3223492 CAATTGATTT
**
3223502 TTTTTTAATTTTTTAAA
1 TTTTTTAATGATTTAAA
3223519 TTTTTTAATGATTTAAA
1 TTTTTTAATGATTTAAA
3223536 CCTTTATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTTAATGATTTAAA
Found at i:3224547 original size:21 final size:21
Alignment explanation
Indices: 3224480--3224550 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
3224470 ATAAAAACAA
*
3224480 CAAAATAGTAACAATATAATAG
1 CAAAATAGTAGCAA-ATAATAG
* * ** *
3224502 TAAACTAGTAGCAAATAGCAA
1 CAAAATAGTAGCAAATAATAG
*
3224523 CAAAATAGTAGCAAACAATAG
1 CAAAATAGTAGCAAATAATAG
3224544 CAAAATA
1 CAAAATA
3224551 ACACTGAAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
21 26 0.70
22 11 0.30
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (21 bp):
CAAAATAGTAGCAAATAATAG
Found at i:3224550 original size:32 final size:33
Alignment explanation
Indices: 3224480--3224550 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
3224470 ATAAAAACAA
* * * *
3224480 CAAAATAGTAACAATATAATAGTAAACTAGTAG
1 CAAAATAGCAACAAAATAATAGCAAACTAATAG
*
3224513 C-AAATAGCAACAAAATAGTAGCAAAC-AATAG
1 CAAAATAGCAACAAAATAATAGCAAACTAATAG
3224544 CAAAATA
1 CAAAATA
3224551 ACACTGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 5 0.16
32 26 0.81
33 1 0.03
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (33 bp):
CAAAATAGCAACAAAATAATAGCAAACTAATAG
Found at i:3232372 original size:31 final size:35
Alignment explanation
Indices: 3232311--3232373 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 35
3232301 TACATTTGTA
*
3232311 TTATATATATAATTAGTAAAAATATATTTTATTAT
1 TTATATATATAATTAGTAAAAAGATATTTTATTAT
3232346 TTAT-TAT-TAATTAGT-AAAAGAT-TTTTAT
1 TTATATATATAATTAGTAAAAAGATATTTTAT
3232374 ATGATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 6 0.22
32 6 0.22
33 8 0.30
34 3 0.11
35 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (35 bp):
TTATATATATAATTAGTAAAAAGATATTTTATTAT
Found at i:3232692 original size:11 final size:11
Alignment explanation
Indices: 3232678--3232719 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3232668 ATAAAAGCAT
3232678 AAAAAGAAACA
1 AAAAAGAAACA
*
3232689 AAAAAGAAA-T
1 AAAAAGAAACA
*
3232699 AGAAAGAAACA
1 AAAAAGAAACA
*
3232710 AAATAGAAAC
1 AAAAAGAAAC
3232720 GAATAGGGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.76, C:0.07, G:0.12, T:0.05
Consensus pattern (11 bp):
AAAAAGAAACA
Found at i:3232958 original size:29 final size:29
Alignment explanation
Indices: 3232911--3232968 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3232901 TTTTTTAGTT
3232911 GGGTTTATGTTGAATAAATGATTGAATTAG
1 GGGTTTATGTTGAATAAATGATTG-ATTAG
*
3232941 GGGTTTAT-TTG-ATGAAATTATTGATTAG
1 GGGTTTATGTTGAAT-AAATGATTGATTAG
3232969 AATTGATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 11 0.42
30 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (29 bp):
GGGTTTATGTTGAATAAATGATTGATTAG
Found at i:3243107 original size:16 final size:16
Alignment explanation
Indices: 3243086--3243121 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3243076 TTTGGTTCGC
*
3243086 TGTATTGGATTAGAGG
1 TGTATTGGATTAAAGG
3243102 TGTATTGGATTAAAGG
1 TGTATTGGATTAAAGG
3243118 TGTA
1 TGTA
3243122 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAAAGG
Found at i:3243185 original size:44 final size:44
Alignment explanation
Indices: 3243135--3243236 Score: 160
Period size: 39 Copynumber: 2.4 Consensus size: 44
3243125 GCAAATCAAC
3243135 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
1 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
*
3243179 TGTTTGG-T---TG-AATGGAATAGAGGTGTAATAGTAATCTTG
1 TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
3243218 TGTTTGGTTGAATGTAATG
1 TGTTTGGTTGAATGTAATG
3243237 TTAAGATCCG
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
39 35 0.67
40 3 0.06
43 3 0.06
44 11 0.21
ACGTcount: A:0.27, C:0.03, G:0.30, T:0.39
Consensus pattern (44 bp):
TGTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCTTG
Found at i:3243921 original size:22 final size:22
Alignment explanation
Indices: 3243874--3243922 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
3243864 TTCCATTTGC
* * *
3243874 TCTCTTTTTCTTGATTTTGTAT
1 TCTCTTTTTCTTCATTTTCTAA
3243896 TCTCTTTTT-TTCATTTCTCTAA
1 TCTCTTTTTCTTCATTT-TCTAA
3243918 TCTCT
1 TCTCT
3243923 CTCCGCAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.10, C:0.20, G:0.04, T:0.65
Consensus pattern (22 bp):
TCTCTTTTTCTTCATTTTCTAA
Found at i:3246685 original size:32 final size:32
Alignment explanation
Indices: 3246639--3246712 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
3246629 AGGTTCAAAT
*
3246639 CTTGTTGGTAACAATTTTAAATCTTTTTTGTA
1 CTTGTTGCTAACAATTTTAAATCTTTTTTGTA
*
3246671 CTTGTTGCTGACAATTTTAAATCTTTTTTGTA
1 CTTGTTGCTAACAATTTTAAATCTTTTTTGTA
3246703 CTTGTTGCTA
1 CTTGTTGCTA
3246713 TTGATGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (32 bp):
CTTGTTGCTAACAATTTTAAATCTTTTTTGTA
Found at i:3260658 original size:16 final size:16
Alignment explanation
Indices: 3260628--3260661 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3260618 TTTTTTCAAA
3260628 TTTATTAAAATATTAT
1 TTTATTAAAATATTAT
3260644 TTTA-TAAAATAATTAT
1 TTTATTAAAAT-ATTAT
3260660 TT
1 TT
3260662 CCATCCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATTAAAATATTAT
Found at i:3263797 original size:46 final size:45
Alignment explanation
Indices: 3263730--3264137 Score: 444
Period size: 46 Copynumber: 9.6 Consensus size: 45
3263720 TTTGAGTACT
* * *
3263730 TCTGATCAAGAGATAAAGTGATAGGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
3263776 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
3263812 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
3263858 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
3263894 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
3263930 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
3263976 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGTTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
3264022 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
3264068 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCT-TAGCTACACTTA
*
3264113 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
3264138 ATCATACGTA
Statistics
Matches: 324, Mismatches: 17, Indels: 45
0.84 0.04 0.12
Matches are distributed among these distances:
36 94 0.29
37 2 0.01
38 1 0.00
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.02
43 14 0.04
44 7 0.02
45 20 0.06
46 173 0.53
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:3263807 original size:36 final size:36
Alignment explanation
Indices: 3263766--3263956 Score: 247
Period size: 36 Copynumber: 5.0 Consensus size: 36
3263756 GGTAGCTTTA
3263766 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
3263802 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
3263847 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
3263884 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
3263920 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
3263956 G
1 G
3263957 TTAGCCTTAG
Statistics
Matches: 139, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 101 0.73
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:3263867 original size:82 final size:82
Alignment explanation
Indices: 3263730--3264137 Score: 419
Period size: 82 Copynumber: 4.9 Consensus size: 82
3263720 TTTGAGTACT
* * *
3263730 TCTGATCAAGAGATAAAGTGATAGGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
3263795 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
3263812 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
3263877 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* *
3263894 TCTGATCAAGTGAAAAAGTGATAA---GT-GC--TA--T--ACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
3263949 GATAAGTGTTAGCCTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* * * *
3263976 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGTTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
3264041 GATAAGTGTTAGCCTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* * *
3264068 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TCTAGCTACACTTATCTGATC-AG-GGACAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
3264130 GATAAGTG
66 GATAAGTG
3264138 ATCATACGTA
Statistics
Matches: 291, Mismatches: 15, Indels: 43
0.83 0.04 0.12
Matches are distributed among these distances:
72 26 0.09
73 1 0.00
74 1 0.00
76 2 0.01
78 4 0.01
79 3 0.01
80 1 0.00
81 1 0.00
82 133 0.46
83 2 0.01
85 2 0.01
86 2 0.01
88 3 0.01
89 8 0.03
90 3 0.01
91 18 0.06
92 81 0.28
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:3263904 original size:21 final size:20
Alignment explanation
Indices: 3263876--3263941 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
3263866 AGTGAAAAAG
3263876 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
3263896 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
3263912 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
3263932 TGATCAAGTG
1 TGAT-AAGTG
3263942 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:3264965 original size:21 final size:20
Alignment explanation
Indices: 3264941--3264992 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3264931 GCACAAAAAT
*
3264941 AAAAAATGTTAACTTATGGA
1 AAAAAATGTTAAATTATGGA
* *
3264961 AAAAAATGATTAAATTTTGTAA
1 AAAAAATG-TTAAATTATG-GA
3264983 AAAAAATGTT
1 AAAAAATGTT
3264993 TGTTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.30
21 10 0.37
22 9 0.33
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAAAATGTTAAATTATGGA
Found at i:3267890 original size:48 final size:48
Alignment explanation
Indices: 3267808--3267899 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
3267798 AAAATTAGAA
** *
3267808 TAAAAATTATAAAAATAAAATTATTAATATTAAATT-TATATAAACTTC
1 TAAAAATTATAAAAATAAAATTAAAAATAATAAATTATA-ATAAACTTC
*
3267856 TAAAAATTATAAAAA-AATATATAAAAATAATAAATTATAATAAA
1 TAAAAATTATAAAAATAAAAT-TAAAAATAATAAATTATAATAAA
3267900 ATAATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 4 0.11
48 32 0.84
49 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (48 bp):
TAAAAATTATAAAAATAAAATTAAAAATAATAAATTATAATAAACTTC
Found at i:3267908 original size:48 final size:48
Alignment explanation
Indices: 3267806--3267908 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 48
3267796 TAAAAATTAG
** * *
3267806 AATAAAAATTATAAAAATAAAATTATTAATATTAAATTTATATAAACT
1 AATAAAAATTATAAAAATAAAATTAAAAATAATAAATTTATATAAAAT
** *
3267854 TCTAAAAATTATAAAAA-AATATATAAAAATAATAAA-TTATAATAAAAT
1 AATAAAAATTATAAAAATAAAAT-TAAAAATAATAAATTTAT-ATAAAAT
3267902 AATAAAA
1 AATAAAA
3267909 TATTTTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
47 8 0.18
48 36 0.82
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (48 bp):
AATAAAAATTATAAAAATAAAATTAAAAATAATAAATTTATATAAAAT
Found at i:3267921 original size:21 final size:20
Alignment explanation
Indices: 3267856--3267942 Score: 63
Period size: 21 Copynumber: 4.3 Consensus size: 20
3267846 TATAAACTTC
* * *
3267856 TAAAAATTATAAAAAAATATA
1 TAAAAATAAT-AAAAATTTTA
*
3267877 TAAAAATAAT--AAATTATA
1 TAAAAATAATAAAAATTTTA
*
3267895 -ATAAAATAATAAAATATTTTT
1 TA-AAAATAATAAAA-ATTTTA
* *
3267916 TAAAAATATTTAAAATTTTA
1 TAAAAATAATAAAAATTTTA
3267936 TAAAAAT
1 TAAAAAT
3267943 TTTAAAAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.02
18 15 0.28
20 14 0.26
21 23 0.43
22 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATAATAAAAATTTTA
Found at i:3267929 original size:10 final size:9
Alignment explanation
Indices: 3267913--3267962 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
3267903 ATAAAATATT
3267913 TTTTAAAAA
1 TTTTAAAAA
*
3267922 TATTTAAAAT
1 T-TTTAAAAA
3267932 TTTATAAAAA
1 TTT-TAAAAA
3267942 TTTTAAAAA
1 TTTTAAAAA
**
3267951 TCATAAAAA
1 TTTTAAAAA
3267960 TTT
1 TTT
3267963 GAATTGGACC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:3267933 original size:20 final size:19
Alignment explanation
Indices: 3267910--3267962 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
3267900 ATAATAAAAT
*
3267910 ATTTTTTAAAAATATTTAAA
1 ATTTTATAAAAAT-TTTAAA
3267930 ATTTTATAAAAATTTTAAA
1 ATTTTATAAAAATTTTAAA
* *
3267949 A-ATCATAAAAATTT
1 ATTTTATAAAAATTT
3267963 GAATTGGACC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 11 0.37
19 7 0.23
20 12 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTATAAAAATTTTAAA
Found at i:3271956 original size:54 final size:54
Alignment explanation
Indices: 3271898--3272280 Score: 439
Period size: 54 Copynumber: 7.1 Consensus size: 54
3271888 GCAACACCAG
* * * *
3271898 CAACAATGAAAATGCGGGTCAGGACGAGAAGAATGCCACTCAGAGTAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* * *
3271952 CAACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCTCAGAGCAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* * * * * *
3272006 GAACAATGAAAATGCGGGTCAGAATGAGAGCAATGCTGCTCAGAGAAACACCGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* ** * *
3272060 GAACAATGAAAATGCAAGTCAGAACGAGAGCAATGCAACTCAGAGCAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
* * * * * *
3272114 GAACAATGAGAATGCGGATCAGAACGAGCACAATGCTGCTCCA-AGTAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACT-CAGAGCAACACTGA
* * * * *
3272168 GAACAATGAGAATGCGGGTCAGAACGAGAACAATGCCACTCCA-AGTAACACCGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACT-CAGAGCAACACTGA
* *
3272222 CAACAATGAGAATGCAGGTCAGAACGAGAACAATG-TGACTCAGAGCAACACTGA
1 CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCT-ACTCAGAGCAACACTGA
3272276 CAACA
1 CAACA
3272281 GCAACAGCAA
Statistics
Matches: 288, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 284 0.99
55 2 0.01
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (54 bp):
CAACAATGAAAATGCGGGTCAGAACGAGAACAATGCTACTCAGAGCAACACTGA
Found at i:3272087 original size:27 final size:27
Alignment explanation
Indices: 3272057--3272256 Score: 101
Period size: 27 Copynumber: 7.4 Consensus size: 27
3272047 AGAGAAACAC
*
3272057 CGAGAACAATGAAAATGCAAGTCAGAA
1 CGAGAACAATGAGAATGCAAGTCAGAA
* *
3272084 CGAGAGCAATGCA-ACT-CAGAG-CA-ACA
1 CGAGAACAATG-AGAATGCA-AGTCAGA-A
*
3272110 CTGAGAACAATGAGAATGC-GGATCAGAA
1 C-GAGAACAATGAGAATGCAAG-TCAGAA
* * * *
3272138 CGAGCACAATGCTG-CTCCAAGT-A-ACA
1 CGAGAACAATG-AGAATGCAAGTCAGA-A
**
3272164 CTGAGAACAATGAGAATGCGGGTCAGAA
1 C-GAGAACAATGAGAATGCAAGTCAGAA
** * * * * *
3272192 CGAGAACAATGCCACTCCAAGTAACAC
1 CGAGAACAATGAGAATGCAAGTCAGAA
* *
3272219 CGACAACAATGAGAATGCAGGTCAGAA
1 CGAGAACAATGAGAATGCAAGTCAGAA
3272246 CGAGAACAATG
1 CGAGAACAATG
3272257 TGACTCAGAG
Statistics
Matches: 122, Mismatches: 35, Indels: 32
0.65 0.19 0.17
Matches are distributed among these distances:
25 2 0.02
26 12 0.10
27 95 0.78
28 11 0.09
29 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (27 bp):
CGAGAACAATGAGAATGCAAGTCAGAA
Found at i:3272149 original size:162 final size:161
Alignment explanation
Indices: 3271875--3272280 Score: 512
Period size: 162 Copynumber: 2.5 Consensus size: 161
3271865 TTCAAATGAA
* * * * *
3271875 AATGCTGCACAAAGCAACACC-AGCAACAATGAAAATGCGGGTCAGGACGAGAAG-AATGCCACT
1 AATGCTGCTC-AAGAAACACCGAG-AACAATGAAAATGCAGGTCAGAACGAG-AGCAATGCAACT
* * * *
3271938 CAGAGTAACACTGACAACAATGAAAATGTGGGTCAGAATGAGAACAATGCTGCT-CAGAGCAACA
63 CAGAGCAACACTGACAACAATGAAAATGCGGATCAGAACGAGAACAATGCTGCTCCA-AGCAACA
* *
3272002 CTGAGAACAATGAAAATGCGGGTCAGAATGAGAGC
127 CTGAGAACAATGAAAATGCGGGTCAGAACGAGAAC
*
3272037 AATGCTGCTCAGAGAAACACCGAGAACAATGAAAATGCAAGTCAGAACGAGAGCAATGCAACTCA
1 AATGCTGCTCA-AGAAACACCGAGAACAATGAAAATGCAGGTCAGAACGAGAGCAATGCAACTCA
* * * *
3272102 GAGCAACACTGAGAACAATGAGAATGCGGATCAGAACGAGCACAATGCTGCTCCAAGTAACACTG
65 GAGCAACACTGACAACAATGAAAATGCGGATCAGAACGAGAACAATGCTGCTCCAAGCAACACTG
*
3272167 AGAACAATGAGAATGCGGGTCAGAACGAGAAC
130 AGAACAATGAAAATGCGGGTCAGAACGAGAAC
** * * * * **
3272199 AATGCCACTCCAAGTAACACCGACAACAATGAGAATGCAGGTCAGAACGAGAACAATGTGACTCA
1 AATGCTGCT-CAAGAAACACCGAGAACAATGAAAATGCAGGTCAGAACGAGAGCAATGCAACTCA
3272264 GAGCAACACTGACAACA
65 GAGCAACACTGACAACA
3272281 GCAACAGCAA
Statistics
Matches: 212, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
161 3 0.01
162 203 0.96
163 6 0.03
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (161 bp):
AATGCTGCTCAAGAAACACCGAGAACAATGAAAATGCAGGTCAGAACGAGAGCAATGCAACTCAG
AGCAACACTGACAACAATGAAAATGCGGATCAGAACGAGAACAATGCTGCTCCAAGCAACACTGA
GAACAATGAAAATGCGGGTCAGAACGAGAAC
Found at i:3272347 original size:51 final size:51
Alignment explanation
Indices: 3272292--3272390 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 51
3272282 CAACAGCAAC
3272292 AACAACAACGAAAATGCAAGTCAGAACGAGAACAATGC-TGCTCAGAGCAGT
1 AACAACAACGAAAATGCAAGTCAGAACGAGAACAATGCAT-CTCAGAGCAGT
* * *
3272343 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGC
1 AACAACAACGAAAATGCAAGTCAGAACGAGAACAATGCATCTCAGAGC
3272391 TTCACCGACA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (51 bp):
AACAACAACGAAAATGCAAGTCAGAACGAGAACAATGCATCTCAGAGCAGT
Found at i:3272442 original size:63 final size:63
Alignment explanation
Indices: 3272343--3272469 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
3272333 TCAGAGCAGT
* * * *
3272343 AACAACAATGAAAATGCAAGTCAGGATGAGAACAATGCATCTCAGAGCTTCACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCTACACCGACACCACC
*
3272406 AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCTTCTCAGAGCTACACCGACACCACC
1 AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCTACACCGACACCACC
3272469 A
1 A
3272470 CCAATGAGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.43, C:0.28, G:0.16, T:0.13
Consensus pattern (63 bp):
AACAACAATGAAAATGCAAGTCAGAACGAAAACAATGCATCTCAGAGCTACACCGACACCACC
Found at i:3274178 original size:31 final size:31
Alignment explanation
Indices: 3274143--3274202 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3274133 CTGAATTTAG
*
3274143 CAACTAGGTCCACTTTGGTATTTGAACTTGA
1 CAACTAGATCCACTTTGGTATTTGAACTTGA
* *
3274174 CAACTAGATCCATTTTGGTCTTTGAACTT
1 CAACTAGATCCACTTTGGTATTTGAACTT
3274203 AGATTCTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (31 bp):
CAACTAGATCCACTTTGGTATTTGAACTTGA
Found at i:3281355 original size:13 final size:13
Alignment explanation
Indices: 3281283--3281359 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 13
3281273 TTAAAAAATA
*
3281283 TTTTA-TTTATCT
1 TTTTATTTTATTT
*
3281295 ATTTATTTTATTT
1 TTTTATTTTATTT
*
3281308 TCTTAATTTTATTT
1 T-TTTATTTTATTT
**
3281322 TTGCATTTTCGAATATT
1 TTTTATTTT---AT-TT
3281339 TTTTATTTTATTT
1 TTTTATTTTATTT
3281352 TTTTATTT
1 TTTTATTT
3281360 CCCTATTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.08
13 22 0.43
14 14 0.27
16 2 0.04
17 9 0.18
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:3288212 original size:5 final size:5
Alignment explanation
Indices: 3288197--3288230 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
3288187 AATTTTTTTA
3288197 GCCCGG GCCCG GCCCG GCCCG GCCCG GCCCG GCC
1 GCCC-G GCCCG GCCCG GCCCG GCCCG GCCCG GCC
3288231 TGAATTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.59, G:0.41, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:3289767 original size:76 final size:76
Alignment explanation
Indices: 3289641--3289791 Score: 284
Period size: 76 Copynumber: 2.0 Consensus size: 76
3289631 GGTTTGCCAG
*
3289641 AATTGTTTGTAATTACTTGTGCATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTACATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
3289706 AAATTCAAATT
66 AAATTCAAATT
*
3289717 AATTGTTTGTAATTACTTGTATATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
1 AATTGTTTGTAATTACTTGTACATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
3289782 AAATTCAAAT
66 AAATTCAAAT
3289792 AAGTAATCTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (76 bp):
AATTGTTTGTAATTACTTGTACATTATAATCATTTTTTATTTTTAAGATTTGATTGTTTGTAATT
AAATTCAAATT
Found at i:3289884 original size:16 final size:16
Alignment explanation
Indices: 3289863--3289896 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3289853 ATATAAATTC
3289863 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
3289879 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
3289895 AA
1 AA
3289897 CTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:3290533 original size:13 final size:13
Alignment explanation
Indices: 3290515--3290547 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3290505 ATTTTTGAAT
3290515 TATTTAGCT-ATAA
1 TATTTAG-TGATAA
3290528 TATTTAGTGATAA
1 TATTTAGTGATAA
3290541 TATTTAG
1 TATTTAG
3290548 GAAAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.05
13 18 0.95
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:3291446 original size:12 final size:12
Alignment explanation
Indices: 3291431--3291461 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3291421 TTTATTTTTG
3291431 TATTTTTGAATA
1 TATTTTTGAATA
3291443 TATTTTTGAATA
1 TATTTTTGAATA
3291455 TATTTTT
1 TATTTTT
3291462 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (12 bp):
TATTTTTGAATA
Found at i:3292662 original size:16 final size:16
Alignment explanation
Indices: 3292641--3292708 Score: 102
Period size: 16 Copynumber: 4.2 Consensus size: 16
3292631 TTTGGTTCGC
3292641 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGA
3292657 TGTATTGGATTAGA-A
1 TGTATTGGATTAGAGA
*
3292672 GTGTATTGGATTAGAGG
1 -TGTATTGGATTAGAGA
*
3292689 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGA
3292705 TGTA
1 TGTA
3292709 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
15 1 0.02
16 48 0.98
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGA
Found at i:3292682 original size:32 final size:32
Alignment explanation
Indices: 3292641--3292708 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
3292631 TTTGGTTCGC
3292641 TGTATTGGATTAGAGATGTATTGGATTAGAAG
1 TGTATTGGATTAGAGATGTATTGGATTAGAAG
* *
3292673 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGATGTATTGGATTAGAAG
3292705 TGTA
1 TGTA
3292709 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGATGTATTGGATTAGAAG
Found at i:3293032 original size:157 final size:157
Alignment explanation
Indices: 3292838--3293147 Score: 539
Period size: 157 Copynumber: 2.0 Consensus size: 157
3292828 CCCTTAGCAT
*
3292838 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
3292903 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
3292968 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
* * * *
3292995 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
3293060 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
3293125 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
3293148 ATATTCTTAT
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 144 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:3293144 original size:82 final size:81
Alignment explanation
Indices: 3292901--3293150 Score: 186
Period size: 76 Copynumber: 3.1 Consensus size: 81
3292891 TATTATTATC
* * *
3292901 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTAT-ATTAAAATATAT
3292966 AATTTAATAAAATTCTT
65 AATTTAATAAAATTCTT
* * * * *
3292983 AATAATTACCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT-TTAAAT
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAATATATTATATTAAAA
* * * * *
3293037 TTTGATAAGATT-AT-TAA-TATG
60 TAT-ATAA-TTTAATAAAATTCTT
3293058 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATA-TTAAAATATAT
3293123 AATTTAATAAAATTCTT
65 AATTTAATAAAATTCTT
*
3293140 AATAATTAATA
1 AATAATAAATA
3293151 TTCTTATATG
Statistics
Matches: 121, Mismatches: 24, Indels: 46
0.63 0.13 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 10 0.08
76 21 0.17
77 6 0.05
78 8 0.07
79 8 0.07
80 6 0.05
81 21 0.17
82 20 0.17
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (81 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATATTAAAATATATA
ATTTAATAAAATTCTT
Found at i:3298876 original size:41 final size:41
Alignment explanation
Indices: 3298811--3299003 Score: 287
Period size: 41 Copynumber: 4.7 Consensus size: 41
3298801 TCTTTCGGGG
**
3298811 CTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
3298852 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* * * * * *
3298893 CTTTAGTGGCGTTTCTAGAAAAGTGCCGCTAAAGCTCAGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* *
3298934 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGTT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
3298975 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
3299004 AAAAACATTT
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Found at i:3299394 original size:22 final size:23
Alignment explanation
Indices: 3299344--3299394 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
3299334 ATATGATTTA
3299344 GAGTTTAAGGTTTAGGAGTTACT
1 GAGTTTAAGGTTTAGGAGTTACT
*
3299367 -ATTTTAAGGTTTATGGA-TTA-T
1 GAGTTTAAGGTTTA-GGAGTTACT
3299388 GAGTTTA
1 GAGTTTA
3299395 GGGGTTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (23 bp):
GAGTTTAAGGTTTAGGAGTTACT
Found at i:3299662 original size:16 final size:17
Alignment explanation
Indices: 3299643--3299684 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
3299633 AAATTCTTTA
3299643 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
3299659 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
3299676 TAAAATAAT
1 T-AAATAAT
3299685 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:3299895 original size:21 final size:22
Alignment explanation
Indices: 3299877--3299917 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3299867 ATGGTTTATT
3299877 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
*
3299898 GTTTAGGGGTTAGGGATTTA
1 GTTTAAGGGTTAGGGATTTA
3299918 GGGTTTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:3300172 original size:23 final size:23
Alignment explanation
Indices: 3300144--3300190 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
3300134 AACTAATAAT
3300144 TTTTAACAAATAAAATAAA-AAAA
1 TTTTAACAAAT-AAATAAATAAAA
3300167 TTTTAACAAATAAATAAATAAAA
1 TTTTAACAAATAAATAAATAAAA
3300190 T
1 T
3300191 CACTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
TTTTAACAAATAAATAAATAAAA
Found at i:3300276 original size:38 final size:39
Alignment explanation
Indices: 3300193--3300277 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
3300183 AATAAAATCA
*
3300193 CTAAAAATAAGCATTAGCGGCGCTTTTCGGAAAACGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
* * *
3300232 CTAAAAATGAGCATTAGTGGCG-TTTTTAGAAAAGCGCCG
1 CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAA-CGCCG
*
3300271 CAAAAAA
1 CTAAAAA
3300278 ACTAGGCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.22
39 31 0.77
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGCGGCGCTTTTCAGAAAACGCCG
Found at i:3301145 original size:38 final size:38
Alignment explanation
Indices: 3301065--3301146 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
3301055 GGTTACAAAC
* * * *
3301065 TTTATCTGTTTTTTATATGTTTATCTCACAAATTTTCT
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
3301103 TTTATCTGCTTTTTACATGTTTATCTCACAAA-GTTCGG
1 TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTC-G
3301141 TTTATC
1 TTTATC
3301147 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (38 bp):
TTTATCTGCTTTTTACATGTTTATCTCACAAATGTTCG
Found at i:3303726 original size:5 final size:5
Alignment explanation
Indices: 3303716--3303741 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3303706 TTTATCCTTA
3303716 AAAAC AAAAC AAAAC AAAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC AAAAC A
3303742 TAATATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:3303913 original size:43 final size:43
Alignment explanation
Indices: 3303866--3304050 Score: 255
Period size: 43 Copynumber: 4.3 Consensus size: 43
3303856 TTTGTTTTTT
* * *
3303866 AAGCGTCGCTAAAGGTCAGGGTCTTTAGCGGCATTTGTCGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
* * * *
3303909 AAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGAAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
*
3303952 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
* ** *
3303995 AAGCGCCGCTAAAGGTTATGACCTTTAGCGGCGTTTGT-GGGA
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
3304037 AAGCGCCGCTAAAG
1 AAGCGCCGCTAAAG
3304051 TTAGCGACGC
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
42 17 0.13
43 111 0.87
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAA
Found at i:3303921 original size:85 final size:85
Alignment explanation
Indices: 3303805--3304050 Score: 246
Period size: 86 Copynumber: 2.9 Consensus size: 85
3303795 AAAGCCATGT
** * * *****
3303805 TTTAGCGGCGTTTGTTAAAAAGCGCCGCTAAAACTCATCTTCATT-GTGGCGTTTGTTTTTTAAG
1 TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAACTCATCGTCATTAGCGGCGTTTGTCGAAAAAG
*
3303869 CGTCGCTAAAGGTCAGGGTC
66 CGCCGCTAAAGGTCAGGGTC
* * * *
3303889 TTTAGCGGCATTTGTCGGAAAAGCGTCGCTAAAAGTCATCGTCTTTAGCGGCGTTTGTCGAAAAA
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAACTCATCGTCATTAGCGGCGTTTGTCGAAAAA
*
3303954 GCGCCGCTAAAGGTCATGGTC
65 GCGCCGCTAAAGGTCAGGGTC
** * * * **
3303975 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTAT-GACCTTTAGCGGCGTTTGT-GGGAA
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAACTCATCG-TCATTAGCGGCGTTTGTCGAAAA
3304038 AGCGCCGCTAAAG
64 AGCGCCGCTAAAG
3304051 TTAGCGACGC
Statistics
Matches: 136, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
84 14 0.10
85 41 0.30
86 81 0.60
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (85 bp):
TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAACTCATCGTCATTAGCGGCGTTTGTCGAAAAAG
CGCCGCTAAAGGTCAGGGTC
Found at i:3307872 original size:23 final size:25
Alignment explanation
Indices: 3307837--3307891 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
3307827 AAAATAAAAA
3307837 TATATAATAATTTTAT-ATTAATATT
1 TATATAATAATTTTATAATTAA-ATT
3307862 TATAT-AT-ATTTTATAATTAAATT
1 TATATAATAATTTTATAATTAAATT
*
3307885 TAAATAA
1 TATATAA
3307892 AAATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 14 0.52
24 8 0.30
25 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATAATAATTTTATAATTAAATT
Found at i:3308298 original size:34 final size:35
Alignment explanation
Indices: 3308254--3308320 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
3308244 CAGTAAAATA
*
3308254 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
3308288 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
3308321 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:3308978 original size:21 final size:20
Alignment explanation
Indices: 3308940--3308978 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3308930 AAAAAATGAT
* *
3308940 AAAATTATATTTTTATTCAA
1 AAAATTATAATTTAATTCAA
3308960 AAAATTTATAATTTAATTC
1 AAAA-TTATAATTTAATTC
3308979 TTTCCTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTATAATTTAATTCAA
Found at i:3316655 original size:16 final size:16
Alignment explanation
Indices: 3316617--3316648 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3316607 TCCAAACGTT
3316617 TTCTTT-TTTGATTTC
1 TTCTTTCTTTGATTTC
3316632 TTCTTTCTTTGATTTC
1 TTCTTTCTTTGATTTC
3316648 T
1 T
3316649 GTTTTCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.72
Consensus pattern (16 bp):
TTCTTTCTTTGATTTC
Found at i:3317137 original size:40 final size:40
Alignment explanation
Indices: 3317082--3317171 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
3317072 GGCGTGTGGC
* * *
3317082 TGGCCGTGTGTGAGACATGGCCGTGTGACTGTCGTAGGTG
1 TGGCCGTGTGCGAGACACGACCGTGTGACTGTCGTAGGTG
* *
3317122 TGGCTGTGTGCGAGACACGATCGTGTGACTGTCGTAGGTG
1 TGGCCGTGTGCGAGACACGACCGTGTGACTGTCGTAGGTG
3317162 TGGCCGTGTG
1 TGGCCGTGTG
3317172 ACGGAATGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.12, C:0.18, G:0.42, T:0.28
Consensus pattern (40 bp):
TGGCCGTGTGCGAGACACGACCGTGTGACTGTCGTAGGTG
Found at i:3324345 original size:44 final size:43
Alignment explanation
Indices: 3324247--3324361 Score: 142
Period size: 44 Copynumber: 2.7 Consensus size: 43
3324237 ATTTCGTACA
* * *
3324247 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATTACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
* * **
3324290 ATGCCACTGTCCTAGACAAGGTCTTACATGTAAGTCACA-AGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAA-TCACATA-TCG
3324334 ATGCCAATGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
3324362 CGATAACACA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 28 0.47
44 31 0.53
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
Found at i:3333268 original size:11 final size:11
Alignment explanation
Indices: 3333252--3333281 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3333242 TTAATCAATT
3333252 TTATTTTTATC
1 TTATTTTTATC
*
3333263 TTATTTTTATT
1 TTATTTTTATC
3333274 TTATTTTT
1 TTATTTTT
3333282 CTCTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTATC
Found at i:3337273 original size:32 final size:32
Alignment explanation
Indices: 3337237--3337344 Score: 103
Period size: 32 Copynumber: 3.2 Consensus size: 32
3337227 GTGATGAGAA
3337237 TTGAGTATGGTATGAAATGATGTATTCATGAG
1 TTGAGTATGGTATGAAATGATGTATTCATGAG
* * * * *
3337269 TTGAGTATTGAATGGCTAATGCCATTGTGA-TGA-GAA
1 TTGAGTATGGTAT-G-AAATG--A-TGT-ATTCATGAG
3337305 TTGAGTATGGTATGAAATGATGTATTCATGAG
1 TTGAGTATGGTATGAAATGATGTATTCATGAG
3337337 TTGAGTAT
1 TTGAGTAT
3337345 TGAATGGCTA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
30 1 0.02
31 5 0.09
32 22 0.38
33 1 0.02
34 8 0.14
35 1 0.02
36 14 0.24
37 5 0.09
38 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.37
Consensus pattern (32 bp):
TTGAGTATGGTATGAAATGATGTATTCATGAG
Found at i:3337310 original size:68 final size:68
Alignment explanation
Indices: 3337227--3337364 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
3337217 TATATAGCAA
3337227 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
1 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
3337292 ATT
66 ATT
3337295 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
1 GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
3337360 ATT
66 ATT
3337363 GT
1 GT
3337365 ACAAACAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.36
Consensus pattern (68 bp):
GTGATGAGAATTGAGTATGGTATGAAATGATGTATTCATGAGTTGAGTATTGAATGGCTAATGCC
ATT
Found at i:3340257 original size:6 final size:6
Alignment explanation
Indices: 3340242--3340270 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3340232 CAAACTATCC
3340242 GAAAAA -AAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
3340271 AGCTAAACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:3353076 original size:16 final size:15
Alignment explanation
Indices: 3353030--3353073 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
3353020 CTATAAATTA
3353030 AATCTTTGTATTTTT
1 AATCTTTGTATTTTT
*
3353045 -AT-TTAGTCATTTTT
1 AATCTTTGT-ATTTTT
3353059 AATCTTTGTATTTTT
1 AATCTTTGTATTTTT
3353074 TAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 8 0.33
16 4 0.17
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
AATCTTTGTATTTTT
Found at i:3362028 original size:26 final size:26
Alignment explanation
Indices: 3361977--3362029 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
3361967 AACTTTTGTC
* *
3361977 AAATGTGGGTACCACATTGGATCAAA
1 AAATGTGAGTACCACATTAGATCAAA
3362003 AAATGATGAGTACCACATTAGA-CAAA
1 AAATG-TGAGTACCACATTAGATCAAA
3362029 A
1 A
3362030 GATATCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (26 bp):
AAATGTGAGTACCACATTAGATCAAA
Found at i:3380915 original size:3 final size:3
Alignment explanation
Indices: 3380907--3380938 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3380897 AACAAATAGG
3380907 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3380939 GGACTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3389087 original size:18 final size:18
Alignment explanation
Indices: 3389053--3389091 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3389043 AAAAAGATTT
3389053 AATTTATAAAATGTTAACA
1 AATTTATAAAATGTTAA-A
*
3389072 AATTTA-AAAATTTTAAA
1 AATTTATAAAATGTTAAA
3389089 AAT
1 AAT
3389092 AATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTTATAAAATGTTAAA
Found at i:3391699 original size:29 final size:28
Alignment explanation
Indices: 3391667--3391732 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
3391657 GCTAGAAGTG
3391667 TTTTATAAAAAACGA-CTCATTCCCGTAAT
1 TTTTA-AAAAAACGACCT-ATTCCCGTAAT
* *
3391696 TTTTAAAAAATCGACCTATTTCCGTAA-
1 TTTTAAAAAAACGACCTATTCCCGTAAT
3391723 TTTTAAAAAA
1 TTTTAAAAAA
3391733 TAATTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 10 0.29
28 17 0.50
29 7 0.21
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (28 bp):
TTTTAAAAAAACGACCTATTCCCGTAAT
Found at i:3391726 original size:27 final size:28
Alignment explanation
Indices: 3391667--3391733 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 28
3391657 GCTAGAAGTG
3391667 TTTTATAAAAAA-CGACTCATTCCCGTAA
1 TTTT-TAAAAAATCGACTCATTCCCGTAA
*
3391695 TTTTTAAAAAATCGAC-CTATTTCCGTAA
1 TTTTTAAAAAATCGACTC-ATTCCCGTAA
3391723 -TTTTAAAAAAT
1 TTTTTAAAAAAT
3391734 AATTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 19 0.53
28 17 0.47
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (28 bp):
TTTTTAAAAAATCGACTCATTCCCGTAA
Found at i:3411145 original size:17 final size:19
Alignment explanation
Indices: 3411112--3411147 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
3411102 TTAAAATTCA
3411112 TTAATAAATTAATTATTTT
1 TTAATAAATTAATTATTTT
3411131 TTAATAAA-T-ATTATTTT
1 TTAATAAATTAATTATTTT
3411148 AACCAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATAAATTAATTATTTT
Found at i:3415003 original size:20 final size:20
Alignment explanation
Indices: 3414966--3415004 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3414956 TTTTAGTTTC
** *
3414966 TTGATAAATTATATATTATT
1 TTGATAAAAAATAAATTATT
3414986 TTGATAAAAAATAAATTAT
1 TTGATAAAAAATAAATTAT
3415005 ACGTTATACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TTGATAAAAAATAAATTATT
Found at i:3416510 original size:31 final size:31
Alignment explanation
Indices: 3416475--3416542 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3416465 AAAATATTTT
3416475 TTTAAAAAATAAAATATAATAATAAATAAGA
1 TTTAAAAAATAAAATATAATAATAAATAAGA
* ** * * *
3416506 TTTAAATAATTTAATATAATGATAAATGATA
1 TTTAAAAAATAAAATATAATAATAAATAAGA
3416537 TTTAAA
1 TTTAAA
3416543 TAGTTAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (31 bp):
TTTAAAAAATAAAATATAATAATAAATAAGA
Found at i:3416543 original size:31 final size:30
Alignment explanation
Indices: 3416487--3416554 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
3416477 TAAAAAATAA
*
3416487 AATATAATAATAAATAAGATTTAAATAATTT
1 AATATAATAATAAATAAGATTTAAAT-AGTT
* * *
3416518 AATATAATGATAAATGATATTTAAATAGTT
1 AATATAATAATAAATAAGATTTAAATAGTT
3416548 AATATAA
1 AATATAA
3416555 ATAACGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (30 bp):
AATATAATAATAAATAAGATTTAAATAGTT
Found at i:3421526 original size:59 final size:59
Alignment explanation
Indices: 3421402--3421526 Score: 134
Period size: 59 Copynumber: 2.1 Consensus size: 59
3421392 TTGGTACATG
*
3421402 ATTTTTT-TTATTAAATTTGATACTCGAGTTTTTTTTGTCTCAATTAAGTACCAAAGTT
1 ATTTTTTAATATTAAATTTGATACTCGAGTTTTTTTTGTCTCAATTAAGTACCAAAGTT
* * * *
3421460 -TGATTTTAATATTCAATTTGATAC-CTGAGCTTTTTTTATG-C-CAATTAAGTACCTATGTT
1 AT-TTTTTAATATTAAATTTGATACTC-GAG-TTTTTTT-TGTCTCAATTAAGTACCAAAGTT
3421519 ATTTTTTA
1 ATTTTTTA
3421527 TTAGAGCAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
57 1 0.02
58 5 0.09
59 38 0.69
60 9 0.16
61 2 0.04
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.51
Consensus pattern (59 bp):
ATTTTTTAATATTAAATTTGATACTCGAGTTTTTTTTGTCTCAATTAAGTACCAAAGTT
Found at i:3421629 original size:25 final size:25
Alignment explanation
Indices: 3421578--3421630 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3421568 ATTTGGTTTG
** **
3421578 AGTACCAAATTGGACATTAAATTCA
1 AGTACCAAATTAAACATTAAAACCA
3421603 AGTACCAAATTAAACATTAAAACCA
1 AGTACCAAATTAAACATTAAAACCA
3421628 AGT
1 AGT
3421631 GCAGATACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (25 bp):
AGTACCAAATTAAACATTAAAACCA
Found at i:3422819 original size:39 final size:39
Alignment explanation
Indices: 3422765--3422844 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
3422755 ACACTAAAGA
*
3422765 AAGAGAAATTTTTTTCCAAATAAAAACAATATATTCAAT
1 AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
3422804 AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
1 AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
3422843 AA
1 AA
3422845 TTGATTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (39 bp):
AAGAGAAATTTTTTTCCAAATAAAAACAACATATTCAAT
Found at i:3425199 original size:20 final size:19
Alignment explanation
Indices: 3425156--3425201 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3425146 ATGAAAACAC
*
3425156 AAATAAATAAACAAATAAA
1 AAATAAACAAACAAATAAA
3425175 AAATAAACAAA-AAATATAA
1 AAATAAACAAACAAATA-AA
3425194 AGAATAAA
1 A-AATAAA
3425202 AAGTACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 13 0.54
20 6 0.25
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (19 bp):
AAATAAACAAACAAATAAA
Found at i:3426795 original size:13 final size:13
Alignment explanation
Indices: 3426777--3426814 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
3426767 TAGGGTTTTT
*
3426777 GCCACTATTTTGG
1 GCCACTGTTTTGG
3426790 GCCACTGTATTTGG
1 GCCACTGT-TTTGG
3426804 GCCACTGTTTT
1 GCCACTGTTTT
3426815 TGTATTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39
Consensus pattern (13 bp):
GCCACTGTTTTGG
Found at i:3433032 original size:12 final size:12
Alignment explanation
Indices: 3433017--3433050 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
3433007 AATATTTTAT
3433017 AAAAAAAGGAAA
1 AAAAAAAGGAAA
3433029 AAAAAAA-GAAA
1 AAAAAAAGGAAA
3433040 AACAAAAAGGA
1 AA-AAAAAGGA
3433051 GAGGTCAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.30
12 12 0.60
13 2 0.10
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGAAA
Found at i:3433983 original size:44 final size:44
Alignment explanation
Indices: 3433933--3434155 Score: 141
Period size: 44 Copynumber: 4.9 Consensus size: 44
3433923 TATCATGGCG
**
3433933 AATCTTATCTCCCTGAAGTTACAGTGAAGCAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCCACT
* * *
3433977 AATCTTATAC-CCCTAAAGTTGTAGTG--GGATGAATTGAAGTCATCCTAGT
1 AATCTTAT-CTCCCTGAAGTTGTAGTGAAGCA-G-ATTGAAG----CC-ACT
* * *
3434026 GAATCTTATCTCCTTGAAGATGTAGTGGAGCA-AGTTGAAGCCACT
1 -AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGA-TTGAAGCCACT
* * * ** *
3434071 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCCA-CT
* * * *
3434116 AATCTTATTTCCCAGAAGTTATAGTGGAA-TAGATTGAAGC
1 AATCTTATCTCCCTGAAGTTGTAGT-GAAGCAGATTGAAGC
3434156 TATAAATAAC
Statistics
Matches: 138, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
42 2 0.01
43 1 0.01
44 62 0.45
45 34 0.25
46 4 0.03
48 2 0.01
49 4 0.03
50 27 0.20
52 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCCACT
Found at i:3434064 original size:94 final size:94
Alignment explanation
Indices: 3433878--3434097 Score: 282
Period size: 94 Copynumber: 2.3 Consensus size: 94
3433868 GTCAGTAAAA
* * * * *
3433878 CCACAAATCCTATACCCCTAAAGTTGCAGTGGGATGAATTGAAGTTATCATGGCGAATCTTATCT
1 CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCATAGCGAATCTTATCT
*
3433943 CCCTGAAGTTACAGTGAAGCAGATTGAAG
66 CCCTGAAGATACAGTGAAGCAGATTGAAG
* *
3433972 CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCCTAGTGAATCTTATCT
1 CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCATAGCGAATCTTATCT
* ** *
3434037 CCTTGAAGATGTAGTGGAGCA-AGTTGAAG
66 CCCTGAAGATACAGTGAAGCAGA-TTGAAG
* *
3434066 CCACTAGTCTTAT-CTCCCTGAAGTTGTAGTGG
1 CCACTAATCTTATAC-CCCTAAAGTTGTAGTGG
3434098 AGCAGACTGA
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
93 2 0.02
94 108 0.98
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (94 bp):
CCACTAATCTTATACCCCTAAAGTTGTAGTGGGATGAATTGAAGTCATCATAGCGAATCTTATCT
CCCTGAAGATACAGTGAAGCAGATTGAAG
Found at i:3434313 original size:44 final size:44
Alignment explanation
Indices: 3434220--3434333 Score: 138
Period size: 44 Copynumber: 2.6 Consensus size: 44
3434210 TTTTATCTTT
* *
3434220 CTGAAGTTGCAGTGGAGCAGGTTAAAGATACCAATCTTATATCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAGATACCAATCCTATATCC
* * * * ** *
3434264 TTGAAGTTGCAGTGGCGCAGATTGAAGCTATTAATCCTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAGATACCAATCCTATATCC
*
3434308 CTGAAGTTGCAGTGGAGCGGATTAAA
1 CTGAAGTTGCAGTGGAGCAGATTAAA
3434334 ATGATAAATC
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATTAAAGATACCAATCCTATATCC
Found at i:3434344 original size:44 final size:44
Alignment explanation
Indices: 3434220--3434377 Score: 121
Period size: 44 Copynumber: 3.6 Consensus size: 44
3434210 TTTTATCTTT
*
3434220 CTGAAGTTGCAGTGGAGCAGG-TT-AAA-GATACCAATCTTATATCC
1 CTGAAGTTGCAGTGGAGC-GGATTAAAATGATA--AATCCTATATCC
* * * ** * *
3434264 TTGAAGTTGCAGTGGCGCAGATTGAAGCT-ATTAATCCTATCTCC
1 CTGAAGTTGCAGTGGAGCGGATT-AAAATGATAAATCCTATATCC
*
3434308 CTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCCTTTA-CC
1 CTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCCTATATCC
* *
3434351 TCTGAGGTTGCAGTAGG-TCGGATTAAA
1 -CTGAAGTTGCAGT-GGAGCGGATTAAA
3434378 TCTATCATAG
Statistics
Matches: 89, Mismatches: 18, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
43 6 0.07
44 78 0.88
45 2 0.02
46 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCCTATATCC
Found at i:3434601 original size:181 final size:179
Alignment explanation
Indices: 3434030--3434654 Score: 539
Period size: 181 Copynumber: 3.4 Consensus size: 179
3434020 CCTAGTGAAT
* * * * ** * * *
3434030 CTTATCTCCTTGAAGATGTAGTGGAGCAAGTTGAAGCCACTAGTCTTATCTCCCTGAAGTTGTAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCT-CTTGAAGTTGCAG
* * * * *
3434095 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCCAGAAGTTATAGTGGAATAGATTGAAGCTATA
65 TGGAGCAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTATAGTGGAACAGATTGAAGATGTA
* * * *
3434160 AATAACATATCTTATCTCTCTGAAGTTGCAATAGTGTAGATCATATAAAAT
130 AATAACA-ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATATCAAAC
* ** * *
3434211 TTTATCTTTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCAA-TCTTATATCCTTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CAAGTCTTATCT-CTTGAAGTTGCA
* * * * * * ** * * *
3434275 GTGGCGCAGATTGAAGCTA-TTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAATGA
64 GTGGAGCAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTATAGTGGAACAGATTGAAGATG-
* * * *
3434338 TAAAT--C-CT-TTA-C-CTCTGAGGTTGCAGTAGGTCGGATTAAATCTATCATAGCAAAC
128 TAAATAACAATCTTATCTCTCTGAAGTTGCAGTA-----GAGTAGATC-AT-AT--CAAAC
* * *
3434393 CTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAGATACAAGTCTTATCTCTGTGAAGTTACAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCT-TGAAGTTGCAG
* * * *
3434458 TGGAGCAGACTGAAGATAGTGAATCTTATTTTCTTGAAGTTATAGTGGAACAAATTGAAGTTGTA
65 TGGAGCAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTATAGTGGAACAGATTGAAGATGTA
*
3434523 AATAACAAATCTTATCTATCTGAAGTTGCAGTAGAGTAGATCATATCAAAC
130 AATAAC-AATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATATCAAAC
* * * * * * *
3434574 CTTATCTCCCTGAAGTTGCAATGGAGTAGGTTGGAGCTGCAAATCTTATATTCTTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTAT-CTCTTGAAGTTGCAG
* *
3434639 TGGGGCAGATTGAAGA
65 TGGAGCAGACTGAAGA
3434655 CGGGCTACAA
Statistics
Matches: 345, Mismatches: 76, Indels: 46
0.74 0.16 0.10
Matches are distributed among these distances:
173 14 0.04
174 1 0.00
175 3 0.01
176 1 0.00
178 7 0.02
179 5 0.01
180 34 0.10
181 140 0.41
182 73 0.21
183 34 0.10
184 6 0.02
185 8 0.02
187 1 0.00
188 3 0.01
189 1 0.00
190 14 0.04
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (179 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCTTGAAGTTGCAGT
GGAGCAGACTGAAGATAGTGAATCTTATTTCCCTGAAGTTATAGTGGAACAGATTGAAGATGTAA
ATAACAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATATCAAAC
Found at i:3434621 original size:363 final size:366
Alignment explanation
Indices: 3434030--3434701 Score: 909
Period size: 363 Copynumber: 1.8 Consensus size: 366
3434020 CCTAGTGAAT
* ** * * **
3434030 CTTATCTCCTTGAAGATGTAGTGGAGCAAGTTGAAGCCACTAGTCTTATCTCCCTGAAGTTGTAG
1 CTTATCTCCCTGAAGATACAGTGGAGCAAGTTGAAGACACAAGTCTTATCTCCCTGAAGTTACAG
* *
3434095 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCCAGAAGTTATAGTGGAATAGATTGAAGCTATA
66 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCCAGAAGTTATAGTGGAACAAATTGAAGCTATA
* * * ** **
3434160 AATAACATATCTTATCTCTCTGAAGTTGCAATAGTGTAGATCATATAAAATTTTATCTTTCTGAA
131 AATAACAAATCTTATCTATCTGAAGTTGCAATAGAGTAGATCATATAAAACCTTATCTCCCTGAA
* *
3434225 GTTGCAGTGGAGCAGGTTAAAGATACCAATCTTATATCCTTGAAGTTGCAGTGGCGCAGATTG-A
196 GTTGCAATGGAGCAGGTTAAAGATACAAATCTTATATCCTTGAAGTTGCAGTGGCGCAGATTGAA
** *
3434289 -A-GCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCCTTTACCT
261 GAGGCTACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAAATCCTTTACCT
3434352 CTGAGGTTGCAGTAGGTCGGATTAAATCTATCATAGCAAAC
326 CTGAGGTTGCAGTAGGTCGGATTAAATCTATCATAGCAAAC
* * * * **
3434393 CTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAGATACAAGTCTTATCTCTGTGAAGTTACAG
1 CTTATCTCCCTGAAGATACAGTGGAGCAAGTTGAAGACACAAGTCTTATCTCCCTGAAGTTACAG
* * ** * *
3434458 TGGAGCAGACTGAAGATAGTGAATCTTATTTTCTTGAAGTTATAGTGGAACAAATTGAAGTTGTA
66 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCCAGAAGTTATAGTGGAACAAATTGAAGCTATA
* *
3434523 AATAACAAATCTTATCTATCTGAAGTTGCAGTAGAGTAGATCATATCAAACCTTATCTCCCTGAA
131 AATAACAAATCTTATCTATCTGAAGTTGCAATAGAGTAGATCATATAAAACCTTATCTCCCTGAA
* ** * * * *
3434588 GTTGCAATGGAGTAGGTTGGAGCTGCAAATCTTATATTCTTGAAGTTGCAGTGGGGCAGATTGAA
196 GTTGCAATGGAGCAGGTTAAAGATACAAATCTTATATCCTTGAAGTTGCAGTGGCGCAGATTGAA
* *
3434653 GACGGGCTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAA
261 GA--GGCTACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
3434702 GCCGCAAACC
Statistics
Matches: 260, Mismatches: 44, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
363 219 0.84
364 1 0.00
365 1 0.00
368 39 0.15
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (366 bp):
CTTATCTCCCTGAAGATACAGTGGAGCAAGTTGAAGACACAAGTCTTATCTCCCTGAAGTTACAG
TGGAGCAGACTGAAGATAGCGAATCTTATTTCCCAGAAGTTATAGTGGAACAAATTGAAGCTATA
AATAACAAATCTTATCTATCTGAAGTTGCAATAGAGTAGATCATATAAAACCTTATCTCCCTGAA
GTTGCAATGGAGCAGGTTAAAGATACAAATCTTATATCCTTGAAGTTGCAGTGGCGCAGATTGAA
GAGGCTACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAAATCCTTTACCT
CTGAGGTTGCAGTAGGTCGGATTAAATCTATCATAGCAAAC
Found at i:3434836 original size:41 final size:41
Alignment explanation
Indices: 3434779--3434888 Score: 161
Period size: 41 Copynumber: 2.7 Consensus size: 41
3434769 ATTGCAGATA
*
3434779 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCATA-TCAAACC
1 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGT-AAACC
3434820 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGTAAACC
1 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGTAAACC
* *
3434861 TTATCTC-CTTGAAGTTGCAGTGGAGCAG
1 TTATCTCTC-TGAAGTTGTAGTAGAGCAG
3434889 GTTGAATATA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
40 1 0.02
41 62 0.97
42 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (41 bp):
TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGTAAACC
Found at i:3434923 original size:44 final size:45
Alignment explanation
Indices: 3434860--3435017 Score: 135
Period size: 44 Copynumber: 3.6 Consensus size: 45
3434850 CAGAGTAAAC
* * * *
3434860 CTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAATA-TACCAA-T
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAAATTA-CAAGT
* **
3434904 CTTATCTCCCTAAAATTGCAGTGGAGCTTATT-AAAATTACAAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAAATTACAAGT
* * * **
3434948 CTTATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGACAACTAA-T
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAAATTAC-AAGT
* * *
3434993 CCTATCTCCTTGAAGTTGCAGTGGA
1 CTTATCTCCCTAAAGTTGCAGTGGA
3435018 ACGGATTAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
43 6 0.07
44 56 0.62
45 26 0.29
46 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (45 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAAATTACAAGT
Found at i:3438791 original size:89 final size:89
Alignment explanation
Indices: 3438640--3438818 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
3438630 AATAAACCCC
*
3438640 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGTCTGCTGGTCT
1 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
*
3438705 GGTGGATAAATAGAGTGGCAAGTA
66 AGTGGATAAATAGAGTGGCAAGTA
3438729 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
1 TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
3438794 AGTGGATAAATAGAGTGGCAAGTA
66 AGTGGATAAATAGAGTGGCAAGTA
3438818 T
1 T
3438819 CAGAGGTCTT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (89 bp):
TATCTTTAGCCAGTAGGCTTATAAATAAATGTTAGTGAAATATGTTAGAATGGGCCTGCTGGTCT
AGTGGATAAATAGAGTGGCAAGTA
Found at i:3440235 original size:27 final size:27
Alignment explanation
Indices: 3440192--3440258 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
3440182 CCAAACTGAT
* *
3440192 ATAAAATAACTGTTATGCCCCCACGTG
1 ATAAAATGACTGCTATGCCCCCACGTG
* * * *
3440219 GTAAAATGACTGCTATGCCCCTATGTT
1 ATAAAATGACTGCTATGCCCCCACGTG
3440246 ATAAAATGACTGC
1 ATAAAATGACTGC
3440259 ATACTCTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (27 bp):
ATAAAATGACTGCTATGCCCCCACGTG
Found at i:3442505 original size:22 final size:23
Alignment explanation
Indices: 3442453--3442506 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3442443 CGGTTTTAAT
*
3442453 TAAAATTAAAATTATATCTGTAA
1 TAAAATTAAAACTATATCTGTAA
*
3442476 TAAAATTAAAACTA-AT-TGTTA
1 TAAAATTAAAACTATATCTGTAA
3442497 TCAAAATTAA
1 T-AAAATTAA
3442507 TTGTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.18
22 10 0.36
23 13 0.46
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (23 bp):
TAAAATTAAAACTATATCTGTAA
Found at i:3442507 original size:16 final size:16
Alignment explanation
Indices: 3442483--3442520 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3442473 TAATAAAATT
*
3442483 AAAACTAATTGTTATC
1 AAAATTAATTGTTATC
*
3442499 AAAATTAATTGTTATT
1 AAAATTAATTGTTATC
3442515 AAAATT
1 AAAATT
3442521 GTATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATTAATTGTTATC
Found at i:3442762 original size:52 final size:52
Alignment explanation
Indices: 3442684--3442787 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
3442674 ATTGCATGTT
*
3442684 CACCATCCTGTTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
1 CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
3442736 CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
1 CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
3442788 ATTAAAAGAA
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:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (52 bp):
CACCATCCTATTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
Found at i:3442983 original size:16 final size:16
Alignment explanation
Indices: 3442962--3442995 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3442952 TTTATAGCAA
3442962 TAAACATACTTAATTT
1 TAAACATACTTAATTT
3442978 TAAACATACTTAATTT
1 TAAACATACTTAATTT
3442994 TA
1 TA
3442996 TCCTGTCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAACATACTTAATTT
Found at i:3443198 original size:9 final size:9
Alignment explanation
Indices: 3443181--3443214 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3443171 ACTGAAGAAA
*
3443181 CATCATCAT
1 CATCGTCAT
3443190 CATCGTCAT
1 CATCGTCAT
*
3443199 CATCGTCGT
1 CATCGTCAT
3443208 CATCGTC
1 CATCGTC
3443215 CCTTTTGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (9 bp):
CATCGTCAT
Found at i:3445502 original size:45 final size:45
Alignment explanation
Indices: 3445438--3445533 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 45
3445428 AGCAAGGCAA
3445438 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
1 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
* *
3445483 TAATGTGAAATTT-TGAGCTAATTTTCCATTATATAAACAATCGGC
1 TAATGTGAAATTTCT-AGCTAATGTTCCATTATATAAACAATAGGC
3445528 TAATGT
1 TAATGT
3445534 TCCATTTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (45 bp):
TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
Found at i:3445892 original size:21 final size:21
Alignment explanation
Indices: 3445876--3445919 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3445866 AAATTTTTTT
3445876 TAAAAATTTATATATTTAAAA
1 TAAAAATTTATATATTTAAAA
3445897 TAAAAATTTATATATTTAAAA
1 TAAAAATTTATATATTTAAAA
3445918 TA
1 TA
3445920 TTCTCGGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAAATTTATATATTTAAAA
Found at i:3449065 original size:13 final size:13
Alignment explanation
Indices: 3449047--3449077 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3449037 AATTAAGCTA
3449047 CCAAAACTTAGTC
1 CCAAAACTTAGTC
3449060 CCAAAACTTAGTC
1 CCAAAACTTAGTC
3449073 CCAAA
1 CCAAA
3449078 TACCGTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.32, G:0.06, T:0.19
Consensus pattern (13 bp):
CCAAAACTTAGTC
Found at i:3450601 original size:9 final size:10
Alignment explanation
Indices: 3450578--3450603 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3450568 TAAAAAGTCT
3450578 TTTTTATTAA
1 TTTTTATTAA
3450588 TTTTTATTAA
1 TTTTTATTAA
3450598 TTTTTA
1 TTTTTA
3450604 ATTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:3451163 original size:22 final size:23
Alignment explanation
Indices: 3451131--3451173 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3451121 AAATTTATAA
3451131 TTATAAATTTTTATAACTTTTGT
1 TTATAAATTTTTATAACTTTTGT
* *
3451154 TTAT-AATTTTTGTAATTTTT
1 TTATAAATTTTTATAACTTTT
3451174 AATAGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (23 bp):
TTATAAATTTTTATAACTTTTGT
Found at i:3452349 original size:9 final size:9
Alignment explanation
Indices: 3452314--3452355 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
3452304 CCACATCAAG
3452314 AAATAATTTA
1 AAAT-ATTTA
3452324 AAAT-TTATA
1 AAATATT-TA
3452333 AAAGTATTTA
1 AAA-TATTTA
3452343 AAATATTTA
1 AAATATTTA
3452352 AAAT
1 AAAT
3452356 TAAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.07
9 15 0.52
10 10 0.34
11 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
AAATATTTA
Found at i:3459580 original size:46 final size:46
Alignment explanation
Indices: 3459408--3459579 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
3459398 AAGTAAGTTA
* *
3459408 ACTCTACTAACAGTTCGTGGGATCGAATGATAAAAGAACTCGATACT
1 ACTCTACTAACAGCTCGTGGGATCGAATGGTAAAA-AACTCGATACT
* * * *
3459455 ACTCTATTAACAGCTCGTGGAATTGAATGGTAAAAAACTCAATACT
1 ACTCTACTAACAGCTCGTGGGATCGAATGGTAAAAAACTCGATACT
* ** * * *
3459501 ACTCTACCAGTAGCTCGTGGGATCAAATGGTAAGAAACTCGATGCT
1 ACTCTACTAACAGCTCGTGGGATCGAATGGTAAAAAACTCGATACT
*
3459547 ACTCTACTAACCA-CTCGTGAGATCGAATGGTAA
1 ACTCTACTAA-CAGCTCGTGGGATCGAATGGTAA
3459580 GTAGCTCGAT
Statistics
Matches: 103, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
46 72 0.70
47 31 0.30
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (46 bp):
ACTCTACTAACAGCTCGTGGGATCGAATGGTAAAAAACTCGATACT
Found at i:3468341 original size:39 final size:37
Alignment explanation
Indices: 3468274--3468366 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
3468264 ACCAGAATTG
* *
3468274 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
3468313 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
3468350 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
3468367 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:3468730 original size:3 final size:3
Alignment explanation
Indices: 3468722--3468760 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
3468712 ATTCCCACTC
* * *
3468722 ATA ATA ATA ATA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3468761 CTTACCTCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3469437 original size:11 final size:11
Alignment explanation
Indices: 3469423--3469448 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3469413 CTTTTTCTTC
3469423 TTTCTCCCCTG
1 TTTCTCCCCTG
3469434 TTTCTCCCCTG
1 TTTCTCCCCTG
3469445 TTTC
1 TTTC
3469449 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:3469830 original size:21 final size:21
Alignment explanation
Indices: 3469806--3469848 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3469796 AATAATAACT
3469806 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
3469827 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
3469848 A
1 A
3469849 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:3473795 original size:13 final size:13
Alignment explanation
Indices: 3473777--3473809 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3473767 TTACTTTCTC
3473777 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
3473790 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
*
3473803 TTCCTTT
1 TTTCTTT
3473810 CTTTTTGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTTCTTT
Found at i:3473803 original size:6 final size:6
Alignment explanation
Indices: 3473771--3473815 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
3473761 TTTAGTTTAC
* *
3473771 TTTCTC TTTCTT TTTCTTT TTTCTT TTTCTT TTTC-C TTTCTT TTT
1 TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTT
3473816 GCACTTGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 4 0.12
6 24 0.71
7 6 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:3479839 original size:39 final size:39
Alignment explanation
Indices: 3479796--3479882 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
3479786 GAACACTTAA
*
3479796 ACTTACCCCATGATACTTCTTGAAGTTATATAATTAACG
1 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
*
3479835 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAATG
1 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
3479874 ACTTACCCC
1 ACTTACCCC
3479883 TCCTCCACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (39 bp):
ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
Found at i:3492820 original size:11 final size:11
Alignment explanation
Indices: 3492804--3492831 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3492794 TTACATTCAT
3492804 ATCATAAATCA
1 ATCATAAATCA
3492815 ATCATAAATCA
1 ATCATAAATCA
3492826 ATCATA
1 ATCATA
3492832 TTGTCCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
ATCATAAATCA
Found at i:3494739 original size:75 final size:74
Alignment explanation
Indices: 3494612--3494790 Score: 259
Period size: 75 Copynumber: 2.4 Consensus size: 74
3494602 TGATTCCCCC
* * * * *
3494612 AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATA
3494677 TTAAATGTGA
66 TTAAATGT-A
* * *
3494687 AAGGGTTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATA
3494752 TTAAATGTA
66 TTAAATGTA
3494761 AAGGGGGTTGCTAAGTGCTGATTCTCCCGA
1 AA-GGGGTTGCTAAGTGCTGATTC-CCCGA
3494791 GGGGTTGCTA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
74 3 0.03
75 84 0.91
76 5 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATA
TTAAATGTA
Found at i:3494801 original size:27 final size:26
Alignment explanation
Indices: 3494764--3494816 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
3494754 AAATGTAAAG
* *
3494764 GGGGTTGCTAAGTGCTGATTCTCCCGA
1 GGGGTTGCTAAGAGCTGAATC-CCCGA
3494791 GGGGTTGCTAAGAGCTGAATCCCCGA
1 GGGGTTGCTAAGAGCTGAATCCCCGA
3494817 ATCATTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (26 bp):
GGGGTTGCTAAGAGCTGAATCCCCGA
Found at i:3494801 original size:102 final size:101
Alignment explanation
Indices: 3494688--3494892 Score: 286
Period size: 102 Copynumber: 2.0 Consensus size: 101
3494678 TAAATGTGAA
* * * * * * *
3494688 AGGGTTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGAGCTGAATCCCCGAATCATTGGTGATTACAAAGAGCTGATACCACCGTATCT
*
3494753 TAAATGT-AAAGGGGGTTGCTAAGTGCTGATTCTCCCG
66 TAAATGTGAAA-GGGGTTGCTAAGTGATGATTC-CCCG
* * *
3494790 AGGGGTTGCTAAGAGCTGAATCCCCGAATCATTGGTGATTGCTAAGTGCTGATACCACCGTATCT
1 AGGGGTTGCTAAGAGCTGAATCCCCGAATCATTGGTGATTACAAAGAGCTGATACCACCGTATCT
3494855 TAAATGTGAAAGGGGTTGCTAAGTGATGATTCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTGATGATTCCCCG
3494891 AG
1 AG
3494893 TCATTGGTGG
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
101 6 0.07
102 82 0.90
103 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (101 bp):
AGGGGTTGCTAAGAGCTGAATCCCCGAATCATTGGTGATTACAAAGAGCTGATACCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGATGATTCCCCG
Found at i:3494878 original size:177 final size:177
Alignment explanation
Indices: 3494582--3494904 Score: 522
Period size: 177 Copynumber: 1.8 Consensus size: 177
3494572 ACATTGAATA
** * *
3494582 TAAAGGGGGTTGCTAAGTTTTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTG
1 TAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGAGCTGAATCCCCAATTCATTG
* * * *
3494647 GTGGTTGCTAAGTGCTGATTCCACCGTATATTAAATGTGAAAGGGTTTGCTAAGTGTTGATTCCC
66 GTGATTGCTAAGTGCTGATACCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGATGATTCCC
3494712 CGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATCTTAAATG
131 CGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATCTTAAATG
* *
3494759 TAAAGGGGGTTGCTAAGTGCTGATTCTCCCGAGGGGTTGCTAAGAGCTGAATCCCCGAA-TCATT
1 TAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGAGCTGAATCCCC-AATTCATT
*
3494823 GGTGATTGCTAAGTGCTGATACCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGATGATTCC
65 GGTGATTGCTAAGTGCTGATACCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGATGATTCC
*
3494888 CCGAGTCATTGGTGGTT
130 CCGACTCATTGGTGGTT
3494905 GCTAAGTGCT
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
177 131 0.98
178 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (177 bp):
TAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGAGCTGAATCCCCAATTCATTG
GTGATTGCTAAGTGCTGATACCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGATGATTCCC
CGACTCATTGGTGGTTACAAAGAGCTGATTCCACCGTATCTTAAATG
Found at i:3495424 original size:101 final size:101
Alignment explanation
Indices: 3495293--3495521 Score: 370
Period size: 101 Copynumber: 2.3 Consensus size: 101
3495283 GAATATAAAG
* * *
3495293 GGGGTTGCTAAGTGCTGATTCCCCTAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCC-GAGGGGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGT
*
3495358 TGCAAAGTGCTGATTCCACCGTATCTTAAATGTG-AA
65 TGCAAAGTGCTGATCCCACCGTATCTTAAATGTGAAA
*
3495394 GGGGTTGCTAAGTGCTGATTCTCCCGAGGGGTTGCTAAGTGTTAATTCCCCGAATCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTC-CCCGAGGGGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGT
*
3495459 TGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAA
65 TGCAAAGTGCTGATCCCACCGTATCTTAAATGTGAAA
*
3495496 GTGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
3495522 CTCATTGGTG
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
101 94 0.79
102 25 0.21
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (101 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTT
GCAAAGTGCTGATCCCACCGTATCTTAAATGTGAAA
Found at i:3495441 original size:27 final size:26
Alignment explanation
Indices: 3495393--3495446 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
3495383 TTAAATGTGA
*
3495393 AGGGGTTGCTAAGTGCTGATTCTCCCG
1 AGGGGTTGCTAAGTGCTAATTC-CCCG
*
3495420 AGGGGTTGCTAAGTGTTAATTCCCCG
1 AGGGGTTGCTAAGTGCTAATTCCCCG
3495446 A
1 A
3495447 ATCATTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTAATTCCCCG
Found at i:3495861 original size:26 final size:27
Alignment explanation
Indices: 3495832--3495885 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3495822 CACCAATGAT
3495832 TCGGG-GAATCAACACTTAGCAACCCC
1 TCGGGAGAATCAACACTTAGCAACCCC
3495858 TCGGGAGAATCAACACTTAGCAACCCC
1 TCGGGAGAATCAACACTTAGCAACCCC
3495885 T
1 T
3495886 TCACATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (27 bp):
TCGGGAGAATCAACACTTAGCAACCCC
Found at i:3495922 original size:41 final size:41
Alignment explanation
Indices: 3495864--3496035 Score: 151
Period size: 33 Copynumber: 4.6 Consensus size: 41
3495854 CCCCTCGGGA
*
3495864 GAATCAACACTTAGCAACCCCTTCACATTTAAGATACGGTG
1 GAATCAGCACTTAGCAACCCCTTCACATTTAAGATACGGTG
* * *
3495905 GAATCAGCACTTTGCAACCAC--CA-A--TGAG-T-CGG-G
1 GAATCAGCACTTAGCAACCCCTTCACATTTAAGATACGGTG
*
3495938 GAATCAGCACTTAGCAACCCCTTTCACATTTAATATACGGTG
1 GAATCAGCACTTAGCAACCCC-TTCACATTTAAGATACGGTG
* * *
3495980 AAATCAGCACTTAACAACCAC--CA-A--TAA-AT-CGG-G
1 GAATCAGCACTTAGCAACCCCTTCACATTTAAGATACGGTG
3496013 GAATCAGCACTTAGCAACCCCTT
1 GAATCAGCACTTAGCAACCCCTT
3496036 AGGGGAATCA
Statistics
Matches: 106, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
33 39 0.37
34 6 0.06
35 3 0.03
36 8 0.08
37 1 0.01
38 2 0.02
39 6 0.06
40 1 0.01
41 21 0.20
42 19 0.18
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (41 bp):
GAATCAGCACTTAGCAACCCCTTCACATTTAAGATACGGTG
Found at i:3495937 original size:101 final size:101
Alignment explanation
Indices: 3495757--3495959 Score: 336
Period size: 101 Copynumber: 2.0 Consensus size: 101
3495747 CACCAATGAG
* * *
3495757 TCGGGGAATCAGCACTTAGCAACCACTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAAC
1 TCGGGGAATCAACACTTAGCAACCACCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAAC
*
3495822 CACCAATGATTCGGGGAATCAACACTTAGCAACCCC
66 CACCAATGAGTCGGGGAATCAACACTTAGCAACCCC
*
3495858 TCGGGAGAATCAACACTTAGCAACC-CCTTCACATTTAAGATACGGTGGAATCAGCACTTTGCAA
1 TCGGG-GAATCAACACTTAGCAACCACCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAA
*
3495922 CCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCC
65 CCACCAATGAGTCGGGGAATCAACACTTAGCAACCCC
3495959 T
1 T
3495960 TTCACATTTA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 77 0.81
102 18 0.19
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (101 bp):
TCGGGGAATCAACACTTAGCAACCACCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAAC
CACCAATGAGTCGGGGAATCAACACTTAGCAACCCC
Found at i:3495985 original size:75 final size:75
Alignment explanation
Indices: 3495858--3496035 Score: 277
Period size: 75 Copynumber: 2.4 Consensus size: 75
3495848 TAGCAACCCC
* * **
3495858 TCGGGAGAATCAACACTTAGCAACCCC-TTCACATTTAAGATACGGTGGAATCAGCACTTTGCAA
1 TCGGG-GAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGAAATCAGCACTTAACAA
* *
3495922 CCACCAATGAG
65 CCACCAATAAA
*
3495933 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAATATACGGTGAAATCAGCACTTAACAAC
1 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGAAATCAGCACTTAACAAC
3495998 CACCAATAAA
66 CACCAATAAA
3496008 TCGGGGAATCAGCACTTAGCAACCCCTT
1 TCGGGGAATCAGCACTTAGCAACCCCTT
3496036 AGGGGAATCA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 20 0.21
75 75 0.79
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.22
Consensus pattern (75 bp):
TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGAAATCAGCACTTAACAAC
CACCAATAAA
Found at i:3496026 original size:176 final size:176
Alignment explanation
Indices: 3495726--3496060 Score: 546
Period size: 176 Copynumber: 1.9 Consensus size: 176
3495716 TCCGTTATCA
*
3495726 GTGGATTCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCACTTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCACTTTCACAT
** * * *
3495791 TTAAGATACGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACC
66 TTAAGATACGGTGAAATCAGCACTTAACAACCACCAATAAATCGGGGAATCAACACTTAGCAACC
*
3495856 CC-TCGGGAGAATCAACACTTAGCAACCCCTTCACATTTAAGATACG
131 CCTTAGGG-GAATCAACACTTAGCAACCCCTTCACATTTAAGATACG
* *
3495902 GTGGAATCAGCACTTTGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCACTTTCACAT
* *
3495967 TTAATATACGGTGAAATCAGCACTTAACAACCACCAATAAATCGGGGAATCAGCACTTAGCAACC
66 TTAAGATACGGTGAAATCAGCACTTAACAACCACCAATAAATCGGGGAATCAACACTTAGCAACC
*
3496032 CCTTAGGGGAATCAGCACTTAGCAACCCC
131 CCTTAGGGGAATCAACACTTAGCAACCCC
3496061 CTTTATATTC
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 142 0.97
177 4 0.03
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (176 bp):
GTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCACTTTCACAT
TTAAGATACGGTGAAATCAGCACTTAACAACCACCAATAAATCGGGGAATCAACACTTAGCAACC
CCTTAGGGGAATCAACACTTAGCAACCCCTTCACATTTAAGATACG
Done.