Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 89 of 226
Found at i:28076128 original size:27 final size:27
Alignment explanation
Indices: 28076091--28076143 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
28076081 GACATTAATA
28076091 AGAGACATTCAATCAACAATTTCTTTG
1 AGAGACATTCAATCAACAATTTCTTTG
*
28076118 AGAGACGTTCAATCAACAATTTCTTT
1 AGAGACATTCAATCAACAATTTCTTT
28076144 AAACCATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (27 bp):
AGAGACATTCAATCAACAATTTCTTTG
Found at i:28082986 original size:51 final size:52
Alignment explanation
Indices: 28082905--28083009 Score: 203
Period size: 51 Copynumber: 2.0 Consensus size: 52
28082895 CTGAATATTG
28082905 TAGAGTTATACTCACAGTTTAAAAAAAAATTACAACTTTAGGTGCATCCAAC
1 TAGAGTTATACTCACAGTTTAAAAAAAAATTACAACTTTAGGTGCATCCAAC
28082957 TAGAGTTATACTCACAGTTT-AAAAAAAATTACAACTTTAGGTGCATCCAAC
1 TAGAGTTATACTCACAGTTTAAAAAAAAATTACAACTTTAGGTGCATCCAAC
28083008 TA
1 TA
28083010 TAACGAGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 33 0.62
52 20 0.38
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (52 bp):
TAGAGTTATACTCACAGTTTAAAAAAAAATTACAACTTTAGGTGCATCCAAC
Found at i:28084226 original size:19 final size:19
Alignment explanation
Indices: 28084167--28084236 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 19
28084157 TATAATTCGG
* *
28084167 ATTTTTATAGTATTTAATAA
1 ATTTATATATTATTTAA-AA
* **
28084187 ATATTATAAATT-TTTGTAA
1 AT-TTATATATTATTTAAAA
28084206 ATTTATATATTATTTAAAA
1 ATTTATATATTATTTAAAA
28084225 A--TATATATTATT
1 ATTTATATATTATT
28084237 AACTATTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
17 11 0.28
18 8 0.20
19 10 0.25
20 5 0.12
21 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTATATATTATTTAAAA
Found at i:28087608 original size:26 final size:26
Alignment explanation
Indices: 28087534--28087613 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 26
28087524 TTGTCAAAAA
* *
28087534 TATAACAA-ATATATATGTATATATAAAT
1 TATAA-AATATATATAAGTATATGT--AT
*
28087562 TATAAAATATATGTACA-TATATGTAT
1 TATAAAATATATATA-AGTATATGTAT
28087588 TATAAAATATATATAAGTATATGTAT
1 TATAAAATATATATAAGTATATGTAT
28087614 ATTTTAAGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 25 0.56
27 2 0.04
28 17 0.38
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (26 bp):
TATAAAATATATATAAGTATATGTAT
Found at i:28087616 original size:28 final size:28
Alignment explanation
Indices: 28087534--28087631 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
28087524 TTGTCAAAAA
* * *
28087534 TATAACAA-ATATATATGTATATATAAAT
1 TATAA-AATATATATAAGTATATGTATAT
*
28087562 TATAAAATATATGTACA-TATATG--TAT
1 TATAAAATATATATA-AGTATATGTATAT
28087588 TATAAAATATATATAAGTATATGTATAT
1 TATAAAATATATATAAGTATATGTATAT
* *
28087616 TTTAAGATAATATATA
1 TATAAAAT-ATATATA
28087632 CAAAAAAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
25 1 0.02
26 22 0.39
27 2 0.04
28 25 0.44
29 7 0.12
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (28 bp):
TATAAAATATATATAAGTATATGTATAT
Found at i:28087714 original size:58 final size:56
Alignment explanation
Indices: 28087637--28087745 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
28087627 ATATACAAAA
* * *
28087637 AAGAATATATGTATGTATATATATATAGGAGTTATAAAATGTAAAACACATATATTAT
1 AAGAATATATGTATATATATAT-TATA-AAGTTATAAAATATAAAACACATATATTAT
* *
28087695 AAGAAT-TCATGTATATATATATTTTAAAGTTATAGAATATAAAACACATAT
1 AAGAATAT-ATGTATATATATATTATAAAGTTATAAAATATAAAACACATAT
28087746 GTATGTATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
56 22 0.49
57 4 0.09
58 19 0.42
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (56 bp):
AAGAATATATGTATATATATATTATAAAGTTATAAAATATAAAACACATATATTAT
Found at i:28089484 original size:44 final size:44
Alignment explanation
Indices: 28089436--28089743 Score: 167
Period size: 44 Copynumber: 7.2 Consensus size: 44
28089426 GTTTTAATCC
* * *
28089436 GCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTTTGTTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
* ** * *
28089480 GCTCCACTACTGCTT-AGGGAGATAAGACTT-G-ATC---CGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTCTTTTG-TCT
** ** * * ** *
28089520 GCTTTACTGCAACTTCAAAGAGATAAGATTTGTGGT-TTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGT-TTCTTTTGTCT
*
28089564 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
* ** * *
28089608 GCTCCACTACTGCTT-AGGGAGATAAGACTT-GATGC----GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTCTTTTG-TCT
* * * * * ** *
28089648 GCTCTACTGCAACTTAAGAGAGATAAGATTTGTGGT-TTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGT-TTCTTTTGTCT
* *
28089692 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
28089736 GCTCCACT
1 GCTCCACT
28089744 ACTGCTTAGG
Statistics
Matches: 190, Mismatches: 54, Indels: 40
0.67 0.19 0.14
Matches are distributed among these distances:
39 2 0.01
40 30 0.16
41 23 0.12
42 2 0.01
43 29 0.15
44 104 0.55
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
Found at i:28089628 original size:128 final size:128
Alignment explanation
Indices: 28089426--28089853 Score: 750
Period size: 128 Copynumber: 3.3 Consensus size: 128
28089416 ATGATTCATC
*
28089426 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
* *
28089491 GCTTAGGGAGATAAGACTTGATCCGATCTGCTTTACTGCAACTTCAAAGAGATAAGATTTGTG
66 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTG
*
28089554 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
28089619 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTT-AAGAGAGATAAGATTTGTG
66 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAA-AGAGATAAGATTTGTG
28089682 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
* * * *
28089747 GCTTAGGGATATAATACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTG
66 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTG
* *
28089810 GTTTTAATCCGCTCCACTACAACTTCAGAGAGATAGGATTGGTT
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
28089854 CTTCCGATCT
Statistics
Matches: 287, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
127 2 0.01
128 284 0.99
129 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (128 bp):
GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTTTGCTCCACTACT
GCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGTG
Found at i:28089930 original size:45 final size:45
Alignment explanation
Indices: 28089898--28090046 Score: 246
Period size: 45 Copynumber: 3.3 Consensus size: 45
28089888 AAAATTTACT
28089898 ATCTTCGACCTACTTCGCTGCCAATATCGGAAGACAAGATCTACA
1 ATCTTCGACCTACTTCGCTGCCAATATCGGAAGACAAGATCTACA
* * *
28089943 ATCTTCGACCTACTTCGTTACAAATA-CAGGAAGACAAGATCTACA
1 ATCTTCGACCTACTTCGCTGCCAATATC-GGAAGACAAGATCTACA
*
28089988 ATCTTCGACCTACTTCGCTGCCAATATAGGAAGACAAGATCTACA
1 ATCTTCGACCTACTTCGCTGCCAATATCGGAAGACAAGATCTACA
28090033 ATCTTCGACCTACT
1 ATCTTCGACCTACT
28090047 CCACTGCTGT
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
44 1 0.01
45 94 0.99
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (45 bp):
ATCTTCGACCTACTTCGCTGCCAATATCGGAAGACAAGATCTACA
Found at i:28090030 original size:90 final size:90
Alignment explanation
Indices: 28089877--28090046 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 90
28089867 TCACTGCCAG
* * * *
28089877 TACAGGAAGGCAAAATTTACTATCTTCGACCTACTTCGCTGCCAATATCGGAAGACAAGATCTAC
1 TACAGGAAGACAAAATCTACAATCTTCGACCTACTTCGCTGCCAATATAGGAAGACAAGATCTAC
28089942 AATCTTCGACCTACTTCGTTACAAA
66 AATCTTCGACCTACTTCGTTACAAA
*
28089967 TACAGGAAGACAAGATCTACAATCTTCGACCTACTTCGCTGCCAATATAGGAAGACAAGATCTAC
1 TACAGGAAGACAAAATCTACAATCTTCGACCTACTTCGCTGCCAATATAGGAAGACAAGATCTAC
28090032 AATCTTCGACCTACT
66 AATCTTCGACCTACT
28090047 CCACTGCTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (90 bp):
TACAGGAAGACAAAATCTACAATCTTCGACCTACTTCGCTGCCAATATAGGAAGACAAGATCTAC
AATCTTCGACCTACTTCGTTACAAA
Found at i:28091080 original size:16 final size:16
Alignment explanation
Indices: 28091059--28091092 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28091049 TTTTTCGTTC
28091059 TTCTTTTCT-TTTCTTT
1 TTCTTTT-TGTTTCTTT
28091075 TTCTTTTTGTTTCTTT
1 TTCTTTTTGTTTCTTT
28091091 TT
1 TT
28091093 TCAAGTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTTTTGTTTCTTT
Found at i:28091544 original size:7 final size:7
Alignment explanation
Indices: 28091528--28091576 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
28091518 GGTAGAGGTT
28091528 TTTTTATG
1 TTTTT-TG
28091536 TTTTTTG
1 TTTTTTG
28091543 TTTTTTG
1 TTTTTTG
*
28091550 TTTTTTA
1 TTTTTTG
28091557 TTTTTT-
1 TTTTTTG
28091563 TTATTTT-
1 TT-TTTTG
28091570 TTTTTTG
1 TTTTTTG
28091577 CCTCTACTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
6 6 0.16
7 27 0.71
8 5 0.13
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (7 bp):
TTTTTTG
Found at i:28091556 original size:23 final size:22
Alignment explanation
Indices: 28091526--28091575 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
28091516 CCGGTAGAGG
*
28091526 TTTTTTTATGTTTTTTGTTTTT
1 TTTTTTTATGTTTTTTATTTTT
*
28091548 TGTTTTTTATTTTTTTTATTTTT
1 T-TTTTTTATGTTTTTTATTTTT
28091571 TTTTT
1 TTTTT
28091576 GCCTCTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (22 bp):
TTTTTTTATGTTTTTTATTTTT
Found at i:28095663 original size:26 final size:26
Alignment explanation
Indices: 28095630--28095693 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
28095620 AAAAATATAA
** *
28095630 AAAATATATATGTATTTATAAATTAT
1 AAAATATATATACATATATAAATTAT
* **
28095656 AAAATATATGTACATATATGTATTAT
1 AAAATATATATACATATATAAATTAT
28095682 AAAATATATATA
1 AAAATATATATA
28095694 TAAGTATACG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (26 bp):
AAAATATATATACATATATAAATTAT
Found at i:28095701 original size:28 final size:26
Alignment explanation
Indices: 28095651--28095706 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
28095641 GTATTTATAA
* * *
28095651 ATTATAAAATATATGTACATATATGT
1 ATTATAAAATATATATAAATATACGT
28095677 ATTATAAAATATATATATAAGTATACGT
1 ATTATAAAATATATATA-AA-TATACGT
28095705 AT
1 AT
28095707 ATTTTAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.64
27 1 0.04
28 8 0.32
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (26 bp):
ATTATAAAATATATATAAATATACGT
Found at i:28103469 original size:11 final size:11
Alignment explanation
Indices: 28103453--28103477 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28103443 TACATTTCAT
28103453 AAATTATAATA
1 AAATTATAATA
28103464 AAATTATAATA
1 AAATTATAATA
28103475 AAA
1 AAA
28103478 GCGTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTATAATA
Found at i:28106636 original size:20 final size:20
Alignment explanation
Indices: 28106605--28106664 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
28106595 ATTTTAAAAT
*
28106605 CAAGTGAAAATGATTTTAAC
1 CAAGTTAAAATGATTTTAAC
* *
28106625 CAA-TTCAAAATGATTTCAAT
1 CAAGTT-AAAATGATTTTAAC
*
28106645 CAAGTTAAAATTATTTTAAC
1 CAAGTTAAAATGATTTTAAC
28106665 ACATCAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (20 bp):
CAAGTTAAAATGATTTTAAC
Found at i:28106661 original size:40 final size:40
Alignment explanation
Indices: 28106602--28106696 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
28106592 ATAATTTTAA
* *
28106602 AATCAAGTGAAAATGATTTTAAC-CAATTCAAAATGA-TTTC
1 AATCAAGTTAAAATTATTTTAACAC-A-TCAAAATGATTTTC
*
28106642 AATCAAGTTAAAATTATTTTAACACATCAAAATTATTTTC
1 AATCAAGTTAAAATTATTTTAACACATCAAAATGATTTTC
* *
28106682 AAACAAGTTAGAATT
1 AATCAAGTTAAAATT
28106697 GCTCCAGGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 8 0.17
40 39 0.81
41 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (40 bp):
AATCAAGTTAAAATTATTTTAACACATCAAAATGATTTTC
Found at i:28106696 original size:21 final size:21
Alignment explanation
Indices: 28106590--28106696 Score: 64
Period size: 20 Copynumber: 5.2 Consensus size: 21
28106580 GAAAATTTTG
* * *
28106590 AAATAATTTTAAAATCAAGTGA
1 AAATTATTTTCAAA-CAAGTTA
* *
28106612 AAATGATTTT-AACCAA-TTCA
1 AAATTATTTTCAAACAAGTT-A
* *
28106632 AAATGA-TTTCAATCAAGTTA
1 AAATTATTTTCAAACAAGTTA
*
28106652 AAATTATTTT--AACACA-TCA
1 AAATTATTTTCAAACA-AGTTA
28106671 AAATTATTTTCAAACAAGTTA
1 AAATTATTTTCAAACAAGTTA
*
28106692 GAATT
1 AAATT
28106697 GCTCCAGGCC
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 19 0.28
20 23 0.34
21 17 0.25
22 9 0.13
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (21 bp):
AAATTATTTTCAAACAAGTTA
Found at i:28110741 original size:16 final size:17
Alignment explanation
Indices: 28110708--28110745 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
28110698 AGCATTTTTA
28110708 TTAAAAAAAAACTTATTT
1 TTAAAAAAAAAC-TATTT
*
28110726 TTAAAATAAAAC-ATTT
1 TTAAAAAAAAACTATTT
28110742 TTAA
1 TTAA
28110746 TTTGACAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAAAAACTATTT
Found at i:28126625 original size:3 final size:3
Alignment explanation
Indices: 28126617--28126644 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28126607 TCCAACTACC
28126617 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
28126645 GCGTGTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:28130201 original size:30 final size:31
Alignment explanation
Indices: 28130167--28130226 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28130157 AAACCTTTTA
*
28130167 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
28130197 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
28130227 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:28131887 original size:95 final size:92
Alignment explanation
Indices: 28131728--28131905 Score: 250
Period size: 94 Copynumber: 1.9 Consensus size: 92
28131718 AACTAATTAT
* * * ** * *
28131728 ATTATAAAAATAGATAAAATTTATTTCAAATTAAATTATAGTGACAATCTCAAATCCTAATATAA
1 ATTATAAAAATAGAAAAAAATTATGTCAAATTAAATTATAGAAAAAATCTCAAATCCAAATATAA
28131793 T-AAAAAGACCAAAACCACAATTTAAA
66 TAAAAAAGACCAAAACCACAATTTAAA
28131819 ATTATAAAAATAAAGAAAAAAAATTATGTCAAATTAAATTATAAGAAAAAATCTCAAATCCAAAT
1 ATTATAAAAAT--AG-AAAAAAATTATGTCAAATTAAATTAT-AGAAAAAATCTCAAATCCAAAT
28131884 ATAATAAAAAAGACCAAAACCA
62 ATAATAAAAAAGACCAAAACCA
28131906 TACTTTGACA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
91 11 0.15
93 2 0.03
94 23 0.31
95 23 0.31
96 16 0.21
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.26
Consensus pattern (92 bp):
ATTATAAAAATAGAAAAAAATTATGTCAAATTAAATTATAGAAAAAATCTCAAATCCAAATATAA
TAAAAAAGACCAAAACCACAATTTAAA
Found at i:28132317 original size:17 final size:18
Alignment explanation
Indices: 28132295--28132336 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
28132285 GTTCAAGGTG
28132295 TAATTAATTTAAA-TT-TT
1 TAATTAA-TTAAATTTATT
28132312 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
28132330 TAATTAA
1 TAATTAA
28132337 AAACCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:28132332 original size:14 final size:14
Alignment explanation
Indices: 28132295--28132337 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
28132285 GTTCAAGGTG
28132295 TAATTAATTTAAATTTT
1 TAATTAA-TTAAA--TT
28132312 TAATTAATTAAATT
1 TAATTAATTAAATT
*
28132326 TATTTAATTAAA
1 TAATTAATTAAA
28132338 AACCTATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:28142401 original size:20 final size:19
Alignment explanation
Indices: 28142376--28142446 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
28142366 ATGTGCAGTC
28142376 AGAGCATCGTAATGCAAACA
1 AGAGCATCGTAATGC-AACA
* * **
28142396 AGAGCAT-GAATATGCTATT
1 AGAGCATCGTA-ATGCAACA
*
28142415 AGAAGCATCGTAGTGCTAACA
1 AG-AGCATCGTAATGC-AACA
28142436 AGAGCATCGTA
1 AGAGCATCGTA
28142447 GTACTATCAG
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (19 bp):
AGAGCATCGTAATGCAACA
Found at i:28147313 original size:24 final size:24
Alignment explanation
Indices: 28147281--28147329 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28147271 GACAATGACA
28147281 TAGTTACAGCATGAAAGGGTAGTT
1 TAGTTACAGCATGAAAGGGTAGTT
28147305 TAGTTACAGCATGAAAGGGTAGTT
1 TAGTTACAGCATGAAAGGGTAGTT
28147329 T
1 T
28147330 GGTTCCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.31
Consensus pattern (24 bp):
TAGTTACAGCATGAAAGGGTAGTT
Found at i:28150038 original size:12 final size:11
Alignment explanation
Indices: 28150010--28150037 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28150000 TAAAGAGATG
28150010 AAAAAAGAAAA
1 AAAAAAGAAAA
28150021 AAAAAAGAAAA
1 AAAAAAGAAAA
28150032 AAAAAA
1 AAAAAA
28150038 AAGGAAAGAA
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:28152124 original size:24 final size:22
Alignment explanation
Indices: 28152047--28152121 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
28152037 CAAGTAAAAA
*
28152047 TAATTAACAAATACTATATAATT
1 TAATTAATAAATACTATATAA-T
* * *
28152070 TAATTGAAATTAGTA-TAAATAAT
1 TAATT--AATAAATACTATATAAT
*
28152093 TTA-TAATAAATACTATATAAT
1 TAATTAATAAATACTATATAAT
28152114 GTAATTAA
1 -TAATTAA
28152122 ATATTTAGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
20 6 0.16
21 7 0.18
22 3 0.08
23 11 0.29
24 6 0.16
25 5 0.13
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAATTAATAAATACTATATAAT
Found at i:28157039 original size:107 final size:109
Alignment explanation
Indices: 28156918--28157169 Score: 280
Period size: 110 Copynumber: 2.3 Consensus size: 109
28156908 CATCTTTTTT
* * *
28156918 TTTTTTTTAGTTTGGGACACTGATGACCGGCACCAATGT-ATT-TAAAAAATTTTGGGTGCTGGC
1 TTTTTTTTACTTTGGGACACTGATGACCGGCACCAATGTCATTAAAAAAAATTTGGGGTGCTGGC
* * * *
28156981 CAGTAGATGGCTGACACCAAGTACAATTTTTA-GTTC-CTAATGCA
66 AAGTAGATGACCGACACCAAGTAC-ATTTTTAGGCTCTC-AATGCA
* * * *
28157025 TTTTTTTTATTTTGGGACACTAAT-AGCCAGCACCAGTGTCATTAAAAAAAAATTTGGGGTGCTG
1 TTTTTTTTACTTTGGGACACTGATGA-CCGGCACCAATGTCATT-AAAAAAAATTTGGGGTGCTG
* * *
28157089 GCAAGTAGATGACCGGCATCAAGTACATTTTTCGGCTCTCAATGCA
64 GCAAGTAGATGACCGACACCAAGTACATTTTTAGGCTCTCAATGCA
* * *
28157135 TTTTTTTTACTTTGGGATACTGATGGCCGACACCA
1 TTTTTTTTACTTTGGGACACTGATGACCGGCACCA
28157170 CCTTTTTCGG
Statistics
Matches: 119, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
106 1 0.01
107 33 0.28
108 3 0.03
109 6 0.05
110 75 0.63
111 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (109 bp):
TTTTTTTTACTTTGGGACACTGATGACCGGCACCAATGTCATTAAAAAAAATTTGGGGTGCTGGC
AAGTAGATGACCGACACCAAGTACATTTTTAGGCTCTCAATGCA
Found at i:28160414 original size:22 final size:22
Alignment explanation
Indices: 28160389--28160457 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
28160379 AATACCATAT
28160389 ACATGCATATTTAATTTAAAGC
1 ACATGCATATTTAATTTAAAGC
* * ** *
28160411 ACAT-TAAATTATAATACAATA-T
1 ACATGCATATT-TAATTTAA-AGC
28160433 ACATGCATATTTAATTTAAAGC
1 ACATGCATATTTAATTTAAAGC
28160455 ACA
1 ACA
28160458 ATAAATTATA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
21 5 0.15
22 23 0.70
23 5 0.15
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (22 bp):
ACATGCATATTTAATTTAAAGC
Found at i:28160418 original size:44 final size:44
Alignment explanation
Indices: 28160356--28160613 Score: 408
Period size: 44 Copynumber: 5.9 Consensus size: 44
28160346 TTCTTATTCC
* * * *
28160356 TAATTTAAAACACGTTAAATTATAATACCATATACATGCATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
*
28160400 TAATTTAAAGCACATTAAATTATAATACAATATACATGCATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
*
28160444 TAATTTAAAGCACAATAAATTATAATACAATATACATACATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
* *
28160488 TATTTTAAAGCACATTAAATTATAATACAATATACATAAATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
*
28160532 TAATTTAAAGCACGTTAAATTATAATACAATATACATACATATT
1 TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
* * *
28160576 TATTTTAAAACTCATTAAATTATAATACAATATACATA
1 TAATTTAAAGCACATTAAATTATAATACAATATACATA
28160614 ACATGTCGAA
Statistics
Matches: 199, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 199 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (44 bp):
TAATTTAAAGCACATTAAATTATAATACAATATACATACATATT
Found at i:28161422 original size:16 final size:16
Alignment explanation
Indices: 28161401--28161436 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28161391 AATAGGCTAA
28161401 AAATAATAAACAAAAC
1 AAATAATAAACAAAAC
**
28161417 AAATAATAAGGAAAAC
1 AAATAATAAACAAAAC
28161433 AAAT
1 AAAT
28161437 TAAAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAATAAACAAAAC
Found at i:28161756 original size:27 final size:27
Alignment explanation
Indices: 28161713--28161786 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
28161703 GGAAAGTGGC
* * * **
28161713 TGGCGGCACCAAAGGTGCCAATGTGAT
1 TGGCGGCACCGATGGTGCCAAAGAAAT
28161740 TGGCGGCACCGATGGTGCCAAAGAAAT
1 TGGCGGCACCGATGGTGCCAAAGAAAT
* *
28161767 TGGTGGCACAGATGGTGCCA
1 TGGCGGCACCGATGGTGCCA
28161787 TACTAAGTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.35, T:0.18
Consensus pattern (27 bp):
TGGCGGCACCGATGGTGCCAAAGAAAT
Found at i:28161801 original size:27 final size:27
Alignment explanation
Indices: 28161740--28161802 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28161730 CCAATGTGAT
* * *
28161740 TGGCGGCACCGATGGTGCCAAAGAAAT
1 TGGCGGCACAGATGGTGCCAAACAAAG
* * *
28161767 TGGTGGCACAGATGGTGCCATACTAAG
1 TGGCGGCACAGATGGTGCCAAACAAAG
28161794 TGGCGGCAC
1 TGGCGGCAC
28161803 TACTCGTGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.35, T:0.17
Consensus pattern (27 bp):
TGGCGGCACAGATGGTGCCAAACAAAG
Found at i:28162230 original size:28 final size:28
Alignment explanation
Indices: 28162171--28162275 Score: 115
Period size: 28 Copynumber: 3.8 Consensus size: 28
28162161 TATTTTGGTA
* **
28162171 TTTTTTGTAATATTTTAGTAAA-AAACCC
1 TTTTTTGTAATATTTTGGTAAATAAA-TT
*
28162199 TTTTTTGTATTATTTTGGTAAATAAATT
1 TTTTTTGTAATATTTTGGTAAATAAATT
* * *
28162227 TTTTTTATAATATTTTGGTATAT-TATT
1 TTTTTTGTAATATTTTGGTAAATAAATT
*
28162254 ATTTTTGTAATATTTTGGTAAA
1 TTTTTTGTAATATTTTGGTAAA
28162276 AAAACCCGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 22 0.34
28 40 0.62
29 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (28 bp):
TTTTTTGTAATATTTTGGTAAATAAATT
Found at i:28165524 original size:14 final size:14
Alignment explanation
Indices: 28165505--28165547 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
28165495 TAACTAAAAC
28165505 TAGAATAATTAAAT
1 TAGAATAATTAAAT
28165519 TAGAATAATTAAAT
1 TAGAATAATTAAAT
*
28165533 TGGAATAATTAAAT
1 TAGAATAATTAAAT
28165547 T
1 T
28165548 TATACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:28165977 original size:12 final size:12
Alignment explanation
Indices: 28165941--28165993 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
28165931 TTGTTTCGAA
28165941 TCTGGCTGGGGC
1 TCTGGCTGGGGC
* *
28165953 ACTGGCTGTGGC
1 TCTGGCTGGGGC
*
28165965 TCTGGTTGGGGC
1 TCTGGCTGGGGC
*
28165977 TCCT-GCTCGGGC
1 T-CTGGCTGGGGC
28165989 TCTGG
1 TCTGG
28165994 TGGTTCCGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.02, C:0.26, G:0.43, T:0.28
Consensus pattern (12 bp):
TCTGGCTGGGGC
Found at i:28168973 original size:23 final size:22
Alignment explanation
Indices: 28168939--28169020 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
28168929 CCTTCCCTCT
* *
28168939 TCTTCTTCTTTCTTTTTTTTTTC
1 TCTTC-TCTTTCTTTTTCTTTCC
*
28168962 TCTTCTCATTTCCTTTTCTTTCC
1 TCTTCTC-TTTCTTTTTCTTTCC
*
28168985 TCTTTTTCTTTCTTTTTCTTCTCC
1 TC-TTCTCTTTCTTTTTCTT-TCC
28169009 T-TTC-CTTTCTTT
1 TCTTCTCTTTCTTT
28169021 CTTTCCCTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 8 0.16
22 4 0.08
23 30 0.60
24 8 0.16
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (22 bp):
TCTTCTCTTTCTTTTTCTTTCC
Found at i:28168981 original size:39 final size:39
Alignment explanation
Indices: 28168911--28169021 Score: 117
Period size: 39 Copynumber: 2.9 Consensus size: 39
28168901 TTACCTTTTT
* * *
28168911 TTTCTTTTTTTTTTC-CTTC-CTTCCCTCTTC-TTCTTC
1 TTTCTTTTTTTTTTCTCTTCTCTTTCCTTTTCTTTCCTC
28168947 TTTCTTTTTTTTTTCTCTTCTCATTTCCTTTTCTTTCCTC
1 TTTCTTTTTTTTTTCTCTTCTC-TTTCCTTTTCTTTCCTC
*
28168987 TTT-TTCTTTCTTTT-TCTTCTCCTTTCC-TTTCTTTC
1 TTTCTT-TTTTTTTTCTCTTCT-CTTTCCTTTTCTTTC
28169022 TTTCCCTCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
36 15 0.23
37 4 0.06
38 9 0.14
39 21 0.32
40 16 0.25
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (39 bp):
TTTCTTTTTTTTTTCTCTTCTCTTTCCTTTTCTTTCCTC
Found at i:28168995 original size:18 final size:17
Alignment explanation
Indices: 28168938--28169018 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
28168928 TCCTTCCCTC
28168938 TTCTTCTTCTTTCT-TTT
1 TTCTT-TTCTTTCTCTTT
*
28168955 TT-TTTTCTCTTCTCATT
1 TTCTTTTCT-TTCTCTTT
*
28168972 TCCTTTTCTTTCCTCTTT
1 TTCTTTTCTTT-CTCTTT
* *
28168990 TTC-TTTCTTTTTCTTC
1 TTCTTTTCTTTCTCTTT
* *
28169006 TCCTTTCCTTTCT
1 TTCTTTTCTTTCT
28169019 TTCTTTCCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
15 4 0.08
16 12 0.24
17 21 0.42
18 13 0.26
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTTTCTTTCTCTTT
Found at i:28168998 original size:17 final size:16
Alignment explanation
Indices: 28168905--28169018 Score: 56
Period size: 16 Copynumber: 7.0 Consensus size: 16
28168895 TAAAAATTAC
28168905 CTTTTT-TTTCTTT-T
1 CTTTTTCTTTCTTTCT
* * *
28168919 TTTTTTCCTTCCTTCCCT
1 CTTTTT-CTTTCTT-TCT
*
28168937 CTTCTTC-TTCTTTCT
1 CTTTTTCTTTCTTTCT
*
28168952 -TTTTTTTTTCTCTTCT
1 CTTTTTCTTTCT-TTCT
* *
28168968 CATTTCCTTTTCTTTCCT
1 CTTTTTC-TTTCTTT-CT
*
28168986 CTTTTTCTTTCTTTTT
1 CTTTTTCTTTCTTTCT
* *
28169002 CTTCTCCTTTCCTTTCT
1 CTTTTTCTTT-CTTTCT
28169019 TTCTTTCCCT
Statistics
Matches: 72, Mismatches: 18, Indels: 17
0.67 0.17 0.16
Matches are distributed among these distances:
14 9 0.12
15 6 0.08
16 22 0.31
17 18 0.25
18 17 0.24
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTTTTCTTTCTTTCT
Found at i:28169002 original size:29 final size:29
Alignment explanation
Indices: 28168955--28169025 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
28168945 TCTTTCTTTT
*
28168955 TTTTTTCTCTTCTCATTTCCTT-TTCTTTCC
1 TTTTTTCT-TTCTCATTT-CTTCTCCTTTCC
*
28168985 TCTTTTTCTTTCT-TTTTCTTCTCCTTTCC
1 T-TTTTTCTTTCTCATTTCTTCTCCTTTCC
28169014 TTTCTTTCTTTC
1 TTT-TTTCTTTC
28169026 CCTCTCCTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 5 0.14
29 19 0.53
30 5 0.14
31 7 0.19
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTTCTTTCTCATTTCTTCTCCTTTCC
Found at i:28169024 original size:13 final size:13
Alignment explanation
Indices: 28168976--28169026 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
28168966 CTCATTTCCT
28168976 TTTCTTTCCTCTT-
1 TTTCTTTCCT-TTC
*
28168989 TTTCTTTCTTTTTC
1 TTTCTTTC-CTTTC
28169003 TTCTCCTTTCCTTTC
1 TT-T-CTTTCCTTTC
28169018 TTTCTTTCC
1 TTTCTTTCC
28169027 CTCTCCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 16 0.50
14 4 0.12
15 7 0.22
16 5 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTTTCCTTTC
Found at i:28169033 original size:19 final size:21
Alignment explanation
Indices: 28168992--28169034 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28168982 TCCTCTTTTT
* *
28168992 CTTTCTTTTTCTTCTCCTTTC
1 CTTTCTTTCTCTTCTCCTCTC
28169013 CTTTCTTTCT-TTC-CCTCTC
1 CTTTCTTTCTCTTCTCCTCTC
28169032 CTT
1 CTT
28169035 CTCCCCCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCTTTCTCTTCTCCTCTC
Found at i:28169177 original size:10 final size:10
Alignment explanation
Indices: 28169149--28169184 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
28169139 GGTGCAGGCT
*
28169149 TTTTTTTTCTA
1 TTTTTTTT-TG
28169160 TTTTTTTTTG
1 TTTTTTTTTG
28169170 TTTTTTTTTG
1 TTTTTTTTTG
28169180 TTTTT
1 TTTTT
28169185 GGTATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:28170425 original size:9 final size:9
Alignment explanation
Indices: 28170411--28170441 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28170401 GTTAAACGAA
28170411 TCGAGTTAT
1 TCGAGTTAT
*
28170420 TCGAGTTAA
1 TCGAGTTAT
28170429 TCGAGTTAT
1 TCGAGTTAT
28170438 TCGA
1 TCGA
28170442 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28170513 original size:9 final size:9
Alignment explanation
Indices: 28170496--28170532 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28170486 TGAGTTTTCG
28170496 AATTCGAAT
1 AATTCGAAT
*
28170505 AACTCGAAT
1 AATTCGAAT
28170514 AATTCGAAT
1 AATTCGAAT
28170523 AATTCGAAT
1 AATTCGAAT
28170532 A
1 A
28170533 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28171008 original size:39 final size:40
Alignment explanation
Indices: 28170914--28171008 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
28170904 GTTTGGAACA
* * *
28170914 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTAGCC
1 AAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTTAGAC
* * * * *
28170954 AAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTATAT
1 AAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTTAGAC
28170993 AAAGCGCCACAAAAAA
1 AAAGCGCCACAAAAAA
28171009 CCTAAGACCA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
39 29 0.64
40 16 0.36
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (40 bp):
AAAGCGCCACAAAAAATAGAGAATTAGCGGCGATTTAGAC
Found at i:28171103 original size:41 final size:41
Alignment explanation
Indices: 28171046--28171308 Score: 305
Period size: 41 Copynumber: 6.4 Consensus size: 41
28171036 ATTTTTTAAA
* *
28171046 CCTTTAGTGGCGTTTTTATCTAAGCGCCGCTAATTCTCTGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* *
28171087 CCTTTAGCGGCGTTTTTATCTAAGCGCCGATAATGCTCAGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* * *
28171128 TCTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* *
28171169 CCTTTGGCGGCGTTTTTATATAAGCGCCGCTAATGCTC-GG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* * * * * * *
28171209 ATCTTTAGCGGCGTTTTTAACTGAGCGCCACGAATTCTCTTG
1 -CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
* * * **
28171251 TCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCAT-TTA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGC-TCTGG
28171292 CCTTTAGCGGCGTTTTT
1 CCTTTAGCGGCGTTTTT
28171309 GCCGAAACGC
Statistics
Matches: 187, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
40 2 0.01
41 183 0.98
42 2 0.01
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCTGG
Found at i:28171184 original size:82 final size:82
Alignment explanation
Indices: 28171047--28171308 Score: 357
Period size: 82 Copynumber: 3.2 Consensus size: 82
28171037 TTTTTTAAAC
* *
28171047 CTTTAGTGGCGTTTTTATCTAAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
*
28171112 GCCGATAATGCTCAGG-T
66 GCCGCTAATGCTC-GGAT
* *
28171129 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTGGCGGCGTTTTTATATAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
28171194 GCCGCTAATGCTCGGAT
66 GCCGCTAATGCTCGGAT
* * * * * * *
28171211 CTTTAGCGGCGTTTTTAACTGAGCGCCACGAATTCTCTTGTCTTTAGCGGCGTTTGTAGCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
** *
28171276 GCCGCTAATGCAT-TTAC
66 GCCGCTAATGC-TCGGAT
28171293 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
28171309 GCCGAAACGC
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
81 2 0.01
82 158 0.98
83 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCTGGCCTTTAGCGGCGTTTTTATCTAAGC
GCCGCTAATGCTCGGAT
Found at i:28171817 original size:14 final size:14
Alignment explanation
Indices: 28171798--28171865 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 14
28171788 TACGGGGTAT
28171798 AGATTTAAGGTTTG
1 AGATTTAAGGTTTG
28171812 AGATTTAAGG-TT-
1 AGATTTAAGGTTTG
* *
28171824 A-ATTTAGGGGTTAG
1 AGATTTA-AGGTTTG
* *
28171838 AGGTTTAGGGGTTTG
1 AGATTTA-AGGTTTG
28171853 AGATTTAAGGTTT
1 AGATTTAAGGTTT
28171866 CAATGGTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
11 5 0.11
12 3 0.07
13 3 0.07
14 16 0.36
15 17 0.39
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.41
Consensus pattern (14 bp):
AGATTTAAGGTTTG
Found at i:28175909 original size:17 final size:18
Alignment explanation
Indices: 28175858--28175950 Score: 55
Period size: 21 Copynumber: 4.8 Consensus size: 18
28175848 ATTGCTTACA
28175858 TTACTTACTAAAATATAT
1 TTACTTACTAAAATATAT
* *
28175876 TACATAATTACTTAAATAT-T
1 T---TACTTACTAAAATATAT
*
28175896 TTACTTACTAAAATTTATAAC
1 TTACTTACTAAAA--TAT-AT
*
28175917 TTACATTACTTAAATATA-
1 TTAC-TTACTAAAATATAT
28175935 TTACATTACTTAAAAT
1 TTAC-TTAC-TAAAAT
28175951 TTATATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
17 10 0.17
18 10 0.17
19 9 0.15
20 5 0.08
21 17 0.29
22 8 0.14
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (18 bp):
TTACTTACTAAAATATAT
Found at i:28175977 original size:45 final size:39
Alignment explanation
Indices: 28175857--28175977 Score: 129
Period size: 38 Copynumber: 3.0 Consensus size: 39
28175847 CATTGCTTAC
* *
28175857 ATTACTTACTAAAATATATTACA-TA-ATTACTTAAATAT
1 ATTACTTACTAAAATTTA-TAAATTACATTACTTAAATAT
* *
28175895 TTTACTTACTAAAATTTATAACTTACATTACTTAAATAT
1 ATTACTTACTAAAATTTATAAATTACATTACTTAAATAT
28175934 ATTACATTACTTAAAATTTATATATATATTACATTACTTAAATA
1 ATTAC-TTAC-TAAAA-TT-TATA-A-ATTACATTACTTAAATA
28175978 AAAATTAGCT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
37 2 0.03
38 18 0.26
39 17 0.25
40 4 0.06
41 5 0.07
42 2 0.03
43 4 0.06
44 1 0.01
45 16 0.23
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (39 bp):
ATTACTTACTAAAATTTATAAATTACATTACTTAAATAT
Found at i:28176548 original size:34 final size:34
Alignment explanation
Indices: 28176505--28176569 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
28176495 CATAACTTAA
28176505 TTAATTAATTAATATTATACATAAATTACATCAC
1 TTAATTAATTAATATTATACATAAATTACATCAC
*
28176539 TTAATTAATTAATATTATACATAACTTACAT
1 TTAATTAATTAATATTATACATAAATTACAT
28176570 TAATATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (34 bp):
TTAATTAATTAATATTATACATAAATTACATCAC
Found at i:28176574 original size:22 final size:22
Alignment explanation
Indices: 28176541--28176591 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
28176531 TACATCACTT
28176541 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
28176562 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
28176584 AATTACAT
1 AATTACAT
28176592 AACTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:28176580 original size:56 final size:56
Alignment explanation
Indices: 28176512--28176625 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
28176502 TAATTAATTA
*
28176512 ATTAATATTATACATAAATTACATCACTTAATTAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
28176568 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
28176624 AT
1 AT
28176626 AACTTACAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.41
Consensus pattern (56 bp):
ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
Found at i:28176592 original size:9 final size:9
Alignment explanation
Indices: 28176578--28176829 Score: 109
Period size: 9 Copynumber: 30.2 Consensus size: 9
28176568 ATTAATATTA
*
28176578 TACATAAAT
1 TACATAACT
28176587 TACATAACT
1 TACATAACT
28176596 TA-ATTAA-T
1 TACA-TAACT
*
28176604 TA-AT-ATT
1 TACATAACT
28176611 ATACATAACT
1 -TACATAACT
28176621 TACATAACT
1 TACATAACT
28176630 TAC--AACT
1 TACATAACT
28176637 TACATAACT
1 TACATAACT
***
28176646 TACATTTTTT
1 TACA-TAACT
*
28176656 TA-ATTA-T
1 TACATAACT
*
28176663 T-CATAAAT
1 TACATAACT
28176671 TACATAACT
1 TACATAACT
* *
28176680 TACTTAATT
1 TACATAACT
*
28176689 TTCATAA--
1 TACATAACT
*
28176696 TAAATAACT
1 TACATAACT
*
28176705 TACACAACT
1 TACATAACT
28176714 TACATAA--
1 TACATAACT
*
28176721 TACTTAACT
1 TACATAACT
* *
28176730 TATATGACT
1 TACATAACT
28176739 TACATAACT
1 TACATAACT
28176748 TACAT-A--
1 TACATAACT
* *
28176754 -GCATAATT
1 TACATAACT
*
28176762 TTCATAA--
1 TACATAACT
*
28176769 TACACAACT
1 TACATAACT
*
28176778 TACATAATT
1 TACATAACT
*
28176787 TTCATAA--
1 TACATAACT
*
28176794 TAAATAACT
1 TACATAACT
28176803 TACATAA--
1 TACATAACT
28176810 TACATAACT
1 TACATAACT
*
28176819 TACATAGCT
1 TACATAACT
28176828 TA
1 TA
28176830 ATTATACTTA
Statistics
Matches: 184, Mismatches: 34, Indels: 50
0.69 0.13 0.19
Matches are distributed among these distances:
5 3 0.02
6 2 0.01
7 42 0.23
8 12 0.07
9 119 0.65
10 6 0.03
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:28176638 original size:16 final size:16
Alignment explanation
Indices: 28176617--28176649 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28176607 TATTATACAT
28176617 AACTTACATAACTTAC
1 AACTTACATAACTTAC
28176633 AACTTACATAACTTAC
1 AACTTACATAACTTAC
28176649 A
1 A
28176650 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:28176640 original size:25 final size:25
Alignment explanation
Indices: 28176612--28176753 Score: 80
Period size: 25 Copynumber: 5.6 Consensus size: 25
28176602 ATTAATATTA
28176612 TACATAACTTACATAACTTACAACT
1 TACATAACTTACATAACTTACAACT
** **
28176637 TACATAACTTACAT-TTTTTTAA-T
1 TACATAACTTACATAACTTACAACT
* *
28176660 TATTCATAAATTACATAACTTACTTAATT
1 TA--CATAACTTACATAACTTAC--AACT
* *
28176689 TTCATAA--TAAATAACTTACACAACT
1 TACATAACTTACATAACTT--ACAACT
* *
28176714 TACATAA--TACTTAACTTATATGACT
1 TACATAACTTACATAACTTACA--ACT
28176739 TACATAACTTACATA
1 TACATAACTTACATA
28176754 GCATAATTTT
Statistics
Matches: 88, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
23 5 0.06
24 4 0.05
25 61 0.69
26 2 0.02
27 12 0.14
28 2 0.02
29 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (25 bp):
TACATAACTTACATAACTTACAACT
Found at i:28176650 original size:34 final size:33
Alignment explanation
Indices: 28176612--28176824 Score: 111
Period size: 34 Copynumber: 6.5 Consensus size: 33
28176602 ATTAATATTA
* *
28176612 TACATAACTTACATAACTTACAACTTACATAACT
1 TACATAATTTACATAA-TTATAACTTACATAACT
** * *
28176646 TACATTTTTTTA-ATTATTCATAAATTACATAACT
1 TACA-TAATTTACATAATT-ATAACTTACATAACT
* * * *
28176680 TACTTAATTTTCATAATAAATAACTTACACAACT
1 TACATAATTTACATAAT-TATAACTTACATAACT
*
28176714 TACATAA--TACTTAACTTATATGACTTACATAACT
1 TACATAATTTACATAA-TTATA--ACTTACATAACT
*** * *
28176748 TACATAGCATA-AT-TTTCATAA--TACACAACT
1 TACATAATTTACATAATT-ATAACTTACATAACT
* *
28176778 TACATAATTTTCATAATAAATAACTTACATAA--
1 TACATAATTTACATAAT-TATAACTTACATAACT
*
28176810 TACATAACTTACATA
1 TACATAATTTACATA
28176825 GCTTAATTAT
Statistics
Matches: 132, Mismatches: 32, Indels: 32
0.67 0.16 0.16
Matches are distributed among these distances:
30 15 0.11
31 2 0.02
32 27 0.20
33 9 0.07
34 72 0.55
35 5 0.04
36 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (33 bp):
TACATAATTTACATAATTATAACTTACATAACT
Found at i:28176729 original size:84 final size:84
Alignment explanation
Indices: 28176574--28176731 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
28176564 TTACATTAAT
* * * *
28176574 ATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATAACTTACAACTTA
1 ATTATACATAAATTACATAACTTAATTAATTAATATAATAAATAACTTACACAACTTACAACATA
28176639 CATAACTTACATTTTTTTA
66 CATAACTTACATTTTTTTA
* * *
28176658 ATTATTCATAAATTACATAACTTACTTAATT-TTCATAATAAATAACTTACACAACTTACATA-A
1 ATTATACATAAATTACATAACTTAATTAATTAAT-ATAATAAATAACTTACACAACTTACA-ACA
*
28176721 TACTTAACTTA
64 TACATAACTTA
28176732 TATGACTTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 1 0.02
84 62 0.97
85 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (84 bp):
ATTATACATAAATTACATAACTTAATTAATTAATATAATAAATAACTTACACAACTTACAACATA
CATAACTTACATTTTTTTA
Found at i:28176784 original size:25 final size:25
Alignment explanation
Indices: 28176755--28176810 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
28176745 ACTTACATAG
*
28176755 CATAATTTTCATAATACACAACTTA
1 CATAATTTTCATAATAAACAACTTA
*
28176780 CATAATTTTCATAATAAATAACTTA
1 CATAATTTTCATAATAAACAACTTA
28176805 CATAAT
1 CATAAT
28176811 ACATAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (25 bp):
CATAATTTTCATAATAAACAACTTA
Found at i:28176800 original size:16 final size:16
Alignment explanation
Indices: 28176789--28176824 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28176779 ACATAATTTT
28176789 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
28176805 CATAATACATAACTTA
1 CATAATAAATAACTTA
28176821 CATA
1 CATA
28176825 GCTTAATTAT
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:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:28182312 original size:21 final size:21
Alignment explanation
Indices: 28182286--28182377 Score: 85
Period size: 21 Copynumber: 4.2 Consensus size: 21
28182276 AACTTAAAGT
* *
28182286 AGAGGCGGCAGCGAGGGAAGC
1 AGAGGCCGCAGCGAGAGAAGC
**
28182307 AGAGGCTACAGCGAGAGAAGC
1 AGAGGCCGCAGCGAGAGAAGC
*
28182328 AGAGGCCGCAGAGAGAGAAGC
1 AGAGGCCGCAGCGAGAGAAGC
** *
28182349 AGCGAGAGAAGCAGCGATAGAAGC
1 A--GAG-GCCGCAGCGAGAGAAGC
28182373 AGAGG
1 AGAGG
28182378 TTCAAAAGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
21 38 0.66
22 3 0.05
23 3 0.05
24 14 0.24
ACGTcount: A:0.37, C:0.17, G:0.43, T:0.02
Consensus pattern (21 bp):
AGAGGCCGCAGCGAGAGAAGC
Found at i:28182355 original size:12 final size:12
Alignment explanation
Indices: 28182315--28182374 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
28182305 GCAGAGGCTA
28182315 CAGCGAGAGAAG
1 CAGCGAGAGAAG
**
28182327 CA--GAG-GCCG
1 CAGCGAGAGAAG
*
28182336 CAGAGAGAGAAG
1 CAGCGAGAGAAG
28182348 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
28182360 CAGCGATAGAAG
1 CAGCGAGAGAAG
28182372 CAG
1 CAG
28182375 AGGTTCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 29 0.74
ACGTcount: A:0.40, C:0.18, G:0.40, T:0.02
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:28182867 original size:43 final size:42
Alignment explanation
Indices: 28182795--28182992 Score: 229
Period size: 42 Copynumber: 4.6 Consensus size: 42
28182785 ATCAAATAGT
* * *
28182795 GGCGTTTTTGACC-AAGCGCCGCTATAGAACATTA-CTTTTAGC
1 GGCGTTTTT-TCCTAAGCGCCGCTAAAGAACATGATC-TTTAGC
*
28182837 GGCGTTTTCTTCCTAAGCGCCTCTAAAGAACATGATCTTTAGC
1 GGCGTTTT-TTCCTAAGCGCCGCTAAAGAACATGATCTTTAGC
* *
28182880 GGCGTTTTTTCCCAAGCGCCGCCAAAGAACATGATCTTTAGC
1 GGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGC
** * *
28182922 GGTATTTTTTCCTAAGCGCTGCTAAAGAACATGATCCTTAGC
1 GGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGC
* *
28182964 GGCGTTTTTTTCTGTAAGCGCCGCAAAAG
1 GGCG-TTTTTTC-CTAAGCGCCGCTAAAG
28182993 TTAGTGACGT
Statistics
Matches: 133, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
42 79 0.59
43 40 0.30
44 14 0.11
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (42 bp):
GGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGC
Found at i:28182895 original size:85 final size:84
Alignment explanation
Indices: 28182795--28182973 Score: 245
Period size: 85 Copynumber: 2.1 Consensus size: 84
28182785 ATCAAATAGT
* * * * *
28182795 GGCGTTTTTGACCAAGCGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTCTTCCTAAGCGCCT
1 GGCGTTTTTTACCAAGCGCCGCCAAAGAACATGATC-TTTAGCGGCATTTT-TTCCTAAGCG-CT
*
28182859 -CTAAAGAACATGATCTTTAGC
63 GCTAAAGAACATGATCCTTAGC
* *
28182880 GGCGTTTTTTCCCAAGCGCCGCCAAAGAACATGATCTTTAGCGGTATTTTTTCCTAAGCGCTGCT
1 GGCGTTTTTTACCAAGCGCCGCCAAAGAACATGATCTTTAGCGGCATTTTTTCCTAAGCGCTGCT
28182945 AAAGAACATGATCCTTAGC
66 AAAGAACATGATCCTTAGC
28182964 GGCGTTTTTT
1 GGCGTTTTTT
28182974 TCTGTAAGCG
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
83 2 0.02
84 40 0.48
85 41 0.49
86 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (84 bp):
GGCGTTTTTTACCAAGCGCCGCCAAAGAACATGATCTTTAGCGGCATTTTTTCCTAAGCGCTGCT
AAAGAACATGATCCTTAGC
Found at i:28184083 original size:15 final size:16
Alignment explanation
Indices: 28184055--28184088 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28184045 ATACATATTT
28184055 AAATGAAATGAGAAAA
1 AAATGAAATGAGAAAA
*
28184071 AAAT-AAATTAGAAAA
1 AAATGAAATGAGAAAA
28184086 AAA
1 AAA
28184089 GATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AAATGAAATGAGAAAA
Found at i:28184113 original size:11 final size:11
Alignment explanation
Indices: 28184097--28184164 Score: 79
Period size: 11 Copynumber: 6.3 Consensus size: 11
28184087 AAGATAATTT
*
28184097 AAATGAAATGG
1 AAATGAAATAG
28184108 AAATGAAAT-G
1 AAATGAAATAG
*
28184118 AGATGGAAATAG
1 AAAT-GAAATAG
28184130 AAATGAAAT-G
1 AAATGAAATAG
28184140 AAATGGAAATAG
1 AAAT-GAAATAG
28184152 AAATGAAAT-G
1 AAATGAAATAG
28184162 AAA
1 AAA
28184165 AAAAAAAGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
10 13 0.25
11 29 0.57
12 9 0.18
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (11 bp):
AAATGAAATAG
Found at i:28184115 original size:5 final size:5
Alignment explanation
Indices: 28184097--28184164 Score: 82
Period size: 5 Copynumber: 12.6 Consensus size: 5
28184087 AAGATAATTT
*
28184097 AAATG AAATGG AAATG AAATG AGATGG AAATAG AAATG AAATG AAATGG
1 AAATG AAAT-G AAATG AAATG AAAT-G AAAT-G AAATG AAATG AAAT-G
28184146 AAATAG AAATG AAATG AAA
1 AAAT-G AAATG AAATG AAA
28184165 AAAAAAAGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
5 32 0.57
6 24 0.43
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:28184132 original size:22 final size:22
Alignment explanation
Indices: 28184097--28184164 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
28184087 AAGATAATTT
*
28184097 AAAT-GAAATGGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
*
28184118 AGATGGAAATAGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
28184140 AAATGGAAATAGAAATGAAATG
1 AAATGGAAATAGAAATGAAATG
28184162 AAA
1 AAA
28184165 AAAAAAAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 3 0.07
22 40 0.93
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (22 bp):
AAATGGAAATAGAAATGAAATG
Found at i:28184701 original size:25 final size:26
Alignment explanation
Indices: 28184651--28184704 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
28184641 AGGAAATGAG
*
28184651 AAAATTTTGAAATTTAAATGAAATTT
1 AAAATTTTGAAATTGAAATGAAATTT
* *
28184677 AAAATTTTGAAA-TGGAATGATATTT
1 AAAATTTTGAAATTGAAATGAAATTT
28184702 AAA
1 AAA
28184705 TTGAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (26 bp):
AAAATTTTGAAATTGAAATGAAATTT
Found at i:28184902 original size:21 final size:21
Alignment explanation
Indices: 28184872--28184923 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28184862 TTGTATATTA
28184872 GGAAA-AAAATAAATTTAAAT
1 GGAAATAAAATAAATTTAAAT
28184892 GGAAATAAAATAAATTTAAAT
1 GGAAATAAAATAAATTTAAAT
*
28184913 GGAAATGAAAT
1 GGAAATAAAAT
28184924 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (21 bp):
GGAAATAAAATAAATTTAAAT
Found at i:28191131 original size:22 final size:22
Alignment explanation
Indices: 28191103--28191153 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
28191093 AGGTAGGTAA
28191103 CTTTTTTTTGCGGTTTTTGCTT
1 CTTTTTTTTGCGGTTTTTGCTT
28191125 CTTTTTTTTGCGGTTTTTGCTT
1 CTTTTTTTTGCGGTTTTTGCTT
28191147 -TTTTTTT
1 CTTTTTTT
28191154 AAAGAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.73
Consensus pattern (22 bp):
CTTTTTTTTGCGGTTTTTGCTT
Found at i:28191706 original size:31 final size:31
Alignment explanation
Indices: 28191671--28191732 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28191661 AGGAAAATTA
28191671 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
28191702 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
28191733 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:28193036 original size:89 final size:88
Alignment explanation
Indices: 28192943--28193271 Score: 408
Period size: 90 Copynumber: 3.7 Consensus size: 88
28192933 ATTCTACAAT
* * * * * * * *
28192943 ATTAATACACAAAAATATAAAATT-AAAATAAAAATATTACGTACTAAGTTAAATTTAAGCACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTAAATATAATACG-ACTAAATTAAATTTAAACACCC
*
28193007 AACAAACTACAAACATATAGGTAAA
65 AACAAACTACAAACAGAT-GGTAAA
* *
28193032 ATTAATATACGAAAATTTTAAATTCAAACTACATATAATACGAACTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTAAATATAATACG-ACTAAATTAAATTTAAACACCC
28193097 AACAAACTACAAACAGATGGATAAA
65 AACAAACTACAAACAGATGG-TAAA
* * * * * * *
28193122 ATTAGTGCATGAAATTTTTAAATTCAAACGATATATAACACAGACTAAATTAAATTTAAACACCC
1 ATTAATACACGAAAATTTTAAATTCAAACTAAATATAATAC-GACTAAATTAAATTTAAACACCC
28193187 AACAAACTACAAACAGATGGGTAAA
65 AACAAACTACAAACAGAT-GGTAAA
* *
28193212 ATTAATACACGAAAATTTTAAATTCAAACTACATATAATATAGACTAAATTAAATTTAAA
1 ATTAATACACGAAAATTTTAAATTCAAACTAAATATAATA-CGACTAAATTAAATTTAAA
28193272 GATACAAAAA
Statistics
Matches: 207, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
89 22 0.11
90 182 0.88
91 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (88 bp):
ATTAATACACGAAAATTTTAAATTCAAACTAAATATAATACGACTAAATTAAATTTAAACACCCA
ACAAACTACAAACAGATGGTAAA
Found at i:28193096 original size:90 final size:90
Alignment explanation
Indices: 28192985--28193271 Score: 418
Period size: 90 Copynumber: 3.2 Consensus size: 90
28192975 AATATTACGT
* * * *
28192985 ACTAAGTTAAATTTAAGCACCCAACAAACTACAAACATATAGGTAAAATTAATATACGAAAATTT
1 ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGAT-GGTAAAATTAATACACGAAAATTT
28193050 TAAATTCAAACTACATATAATACGA-
65 TAAATTCAAACTACATATAATACGAG
* * * *
28193075 ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGATAAAATTAGTGCATGAAATTTT
1 ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGG-TAAAATTAATACACGAAAATTT
* * *
28193140 TAAATTCAAACGATATATAACAC-AG
65 TAAATTCAAACTACATATAATACGAG
28193165 ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATACACGAAAATTT
1 ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGAT-GGTAAAATTAATACACGAAAATTT
*
28193230 TAAATTCAAACTACATATAATA-TAG
65 TAAATTCAAACTACATATAATACGAG
28193255 ACTAAATTAAATTTAAA
1 ACTAAATTAAATTTAAA
28193272 GATACAAAAA
Statistics
Matches: 175, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
89 3 0.02
90 170 0.97
91 2 0.01
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (90 bp):
ACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGTAAAATTAATACACGAAAATTTT
AAATTCAAACTACATATAATACGAG
Found at i:28194199 original size:113 final size:113
Alignment explanation
Indices: 28193928--28194262 Score: 352
Period size: 113 Copynumber: 2.9 Consensus size: 113
28193918 GAAAAAGGTA
* * ** * **
28193928 GTGTCGGCCAACAGTGTCCCAAAGTAAAAAGAAAAT-TGCATTGGGAGACAAAAAATGTATTTGG
1 GTGTCGACCATCAGTGTCCCAAAGTAAAAA-AAAATGT-C-TTGGGACCCGAAAAATGTACCTGG
* * **** * *
28193992 TGCCGGCCATCTACTGGCCAGCACTCCAAAAAAAATATTTTT-AATAGACACTG
63 TGCCGACCACCTACTGGCCAGCAC-CC--AATTTTTTTTTTTAAATTGACACTG
* * * *
28194045 ATG-CTGGCTATCAGTGTCCCAAAGTAAAAAAAAATGTCTTGGGACTCGAAAAATGTACCTGGTG
1 GTGTC-GACCATCAGTGTCCCAAAGTAAAAAAAAATGTCTTGGGACCCGAAAAATGTACCTGGTG
* * * *
28194109 TCGACCATCTATTGGCCAGCATCCAATTTTTTTTTTTAAATTGACACTG
65 CCGACCACCTACTGGCCAGCACCCAATTTTTTTTTTTAAATTGACACTG
* *
28194158 GTGTCGACCATCAGTGTCCCAAAGTAAAAAGAATTGTCTTGGGACCCGAAAAATGTACCTGGTGC
1 GTGTCGACCATCAGTGTCCCAAAGTAAAAAAAAATGTCTTGGGACCCGAAAAATGTACCTGGTGC
*
28194223 CGACCACCTACTGGCTAGCACCCAATTTTTTTTTTTAAAT
66 CGACCACCTACTGGCCAGCACCCAATTTTTTTTTTTAAAT
28194263 GTCTCTGGTG
Statistics
Matches: 185, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
112 8 0.04
113 102 0.55
114 3 0.02
115 39 0.21
116 7 0.04
117 26 0.14
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (113 bp):
GTGTCGACCATCAGTGTCCCAAAGTAAAAAAAAATGTCTTGGGACCCGAAAAATGTACCTGGTGC
CGACCACCTACTGGCCAGCACCCAATTTTTTTTTTTAAATTGACACTG
Found at i:28195295 original size:9 final size:9
Alignment explanation
Indices: 28195283--28195325 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
28195273 TAAAAATTAA
28195283 TAAAAAAAT
1 TAAAAAAAT
28195292 TAAATAAAAT
1 TAAA-AAAAT
* *
28195302 TCAAAAAGT
1 TAAAAAAAT
28195311 TAAAAAAA-
1 TAAAAAAAT
28195319 TAAAAAA
1 TAAAAAA
28195326 TGAATCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:28195325 original size:18 final size:18
Alignment explanation
Indices: 28195281--28195325 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
28195271 TTTAAAAATT
28195281 AATAAAAAAATTAAATAA
1 AATAAAAAAATTAAATAA
* *
28195299 AATTCAAAAAGTTAAA-AA
1 AA-TAAAAAAATTAAATAA
28195317 AATAAAAAA
1 AATAAAAAA
28195326 TGAATCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAAAAAATTAAATAA
Found at i:28196127 original size:18 final size:18
Alignment explanation
Indices: 28196088--28196131 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
28196078 TTCATTTTAT
* *
28196088 ATTTTAA-ATTTTTTTAC
1 ATTTTAATATTTTTATAA
*
28196105 TTTTTAATATTTTTATAA
1 ATTTTAATATTTTTATAA
28196123 ATTTTAATA
1 ATTTTAATA
28196132 ATGTTATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTAATATTTTTATAA
Found at i:28196589 original size:19 final size:20
Alignment explanation
Indices: 28196558--28196596 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28196548 AAAAATCTAA
28196558 ATAAACAAATTAAA-AATAT
1 ATAAACAAATTAAATAATAT
28196577 ATAAA-AAATTTAAATAATAT
1 ATAAACAAA-TTAAATAATAT
28196597 GTACAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 10 0.56
20 5 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAACAAATTAAATAATAT
Found at i:28196660 original size:4 final size:4
Alignment explanation
Indices: 28196640--28196676 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
28196630 AGTTCTTCAT
28196640 ATAA ATTAA AT-A ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA A-TAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
28196677 AGAAGTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:28200788 original size:26 final size:26
Alignment explanation
Indices: 28200759--28200815 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
28200749 CCATTTTTTT
* * *
28200759 AATAAACACCAAAAAGTTATTTTAAA
1 AATAAAAACAAAAAAATTATTTTAAA
*
28200785 AATAAAAAATAAAAAAATTATTTTAAA
1 AAT-AAAAACAAAAAAATTATTTTAAA
28200812 AATA
1 AATA
28200816 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (26 bp):
AATAAAAACAAAAAAATTATTTTAAA
Found at i:28213779 original size:21 final size:22
Alignment explanation
Indices: 28213729--28213780 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
28213719 AAAAAAAACC
* * *
28213729 CCTTACACCCATCACATCCTAA
1 CCTTTCACCCATCAAATCCAAA
28213751 CCTTTCACCCATCAAAT-CAAA
1 CCTTTCACCCATCAAATCCAAA
*
28213772 CTTTTCACC
1 CCTTTCACC
28213781 TAGAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (22 bp):
CCTTTCACCCATCAAATCCAAA
Found at i:28213891 original size:22 final size:22
Alignment explanation
Indices: 28213866--28213913 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
28213856 AAACAAAAAC
28213866 CCTTACACCCATCAAATCCTAA
1 CCTTACACCCATCAAATCCTAA
* * *
28213888 CCTTTCACCCATCACATCCTAG
1 CCTTACACCCATCAAATCCTAA
28213910 CCTT
1 CCTT
28213914 CTCTTTACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.44, G:0.02, T:0.27
Consensus pattern (22 bp):
CCTTACACCCATCAAATCCTAA
Found at i:28225649 original size:21 final size:23
Alignment explanation
Indices: 28225623--28225664 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
28225613 TTCACTGGAT
*
28225623 ACGACGGTG-CCTA-TGGTTGCA
1 ACGACGGCGTCCTAGTGGTTGCA
28225644 ACGACGGCGTCCTAGTGGTTG
1 ACGACGGCGTCCTAGTGGTTG
28225665 GTGGCAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.17, C:0.24, G:0.36, T:0.24
Consensus pattern (23 bp):
ACGACGGCGTCCTAGTGGTTGCA
Found at i:28229276 original size:42 final size:42
Alignment explanation
Indices: 28229230--28229409 Score: 201
Period size: 42 Copynumber: 4.3 Consensus size: 42
28229220 AGATCCCATA
* *
28229230 TATGGTCTTACATGCTATCAT-ATATCGATGCCAATAGT-C-AGC
1 TATGGTCTTACATG-AATC-TCATATCGATGCCAAT-GTCCAAAC
*
28229272 TATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAAAC
1 TATGGTCTTACATGAATCTCATATCGATGCCAATGT-CCAAAC
28229315 -ATGGTCTTACATGAATCTCATATCGATGCCAATGTCCCAAAC
1 TATGGTCTTACATGAATCTCATATCGATGCCAATGT-CCAAAC
* * * *
28229357 -ATGGTCTTACATGAATCACATAACAATGCCAATGTCCCAGAC
1 TATGGTCTTACATGAATCTCATATCGATGCCAATGT-CCAAAC
28229399 -ATGGTCTTACA
1 TATGGTCTTACA
28229410 CGTAATCACA
Statistics
Matches: 126, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
40 3 0.02
41 17 0.13
42 104 0.83
43 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
TATGGTCTTACATGAATCTCATATCGATGCCAATGTCCAAAC
Found at i:28229324 original size:84 final size:83
Alignment explanation
Indices: 28229231--28229409 Score: 229
Period size: 84 Copynumber: 2.1 Consensus size: 83
28229221 GATCCCATAT
* * *
28229231 ATGGTCTTACATGCTATCAT-ATATCGATGCCAATAGT-C-AGCTATGGTCTTACACGAATCTCA
1 ATGGTCTTACATG-AATC-TCATATCGATGCCAAT-GTCCAAAC-ATGGTCTTACACGAATCACA
* *
28229293 TATCGATGCCAATGTCCCAAAC
62 TAACAATGCCAATGTCCCAAAC
*
28229315 ATGGTCTTACATGAATCTCATATCGATGCCAATGTCCCAAACATGGTCTTACATGAATCACATAA
1 ATGGTCTTACATGAATCTCATATCGATGCCAATGT-CCAAACATGGTCTTACACGAATCACATAA
*
28229380 CAATGCCAATGTCCCAGAC
65 CAATGCCAATGTCCCAAAC
28229399 ATGGTCTTACA
1 ATGGTCTTACA
28229410 CGTAATCACA
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
82 3 0.04
83 17 0.20
84 62 0.74
85 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (83 bp):
ATGGTCTTACATGAATCTCATATCGATGCCAATGTCCAAACATGGTCTTACACGAATCACATAAC
AATGCCAATGTCCCAAAC
Found at i:28237904 original size:30 final size:30
Alignment explanation
Indices: 28237834--28237911 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
28237824 AAAGAATAAG
* * * *
28237834 AAATGAAATGGAAA-AAGAAAATTTGAGAA
1 AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
28237863 AAATGAAGTG-AAAGAAAAAAAGTTGAGAA
1 AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
28237892 AAGA-GAAAGTGAAAAGAAAA
1 AA-ATG-AAGTGAAAAGAAAA
28237912 CAAAAATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.07
29 25 0.60
30 6 0.14
31 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (30 bp):
AAATGAAGTGAAAAGAAAAAAAGTTGAGAA
Found at i:28242441 original size:29 final size:30
Alignment explanation
Indices: 28242406--28242473 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
28242396 TGAAAACTTC
28242406 ATGTATAAAATTACACA-AAATCAAAGTTT
1 ATGTATAAAATTACACATAAATCAAAGTTT
* *
28242435 ATTTATAACATTACACATTAAATCAAAGTTT
1 ATGTATAAAATTACACA-TAAATCAAAGTTT
28242466 ATGTATAA
1 ATGTATAA
28242474 TTTTGAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (30 bp):
ATGTATAAAATTACACATAAATCAAAGTTT
Found at i:28248075 original size:26 final size:23
Alignment explanation
Indices: 28248024--28248077 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
28248014 TGTTTATGCT
**
28248024 AATTACTTTAAATAGTAAAAGTA
1 AATTACTTTAAATAGTAAAACAA
28248047 AATTACTATTAAATAGAATAAAACAA
1 AATTACT-TTAAATAG--TAAAACAA
28248073 AATTA
1 AATTA
28248078 TTAATATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 8 0.31
26 11 0.42
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
AATTACTTTAAATAGTAAAACAA
Found at i:28249749 original size:2 final size:2
Alignment explanation
Indices: 28249742--28249784 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28249732 TTTATAACGT
28249742 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28249784 T
1 T
28249785 CTAACTTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:28251118 original size:24 final size:25
Alignment explanation
Indices: 28251080--28251143 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 25
28251070 AAATAGAAAA
**
28251080 GAAAAGAAGGGAAAATGAAATAA-G
1 GAAAAGAAGAAAAAATGAAATAATG
*
28251104 GAAAAGAAGACAAAA--AAATAATG
1 GAAAAGAAGAAAAAATGAAATAATG
* *
28251127 TAAAAGAAAAAAAAATG
1 GAAAAGAAGAAAAAATG
28251144 TTCAGGAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 6 0.19
23 13 0.41
24 13 0.41
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (25 bp):
GAAAAGAAGAAAAAATGAAATAATG
Found at i:28251140 original size:22 final size:22
Alignment explanation
Indices: 28251097--28251141 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28251087 AGGGAAAATG
*
28251097 AAATAAGGAAAAGAAGACAAAA
1 AAATAAGGAAAAGAAGAAAAAA
*
28251119 AAATAATGTAAAAGAA-AAAAAA
1 AAATAA-GGAAAAGAAGAAAAAA
28251141 A
1 A
28251142 TGTTCAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.09
Consensus pattern (22 bp):
AAATAAGGAAAAGAAGAAAAAA
Found at i:28257195 original size:30 final size:31
Alignment explanation
Indices: 28257149--28257208 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28257139 TATTTTATTG
* *
28257149 TTAATTTTTTTTATTATTTTAAAGGCATTTA
1 TTAATTTTTGTTATTATTTTAAAGCCATTTA
*
28257180 TTAA-TTTTGTTATTATTTTAGAGCCATTT
1 TTAATTTTTGTTATTATTTTAAAGCCATTT
28257209 GTTTGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.60
Consensus pattern (31 bp):
TTAATTTTTGTTATTATTTTAAAGCCATTTA
Found at i:28260435 original size:18 final size:19
Alignment explanation
Indices: 28260414--28260450 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28260404 AAAGGAAGAT
28260414 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATCAAAAA
*
28260432 AGAAAAAGAGAATGAAAAA
1 AGAAAAAGAGAATCAAAAA
28260451 GAGCCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAGAATCAAAAA
Found at i:28262287 original size:33 final size:34
Alignment explanation
Indices: 28262223--28262297 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
28262213 AAGTTAGTTT
*
28262223 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
28262256 ATTAATTTTAGTTCAGCTTAAATAATTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
28262290 ATTAATTT
1 ATTAATTT
28262298 GTTTAAATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (34 bp):
ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:28273267 original size:21 final size:22
Alignment explanation
Indices: 28273243--28273292 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
28273233 ATTTAAAATA
*
28273243 TTAAAAAAGTTGTAA-AAATTC
1 TTAAAAAAATTGTAACAAATTC
*
28273264 TTAAAAAAATTGTAACAAATTG
1 TTAAAAAAATTGTAACAAATTC
28273286 TTAAAAA
1 TTAAAAA
28273293 CTATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (22 bp):
TTAAAAAAATTGTAACAAATTC
Found at i:28273404 original size:18 final size:19
Alignment explanation
Indices: 28273365--28273414 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
28273355 ATTTTTAAAA
*
28273365 AAAAATGATTAAACATTGT
1 AAAAATGATTAAACATTAT
28273384 AAAAATGA-TAAGA-ATTAT
1 AAAAATGATTAA-ACATTAT
* *
28273402 AAACATTATTAAA
1 AAAAATGATTAAA
28273415 GAATTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (19 bp):
AAAAATGATTAAACATTAT
Found at i:28273670 original size:18 final size:18
Alignment explanation
Indices: 28273638--28273672 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28273628 GTAAAATTAT
**
28273638 TATAATTTTTTCAATTTA
1 TATAATTTTCACAATTTA
28273656 TATAATTTTCACAATTT
1 TATAATTTTCACAATTT
28273673 TTAAATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATTTTCACAATTTA
Found at i:28275210 original size:15 final size:17
Alignment explanation
Indices: 28275192--28275223 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28275182 CAGAATAGAA
28275192 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
28275207 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
28275224 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:28287478 original size:22 final size:20
Alignment explanation
Indices: 28287457--28287497 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28287447 TTTTTTTATA
28287457 AAATAAAAAAATTATAAATAT
1 AAAT-AAAAAATTATAAATAT
* *
28287478 ATATTAAAAATTATAAATAT
1 AAATAAAAAATTATAAATAT
28287498 TTTGTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAAAAAATTATAAATAT
Found at i:28288685 original size:29 final size:29
Alignment explanation
Indices: 28288653--28288721 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
28288643 GTTGGGCTCG
* * *
28288653 TTTTAATAAAATTGACCCATTTCTGTTAA
1 TTTTAATAAAAGTGACACATTTCTATTAA
* *
28288682 TTTTAATAAAAGTGACATATTTCTATTAT
1 TTTTAATAAAAGTGACACATTTCTATTAA
*
28288711 TTTTAAAAAAA
1 TTTTAATAAAA
28288722 ATGAGATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (29 bp):
TTTTAATAAAAGTGACACATTTCTATTAA
Found at i:28297358 original size:21 final size:22
Alignment explanation
Indices: 28297315--28297360 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
28297305 TTTATTAAAA
28297315 TAATAAATTATATTAATCATAT
1 TAATAAATTATATTAATCATAT
*
28297337 TAAT-AATT-TATTATATCTTAT
1 TAATAAATTATATTA-ATCATAT
28297358 TAA
1 TAA
28297361 ATATAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATAAATTATATTAATCATAT
Found at i:28297528 original size:20 final size:20
Alignment explanation
Indices: 28297491--28297528 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28297481 ATTAACTTAC
*
28297491 AATTTTTAAAAGATAAAATT
1 AATTTTTAAAAGAAAAAATT
28297511 AATTTTTAGAAA-AAAAAA
1 AATTTTTA-AAAGAAAAAA
28297529 GCTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AATTTTTAAAAGAAAAAATT
Found at i:28308959 original size:20 final size:21
Alignment explanation
Indices: 28308915--28308961 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
28308905 TAATTGTTAT
*
28308915 ATTTTA-ATATTTAAAATATA
1 ATTTTATATATTCAAAATATA
*
28308935 A-TTTATATATTCAAATTA-A
1 ATTTTATATATTCAAAATATA
28308954 ATTTTATA
1 ATTTTATA
28308962 AATAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTATATATTCAAAATATA
Found at i:28310857 original size:31 final size:31
Alignment explanation
Indices: 28310819--28310934 Score: 94
Period size: 31 Copynumber: 3.6 Consensus size: 31
28310809 AATTTAATAA
28310819 AAATATATAATTTAATAAAATTCTTAATATT
1 AAATATATAATTTAATAAAATTCTTAATATT
* *
28310850 AAATATATGAATTTACTAAAA-TCATAATATAT
1 AAATATAT-AATTTAATAAAATTCTTAATAT-T
* * ** *
28310882 AATACTATAAAATATAATTTAAAATAATTATTATT
1 AA-A-TATATAATTTAA--TAAAATTCTTAATATT
28310917 -AA-ATATAATTTAATAAAA
1 AAATATATAATTTAATAAAA
28310935 ATATATAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
29 5 0.07
31 25 0.37
32 14 0.21
33 7 0.10
34 5 0.07
35 6 0.09
36 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (31 bp):
AAATATATAATTTAATAAAATTCTTAATATT
Found at i:28314088 original size:23 final size:23
Alignment explanation
Indices: 28314059--28314106 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
28314049 CATGGGTTGC
*
28314059 TGTTTTTTTTCTCTTTTCTGGGT
1 TGTTTTTTTTCTCTTTTATGGGT
28314082 TGTTTTTTTTCTCTTTTATGGGT
1 TGTTTTTTTTCTCTTTTATGGGT
28314105 TG
1 TG
28314107 CTGTTTCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.02, C:0.10, G:0.19, T:0.69
Consensus pattern (23 bp):
TGTTTTTTTTCTCTTTTATGGGT
Found at i:28314265 original size:25 final size:26
Alignment explanation
Indices: 28314226--28314389 Score: 171
Period size: 25 Copynumber: 6.6 Consensus size: 26
28314216 AAACTTACAC
*
28314226 GGCGATGC-GGCAGAGGACTGTCGAT
1 GGCGATGCAGACAGAGGACTGTCGAT
* *
28314251 GGCGATGTAGA-AGAGGACTATCGAT
1 GGCGATGCAGACAGAGGACTGTCGAT
* * *
28314276 GGCAATGC-GATAGAGGACTTTCGAT
1 GGCGATGCAGACAGAGGACTGTCGAT
* *
28314301 GGCAATGCA-ACAGAGGACTTTCGAT
1 GGCGATGCAGACAGAGGACTGTCGAT
* *
28314326 GACGATGC-GGCAGAGGACTGTCGAT
1 GGCGATGCAGACAGAGGACTGTCGAT
*
28314351 GGTGATGCA-ACAGAGGACTGTCGAT
1 GGCGATGCAGACAGAGGACTGTCGAT
*
28314376 GGCAATGCAG-CAGA
1 GGCGATGCAGACAGA
28314390 CGTTCAGGGA
Statistics
Matches: 117, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.02
25 114 0.97
26 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.36, T:0.18
Consensus pattern (26 bp):
GGCGATGCAGACAGAGGACTGTCGAT
Found at i:28314350 original size:75 final size:75
Alignment explanation
Indices: 28314236--28314389 Score: 200
Period size: 75 Copynumber: 2.1 Consensus size: 75
28314226 GGCGATGCGG
* * * * *
28314236 CAGAGGACTGTCGATGGCGATGTAGAAGAGGACTATCGATGGCAATGCGATAGAGGACTTTCGAT
1 CAGAGGACTGTCGATGACGATGCAGAAGAGGACTATCGATGGCAATGCAACAGAGGACTGTCGAT
28314301 GGCAATGCAA
66 GGCAATGCAA
* * * * **
28314311 CAGAGGACTTTCGATGACGATGCGGCAGAGGACTGTCGATGGTGATGCAACAGAGGACTGTCGAT
1 CAGAGGACTGTCGATGACGATGCAGAAGAGGACTATCGATGGCAATGCAACAGAGGACTGTCGAT
*
28314376 GGCAATGCAG
66 GGCAATGCAA
28314386 CAGA
1 CAGA
28314390 CGTTCAGGGA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (75 bp):
CAGAGGACTGTCGATGACGATGCAGAAGAGGACTATCGATGGCAATGCAACAGAGGACTGTCGAT
GGCAATGCAA
Found at i:28314389 original size:50 final size:50
Alignment explanation
Indices: 28314230--28314389 Score: 205
Period size: 50 Copynumber: 3.2 Consensus size: 50
28314220 TTACACGGCG
*
28314230 ATGCGGCAGAGGACTGTCGATGGCGATGTAGA-AGAGGACTATCGATGGCA
1 ATGCGGCAGAGGACTGTCGATGGCGATGCA-ACAGAGGACTATCGATGGCA
** * * * * *
28314280 ATGCGATAGAGGACTTTCGATGGCAATGCAACAGAGGACTTTCGATGACG
1 ATGCGGCAGAGGACTGTCGATGGCGATGCAACAGAGGACTATCGATGGCA
* *
28314330 ATGCGGCAGAGGACTGTCGATGGTGATGCAACAGAGGACTGTCGATGGCA
1 ATGCGGCAGAGGACTGTCGATGGCGATGCAACAGAGGACTATCGATGGCA
*
28314380 ATGCAGCAGA
1 ATGCGGCAGA
28314390 CGTTCAGGGA
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 91 0.99
ACGTcount: A:0.29, C:0.17, G:0.35, T:0.19
Consensus pattern (50 bp):
ATGCGGCAGAGGACTGTCGATGGCGATGCAACAGAGGACTATCGATGGCA
Found at i:28315079 original size:21 final size:21
Alignment explanation
Indices: 28315055--28315100 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
28315045 TTTGTTACAA
*
28315055 ACATAACAAATATGCCATTTT
1 ACATAACAAAGATGCCATTTT
* * *
28315076 ACATAATAGAGCTGCCATTTT
1 ACATAACAAAGATGCCATTTT
28315097 ACAT
1 ACAT
28315101 CCTTCTCTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (21 bp):
ACATAACAAAGATGCCATTTT
Found at i:28315217 original size:39 final size:37
Alignment explanation
Indices: 28315159--28315295 Score: 127
Period size: 39 Copynumber: 3.5 Consensus size: 37
28315149 CCCATCCCTT
*
28315159 TCCTTCTTCCCACCATCCCTCCCCCTTACTTCGATTCTC
1 TCCTTCTCCCCACCATCCCT-CCCCTTAC-TCGATTCTC
*
28315198 TCCTTCTCCCCACCGTCCCTCCCCTTACTCTGATTCTCAC
1 TCCTTCTCCCCACCATCCCTCCCCTTACTC-GATTCT--C
*
28315238 TCTCTTCT--CCACCATCCCTCACCTTACTC-ATCTTCTC
1 TC-CTTCTCCCCACCATCCCTCCCCTTACTCGA--TTCTC
* *
28315275 TCCCTCTCTCCCACCGTCCCT
1 TCCTTCTC-CCCACCATCCCT
28315296 TTCTCTCTAC
Statistics
Matches: 83, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
36 4 0.05
37 6 0.07
38 14 0.17
39 51 0.61
40 3 0.04
41 5 0.06
ACGTcount: A:0.10, C:0.53, G:0.03, T:0.34
Consensus pattern (37 bp):
TCCTTCTCCCCACCATCCCTCCCCTTACTCGATTCTC
Found at i:28316705 original size:29 final size:32
Alignment explanation
Indices: 28316670--28316752 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 32
28316660 AATCTCAAAG
28316670 TTATATAT-TAATTTTGATTTAAAGT-TAAAT
1 TTATATATATAATTTTGATTTAAAGTATAAAT
*
28316700 TT-TATATATAAATTTTGATTT--TGTATAAAT
1 TTATATATAT-AATTTTGATTTAAAGTATAAAT
*
28316730 TTATATATAAAATTTTGATTTAA
1 TTATATATATAATTTTGATTTAA
28316753 TGCAATTCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 7 0.16
30 21 0.47
31 17 0.38
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (32 bp):
TTATATATATAATTTTGATTTAAAGTATAAAT
Found at i:28316708 original size:31 final size:31
Alignment explanation
Indices: 28316670--28316752 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
28316660 AATCTCAAAG
*
28316670 TTATATATTAATTTTGATTTAAAGT-TAAATT
1 TTATATATAAATTTTGATTTAAAGTATAAA-T
*
28316701 TTATATATAAATTTTGATTT--TGTATAAAT
1 TTATATATAAATTTTGATTTAAAGTATAAAT
28316730 TTATATATAAAATTTTGATTTAA
1 TTATATAT-AAATTTTGATTTAA
28316753 TGCAATTCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
29 11 0.24
30 16 0.35
31 19 0.41
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (31 bp):
TTATATATAAATTTTGATTTAAAGTATAAAT
Found at i:28317610 original size:22 final size:22
Alignment explanation
Indices: 28317585--28317665 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
28317575 ATTTTGTATT
*
28317585 ATATAACATATCAGAGAATATA
1 ATATAACATATCAGAGAATATC
** *
28317607 ATATAACATATTGGAGCATATC
1 ATATAACATATCAGAGAATATC
** *
28317629 ATATAACATATTGGAGTATATC
1 ATATAACATATCAGAGAATATC
28317651 ATATAACATATCAGA
1 ATATAACATATCAGA
28317666 ACATATCTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (22 bp):
ATATAACATATCAGAGAATATC
Found at i:28317671 original size:44 final size:44
Alignment explanation
Indices: 28317585--28317672 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
28317575 ATTTTGTATT
** *
28317585 ATATAACATATCAGAGAATATAATATAACATATTGGAGCATATC
1 ATATAACATATCAGAGAATATAATATAACATATCAGAACATATC
** * *
28317629 ATATAACATATTGGAGTATATCATATAACATATCAGAACATATC
1 ATATAACATATCAGAGAATATAATATAACATATCAGAACATATC
28317673 TTACTCCCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (44 bp):
ATATAACATATCAGAGAATATAATATAACATATCAGAACATATC
Found at i:28320452 original size:232 final size:233
Alignment explanation
Indices: 28320045--28320509 Score: 923
Period size: 232 Copynumber: 2.0 Consensus size: 233
28320035 GAAGTTGTGT
28320045 ATTATTTGTATATTTACATTAAATAAATTATGTTGAAACATCAACATTTCTTGAGTTCCTTGGAG
1 ATTATTTGTATATTTACATTAAATAAATTATGTTGAAACATCAACATTTCTTGAGTTCCTTGGAG
28320110 CCCCAAGCATTGGACTAGAACCTGAAATAACCTTTGATTCCACAAACAGTTTCCTCATTAGGCTT
66 CCCCAAGCATTGGACTAGAACCTGAAATAACCTTTGATTCCACAAACAGTTTCCTCATTAGGCTT
28320175 TACAACAGAGAAATCATCTAAAGACACATGAATAT-CCCTTTTTTTTTTCTAAAGTATCTATAGG
131 TACAACAGAGAAATCATCTAAAGACACATGAATATCCCCTTTTTTTTTTCTAAAGTATCTATAGG
28320239 AGTGAGCTTAACAATTAATCTTTCACATCTCATAATCC
196 AGTGAGCTTAACAATTAATCTTTCACATCTCATAATCC
28320277 ATTATTTGTATATTTACATTAAATAAATTATGTTGAAACATCAACATTTCTTGAGTTCCTTGGAG
1 ATTATTTGTATATTTACATTAAATAAATTATGTTGAAACATCAACATTTCTTGAGTTCCTTGGAG
28320342 CCCCAAGCATTGGACTAGAACCTGAAATAACCTTTGATTCCACAAACAGTTTCCTCATTAGGCTT
66 CCCCAAGCATTGGACTAGAACCTGAAATAACCTTTGATTCCACAAACAGTTTCCTCATTAGGCTT
28320407 TACAACAGAGAAATCATCTAAAGACACATGAATATCCCCTTTTTTTTTTCTAAAGTATCTATAGG
131 TACAACAGAGAAATCATCTAAAGACACATGAATATCCCCTTTTTTTTTTCTAAAGTATCTATAGG
28320472 AGTGAGCTTAACAATTAATCTTTCACATCTCATAATCC
196 AGTGAGCTTAACAATTAATCTTTCACATCTCATAATCC
28320510 CGTTAAGGGT
Statistics
Matches: 232, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
232 165 0.71
233 67 0.29
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (233 bp):
ATTATTTGTATATTTACATTAAATAAATTATGTTGAAACATCAACATTTCTTGAGTTCCTTGGAG
CCCCAAGCATTGGACTAGAACCTGAAATAACCTTTGATTCCACAAACAGTTTCCTCATTAGGCTT
TACAACAGAGAAATCATCTAAAGACACATGAATATCCCCTTTTTTTTTTCTAAAGTATCTATAGG
AGTGAGCTTAACAATTAATCTTTCACATCTCATAATCC
Done.