Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004693.1 Hibiscus syriacus cultivar Beakdansim tig00010533_pilon, whole genome shotgun sequence
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: 2620943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 6 of 12
Found at i:1164611 original size:14 final size:15
Alignment explanation
Indices: 1164477--1164617 Score: 139
Period size: 15 Copynumber: 9.2 Consensus size: 15
1164467 TATTAAAATA
1164477 ATTTT-AAATAATTT
1 ATTTTAAAATAATTT
* *
1164491 A--ATAAAGTAATTT
1 ATTTTAAAATAATTT
1164504 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
1164519 ATTTTAAAAT-ATTT
1 ATTTTAAAATAATTT
*
1164533 TTTTATAAAATAATTT
1 ATTT-TAAAATAATTT
1164549 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
*
1164564 ATTATAAAATATGGATTGATTT
1 ATT-TTAAA-AT--A---ATTT
1164586 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
1164601 ATTTT-AAATAATTT
1 ATTTTAAAATAATTT
1164615 ATT
1 ATT
1164618 AGTATGGATT
Statistics
Matches: 107, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
12 1 0.01
13 9 0.08
14 20 0.19
15 49 0.46
16 11 0.10
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 7 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTTAAAATAATTT
Found at i:1164635 original size:32 final size:31
Alignment explanation
Indices: 1164597--1164850 Score: 127
Period size: 32 Copynumber: 8.4 Consensus size: 31
1164587 TTTTAAAATA
1164597 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
1164629 ATTTATTTT--A-AA---A-TATA--GATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
* *
1164651 ATTAATTTTAAATAATTTATTAATATGAATTG
1 ATTTATTTTAAATAATTTATT-ATATGGATTG
* * **
1164683 ATTTATTTTAAAATTTGAATTGATTTATTTTAAAATATAG
1 ATTTATTTT-AAA--T-AATTTA-TTA-TAT-GGAT-T-G
* * * *
1164723 ATTGA-TTT--ATTATTGTAGTTGTATGTATTG
1 ATTTATTTTAAATAATT-TA-TTATATGGATTG
1164753 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
1164785 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
*
1164807 GTTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
1164839 ATTTATTTTAAA
1 ATTTATTTTAAA
1164851 ATATGGATTG
Statistics
Matches: 168, Mismatches: 20, Indels: 68
0.66 0.08 0.27
Matches are distributed among these distances:
22 26 0.15
23 4 0.02
24 3 0.02
25 5 0.03
26 4 0.02
28 4 0.02
29 4 0.02
30 9 0.05
31 10 0.06
32 58 0.35
33 13 0.08
34 4 0.02
35 1 0.01
36 7 0.04
37 4 0.02
38 3 0.02
39 4 0.02
40 5 0.03
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTATATGGATTG
Found at i:1164649 original size:22 final size:22
Alignment explanation
Indices: 1164624--1164733 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
1164614 TATTAGTATG
1164624 GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
*
1164646 GATTGATTAATTTTAAATAATTTATTA
1 GATTGATTTATTTT-AA-AA--TA-TA
* *
1164673 -ATATGAATTGATTTATTTTAAAAT-TT
1 GAT-TG-ATTTA-TT---TTAAAATATA
1164699 GAATTGATTTATTTTAAAATATA
1 G-ATTGATTTATTTTAAAATATA
1164722 GATTGATTTATT
1 GATTGATTTATT
1164734 ATTGTAGTTG
Statistics
Matches: 69, Mismatches: 5, Indels: 28
0.68 0.05 0.27
Matches are distributed among these distances:
22 31 0.45
23 4 0.06
24 2 0.03
25 2 0.03
26 9 0.13
27 6 0.09
28 7 0.10
29 2 0.03
30 2 0.03
31 2 0.03
32 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:1164667 original size:54 final size:54
Alignment explanation
Indices: 1164597--1164867 Score: 335
Period size: 54 Copynumber: 5.1 Consensus size: 54
1164587 TTTTAAAATA
1164597 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* * * *
1164651 ATTAATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAAT-TTGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAG-ATTG
* * * ** *
1164705 ATTTATTTT-AA-AA--TA-TAG-ATTGATTTA-TTATTGT-AGTTGTATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATA-G-ATTG
*
1164753 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* *
1164807 GTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1164861 ATTTATT
1 ATTTATT
1164868 ATTGTAGTTG
Statistics
Matches: 183, Mismatches: 23, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
46 2 0.01
47 7 0.04
48 20 0.11
49 4 0.02
50 4 0.02
52 4 0.02
53 7 0.04
54 125 0.68
55 7 0.04
56 3 0.02
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
Found at i:1164792 original size:22 final size:22
Alignment explanation
Indices: 1164776--1164818 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1164766 AATTTATTAG
1164776 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1164798 TATGGATTGGTTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1164819 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1164844 original size:18 final size:18
Alignment explanation
Indices: 1164821--1164868 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1164811 ATTTTAAATA
*
1164821 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1164839 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1164861 ATTTATTA
1 ATTTATTA
1164869 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1164918 original size:32 final size:32
Alignment explanation
Indices: 1164877--1164940 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1164867 TATTGTAGTT
*
1164877 GTATGGATTGATTTATTTTAGATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1164909 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1164941 TTATAGTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1164924 original size:18 final size:17
Alignment explanation
Indices: 1164875--1164925 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
1164865 ATTATTGTAG
1164875 TTGTATGGATTGATTTA
1 TTGTATGGATTGATTTA
* *
1164892 TT-T-TAGA-TAATTTA
1 TTGTATGGATTGATTTA
1164906 TTAGTATGGATTGATTTA
1 TT-GTATGGATTGATTTA
1164924 TT
1 TT
1164926 TTAAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 2 0.08
17 5 0.19
18 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
TTGTATGGATTGATTTA
Found at i:1168634 original size:20 final size:20
Alignment explanation
Indices: 1168577--1168634 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
1168567 GTCTACGTAA
*
1168577 TTTATAACTTTAATTCATGTT
1 TTTATAA-TTTAATTTATGTT
* *
1168598 TTTA-ATATATCATTTTATGTT
1 TTTATA-AT-TTAATTTATGTT
1168619 TTTATAATTTAATTTA
1 TTTATAATTTAATTTA
1168635 ATCATATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 8 0.28
21 20 0.69
22 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTATAATTTAATTTATGTT
Found at i:1175683 original size:23 final size:24
Alignment explanation
Indices: 1175656--1175714 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
1175646 AAATTTAATA
1175656 AATATTGAATTATA-TTTTATAT-T
1 AATATTGAATTATACTTTTAT-TCT
* *
1175679 AATATTGGATTACACTTTTATTCT
1 AATATTGAATTATACTTTTATTCT
1175703 AAT-TTGAATTAT
1 AATATTGAATTAT
1175715 TGAAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.53
Consensus pattern (24 bp):
AATATTGAATTATACTTTTATTCT
Found at i:1191659 original size:30 final size:30
Alignment explanation
Indices: 1191613--1191676 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1191603 GAAGGACCTG
* *
1191613 TCCAGAGGTTACAAAGA-ACCCCGGTAACTA
1 TCCAGAGGTCACAAAGATA-CCCGGCAACTA
* *
1191643 TCCAGAGGTCATAAAGATACTCGGCAACTA
1 TCCAGAGGTCACAAAGATACCCGGCAACTA
1191673 TCCA
1 TCCA
1191677 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGATACCCGGCAACTA
Found at i:1192435 original size:19 final size:19
Alignment explanation
Indices: 1192411--1192462 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1192401 TTTTAAAAGG
1192411 ATGCATCGATGCATTATCT
1 ATGCATCGATGCATTATCT
1192430 ATGCATCGATGCATTATCT
1 ATGCATCGATGCATTATCT
1192449 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1192463 CAAAGGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (19 bp):
ATGCATCGATGCATTATCT
Found at i:1192488 original size:83 final size:84
Alignment explanation
Indices: 1192346--1192511 Score: 230
Period size: 83 Copynumber: 2.0 Consensus size: 84
1192336 TCAATGAAGG
* * * *
1192346 TATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTAAAAGG
1 TATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-AAAGG
1192411 -ATGCATCGATGCA-TTATC
65 AATGCATCGATGCACTTATC
* * *
1192429 TATGCATCGATGCATTA-TCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTAAAGG
1 TATGCATCGATGCACTACT-TATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAGG
1192493 AATGCATCGATGCACTTAT
65 AATGCATCGATGCACTTAT
1192512 GAATGTGCAT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
82 6 0.08
83 63 0.86
84 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (84 bp):
TATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAGGA
ATGCATCGATGCACTTATC
Found at i:1198456 original size:6 final size:6
Alignment explanation
Indices: 1198445--1198742 Score: 447
Period size: 6 Copynumber: 50.0 Consensus size: 6
1198435 TAATTTATGC
* *
1198445 ATGTGT ATGTGT ATGTGT ACGTAT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
* * * * *
1198493 ACGTGT ATGTGT ATGTGT ACGTGT ATGTAT AGGTGT ATGTGT AGGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
* * * * * * * *
1198541 ACGTGT AGGTAT AGGTGT ACGTGT ATGTGT AAGTGT AGGTGT ACGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1198589 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1198637 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTG- -TGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1198683 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1198731 ATGTGT ATGTGT
1 ATGTGT ATGTGT
1198743 GTAAAAGCTA
Statistics
Matches: 267, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
4 4 0.01
6 263 0.99
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.46
Consensus pattern (6 bp):
ATGTGT
Found at i:1201073 original size:17 final size:18
Alignment explanation
Indices: 1201051--1201084 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1201041 TATATTATTT
1201051 AATTATTA-AAAATATAA
1 AATTATTATAAAATATAA
1201068 AATTATTATAAAATATA
1 AATTATTATAAAATATA
1201085 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATTATAAAATATAA
Found at i:1201085 original size:20 final size:19
Alignment explanation
Indices: 1201051--1201094 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1201041 TATATTATTT
1201051 AATTATTA-AAAATATA-A
1 AATTATTATAAAATATATA
*
1201068 AATTATTATAAAATATATT
1 AATTATTATAAAATATATA
1201087 AATT-TTAT
1 AATTATTAT
1201095 CGTTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATTATAAAATATATA
Found at i:1201094 original size:18 final size:19
Alignment explanation
Indices: 1201030--1201094 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
1201020 TTTATTTTTA
*
1201030 TATTATGAAAATATATTATT
1 TATTAT-AAAATATATTAAT
*
1201050 TAATTATTAAAA-ATATAAAAT
1 T-ATTA-TAAAATATAT-TAAT
1201071 TATTATAAAATATATTAAT
1 TATTATAAAATATATTAAT
1201090 T-TTAT
1 TATTAT
1201095 CGTTTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
18 4 0.11
19 9 0.24
20 13 0.34
21 11 0.29
22 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTATAAAATATATTAAT
Found at i:1201104 original size:41 final size:42
Alignment explanation
Indices: 1201030--1201131 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 42
1201020 TTTATTTTTA
*
1201030 TATTATGAAAATATATTATTTAATTATTAAAAATATAA-A-AT
1 TATTAT-AAAATATATTATTTAATCATTAAAAATATAATACAT
* * *
1201071 TATTATAAAATATATTAATTTTATCGTTTAAAATATAATACAT
1 TATTATAAAATATATT-ATTTAATCATTAAAAATATAATACAT
* *
1201114 AATTAT-AAATATCTTATT
1 TATTATAAAATATATTATT
1201132 ATAAAATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
40 10 0.19
41 26 0.50
42 9 0.17
43 7 0.13
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (42 bp):
TATTATAAAATATATTATTTAATCATTAAAAATATAATACAT
Found at i:1201518 original size:22 final size:22
Alignment explanation
Indices: 1201483--1201532 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1201473 CTACAACTAA
1201483 CTTAAAACCCTAAA-CTCTAAAC
1 CTTAAAACCCTAAATCT-TAAAC
* *
1201505 CTTAAAATCTTAAATCTTAAAC
1 CTTAAAACCCTAAATCTTAAAC
*
1201527 ATTAAA
1 CTTAAA
1201533 CTCTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (22 bp):
CTTAAAACCCTAAATCTTAAAC
Found at i:1205844 original size:9 final size:9
Alignment explanation
Indices: 1205830--1205865 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
1205820 GGGCGACGAA
1205830 GATGAGGAT
1 GATGAGGAT
*
1205839 GATGAGGAA
1 GATGAGGAT
1205848 GATGAGGAT
1 GATGAGGAT
1205857 GATGAGGAT
1 GATGAGGAT
1205866 AAACTACAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.19
Consensus pattern (9 bp):
GATGAGGAT
Found at i:1205850 original size:18 final size:18
Alignment explanation
Indices: 1205827--1205864 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1205817 ACAGGGCGAC
1205827 GAAGATGAGGATGATGAG
1 GAAGATGAGGATGATGAG
1205845 GAAGATGAGGATGATGAG
1 GAAGATGAGGATGATGAG
1205863 GA
1 GA
1205865 TAAACTACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.45, T:0.16
Consensus pattern (18 bp):
GAAGATGAGGATGATGAG
Found at i:1222531 original size:2 final size:2
Alignment explanation
Indices: 1222524--1222555 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1222514 ATAAACTTTA
1222524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1222556 CCAAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1223453 original size:41 final size:41
Alignment explanation
Indices: 1223397--1223534 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
1223387 CGAATTGGGG
* *
1223397 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
1223438 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** * * * *
1223480 --TTTCGCAACGCGATTCTAACTTTCGTAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
1223519 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1223535 TTTCAAAGTT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.02
40 30 0.37
41 47 0.58
42 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1223501 original size:20 final size:20
Alignment explanation
Indices: 1223401--1223514 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
1223391 TTGGGGAAAA
* *
1223401 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
1223421 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
1223442 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1223462 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
1223482 TCGCAACGCGATTCTAACTT
1 TCGCAACGCGATACTGACTT
* *
1223502 TCGTAACGAGATA
1 TCGCAACGCGATA
1223515 ATACAGAATC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1223687 original size:12 final size:12
Alignment explanation
Indices: 1223668--1223701 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1223658 CTCTCTGGCG
1223668 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1223680 ATATCCGTTCCT
1 ACATCCGTTCCT
1223692 ACATCC-TTCC
1 ACATCCGTTCC
1223702 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1223875 original size:20 final size:20
Alignment explanation
Indices: 1223850--1223887 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1223840 ATTCATTTGA
*
1223850 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
1223870 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
1223888 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:1223947 original size:19 final size:16
Alignment explanation
Indices: 1223906--1223957 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 16
1223896 GAAATGAAAA
1223906 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1223922 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
*
1223936 ATTTCGCATTGCGATTCTC
1 ---TCGCATTGCGATTTTC
1223955 TCG
1 TCG
1223958 TTACGATAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 11 0.37
16 6 0.20
17 3 0.10
19 10 0.33
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:1224110 original size:14 final size:14
Alignment explanation
Indices: 1224091--1224127 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1224081 CATCAATTAA
1224091 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1224105 ACAAATCATCTTTT
1 ACAAATCAACATTT
1224119 ACAAATCAA
1 ACAAATCAA
1224128 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1226031 original size:19 final size:20
Alignment explanation
Indices: 1225992--1226042 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1225982 CACGAAACTT
*
1225992 AAAATCGCAACGCGAAAATG
1 AAAATCGCAATGCGAAAATG
**
1226012 ACTATCGCAATGCG-AAATG
1 AAAATCGCAATGCGAAAATG
1226031 AAAATCGCAATG
1 AAAATCGCAATG
1226043 ACAAAATCGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAATGCGAAAATG
Found at i:1226078 original size:32 final size:33
Alignment explanation
Indices: 1226015--1226093 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1226005 GAAAATGACT
*
1226015 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1226048 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1226080 ATCGTAACGCGAAA
1 ATCGCAATGCGAAA
1226094 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 27 0.63
33 16 0.37
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1226083 original size:14 final size:14
Alignment explanation
Indices: 1226031--1226088 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1226021 ATGCGAAATG
*
1226031 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
1226045 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1226061 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1226077 AAAATCGTAACG
1 AAAATCGCAACG
1226089 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1226122 original size:19 final size:19
Alignment explanation
Indices: 1226100--1226182 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
1226090 GAAACACAAA
1226100 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1226119 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
** *
1226138 TCGCATTGC-AACTT--TG
1 TCGCATTGCGATTTTCATT
*
1226154 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
1226171 TCGCATTGCGAT
1 TCGCATTGCGAT
1226183 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 33 0.65
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1226190 original size:19 final size:20
Alignment explanation
Indices: 1226168--1226210 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1226158 TGCGATTTTT
1226168 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
1226187 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
1226207 ATTT
1 ATTT
1226211 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:1226201 original size:20 final size:20
Alignment explanation
Indices: 1226176--1226221 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1226166 TTATTTCGCA
1226176 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1226196 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1226216 TTGCGA
1 TTGCGA
1226222 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1226728 original size:18 final size:18
Alignment explanation
Indices: 1226702--1226746 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1226692 GTCGATCAGA
* * *
1226702 TGATGGCTCTGGGTGATG
1 TGATAGCTCTGGGCGAGG
1226720 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
*
1226738 TGATTGCTC
1 TGATAGCTC
1226747 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.16, G:0.40, T:0.31
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:1228100 original size:20 final size:21
Alignment explanation
Indices: 1228067--1228124 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
1228057 AATAGTTTCT
**
1228067 GAAAATGAAAATCGCAACA-C
1 GAAAATGACTATCGCAACAGC
1228087 GAAAATGACTATCGCAA-AGC
1 GAAAATGACTATCGCAACAGC
**
1228107 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
1228125 GAGAGAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (21 bp):
GAAAATGACTATCGCAACAGC
Found at i:1228651 original size:20 final size:20
Alignment explanation
Indices: 1228626--1228671 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1228616 TATTATCATA
1228626 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCG
* *
1228646 TTGCGAAAGTCAGTATCTCG
1 TTGCGAAAGTCAGAATCGCG
1228666 TTGCGA
1 TTGCGA
1228672 TTTTGTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
TTGCGAAAGTCAGAATCGCG
Found at i:1228705 original size:20 final size:20
Alignment explanation
Indices: 1228680--1228733 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1228670 GATTTTGTAT
1228680 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1228700 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1228720 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1228734 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1228705 original size:61 final size:61
Alignment explanation
Indices: 1228599--1228736 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
1228589 CGCTTAGAAA
* * * *
1228599 ATCGCATTGCGATTATGTATTATCATATTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
1228660 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1228721 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1228737 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1228752 original size:61 final size:61
Alignment explanation
Indices: 1228625--1228754 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 61
1228615 GTATTATCAT
* * * * * ** *
1228625 ATTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGC
1 ATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGC
* *
1228686 ATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGC
1 ATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGC
*
1228747 GTTGCGAT
1 ATTGCGAT
1228755 TTACTTATTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 55 0.96
62 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGC
Found at i:1228844 original size:21 final size:21
Alignment explanation
Indices: 1228804--1228844 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1228794 ACTGTAGACC
** *
1228804 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1228825 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1228845 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1233110 original size:71 final size:71
Alignment explanation
Indices: 1232969--1233103 Score: 261
Period size: 71 Copynumber: 1.9 Consensus size: 71
1232959 TAGTGTTTAA
1232969 TTTTGATTCATATGTATAATTAATTAAAACATATGAACATTACATACATAAATCTGGTTAGCTTA
1 TTTTGATTCATATGTATAATTAATTAAAACATATGAACATTACATACATAAATCTGGTTAGCTTA
1233034 GAAAGT
66 GAAAGT
*
1233040 TTTTGATTCATATGTATAATTAATTAAAACATATGAACATTACATACATAGATCTGGTTAGCTT
1 TTTTGATTCATATGTATAATTAATTAAAACATATGAACATTACATACATAAATCTGGTTAGCTT
1233104 TAAAAGTAGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (71 bp):
TTTTGATTCATATGTATAATTAATTAAAACATATGAACATTACATACATAAATCTGGTTAGCTTA
GAAAGT
Found at i:1233434 original size:20 final size:20
Alignment explanation
Indices: 1233409--1233582 Score: 199
Period size: 20 Copynumber: 8.7 Consensus size: 20
1233399 CGATTTTCCA
* *
1233409 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
1233429 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1233449 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1233469 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1233489 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1233509 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
1233529 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1233549 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1233570 AAATCGCAACGCG
1 AAATCGCAACGCG
1233583 ATATTTAAAG
Statistics
Matches: 128, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 109 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1233492 original size:60 final size:60
Alignment explanation
Indices: 1233409--1233582 Score: 224
Period size: 60 Copynumber: 2.9 Consensus size: 60
1233399 CGATTTTCCA
** * *
1233409 AAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGATAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
1233469 AAATCGCAACGCGT-ATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCGGT
1 AAATCGCAACG-ATAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
*
1233529 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGATAATACAT-AAATCGCAATGCGTATCCGTAAATCGCAACGCG
1233583 ATATTTAAAG
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.01
60 64 0.67
61 31 0.32
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGATAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:1234004 original size:33 final size:33
Alignment explanation
Indices: 1233965--1234035 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1233955 TTCACTTAGA
1233965 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1233998 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1234031 TTTCA
1 TTTCA
1234036 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1234153 original size:14 final size:14
Alignment explanation
Indices: 1234134--1234223 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1234124 GATAAATGAA
1234134 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1234148 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
1234167 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1234181 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1234200 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1234214 AATCGCAACG
1 AATCGCAACG
1234224 CGAAACCAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1234171 original size:33 final size:33
Alignment explanation
Indices: 1234127--1234239 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
1234117 GCAACGAGAT
1234127 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
*
1234160 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1234193 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1234226 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1234240 TTGCGATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1234172 original size:19 final size:19
Alignment explanation
Indices: 1234148--1234209 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1234138 GCAACGAGAG
*
1234148 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
1234167 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1234181 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1234200 AATCGCAACG
1 AATCGCAACG
1234210 AGAGAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.56
ACGTcount: A:0.44, C:0.24, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1234276 original size:14 final size:14
Alignment explanation
Indices: 1234257--1234346 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1234247 TTTTATTTCG
1234257 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1234271 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1234290 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1234304 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1234323 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1234337 CGTTGCGATT
1 CGTTGCGATT
1234347 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1234282 original size:33 final size:33
Alignment explanation
Indices: 1234240--1234354 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1234230 CAAAATCGCA
*
1234240 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1234273 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1234306 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1234339 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1234355 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1234295 original size:19 final size:19
Alignment explanation
Indices: 1234235--1234332 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1234225 GAAACCAAAA
* *
1234235 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1234254 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1234268 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1234287 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1234301 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1234320 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1234333 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1236210 original size:93 final size:93
Alignment explanation
Indices: 1236051--1236333 Score: 532
Period size: 93 Copynumber: 3.1 Consensus size: 93
1236041 TAGATTGCTT
*
1236051 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1236116 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1236144 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1236209 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1236237 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTATATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1236302 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1236329 AGTAA
1 AGTAA
1236334 TGCAATCCAT
Statistics
Matches: 187, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
92 6 0.03
93 181 0.97
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1236406 original size:20 final size:19
Alignment explanation
Indices: 1236381--1236457 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
1236371 TAGTTTACTT
**
1236381 TCGCAACACGAAAGTTAAAA
1 TCGCAACACGAAA-CCAAAA
*
1236401 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
*
1236420 TCGC-A-ACG--A-CAAGA
1 TCGCAACACGAAACCAAAA
*
1236434 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
1236453 TCGCA
1 TCGCA
1236458 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
14 8 0.18
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 17 0.38
20 12 0.27
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Found at i:1236421 original size:19 final size:19
Alignment explanation
Indices: 1236397--1236457 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
1236387 CACGAAAGTT
1236397 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1236416 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1236430 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1236449 AAAATCGCA
1 AAAATCGCA
1236458 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.48, C:0.30, G:0.16, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1236475 original size:19 final size:19
Alignment explanation
Indices: 1236453--1236587 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1236443 GAAACCAAAA
*
1236453 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1236472 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1236488 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1236505 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1236521 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1236538 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1236557 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1236577 TCGTGTTGCGA
1 TCGCGTTGCGA
1236588 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1236494 original size:14 final size:14
Alignment explanation
Indices: 1236475--1236531 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1236465 TTTCATTTCG
1236475 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1236489 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1236506 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1236522 CGTTGCGATT
1 CGTTGCGATT
1236532 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1236500 original size:33 final size:33
Alignment explanation
Indices: 1236458--1236550 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1236448 CAAAATCGCA
*
1236458 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1236491 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1236524 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1236551 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1238520 original size:14 final size:14
Alignment explanation
Indices: 1238501--1238536 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1238491 CTTATTTAAT
1238501 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1238515 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1238529 TGATTTGT
1 TGATTTGT
1238537 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1238719 original size:20 final size:19
Alignment explanation
Indices: 1238643--1238726 Score: 115
Period size: 19 Copynumber: 4.6 Consensus size: 19
1238633 AAAAATGACT
1238643 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1238662 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1238681 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1238695 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1238715 ATCGCAATGCGA
1 ATCGCAATGCGA
1238727 TTTTCATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 1 0.02
17 3 0.05
19 29 0.51
20 13 0.23
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1238744 original size:19 final size:19
Alignment explanation
Indices: 1238716--1239089 Score: 536
Period size: 19 Copynumber: 20.7 Consensus size: 19
1238706 GAAATGAAAA
*
1238716 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1238735 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1238751 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238768 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238787 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238806 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238825 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238844 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238863 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238882 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238901 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238920 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238939 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1238958 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1238974 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1238991 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1239010 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1239026 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1239043 TCCGCATTGCGAATTTCA--
1 T-CGCATTGCGATTTTCATT
*
1239061 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1239077 TCGCGTTGCGATT
1 TCGCATTGCGATT
1239090 GTAATTTCCG
Statistics
Matches: 323, Mismatches: 11, Indels: 42
0.86 0.03 0.11
Matches are distributed among these distances:
14 28 0.09
16 23 0.07
17 20 0.06
18 3 0.01
19 238 0.74
20 11 0.03
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1241390 original size:12 final size:12
Alignment explanation
Indices: 1241373--1241397 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1241363 TCTTCGGGGA
1241373 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1241385 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1241397 C
1 C
1241398 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1241606 original size:24 final size:24
Alignment explanation
Indices: 1241572--1241618 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1241562 CTGAAACATC
1241572 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1241596 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1241619 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1242329 original size:20 final size:20
Alignment explanation
Indices: 1242301--1242510 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
1242291 AAATTTCAGT
* * *
1242301 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1242321 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1242341 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1242361 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1242381 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
1242401 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
1242421 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1242441 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1242461 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1242481 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1242501 GTTGCGATTT
1 GTTGCGATTT
1242511 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1242567 original size:21 final size:20
Alignment explanation
Indices: 1242477--1242573 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
1242467 ATTTATGTGT
* *
1242477 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
1242497 TCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTT-CAAAA
** * * **
1242518 TCGCAATGCGAATTTGACTA
1 TCGCGTTGCGATTTTCAAAA
*
1242538 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
*
1242559 TCGCGTTGCAATTTT
1 TCGCGTTGCGATTTT
1242574 GGACACTGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.53
21 28 0.47
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:1244992 original size:4 final size:4
Alignment explanation
Indices: 1244985--1245031 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
1244975 CAGTGTATGT
1244985 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1245032 TATAGTTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1250469 original size:30 final size:30
Alignment explanation
Indices: 1250412--1250469 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1250402 CCGAATCGTC
* *
1250412 CGTCGTTTTCGTCCTCGTCATCGTCTTCGA
1 CGTCGTTTTCGTCCTCGCCATCATCTTCGA
*
1250442 CGTCGTTTTCGTCAC-CGCCGTCATCTTC
1 CGTCGTTTTCGTC-CTCGCCATCATCTTC
1250470 TTCTTCGTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.07, C:0.36, G:0.19, T:0.38
Consensus pattern (30 bp):
CGTCGTTTTCGTCCTCGCCATCATCTTCGA
Found at i:1250472 original size:33 final size:30
Alignment explanation
Indices: 1250412--1250486 Score: 78
Period size: 33 Copynumber: 2.4 Consensus size: 30
1250402 CCGAATCGTC
*
1250412 CGTCGTTTTCGTCCTCGTCATCGTCTTCGA
1 CGTCGTTTTCGTCCCCGTCATCGTCTTCGA
* **
1250442 CGTCGTTTTCGTCACCGCCGTCATCTTCTTCTT
1 CGTCGTTTTCGT--CC-CCGTCATCGTCTTCGA
*
1250475 CGTCGATTTCGT
1 CGTCGTTTTCGT
1250487 TGGTGTTCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 12 0.32
32 2 0.05
33 23 0.62
ACGTcount: A:0.07, C:0.33, G:0.19, T:0.41
Consensus pattern (30 bp):
CGTCGTTTTCGTCCCCGTCATCGTCTTCGA
Found at i:1254597 original size:23 final size:23
Alignment explanation
Indices: 1254567--1254616 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1254557 CGGGATTTTT
*
1254567 ACTGTTTTGTTAAATCATTCATC
1 ACTGTTTTGTTAAATCAGTCATC
*
1254590 ACTGTTTTGTTGAATCAGTCATC
1 ACTGTTTTGTTAAATCAGTCATC
1254613 ACTG
1 ACTG
1254617 AATCATACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (23 bp):
ACTGTTTTGTTAAATCAGTCATC
Found at i:1256089 original size:33 final size:30
Alignment explanation
Indices: 1256019--1256097 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 30
1256009 TTTAAAATAG
*
1256019 TTATTATATTTTATATTAATATATTTATGTAA
1 TTATTAT-TTTT-TATTAATATATTTATATAA
*
1256051 ATATTATTTTTTATTAAAATAATATTTATATAA
1 TTATTATTTTTTATT--AAT-ATATTTATATAA
1256084 TTATTATTTATTTA
1 TTATTATTT-TTTA
1256098 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 9 0.22
33 19 0.47
34 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TTATTATTTTTTATTAATATATTTATATAA
Found at i:1256260 original size:17 final size:17
Alignment explanation
Indices: 1256238--1256291 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1256228 AATGTTAATA
1256238 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1256255 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1256272 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1256289 TTT
1 TTT
1256292 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1257851 original size:21 final size:21
Alignment explanation
Indices: 1257821--1257868 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1257811 GCAGGGGTAC
* *
1257821 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1257842 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1257863 ATGCCA
1 ATGCCA
1257869 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1257898 original size:21 final size:21
Alignment explanation
Indices: 1257872--1257941 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
1257862 TATGCCATCT
*
1257872 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
1257893 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
1257914 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
1257935 CCGCAGG
1 CCGCAGG
1257942 ATTTTATACC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.36, G:0.27, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1258516 original size:34 final size:35
Alignment explanation
Indices: 1258466--1258570 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 35
1258456 AAATGTTTTT
*
1258466 AAAATACAAATTATATTATTCGAAATTTAAAA-TA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATTA
* *
1258500 AAAATAAAAATAATATTATTCGAAA-TTAAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATTA
* * *
1258534 AAAATATAAATTATAGTATTCGAAATTTAACATTA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATTA
1258569 AA
1 AA
1258571 TTTCAACTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
33 6 0.10
34 46 0.75
35 9 0.15
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (35 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATTA
Found at i:1260139 original size:128 final size:127
Alignment explanation
Indices: 1259906--1260525 Score: 1009
Period size: 128 Copynumber: 4.9 Consensus size: 127
1259896 TTACCTGATT
1259906 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * ***
1259971 TGACAAAATAATGGAAGGCGCCCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGT-GAATGAGAAATAATAGG
*
1260034 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
1260099 TGACAAAATAATGGAAGGCGCCCCCCCGGGAACGCACCTTCATGTGAAT-AGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTGAATGAG--AAATAATAGG
1260162 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1260227 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTGAAT-GAGAAATAATAGG
* *
1260290 TACTGATATGTCTAGTGTCTCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
1260355 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT----ATTAAAAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTGAATGAGAAATAATAGG
1260413 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1260477 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTGAAT
1260526 AGTACTCCGA
Statistics
Matches: 471, Mismatches: 17, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
122 49 0.10
123 69 0.15
126 2 0.00
127 1 0.00
128 349 0.74
130 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.23
Consensus pattern (127 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTGAATGAGAAATAATAGG
Found at i:1264320 original size:2 final size:2
Alignment explanation
Indices: 1264313--1264355 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1264303 ATTTTTAAGA
1264313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1264355 A
1 A
1264356 AATTTATGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1270506 original size:21 final size:21
Alignment explanation
Indices: 1270480--1270522 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1270470 CCGGAAATAT
*
1270480 TAAAAAAAATGATGTTTTAGG
1 TAAAAAAAATAATGTTTTAGG
*
1270501 TAAAAATAATAATGTTTTAGG
1 TAAAAAAAATAATGTTTTAGG
1270522 T
1 T
1270523 TATTTTTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (21 bp):
TAAAAAAAATAATGTTTTAGG
Found at i:1273392 original size:17 final size:19
Alignment explanation
Indices: 1273370--1273404 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1273360 TAAATTCATT
1273370 TTATATTT-TTAT-TATAA
1 TTATATTTGTTATCTATAA
1273387 TTATATTTGTTATCTATA
1 TTATATTTGTTATCTATA
1273405 TTTCTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TTATATTTGTTATCTATAA
Found at i:1273530 original size:15 final size:15
Alignment explanation
Indices: 1273512--1273561 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1273502 TCTTATTGAC
1273512 AATATAAATATTAAT
1 AATATAAATATTAAT
**
1273527 AATATAAA-ATTTTT
1 AATATAAATATTAAT
*
1273541 AGA-ATACATATTAAT
1 A-ATATAAATATTAAT
1273556 AATATA
1 AATATA
1273562 TTTCTATCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
AATATAAATATTAAT
Found at i:1276242 original size:2 final size:2
Alignment explanation
Indices: 1276235--1276263 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1276225 TTCAACTTGC
1276235 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1276264 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1278343 original size:3 final size:3
Alignment explanation
Indices: 1278337--1278421 Score: 161
Period size: 3 Copynumber: 28.3 Consensus size: 3
1278327 GGTTGTTGAA
1278337 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1278385 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1278422 GTTTTATTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1285629 original size:2 final size:2
Alignment explanation
Indices: 1285624--1285653 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1285614 TATAAAGGAG
1285624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1285654 CTTAGATCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1290858 original size:18 final size:18
Alignment explanation
Indices: 1290835--1290872 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1290825 GTTCACTTGC
*
1290835 TCCACCTCAAAATTAGTG
1 TCCACCTCAAAATCAGTG
*
1290853 TCCACCTTAAAATCAGTG
1 TCCACCTCAAAATCAGTG
1290871 TC
1 TC
1290873 TGTCTCAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (18 bp):
TCCACCTCAAAATCAGTG
Found at i:1294753 original size:183 final size:186
Alignment explanation
Indices: 1294432--1294820 Score: 587
Period size: 183 Copynumber: 2.1 Consensus size: 186
1294422 TTTTCTAATT
* * *
1294432 TATATAA-A-ATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATAAATAAT
*
1294495 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGATATT
*
1294560 AGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTT-AGCCCATATG-T-TA
131 AGATCTTAAATTATTAATTGGATTTTAAATGATTTGGG-TTGAGCCCATATGTTATA
* *
1294614 TATATAATATATTTAATATTTTTTAATT-AAAAAATAATTTACAATTAATTTAAATAGTATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AATTTACAATTAATTTAAATAATAAATAA
* *
1294678 TTATAAAATAAAGAA-TTTA-TTTAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGATA
65 TTATAAAATAAA-AATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGATA
* *
1294741 TTAGATCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGTTATA
129 TTAGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGTTGAGCCCATATGTTATA
1294799 TATAATAATATATTTAATATTT
1 TAT-ATAATATATTTAATATTT
1294821 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
182 9 0.05
183 95 0.51
184 59 0.31
185 7 0.04
186 18 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATAAATAAT
TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGATATT
AGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGTTGAGCCCATATGTTATA
Found at i:1295617 original size:31 final size:31
Alignment explanation
Indices: 1295579--1295646 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1295569 AAAGGCTGAA
1295579 GGACTAAAATCAAATAGATCGATAATATTAG
1 GGACTAAAATCAAATAGATCGATAATATTAG
** * * *
1295610 GGACTAAAATCGGATGGATCGATAATGTTAT
1 GGACTAAAATCAAATAGATCGATAATATTAG
1295641 GGACTA
1 GGACTA
1295647 TTCCCCCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.26
Consensus pattern (31 bp):
GGACTAAAATCAAATAGATCGATAATATTAG
Found at i:1300179 original size:227 final size:227
Alignment explanation
Indices: 1299759--1300213 Score: 799
Period size: 227 Copynumber: 2.0 Consensus size: 227
1299749 CCCTTAAAAG
*
1299759 AATTCTTTCAAAAATATCTTTATTATGTTATTGAATAATAAAAATTCTACGAAGATTAAATTACA
1 AATTCTTTCAAAAATATCCTTATTATGTTATTGAATAATAAAAATTCTACGAAGATTAAATTACA
*
1299824 AATTTATTCTTAAATTATTTTAGATTTACAAAAAAATATCTATAATTAAAATTGTATATGAAATT
66 AATTTATTCTTAAACTATTTTAGATTTACAAAAAAATATCTATAATTAAAATTGTATATGAAATT
* *
1299889 CAGGGTTAAAATAAAATTTTATCATTTCATTAAATCTTTTTATATTTTTAATTTTGTAAAAATAT
131 CAGGGTTAAAATAAAATTTTACCATTTCATTAAATCTTTTTATATTTTCAATTTTGTAAAAATAT
1299954 ATATATAAATTTTATGAATTTAAATTTTTTAA
196 ATATATAAATTTTATGAATTTAAATTTTTTAA
1299986 AATTCTTTCAAAAATATCCTTATTATGTTATTGAATAATAAAAATTCTACGAATG-TTAAATTAC
1 AATTCTTTCAAAAATATCCTTATTATGTTATTGAATAATAAAAATTCTACGAA-GATTAAATTAC
* *
1300050 AAATTTATTCTTAAACTATTTTAGATTTAC-AAAAAA-ATCTATAATTAAAATTTTATATGAAGT
65 AAATTTATTCTTAAACTATTTTAGATTTACAAAAAAATATCTATAATTAAAATTGTATATGAAAT
*
1300113 TCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAATCTTTTTATATTTTCAATTTTGTAAAAAA
130 TCA-GGGTTAAAATAAAATTTTACCATTTCATTAAATCTTTTTATATTTTCAATTTTGT-AAAAA
1300178 TATATATATAAATTTTATGAATTTAAATTTTTTAA
193 TATATATATAAATTTTATGAATTTAAATTTTTTAA
1300213 A
1 A
1300214 GAAAATATAT
Statistics
Matches: 218, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
225 28 0.13
226 58 0.27
227 131 0.60
228 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (227 bp):
AATTCTTTCAAAAATATCCTTATTATGTTATTGAATAATAAAAATTCTACGAAGATTAAATTACA
AATTTATTCTTAAACTATTTTAGATTTACAAAAAAATATCTATAATTAAAATTGTATATGAAATT
CAGGGTTAAAATAAAATTTTACCATTTCATTAAATCTTTTTATATTTTCAATTTTGTAAAAATAT
ATATATAAATTTTATGAATTTAAATTTTTTAA
Found at i:1300409 original size:20 final size:20
Alignment explanation
Indices: 1300384--1300421 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1300374 ATCGTATTCT
1300384 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1300404 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1300422 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1301074 original size:20 final size:20
Alignment explanation
Indices: 1301049--1301086 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1301039 ATCCTATTCG
1301049 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
1301069 CTGGTAATCTTATATTCC
1 CTGGTAATCTTACATTCC
1301087 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1302232 original size:19 final size:19
Alignment explanation
Indices: 1302208--1302245 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1302198 CATATACTCA
1302208 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
1302227 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
1302246 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:1302304 original size:32 final size:32
Alignment explanation
Indices: 1302260--1302330 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
1302250 CATATACTCA
* *
1302260 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
1302292 CCATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
1302324 CCATGCA
1 CCATGCA
1302331 GTCTGGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.30, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:1302421 original size:29 final size:29
Alignment explanation
Indices: 1302318--1302412 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
1302308 GCCAATAGAG
* **
1302318 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1302347 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1302376 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1302405 AGGTCGCC
1 AGGTCGCC
1302413 CCGGCGTCCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:1302511 original size:49 final size:49
Alignment explanation
Indices: 1302439--1302553 Score: 177
Period size: 49 Copynumber: 2.4 Consensus size: 49
1302429 CCCGAGACCA
1302439 TGCATG-C-ACATGCA-GCCAAATAACTTCACGTGCTCCTGCT-CCCGC
1 TGCATGCCTACATGCATGCCAAATAACTTCACGTGCTCCTGCTCCCCGC
*
1302484 TGCATGCCTGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAA-ATAACTTCACGTGCTCCTGCTCCCCGC
1302534 TGCATGCCTACA-GCATGCCA
1 TGCATGCCTACATGCATGCCA
1302554 TGTGATCCTA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
45 6 0.10
46 1 0.02
47 6 0.10
48 5 0.08
49 29 0.46
50 16 0.25
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (49 bp):
TGCATGCCTACATGCATGCCAAATAACTTCACGTGCTCCTGCTCCCCGC
Found at i:1302778 original size:16 final size:18
Alignment explanation
Indices: 1302757--1302795 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1302747 GGAGATAAGG
*
1302757 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
1302773 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
1302791 TAAAT
1 TAAAT
1302796 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:1302964 original size:41 final size:40
Alignment explanation
Indices: 1302859--1302968 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 40
1302849 TACATAAATT
* *
1302859 AAAAATTATTTAATTAGTATATGTTTGATAGTTATATAGTTAA
1 AAAAATTATTTAATTAGT-TTTG-TTAATAGTTATATAG-TAA
* * *
1302902 AAATAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATA-TAA
1 AAA-AATTATTTAATTAGTTTTGTTAATAGTTA--TATAGTAA
1302944 AAAAATTATTTAATTAGTTTTGTTA
1 AAAAATTATTTAATTAGTTTTGTTA
1302969 GTTAAATAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
41 19 0.34
42 15 0.27
43 6 0.11
44 16 0.29
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (40 bp):
AAAAATTATTTAATTAGTTTTGTTAATAGTTATATAGTAA
Found at i:1302973 original size:45 final size:46
Alignment explanation
Indices: 1302900--1302988 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 46
1302890 TTATATAGTT
*
1302900 AAAAATAATTAATTAGTTTGTTTTGTT-AATAGTT-AGTTATATAA
1 AAAAATAATTAATTAGTTTGTTTAGTTAAATAGTTAAGTTATATAA
*
1302944 AAAAATTATTTAATTAGTTT-TGTTAGTTAAATAGTTAAGTTATAT
1 AAAAA-TAATTAATTAGTTTGT-TTAGTTAAATAGTTAAGTTATAT
1302989 TTGTTTGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 6 0.15
45 18 0.46
46 7 0.18
47 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (46 bp):
AAAAATAATTAATTAGTTTGTTTAGTTAAATAGTTAAGTTATATAA
Found at i:1303033 original size:12 final size:12
Alignment explanation
Indices: 1303016--1303068 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
1303006 ATTATAAAAA
1303016 ATTAGTTAGTTT
1 ATTAGTTAGTTT
1303028 ATTAGTTAGTTTT
1 ATTAGTTAG-TTT
*
1303041 AGTTAGTAAGTTT
1 A-TTAGTTAGTTT
*
1303054 ATTAG-TAGTAT
1 ATTAGTTAGTTT
1303065 ATTA
1 ATTA
1303069 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 8 0.22
12 13 0.36
13 8 0.22
14 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (12 bp):
ATTAGTTAGTTT
Found at i:1303195 original size:16 final size:16
Alignment explanation
Indices: 1303163--1303209 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1303153 TTTAAAAAGT
*
1303163 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
1303179 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
1303195 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
1303210 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:1303204 original size:15 final size:14
Alignment explanation
Indices: 1303184--1303214 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1303174 GTTTATTAGT
1303184 TTATTATATTATAAG
1 TTATTATATTA-AAG
1303199 TTATTATATTAAAG
1 TTATTATATTAAAG
1303213 TT
1 TT
1303215 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:1305368 original size:16 final size:17
Alignment explanation
Indices: 1305349--1305380 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1305339 CAATGATGTT
1305349 TAGTATC-AATAATTAC
1 TAGTATCAAATAATTAC
1305365 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
1305381 GTATTAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:1305399 original size:21 final size:21
Alignment explanation
Indices: 1305375--1305418 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1305365 TAGTATCAAA
* *
1305375 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
1305396 TAATAATTAGTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
1305417 TA
1 TA
1305419 TCAATCATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:1305430 original size:21 final size:21
Alignment explanation
Indices: 1305383--1305447 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1305373 AATAATTAGT
*
1305383 ATTAAATCATTAGTAATAATT
1 ATTAAATCATTAGTAATAATC
*
1305404 AGTAAATCATTAGT-ATCAATC
1 ATTAAATCATTAGTAAT-AATC
*
1305425 ATTAAAT-ATT--TAAAAATC
1 ATTAAATCATTAGTAATAATC
1305443 ATTAA
1 ATTAA
1305448 TAAATTCGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 10 0.26
19 1 0.03
20 5 0.13
21 22 0.58
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTAAATCATTAGTAATAATC
Found at i:1305609 original size:12 final size:12
Alignment explanation
Indices: 1305526--1305713 Score: 69
Period size: 11 Copynumber: 16.2 Consensus size: 12
1305516 ATTATTAGTA
1305526 ATTATTA-AATC
1 ATTATTATAATC
*
1305537 ATTATTATAATA
1 ATTATTATAATC
*
1305549 ATTACTA-AAT-
1 ATTATTATAATC
* ** *
1305559 AATAACATAATT
1 ATTATTATAATC
*
1305571 ATTA-TAAAATC
1 ATTATTATAATC
*
1305582 ATTATTATAATG
1 ATTATTATAATC
1305594 ATTA-TATCAATC
1 ATTATTAT-AATC
* *
1305606 ATTACTAAACATC
1 ATTATTATA-ATC
*
1305619 AAATCATTA-AAT-
1 --ATTATTATAATC
1305631 A-T-TTA-AATC
1 ATTATTATAATC
1305640 ATTATTA-AATC
1 ATTATTATAATC
* *
1305651 ATTTTTATAATG
1 ATTATTATAATC
1305663 ATTATTACTAAATC
1 ATTATTA-T-AATC
* *
1305677 ATTACTATAATG
1 ATTATTATAATC
*
1305689 ATTTATCA-AATC
1 A-TTATTATAATC
*
1305701 ATTACTA-AATC
1 ATTATTATAATC
1305712 AT
1 AT
1305714 CAAATCATTA
Statistics
Matches: 134, Mismatches: 27, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
8 6 0.04
9 1 0.01
10 6 0.04
11 47 0.35
12 46 0.34
13 13 0.10
14 10 0.07
15 5 0.04
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (12 bp):
ATTATTATAATC
Found at i:1305674 original size:26 final size:26
Alignment explanation
Indices: 1305640--1305707 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
1305630 TATTTAAATC
* **
1305640 ATTATTAAATCATTTTTATAATGATT
1 ATTACTAAATCATTACTATAATGATT
1305666 ATTACTAAATCATTACTATAATGA-T
1 ATTACTAAATCATTACTATAATGATT
1305691 -TTA-TCAAATCATTACTA
1 ATTACT-AAATCATTACTA
1305708 AATCATCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 1 0.03
24 15 0.39
25 1 0.03
26 21 0.55
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTACTAAATCATTACTATAATGATT
Found at i:1305701 original size:95 final size:95
Alignment explanation
Indices: 1305568--1305761 Score: 331
Period size: 95 Copynumber: 2.0 Consensus size: 95
1305558 TAATAACATA
*
1305568 ATTATTATAAAATCATTATTATAATGATTATATCAATCATTACTAAA-CATCAAATCATTAAATA
1 ATTATTATAAAATCATTACTATAATGATTATATCAATCATTACTAAATCATCAAATCATTAAATA
1305632 TTTAAATCATTATTAAATCATTTTTATAATG
66 TTTAAATCATTATT-AATCATTTTTATAATG
1305663 ATTATTACT-AAATCATTACTATAATGATT-TATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTA-TAAAATCATTACTATAATGATTATATC-AATCATTACTAAATCATCAAATCATTAAA
1305726 TATTTAAATCATTATTAATCATTTTTATAATG
64 TATTTAAATCATTATTAATCATTTTTATAATG
1305758 ATTA
1 ATTA
1305762 CTAATCATTG
Statistics
Matches: 95, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
94 4 0.04
95 59 0.62
96 32 0.34
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (95 bp):
ATTATTATAAAATCATTACTATAATGATTATATCAATCATTACTAAATCATCAAATCATTAAATA
TTTAAATCATTATTAATCATTTTTATAATG
Found at i:1305704 original size:24 final size:23
Alignment explanation
Indices: 1305526--1305707 Score: 83
Period size: 23 Copynumber: 7.8 Consensus size: 23
1305516 ATTATTAGTA
* * *
1305526 ATTATTAAATCATTATTATAATA
1 ATTATCAAATCATTACTATAATG
* * *
1305549 ATTA-CTAAATAATAAC-ATAATT
1 ATTATC-AAATCATTACTATAATG
* *
1305571 ATTATAAAATCATTATTATAATG
1 ATTATCAAATCATTACTATAATG
1305594 ATTAT-ATCAATCATTAC--TAA--
1 ATTATCA--AATCATTACTATAATG
* * *
1305614 A-CATCAAATCATTAAATATTTAAATC
1 ATTATCAAATCATT-ACTA--T-AATG
* **
1305640 ATTATTAAATCATTTTTATAATG
1 ATTATCAAATCATTACTATAATG
1305663 ATTATTACTAAATCATTACTATAATG
1 ATTA-T-C-AAATCATTACTATAATG
1305689 ATTTATCAAATCATTACTA
1 A-TTATCAAATCATTACTA
1305708 AATCATCAAA
Statistics
Matches: 119, Mismatches: 21, Indels: 37
0.67 0.12 0.21
Matches are distributed among these distances:
18 7 0.06
19 3 0.03
20 2 0.02
22 20 0.17
23 29 0.24
24 24 0.20
25 1 0.01
26 20 0.17
27 13 0.11
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTATCAAATCATTACTATAATG
Found at i:1305766 original size:22 final size:21
Alignment explanation
Indices: 1305728--1305770 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1305718 TCATTAAATA
*
1305728 TTTAAATCATTATTAATCATT
1 TTTAAATCATTACTAATCATT
*
1305749 TTTATAATGATTACTAATCATT
1 TTTA-AATCATTACTAATCATT
1305771 GTTCATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTAAATCATTACTAATCATT
Found at i:1305875 original size:14 final size:14
Alignment explanation
Indices: 1305856--1305901 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 14
1305846 TTCAAGTCGT
1305856 AATCATTACTATCA
1 AATCATTACTATCA
1305870 AATCATTAC--T-A
1 AATCATTACTATCA
1305881 AATCATTA-TATCA
1 AATCATTACTATCA
1305894 AATCATTA
1 AATCATTA
1305902 AATATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.31
12 2 0.07
13 9 0.31
14 9 0.31
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (14 bp):
AATCATTACTATCA
Found at i:1305921 original size:20 final size:20
Alignment explanation
Indices: 1305898--1305937 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1305888 ATATCAAATC
*
1305898 ATTAAATATTAATAATAATT
1 ATTAAAAATTAATAATAATT
1305918 ATTAAAAATTAATAATAATT
1 ATTAAAAATTAATAATAATT
1305938 TCATTATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAAAATTAATAATAATT
Found at i:1306035 original size:13 final size:11
Alignment explanation
Indices: 1305943--1306260 Score: 71
Period size: 11 Copynumber: 27.6 Consensus size: 11
1305933 TAATTTCATT
1305943 ATTACT-AATC
1 ATTACTAAATC
1305953 ATTACTAAATC
1 ATTACTAAATC
1305964 ATTACTATCAAATC
1 ATTAC--T-AAATC
* *
1305978 A-TACATAATTA
1 ATTAC-TAAATC
* * ** *
1305989 ATAAGTTCATT
1 ATTACTAAATC
1306000 ATTACT-AATC
1 ATTACTAAATC
1306010 ATTACTAAATC
1 ATTACTAAATC
1306021 ATTACTATCAATC
1 ATTACTA--AATC
** *
1306034 ATTAAAAAATA
1 ATTACTAAATC
* * ** *
1306045 ATAATTTCATT
1 ATTACTAAATC
1306056 ATTACT-AATC
1 ATTACTAAATC
1306066 ATTACTAAATC
1 ATTACTAAATC
1306077 A-TACTATCAATC
1 ATTACTA--AATC
*
1306089 A-TAC-ATAATT
1 ATTACTA-AATC
* * *
1306099 AATAATAATTTC
1 ATTACTAA-ATC
*
1306111 ATTATTACTAATC
1 ATTACTA--AATC
1306124 ATTACTAAATC
1 ATTACTAAATC
1306135 ATTACTATCAAATC
1 ATTAC--T-AAATC
*
1306149 A-TAC-ATAATT
1 ATTACTA-AATC
* * *
1306159 AATAATAATTTC
1 ATTACTAA-ATC
*
1306171 ATTATTACTAATC
1 ATTACTA--AATC
1306184 ATTACTAAATC
1 ATTACTAAATC
1306195 ATTACTATCAAATC
1 ATTAC--T-AAATC
* *
1306209 ATTA-AAAATT
1 ATTACTAAATC
* * *
1306219 AATAATAATTC
1 ATTACTAAATC
*
1306230 ATTATTACTAATC
1 ATTACTA--AATC
1306243 ATTACTAAATC
1 ATTACTAAATC
1306254 ATTACTA
1 ATTACTA
1306261 CAAATCATAC
Statistics
Matches: 225, Mismatches: 52, Indels: 61
0.67 0.15 0.18
Matches are distributed among these distances:
9 1 0.00
10 42 0.19
11 91 0.40
12 25 0.11
13 43 0.19
14 23 0.10
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:1306260 original size:59 final size:60
Alignment explanation
Indices: 1305924--1306430 Score: 830
Period size: 59 Copynumber: 8.7 Consensus size: 60
1305914 AATTATTAAA
1305924 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
*
1305984 AA-T--TAATAAGTTCATTATTACTAATCATTACTAAATCATTACTATC-AATCATTA-A-
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCA-TACAT
1306039 AA--AATAATAATTTCATTATTACTAATCATTACTAAATCA-TACTATC-AATCATACAT
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
1306095 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
*
1306155 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTA-AA
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCA-TACAT
1306215 AATTAATAATAA-TTCATTATTACTAATCATTACTAAATCATTACTA-CAAATCATACAT
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
1306273 AATTAATAATAATTTCATTATTACTAATC-TTACTAAATCATTACTATCAAATCATACAT
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
* *
1306332 AATTAATAATAATTTCATCATTACTAATCATTACTAAATCATTACTATCAAATCATTA-AA
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCA-TACAT
*
1306392 AATTAATAAT-ATTTCATCATTACTAATCATTACTAAATC
1 AATTAATAATAATTTCATTATTACTAATCATTACTAAATC
1306431 TTATAAATAC
Statistics
Matches: 426, Mismatches: 6, Indels: 31
0.92 0.01 0.07
Matches are distributed among these distances:
54 2 0.00
55 15 0.04
56 42 0.10
57 46 0.11
58 74 0.17
59 127 0.30
60 116 0.27
61 4 0.01
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (60 bp):
AATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATACAT
Found at i:1306373 original size:11 final size:11
Alignment explanation
Indices: 1306348--1306378 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1306338 TAATAATTTC
1306348 ATCATTACT-A
1 ATCATTACTAA
1306358 ATCATTACTAA
1 ATCATTACTAA
1306369 ATCATTACTA
1 ATCATTACTA
1306379 TCAAATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (11 bp):
ATCATTACTAA
Found at i:1309481 original size:28 final size:28
Alignment explanation
Indices: 1309450--1309503 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1309440 ATAATCTAAT
*
1309450 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
1309478 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1309504 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1309510 original size:28 final size:28
Alignment explanation
Indices: 1309446--1309510 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
1309436 TTATATAATC
*
1309446 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
1309474 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
1309502 TAATTTATA
1 TAATATATA
1309511 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:1309513 original size:21 final size:21
Alignment explanation
Indices: 1309480--1309528 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1309470 TTAATATAAT
1309480 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1309501 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1309522 ATTAACT
1 A-TAACT
1309529 AATTTCTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1310169 original size:30 final size:30
Alignment explanation
Indices: 1310129--1310230 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
1310119 TTTGGCGAGC
1310129 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
1310159 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
1310189 TGGGCATGCATGGAGGTCGTTGGGCGTG-A
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1310218 TGGGCGTGCATGG
1 TGGGCGTGCATGG
1310231 GGGCATGGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 12 0.19
30 52 0.81
ACGTcount: A:0.11, C:0.18, G:0.48, T:0.24
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:1310324 original size:26 final size:26
Alignment explanation
Indices: 1310288--1310346 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
1310278 GTGGTCGCCC
1310288 GCGACCTGGTTGGGCGGGCGTGCATG
1 GCGACCTGGTTGGGCGGGCGTGCATG
*
1310314 GCGACCTGGTTGGTCGGGCGTGCATG
1 GCGACCTGGTTGGGCGGGCGTGCATG
1310340 GCGACCT
1 GCGACCT
1310347 ACCCCCGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.08, C:0.25, G:0.46, T:0.20
Consensus pattern (26 bp):
GCGACCTGGTTGGGCGGGCGTGCATG
Found at i:1310921 original size:21 final size:21
Alignment explanation
Indices: 1310877--1310921 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1310867 ACTTAACTCG
* *
1310877 TTTAATACTTAAACTATCAGT
1 TTTAATACCTAAACTATCAAT
* *
1310898 TTTAATACCTAAACTTTTAAT
1 TTTAATACCTAAACTATCAAT
1310919 TTT
1 TTT
1310922 TTTCAAAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTAATACCTAAACTATCAAT
Found at i:1321090 original size:2 final size:2
Alignment explanation
Indices: 1321083--1321121 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1321073 ATCTTTGCTC
1321083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1321122 ATTAGTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1321280 original size:19 final size:17
Alignment explanation
Indices: 1321258--1321293 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
1321248 TAAATTATTA
1321258 ATAAAAAAATATTTAAATT
1 ATAAAAAAA-A-TTAAATT
1321277 ATAAAAAAAATTAAATT
1 ATAAAAAAAATTAAATT
1321294 TTCCAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAAAAATTAAATT
Found at i:1321579 original size:20 final size:21
Alignment explanation
Indices: 1321548--1321591 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
1321538 TAGATTCAAA
1321548 ATTAATATTATTTTAAAAAAT
1 ATTAATATTATTTTAAAAAAT
1321569 ATTAA-ATTATTTTAAAAAAT
1 ATTAATATTATTTTAAAAAAT
1321589 ATT
1 ATT
1321592 GTATATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAATATTATTTTAAAAAAT
Found at i:1330421 original size:19 final size:18
Alignment explanation
Indices: 1330385--1330423 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1330375 GTTTAAACCG
*
1330385 AAGTTGAAGTTCAGATAA
1 AAGTTGAAGTTCACATAA
*
1330403 AAGTTGCAAGTTTACATAA
1 AAGTTG-AAGTTCACATAA
1330422 AA
1 AA
1330424 AATCAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (18 bp):
AAGTTGAAGTTCACATAA
Done.