Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1594612 original size:20 final size:21
Alignment explanation
Indices: 1594589--1594628 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1594579 AATTTGTGTA
1594589 TTTATA-TTATAATTATATAT
1 TTTATAGTTATAATTATATAT
1594609 TTTATATGTTATAATTATAT
1 TTTATA-GTTATAATTATAT
1594629 TTAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTATAGTTATAATTATATAT
Found at i:1594623 original size:22 final size:22
Alignment explanation
Indices: 1594595--1594683 Score: 74
Period size: 22 Copynumber: 3.9 Consensus size: 22
1594585 TGTATTTATA
*
1594595 TTATAATTATATATTTTATATG
1 TTATAATTATATATTATATATG
* *
1594617 TTATAATTATAT-TTAAAATATT
1 TTATAATTATATATT-ATATATG
* *
1594639 TTATATTTATATTAATTTTAATATG
1 TTATAATTATA-T-ATTAT-ATATG
1594664 TTAATAATT-TATATTATATA
1 TT-ATAATTATATATTATATA
1594684 AATTTTTAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
21 2 0.04
22 29 0.56
23 5 0.10
24 1 0.02
25 10 0.19
26 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATAATTATATATTATATATG
Found at i:1595181 original size:19 final size:20
Alignment explanation
Indices: 1595153--1595231 Score: 78
Period size: 19 Copynumber: 4.2 Consensus size: 20
1595143 CTCGCATTAA
*
1595153 AAAAAAATTA-AAATATAAT
1 AAAAATATTATAAATATAAT
*
1595172 AAAAATATTATATA-AT-AT
1 AAAAATATTATAAATATAAT
*
1595190 -AAAATATTATAAATATCAT
1 AAAAATATTATAAATATAAT
* *
1595209 ATAAATA-TATAAATATATT
1 AAAAATATTATAAATATAAT
1595228 AAAA
1 AAAA
1595232 TTTATATAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 12 0.24
18 4 0.08
19 26 0.53
20 7 0.14
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATATTATAAATATAAT
Found at i:1595184 original size:16 final size:17
Alignment explanation
Indices: 1595165--1595294 Score: 85
Period size: 16 Copynumber: 7.6 Consensus size: 17
1595155 AAAAATTAAA
1595165 ATATAATA-AAAATATT
1 ATATAATATAAAATATT
1595181 ATATAATATAAAATATT
1 ATATAATATAAAATATT
*
1595198 ATAAATATCATATAAATA-T
1 ATATA-AT-ATA-AAATATT
*
1595217 ATAAATATATTAAAAT-TT
1 ATATA-ATA-TAAAATATT
* *
1595235 ATATAACATAAATTATT
1 ATATAATATAAAATATT
* *
1595252 A-AT-GTGTCAAAAT-TT
1 ATATAATAT-AAAATATT
1595267 ATATAAATATAAAATATT
1 ATAT-AATATAAAATATT
*
1595285 TTA-AATATAA
1 ATATAATATAA
1595295 TTATGATATA
Statistics
Matches: 91, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
15 4 0.04
16 28 0.31
17 22 0.24
18 18 0.20
19 14 0.15
20 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATATAAAATATT
Found at i:1595237 original size:37 final size:36
Alignment explanation
Indices: 1595155--1595237 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 36
1595145 CGCATTAAAA
* *
1595155 AAAAATTA-AAATATAATAAAAATATTATATAATAT
1 AAAATTTATAAATATAATAAAAATATTAAATAATAT
* *
1595190 AAAATATTATAAATATCATATAAATATATAAAT-ATATT
1 AAAAT-TTATAAATATAATAAAAATAT-TAAATAATA-T
1595228 AAAATTTATA
1 AAAATTTATA
1595238 TAACATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 4 0.10
36 3 0.08
37 23 0.57
38 10 0.25
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (36 bp):
AAAATTTATAAATATAATAAAAATATTAAATAATAT
Found at i:1595277 original size:87 final size:88
Alignment explanation
Indices: 1595173--1595332 Score: 222
Period size: 87 Copynumber: 1.8 Consensus size: 88
1595163 AAATATAATA
*
1595173 AAAATATTATATAATATAAAATATTATAAATATCA-TATAAATATATAAATATATTA-AAATT-T
1 AAAATATTATATAATATAAAATATTATAAATATAATTAT-AATATATAAA-ATA-TACAAATTCT
1595235 ATAT-AACATAAATTATTAATGTGTC
63 ATATGAACATAAATTATTAATGTGTC
* *
1595260 AAAAT-TTATATAAATATAAAATATTTTAAATATAATTATGATATATAAAATATACAAATTCTAT
1 AAAATATTATAT-AATATAAAATATTATAAATATAATTATAATATATAAAATATACAAATTCTAT
1595324 ATGAACATA
65 ATGAACATA
1595333 TAAATTTTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
85 2 0.03
86 14 0.22
87 40 0.62
88 9 0.14
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (88 bp):
AAAATATTATATAATATAAAATATTATAAATATAATTATAATATATAAAATATACAAATTCTATA
TGAACATAAATTATTAATGTGTC
Found at i:1596054 original size:27 final size:27
Alignment explanation
Indices: 1596024--1596085 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1596014 AAAATCGAAA
** *
1596024 TAAATATATTTAATTTTTTAATATAT-T
1 TAAATATATTT-ATAATTAAATATATAT
*
1596051 TAAAAATATTTATAATTAAATATATAT
1 TAAATATATTTATAATTAAATATATAT
1596078 TAAATATA
1 TAAATATA
1596086 AATATTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAATATATTTATAATTAAATATATAT
Found at i:1596092 original size:13 final size:13
Alignment explanation
Indices: 1596065--1596103 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1596055 AATATTTATA
1596065 ATTAAATAT--AT
1 ATTAAATATAAAT
1596076 ATTAAATATAAAT
1 ATTAAATATAAAT
*
1596089 ATTAAATACAAAT
1 ATTAAATATAAAT
1596102 AT
1 AT
1596104 CTTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAAATATAAAT
Found at i:1598329 original size:6 final size:6
Alignment explanation
Indices: 1598318--1598361 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
1598308 ATATCTCTTT
*
1598318 ATATAA ATATAA TTAT-A ATATAA A-A-AA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
1598362 GATACATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 6 0.18
6 24 0.73
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:1601604 original size:16 final size:15
Alignment explanation
Indices: 1601565--1601607 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1601555 CATGCAGTTC
1601565 TTTTAAAAAAAAAAA
1 TTTTAAAAAAAAAAA
* *
1601580 TTTTAAAAATAATAA
1 TTTTAAAAAAAAAAA
1601595 TTTTATAAAAAAA
1 TTTTA-AAAAAAA
1601608 TTATCAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTTTAAAAAAAAAAA
Found at i:1608524 original size:31 final size:31
Alignment explanation
Indices: 1608486--1608577 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 31
1608476 TTTCAAAATG
* *
1608486 TGCCACCGGTTATGAATAGTAGTTTTTATTA
1 TGCCACCGGATAAGAATAGTAGTTTTTATTA
* **
1608517 TGCCACCGAATAAGAATAGTAGTTTTTATCG
1 TGCCACCGGATAAGAATAGTAGTTTTTATTA
* * *
1608548 TGCTATCGGATAAGAATAGCAGTTTTTATT
1 TGCCACCGGATAAGAATAGTAGTTTTTATT
1608578 CCAACTAGTG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (31 bp):
TGCCACCGGATAAGAATAGTAGTTTTTATTA
Found at i:1609282 original size:14 final size:14
Alignment explanation
Indices: 1609263--1609319 Score: 64
Period size: 13 Copynumber: 4.1 Consensus size: 14
1609253 GATTTTTTAT
1609263 ATAAAATTAAAAAA
1 ATAAAATTAAAAAA
*
1609277 ATAAAA-CAAAAAA
1 ATAAAATTAAAAAA
*
1609290 ATCAAATT-AAAAA
1 ATAAAATTAAAAAA
*
1609303 ATCAAAAATAAAAAA
1 AT-AAAATTAAAAAA
1609318 AT
1 AT
1609320 CATGAAATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 18 0.51
14 10 0.29
15 7 0.20
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (14 bp):
ATAAAATTAAAAAA
Found at i:1609315 original size:28 final size:27
Alignment explanation
Indices: 1609266--1609321 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
1609256 TTTTTATATA
1609266 AAATTAAAAAAATAAAACAAAAAAATC
1 AAATTAAAAAAATAAAACAAAAAAATC
*
1609293 AAATT-AAAAAATCAAAAATAAAAAAATC
1 AAATTAAAAAAAT--AAAACAAAAAAATC
1609321 A
1 A
1609322 TGAAATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.27
27 5 0.19
28 14 0.54
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (27 bp):
AAATTAAAAAAATAAAACAAAAAAATC
Found at i:1610412 original size:24 final size:24
Alignment explanation
Indices: 1610384--1610442 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1610374 AACAAGCAAT
1610384 ACGAGCAAAAGAGAGCAGCAAAAGG
1 ACGAGCAAAAGAGAGCAGC-AAAGG
*
1610409 -CGAGCAAAGGAGAGCAGCAAAGG
1 ACGAGCAAAAGAGAGCAGCAAAGG
*
1610432 ATGAGCAAAAG
1 ACGAGCAAAAG
1610443 GGAAGACGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.49, C:0.15, G:0.34, T:0.02
Consensus pattern (24 bp):
ACGAGCAAAAGAGAGCAGCAAAGG
Found at i:1610430 original size:13 final size:13
Alignment explanation
Indices: 1610387--1610438 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
1610377 AAGCAATACG
*
1610387 AGCAAAAGAGAGC
1 AGCAAAGGAGAGC
1610400 AGCAAA--AG-GC
1 AGCAAAGGAGAGC
1610410 GAGCAAAGGAGAGC
1 -AGCAAAGGAGAGC
1610424 AGCAAAGGATGAGC
1 AGCAAAGGA-GAGC
1610438 A
1 A
1610439 AAAGGGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.06
11 8 0.24
13 17 0.50
14 7 0.21
ACGTcount: A:0.48, C:0.15, G:0.35, T:0.02
Consensus pattern (13 bp):
AGCAAAGGAGAGC
Found at i:1615843 original size:10 final size:10
Alignment explanation
Indices: 1615828--1615867 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
1615818 ATCTCTCTTC
*
1615828 AAAAAAGAAAA
1 AAAAAA-AAAG
1615839 AAAAAGAAAAG
1 AAAAA-AAAAG
1615850 AAAAAAAAAG
1 AAAAAAAAAG
1615860 AAAAAAAA
1 AAAAAAAA
1615868 CCTTTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 13 0.48
11 13 0.48
12 1 0.04
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1615850 original size:15 final size:15
Alignment explanation
Indices: 1615830--1615867 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1615820 CTCTCTTCAA
1615830 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
1615845 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
1615860 AAAA-AAAA
1 AAAAGAAAA
1615868 CCTTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:1616410 original size:10 final size:10
Alignment explanation
Indices: 1616395--1616419 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1616385 CCAAATCTAA
1616395 AAAAAAAACC
1 AAAAAAAACC
1616405 AAAAAAAACC
1 AAAAAAAACC
1616415 AAAAA
1 AAAAA
1616420 CATATGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACC
Found at i:1616741 original size:13 final size:13
Alignment explanation
Indices: 1616723--1616747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1616713 GCTTTTTGTG
1616723 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
1616736 AAAAGAGAAAAA
1 AAAAGAGAAAAA
1616748 GAATGAAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAA
Found at i:1621475 original size:13 final size:13
Alignment explanation
Indices: 1621457--1621483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1621447 ACATTATGCT
1621457 TTGTATCGATACA
1 TTGTATCGATACA
1621470 TTGTATCGATACA
1 TTGTATCGATACA
1621483 T
1 T
1621484 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1624506 original size:13 final size:13
Alignment explanation
Indices: 1624488--1624513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1624478 TACACAAAAT
1624488 ATGTATCGATACA
1 ATGTATCGATACA
1624501 ATGTATCGATACA
1 ATGTATCGATACA
1624514 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1624535 original size:35 final size:32
Alignment explanation
Indices: 1624470--1624535 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
1624460 TAGCCAAACT
*
1624470 TGTATCGATACACAAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
1624502 TGTATCGATACACAAAAAAAATTGTATCGATACA
1 TGTATCGATACAC--AAAAAA-TGTATCGATACA
1624536 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
34 5 0.17
35 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:1628581 original size:15 final size:15
Alignment explanation
Indices: 1628561--1628591 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1628551 TAAAAATATC
*
1628561 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1628576 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1628591 C
1 C
1628592 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1630691 original size:13 final size:13
Alignment explanation
Indices: 1630673--1630710 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1630663 CATTTTTCTT
1630673 TGTATCGATACAA
1 TGTATCGATACAA
*
1630686 TGTATCGATACAC
1 TGTATCGATACAA
1630699 TGTATCGATACA
1 TGTATCGATACA
1630711 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1632352 original size:22 final size:20
Alignment explanation
Indices: 1632318--1632358 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1632308 TGTTTAATGT
*
1632318 TTTGCTTGACTTTGTATTTA
1 TTTGCTTGACTTTGAATTTA
1632338 TTTGCATTGTACTTTGAATTT
1 TTTGC-TTG-ACTTTGAATTT
1632359 TAATCTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.59
Consensus pattern (20 bp):
TTTGCTTGACTTTGAATTTA
Found at i:1633284 original size:13 final size:13
Alignment explanation
Indices: 1633266--1633291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1633256 TACACAAAAT
1633266 ATGTATCGATACA
1 ATGTATCGATACA
1633279 ATGTATCGATACA
1 ATGTATCGATACA
1633292 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1633289 original size:32 final size:34
Alignment explanation
Indices: 1633248--1633312 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
1633238 TAGCCAAACT
*
1633248 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
1633280 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
1633313 TTGGATTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:1633672 original size:34 final size:35
Alignment explanation
Indices: 1633634--1633700 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1633624 CCTTACAACA
1633634 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1633668 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1633701 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1634176 original size:13 final size:13
Alignment explanation
Indices: 1634158--1634183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1634148 CAATTTTTTG
1634158 TGTATCGATACAT
1 TGTATCGATACAT
1634171 TGTATCGATACAT
1 TGTATCGATACAT
1634184 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1634195 original size:32 final size:33
Alignment explanation
Indices: 1634138--1634201 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1634128 TACAAGCCAA
**
1634138 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1634171 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1634202 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1634922 original size:21 final size:21
Alignment explanation
Indices: 1634879--1634924 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1634869 TAATTCACGC
* *
1634879 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
1634900 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
1634921 ATTC
1 ATTC
1634925 ATATCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:1639247 original size:13 final size:13
Alignment explanation
Indices: 1639229--1639254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1639219 CAATTTTTTG
1639229 TGTATCGATACAT
1 TGTATCGATACAT
1639242 TGTATCGATACAT
1 TGTATCGATACAT
1639255 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1639266 original size:32 final size:33
Alignment explanation
Indices: 1639209--1639272 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1639199 TACAAGCCAA
**
1639209 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1639242 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1639273 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1641356 original size:185 final size:185
Alignment explanation
Indices: 1641044--1641397 Score: 663
Period size: 185 Copynumber: 1.9 Consensus size: 185
1641034 ACATTATCAT
* *
1641044 GACTTCTAGAATTTTGTAACTAGTTAACATCAACTTATTTGGTCTAACTAAAACGCAAAGTGTAG
1 GACTTCTAGAATTTTGCAACTAGTTAACATCAACTTATTTGGTCTAACTAAAACGCAAAGTCTAG
*
1641109 GTGGTAAAAGATATGGATTTGTTATTGTGGATGATTATTCTAGATATATTTGGGTTTTATTCTTA
66 GTGGTAAAAGATATGGATTTGTTATTGTAGATGATTATTCTAGATATATTTGGGTTTTATTCTTA
1641174 AGCACTAAAGATGAAGCTTTAGAAAAATTCATCACTTTTGCAACTAGTTATTGTG
131 AGCACTAAAGATGAAGCTTTAGAAAAATTCATCACTTTTGCAACTAGTTATTGTG
* *
1641229 GACTTCTAGAATTTTGCAACTAGTTAACATCGACTTATTTGGTCTAACTAGAACGCAAAGTCTAG
1 GACTTCTAGAATTTTGCAACTAGTTAACATCAACTTATTTGGTCTAACTAAAACGCAAAGTCTAG
1641294 GTGGTAAAAGATATGGATTTGTTATTGTAGATGATTATTCTAGATATATTTGGGTTTTATTCTTA
66 GTGGTAAAAGATATGGATTTGTTATTGTAGATGATTATTCTAGATATATTTGGGTTTTATTCTTA
1641359 AGCACTAAAGATGAAGCTTTAGAAAAATTCATCACTTTT
131 AGCACTAAAGATGAAGCTTTAGAAAAATTCATCACTTTT
1641398 TGTAAAATTG
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 164 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (185 bp):
GACTTCTAGAATTTTGCAACTAGTTAACATCAACTTATTTGGTCTAACTAAAACGCAAAGTCTAG
GTGGTAAAAGATATGGATTTGTTATTGTAGATGATTATTCTAGATATATTTGGGTTTTATTCTTA
AGCACTAAAGATGAAGCTTTAGAAAAATTCATCACTTTTGCAACTAGTTATTGTG
Found at i:1644748 original size:7 final size:7
Alignment explanation
Indices: 1644736--1644776 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
1644726 TTATATTAAA
1644736 TGGCACT
1 TGGCACT
1644743 TGGCACT
1 TGGCACT
*
1644750 TGGTACT
1 TGGCACT
1644757 TGGCACT
1 TGGCACT
1644764 TGGCACT
1 TGGCACT
1644771 TGGCAC
1 TGGCAC
1644777 GTGCAGGTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (7 bp):
TGGCACT
Found at i:1647578 original size:13 final size:13
Alignment explanation
Indices: 1647560--1647590 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1647550 CGATACATAG
*
1647560 TACATTTTATCGA
1 TACATTGTATCGA
1647573 TACATTGTATCGA
1 TACATTGTATCGA
1647586 TACAT
1 TACAT
1647591 AGTGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1647609 original size:33 final size:33
Alignment explanation
Indices: 1647544--1647610 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1647534 TTACCACTAT
*** *
1647544 TTGTATCGATACATAGTACATTTTATCGATACA
1 TTGTATCGATACATAGTACAAAGTATCAATACA
1647577 TTGTATCGATACATAGTGA-AAAGTATCAATACA
1 TTGTATCGATACATAGT-ACAAAGTATCAATACA
1647610 T
1 T
1647611 CGTCCTAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATAGTACAAAGTATCAATACA
Found at i:1650062 original size:55 final size:55
Alignment explanation
Indices: 1649972--1650544 Score: 822
Period size: 55 Copynumber: 10.4 Consensus size: 55
1649962 CTCTATCCGC
*
1649972 TTTCCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAT
1650027 TTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAT
* * *
1650082 TTTTCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-T
* *
1650138 TTT-CAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAT
*
1650192 CTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAT
* *
1650247 TTTTCAGTCCTCAAAGAGCAGGACTCCT-TTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAT
* *
1650302 TTTCCAGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAACTTGGTGGCAT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAT
*
1650357 TTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-T
* * *
1650413 TTT-CATTCCACAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA-T
* *
1650468 TTT-CAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACT
1 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA-T
* * *
1650523 TTT-TACTCCTCAATGAGCAGGA
1 TTTCCAGTCCTCAAAGAGCAGGA
1650545 TACAGTTTAT
Statistics
Matches: 481, Mismatches: 29, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
54 8 0.02
55 463 0.96
56 10 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
TTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAT
Found at i:1650469 original size:29 final size:29
Alignment explanation
Indices: 1650325--1650472 Score: 89
Period size: 29 Copynumber: 5.3 Consensus size: 29
1650315 AAGAACAGGA
*
1650325 CACCTTTCAAAGCCCACACAACTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
* * * * * **
1650354 CA-TTTTC-CAGTCCTCA-AAG-AGCAGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
1650379 ACACCTCTT-AAAGCCCACACAAGTTGGTGG
1 -CACCT-TTCAAAGCCCACACAAGTTGGTGG
** * **
1650409 CACCTTTC--ATTCCACA-AAG-AGCAGG
1 CACCTTTCAAAGCCCACACAAGTTGGTGG
1650434 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTCAAAGCCCACACAAGTTGGTGG
1650464 CACCTTTCA
1 CACCTTTCA
1650473 GTCCTCAAAG
Statistics
Matches: 82, Mismatches: 25, Indels: 24
0.63 0.19 0.18
Matches are distributed among these distances:
25 6 0.07
26 15 0.18
27 13 0.16
28 20 0.24
29 22 0.27
30 6 0.07
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:1651203 original size:19 final size:19
Alignment explanation
Indices: 1651179--1651278 Score: 107
Period size: 19 Copynumber: 5.9 Consensus size: 19
1651169 AATTCAACGA
1651179 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1651198 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1651213 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1651230 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1651245 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1651262 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1651279 TTAGCTACTG
Statistics
Matches: 69, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.32
15 4 0.06
17 4 0.06
19 39 0.57
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1651217 original size:32 final size:32
Alignment explanation
Indices: 1651181--1651275 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
1651171 TTCAACGATT
1651181 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
1651213 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
1651245 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTTTTGTATCGATACA
1651276 TAATTAGCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:1651218 original size:13 final size:13
Alignment explanation
Indices: 1651200--1651256 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1651190 ACATAAGTTT
1651200 TGTATCGATACAA
1 TGTATCGATACAA
1651213 TGTATCGATACATAA
1 TGTATCGATAC--AA
1651228 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
1651245 TGTATCGATACA
1 TGTATCGATACA
1651257 TAAGTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1651336 original size:13 final size:13
Alignment explanation
Indices: 1651318--1651343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1651308 CATTTTTCTG
1651318 TGTATCGATACAT
1 TGTATCGATACAT
1651331 TGTATCGATACAT
1 TGTATCGATACAT
1651344 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1651340 original size:33 final size:33
Alignment explanation
Indices: 1651298--1651364 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1651288 GCCAAGGAAA
***
1651298 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1651331 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1651364 T
1 T
1651365 TGAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1654050 original size:80 final size:80
Alignment explanation
Indices: 1653899--1654053 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 80
1653889 TCTCATAATT
* * * * * ** * * *
1653899 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTTCTAATCAT
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGAACACTCCAACCCCGATTATCATCTTCAAAACAT
*
1653964 CGATTTCTCACAACC
66 CAATTTCTCACAACC
*
1653979 GGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG-TTATCATCTTCAAAACAT
1 GGGGATACTCCAACCCCGTTATTTTCAAGGGAACACTCCAACCCCGATTATCATCTTCAAAACAT
1654043 CAAATTTCTCA
66 C-AATTTCTCA
1654054 TCGGGAAATA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
79 13 0.21
80 49 0.79
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGTTATTTTCAAGGGAACACTCCAACCCCGATTATCATCTTCAAAACAT
CAATTTCTCACAACC
Found at i:1658950 original size:111 final size:111
Alignment explanation
Indices: 1658756--1658979 Score: 448
Period size: 111 Copynumber: 2.0 Consensus size: 111
1658746 AACAGGATAA
1658756 AAGAAAAAGATCATGGCAATTATATAAGCCATCAAAATTGTAAATCATTTCATAGTTGACTATAA
1 AAGAAAAAGATCATGGCAATTATATAAGCCATCAAAATTGTAAATCATTTCATAGTTGACTATAA
1658821 AATGACTAGAAAAGTCAATAAAAATATATAGTTTTACAAAAATAGT
66 AATGACTAGAAAAGTCAATAAAAATATATAGTTTTACAAAAATAGT
1658867 AAGAAAAAGATCATGGCAATTATATAAGCCATCAAAATTGTAAATCATTTCATAGTTGACTATAA
1 AAGAAAAAGATCATGGCAATTATATAAGCCATCAAAATTGTAAATCATTTCATAGTTGACTATAA
1658932 AATGACTAGAAAAGTCAATAAAAATATATAGTTTTACAAAAATAGT
66 AATGACTAGAAAAGTCAATAAAAATATATAGTTTTACAAAAATAGT
1658978 AA
1 AA
1658980 AAGCGATCTA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (111 bp):
AAGAAAAAGATCATGGCAATTATATAAGCCATCAAAATTGTAAATCATTTCATAGTTGACTATAA
AATGACTAGAAAAGTCAATAAAAATATATAGTTTTACAAAAATAGT
Found at i:1661833 original size:2 final size:2
Alignment explanation
Indices: 1661826--1661855 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1661816 TACTAAAATA
1661826 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
1661856 CCAACACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1662726 original size:38 final size:38
Alignment explanation
Indices: 1662670--1662807 Score: 109
Period size: 38 Copynumber: 3.6 Consensus size: 38
1662660 AGTTATAAAC
* * *
1662670 AAAAACCACTACTT-TAAACAGGTGACATGGTTCGAAAT
1 AAAAATCACTA-TTCTAAACCGGTGACATGGTTCAAAAT
* * * *
1662708 GAAAA-CTATTATTCTAAACCGATGACACGGTTCAAAAT
1 AAAAATC-ACTATTCTAAACCGGTGACATGGTTCAAAAT
* * * * *
1662746 AAAAATCACTATTTTAAACCGGTGGCATGGTTTAATAC
1 AAAAATCACTATTCTAAACCGGTGACATGGTTCAAAAT
* * *
1662784 AAAAACCACTATTCTTATCCGGTG
1 AAAAATCACTATTCTAAACCGGTG
1662808 GCACAATTCA
Statistics
Matches: 78, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
37 3 0.04
38 74 0.95
39 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (38 bp):
AAAAATCACTATTCTAAACCGGTGACATGGTTCAAAAT
Found at i:1662808 original size:38 final size:38
Alignment explanation
Indices: 1662717--1662886 Score: 180
Period size: 38 Copynumber: 4.5 Consensus size: 38
1662707 TGAAAACTAT
* * * * * * *
1662717 TATTCTAAACCGATGACACGGTTCAAAATAAAAATCAC
1 TATTCTTAACCGGTGGCACAGTTCAATACAAAAACCAC
** *
1662755 TATT-TTAAACCGGTGGCATGGTTTAATACAAAAACCAC
1 TATTCTT-AACCGGTGGCACAGTTCAATACAAAAACCAC
* * *
1662793 TATTCTTATCCGGTGGCACAATTCATTACAAAAACCAC
1 TATTCTTAACCGGTGGCACAGTTCAATACAAAAACCAC
* *
1662831 TATTCTTATCCGGTGGCACAGCTCAATACAAAAACCAC
1 TATTCTTAACCGGTGGCACAGTTCAATACAAAAACCAC
*
1662869 TATTCTTAACCTGTGGCA
1 TATTCTTAACCGGTGGCA
1662887 TGATTTGAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
37 1 0.01
38 108 0.97
39 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.28
Consensus pattern (38 bp):
TATTCTTAACCGGTGGCACAGTTCAATACAAAAACCAC
Found at i:1667011 original size:2 final size:2
Alignment explanation
Indices: 1667004--1667043 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1666994 GCTTCAATGC
1667004 TA TA TA TA TA 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 TA TA TA TA TA
1667044 GAGAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1669651 original size:2 final size:2
Alignment explanation
Indices: 1669644--1669674 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1669634 ATGGTAAAAT
1669644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1669675 TTCCAACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1676803 original size:18 final size:19
Alignment explanation
Indices: 1676776--1676812 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1676766 TTTAAAATTT
1676776 AAAATCATTT-CTTTAAAA
1 AAAATCATTTGCTTTAAAA
*
1676794 AAAATTATTTGCTTTAAAA
1 AAAATCATTTGCTTTAAAA
1676813 TTGTGCACCC
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:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAATCATTTGCTTTAAAA
Found at i:1678605 original size:32 final size:32
Alignment explanation
Indices: 1678525--1678606 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
1678515 ACCCTATATT
* * *
1678525 TTTCCAAATAGGTCAAAA-GTCCACTTGTATC
1 TTTCTAAATAGGTCAAAATATCAACTTGTATC
* * *
1678556 TTTCTAAACA-ATCCAAAATATGAACTTGTATC
1 TTTCTAAATAGGT-CAAAATATCAACTTGTATC
1678588 TTTCTAAATAGGTCAAAAT
1 TTTCTAAATAGGTCAAAAT
1678607 CCCAAACTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
30 1 0.03
31 13 0.32
32 25 0.62
33 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (32 bp):
TTTCTAAATAGGTCAAAATATCAACTTGTATC
Found at i:1678783 original size:65 final size:64
Alignment explanation
Indices: 1678642--1678815 Score: 180
Period size: 65 Copynumber: 2.7 Consensus size: 64
1678632 TCTATATCTC
* * *
1678642 CAAATATGTCAAAAGTTC-AACTTGTATCTTTTC-AAACAAGC-TAAAATCTGAATCGATATCTT
1 CAAATAGGTCAAAAG-TCAAACTTGTATC-TTTCGAAACAAGCAAAAAATCTAAATCGATATCTT
1678704 T
64 T
*
1678705 CAAATAGGTCAAAAGTCAAACTTGTATCATTCGAAACAAGACAAAAAATC-AAAT-GTATATCTT
1 CAAATAGGTCAAAAGTCAAACTTGTATCTTTCGAAACAAG-CAAAAAATCTAAATCG-ATATCTT
1678768 T
64 T
* * * *
1678769 CTAAATAGGTCAAAAATCAAATTTGAATCTTTGCG-AACAAGCCAAAA
1 C-AAATAGGTCAAAAGTCAAACTTGTATCTTT-CGAAACAAGCAAAAA
1678816 TCCTATTAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
62 5 0.05
63 32 0.34
64 18 0.19
65 38 0.40
66 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (64 bp):
CAAATAGGTCAAAAGTCAAACTTGTATCTTTCGAAACAAGCAAAAAATCTAAATCGATATCTTT
Found at i:1678789 original size:32 final size:30
Alignment explanation
Indices: 1678697--1678791 Score: 91
Period size: 33 Copynumber: 3.0 Consensus size: 30
1678687 ATCTGAATCG
*
1678697 ATATCTTTCAAATAGGTCAAAAGTCAAACTT
1 ATATCTTTCAAATAGGTCAAAAATCAAA-TT
* * * * *
1678728 GTATCATTCGAAACAAGACAAAAAATCAAATGT
1 ATATCTTTC-AAATAGGTC-AAAAATCAAAT-T
1678761 ATATCTTTCTAAATAGGTCAAAAATCAAATT
1 ATATCTTTC-AAATAGGTCAAAAATCAAATT
1678792 TGAATCTTTG
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
31 8 0.16
32 18 0.37
33 23 0.47
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (30 bp):
ATATCTTTCAAATAGGTCAAAAATCAAATT
Found at i:1678799 original size:32 final size:31
Alignment explanation
Indices: 1678699--1678800 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 31
1678689 CTGAATCGAT
* * *
1678699 ATCTTTCAAATAGGTCAAAAGTCAAACTTGT
1 ATCTTTCAAATAGGTCAAAAATCAAATTTGA
* * * * *
1678730 ATCATTCGAAACAAGACAAAAAATCAAATGT-A
1 ATCTTTC-AAATAGGTC-AAAAATCAAATTTGA
1678762 TATCTTTCTAAATAGGTCAAAAATCAAATTTGA
1 -ATCTTTC-AAATAGGTCAAAAATCAAATTTGA
1678795 ATCTTT
1 ATCTTT
1678801 GCGAACAAGC
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
31 6 0.11
32 24 0.45
33 23 0.43
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (31 bp):
ATCTTTCAAATAGGTCAAAAATCAAATTTGA
Found at i:1682885 original size:18 final size:18
Alignment explanation
Indices: 1682862--1682897 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1682852 GTAACCTATA
1682862 ATCTAATATGCACAACTT
1 ATCTAATATGCACAACTT
1682880 ATCTAATATGCACAACTT
1 ATCTAATATGCACAACTT
1682898 CAAGAAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (18 bp):
ATCTAATATGCACAACTT
Found at i:1684931 original size:13 final size:13
Alignment explanation
Indices: 1684909--1684940 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1684899 TTATGAATCA
*
1684909 ATACATTGTATCG
1 ATACAATGTATCG
1684922 ATACAATGTATCG
1 ATACAATGTATCG
1684935 ATACAA
1 ATACAA
1684941 AGAACATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (13 bp):
ATACAATGTATCG
Found at i:1685004 original size:20 final size:21
Alignment explanation
Indices: 1684969--1685008 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1684959 ATCTGGGTTT
*
1684969 TTTCAGATGTATCGATACATC
1 TTTCAGATGCATCGATACATC
1684990 TTTCA-ATGCATCGATACAT
1 TTTCAGATGCATCGATACAT
1685009 TCTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (21 bp):
TTTCAGATGCATCGATACATC
Found at i:1695526 original size:72 final size:72
Alignment explanation
Indices: 1695409--1695657 Score: 417
Period size: 72 Copynumber: 3.5 Consensus size: 72
1695399 TCCTGTTGCT
* * * *
1695409 ATGTATTGATACAATTCATAAGGTATCGATATATGCATTTGAAATTATAGCCGTTAATAGCCGTT
1 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTTATAGCCGTT
1695474 TGGGACA
66 TGGGACA
*
1695481 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTTATAACCGTT
1 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTTATAGCCGTT
1695546 TGGGACA
66 TGGGACA
* *
1695553 ATGTATCGATACAATTCATAATATATCGATACATGCATTTGAAATTATAGCCATTTATAGCCGTT
1 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTTATAGCCGTT
1695618 TGGGACA
66 TGGGACA
* *
1695625 ATGTATCGATACAATTCTTCATGTATCGATACA
1 ATGTATCGATACAATTCATAATGTATCGATACA
1695658 ATGTGCCATG
Statistics
Matches: 166, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 166 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (72 bp):
ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTTATAGCCGTT
TGGGACA
Found at i:1695650 original size:20 final size:20
Alignment explanation
Indices: 1695625--1695678 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
1695615 GTTTGGGACA
1695625 ATGTATCGATACAAT-T-CTTC
1 ATGTATCGATACAATGTGC--C
1695645 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
1695665 ATGTATCGATACAA
1 ATGTATCGATACAA
1695679 ATAGTAGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:1700989 original size:51 final size:52
Alignment explanation
Indices: 1700863--1701001 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 52
1700853 ATTTGCCTGC
* *
1700863 ATGTATCGATACATTGAAGAATATATCGATACATTTGGGTCAAAAACCCAAA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCCAAA
* * * * * *
1700915 ATGTATTGATACAATGGAGAATGTATC-AGTATATTTGGGTC-AAAATCTAGA
1 ATGTATCGATACAATGAAGAATGTATCGA-TACATTTGGGTCAAAAACCCAAA
*
1700966 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAAGAATGTATCGATACATTT
1701002 TTATTCCAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
51 38 0.52
52 35 0.48
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (52 bp):
ATGTATCGATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCCAAA
Found at i:1701080 original size:20 final size:20
Alignment explanation
Indices: 1701037--1701094 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1701027 GACATGGTCT
*
1701037 TGTATCGATACATTTCAGAC-A
1 TGTATCGATACA-TTCA-CCTA
*
1701058 TGTATCGATACGTTCACCTA
1 TGTATCGATACATTCACCTA
1701078 TGTATCGATACATTCAC
1 TGTATCGATACATTCAC
1701095 TTACTATAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 21 0.64
21 11 0.33
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATTCACCTA
Found at i:1702710 original size:51 final size:51
Alignment explanation
Indices: 1702629--1702745 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
1702619 CTTATAACGG
* * * *
1702629 GGTTGGAGTATCCCTAATTGTGAAAAATTGATGTTTTGGAAATAAAATCG-
1 GGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAATCGA
* *
1702679 GAGTTAGAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAATCGA
1 G-GTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAATCGA
*
1702731 GGTTGGAGTATCCCC
1 GGTTAGAGTATCCCC
1702746 TTGGAAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
50 1 0.02
51 56 0.97
52 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAATCGA
Found at i:1702951 original size:51 final size:51
Alignment explanation
Indices: 1702893--1703004 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 51
1702883 AACGAGATTA
* *
1702893 GAGTATCCCCGATGGGGAAAAATCGATGTTTTGGAAATCAAACCGAGGTTG
1 GAGTATCCCCGATGGGGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTG
* * * * *
1702944 GAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTG
1 GAGTATCCCCGATGGGGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTG
1702995 GAGTATCCCC
1 GAGTATCCCC
1703005 TTGAAAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (51 bp):
GAGTATCCCCGATGGGGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTG
Found at i:1702988 original size:130 final size:130
Alignment explanation
Indices: 1702622--1703083 Score: 606
Period size: 130 Copynumber: 3.6 Consensus size: 130
1702612 GTATCCCCTT
* ** * * * *
1702622 ATAACGGGGTTGGAGTATCCCTAATTGTGAAAAATTGATGTTTTGGAAATAAAATCG-GAGTTAG
1 ATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCGAG-GTTGG
*
1702686 AGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTTGGA
65 AGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTTGGA
1702751 A
130 A
** *
1702752 ATAACGGGGTTAGAGTATCTTCGATGGTG-AAAATCAATGTTTTGGAAATAAAACCGAGGTTGGA
1 ATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGA
* * * * *
1702816 GTATCTCTGATTATGAAAAATTGATGTTTTAGAAATAAAATCGAAGTTAGAGTATCCCGTTGGAA
66 GTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTTGGAA
* * * *
1702881 ATAACGAGATTAGAGTATCCCCGATGGGGAAAAATCGATGTTTTGGAAATCAAACCGAGGTTGGA
1 ATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGA
* * *
1702946 GTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTGAAA
66 GTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTTGGAA
* * ** * * * *
1703011 ATAACGGGGTTGGAGTATCCCCAATTATGAAAAAT-TAGTATTTTGAAAATAAAACCGGGGTTGG
1 ATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGA-TGTTTTGGAAATAAAACCGAGGTTGG
1703075 AGTATCCCC
65 AGTATCCCC
1703084 TCGAAAATAA
Statistics
Matches: 286, Mismatches: 43, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
129 113 0.40
130 173 0.60
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (130 bp):
ATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGA
GTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTTGGAA
Found at i:1703070 original size:79 final size:78
Alignment explanation
Indices: 1702936--1703143 Score: 301
Period size: 79 Copynumber: 2.6 Consensus size: 78
1702926 GAAATCAAAC
* *
1702936 CGAGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGAGGTTGGAGTATCCCCGATTGTGAAAAATTG-TATTTTAGAAATAAAACCGGGGTTGGAGTAT
*
1703001 CCCCTTGAAAATAA
65 CCCCTCGAAAATAA
* * *
1703015 CGGGGTTGGAGTATCCCCAATTATGAAAAATTAGTATTTT-GAAAATAAAACCGGGGTTGGAGTA
1 CGAGGTTGGAGTATCCCCGATTGTGAAAAATT-GTATTTTAG-AAATAAAACCGGGGTTGGAGTA
1703079 TCCCCTCGAAAATAA
64 TCCCCTCGAAAATAA
* *
1703094 CGAGGTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTAGAAATAAAA
1 CGAGGTTGGAGTATCCCCGATTGTGAAAAATT-GTATTTTAGAAATAAAA
1703144 ACATGAATGA
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 111 0.97
80 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (78 bp):
CGAGGTTGGAGTATCCCCGATTGTGAAAAATTGTATTTTAGAAATAAAACCGGGGTTGGAGTATC
CCCTCGAAAATAA
Found at i:1710716 original size:32 final size:32
Alignment explanation
Indices: 1710680--1710851 Score: 161
Period size: 32 Copynumber: 5.4 Consensus size: 32
1710670 TCTCTTTTTT
*
1710680 AAGTCCACGACTTAGTGGCATCCTTTTCTTCC
1 AAGTCCACAACTTAGTGGCATCCTTTTCTTCC
* * * **
1710712 AAGTCCATAACTCAGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTTAGTGGCATCCTTTT-CTTCC
* * *
1710745 AAGTCCATACCATAGTGGCATCTCTTTTC-T--
1 AAGTCCACAACTTAGTGGCATC-CTTTTCTTCC
*
1710775 AAGTCCACGACTTAGTGGCATCCTTTTCTTCC
1 AAGTCCACAACTTAGTGGCATCCTTTTCTTCC
* * * **
1710807 AAGTCCACAACTCAGTGACATCTTTTTTCTTTT
1 AAGTCCACAACTTAGTGGCATC-CTTTTCTTCC
1710840 AAGTCCACAACT
1 AAGTCCACAACT
1710852 CCATGGCACT
Statistics
Matches: 114, Mismatches: 20, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
29 6 0.05
30 19 0.17
32 43 0.38
33 42 0.37
34 4 0.04
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.37
Consensus pattern (32 bp):
AAGTCCACAACTTAGTGGCATCCTTTTCTTCC
Found at i:1710762 original size:33 final size:32
Alignment explanation
Indices: 1710692--1710851 Score: 116
Period size: 33 Copynumber: 5.0 Consensus size: 32
1710682 GTCCACGACT
*
1710692 TAGTGGCATCCTTTT-CTTCCAAGTCCATAAC
1 TAGTGGCATCTTTTTCCTTCCAAGTCCATAAC
** *
1710723 TCAGTGGCATCTTTTTCCTTTTAAGTCCATACC
1 T-AGTGGCATCTTTTTCCTTCCAAGTCCATAAC
**
1710756 ATAGTGGCATCTCTTTT-C-T--AAGTCCACGAC
1 -TAGTGGCATCT-TTTTCCTTCCAAGTCCATAAC
* *
1710786 TTAGTGGCATCCTTTT-CTTCCAAGTCCACAAC
1 -TAGTGGCATCTTTTTCCTTCCAAGTCCATAAC
* * ** *
1710818 TCAGTGACATCTTTTTTCTTTTAAGTCCACAAC
1 T-AGTGGCATCTTTTTCCTTCCAAGTCCATAAC
1710851 T
1 T
1710852 CCATGGCACT
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.05
30 19 0.18
31 2 0.02
32 36 0.34
33 39 0.37
34 5 0.05
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (32 bp):
TAGTGGCATCTTTTTCCTTCCAAGTCCATAAC
Found at i:1710832 original size:95 final size:95
Alignment explanation
Indices: 1710669--1710846 Score: 320
Period size: 95 Copynumber: 1.9 Consensus size: 95
1710659 AATTCTTCAA
* * *
1710669 ATCTCTTTTTTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATAACTCAGTGGCATC
1 ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
1710734 TTTTTCCTTTTAAGTCCATACCATAGTGGC
66 TTTTTCCTTTTAAGTCCATACCATAGTGGC
1710764 ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
1 ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
*
1710829 TTTTTTCTTTTAAGTCCA
66 TTTTTCCTTTTAAGTCCA
1710847 CAACTCCATG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.39
Consensus pattern (95 bp):
ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
TTTTTCCTTTTAAGTCCATACCATAGTGGC
Found at i:1710852 original size:33 final size:33
Alignment explanation
Indices: 1710676--1710920 Score: 227
Period size: 34 Copynumber: 7.5 Consensus size: 33
1710666 CAAATCTCTT
* * *
1710676 TTTTAAGTCCACGACTTAGTGGCATC-CTTTTC
1 TTTTAAGTCCACAACTCAGTGGCATCTTTTTTC
** * *
1710708 TTCCAAGTCCATAACTCAGTGGCATCTTTTTCC
1 TTTTAAGTCCACAACTCAGTGGCATCTTTTTTC
* * *
1710741 TTTTAAGTCCATACCAT-AGTGGCATCTCTTTTC
1 TTTTAAGTCCACAAC-TCAGTGGCATCTTTTTTC
* * *
1710774 ---TAAGTCCACGACTTAGTGGCATC-CTTTTC
1 TTTTAAGTCCACAACTCAGTGGCATCTTTTTTC
** *
1710803 TTCCAAGTCCACAACTCAGTGACATCTTTTTTC
1 TTTTAAGTCCACAACTCAGTGGCATCTTTTTTC
*
1710836 TTTTAAGTCCACAACTCCA-TGGCACTCTTTTTGC
1 TTTTAAGTCCACAACT-CAGTGGCA-TCTTTTTTC
*
1710870 TTTTAAGTCCACAACTCCA-TGGCACTCTTTTTGC
1 TTTTAAGTCCACAACT-CAGTGGCA-TCTTTTTTC
1710904 TTTTAAGTCCACAACTC
1 TTTTAAGTCCACAACTC
1710921 CATGGCACCT
Statistics
Matches: 180, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
29 7 0.04
30 18 0.10
32 40 0.22
33 54 0.30
34 61 0.34
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (33 bp):
TTTTAAGTCCACAACTCAGTGGCATCTTTTTTC
Found at i:1710859 original size:95 final size:95
Alignment explanation
Indices: 1710669--1710866 Score: 303
Period size: 95 Copynumber: 2.1 Consensus size: 95
1710659 AATTCTTCAA
* * *
1710669 ATCTCTTTTTTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCATAACTCAGTGGCATC
1 ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
* *
1710734 TTTTTCCTTTTAAGTCCATACCATAGTGGC
66 TTTTTCCTTTTAAGTCCAAACCACAGTGGC
1710764 ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
1 ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
*
1710829 TTTTTTCTTTTAAGTCCACAACTC-CA-TGGC
66 TTTTTCCTTTTAAGTCCA-AAC-CACAGTGGC
1710859 A-CTCTTTT
1 ATCTCTTTT
1710867 TGCTTTTAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
94 7 0.07
95 84 0.88
96 3 0.03
97 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.39
Consensus pattern (95 bp):
ATCTCTTTTCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGACATC
TTTTTCCTTTTAAGTCCAAACCACAGTGGC
Found at i:1710913 original size:68 final size:66
Alignment explanation
Indices: 1710676--1710932 Score: 203
Period size: 65 Copynumber: 3.9 Consensus size: 66
1710666 CAAATCTCTT
* * * * ** * *
1710676 TTTTAAGTCCACGACTTAGTGGCATCCTTTT-CTTCCAAGTCCATAACT-CAGTGGCATCTTTTT
1 TTTTAAGTCCACAACTCAGTGACATCTTTTTGCTTTTAAGTCCACAACTCCA-TGGCACCTTTTT
*
1710739 CC
65 GC
* * * * *
1710741 TTTTAAGTCCATACCAT-AGTGGCATCTCTTTT-C---TAAGTCCACGACT-TAGTGGCATCC-T
1 TTTTAAGTCCACAAC-TCAGTGACATCT-TTTTGCTTTTAAGTCCACAACTCCA-TGGCA-CCTT
1710799 TTT-C
62 TTTGC
** *
1710803 TTCCAAGTCCACAACTCAGTGACATCTTTTTTCTTTTAAGTCCACAACTCCATGGCACTCTTTTT
1 TTTTAAGTCCACAACTCAGTGACATCTTTTTGCTTTTAAGTCCACAACTCCATGGCAC-CTTTTT
1710868 GC
65 GC
*
1710870 TTTTAAGTCCACAACTCCA-TGGCACTCTTTTTGCTTTTAAGTCCACAACTCCATGGCACCTTT
1 TTTTAAGTCCACAACT-CAGTGACA-TCTTTTTGCTTTTAAGTCCACAACTCCATGGCACCTTT
1710933 AAGTCTAATA
Statistics
Matches: 158, Mismatches: 20, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
61 5 0.03
62 22 0.14
63 21 0.13
64 2 0.01
65 39 0.25
66 11 0.07
67 23 0.15
68 35 0.22
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.38
Consensus pattern (66 bp):
TTTTAAGTCCACAACTCAGTGACATCTTTTTGCTTTTAAGTCCACAACTCCATGGCACCTTTTTG
C
Found at i:1711018 original size:49 final size:49
Alignment explanation
Indices: 1710946--1711685 Score: 658
Period size: 49 Copynumber: 15.4 Consensus size: 49
1710936 TCTAATATCA
* **
1710946 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTGAGACTGATGTCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * *
1710995 CTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * *
1711038 CTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC-TTGAGTCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGACCAATGTCG
* *
1711089 CTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTTG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * *
1711137 CGGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * * *
1711186 CTAGCCTTGAATCAGCACATTGG------CA----TAAGCCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * *
1711225 TTGGCTTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * * *
1711273 CTGTCCTTGAATCAGCATATTGG------CA-C---AAGCCCAGTATCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * * *
1711312 CTGGCCTTGAATCAGCATATTGGAACCTTTATCTTTAAGATCGATGTCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * * * * * * *
1711361 TTGGCCTTGAATGAGCACATCGACACCTCAACCATCTTTAAGCCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCACCT---TCATCTTTAAGACCAATGTCG
* * *
1711413 CTGACCTTGAATCAGCATATTGGCA-CATCATCTTTAAGTCCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * * *
1711461 CTGGCCTTGAATCAGCACATTGGTACCTTCATCTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* *
1711510 CTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTCG
1 CTGGCCTTGAATCAGCATATTGGCACC-T--TCATCTTTAAGACCAATGTCG
* * * *
1711562 CTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
* * *
1711611 CTGGCCTTGAATCAGCATATTGGCGTCTTCGTCATCTTTAAAACCTAATGTCG
1 CTGGCCTTGAATCAGCATATTGGC-AC--CTTCATCTTTAAGACC-AATGTCG
* *
1711664 TTGGCCTTGAATCAGCACATTG
1 CTGGCCTTGAATCAGCATATTG
1711686 ACATTTTTCT
Statistics
Matches: 560, Mismatches: 88, Indels: 82
0.77 0.12 0.11
Matches are distributed among these distances:
39 63 0.11
42 1 0.00
43 37 0.07
45 2 0.00
46 1 0.00
47 2 0.00
48 110 0.20
49 180 0.32
50 3 0.01
51 43 0.08
52 92 0.16
53 26 0.05
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (49 bp):
CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCG
Found at i:1711281 original size:87 final size:86
Alignment explanation
Indices: 1711139--1711380 Score: 331
Period size: 87 Copynumber: 2.8 Consensus size: 86
1711129 CAATGTTGCG
*
1711139 GGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCAC
1 GGCCTTGAATCAGCATATTGGCAC-CTTATCTTTAAGACCAATGTCGCT-GCCTTGAATCAGCAC
* *
1711204 ATTGGCATAAGCCCAATATCGTT
64 ATTGGCACAAGCCCAATATCGCT
* * *
1711227 GGCTTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGTCCTTGAATCAGCATA
1 GGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG-CCTTGAATCAGCACA
*
1711292 TTGGCACAAGCCCAGTATCGCT
65 TTGGCACAAGCCCAATATCGCT
* * * * *
1711314 GGCCTTGAATCAGCATATTGGAACCTTTATCTTTAAGATCGATGTCGTTGGCCTTGAATGAGCAC
1 GGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCGCT-GCCTTGAATCAGCAC
1711379 AT
64 AT
1711381 CGACACCTCA
Statistics
Matches: 136, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
86 1 0.01
87 78 0.57
88 56 0.41
89 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (86 bp):
GGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTGCCTTGAATCAGCACAT
TGGCACAAGCCCAATATCGCT
Found at i:1711582 original size:101 final size:101
Alignment explanation
Indices: 1711307--1711685 Score: 495
Period size: 101 Copynumber: 3.8 Consensus size: 101
1711297 ACAAGCCCAG
** * *
1711307 TATCGCTGGCCTTGAATCAGCATATTGGAACCTT--T-ATCTTTAAGAT-CGATGTCGTTGGCCT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAG-TCCAATGTCGCTGGCCT
* * * * *
1711368 TGAATGAGCACATCGACACCTCAACCATCTTTAAGCCCAA
65 TGAATCAGCACATTGGCACCT---TCATCTTTAAGTCCAA
* * *
1711408 TATCGCTGACCTTGAATCAGCATATT-G-G-C-ACATCATCTTTAAGTCCAATGTCGCTGGCCTT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCTT
*
1711469 GAATCAGCACATTGGTACCTTCATCTTTAAGTCCAA
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
1711505 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCTT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCTT
*
1711570 GAATCAGCACATTGGCACCTTCATTTTTAAGTCCAA
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* ** *
1711606 TATCGCTGGCCTTGAATCAGCATATTGGCGTCTTCGTCATCTTTAAAACCTAATGTCGTTGGCCT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCC-AATGTCGCTGGCCT
1711671 TGAATCAGCACATTG
65 TGAATCAGCACATTG
1711686 ACATTTTTCT
Statistics
Matches: 249, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
97 39 0.16
98 2 0.01
99 3 0.01
100 41 0.16
101 136 0.55
102 28 0.11
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (101 bp):
TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGTCCAATGTCGCTGGCCTT
GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
Found at i:1711584 original size:149 final size:150
Alignment explanation
Indices: 1711307--1711688 Score: 437
Period size: 149 Copynumber: 2.5 Consensus size: 150
1711297 ACAAGCCCAG
* * * *
1711307 TATCGCTGGCCTTGAATCAGCATATTGGAACCTTTATCTTTAAGATCGATGTCGTTGGCCTTGAA
1 TATCGCTGGCCTTGAATCAGCATATTGGAACCTTCATCTTTAAGATCAATATCGCTGGCCTTGAA
* *
1711372 TGAGCACATCGACACCTCAACCATCTTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTGGC
66 TCAGCACATCGACACCTCAACCATCTTTAAGCCCAATATCGCTGACCTTGAATCAGCACATTGGC
1711437 A-CATCATCTTTAAGTCCAA
131 ACCATCATCTTTAAGTCCAA
* * *
1711456 TGTCGCTGGCCTTGAATCAGCACATTGGTACCTTCATCTTTAAG-TCCAATATCGCTGGCCTTGA
1 TATCGCTGGCCTTGAATCAGCATATTGGAACCTTCATCTTTAAGAT-CAATATCGCTGGCCTTGA
* * * * ** * * *
1711520 ATCAGCATATTGGCGCCTTC-GTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
65 ATCAGCACATCGACACC-TCAACCATCTTTAAGCCCAATATCGCTGACCTTGAATCAGCACATTG
* *
1711584 GCACCTTCATTTTTAAGTCCAA
129 GCACCATCATCTTTAAGTCCAA
** * * * * *
1711606 TATCGCTGGCCTTGAATCAGCATATTGGCGTCTTCGTCATCTTTAAAACCTAATGTCGTTGGCCT
1 TATCGCTGGCCTTGAATCAGCATATTGG-AAC--CTTCATCTTTAAGATC-AATATCGCTGGCCT
*
1711671 TGAATCAGCACATTGACA
62 TGAATCAGCACATCGACA
1711689 TTTTTCTCAT
Statistics
Matches: 193, Mismatches: 32, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
148 1 0.01
149 108 0.56
150 44 0.23
151 1 0.01
153 12 0.06
154 27 0.14
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (150 bp):
TATCGCTGGCCTTGAATCAGCATATTGGAACCTTCATCTTTAAGATCAATATCGCTGGCCTTGAA
TCAGCACATCGACACCTCAACCATCTTTAAGCCCAATATCGCTGACCTTGAATCAGCACATTGGC
ACCATCATCTTTAAGTCCAA
Found at i:1716525 original size:24 final size:20
Alignment explanation
Indices: 1716481--1716581 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 20
1716471 AAAATGCCTG
1716481 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
1716501 AATGTATCGATACATCTGGGTAAAACCA
1 AATGTATCGATACAT-T--G---AA--A
* *
1716529 GAATGTATCGATACAATGAAT
1 -AATGTATCGATACATTGAAA
* *
1716550 AATGTATCGATACAATGAAT
1 AATGTATCGATACATTGAAA
1716570 AATGTATCGATA
1 AATGTATCGATA
1716582 TATCTGGGTA
Statistics
Matches: 70, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
20 47 0.67
21 1 0.01
23 3 0.04
26 3 0.04
28 2 0.03
29 14 0.20
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1716563 original size:69 final size:70
Alignment explanation
Indices: 1716481--1716632 Score: 252
Period size: 69 Copynumber: 2.2 Consensus size: 70
1716471 AAAATGCCTG
*
1716481 AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAA-CCAGAATGTATCGATACAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAGAATGTATCGATACAA
*
1716545 TGAAT
66 TGAAC
* * *
1716550 AATGTATCGATACAATGAATAATGTATCGATATATCTGGGTAAAACCCAGAATGTATCGATATAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAGAATGTATCGATACAA
1716615 TGAAC
66 TGAAC
1716620 AATGTATCGATAC
1 AATGTATCGATAC
1716633 TAATTGTAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 42 0.55
70 35 0.45
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (70 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCCAGAATGTATCGATACAA
TGAAC
Found at i:1716686 original size:20 final size:20
Alignment explanation
Indices: 1716661--1716710 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1716651 ATTTTTGATA
1716661 TATCGATACAATGAACAATG
1 TATCGATACAATGAACAATG
*
1716681 TATCGATACAATGAATAATG
1 TATCGATACAATGAACAATG
1716701 TATCGATACA
1 TATCGATACA
1716711 TCTGGGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (20 bp):
TATCGATACAATGAACAATG
Found at i:1716698 original size:127 final size:127
Alignment explanation
Indices: 1716534--1716785 Score: 486
Period size: 127 Copynumber: 2.0 Consensus size: 127
1716524 AACCAGAATG
* *
1716534 TATCGATACAATGAATAATGTATCGATACAATGAATAATGTATCGATATATCTGGGTAAAACCCA
1 TATCGATACAATGAACAATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAACCCA
1716599 GAATGTATCGATATAATGAACAATGTATCGATACTAATTGTAAAAATTTTGAATTTTTGATA
66 GAATGTATCGATATAATGAACAATGTATCGATACTAATTGTAAAAATTTTGAATTTTTGATA
1716661 TATCGATACAATGAACAATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAACCCA
1 TATCGATACAATGAACAATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAACCCA
1716726 GAATGTATCGATATAATGAACAATGTATCGATACTAATTGTAAAAATTTTGAATTTTTGA
66 GAATGTATCGATATAATGAACAATGTATCGATACTAATTGTAAAAATTTTGAATTTTTGA
1716786 CTGTTGGGAC
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (127 bp):
TATCGATACAATGAACAATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAACCCA
GAATGTATCGATATAATGAACAATGTATCGATACTAATTGTAAAAATTTTGAATTTTTGATA
Found at i:1717265 original size:52 final size:51
Alignment explanation
Indices: 1717208--1717872 Score: 228
Period size: 52 Copynumber: 12.6 Consensus size: 51
1717198 GGTGCTAATG
* * * *
1717208 TGCTGATTCAAGACTAGTGACATTAGGCTTGAAAATGAGAAAAATGCGAATA
1 TGCTGATTCAAGGCTAGTGACATT-GGCTTAAAAATGACAAAAATGCCAATA
* * * * *
1717260 TGCTGATTCAAGGCCAGTAACATTAGACTTAAAAATGACAAAAGTGCCAATG
1 TGCTGATTCAAGGCTAGTGACATT-GGCTTAAAAATGACAAAAATGCCAATA
** ** * *
1717312 TGCTGATTTCAA-GCTA-AAACATTGAGCTTAAAAATGACAAAGGTGCCTATG
1 TGCTGA-TTCAAGGCTAGTGACATTG-GCTTAAAAATGACAAAAATGCCAATA
* *
1717363 TGCTGATTCAAGGGTAGTGACATTGGACTTAGAAAGA-GA-AAAAAGTGCTAATA
1 TGCTGATTCAAGGCTAGTGACATTGG-CTTA-AAA-ATGACAAAAA-TGCCAATA
* * *
1717416 TGCTGATTGAAGGCTAGTGATATTGGACTTAAAGATGATAAGGGTA-AAAAGAGTGCCAATG
1 TGCTGATTCAAGGCTAGTGACATTGG-CTTAAA-A--AT----G-ACAAAA-A-TGCCAATA
* * * * * * ** *
1717477 TGCTGATTCACGGCTAGCGACATTGGACTTGAAGATGAGAAGAATGCTGATG
1 TGCTGATTCAAGGCTAGTGACATTGG-CTTAAAAATGACAAAAATGCCAATA
* * * * * * * * *
1717529 TGCTGATTCACA-ACCAGCGACATTGGACTTGAAGATAAGAAGAATGCCAATG
1 TGCTGATTCA-AGGCTAGTGACATTGG-CTTAAAAATGACAAAAATGCCAATA
* * * * * * * *
1717581 TGCTGATTCAAGG-TCAATGATATTGGACTTAAATATTAGAAGAATGCGAATG
1 TGCTGATTCAAGGCT-AGTGACATTGG-CTTAAAAATGACAAAAATGCCAATA
* * * * *** ** * *
1717633 TACTGATTTAGGGCCAACAACATTAGGCTTAGGAATGATAAAGATGCCAATA
1 TGCTGATTCAAGGCTAGTGACATT-GGCTTAAAAATGACAAAAATGCCAATA
* ** * * * * * * * **
1717685 TGTTGATTCAAGGCCGGCGATATCAGACTTAAAGATAACTAAGGTGCCAATA
1 TGCTGATTCAAGGCTAGTGACAT-TGGCTTAAAAATGACAAAAATGCCAATA
* * * * ** * *
1717737 TGCTGATTCAAGGTTAGCGATATTGGACTTAAAGATGACAAAGGTGCTAATG
1 TGCTGATTCAAGGCTAGTGACATTGG-CTTAAAAATGACAAAAATGCCAATA
* * * * * **
1717789 TGCTGATTCAAGGCCAGTAACATTGGACTTAAAGATAATAAAGGTGCCAATA
1 TGCTGATTCAAGGCTAGTGACATTGG-CTTAAAAATGACAAAAATGCCAATA
* * * *
1717841 TGCTAATTCAAGACCAGTGATATTGGACTTAA
1 TGCTGATTCAAGGCTAGTGACATTGG-CTTAA
1717873 GAAAAAAAGA
Statistics
Matches: 481, Mismatches: 107, Indels: 50
0.75 0.17 0.08
Matches are distributed among these distances:
50 6 0.01
51 41 0.09
52 335 0.70
53 48 0.10
54 7 0.01
58 2 0.00
59 1 0.00
60 5 0.01
61 36 0.07
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (51 bp):
TGCTGATTCAAGGCTAGTGACATTGGCTTAAAAATGACAAAAATGCCAATA
Found at i:1717502 original size:61 final size:60
Alignment explanation
Indices: 1717401--1717514 Score: 156
Period size: 61 Copynumber: 1.9 Consensus size: 60
1717391 TTAGAAAGAG
* * * *
1717401 AAAAAAGTGCTAATATGCTGATTGAAGGCTAGTGATATTGGACTTAAAGATGATAAGGGT
1 AAAAAAGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGATAAGGGT
* * *
1717461 AAAAAGAGTGCCAATGTGCTGATTCACGGCTAGCGACATTGGACTTGAAGATGA
1 AAAAA-AGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGA
1717515 GAAGAATGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 5 0.11
61 41 0.89
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.25
Consensus pattern (60 bp):
AAAAAAGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGATAAGGGT
Found at i:1717863 original size:156 final size:156
Alignment explanation
Indices: 1717573--1717923 Score: 343
Period size: 156 Copynumber: 2.3 Consensus size: 156
1717563 ATAAGAAGAA
* * * * *
1717573 TGCCAATGTGCTGATTCAAGGTCAATGATATTGGACTTAAATATTAGAAGAATGCGAATGTACTG
1 TGCCAATATGCTGATTCAAGGTCAACGATATTGGACTTAAAGATGAAAAGAATGCGAATGTACTG
* * * * * * * *
1717638 ATTTAGGGCCAACAACATTAGGCTTAGGAATGATAAAGATGCCAATATGTTGATTCAAGGCCGGC
66 ATTCAAGGCCAACAACATTAGGCTTAAGAATAATAAAGATGCCAATATGCTAATTCAAGACCAGC
1717703 GATATCAGACTTAAAGATAACTAAGG
131 GATATCAGACTTAAAGATAACTAAGG
* * * * *
1717729 TGCCAATATGCTGATTCAAGGTTAGCGATATTGGACTTAAAGATGACAAAG-GTGCTAATGTGCT
1 TGCCAATATGCTGATTCAAGGTCAACGATATTGGACTTAAAGATGA-AAAGAATGCGAATGTACT
** *
1717793 GATTCAAGGCCAGTAACATT-GGACTTAA-AGATAATAAAGGTGCCAATATGCTAATTCAAGACC
65 GATTCAAGGCCAACAACATTAGG-CTTAAGA-ATAATAAAGATGCCAATATGCTAATTCAAGACC
* ** ** *
1717856 AGTGATATTGGACTT-AAGA-AAAAAAGA
128 AGCGATATCAGACTTAAAGATAACTAAGG
* * * ** *
1717883 TGACAATGTGCTGAATCAAGCCCAACGACATTGGACTTAAA
1 TGCCAATATGCTGATTCAAGGTCAACGATATTGGACTTAAA
1717924 AAGAGATGCC
Statistics
Matches: 157, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
154 38 0.24
155 7 0.04
156 109 0.69
157 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (156 bp):
TGCCAATATGCTGATTCAAGGTCAACGATATTGGACTTAAAGATGAAAAGAATGCGAATGTACTG
ATTCAAGGCCAACAACATTAGGCTTAAGAATAATAAAGATGCCAATATGCTAATTCAAGACCAGC
GATATCAGACTTAAAGATAACTAAGG
Found at i:1717927 original size:104 final size:104
Alignment explanation
Indices: 1717710--1717923 Score: 265
Period size: 104 Copynumber: 2.1 Consensus size: 104
1717700 GGCGATATCA
* *** *
1717710 GACTTAAAGATAACTAAGGTGCCAATATGCTGATTCAAGGTTAGCGATATTGGACTTAAAGATGA
1 GACTTAAAGATAACTAAGGTGCCAATATGCTAATTCAAGACCAGCGATATTGGACTTAAAGATAA
* * * * **
1717775 CAAAGGTGCTAATGTGCTGATTCAAGGCCAGTAACATTG
66 AAAAGATGCTAATGTGCTGAATCAAGCCCAACAACATTG
*
1717814 GACTTAAAGATAA-TAAAGGTGCCAATATGCTAATTCAAGACCAGTGATATTGGACTT-AAGA-A
1 GACTTAAAGATAACT-AAGGTGCCAATATGCTAATTCAAGACCAGCGATATTGGACTTAAAGATA
*
1717876 AAAAAGATGAC-AATGTGCTGAATCAAGCCCAACGACATTG
65 AAAAAGATG-CTAATGTGCTGAATCAAGCCCAACAACATTG
1717916 GACTTAAA
1 GACTTAAA
1717924 AAGAGATGCC
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
102 39 0.41
103 6 0.06
104 50 0.53
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (104 bp):
GACTTAAAGATAACTAAGGTGCCAATATGCTAATTCAAGACCAGCGATATTGGACTTAAAGATAA
AAAAGATGCTAATGTGCTGAATCAAGCCCAACAACATTG
Found at i:1718024 original size:35 final size:32
Alignment explanation
Indices: 1717919--1718052 Score: 130
Period size: 32 Copynumber: 4.2 Consensus size: 32
1717909 GACATTGGAC
* *
1717919 TTAAAAAGAGATGCCACTGACTTGTGTGGGCT
1 TTAAAAAGAGTTGCCACCGACTTGTGTGGGCT
* * *
1717951 TTGAAAAGAGTTTCCATCGACTTGTGTGGGCT
1 TTAAAAAGAGTTGCCACCGACTTGTGTGGGCT
* *
1717983 CT-AAAAGGGTTGCCACCGACTTGTGTGTGTGCT
1 TTAAAAAGAGTTGCCACCGACTTGTGTG-G-GCT
* **
1718016 TTAAAAAAGGGTTGCCACTAAC-T-TGTGGGCT
1 TT-AAAAAGAGTTGCCACCGACTTGTGTGGGCT
1718047 TTAAAA
1 TTAAAA
1718053 TGGTGCCACT
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
30 4 0.05
31 27 0.31
32 30 0.35
33 8 0.09
34 1 0.01
35 16 0.19
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (32 bp):
TTAAAAAGAGTTGCCACCGACTTGTGTGGGCT
Found at i:1718063 original size:28 final size:27
Alignment explanation
Indices: 1718028--1718139 Score: 107
Period size: 28 Copynumber: 4.0 Consensus size: 27
1718018 AAAAAAGGGT
1718028 TGCCACTAACTTGTGGGCTTTAAAATGG
1 TGCCACTAACTTGTGGGCTTTAAAA-GG
*
1718056 TGCCACTAACATGTGGGCTTTGAAAAGG
1 TGCCACTAACTTGTGGGCTTT-AAAAGG
* * * *
1718084 TGCCATTGACTTTTGGGCTTTACAAGGG
1 TGCCACTAACTTGTGGGCTTTA-AAAGG
* * * *
1718112 TGCCAATGACTTATGGGTTTTGAAAAGG
1 TGCCACTAACTTGTGGGCTTT-AAAAGG
1718140 GATACCACGA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.01
28 65 0.92
29 5 0.07
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (27 bp):
TGCCACTAACTTGTGGGCTTTAAAAGG
Found at i:1718274 original size:32 final size:30
Alignment explanation
Indices: 1718238--1718543 Score: 155
Period size: 30 Copynumber: 10.4 Consensus size: 30
1718228 GGTACCATAT
1718238 AGTTGTGGACTTTGAAGAAAAAAGTGCCAAGA
1 AGTTGTGGACTTT-AA-AAAAAAGTGCCAAGA
** *
1718270 AGTTGTGGACTTTAAAAAAGGGTGCCACGA
1 AGTTGTGGACTTTAAAAAAAAGTGCCAAGA
* *
1718300 AATTCTGGACTTT--AAAAAA--G----G-
1 AGTTGTGGACTTTAAAAAAAAGTGCCAAGA
* * * *
1718321 -GTTATGGACTTTGAAAAAAGAGTATGCCATGG
1 AGTTGTGGACTTT-AAAAAAAAG--TGCCAAGA
** * *
1718353 AGTTGTGGACTTT-AAAAGTAGTGCCATGG
1 AGTTGTGGACTTTAAAAAAAAGTGCCAAGA
* * *
1718382 AGTTATGGAC-TTAAAAAAAATGTGTCATTG-
1 AGTTGTGGACTTTAAAAAAAA-GTGCCA-AGA
** * *
1718412 AGTTGTGGACTTT-AAAAATGGTGCCACGG
1 AGTTGTGGACTTTAAAAAAAAGTGCCAAGA
**
1718441 AGTTGTAAAC-TTAAAAAAAAGGTGCCACAGA
1 AGTTGTGGACTTTAAAAAAAA-GTGCCA-AGA
*
1718472 A-TTGTGGACTTT-AAAAAAGGTGCCATAG-
1 AGTTGTGGACTTTAAAAAAAAGTGCCA-AGA
*
1718500 AGTTGTGGACTTTAAAAAAACGGTGCCACA-A
1 AGTTGTGGACTTTAAAAAAA-AGTGCCA-AGA
1718531 AGTTGTGGACTTT
1 AGTTGTGGACTTT
1718544 TTTAAAAAAA
Statistics
Matches: 215, Mismatches: 33, Indels: 53
0.71 0.11 0.18
Matches are distributed among these distances:
20 10 0.05
22 1 0.00
23 5 0.02
26 1 0.00
27 1 0.00
28 10 0.05
29 59 0.27
30 66 0.31
31 38 0.18
32 13 0.06
33 11 0.05
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (30 bp):
AGTTGTGGACTTTAAAAAAAAGTGCCAAGA
Found at i:1718318 original size:59 final size:58
Alignment explanation
Indices: 1718240--1718543 Score: 198
Period size: 59 Copynumber: 5.2 Consensus size: 58
1718230 TACCATATAG
*
1718240 TTGTGGACTTTGAAGAAAAAAGTGCCAAGAAGTTGTGGACTTTAAAAAAGGGTGCCACGAAA
1 TTGTGGACTTT--A-AAAAAAGTGCCAAG-AGTTGTGGACTTTAAAAAAAGGTGCCACGAAA
* * * * * *
1718302 TTCTGGACTTT-AAAAAA--G----G-GTTATGGACTTTGAAAAAAGAGTATGCCATGGAG
1 TTGTGGACTTTAAAAAAAGTGCCAAGAGTTGTGGACTTT-AAAAAA-AG-GTGCCACGAAA
** * * * * * * *
1718355 TTGTGGACTTTAAAAGTAGTGCCATGGAGTTATGGACTTAAAAAAAATGTGTCATTG-AG
1 TTGTGGACTTTAAAAAAAGTGCCA-AGAGTTGTGGACTTTAAAAAAAGGTGCCA-CGAAA
** * ** *
1718414 TTGTGGACTTTAAAAATGGTGCCACGGAGTTGTAAACTTAAAAAAAAGGTGCCAC-AGAA
1 TTGTGGACTTTAAAAAAAGTGCCA-AGAGTTGTGGACTTTAAAAAAAGGTGCCACGA-AA
*
1718473 TTGTGGACTTTAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAACGGTGCCAC-AAA
1 TTGTGGACTTTAAAAAAAGTGCCA-AGAGTTGTGGACTTTAAAAAAA-GGTGCCACGAAA
1718532 GTTGTGGACTTT
1 -TTGTGGACTTT
1718544 TTTAAAAAAA
Statistics
Matches: 195, Mismatches: 30, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
50 11 0.06
51 6 0.03
52 2 0.01
53 17 0.09
54 4 0.02
56 2 0.01
58 6 0.03
59 96 0.49
60 23 0.12
61 7 0.04
62 21 0.11
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (58 bp):
TTGTGGACTTTAAAAAAAGTGCCAAGAGTTGTGGACTTTAAAAAAAGGTGCCACGAAA
Found at i:1718346 original size:20 final size:20
Alignment explanation
Indices: 1718305--1718343 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1718295 CACGAAATTC
*
1718305 TGGACTTTAAAAAAGGGTTA
1 TGGACTTTAAAAAAGAGTTA
1718325 TGGACTTTGAAAAAAGAGT
1 TGGACTTT-AAAAAAGAGT
1718344 ATGCCATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (20 bp):
TGGACTTTAAAAAAGAGTTA
Found at i:1718379 original size:29 final size:30
Alignment explanation
Indices: 1718325--1718733 Score: 233
Period size: 29 Copynumber: 13.4 Consensus size: 30
1718315 AAAAGGGTTA
*
1718325 TGGACTTTGAAAAAAGAGTATGCCATGGAGTTG
1 TGGACTTT-AAAAAA-AG-GTGCCATGGAGTTG
** *
1718358 TGGACTTTAAAAGTA-GTGCCATGGAGTTA
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
* * * *
1718387 TGGACTTAAAAAAAATGTGTCATTGAGTTG
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
* *
1718417 TGGACTTT-AAAAATGGTGCCACGGAGTTG
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
** * ** *
1718446 TAAACTTAAAAAAAAGGTGCCACAGAATTG
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
*
1718476 TGGACTTT-AAAAAAGGTGCCATAGAGTTG
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
***
1718505 TGGACTTTAAAAAAACGGTGCCACAAAGTTG
1 TGGACTTTAAAAAAA-GGTGCCATGGAGTTG
** *
1718536 TGGACTTTTTTAAAAAAAAAGGTGCCACAGAGTGG
1 TGGAC---TTT--AAAAAAAGGTGCCATGGAGTTG
* * * *
1718571 TGGAC-CT-AAAAGA-TTGCCATAGAGTTG
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
* * * * *
1718598 TGAACTTT-AAAAAGGGTACCACGGAGTTT
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
* * *
1718627 TAGACTTCTAAAAAAAAGGTGTCACGGAGTTG
1 TGGACTT-T-AAAAAAAGGTGCCATGGAGTTG
* *
1718659 TGGACTTTTTAAAAAAAAGGGTGTCATGGAGTTA
1 TGGAC--TTT-AAAAAAA-GGTGCCATGGAGTTG
* ** * * *
1718693 TTGACTTT--GCAAAGGTGCCACGAAGTTA
1 TGGACTTTAAAAAAAGGTGCCATGGAGTTG
1718721 TGGACTTTAAAAA
1 TGGACTTTAAAAA
1718734 GGGATGCCAC
Statistics
Matches: 294, Mismatches: 63, Indels: 41
0.74 0.16 0.10
Matches are distributed among these distances:
27 15 0.05
28 29 0.10
29 89 0.30
30 49 0.17
31 20 0.07
32 28 0.10
33 17 0.06
34 22 0.07
35 18 0.06
36 7 0.02
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (30 bp):
TGGACTTTAAAAAAAGGTGCCATGGAGTTG
Found at i:1718391 original size:82 final size:81
Alignment explanation
Indices: 1718243--1718400 Score: 185
Period size: 82 Copynumber: 1.9 Consensus size: 81
1718233 CATATAGTTG
* *
1718243 TGGACTTTGAAGAAAAAAGTGCCAAGAAGTTGTGGACTTTAAAAAAGGGTGCCACGAAATTCTGG
1 TGGACTTTGAAGAAAAAAGTGCCAAGAAGTTGTGGACTTT-AAAAAGAGTGCCACGAAATTATGG
*
1718308 ACTTTAAAAAAGGGTTA
65 ACTTAAAAAAAGGGTTA
* * * * * *
1718325 TGGACTTTGAA-AAAAGAGTATGCCATGGAGTTGTGGACTTT-AAAAGTAGTGCCATGGAGTTAT
1 TGGACTTTGAAGAAAAAAG--TGCCAAGAAGTTGTGGACTTTAAAAAG-AGTGCCACGAAATTAT
1718388 GGACTTAAAAAAA
63 GGACTTAAAAAAA
1718401 ATGTGTCATT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
81 11 0.17
82 34 0.53
83 19 0.30
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (81 bp):
TGGACTTTGAAGAAAAAAGTGCCAAGAAGTTGTGGACTTTAAAAAGAGTGCCACGAAATTATGGA
CTTAAAAAAAGGGTTA
Found at i:1718653 original size:32 final size:32
Alignment explanation
Indices: 1718606--1718699 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 32
1718596 TGTGAACTTT
**
1718606 AAAAAGGGTACCACGGAGTTTTAGACTTCTAAA
1 AAAAAGGGTGTCACGGAGTTTT-GACTTCTAAA
* *
1718639 AAAAA-GGTGTCACGGAGTTGTGGACTTTTTAAA
1 AAAAAGGGTGTCACGGAGTT-TTGAC-TTCTAAA
*
1718672 AAAAAGGGTGTCATGGAGTTATTGACTT
1 AAAAAGGGTGTCACGGAGTT-TTGACTT
1718700 TGCAAAGGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
32 15 0.29
33 19 0.37
34 17 0.33
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.29
Consensus pattern (32 bp):
AAAAAGGGTGTCACGGAGTTTTGACTTCTAAA
Found at i:1718682 original size:34 final size:34
Alignment explanation
Indices: 1718606--1718700 Score: 104
Period size: 34 Copynumber: 2.9 Consensus size: 34
1718596 TGTGAACTTT
** *
1718606 AAAAAGGGTACCACGGAGTTTTAGAC-TTCTAAA
1 AAAAAGGGTGTCACGGAGTTATAGACTTTCTAAA
* * *
1718639 AAAAA-GGTGTCACGGAGTTGTGGACTTTTTAAA
1 AAAAAGGGTGTCACGGAGTTATAGACTTTCTAAA
* *
1718672 AAAAAGGGTGTCATGGAGTTATTGACTTT
1 AAAAAGGGTGTCACGGAGTTATAGACTTT
1718701 GCAAAGGTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
32 16 0.31
33 16 0.31
34 20 0.38
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (34 bp):
AAAAAGGGTGTCACGGAGTTATAGACTTTCTAAA
Found at i:1718734 original size:28 final size:30
Alignment explanation
Indices: 1718708--1718772 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
1718698 TTTGCAAAGG
1718708 TGCCACGAAGTTATGGACTTTAAAAAGGGA
1 TGCCACGAAGTTATGGACTTTAAAAAGGGA
* ** * * *
1718738 TGCCACTAAGTCGTGGACTTTGAGAAGAGA
1 TGCCACGAAGTTATGGACTTTAAAAAGGGA
1718768 TGCCA
1 TGCCA
1718773 TTGAGTCGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (30 bp):
TGCCACGAAGTTATGGACTTTAAAAAGGGA
Found at i:1718848 original size:29 final size:29
Alignment explanation
Indices: 1718721--1718858 Score: 170
Period size: 29 Copynumber: 4.7 Consensus size: 29
1718711 CACGAAGTTA
*
1718721 TGGACTTT-AAAAAGGGATGCCACTAAGTCG
1 TGGACTTTGAAAAA--GATGCCACTGAGTCG
* *
1718751 TGGACTTTGAGAAGAGATGCCATTGAGTCG
1 TGGACTTTGA-AAAAGATGCCACTGAGTCG
* * *
1718781 TGGACTTTGGAAGAGATGTCACTGAGTCG
1 TGGACTTTGAAAAAGATGCCACTGAGTCG
1718810 TGGACTTTGAAAAAGATGCCACTGAGTCG
1 TGGACTTTGAAAAAGATGCCACTGAGTCG
*
1718839 TGGACTTTGAGAAATGATGC
1 TGGACTTTGA-AAAAGATGC
1718859 TTTACTAGAG
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
29 53 0.56
30 38 0.40
31 1 0.01
32 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.26
Consensus pattern (29 bp):
TGGACTTTGAAAAAGATGCCACTGAGTCG
Found at i:1722910 original size:79 final size:78
Alignment explanation
Indices: 1722813--1723436 Score: 497
Period size: 79 Copynumber: 7.9 Consensus size: 78
1722803 TATTCCCTCA
* * * * * *
1722813 GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATTGGTGTTTTGAAAA
1 GAGTATCCCCTGA-AAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGTTTTGAAAA
*
1722878 TAAAATTGGGGTTG
65 TAAAATCGGGGTTG
* * * * * * *
1722892 GAGTATCCTTCTGAAAATAATGGGGATGGAGTATCCTTGATTGTGGAAAATCGGTATTTTGGAAA
1 GAGTATCC-CCTGAAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGTTTTGAAAA
* ** *
1722957 TAAAACCTAGGTTA
65 TAAAATCGGGGTTG
* * * * *
1722971 GAGTATCCCCTTGAAAATAACGGGGTTGGAGTAACCCCGATTATGGAAAATCAATGTTTTGGAAA
1 GAGTATCCCC-TGAAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGTTTTGAAAA
* **
1723036 TAAAACCAAGGTTG
65 TAAAATCGGGGTTG
* * * * * * * *
1723050 GAGTATCCCTTCAGAAATGAGGGGGTTGGAGTATCCTCGATTATGAAAAATCAATGTTTAGAAAA
1 GAGTATCCCCTGA-AAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGTTTTGAAAA
*
1723115 TAAAAACTAGGGGTTG
65 T-AAAA-TCGGGGTTG
* * * * * *
1723131 GAGTATCCTCTCAGAAATAACGGGGTTGGAGTATCCAT-GATGGTAGAAAATCGATATTTTGGAA
1 GAGTATCCCCTGA-AAATAACGGGGTTGGAGTATCC-TCGATTGTGGAAAATCGATGTTTTGAAA
*
1723195 ATAAAA-CTAGGGTTG
64 ATAAAATC-GGGGTTG
* * ** * * * *
1723210 GAGTATCCACTCAGAAATAACAAGGTT-AAGTATCCTCAATTGTGGAAAATTGAT-TTTTTAGAA
1 GAGTATCCCCTGA-AAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGTTTTGA-AA
1723273 ATAAAATCGGGGTTG
64 ATAAAATCGGGGTTG
* * * * * *
1723288 AAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCGATTATGGAAAAT-TATTGTTTTGAAA
1 GAGTATCCCCT-GAAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGA-TGTTTTGAAA
*
1723352 ATAAAATCGAGGTTG
64 ATAAAATCGGGGTTG
* * ** *
1723367 AAGTGTCCCCTCGAAAATAACAAGGTTGGAGTATCCTCG-TTGGTGGAAAATCGATATTTT-AGA
1 GAGTATCCCCT-GAAAATAACGGGGTTGGAGTATCCTCGATT-GTGGAAAATCGATGTTTTGA-A
1723430 AATAAAA
63 AATAAAA
1723437 ACATGAATGA
Statistics
Matches: 440, Mismatches: 88, Indels: 34
0.78 0.16 0.06
Matches are distributed among these distances:
77 5 0.01
78 60 0.14
79 300 0.68
80 17 0.04
81 57 0.13
82 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (78 bp):
GAGTATCCCCTGAAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGTTTTGAAAAT
AAAATCGGGGTTG
Found at i:1723100 original size:158 final size:159
Alignment explanation
Indices: 1722812--1723438 Score: 601
Period size: 158 Copynumber: 4.0 Consensus size: 159
1722802 ATATTCCCTC
* * ***
1722812 AGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATTGGTGTTTTGAAA
1 AGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATGGAAAATCAATGTTTTGAAA
**** * *** * *
1722877 ATAAAATTGGGGTTGGAGTAT-CCTTCTGAAAATAATGGGGATGGAGTATCCTTGATTGTGGAAA
66 ATAAAACCAAGGTTGGAGTATCCCTTCAGAAAATAACAAGGTTGGAGTATCCTCGATTGTGGAAA
* * *
1722941 ATCGGTATTTTGGAAATAAAACCTAGGTT
131 ATCGATATTTTAGAAATAAAAACTAGGTT
* * * *
1722970 AGAGTATCCCCT-TGAAAATAACGGGGTTGGAGTAACCCCGATTATGGAAAATCAATGTTTTGGA
1 AGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATGATGGAAAATCAATGTTTTGAA
* *** * *
1723034 AATAAAACCAAGGTTGGAGTATCCCTTCAG-AAATGAGGGGGTTGGAGTATCCTCGATTATGAAA
65 AATAAAACCAAGGTTGGAGTATCCCTTCAGAAAATAACAAGGTTGGAGTATCCTCGATTGTGGAA
1723098 AATC-A-ATGTTTAGAAAATAAAAACTAGGGGTT
130 AATCGATAT-TTTAG-AAATAAAAACTA--GGTT
* * ** * * * * *
1723130 GGAGTATCCTCTCAGAAATAACGGGGTTGGAGTATCCATGATGGTAGAAAATCGATATTTTGGAA
1 AGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATGGAAAATCAATGTTTTGAAA
* * * *
1723195 ATAAAACTAGGGTTGGAGTATCCAC-TCAG-AAATAACAAGGTT-AAGTATCCTCAATTGTGGAA
66 ATAAAACCAAGGTTGGAGTATCC-CTTCAGAAAATAACAAGGTTGGAGTATCCTCGATTGTGGAA
* * * **
1723257 AATTGATTTTTTAGAAATAAAATCGGGGTT
130 AATCGATATTTTAGAAATAAAAACTAGGTT
* * * * *
1723287 -GAAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCGATTATGGAAAATTATTGTTTTGAA
1 AG-AGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATGGAAAATCAATGTTTTGAA
* * * * *
1723351 AATAAAATCGAGGTTGAAGTGTCCCCTC-GAAAATAACAAGGTTGGAGTATCCTCG-TTGGTGGA
65 AATAAAACCAAGGTTGGAGTATCCCTTCAGAAAATAACAAGGTTGGAGTATCCTCGATT-GTGGA
1723414 AAATCGATATTTTAGAAATAAAAAC
129 AAATCGATATTTTAGAAATAAAAAC
1723439 ATGAATGAAA
Statistics
Matches: 381, Mismatches: 73, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
156 5 0.01
157 93 0.24
158 150 0.39
159 34 0.09
160 96 0.25
161 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (159 bp):
AGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATGGAAAATCAATGTTTTGAAA
ATAAAACCAAGGTTGGAGTATCCCTTCAGAAAATAACAAGGTTGGAGTATCCTCGATTGTGGAAA
ATCGATATTTTAGAAATAAAAACTAGGTT
Found at i:1723396 original size:317 final size:318
Alignment explanation
Indices: 1722813--1723438 Score: 746
Period size: 317 Copynumber: 2.0 Consensus size: 318
1722803 TATTCCCTCA
* * * *
1722813 GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATTGGTGTTTTGAAAA
1 GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCACGATGGTGAAAAATCGATATTTTGAAAA
* * * * *** * **
1722878 TAAAATTGGGGTTGGAGTATCCTTCTGAAAATAATGGGGATGGAGTATCCTTGATTGTGGAAAAT
66 TAAAACTAGGGTTGGAGTATCCCTCAGAAAATAACAAGGATGAAGTATCCTCAATTGTGGAAAAT
* * * **
1722943 CGGTATTTTGGAAATAAAACCTAGGTTAGAGTATCCCCTTGAAAATAACGGGGTTGGAGTAACCC
131 CGATATTTTAGAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTAACCC
* * * * ***
1723008 CGATTATGGAAAATCAATGTTTTGGAAATAAAACCAAGGTTGGAGTATCCCTTCAGAAATGAGGG
196 CGATTATGGAAAATCAATGTTTTGAAAATAAAACCAAGGTTGAAGTATCCCCTCAGAAATAACAA
1723073 GGTTGGAGTATCCTCGATT-ATGAAAAATC-A-ATGTTTAGAAAATAAAAACTAGGGGTTG
261 GGTTGGAGTATCCTCG-TTGATGAAAAATCGATAT-TTTAG-AAATAAAAACTAGGGGTTG
* * *
1723131 GAGTATCCTCTCAGAAATAACGGGGTTGGAGTATCCATGATGGT-AGAAAATCGATATTTTGGAA
1 GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCACGATGGTGA-AAAATCGATATTTTGAAA
*
1723195 ATAAAACTAGGGTTGGAGTATCCACTCAG-AAATAACAAGG-TTAAGTATCCTCAATTGTGGAAA
65 ATAAAACTAGGGTTGGAGTATCC-CTCAGAAAATAACAAGGATGAAGTATCCTCAATTGTGGAAA
* * * * * *
1723258 ATTGATTTTTTAGAAATAAAATCGGGGTT-GAAGTATCCCCTCAAAAATAATGGGGTTGGAGTAT
129 ATCGATATTTTAGAAATAAAACCGAGGTTAG-AGTATCCCCTCAAAAATAACGGGGTTGGAGTAA
* * * * *
1723322 CCCCGATTATGGAAAATTATTGTTTTGAAAATAAAATCGAGGTTGAAGTGTCCCCTC-GAAAATA
193 CCCCGATTATGGAAAATCAATGTTTTGAAAATAAAACCAAGGTTGAAGTATCCCCTCAG-AAATA
* *
1723386 ACAAGGTTGGAGTATCCTCGTTGGTGGAAAATCGATATTTTAGAAATAAAAAC
257 ACAAGGTTGGAGTATCCTCGTTGATGAAAAATCGATATTTTAGAAATAAAAAC
1723439 ATGAATGAAA
Statistics
Matches: 258, Mismatches: 43, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
316 4 0.02
317 159 0.62
318 90 0.35
319 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (318 bp):
GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCACGATGGTGAAAAATCGATATTTTGAAAA
TAAAACTAGGGTTGGAGTATCCCTCAGAAAATAACAAGGATGAAGTATCCTCAATTGTGGAAAAT
CGATATTTTAGAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTAACCC
CGATTATGGAAAATCAATGTTTTGAAAATAAAACCAAGGTTGAAGTATCCCCTCAGAAATAACAA
GGTTGGAGTATCCTCGTTGATGAAAAATCGATATTTTAGAAATAAAAACTAGGGGTTG
Found at i:1725975 original size:13 final size:13
Alignment explanation
Indices: 1725957--1725982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1725947 CAATTTTTTG
1725957 TGTATCGATACAT
1 TGTATCGATACAT
1725970 TGTATCGATACAT
1 TGTATCGATACAT
1725983 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1726675 original size:25 final size:26
Alignment explanation
Indices: 1726628--1726680 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1726618 AAATAAATTT
1726628 AACGAATTTGTACATTCTCCCCCTTA
1 AACGAATTTGTACATTCTCCCCCTTA
1726654 AACGAATTTGTACATTCTCCCCCTTA
1 AACGAATTTGTACATTCTCCCCCTTA
1726680 A
1 A
1726681 TAAGGTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (26 bp):
AACGAATTTGTACATTCTCCCCCTTA
Found at i:1728415 original size:21 final size:21
Alignment explanation
Indices: 1728391--1728437 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1728381 TTTGATGCTG
1728391 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1728411 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1728432 ATTTTG
1 ATTTTG
1728438 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1728576 original size:13 final size:13
Alignment explanation
Indices: 1728558--1728596 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1728548 ATAATCACCC
*
1728558 TGTATCGATACAG
1 TGTATCGATACAA
1728571 TGTATCGATACAA
1 TGTATCGATACAA
1728584 TGTATCGATACAA
1 TGTATCGATACAA
1728597 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1728607 original size:20 final size:20
Alignment explanation
Indices: 1728582--1728660 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1728572 GTATCGATAC
1728582 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1728602 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1728627 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1728647 CATGTATCGATACA
1 AATGTATCGATACA
1728661 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1730694 original size:15 final size:15
Alignment explanation
Indices: 1730674--1730704 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1730664 ATTTTGTTTG
*
1730674 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1730689 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1730704 G
1 G
1730705 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1732537 original size:21 final size:21
Alignment explanation
Indices: 1732508--1732552 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1732498 AAGTTTTCAT
*
1732508 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1732528 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1732550 TTT
1 TTT
1732553 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1734788 original size:13 final size:13
Alignment explanation
Indices: 1734770--1734795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1734760 CAATTTTTTG
1734770 TGTATCGATACAT
1 TGTATCGATACAT
1734783 TGTATCGATACAT
1 TGTATCGATACAT
1734796 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1735281 original size:50 final size:49
Alignment explanation
Indices: 1735217--1735350 Score: 196
Period size: 50 Copynumber: 2.7 Consensus size: 49
1735207 AAAAATGACT
* * *
1735217 GAATGTATCGATACATTGAGAAATGTATTGATACATTTAGGTAAAACCTA
1 GAATGTATCGATACAATGA-AAATGTATTGATACATCTAGGTAAAACCCA
* *
1735267 GAATGTATCAATACAATGAAAAATGTATCGATACATCTAGGTAAAACCCA
1 GAATGTATCGATACAATG-AAAATGTATTGATACATCTAGGTAAAACCCA
1735317 GAATGTATCGATACAATGAAGAATGTATTGATAC
1 GAATGTATCGATACAATGAA-AATGTATTGATAC
1735351 CAATTGTGAA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 2 0.03
50 72 0.96
51 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (49 bp):
GAATGTATCGATACAATGAAAATGTATTGATACATCTAGGTAAAACCCA
Found at i:1736075 original size:61 final size:61
Alignment explanation
Indices: 1735957--1736585 Score: 642
Period size: 61 Copynumber: 10.3 Consensus size: 61
1735947 AAATGTCCTG
* * * ** *
1735957 CTCTTTGGGGACT-AGAATGTGCCA-CAACTTGTGTGGGTTTTGCAAGGAGAAA-ACGTCCTA
1 CTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGACGTCTTA
* * * * *
1736017 CCCTTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGACGTCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
* * * * * *
1736078 CTCTTTGAGGATTGAAAGGTGCCACTAACTTGTGTGGGTTTTAAAAGGAAAAGGCATCATA
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
* * * * * *
1736139 CTCTTTGAGGACTGAAAGGTGCTACCAACTTGTGTAGGCTTTAAAAGAAAAAGGCATCATA
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
* * * * *
1736200 CTCTTTGAGGACT-AGAAGGTGCCATCAACTTGTATAGGCTTTAAAAGGAAAATG-TGTCATA
1 CTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GACGTCTTA
* * * * **
1736261 CTGTTTGAGGACT-AGAAGGTGCCACCAATTTGTATGGGCTTTAAAAGGAAAAAATTTCTTA
1 CTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
* * ** * *
1736322 CTCTTTGAGGACTAAAAAGTGCCATTAACTCGTGTGGGCTTTAAAAGGAAAAGACGTC-CA
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
* * * *
1736382 CCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGGAAAGACATCTTG
1 -CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
* * * * * * *
1736444 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAATAGAAAAAAAGTGTCTTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGA-CGTCTTA
* * * * *
1736506 CTATTTGAGGACTAAAAGGTACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGATGTCTTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
1736567 CTCTTTGAGGACTGAAAGG
1 CTCTTTGAGGACTGAAAGG
1736586 ATAAAAGGTT
Statistics
Matches: 488, Mismatches: 71, Indels: 19
0.84 0.12 0.03
Matches are distributed among these distances:
60 24 0.05
61 409 0.84
62 55 0.11
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (61 bp):
CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTTA
Found at i:1750014 original size:21 final size:21
Alignment explanation
Indices: 1749988--1750063 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1749978 CTGCCAAGAA
*
1749988 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1750009 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1750029 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1750050 ATGTATCGATACAT
1 ATGTATCGATACAT
1750064 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1750034 original size:20 final size:20
Alignment explanation
Indices: 1750009--1750081 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1749999 CATCTTTTTT
1750009 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1750029 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1750050 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1750070 ATGTATCGATAC
1 ATGTATCGATAC
1750082 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1750045 original size:41 final size:41
Alignment explanation
Indices: 1749988--1750081 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1749978 CTGCCAAGAA
*
1749988 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1750029 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1750070 ATGTATCGATAC
1 ATGTATCGATAC
1750082 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1750691 original size:48 final size:48
Alignment explanation
Indices: 1750636--1750731 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1750626 AAATTTTACG
*
1750636 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCT
1750684 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCT
1750732 TTATCTCCCC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.26, C:0.29, G:0.07, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACACATTCTCTCCT
Found at i:1752570 original size:13 final size:13
Alignment explanation
Indices: 1752552--1752590 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1752542 ATAATCACCC
*
1752552 TGTATCGATACAG
1 TGTATCGATACAA
1752565 TGTATCGATACAA
1 TGTATCGATACAA
1752578 TGTATCGATACAA
1 TGTATCGATACAA
1752591 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1752601 original size:20 final size:20
Alignment explanation
Indices: 1752576--1752654 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1752566 GTATCGATAC
1752576 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1752596 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1752621 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1752641 CATGTATCGATACA
1 AATGTATCGATACA
1752655 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1754691 original size:15 final size:15
Alignment explanation
Indices: 1754671--1754701 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1754661 ATTTCGTTTG
*
1754671 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1754686 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1754701 G
1 G
1754702 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1758855 original size:21 final size:21
Alignment explanation
Indices: 1758829--1758904 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1758819 CTGCCAAGAA
*
1758829 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1758850 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1758870 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1758891 ATGTATCGATACAT
1 ATGTATCGATACAT
1758905 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1758875 original size:20 final size:20
Alignment explanation
Indices: 1758850--1758922 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1758840 CATCTTTTTT
1758850 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1758870 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1758891 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1758911 ATGTATCGATAC
1 ATGTATCGATAC
1758923 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1758886 original size:41 final size:41
Alignment explanation
Indices: 1758829--1758922 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1758819 CTGCCAAGAA
*
1758829 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1758870 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1758911 ATGTATCGATAC
1 ATGTATCGATAC
1758923 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1759889 original size:79 final size:79
Alignment explanation
Indices: 1759710--1759905 Score: 225
Period size: 79 Copynumber: 2.5 Consensus size: 79
1759700 ATATTTCCTC
* * * ** *
1759710 GGAGTATTCTCTCAAAAATAACGGGGTTAAAGTATCCCTGATGGTGAGAAATTGATGTTTTGGAA
1 GGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCTGATGGTGAAAAATTGATGTTTTGGAA
** *
1759775 ATAAAATTGGGGTT
66 ATAAAACCGAGGTT
* * * * *
1759789 AGAGTATCTCTTCGAAAATAATGGGGTTGGAGTAT-CCTCGATTGTGAAAAATT-AGTGTTTTGG
1 GGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCT-GATGGTGAAAAATTGA-TGTTTTGG
1759852 AAATAAAACCGAGGTT
64 AAATAAAACCGAGGTT
*
1759868 GGAGTATCCCCTCAAAAATAATGGGATTGGAGTATCCC
1 GGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCC
1759906 CTCGAAAATA
Statistics
Matches: 95, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
78 4 0.04
79 89 0.94
80 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (79 bp):
GGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCTGATGGTGAAAAATTGATGTTTTGGAA
ATAAAACCGAGGTT
Done.