Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 39 of 295
Found at i:11394995 original size:48 final size:45
Alignment explanation
Indices: 11394877--11395011 Score: 146
Period size: 47 Copynumber: 2.8 Consensus size: 45
11394867 CTTTTTCCAG
* * *
11394877 GTGATGTTTCTTTTTCCCTATTTCCCTTTT-TTTCTTTCTTTTTCCGG
1 GTGATGTTTC-TTCTCCCTATTT-CCTTTTCTTTCTTT-TTTGTCCGA
*
11394924 GTGATGTTTCTTCTTCCCTATTTCCATTTTTCTTTCTTTTTTGTCCTA
1 GTGATGTTTCTTC-TCCCTATTTCC--TTTTCTTTCTTTTTTGTCCGA
*
11394972 GTGATGTTTCTTCTCCACAATTTCCTTTTCTCTTCTTTTT
1 GTGATGTTTCTTCTCC-CTATTTCCTTTTCT-TTCTTTTT
11395012 CCCTGTGACC
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
46 10 0.13
47 30 0.39
48 30 0.39
49 7 0.09
ACGTcount: A:0.07, C:0.24, G:0.09, T:0.60
Consensus pattern (45 bp):
GTGATGTTTCTTCTCCCTATTTCCTTTTCTTTCTTTTTTGTCCGA
Found at i:11401168 original size:24 final size:24
Alignment explanation
Indices: 11401140--11401190 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
11401130 AGCTTGTAAA
11401140 AACCATCACTGGAGCATCAAATTG
1 AACCATCACTGGAGCATCAAATTG
* *
11401164 AACCATCACTGTAGTATCAAATTG
1 AACCATCACTGGAGCATCAAATTG
11401188 AAC
1 AAC
11401191 ATATCCCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (24 bp):
AACCATCACTGGAGCATCAAATTG
Found at i:11405572 original size:58 final size:59
Alignment explanation
Indices: 11405503--11405620 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 59
11405493 TTAGGCCCTA
*
11405503 AACTTGGCAATTGTTTTCACATTGGGGCCTGAACTCTT-TTTGCCCAAGTTAGACCTTG
1 AACTTGGCAATTATTTTCACATTGGGGCCTGAACTCTTATTTGCCCAAGTTAGACCTTG
* * * *
11405561 AACTTGGCAATTATTTTCACATTGGGGCTTGAACTTTTATTTGTCCAAGTTAGTCCTTG
1 AACTTGGCAATTATTTTCACATTGGGGCCTGAACTCTTATTTGCCCAAGTTAGACCTTG
11405620 A
1 A
11405621 TGTTTCCTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 35 0.65
59 19 0.35
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (59 bp):
AACTTGGCAATTATTTTCACATTGGGGCCTGAACTCTTATTTGCCCAAGTTAGACCTTG
Found at i:11411603 original size:90 final size:90
Alignment explanation
Indices: 11411445--11411690 Score: 384
Period size: 90 Copynumber: 2.7 Consensus size: 90
11411435 GATCCAAAAA
* * *
11411445 CAAATGAACAAGAAGTTGTACATACAATGGATGTGTGCAATGCTTCAACGGTTGAAGGTTGTCAT
1 CAAAGGAACAAGAAGTTGTACATTCAATGGATGTGTGCAATGCTTCAACGGTTGAAGATTGTCAT
*
11411510 AGAGATGCCATAGAAAATTCTCAAG
66 AGAGAAGCCATAGAAAATTCTCAAG
*
11411535 CAAAGGAACAAGAAGTTGTACATTCAATGGATGTGTGCAATGCTTCAATGGTTGAAGATTGTCAT
1 CAAAGGAACAAGAAGTTGTACATTCAATGGATGTGTGCAATGCTTCAACGGTTGAAGATTGTCAT
11411600 AGAGAAGCCATAGAAAATTCTCAAG
66 AGAGAAGCCATAGAAAATTCTCAAG
**** * * *
11411625 CAAAGGAACAAGAAGTTGTACATTCAATGGATGCACACAATGCTTCACCGGGTGATGATTGTCAT
1 CAAAGGAACAAGAAGTTGTACATTCAATGGATGTGTGCAATGCTTCAACGGTTGAAGATTGTCAT
11411690 A
66 A
11411691 AAGATACTCT
Statistics
Matches: 143, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 143 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (90 bp):
CAAAGGAACAAGAAGTTGTACATTCAATGGATGTGTGCAATGCTTCAACGGTTGAAGATTGTCAT
AGAGAAGCCATAGAAAATTCTCAAG
Found at i:11415754 original size:20 final size:20
Alignment explanation
Indices: 11415729--11415767 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
11415719 AAATTTCATC
11415729 AATTTTTACTATTAAAAATT
1 AATTTTTACTATTAAAAATT
11415749 AATTTTTACTATTAAAAAT
1 AATTTTTACTATTAAAAAT
11415768 CAATCTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTTACTATTAAAAATT
Found at i:11416215 original size:3 final size:3
Alignment explanation
Indices: 11416209--11416243 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
11416199 TTAAACACTA
11416209 ATC ATC A-C ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
11416244 CTCAATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:11420047 original size:12 final size:12
Alignment explanation
Indices: 11420030--11420055 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11420020 AAAAATTGAA
11420030 TAGTGGAGTGAC
1 TAGTGGAGTGAC
11420042 TAGTGGAGTGAC
1 TAGTGGAGTGAC
11420054 TA
1 TA
11420056 ACTTTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.38, T:0.27
Consensus pattern (12 bp):
TAGTGGAGTGAC
Found at i:11423990 original size:17 final size:18
Alignment explanation
Indices: 11423964--11423997 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11423954 TACATTATAT
11423964 AATTTGATTTTT-TTTAC
1 AATTTGATTTTTATTTAC
*
11423981 AATTTTATTTTTATTTA
1 AATTTGATTTTTATTTA
11423998 TAACATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
AATTTGATTTTTATTTAC
Found at i:11427269 original size:21 final size:21
Alignment explanation
Indices: 11427244--11427287 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
11427234 TTTTGTTACA
11427244 ATGGCTTCTACAGATTCATCC
1 ATGGCTTCTACAGATTCATCC
11427265 ATGGCTTCTACAGATTCATCC
1 ATGGCTTCTACAGATTCATCC
11427286 AT
1 AT
11427288 TCTTTGGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (21 bp):
ATGGCTTCTACAGATTCATCC
Found at i:11435716 original size:32 final size:31
Alignment explanation
Indices: 11435657--11435733 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
11435647 AAAATTTTAA
*
11435657 TAAATGAAAAATATATAAATTTATTAAATAT
1 TAAATAAAAAATATATAAATTTATTAAATAT
*
11435688 TAAATAAAAACATATA-AATATTTTTTAAA-A-
1 TAAATAAAAA-ATATATAA-ATTTATTAAATAT
*
11435718 AAAATTAAAAAATATA
1 TAAA-TAAAAAATATA
11435734 AGCAAACTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 8 0.20
31 18 0.45
32 14 0.35
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (31 bp):
TAAATAAAAAATATATAAATTTATTAAATAT
Found at i:11443582 original size:15 final size:15
Alignment explanation
Indices: 11443540--11443582 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
11443530 ATAAATATTT
*
11443540 TATAATTTTTTGAAA
1 TATAATTTTTTTAAA
**
11443555 T-TAATTTACTTAAA
1 TATAATTTTTTTAAA
11443569 TATAATTTTTTTAA
1 TATAATTTTTTTAA
11443583 TAGCTTGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TATAATTTTTTTAAA
Found at i:11450170 original size:21 final size:21
Alignment explanation
Indices: 11450146--11450202 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
11450136 TGTGTTTTAC
11450146 TTTCTGTTCAACTCTT-ATGAG
1 TTTCTGTTCAACT-TTAATGAG
*
11450167 TTTCTGTTCAGCTTTAATGAG
1 TTTCTGTTCAACTTTAATGAG
* *
11450188 CTTCTGTTCAGCTTT
1 TTTCTGTTCAACTTT
11450203 CGAGGTTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (21 bp):
TTTCTGTTCAACTTTAATGAG
Found at i:11450730 original size:23 final size:27
Alignment explanation
Indices: 11450703--11450755 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 27
11450693 TACATATTGG
11450703 TATGAGAATGAG-G-TATAT-TATG-A
1 TATGAGAATGAGTGTTATATGTATGTA
*
11450726 TATGAGCATGAGTGTTATATGTATGTA
1 TATGAGAATGAGTGTTATATGTATGTA
11450753 TAT
1 TAT
11450756 AATTGAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 11 0.44
24 1 0.04
25 5 0.20
26 4 0.16
27 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.40
Consensus pattern (27 bp):
TATGAGAATGAGTGTTATATGTATGTA
Found at i:11454535 original size:19 final size:18
Alignment explanation
Indices: 11454513--11454561 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
11454503 TTAAGTTGAT
11454513 TTAATAAACTTAAGCATAA
1 TTAATAAACTTAAGC-TAA
* **
11454532 TTAATTAACAAAAGCTAA
1 TTAATAAACTTAAGCTAA
*
11454550 TTATTAAACTTA
1 TTAATAAACTTA
11454562 TTTTGCAGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (18 bp):
TTAATAAACTTAAGCTAA
Found at i:11456286 original size:25 final size:25
Alignment explanation
Indices: 11456249--11456310 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 25
11456239 GGATACACAC
* * * *
11456249 AGCTCTTATGAGCATCCTAATATTT
1 AGCTCTCACGAGCATCCCAATACTT
* *
11456274 AGCTCTCACGAGCTTCCCGATACTT
1 AGCTCTCACGAGCATCCCAATACTT
*
11456299 GGCTCTCACGAG
1 AGCTCTCACGAG
11456311 TTTCCTGATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.31
Consensus pattern (25 bp):
AGCTCTCACGAGCATCCCAATACTT
Found at i:11456326 original size:25 final size:25
Alignment explanation
Indices: 11456275--11456330 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
11456265 CTAATATTTA
*
11456275 GCTCTCACGAGCTTCCCGATACTTG
1 GCTCTCACGAGCTTCCCGATACATG
* *
11456300 GCTCTCACGAGTTTCCTGATTA-ATG
1 GCTCTCACGAGCTTCCCGA-TACATG
11456325 GCTCTC
1 GCTCTC
11456331 TTCAGCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.32
Consensus pattern (25 bp):
GCTCTCACGAGCTTCCCGATACATG
Found at i:11456378 original size:25 final size:25
Alignment explanation
Indices: 11456350--11456416 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
11456340 TCGATATTTG
11456350 GCTCACAAGAGCTTCCCGTTATACA
1 GCTCACAAGAGCTTCCCGTTATACA
* **
11456375 GCTCACATGAGCTTCCCGTTATATG
1 GCTCACAAGAGCTTCCCGTTATACA
**
11456400 GCTCGGAAGAGCTTCCC
1 GCTCACAAGAGCTTCCC
11456417 ATTTACATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.25
Consensus pattern (25 bp):
GCTCACAAGAGCTTCCCGTTATACA
Found at i:11456466 original size:17 final size:17
Alignment explanation
Indices: 11456444--11456481 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
11456434 AACATACATG
11456444 TACATGAATTGATGGAT
1 TACATGAATTGATGGAT
11456461 TACATGAATTGATGGAT
1 TACATGAATTGATGGAT
11456478 TACA
1 TACA
11456482 ATTTTGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (17 bp):
TACATGAATTGATGGAT
Found at i:11460228 original size:23 final size:22
Alignment explanation
Indices: 11460177--11460228 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
11460167 CCTCGTCTTT
*
11460177 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
11460199 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
11460222 TTCTTTT
1 TTCTTTT
11460229 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:11464900 original size:17 final size:18
Alignment explanation
Indices: 11464868--11464902 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11464858 CCATGTGGCC
11464868 TGCCCGTGTGGGCCCACA
1 TGCCCGTGTGGGCCCACA
*
11464886 TGCCCTTGT-GGCCCACA
1 TGCCCGTGTGGGCCCACA
11464903 CGGCCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.40, G:0.29, T:0.20
Consensus pattern (18 bp):
TGCCCGTGTGGGCCCACA
Found at i:11474546 original size:36 final size:33
Alignment explanation
Indices: 11474500--11474597 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 33
11474490 ATTTCAAACC
*
11474500 TTCTTCTTTCTTT-TTCTCGATCAGCCTCAAATC
1 TTCTTC-TTCTTTCTTCTCGATCAGCCTCAAATA
* *
11474533 TTCTTCTTCTTTCTTCTCGGTTAGCCTCAAATA
1 TTCTTCTTCTTTCTTCTCGATCAGCCTCAAATA
* *
11474566 TTCTTC-TCTTTGCTTCTTGATCAACCTCAAAT
1 TTCTTCTTCTTT-CTTCTCGATCAGCCTCAAAT
11474598 TTGTCCATCT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 11 0.20
33 45 0.80
ACGTcount: A:0.16, C:0.29, G:0.07, T:0.48
Consensus pattern (33 bp):
TTCTTCTTCTTTCTTCTCGATCAGCCTCAAATA
Found at i:11479188 original size:46 final size:46
Alignment explanation
Indices: 11479130--11479450 Score: 448
Period size: 46 Copynumber: 7.0 Consensus size: 46
11479120 AGTGTGCTCT
11479130 CTGATA-GAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
11479176 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
11479222 TTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
11479268 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
11479314 GTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** ** *
11479360 GTGACGGGGAAATGAATAAGACCATGGTTGAATGATACCATGGCAAC
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
11479407 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
11479451 TCATGTCGAA
Statistics
Matches: 252, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.00
46 211 0.84
47 40 0.16
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:11484068 original size:5 final size:5
Alignment explanation
Indices: 11484058--11484082 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11484048 AACATAAATT
11484058 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
11484083 TATCTTCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:11486658 original size:16 final size:15
Alignment explanation
Indices: 11486628--11486659 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11486618 GTTCTCCATG
11486628 TAAAAATACAGTTTT
1 TAAAAATACAGTTTT
*
11486643 TAAAAATACAATTTT
1 TAAAAATACAGTTTT
11486658 TA
1 TA
11486660 CATCTAACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAAATACAGTTTT
Found at i:11494186 original size:53 final size:53
Alignment explanation
Indices: 11494114--11494219 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
11494104 AAACTTCTAG
*
11494114 GTGAAAATTGTGGATTTTTGGTAAAAGGACCAAAATGTAATGACAACAAAGTT
1 GTGAAAATGGTGGATTTTTGGTAAAAGGACCAAAATGTAATGACAACAAAGTT
*
11494167 GTGAAAATGGTGGATTTTTGGTAAAAGGACCAAAATGTAATTACAACAAAGTT
1 GTGAAAATGGTGGATTTTTGGTAAAAGGACCAAAATGTAATGACAACAAAGTT
11494220 TTCTTCTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (53 bp):
GTGAAAATGGTGGATTTTTGGTAAAAGGACCAAAATGTAATGACAACAAAGTT
Found at i:11494326 original size:11 final size:11
Alignment explanation
Indices: 11494310--11494351 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
11494300 TAGCTATTTA
11494310 TAATAAAATAT
1 TAATAAAATAT
11494321 TAATAAAATATT
1 TAATAAAATA-T
*
11494333 TCATTAAAATAT
1 T-AATAAAATAT
11494345 TAATAAA
1 TAATAAA
11494352 GTAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 15 0.56
12 4 0.15
13 8 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:11494726 original size:3 final size:3
Alignment explanation
Indices: 11494718--11494759 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
11494708 CTACTTCTTA
11494718 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11494760 CCTCAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11495002 original size:13 final size:13
Alignment explanation
Indices: 11494970--11494995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11494960 GTATCATATT
11494970 ATATAAAATTAAA
1 ATATAAAATTAAA
11494983 ATATAAAATTAAA
1 ATATAAAATTAAA
11494996 TAATAAAGTG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAATTAAA
Found at i:11500682 original size:46 final size:46
Alignment explanation
Indices: 11500593--11500701 Score: 132
Period size: 46 Copynumber: 2.4 Consensus size: 46
11500583 TATGTGTGCT
*
11500593 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGCATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGCACGAGAGCC
* * * *
11500639 AGTGTAAGACATGTTTGGGACATGCATC-GGCATTGAG-ACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCA--CAGCACGAGAGCC
*
11500685 GGTGTAAGACATGTCTG
1 AGTGTAAGACATGTCTG
11500702 ACCTGCATCG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 3 0.06
46 49 0.91
47 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGCACGAGAGCC
Found at i:11500882 original size:49 final size:49
Alignment explanation
Indices: 11500775--11500896 Score: 131
Period size: 49 Copynumber: 2.5 Consensus size: 49
11500765 GTGGTGTGTT
* * *
11500775 AGTGTAAGACCTGTCTGGGACATGGCATTGAAACCGATAGATGAGAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATTCAAACCGATAGATGAAAGCC
* * * * *
11500824 AGTGAAAGACCTATCTGGGACATGGTA-TCAACCTCGCT-GTATGAAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATTCAAAC-CGATAG-ATGAAAGCC
11500873 AGTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGACC-TGTCTGGGACAT
11500897 CGCGTTGGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
48 5 0.08
49 44 0.73
50 11 0.18
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATTCAAACCGATAGATGAAAGCC
Found at i:11502944 original size:51 final size:51
Alignment explanation
Indices: 11502889--11503041 Score: 198
Period size: 51 Copynumber: 3.0 Consensus size: 51
11502879 AGAGGCTGAC
* * * *
11502889 ATAGGCGAACCCCTAATTAACTCAAATGGAGTAGAGGACGTATGACCAGAA
1 ATAGGAGAACCCCTAATTAACCCAAATGGAGTAGAAGATGTATGACCAGAA
* * *
11502940 ATAGGAGAATCCCTAATTAACCCAGATGGAGTAAAAGATGTATGACCAGAA
1 ATAGGAGAACCCCTAATTAACCCAAATGGAGTAGAAGATGTATGACCAGAA
** * * *
11502991 GGAGAAGAACCCCTAATTAACCCAAATAGAGTAGATGATGTATGACCAGAA
1 ATAGGAGAACCCCTAATTAACCCAAATGGAGTAGAAGATGTATGACCAGAA
11503042 GAAGGAGTAC
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 87 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (51 bp):
ATAGGAGAACCCCTAATTAACCCAAATGGAGTAGAAGATGTATGACCAGAA
Found at i:11506625 original size:48 final size:47
Alignment explanation
Indices: 11506567--11506738 Score: 220
Period size: 48 Copynumber: 3.6 Consensus size: 47
11506557 ATATCGGTGC
* * *
11506567 CGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATGTCATCAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCA-CAT
*
11506615 CAATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACA-
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATC-ACAT
* * * *
11506662 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCAGAT
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCACAT
11506710 GCCGATGCCATGTCCCAGACATGGTCTTA
1 --CGATGCCATGTCCCAGACATGGTCTTA
11506739 TACGGGATCT
Statistics
Matches: 110, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
47 3 0.03
48 79 0.72
49 27 0.25
50 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCACAT
Found at i:11515874 original size:10 final size:10
Alignment explanation
Indices: 11515859--11515883 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11515849 AGTAGTTATT
11515859 TTTCTGTTAC
1 TTTCTGTTAC
11515869 TTTCTGTTAC
1 TTTCTGTTAC
11515879 TTTCT
1 TTTCT
11515884 TTCCTTGCTT
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:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (10 bp):
TTTCTGTTAC
Found at i:11518263 original size:126 final size:126
Alignment explanation
Indices: 11518030--11518412 Score: 624
Period size: 126 Copynumber: 3.0 Consensus size: 126
11518020 TTTCTGCAAG
* * * *
11518030 AATAATTCTGAGCAGACGTTTCTGGACAAATAATGTCAGAAAACGCTTCAAGCATGATGCACTGT
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTC-GAAAACGCTTCAAGCAGGATGCACTGT
*
11518095 CAGCAAAATTTCTAGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTATTTCGTAGAAA
65 CAGCAAAATTTCTAGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
*
11518157 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAATGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
* * *
11518222 AGCAAAATTTCTAGAAAAAGCTCCTACGTGGATGCTTTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTAGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * *
11518283 AATAATTTTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTTAAGCAGGATGCACTATC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
11518348 AGCAAAA-TTCTGGAAAAAGCTCCCACGCGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTAGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
11518408 AATAA
1 AATAA
11518413 GGGTATAAAT
Statistics
Matches: 238, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
125 53 0.22
126 151 0.63
127 34 0.14
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (126 bp):
AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTCTAGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
Found at i:11521191 original size:41 final size:41
Alignment explanation
Indices: 11521129--11521391 Score: 408
Period size: 41 Copynumber: 6.5 Consensus size: 41
11521119 CGTTTTACCA
** * *
11521129 AAAACGCCGCTAAAA-ATAGAGCAATAGCGGC-CTTTTATGTT
1 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGC-TTT-TGGT
* *
11521170 AAAACGCCGCTAAAA-ACAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
11521210 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
11521251 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
11521292 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
*
11521333 AAAACGCCGCTAAAAGCCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
*
11521374 AAAACGCTGCT-AAAGCCA
1 AAAACGCCGCTAAAAGCCA
11521392 TATAACCCCT
Statistics
Matches: 213, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
40 25 0.12
41 187 0.88
42 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCTAAAAGCCAGAGCACTAGCGGCGCTTTTGGT
Found at i:11521454 original size:22 final size:23
Alignment explanation
Indices: 11521429--11521476 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
11521419 AAAAAATCAT
*
11521429 AAACACT-AA-TCTATAATCCTTA
1 AAACACTAAACTCT-TAAACCTTA
11521451 AAACACTAAACTCTTAAACCTTA
1 AAACACTAAACTCTTAAACCTTA
11521474 AAA
1 AAA
11521477 AATCTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 13 0.57
24 3 0.13
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (23 bp):
AAACACTAAACTCTTAAACCTTA
Found at i:11521725 original size:14 final size:15
Alignment explanation
Indices: 11521691--11521726 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
11521681 TATTTTAAGT
*
11521691 TTTATGGATTATAGA
1 TTTAGGGATTATAGA
11521706 TTTAGGGATTATAG-
1 TTTAGGGATTATAGA
11521720 TTTAGGG
1 TTTAGGG
11521727 GTTAGTGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (15 bp):
TTTAGGGATTATAGA
Found at i:11521994 original size:22 final size:22
Alignment explanation
Indices: 11521943--11521996 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
11521933 ATGATTAAGG
11521943 GTTTAAGGTTTATGAGTTACTA
1 GTTTAAGGTTTATGAGTTACTA
*
11521965 TTTTAAGGTTTATGTA-TTA-TA
1 GTTTAAGGTTTATG-AGTTACTA
11521986 GTTTAAAGGTT
1 GTTT-AAGGTT
11521997 AGGGGTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 22 0.79
23 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (22 bp):
GTTTAAGGTTTATGAGTTACTA
Found at i:11522077 original size:282 final size:271
Alignment explanation
Indices: 11521550--11522185 Score: 716
Period size: 282 Copynumber: 2.3 Consensus size: 271
11521540 GATGTACATC
* * * *
11521550 ATATGTTAAATATTTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAATATTGAATTAA
1 ATATGATAAATATTTTCTTATATAATTGTAAAAGAGATAATATTAATTTAAAAATATTGAATCAA
** *
11521615 TTATCATTATAGTTTAAGGTTTATGATTTAGGGCATATGGTTAAGGGTTTAAGGTTTACGAGTTA
66 TTATCATTATAGTTTAAGGTTTACAATTTAGGGCATATGATTAAGGGTTTAAGGTTTACGAGTTA
* *
11521680 CTATTTTAAGTTTTATGGATTATAGATTTAGGGATTATAGTTTAGGGGTTAGTGGTCTAGGATTA
131 CTATTTTAAGGTTTATGGATTATAGAGTTAGGGATTATAGTTTAGGGGTTAGTGGTCTAGGATTA
* * *
11521745 AGAGTTTATATTTTAGGATTTAGGATTTAGGGTCTAGGGATTAAGGATTAA-GAGTTTAGGGTTT
196 AGAGTTCATATTTTAGGA-TT---ATTTAGAGTCTAGAGATTAAGGATTAATG-GTTTA--G---
11521809 AGTTAATTAATGTTTTTAATTT
251 A-TTAATTAATGTTTTTAATTT
*
11521831 ATATGATAAATATTTTCTTATATAATTGTAAAAAAGATAATATTAATTTAAAAATATTGAATCAA
1 ATATGATAAATATTTTCTTATATAATTGTAAAAGAGATAATATTAATTTAAAAATATTGAATCAA
* * *
11521896 TTAATCATTATAGTTTAGGGTTTACAATTTAGGGTATATGATTAAGGGTTTAAGGTTTATGAGTT
66 TT-ATCATTATAGTTTAAGGTTTACAATTTAGGGCATATGATTAAGGGTTTAAGGTTTACGAGTT
* * *
11521961 ACTATTTTAAGGTTTATGTATTATAGTTTAAAGGTTAGGGGTTATGAG-TTATGGGTTA-TGGGT
130 ACTATTTTAAGGTTTATGGATTATAG-----A-GTTAGGGATTAT-AGTTTAGGGGTTAGT-GGT
* * * * *
11522024 TTAGGGTTAATG-GTTCATATTTTAGGA-T-TTTAGAGTTTAGAGTTTAGGGATTAATGGTTTAG
187 CTAGGATTAA-GAGTTCATATTTTAGGATTATTTAGAGTCTAGAGATTAAGGATTAATGGTTTAG
*
11522086 ATTAATTAGTGTTTTTAATTT
251 ATTAATTAATGTTTTTAATTT
* * * * * *
11522107 ATAT-ATTAAATAATTTCTTATATGATTGTAAAAGAGATAATTTTAATTTTAATAT-TTTAA--A
1 ATATGA-TAAATATTTTCTTATATAATTGTAAAAGAGATAATATTAATTTAAAAATATTGAATCA
*
11522168 ATTATGATTATAGTTTAA
65 ATTATCATTATAGTTTAA
11522186 ATTATTTAAG
Statistics
Matches: 309, Mismatches: 34, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
272 13 0.04
273 4 0.01
275 5 0.02
276 66 0.21
277 1 0.00
280 1 0.00
281 62 0.20
282 106 0.34
283 1 0.00
286 1 0.00
287 2 0.01
288 44 0.14
289 3 0.01
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.45
Consensus pattern (271 bp):
ATATGATAAATATTTTCTTATATAATTGTAAAAGAGATAATATTAATTTAAAAATATTGAATCAA
TTATCATTATAGTTTAAGGTTTACAATTTAGGGCATATGATTAAGGGTTTAAGGTTTACGAGTTA
CTATTTTAAGGTTTATGGATTATAGAGTTAGGGATTATAGTTTAGGGGTTAGTGGTCTAGGATTA
AGAGTTCATATTTTAGGATTATTTAGAGTCTAGAGATTAAGGATTAATGGTTTAGATTAATTAAT
GTTTTTAATTT
Found at i:11522405 original size:7 final size:6
Alignment explanation
Indices: 11522380--11522424 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
11522370 AACAACATTG
*
11522380 ATAACAA ATAAAA ATAAAA TACAAAA ATAAAA ATAAAA TATAAAA
1 ATAA-AA ATAAAA ATAAAA -ATAAAA ATAAAA ATAAAA -ATAAAA
11522425 TAGAGGTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 19 0.56
7 15 0.44
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:11522405 original size:13 final size:12
Alignment explanation
Indices: 11522385--11522426 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
11522375 CATTGATAAC
11522385 AAAT-AAAAATA
1 AAATAAAAAATA
11522396 AAATACAAAAATAA
1 AAATA-AAAAAT-A
*
11522410 AAATAAAATATA
1 AAATAAAAAATA
11522422 AAATA
1 AAATA
11522427 GAGGTTAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.15
12 6 0.22
13 11 0.41
14 6 0.22
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:11522407 original size:19 final size:19
Alignment explanation
Indices: 11522385--11522424 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
11522375 CATTGATAAC
11522385 AAATAAAAATAAAATACAA
1 AAATAAAAATAAAATACAA
*
11522404 AAATAAAAATAAAATATAA
1 AAATAAAAATAAAATACAA
11522423 AA
1 AA
11522425 TAGAGGTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATAAAAATAAAATACAA
Found at i:11527208 original size:43 final size:43
Alignment explanation
Indices: 11527126--11527300 Score: 208
Period size: 43 Copynumber: 4.1 Consensus size: 43
11527116 TTTCATGACT
* * * * *
11527126 TTTAGCGGCATTT-TTGAGAAAAGCACCGCTAAAGACCGTGATC
1 TTTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGGCCATGATC
* *
11527169 TTTAACGGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCGTGATC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCATGATC
* * * * *
11527212 TTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAATGTCATAATT
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCATGATC
* *
11527255 TTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCATGATC
11527298 TTT
1 TTT
11527301 TGTAACAGCC
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
43 111 0.97
44 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGCCATGATC
Found at i:11530400 original size:18 final size:18
Alignment explanation
Indices: 11530377--11530414 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11530367 GGAAAAGGAA
*
11530377 ACATATAAGGGTTAGAAT
1 ACATATAAGGGCTAGAAT
11530395 ACATATAAGGGCTAGAAT
1 ACATATAAGGGCTAGAAT
11530413 AC
1 AC
11530415 GCACCTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGAAT
Found at i:11532084 original size:48 final size:47
Alignment explanation
Indices: 11532008--11532114 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 47
11531998 ATGCAAACAT
* *
11532008 CATAAATGAAAAAAAATCAAACAGTATTG-ATATTGTAATTACAA-TTG
1 CATAAATGAAAAAAAATCAAACAGTATTGCAAATT-TAACTA-AATTTG
* * *
11532055 CATAAATGAATGAAATATCAAATAGTATTGCAAATTTAACTAAATTTG
1 CATAAATGAA-AAAAAATCAAACAGTATTGCAAATTTAACTAAATTTG
*
11532103 CATAAATTAAAA
1 CATAAATGAAAA
11532115 TAGTATCGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
47 13 0.26
48 33 0.66
49 4 0.08
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.31
Consensus pattern (47 bp):
CATAAATGAAAAAAAATCAAACAGTATTGCAAATTTAACTAAATTTG
Found at i:11532290 original size:11 final size:11
Alignment explanation
Indices: 11532274--11532305 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
11532264 TTTTAAACAA
11532274 AGAATTTTGAT
1 AGAATTTTGAT
11532285 AGAATTTTGAT
1 AGAATTTTGAT
*
11532296 GGAATTTTGA
1 AGAATTTTGA
11532306 GAAAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (11 bp):
AGAATTTTGAT
Found at i:11534153 original size:15 final size:14
Alignment explanation
Indices: 11534106--11534153 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
11534096 TGGCCCCCTA
11534106 AAATTATAAAAATT
1 AAATTATAAAAATT
*
11534120 CAAATTATAAATATAT
1 -AAATTATAAAAAT-T
11534136 AAATTATAAAAAATT
1 AAATTAT-AAAAATT
11534151 AAA
1 AAA
11534154 ATTTCACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 23 0.79
16 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTATAAAAATT
Found at i:11535669 original size:44 final size:44
Alignment explanation
Indices: 11535593--11535687 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
11535583 ATCCCCAAAG
* * ** * *
11535593 GATTAGTGGCTTCAATCTGCTCCATTGTAACTTC-AGGAAGATAA
1 GATTTGTGGCTTCAATCTACTCCACAGCAACTTCAAAG-AGATAA
11535637 GATTTGTGGCTTCAATCTACTCCACAGCAACTTCAAAGAGATAA
1 GATTTGTGGCTTCAATCTACTCCACAGCAACTTCAAAGAGATAA
11535681 GATTTGT
1 GATTTGT
11535688 CATAATAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
44 42 0.95
45 2 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
GATTTGTGGCTTCAATCTACTCCACAGCAACTTCAAAGAGATAA
Found at i:11541147 original size:46 final size:44
Alignment explanation
Indices: 11541043--11541150 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
11541033 TGTCTTTAAC
** * * *
11541043 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
11541087 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
11541133 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
11541151 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:11542042 original size:9 final size:9
Alignment explanation
Indices: 11542028--11542062 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
11542018 TTCTATTCTG
11542028 TTTCTTTTC
1 TTTCTTTTC
*
11542037 TTTCTTTTT
1 TTTCTTTTC
*
11542046 TTTCTATTC
1 TTTCTTTTC
11542055 TTTCTTTT
1 TTTCTTTT
11542063 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:11542055 original size:18 final size:19
Alignment explanation
Indices: 11542028--11542067 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
11542018 TTCTATTCTG
*
11542028 TTTCTTTTCTTTCTTTT-T
1 TTTCTATTCTTTCTTTTGT
11542046 TTTCTATTCTTTCTTTTGT
1 TTTCTATTCTTTCTTTTGT
11542065 TTT
1 TTT
11542068 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTCTATTCTTTCTTTTGT
Found at i:11542084 original size:5 final size:5
Alignment explanation
Indices: 11542071--11542143 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
11542061 TTGTTTTATG
11542071 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
11542119 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
11542144 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:11542096 original size:19 final size:19
Alignment explanation
Indices: 11542072--11542114 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
11542062 TGTTTTATGT
11542072 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
11542091 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
11542110 ATATA
1 ATATA
11542115 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:11542124 original size:24 final size:25
Alignment explanation
Indices: 11542078--11542142 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
11542068 ATGTATATAT
* *
11542078 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
11542102 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
11542127 TTACTATAATATAATA
1 ATAATATAATATAATA
11542143 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:11543502 original size:27 final size:23
Alignment explanation
Indices: 11543480--11543528 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
11543470 TCCAAAAAGT
11543480 AACAAGAAGAACACAAGAAC-AAAA
1 AACAAGAAGAA-AC-AGAACAAAAA
*
11543504 ACCAAGAAGAAACAGAACAAAAA
1 AACAAGAAGAAACAGAACAAAAA
11543527 AA
1 AA
11543529 ATAACGTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 7 0.32
24 10 0.45
ACGTcount: A:0.71, C:0.16, G:0.12, T:0.00
Consensus pattern (23 bp):
AACAAGAAGAAACAGAACAAAAA
Found at i:11543528 original size:24 final size:24
Alignment explanation
Indices: 11543482--11543526 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
11543472 CAAAAAGTAA
11543482 CAAGAAGAACACAAGAACAAAAAC
1 CAAGAAGAACACAAGAACAAAAAC
11543506 CAAGAAGAA-AC-AGAACAAAAA
1 CAAGAAGAACACAAGAACAAAAA
11543527 AAATAACGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.69, C:0.18, G:0.13, T:0.00
Consensus pattern (24 bp):
CAAGAAGAACACAAGAACAAAAAC
Found at i:11549064 original size:24 final size:24
Alignment explanation
Indices: 11549037--11549082 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
11549027 TGCAGCTACG
*
11549037 TTTACAGCTGGTCTTGCATTTCCT
1 TTTACAGCTGGTCTAGCATTTCCT
* * *
11549061 TTTAGATCTGTTCTAGCATTTC
1 TTTACAGCTGGTCTAGCATTTC
11549083 TAACCTTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (24 bp):
TTTACAGCTGGTCTAGCATTTCCT
Found at i:11553068 original size:52 final size:54
Alignment explanation
Indices: 11552969--11553071 Score: 124
Period size: 52 Copynumber: 1.9 Consensus size: 54
11552959 AAATGAAAGG
*
11552969 AAAACATAAGTAATATCGAATTTAAATATATATAAAAATAATAAATAAATAGGC
1 AAAACATAAGTAATATCAAATTTAAATATATATAAAAATAATAAATAAATAGGC
* * *
11553023 AAAACA-AA-TAATATTAAATTTAAGTAT-T-TAAAAAGTAAATGAATAAATA
1 AAAACATAAGTAATATCAAATTTAAATATATATAAAAA-T-AATAAATAAATA
11553072 AAATAAGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
50 6 0.14
51 2 0.05
52 27 0.63
53 2 0.05
54 6 0.14
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (54 bp):
AAAACATAAGTAATATCAAATTTAAATATATATAAAAATAATAAATAAATAGGC
Found at i:11561799 original size:177 final size:177
Alignment explanation
Indices: 11561501--11561852 Score: 533
Period size: 177 Copynumber: 2.0 Consensus size: 177
11561491 TCCAAGTTTC
* * *
11561501 ATGGTAGGTTGACTCTTTTTCGTTACCTCCTTTTTAAATTGGTAACTCTAGATATTCTAATATCT
1 ATGGTAGGTTGACTCTTTTTCGTTACCTCCTCTTTAAATTGGTAACTCTAAATACTCTAATATCT
* * **
11561566 ACTTAAAGTTAAGACTTTTATGGGATGACATTCGTTCTTTGATACAGTAGGTACATATCAAAACT
66 ACTGAAAGTTAAGACTTTTATAGGATGACATTCGTTCTTTGATACAACAGGTACATATCAAAACT
* * * *
11561631 CAACATAGACACCATTAGATGGACCACTTCATTTGTAGAGCGGCGTT
131 CAACATAGACACCATCAAACGGACCACTTCATTTGGAGAGCGGCGTT
* *
11561678 ATGGTAGGTTGACTCTTTTTCGTTGCCTCCTCTTTAAATTGGTAACTCTAAATACTCTAATATTT
1 ATGGTAGGTTGACTCTTTTTCGTTACCTCCTCTTTAAATTGGTAACTCTAAATACTCTAATATCT
* * * **
11561743 ACTGAAAGTTAAGACTTTTATAGGATGACATTTGTTCTTTGTTACAACATGTACATATCAGTACT
66 ACTGAAAGTTAAGACTTTTATAGGATGACATTCGTTCTTTGATACAACAGGTACATATCAAAACT
*
11561808 CAACATGGACACCATCAAACGGACCACTTCATTTGGAGAGCGGCG
131 CAACATAGACACCATCAAACGGACCACTTCATTTGGAGAGCGGCG
11561853 GTATTCATGT
Statistics
Matches: 156, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
177 156 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (177 bp):
ATGGTAGGTTGACTCTTTTTCGTTACCTCCTCTTTAAATTGGTAACTCTAAATACTCTAATATCT
ACTGAAAGTTAAGACTTTTATAGGATGACATTCGTTCTTTGATACAACAGGTACATATCAAAACT
CAACATAGACACCATCAAACGGACCACTTCATTTGGAGAGCGGCGTT
Found at i:11563443 original size:19 final size:20
Alignment explanation
Indices: 11563419--11563468 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
11563409 GGCATCGCTC
11563419 ACTCCTCTG-CACCGACGAG
1 ACTCCTCTGCCACCGACGAG
*
11563438 ACTCCTCCCTGCCACCGACGGG
1 ACTCCT--CTGCCACCGACGAG
*
11563460 ACTGCTCTG
1 ACTCCTCTG
11563469 AGCTATTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.23
20 3 0.12
21 3 0.12
22 14 0.54
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (20 bp):
ACTCCTCTGCCACCGACGAG
Found at i:11563453 original size:22 final size:22
Alignment explanation
Indices: 11563420--11563462 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11563410 GCATCGCTCA
11563420 CTCCTCTGCACCGACGAGACTC
1 CTCCTCTGCACCGACGAGACTC
*
11563442 CTCC-CTGCCACCGACGGGACT
1 CTCCTCTG-CACCGACGAGACT
11563463 GCTCTGAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (22 bp):
CTCCTCTGCACCGACGAGACTC
Found at i:11564120 original size:14 final size:14
Alignment explanation
Indices: 11564101--11564129 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11564091 AGCTTAATAG
11564101 TATATTTTAAAAAA
1 TATATTTTAAAAAA
11564115 TATATTTTAAAAAA
1 TATATTTTAAAAAA
11564129 T
1 T
11564130 CCGAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATTTTAAAAAA
Found at i:11564285 original size:12 final size:13
Alignment explanation
Indices: 11564257--11564290 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11564247 GTATATTTTG
*
11564257 AAAAATAAAATCC
1 AAAAATAAAATCA
11564270 AAAAATAAAAT-A
1 AAAAATAAAATCA
11564282 AAAAATAAA
1 AAAAATAAA
11564291 CGGCCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAATCA
Found at i:11564553 original size:146 final size:143
Alignment explanation
Indices: 11564125--11565442 Score: 1697
Period size: 146 Copynumber: 9.1 Consensus size: 143
11564115 TATATTTTAA
* *
11564125 AAAATCCGAAAATAAAA-TAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAATAT
1 AAAATCCGAAAATAAAATTAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAA
11564189 ACTAAAATAATACATATGAAACATTATGTACTAAAATAATA-AAAAAAAT---AT--GAAAATAG
66 ACTAAAATAATAC--ATGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAG
*
11564248 TATATTTTGAAAAAT
129 TATATTTTAAAAAAT
* * * **
11564263 AAAATCCAAAAATAAAATAAAAAATAAACGGCCAAAATCAAAAATTTTTACTAAATTAATATAAA
1 AAAATCCGAAAATAAAAT-TAAAA-AAA-GGCCAAAATCAGAGTTTTTTACTAAATTAATATAAA
*
11564328 AAAACTAAAATAACACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAA
63 AAAACTAAAATAATACA--TGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAA
11564393 TAGTATATTTTAAAAAAT
126 TAGTATATTTTAAAAAAT
* * * *
11564411 AAAATCCGAAAACAAAATTAAAAAAAAGCCAAAATCACAGATTTTTACTAAATTAATATAAAAAA
1 AAAATCCGAAAATAAAATTAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATAT---AAA
* *
11564476 AAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAACAAAATACAAAAATA
63 AAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATA
* **
11564541 ATATATCCTAAAAAAT
128 GTATATTTTAAAAAAT
* * * * *
11564557 AAAATCCGAAAATAAAAAT-AAAAAGGGTCAAAGTCAGAGTTTTTTTTTTCTAAATTAATATAAA
1 AAAATCCGAAAATAAAATTAAAAAAAGGCCAAAATCAGAG---TTTTTTACTAAATTAATATAAA
* *
11564621 AAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAA-CAAATACAAAAATA
63 AAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATA
* *
11564685 ATAAATTTTAAAAAAT
128 GTATATTTTAAAAAAT
* * * *
11564701 AAATTTCGAAAATAAAAAT-AAAAAAGGCCAAAATCAGAGTTTTTTTTCTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAATTAAAAAAAGGCCAAAATCAGAG-TTTTTTACTAAATTAATATAAAAA
* * *
11564765 AACTAAAATAATACATTTGAAACATTATATACTAAAATAATATAAAAGAATAAAATACGAAAAGA
65 AACTAAAATAATACA--TGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATA
11564830 GTATATTTTAAAAAAT
128 GTATATTTTAAAAAAT
** * * *
11564846 AAAATCTAAAAACAAAA-TAAATAAAACGGCCAAAATCACAGATTTTTACTAAATTAATATAAAA
1 AAAATCCGAAAATAAAATTAAA-AAAA-GGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAA
11564910 AAACTAAAATAATACATGAAACATTATGTACTAAAATAATAT--AAAAATAAAATACGAAAATAG
64 AAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAG
11564973 TATATTTTAAAAAAT
129 TATATTTTAAAAAAT
* *
11564988 AAAATCCTAAAATAAAA--AATAAAAAGGGCC-AAATCAGAGTTTTTTTTCTAAATTAATATAAA
1 AAAATCCGAAAATAAAATTAA-AAAAA-GGCCAAAATCAGAG-TTTTTTACTAAATTAATATAAA
* *
11565050 AAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAACAAAATATGAAAATA
63 AAAACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATA
*
11565115 GTATATTTTAGAAAAT
128 GTATATTTTAAAAAAT
* * *
11565131 AAAATTCGAAAATAAAATAAAAAATAAATGGCCAAAATCAGAGTTTTTTATTAAATTAATAT-AA
1 AAAATCCGAAAATAAAAT-TAAAA-AAA-GGCCAAAATCAGAGTTTTTTACTAAATTAATATAAA
11565195 AAAACTAAAATAATACATTTCG-AACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAA
63 AAAACTAAAATAATACA--T-GAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAA
*
11565258 ATAGTATATTTTAAAAAGT
125 ATAGTATATTTTAAAAAAT
* * *
11565277 AAAATCCGAAAATAAAATAAAAAAACAAACGGTCAAAATCAGAGTTTTTTATTAAATTAATATAA
1 AAAATCCGAAAATAAAAT--TAAAA-AAA-GGCCAAAATCAGAGTTTTTTACTAAATTAATATAA
* *
11565342 AAAATACAAAAATAATACATTTGAAACATTATGTACTAAAATAATAT--AAAAATAAAAAACGAA
62 AAAA-ACTAAAATAATACA--TGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAA
*
11565405 AATAATATATTTTAAAAAAT
124 AATAGTATATTTTAAAAAAT
11565425 AAAATCCGAAAATAAAAT
1 AAAATCCGAAAATAAAAT
11565443 AAATACCAAA
Statistics
Matches: 1056, Mismatches: 84, Indels: 70
0.87 0.07 0.06
Matches are distributed among these distances:
138 16 0.02
140 13 0.01
141 76 0.07
142 160 0.15
143 56 0.05
144 117 0.11
145 158 0.15
146 198 0.19
147 91 0.09
148 132 0.12
149 39 0.04
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (143 bp):
AAAATCCGAAAATAAAATTAAAAAAAGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAA
ACTAAAATAATACATGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAGTA
TATTTTAAAAAAT
Found at i:11564701 original size:14 final size:15
Alignment explanation
Indices: 11564679--11564719 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
11564669 AACAAATACA
11564679 AAAATAATAAATTTT
1 AAAATAATAAATTTT
*
11564694 AAAA-AATAAATTTCG
1 AAAATAATAAATTT-T
11564709 AAAATAA-AAAT
1 AAAATAATAAAT
11564720 AAAAAAGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 9 0.39
15 12 0.52
16 2 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAATAATAAATTTT
Found at i:11565055 original size:287 final size:287
Alignment explanation
Indices: 11564125--11565445 Score: 1743
Period size: 287 Copynumber: 4.6 Consensus size: 287
11564115 TATATTTTAA
* * *
11564125 AAAATCCGAAAATAAAATAAAAAAAGGCCAAAATCAGAG-TTTTTTACTAAATTAATATAAATAT
1 AAAATCCGAAAATAAAA-AAAAAAAGGCCAAAATCAGAGTTTTTTTTCTAAATTAATATAAAAAA
*
11564189 ACTAAAATAATACATATGAAACATTATGTACTAAAAT-A-AT--AAAA-AAAATATGAAAATAGT
65 ACTAAAATAATACAT-TGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATAGT
* * * *
11564249 ATATTTTGAAAAATAAAATCCAAAAATAAAATAAAAAATAAACGGCCAAAATCAAAAATTTTTAC
129 ATATTTTAAAAAATAAAATCCGAAAATAAAAT-AAAAATAAACGGCCAAAATCAGAGATTTTTAC
*
11564314 TAAATTAATATAAAAAAACTAAAATAACACATTTGAAACATTATGTACTAAAATAATATAAAAAA
193 TAAATTAATATAAAAAAACTAAAATAATACA-TTGAAACATTATGTACTAAAATAATAT-AAAAA
11564379 ATAAAATACGAAAATAGTATATTTTAAAAAAT
256 ATAAAATACGAAAATAGTATATTTTAAAAAAT
* * * * *
11564411 AAAATCCGAAAACAAAATTAAAAAAAAGCCAAAATCACAG-ATTTTTACTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAA--AAAAAAAGGCCAAAATCAGAGTTTTTTTTCTAAATTAATAT---AA
*
11564475 AAAAACTAAAATAATACA-TGAAACATTATGTACTAAAATAATATAAAAAAACAAAATACAAAAA
61 AAAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATAT-AAAAAACAAAATACGAAAA
* ** * * * * *
11564539 TAATATATCCTAAAAAATAAAATCCGAAAAT-AAA-AATAA-AAAGGGTCAAAGTCAGAGTTTTT
125 TAGTATATTTTAAAAAATAAAATCCGAAAATAAAATAAAAATAAACGGCCAAAATCAGAG---AT
*
11564601 TTTTTCTAAATTAATATAAAAAAACTAAAATAATACA-TGAAACATTATGTACTAAAATAATATA
187 TTTTACTAAATTAATATAAAAAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATATA
* * *
11564665 AAAAA-ACAAATACAAAAATAATAAATTTTAAAAAAT
252 AAAAATA-AAATACGAAAATAGTATATTTTAAAAAAT
* *
11564701 AAATTTCGAAAATAAAAATAAAAAAGGCCAAAATCAGAGTTTTTTTTCTAAATTAATATAAAAAA
1 AAAATCCGAAAATAAAAA-AAAAAAGGCCAAAATCAGAGTTTTTTTTCTAAATTAATATAAAAAA
* * *
11564766 ACTAAAATAATACATTTGAAACATTATATACTAAAATAATATAAAAGAATAAAATACGAAAAGAG
65 ACTAAAATAATACA-TTGAAACATTATGTACTAAAATAATATAAAA-AACAAAATACGAAAATAG
** * * *
11564831 TATATTTTAAAAAATAAAATCTAAAAACAAAATAAATA-AAACGGCCAAAATCACAGATTTTTAC
128 TATATTTTAAAAAATAAAATCCGAAAATAAAATAAAAATAAACGGCCAAAATCAGAGATTTTTAC
11564895 TAAATTAATATAAAAAAACTAAAATAATACA-TGAAACATTATGTACTAAAATAATAT-AAAAAT
193 TAAATTAATATAAAAAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATATAAAAAAT
11564958 AAAATACGAAAATAGTATATTTTAAAAAAT
258 AAAATACGAAAATAGTATATTTTAAAAAAT
*
11564988 AAAATCCTAAAATAAAAAATAAAAAGGGCC-AAATCAGAGTTTTTTTTCTAAATTAATATAAAAA
1 AAAATCCGAAAATAAAAAA-AAAAA-GGCCAAAATCAGAGTTTTTTTTCTAAATTAATATAAAAA
*
11565052 AACTAAAATAATACA-TGAAACATTATGTACTAAAATAATATAAAAAAACAAAATATGAAAATAG
64 AACTAAAATAATACATTGAAACATTATGTACTAAAATAATAT-AAAAAACAAAATACGAAAATAG
* * * *
11565116 TATATTTTAGAAAATAAAATTCGAAAATAAAATAAAAAATAAATGGCCAAAATCAGAGTTTTTTA
128 TATATTTTAAAAAATAAAATCCGAAAATAAAAT-AAAAATAAACGGCCAAAATCAGAGATTTTTA
*
11565181 TTAAATTAATAT-AAAAAACTAAAATAATACATTTCG-AACATTATGTACTAAAATAATATAAAA
192 CTAAATTAATATAAAAAAACTAAAATAATACA-TT-GAAACATTATGTACTAAAATAATATAAAA
*
11565244 AATAAAATACGAAAATAGTATATTTTAAAAAGT
255 AATAAAATACGAAAATAGTATATTTTAAAAAAT
* *
11565277 AAAATCCGAAAATAAAATAAAAAAACAAACGGTCAAAATCAGAGTTTTTTAT-TAAATTAATATA
1 AAAATCCGAAAAT---A-AAAAAAA-AAA-GGCCAAAATCAGAGTTTTTTTTCTAAATTAATATA
*
11565341 AAAAATACAAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAATA-AAAA-ACGA
60 AAAAA-ACTAAAATAATACA-TTGAAACATTATGTACTAAAATAATATAAAAA-ACAAAATACGA
*
11565404 AAATAATATATTTTAAAAAATAAAATCCGAAAATAAAATAAA
122 AAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAATAAA
11565446 TACCAAAATA
Statistics
Matches: 914, Mismatches: 80, Indels: 75
0.86 0.07 0.07
Matches are distributed among these distances:
285 68 0.07
286 44 0.05
287 191 0.21
288 118 0.13
289 130 0.14
290 99 0.11
291 47 0.05
292 3 0.00
293 74 0.08
294 104 0.11
295 9 0.01
296 27 0.03
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (287 bp):
AAAATCCGAAAATAAAAAAAAAAAGGCCAAAATCAGAGTTTTTTTTCTAAATTAATATAAAAAAA
CTAAAATAATACATTGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATAGTAT
ATTTTAAAAAATAAAATCCGAAAATAAAATAAAAATAAACGGCCAAAATCAGAGATTTTTACTAA
ATTAATATAAAAAAACTAAAATAATACATTGAAACATTATGTACTAAAATAATATAAAAAATAAA
ATACGAAAATAGTATATTTTAAAAAAT
Found at i:11571846 original size:78 final size:77
Alignment explanation
Indices: 11571750--11571905 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 77
11571740 TAACACTAAA
11571750 CAAACTATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
1 CAAACTATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
11571815 ACAAAAAAATTAC
66 AC-AAAAAATTAC
11571828 CAAACTATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
1 CAAACTATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
11571893 ACAAAAAATTAC
66 ACAAAAAATTAC
11571905 C
1 C
11571906 TTTTCTTTTC
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 11 0.14
78 67 0.86
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (77 bp):
CAAACTATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
ACAAAAAATTAC
Found at i:11571933 original size:22 final size:22
Alignment explanation
Indices: 11571907--11571948 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11571897 AAAATTACCT
11571907 TTTCTTTTCTTTAT-TCTTCTCC
1 TTTC-TTTCTTTATATCTTCTCC
*
11571929 TTTCTTTCTTTCTATCTTCT
1 TTTCTTTCTTTATATCTTCT
11571949 TCTTCTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTCTTTATATCTTCTCC
Found at i:11572056 original size:27 final size:27
Alignment explanation
Indices: 11572026--11572084 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
11572016 GGGGTTAAAG
**
11572026 CTGTGAGAAAGGCACCACTGGTGCCGC
1 CTGTGAGAAACCCACCACTGGTGCCGC
* ** *
11572053 CTGTGGGGTACCCTCCACTGGTGCCGC
1 CTGTGAGAAACCCACCACTGGTGCCGC
11572080 CTGTG
1 CTGTG
11572085 GGGTACCCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.32, G:0.34, T:0.20
Consensus pattern (27 bp):
CTGTGAGAAACCCACCACTGGTGCCGC
Found at i:11572085 original size:27 final size:27
Alignment explanation
Indices: 11572040--11572097 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
11572030 GAGAAAGGCA
11572040 CCACTGGTGCCGCCTGTGGGGTACCCT
1 CCACTGGTGCCGCCTGTGGGGTACCCT
11572067 CCACTGGTGCCGCCTGTGGGGTACCCT
1 CCACTGGTGCCGCCTGTGGGGTACCCT
11572094 CCAC
1 CCAC
11572098 CCTTATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.09, C:0.40, G:0.31, T:0.21
Consensus pattern (27 bp):
CCACTGGTGCCGCCTGTGGGGTACCCT
Found at i:11572757 original size:31 final size:31
Alignment explanation
Indices: 11572696--11572758 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
11572686 AAGTTTTCAG
* * * *
11572696 GCCCCAATATGGGAATAATTGTCTAGTTTAT
1 GCCCCAATATAGAAATAATTATCTAATTTAT
11572727 GCCCCAATATAGAAATAATTAT-TAAATTTAT
1 GCCCCAATATAGAAATAATTATCT-AATTTAT
11572758 G
1 G
11572759 GTCTATCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (31 bp):
GCCCCAATATAGAAATAATTATCTAATTTAT
Found at i:11573044 original size:30 final size:31
Alignment explanation
Indices: 11572987--11573054 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
11572977 GTTACAAATG
* *
11572987 GTCATTGAATTATTTGAGAGTTTTTATTTAA
1 GTCATTGAACTATTTGAAAGTTTTTATTTAA
11573018 GTCATTGAACTATTTGAAAG-TTTTATTTAA
1 GTCATTGAACTATTTGAAAGTTTTTATTTAA
*
11573048 GTAATTG
1 GTCATTG
11573055 GTTGCTAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (31 bp):
GTCATTGAACTATTTGAAAGTTTTTATTTAA
Found at i:11582306 original size:28 final size:28
Alignment explanation
Indices: 11582274--11582329 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
11582264 GCAGCACAAA
*
11582274 ATCATTCTATTGTTCTTCGTTTCATTAC
1 ATCATTCTATTGTTCTTCCTTTCATTAC
11582302 ATCATTCTATTGTTCTTCCTTTCATTAC
1 ATCATTCTATTGTTCTTCCTTTCATTAC
11582330 TGGTTTTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (28 bp):
ATCATTCTATTGTTCTTCCTTTCATTAC
Found at i:11591436 original size:6 final size:6
Alignment explanation
Indices: 11591422--11591454 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
11591412 TCTTTTTCTT
*
11591422 TTTTG- TTTTAA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
11591455 TTTTTACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (6 bp):
TTTTGA
Found at i:11592124 original size:22 final size:22
Alignment explanation
Indices: 11592087--11592167 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
11592077 ATTTTTTTGA
**
11592087 ATTTTTAAAATTTAAAAAAAAT
1 ATTTTTAAAAAATAAAAAAAAT
*
11592109 ATTTTTAAAAAATAAAAATCATTAAA
1 ATTTTTAAAAAATAAAAA--A--AAT
*
11592135 ATTATTTAAAAACATAAAAAATAT
1 ATT-TTTAAAAA-ATAAAAAAAAT
11592159 -TTTTTAAAA
1 ATTTTTAAAA
11592168 TTTAAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 23 0.48
23 2 0.04
24 2 0.04
26 6 0.12
27 8 0.17
28 7 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTTTAAAAAATAAAAAAAAT
Found at i:11592145 original size:19 final size:19
Alignment explanation
Indices: 11592121--11592160 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11592111 TTTTAAAAAA
* *
11592121 TAAAAATCATTAAAATTATT
1 TAAAAA-CATAAAAAATATT
11592141 TAAAAACATAAAAAATATT
1 TAAAAACATAAAAAATATT
11592160 T
1 T
11592161 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAACATAAAAAATATT
Found at i:11603412 original size:17 final size:17
Alignment explanation
Indices: 11603365--11603437 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
11603355 CCACACATTG
* *
11603365 ACATAGTTCACATATAA
1 ACATAGCTCTCATATAA
* *
11603382 ACACAACT-TGCATATAA
1 ACATAGCTCT-CATATAA
11603399 ACATAGCTCTCATATAA
1 ACATAGCTCTCATATAA
* * **
11603416 ATATAGTTAGCATATAA
1 ACATAGCTCTCATATAA
11603433 ACATA
1 ACATA
11603438 ACTCAGATTG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
17 42 0.98
18 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.29
Consensus pattern (17 bp):
ACATAGCTCTCATATAA
Found at i:11603540 original size:16 final size:16
Alignment explanation
Indices: 11603519--11603550 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11603509 ACAATGATAG
11603519 TTTGCATATTCAAGTA
1 TTTGCATATTCAAGTA
11603535 TTTGCATATTCAAGTA
1 TTTGCATATTCAAGTA
11603551 ATCACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
TTTGCATATTCAAGTA
Found at i:11604843 original size:26 final size:26
Alignment explanation
Indices: 11604811--11604861 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
11604801 GAACAACTGG
11604811 ATTGGCATACCAATTGTATCCTATCA
1 ATTGGCATACCAATTGTATCCTATCA
*
11604837 ATTGGCATACCACTTGTATCCTATC
1 ATTGGCATACCAATTGTATCCTATC
11604862 TTTTCTTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (26 bp):
ATTGGCATACCAATTGTATCCTATCA
Found at i:11611092 original size:28 final size:28
Alignment explanation
Indices: 11611028--11611092 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
11611018 TTATCGAGCT
11611028 TTGTCTCTACGGAGACCACTGTTACTAA
1 TTGTCTCTACGGAGACCACTGTTACTAA
* *
11611056 TTTTCTCTACGGAGACCACTGTTACTGA
1 TTGTCTCTACGGAGACCACTGTTACTAA
*
11611084 TTGTGTCTA
1 TTGTCTCTA
11611093 TAGAGACCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (28 bp):
TTGTCTCTACGGAGACCACTGTTACTAA
Found at i:11611098 original size:28 final size:28
Alignment explanation
Indices: 11611028--11611100 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
11611018 TTATCGAGCT
*
11611028 TTGTCTCTACGGAGACCACTGTTACTAA
1 TTGTCTCTACAGAGACCACTGTTACTAA
* * *
11611056 TTTTCTCTACGGAGACCACTGTTACTGA
1 TTGTCTCTACAGAGACCACTGTTACTAA
* *
11611084 TTGTGTCTATAGAGACC
1 TTGTCTCTACAGAGACC
11611101 TTGGTGTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (28 bp):
TTGTCTCTACAGAGACCACTGTTACTAA
Found at i:11614129 original size:11 final size:11
Alignment explanation
Indices: 11614115--11614139 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11614105 GAAGAGAGAG
11614115 AAAAGAAAATA
1 AAAAGAAAATA
11614126 AAAAGAAAATA
1 AAAAGAAAATA
11614137 AAA
1 AAA
11614140 TAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGAAAATA
Found at i:11618535 original size:156 final size:156
Alignment explanation
Indices: 11618251--11618563 Score: 590
Period size: 156 Copynumber: 2.0 Consensus size: 156
11618241 TGCTCCACGC
11618251 ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
1 ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
11618316 TTTTAGATTATCCCTTAATCCGTCCTCAAATTGGACACACCTCTCATACTCAGTCGCAACCATGC
66 TTTTAGATTATCCCTTAATCCGTCCTCAAATTGGACACACCTCTCATACTCAGTCGCAACCATGC
* *
11618381 CTCGAGTGTAGCGACTTATCCTCAAA
131 CTCGAGTGTAGCGACTCAGCCTCAAA
*
11618407 ACTTAACATCTTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
1 ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
*
11618472 TTTTAGATTATCCCTTAATCCGTCCTCAAATTGGACACATCTCTCATACTCAGTCGCAACCATGC
66 TTTTAGATTATCCCTTAATCCGTCCTCAAATTGGACACACCTCTCATACTCAGTCGCAACCATGC
11618537 CTCGAGTGTAGCGACTCAGCCTCAAA
131 CTCGAGTGTAGCGACTCAGCCTCAAA
11618563 A
1 A
11618564 ACTCGACCTT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.30
Consensus pattern (156 bp):
ACTTAACATCCTTGACTCTCAACCAGAACTGTGAACTCTCACTCTTTTTGTAGAGCAATCAATAC
TTTTAGATTATCCCTTAATCCGTCCTCAAATTGGACACACCTCTCATACTCAGTCGCAACCATGC
CTCGAGTGTAGCGACTCAGCCTCAAA
Found at i:11624115 original size:26 final size:26
Alignment explanation
Indices: 11624049--11624134 Score: 136
Period size: 26 Copynumber: 3.2 Consensus size: 26
11624039 GATAAAAAGC
*
11624049 ATATTTTATAAGGTATATTAAAATGAA
1 ATATTTGATAAGGTATATTAAAATG-A
*
11624076 ATCATTTGATAAGGTATATCAAAATGA
1 AT-ATTTGATAAGGTATATTAAAATGA
11624103 ATATTTGATAAGGTATATTAAAATGA
1 ATATTTGATAAGGTATATTAAAATGA
11624129 ATATTT
1 ATATTT
11624135 AAGTTTTAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 29 0.53
27 5 0.09
28 21 0.38
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (26 bp):
ATATTTGATAAGGTATATTAAAATGA
Found at i:11625202 original size:41 final size:41
Alignment explanation
Indices: 11625157--11625239 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
11625147 TACATCTTCA
11625157 ACTGAATTATATGTAGAGAACAACGAATCATCACCCTTGTC
1 ACTGAATTATATGTAGAGAACAACGAATCATCACCCTTGTC
* *
11625198 ACTGAATTATATGTAGAGAACAATGAATCATCGCCCTTGTC
1 ACTGAATTATATGTAGAGAACAACGAATCATCACCCTTGTC
11625239 A
1 A
11625240 TTGGCCACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (41 bp):
ACTGAATTATATGTAGAGAACAACGAATCATCACCCTTGTC
Found at i:11626665 original size:23 final size:22
Alignment explanation
Indices: 11626637--11626684 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
11626627 ACATTCAATC
11626637 AAAGGGAAAACAAAGGGACAACA
1 AAAGGG-AAACAAAGGGACAACA
**
11626660 AAAGGGAAATGAAGGGACAACA
1 AAAGGGAAACAAAGGGACAACA
11626682 AAA
1 AAA
11626685 CTGCTCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.60, C:0.10, G:0.27, T:0.02
Consensus pattern (22 bp):
AAAGGGAAACAAAGGGACAACA
Found at i:11626776 original size:37 final size:37
Alignment explanation
Indices: 11626722--11626816 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
11626712 CATCAAGTAT
* * *
11626722 AGAGACATGACTATTCAAATACATATGG-ACTAAGTGA
1 AGAGACATGACTTTTCAAATACACACGGAAC-AAGTGA
* *
11626759 AGAGACATGGCTTTTCAACTACACACGGAACAAGTGA
1 AGAGACATGACTTTTCAAATACACACGGAACAAGTGA
*
11626796 AGAGACATGACCTTTCAAATA
1 AGAGACATGACTTTTCAAATA
11626817 TCTTCCATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 47 0.96
38 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (37 bp):
AGAGACATGACTTTTCAAATACACACGGAACAAGTGA
Found at i:11629278 original size:9 final size:9
Alignment explanation
Indices: 11629264--11629288 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11629254 AGTACAATGG
11629264 CATGCTTCT
1 CATGCTTCT
11629273 CATGCTTCT
1 CATGCTTCT
11629282 CATGCTT
1 CATGCTT
11629289 TTCGGTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.32, G:0.12, T:0.44
Consensus pattern (9 bp):
CATGCTTCT
Found at i:11635694 original size:21 final size:22
Alignment explanation
Indices: 11635659--11635699 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
11635649 TTATGTTTGT
11635659 TAAACATCACTTAATTAGTTAG
1 TAAACATCACTTAATTAGTTAG
*
11635681 TAAAC-TCAGTTAATTAGTT
1 TAAACATCACTTAATTAGTT
11635700 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
TAAACATCACTTAATTAGTTAG
Found at i:11637237 original size:21 final size:22
Alignment explanation
Indices: 11637211--11637251 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11637201 TACTAGCCAC
11637211 AGGGGC-ACACGCCCGTGTGGG
1 AGGGGCAACACGCCCGTGTGGG
*
11637232 AGGGGCAACACGCCTGTGTG
1 AGGGGCAACACGCCCGTGTG
11637252 ACCAATTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.27, G:0.44, T:0.12
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGGG
Found at i:11638554 original size:47 final size:46
Alignment explanation
Indices: 11638460--11638578 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 46
11638450 ATGTCTTACA
* *
11638460 TTCCAGACACGTCTTACACTGGCTCTCATCTCAATGCCAATGCCATG
1 TTCCAGACATGTCTTACACTGGCTCTCATAT-AATGCCAATGCCATG
*
11638507 TTCCAGACATGGTCTTACACTGGCTCTCATA-ATATGGCCGATG-CATG
1 TTCCAGACAT-GTCTTACACTGGCTCTCATATA-AT-GCCAATGCCATG
* * *
11638554 TCCCAAACATGTCTTACACTAGCTC
1 TTCCAGACATGTCTTACACTGGCTC
11638579 ACAATAACCC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
46 15 0.24
47 23 0.37
48 25 0.40
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (46 bp):
TTCCAGACATGTCTTACACTGGCTCTCATATAATGCCAATGCCATG
Found at i:11639919 original size:24 final size:25
Alignment explanation
Indices: 11639883--11639929 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
11639873 TATTTATGGA
*
11639883 TAGAACGTCCACAATCTTTAATTGGT
1 TAGAACGTCCAC-ACCTTTAATTGGT
11639909 TAGAAC-T-CACACCTTTAATTG
1 TAGAACGTCCACACCTTTAATTG
11639930 CAAATCCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 1 0.05
26 6 0.30
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (25 bp):
TAGAACGTCCACACCTTTAATTGGT
Found at i:11646965 original size:31 final size:30
Alignment explanation
Indices: 11646907--11646980 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
11646897 AAAAAAACTT
* *
11646907 AATAGTTCAGTGACTCAAATAAAACTTTCA
1 AATAGTTCAATGACTCAAAGAAAACTTTCA
* *
11646937 ACTAGTTCAATGACTTAAACGAAAACTTTCA
1 AATAGTTCAATGACTCAAA-GAAAACTTTCA
*
11646968 AATAATTCAATGA
1 AATAGTTCAATGA
11646981 TCATTTTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (30 bp):
AATAGTTCAATGACTCAAAGAAAACTTTCA
Found at i:11651002 original size:34 final size:33
Alignment explanation
Indices: 11650953--11651032 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 33
11650943 CCATCTTAGT
*
11650953 ACAGTATCAATTATGCAGTAGGGCCTTAGCCCATC
1 ACAGTATC-AGTATGCAGTAGGGCCTTAGCCCA-C
* * *
11650988 ATATTATCAGTATGCATTAGGGCCTTAGCCCAC
1 ACAGTATCAGTATGCAGTAGGGCCTTAGCCCAC
11651021 ACAGTATCAGTA
1 ACAGTATCAGTA
11651033 GTATTCATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 11 0.28
34 22 0.56
35 6 0.15
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (33 bp):
ACAGTATCAGTATGCAGTAGGGCCTTAGCCCAC
Found at i:11665893 original size:24 final size:24
Alignment explanation
Indices: 11665861--11665909 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11665851 TTAGGGTTAG
11665861 CCACCTAGAGCCTTCCCTTTCATT
1 CCACCTAGAGCCTTCCCTTTCATT
11665885 CCACCTAGAGCCTTCCCTTTCATT
1 CCACCTAGAGCCTTCCCTTTCATT
11665909 C
1 C
11665910 TATTCTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.33
Consensus pattern (24 bp):
CCACCTAGAGCCTTCCCTTTCATT
Found at i:11667645 original size:28 final size:27
Alignment explanation
Indices: 11667554--11667659 Score: 90
Period size: 28 Copynumber: 3.7 Consensus size: 27
11667544 ACTTGTAATA
* *
11667554 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
*
11667582 GGGCTAGGCCCAGTATACTATGATATTG-TAAG
1 GGGCTAGGCCCAG-AT--TA--ATATTGAT-AT
11667614 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
11667642 GGGCTAAGGCCCAG-TTAA
1 GGGCT-AGGCCCAGATTAA
11667660 CTCTGATTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
27 11 0.17
28 27 0.42
29 2 0.03
30 3 0.05
31 1 0.02
32 14 0.22
33 7 0.11
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (27 bp):
GGGCTAGGCCCAGATTAATATTGATAT
Found at i:11669994 original size:19 final size:19
Alignment explanation
Indices: 11669966--11670002 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11669956 CATTTTGTTT
11669966 TTATTATTAATAAAAATTA
1 TTATTATTAATAAAAATTA
*
11669985 TTATTTTTAATAAAAATT
1 TTATTATTAATAAAAATT
11670003 TCATCCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTATTAATAAAAATTA
Found at i:11670689 original size:21 final size:20
Alignment explanation
Indices: 11670669--11670753 Score: 57
Period size: 19 Copynumber: 4.3 Consensus size: 20
11670659 TTTTTCAAAT
11670669 AATTATAAAAAAATATTAAA
1 AATTATAAAAAAATATTAAA
* * *
11670689 TATCTAGAAAATAAT-TTAAA
1 AAT-TATAAAAAAATATTAAA
* * * *
11670709 ATTTATTAAAAATTATT-GA
1 AATTATAAAAAAATATTAAA
* * *
11670728 AATTATAAAAAATTAATATA
1 AATTATAAAAAAATATTAAA
11670748 AATTAT
1 AATTAT
11670754 TTAAAAATTA
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
19 22 0.46
20 17 0.35
21 9 0.19
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTATAAAAAAATATTAAA
Found at i:11670730 original size:20 final size:19
Alignment explanation
Indices: 11670711--11670763 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
11670701 AATTTAAAAT
11670711 TTATTAAAAATTAT-TGAAA
1 TTATTAAAAATTATAT-AAA
*
11670730 TTATAAAAAATTAATATAAA
1 TTATTAAAAATT-ATATAAA
11670750 TTATTTAAAAATTA
1 TTA-TTAAAAATTA
11670764 ATCTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 11 0.38
20 9 0.31
21 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TTATTAAAAATTATATAAA
Found at i:11670738 original size:19 final size:18
Alignment explanation
Indices: 11670669--11670763 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 18
11670659 TTTTTCAAAT
*
11670669 AATTATAAAAAAATATTA
1 AATTATAAAAAATTATTA
* * *
11670687 AATATCTAGAAAATAATTTAA
1 AAT-TATAAAAAATTA-TT-A
*
11670708 AATTTATTAAAAATTATTGA
1 AA-TTATAAAAAATTATT-A
11670728 AATTATAAAAAATTAATATA
1 AATTATAAAAAATT-AT-TA
*
11670748 AATTATTTAAAAATTA
1 AATTA-TAAAAAATTA
11670764 ATCTTAATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
18 3 0.05
19 19 0.32
20 16 0.27
21 20 0.34
22 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (18 bp):
AATTATAAAAAATTATTA
Found at i:11670763 original size:11 final size:10
Alignment explanation
Indices: 11670704--11670763 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
11670694 AGAAAATAAT
*
11670704 TTAAAATTTA
1 TTAAAAATTA
11670714 TTAAAAATTA
1 TTAAAAATTA
*
11670724 TT-GAAATTA
1 TTAAAAATTA
*
11670733 TAAAAAATTA
1 TTAAAAATTA
* *
11670743 ATATAAATTA
1 TTAAAAATTA
11670753 TTTAAAAATTA
1 -TTAAAAATTA
11670764 ATCTTAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.18
10 24 0.62
11 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:11671148 original size:18 final size:19
Alignment explanation
Indices: 11671119--11671162 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
11671109 TGTATAATTA
11671119 ATTTTCAATTTTAA-TATTT
1 ATTTT-AATTTTAACTATTT
11671138 ATTTTAATTTTAACTATTT
1 ATTTTAATTTTAACTATTT
11671157 -TTTTAA
1 ATTTTAA
11671163 AAAATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTAATTTTAACTATTT
Found at i:11676180 original size:20 final size:20
Alignment explanation
Indices: 11676130--11676180 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11676120 TTTTCAACAT
11676130 TAAACCCTAAACCTAAACCC
1 TAAACCCTAAACCTAAACCC
* ** * *
11676150 CAAACTATAAACCTATATCC
1 TAAACCCTAAACCTAAACCC
11676170 TAAACCCTAAA
1 TAAACCCTAAA
11676181 TATATATATT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAACCCTAAACCTAAACCC
Found at i:11676365 original size:14 final size:14
Alignment explanation
Indices: 11676348--11676386 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
11676338 GTAAAACAAA
*
11676348 AAACCACAAACTCT
1 AAACCAAAAACTCT
*
11676362 AAACCATAAACTCT
1 AAACCAAAAACTCT
11676376 AAACCAAAAAC
1 AAACCAAAAAC
11676387 AATAAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (14 bp):
AAACCAAAAACTCT
Found at i:11676519 original size:7 final size:7
Alignment explanation
Indices: 11676509--11676542 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
11676499 CCCTAAACTC
11676509 TAAACCA
1 TAAACCA
11676516 TAAACCA
1 TAAACCA
*
11676523 TAAAACA
1 TAAACCA
11676530 TAAACCA
1 TAAACCA
11676537 TAAACC
1 TAAACC
11676543 CTTAACCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCA
Found at i:11677141 original size:41 final size:41
Alignment explanation
Indices: 11677072--11677262 Score: 265
Period size: 41 Copynumber: 4.6 Consensus size: 41
11677062 TTACTTTTTT
* * * * *
11677072 GCGGCATTTTTCCAAAAGTGCCGTTAAAACCTTGATCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* *
11677113 GCGGTGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* * *
11677154 GCTGCGTTTTTCCAAAAGCGCCGCTAAAACATCAACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
11677195 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* *
11677236 GCGGCGTTTTGACCAAAAACGCCGCTA
1 GCGGCGTTTT-TCCAAAAGCGCCGCTA
11677263 CTGCTCAGTT
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 120 0.90
42 14 0.10
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (41 bp):
GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
Found at i:11681275 original size:18 final size:18
Alignment explanation
Indices: 11681248--11681290 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
11681238 CGCATAAAAG
* *
11681248 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
11681266 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
11681284 GAAAGAA
1 GAAAGAA
11681291 GGGGGAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:11693210 original size:19 final size:21
Alignment explanation
Indices: 11693182--11693225 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
11693172 AGAGCGAAAG
11693182 GAAC-GAG-AAACGGGCCAAA
1 GAACAGAGAAAACGGGCCAAA
*
11693201 -AACAGAGAAAATGGGCCAAA
1 GAACAGAGAAAACGGGCCAAA
11693221 GAACA
1 GAACA
11693226 AAATCAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 11 0.52
21 4 0.19
ACGTcount: A:0.52, C:0.18, G:0.27, T:0.02
Consensus pattern (21 bp):
GAACAGAGAAAACGGGCCAAA
Found at i:11698756 original size:208 final size:209
Alignment explanation
Indices: 11698398--11698815 Score: 793
Period size: 208 Copynumber: 2.0 Consensus size: 209
11698388 TCTTTAAAAC
* *
11698398 CTGTCTCGAAAATCATGTATTACCAAACATCTCATGATTCTCCCCTGATCGAGCATAAAAAATGA
1 CTGTCTCAAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCGAGCATAAAAAATGA
*
11698463 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTATTCCTCAACTA
66 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
*
11698528 ACAGAAATTAACTAAATAGAGGATTTAATTAAAATTTAAAAAAAACTAGGGGTAT-AATTGTAAA
131 ACAGAAATTAACTAAATAGAGGATTTAATTAAAATTTAAAAAAAACTAGGGGTATAAATTGCAAA
11698592 TAATAAAAAGTAGG
196 TAATAAAAAGTAGG
11698606 CTGTCTCAAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCGAGCATAAAAAATGA
1 CTGTCTCAAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCGAGCATAAAAAATGA
11698671 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
66 TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
11698736 ACAGAAATTAACTAAATAGAGGATTTAATTAAAATTTAAAAAAAACTAGGGGTATAAATTGCAAA
131 ACAGAAATTAACTAAATAGAGGATTTAATTAAAATTTAAAAAAAACTAGGGGTATAAATTGCAAA
11698801 TAATAAAAAGTAGG
196 TAATAAAAAGTAGG
11698815 C
1 C
11698816 CAATAAGGGT
Statistics
Matches: 205, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
208 182 0.89
209 23 0.11
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (209 bp):
CTGTCTCAAAAATCACGTATTACCAAACATCTCATGATTCTCCCCTGATCGAGCATAAAAAATGA
TTAAACACAATCAACAATCACTTCCATTACAATGAAAAATAAAATCCCAACTTACTCCTCAACTA
ACAGAAATTAACTAAATAGAGGATTTAATTAAAATTTAAAAAAAACTAGGGGTATAAATTGCAAA
TAATAAAAAGTAGG
Found at i:11700028 original size:39 final size:38
Alignment explanation
Indices: 11699945--11700039 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 38
11699935 CTTGAAACCA
*
11699945 ATTACCAGCACAAGCCTGTGGGAATTTAAACCCGGTAT
1 ATTACCAGCACAAGCCTGTGGGAATTTAAACCCGGCAT
* * * *
11699983 AATACCAGCTCGAAGCCTGTGGGACTTT-AGCCCGGACAT
1 ATTACCAGCAC-AAGCCTGTGGGAATTTAAACCCGG-CAT
11700022 ATTACCAGCACATAGCCT
1 ATTACCAGCACA-AGCCT
11700040 ACGGACCTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 16 0.34
39 31 0.66
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (38 bp):
ATTACCAGCACAAGCCTGTGGGAATTTAAACCCGGCAT
Found at i:11700071 original size:39 final size:39
Alignment explanation
Indices: 11700028--11700176 Score: 237
Period size: 39 Copynumber: 3.8 Consensus size: 39
11700018 ACATATTACC
* *
11700028 AGCACATAGCCTACGGACCTTAAGTCC-GATTATAATTCT
1 AGCACATAGCCTGCGGACCCTAAGTCCGGA-TATAATTCT
11700067 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCT
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCT
*
11700106 AGCACATAGCCTGCGGACCTTAAGTCCGGATATAATTCT
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCT
* *
11700145 AGCATATAGCCTGCGGACCCTAAGTCTGGATA
1 AGCACATAGCCTGCGGACCCTAAGTCCGGATA
11700177 AACATCACTG
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
39 101 0.98
40 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (39 bp):
AGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCT
Found at i:11700078 original size:78 final size:78
Alignment explanation
Indices: 11700011--11700168 Score: 239
Period size: 78 Copynumber: 2.0 Consensus size: 78
11700001 GTGGGACTTT
11700011 AGCCCGGACAT-ATTACCAGCACATAGCCTACGGACCTTAAGTCC-GATTATAATTCTAGCACAT
1 AGCCCGGACATAATT-CCAGCACATAGCCTACGGACCTTAAGTCCGGA-TATAATTCTAGCACAT
11700074 AGCCTGCGGACCCTA
64 AGCCTGCGGACCCTA
* * * * *
11700089 AGTCCGGATATAATTCTAGCACATAGCCTGCGGACCTTAAGTCCGGATATAATTCTAGCATATAG
1 AGCCCGGACATAATTCCAGCACATAGCCTACGGACCTTAAGTCCGGATATAATTCTAGCACATAG
11700154 CCTGCGGACCCTA
66 CCTGCGGACCCTA
11700167 AG
1 AG
11700169 TCTGGATAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
78 68 0.93
79 5 0.07
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (78 bp):
AGCCCGGACATAATTCCAGCACATAGCCTACGGACCTTAAGTCCGGATATAATTCTAGCACATAG
CCTGCGGACCCTA
Found at i:11706294 original size:51 final size:49
Alignment explanation
Indices: 11706210--11706335 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 49
11706200 AATCTGCTTT
* * * *
11706210 ACTGCAACTTCAGGGAGATAAGATTAATGGCTTGTAGCTTTAGTCTATTCC
1 ACTGCAACTTCAGGGAAATAAGATTTATAGCTTGTAGCTTTAATC--TTCC
* * *
11706261 ACTGCAACTTCAAGAAAATAAGATTTTTAGCTTGTAGCTTTAATCTTCC
1 ACTGCAACTTCAGGGAAATAAGATTTATAGCTTGTAGCTTTAATCTTCC
*
11706310 ACTACAACTTCAGGGAAATAAGATTT
1 ACTGCAACTTCAGGGAAATAAGATTT
11706336 GTTATCTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 27 0.42
51 38 0.58
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (49 bp):
ACTGCAACTTCAGGGAAATAAGATTTATAGCTTGTAGCTTTAATCTTCC
Found at i:11706345 original size:145 final size:145
Alignment explanation
Indices: 11706062--11706377 Score: 327
Period size: 145 Copynumber: 2.2 Consensus size: 145
11706052 TTTAATCTAT
* * * * ** *
11706062 TCCACTGCAAATTCGAGGAGATGAGATTTGTAGCTTGTAGCTTCAGTCTATTCCACTGCAACTTC
1 TCCACTACAACTTCAAGGAGATAAGATTAATGGCTTGTAGCTTCAGTCTATTCCACTGCAACTTC
* * * * * *
11706127 AGGGAAATAAGACTTGCTATATTAGATTTAATCCAATCCACTGCAACTTCAGAGGTATAGGATTT
66 AAGAAAATAAGACTTGCTATAGTAGATTTAATCCAATCCACTACAACTTCAGAGGAATAAGATTT
*
11706192 GTCGCTTCAATCTGC
131 GTAGCTTCAATCTGC
** * * *
11706207 TTTACTGCAACTTCAGGGAGATAAGATTAATGGCTTGTAGCTTTAGTCTATTCCACTGCAACTTC
1 TCCACTACAACTTCAAGGAGATAAGATTAATGGCTTGTAGCTTCAGTCTATTCCACTGCAACTTC
* * *
11706272 AAGAAAATAAGATTTTTAGCT-T-GTAGCTTTAAT-C-TTCCACTACAACTTCAG-GGAAATAAG
66 AAGAAAATAAGA--CTT-GCTATAGTAGATTTAATCCAATCCACTACAACTTCAGAGG-AATAAG
* *
11706332 ATTTGTTATCTTCAGTCTGC
127 ATTTG-TAGCTTCAATCTGC
*
11706352 TCCACTACAACTTTAAGGAGATAAGA
1 TCCACTACAACTTCAAGGAGATAAGA
11706378 CTTGTAACTT
Statistics
Matches: 139, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
143 2 0.01
144 24 0.17
145 98 0.71
146 9 0.06
147 3 0.02
148 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (145 bp):
TCCACTACAACTTCAAGGAGATAAGATTAATGGCTTGTAGCTTCAGTCTATTCCACTGCAACTTC
AAGAAAATAAGACTTGCTATAGTAGATTTAATCCAATCCACTACAACTTCAGAGGAATAAGATTT
GTAGCTTCAATCTGC
Found at i:11706511 original size:44 final size:44
Alignment explanation
Indices: 11706454--11706719 Score: 271
Period size: 44 Copynumber: 5.9 Consensus size: 44
11706444 ATCTGCTATT
*
11706454 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTAGTAGC
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTAGTAGC
* * *
11706498 TTCAATCTACTCCATTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAAC
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGA--T-T-A---GTAGC
* ** ** * * *
11706549 TTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTTGCTATC
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTAG-TAGC
* * * *
11706594 TTCAATCTACTCCACTACAACTTCAGGGAGATGAGATTTGTGGT
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTAGTAGC
* * *
11706638 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTAGTGGC
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTAGTAGC
* *
11706682 TTCAATCTGCTCTACTACAACTTCAGGGAGATAAGATT
1 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATT
11706720 CTTCATAATG
Statistics
Matches: 183, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
44 108 0.59
45 36 0.20
46 1 0.01
47 1 0.01
48 2 0.01
49 1 0.01
51 34 0.19
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTAGTAGC
Found at i:11706610 original size:140 final size:140
Alignment explanation
Indices: 11706408--11706675 Score: 387
Period size: 140 Copynumber: 1.9 Consensus size: 140
11706398 AGGTTTATAG
* * * *
11706408 CTTTAATCTGCTTTACTATAACTTCAGAAAGATAGGATCTGCTATTTTCAATCTGCTCCACTACA
1 CTTTAATCTGCTTCACTATAACTTCAGAAAGATAAGATCTGCTATCTTCAATCTACTCCACTACA
*
11706473 ACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCATTGCAACTTCAGGGAGATAAGATTTG
66 ACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG
11706538 TAACTTGTAA
131 TAACTTGTAA
* * *
11706548 CTTTAATCTG-TTCCACTGTAACTTCAGGGAA-ATAAGATTTGCTATCTTCAATCTACTCCACTA
1 CTTTAATCTGCTT-CACTATAACTTCA-GAAAGATAAGATCTGCTATCTTCAATCTACTCCACTA
* * * * *
11706611 CAACTTCAGGGAGATGAGATTTGTGGTTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
64 CAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
11706676 AGTGGCTTCA
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
139 2 0.02
140 108 0.96
141 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (140 bp):
CTTTAATCTGCTTCACTATAACTTCAGAAAGATAAGATCTGCTATCTTCAATCTACTCCACTACA
ACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG
TAACTTGTAA
Found at i:11711410 original size:48 final size:48
Alignment explanation
Indices: 11711349--11711721 Score: 602
Period size: 48 Copynumber: 7.8 Consensus size: 48
11711339 TGTTACAACA
* * *
11711349 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
11711397 TTCACATTTGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
11711445 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
11711493 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
11711541 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
11711589 TTCACATTCGTCATTCGGCTTTACCACATATATATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
11711637 TTCACATTAGCCATTCGGCTTTACCACATACACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
11711685 TTCACATTAGCCATTCGGCTTCACCACACATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATAT
11711722 ATTTATCTTG
Statistics
Matches: 303, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 303 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:11726523 original size:46 final size:47
Alignment explanation
Indices: 11726456--11726563 Score: 163
Period size: 46 Copynumber: 2.4 Consensus size: 47
11726446 TTTTTCTGTA
11726456 CATTCTTAGTCTAGATAATTAGTTAATTAAAA-AAAACCCCATTATT
1 CATTCTTAGTCTAGATAATTAGTTAATTAAAACAAAACCCCATTATT
*
11726502 CATTCTTAGTTTAGATAATTAGTTAATTAAAACAAAA-CCC--TATT
1 CATTCTTAGTCTAGATAATTAGTTAATTAAAACAAAACCCCATTATT
*
11726546 -ATTCTTAGGCTAGATAAT
1 CATTCTTAGTCTAGATAAT
11726564 AAAAGATAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
43 16 0.28
44 4 0.07
46 34 0.59
47 4 0.07
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (47 bp):
CATTCTTAGTCTAGATAATTAGTTAATTAAAACAAAACCCCATTATT
Found at i:11749553 original size:103 final size:104
Alignment explanation
Indices: 11749374--11749637 Score: 422
Period size: 103 Copynumber: 2.5 Consensus size: 104
11749364 ACCGTTATTA
* * * *
11749374 GTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAA
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
** *
11749439 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATACG
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
*
11749477 GTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
11749542 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
* **
11749581 GTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
11749638 TTTATGTACA
Statistics
Matches: 148, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 82 0.55
104 66 0.45
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (104 bp):
GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
Found at i:11755431 original size:4 final size:4
Alignment explanation
Indices: 11755422--11755450 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
11755412 TTAGCTTTCA
11755422 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
11755451 AATATAAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Done.