Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 119 of 147
Found at i:21339454 original size:21 final size:20
Alignment explanation
Indices: 21339428--21339466 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21339418 AAAAAATAAT
21339428 TATATATATTTTATTATTTTA
1 TATATATATTTTA-TATTTTA
*
21339449 TATATATTTTTTATATTT
1 TATATATATTTTATATTT
21339467 CAATTACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATATATATTTTATATTTTA
Found at i:21347228 original size:24 final size:23
Alignment explanation
Indices: 21347192--21347237 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
21347182 TATATTTTAA
21347192 TTTTAATTATCAA-ATATAAATAT
1 TTTTAATTATCAATAT-TAAATAT
*
21347215 TTTTAATATGTCAATATTAAATA
1 TTTTAAT-TATCAATATTAAATA
21347238 GTATTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 11 0.55
25 2 0.10
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTAATTATCAATATTAAATAT
Found at i:21347329 original size:20 final size:20
Alignment explanation
Indices: 21347301--21347339 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21347291 ATAATAATAA
* *
21347301 ATATTAATATTATTTTAATT
1 ATATAAATAATATTTTAATT
21347321 ATATAAATAATATTTTAAT
1 ATATAAATAATATTTTAAT
21347340 AACAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATAAATAATATTTTAATT
Found at i:21347356 original size:47 final size:49
Alignment explanation
Indices: 21347284--21347381 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 49
21347274 ATATTGGTAT
* *
21347284 TATTTTAATAATAATAAATATTAATATTATTTTAATTAT-ATA-AATAA
1 TATTTTAATAAAAATAAATATTAATAATATTTTAATTATGATATAATAA
**
21347331 TATTTTAATAACAAATATAA-A-TAATAATATTTTTGTTATGATATAATAA
1 TATTTTAATAA-AAATA-AATATTAATAATATTTTAATTATGATATAATAA
21347380 TA
1 TA
21347382 AATAATTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
47 26 0.60
48 8 0.19
49 9 0.21
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (49 bp):
TATTTTAATAAAAATAAATATTAATAATATTTTAATTATGATATAATAA
Found at i:21347397 original size:21 final size:21
Alignment explanation
Indices: 21347382--21347425 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
21347372 TATAATAATA
*
21347382 AATAATTTTAATATAAGATAT
1 AATAATTTTAATATAAAATAT
*
21347403 AATTATTTTAATAATATAAATAT
1 AATAATTTTAAT-ATA-AAATAT
21347426 TTTTGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATAATTTTAATATAAAATAT
Found at i:21347540 original size:29 final size:30
Alignment explanation
Indices: 21347456--21347546 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 30
21347446 ATATTACTAT
* * * *
21347456 TTTTAATATTATT-ATATTAATAAAAAATA
1 TTTTAAGAATATTAATATAAATAATAAATA
* **
21347485 TTTTAAGAATA-GAA-ATAATATTTTAAATA
1 TTTTAAGAATATTAATATAA-ATAATAAATA
21347514 TTTTAA-AATATTAATATAAATAATAAATA
1 TTTTAAGAATATTAATATAAATAATAAATA
21347543 TTTT
1 TTTT
21347547 TTAAGTGTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
28 7 0.15
29 37 0.77
30 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTTAAGAATATTAATATAAATAATAAATA
Found at i:21347729 original size:13 final size:14
Alignment explanation
Indices: 21347711--21347741 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
21347701 CAAAATTTAA
21347711 AATTTTTAAAAAT-
1 AATTTTTAAAAATC
21347724 AATTTTTAAAAATC
1 AATTTTTAAAAATC
21347738 AATT
1 AATT
21347742 CTCTCAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTTTAAAAATC
Found at i:21349579 original size:19 final size:19
Alignment explanation
Indices: 21349555--21349593 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21349545 CGTTTATATG
21349555 TTATTTAATCAATATAATT
1 TTATTTAATCAATATAATT
* *
21349574 TTATTTTATCAATATCATT
1 TTATTTAATCAATATAATT
21349593 T
1 T
21349594 ATTAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTTAATCAATATAATT
Found at i:21349899 original size:30 final size:31
Alignment explanation
Indices: 21349839--21349899 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
21349829 ATAGTATATA
* *
21349839 ATTTGAAAGTTTAGAATATAAATGATACATT
1 ATTTAAAAGTTTAGAATATAAATAATACATT
*
21349870 ATTTAAAATTTTAGAATAT-AATAATACATT
1 ATTTAAAAGTTTAGAATATAAATAATACATT
21349900 TTATTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTTAAAAGTTTAGAATATAAATAATACATT
Found at i:21357776 original size:2 final size:2
Alignment explanation
Indices: 21357769--21357796 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21357759 AATGCAAAAC
21357769 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
21357797 GAATCGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21360461 original size:15 final size:16
Alignment explanation
Indices: 21360436--21360465 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21360426 ATAGCCCATC
21360436 TGTTGCTTTTTTTTAT
1 TGTTGCTTTTTTTTAT
21360452 TGTT-CTTTTTTTTA
1 TGTTGCTTTTTTTTA
21360466 GGGAAGGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.10, T:0.77
Consensus pattern (16 bp):
TGTTGCTTTTTTTTAT
Found at i:21364437 original size:19 final size:19
Alignment explanation
Indices: 21364413--21364489 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
21364403 GTAATGAGCC
21364413 AAATAATAATTAAAGATAA
1 AAATAATAATTAAAGATAA
***
21364432 AAATAAT-A-T---GAGCC
1 AAATAATAATTAAAGATAA
21364446 AAATAATAATTAAAGATAA
1 AAATAATAATTAAAGATAA
*
21364465 AAATAATAATAATAAG-TAA
1 AAATAATAATTA-AAGATAA
21364484 AAATAA
1 AAATAA
21364490 AATGAAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 29 0.64
20 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (19 bp):
AAATAATAATTAAAGATAA
Found at i:21364438 original size:16 final size:16
Alignment explanation
Indices: 21364417--21364471 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
21364407 TGAGCCAAAT
21364417 AATAATTAAAGATAAA
1 AATAATTAAAGATAAA
* **
21364433 AATAA-TATGAGCCAAA
1 AATAATTA-AAGATAAA
21364449 TAATAATTAAAGATAAA
1 -AATAATTAAAGATAAA
21364466 AATAAT
1 AATAAT
21364472 AATAATAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 2 0.07
16 16 0.53
17 10 0.33
18 2 0.07
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (16 bp):
AATAATTAAAGATAAA
Found at i:21364447 original size:33 final size:33
Alignment explanation
Indices: 21364406--21364472 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
21364396 ATTTAAAGTA
21364406 ATGAGCCAAATAATAATTAAAGATAAAAATAAT
1 ATGAGCCAAATAATAATTAAAGATAAAAATAAT
21364439 ATGAGCCAAATAATAATTAAAGATAAAAATAAT
1 ATGAGCCAAATAATAATTAAAGATAAAAATAAT
21364472 A
1 A
21364473 ATAATAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (33 bp):
ATGAGCCAAATAATAATTAAAGATAAAAATAAT
Found at i:21368593 original size:18 final size:18
Alignment explanation
Indices: 21368551--21368585 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21368541 CATGTCTAAA
21368551 AAATCAATATATAAAGAG
1 AAATCAATATATAAAGAG
21368569 AAATCAATATATAAAGA
1 AAATCAATATATAAAGA
21368586 ATAATCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (18 bp):
AAATCAATATATAAAGAG
Found at i:21372680 original size:19 final size:19
Alignment explanation
Indices: 21372652--21372695 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
21372642 GTAATAAGCG
*
21372652 AAATAATAATTA-AAGATAA
1 AAATAATAATAATAAG-TAA
*
21372671 AAATAGTAATAATAAGTAA
1 AAATAATAATAATAAGTAA
21372690 AAATAA
1 AAATAA
21372696 AAAATCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (19 bp):
AAATAATAATAATAAGTAA
Found at i:21372726 original size:20 final size:20
Alignment explanation
Indices: 21372689--21372733 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
21372679 ATAATAAGTA
**
21372689 AAAATAAAAAATCTAAAAAT
1 AAAATAAAAAATAAAAAAAT
21372709 AAAATAAAAAATAAAAAAAT
1 AAAATAAAAAATAAAAAAAT
*
21372729 CAAAT
1 AAAAT
21372734 CAAATCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAATAAAAAATAAAAAAAT
Found at i:21382112 original size:10 final size:10
Alignment explanation
Indices: 21382097--21382134 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
21382087 CTATAAGGTT
21382097 ATGTTGTTCA
1 ATGTTGTTCA
21382107 ATGTTGTTCA
1 ATGTTGTTCA
21382117 ATGTTGTTCA
1 ATGTTGTTCA
*
21382127 AAGTTGTT
1 ATGTTGTT
21382135 ACAAAATGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (10 bp):
ATGTTGTTCA
Found at i:21383296 original size:131 final size:131
Alignment explanation
Indices: 21383051--21383339 Score: 350
Period size: 131 Copynumber: 2.2 Consensus size: 131
21383041 TTATCTTGGT
* * ** * ** *
21383051 AATTGCCTTCATAAAGGTTTAGCTTGGTCACCTTAGCCAAAAAGCTCATATTGATAAATTACATT
1 AATTG-CTTTATAAAGGCTTAGCTTAATCACCTCAGCCAAAAAGCTCATATCAACAAATTACATT
* * * * *
21383116 CATAAATACCTACTTTAACAAAATAGTTTAATTCAACAAATTATCTTCATAAAAGCTCAATTCAG
65 CATAAATACCTACTTTAACAAAAGAGTTCAATTCAACAAATTATCTTCATAAAAGCCCAACTCAA
21383181 C-
130 CA
* *
21383182 AATTAGCTTTATAAAGGCTTAGCTTAATCACCTCGGCCAAAAAGCTCATATCAACAAATTACCTT
1 AATT-GCTTTATAAAGGCTTAGCTTAATCACCTCAGCCAAAAAGCTCATATCAACAAATTACATT
* * *
21383247 CATAAA-AGCT-CATTTCAATAAAAGAGTTCAATTCAACAAATTATTTTCATAAAAGCCCAACTC
65 CATAAATACCTAC-TTT-AACAAAAGAGTTCAATTCAACAAATTATCTTCATAAAAGCCCAACTC
21383310 AACA
128 AACA
21383314 AATTGCTTTATTAAAGGCTTAGCTTA
1 AATTGCTTTA-TAAAGGCTTAGCTTA
21383340 GCTACCTTGT
Statistics
Matches: 135, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
129 1 0.01
130 6 0.04
131 108 0.80
132 20 0.15
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (131 bp):
AATTGCTTTATAAAGGCTTAGCTTAATCACCTCAGCCAAAAAGCTCATATCAACAAATTACATTC
ATAAATACCTACTTTAACAAAAGAGTTCAATTCAACAAATTATCTTCATAAAAGCCCAACTCAAC
A
Found at i:21388951 original size:98 final size:101
Alignment explanation
Indices: 21388849--21389120 Score: 270
Period size: 98 Copynumber: 2.7 Consensus size: 101
21388839 AAAAGAGTTA
* * *
21388849 AGCTTGATCAAATTTCATTAATAAAATATTAATTTCACTACATTTTCTTAATAAAGGATTAGCTT
1 AGCTTGATCAAATTTCATTAATAAAGTATTAATTTCGCTATATTTTCTTAATAAAGGATTAG-TT
* * * * *
21388914 -AATTAAAGGATATCAATTTGG-TCAA-AAAAT-CTC
65 CAACTAAAAGAGATCAATTCGGCTAAACAAAATGCTC
** * * *
21388947 AGCTT-AGTCAAATTTTTTTAATAAAGTATCAGTTTTGGC-ATATTTTCTTAATAAAGGATTAGT
1 AGCTTGA-TCAAATTTCATTAATAAAGTATTA-ATTTCGCTATATTTTCTTAATAAAGGATTAGT
*
21389010 TCAACTAAAAGAGATCAGTTCGGCTAAACAAAATGCTC
64 TCAACTAAAAGAGATCAATTCGGCTAAACAAAATGCTC
* * * * * *
21389048 AACTCGATCAAATTTCATTGACAAAGTATTAGTTTTGCTATA-TTTCTTTAATAAAGGATTAGTT
1 AGCTTGATCAAATTTCATTAATAAAGTATTAATTTCGCTATATTTTC-TTAATAAAGGATTAGTT
*
21389112 CAGCTAAAA
65 CAACTAAAA
21389121 ACGATTAGTT
Statistics
Matches: 141, Mismatches: 24, Indels: 15
0.78 0.13 0.08
Matches are distributed among these distances:
97 3 0.02
98 63 0.45
99 7 0.05
100 14 0.10
101 53 0.38
102 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (101 bp):
AGCTTGATCAAATTTCATTAATAAAGTATTAATTTCGCTATATTTTCTTAATAAAGGATTAGTTC
AACTAAAAGAGATCAATTCGGCTAAACAAAATGCTC
Found at i:21389608 original size:98 final size:98
Alignment explanation
Indices: 21389399--21389609 Score: 210
Period size: 98 Copynumber: 2.2 Consensus size: 98
21389389 TTAATAAAGG
* * * * * * *
21389399 ATTAGCTTGACCAAAAGAAATTAGCTTAGCCAAATTTTATTGATAAAATATCAGTTTTATCTTAT
1 ATTAGTTTGGCCAAAAGAAATTAGCTTAACCAAATTTCATTAATAAAATATCAGTTTCATCATAT
* **
21389464 TTCTTTAATAAAAGATTAGCTTGGCTAAAACAA
66 TTCTTTAATAAAAGATTAACTAAGCTAAAACAA
* * * * * * *
21389497 ATAAACTCT-GCCAAAAG-AGTTCAGCTTAACTAAATTTCATTAATAAAGTATTAGTTTCATCAT
1 AT-TAGTTTGGCCAAAAGAAATT-AGCTTAACCAAATTTCATTAATAAAATATCAGTTTCATCAT
* * *
21389560 ATTTTTTTAATAAAGGATTAACTAAGCTAAAAGAA
64 ATTTCTTTAATAAAAGATTAACTAAGCTAAAACAA
21389595 ATTAGTTTGGCCAAA
1 ATTAGTTTGGCCAAA
21389610 TTTTATTGAT
Statistics
Matches: 87, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
97 6 0.07
98 79 0.91
99 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (98 bp):
ATTAGTTTGGCCAAAAGAAATTAGCTTAACCAAATTTCATTAATAAAATATCAGTTTCATCATAT
TTCTTTAATAAAAGATTAACTAAGCTAAAACAA
Found at i:21389640 original size:79 final size:79
Alignment explanation
Indices: 21389528--21389688 Score: 200
Period size: 79 Copynumber: 2.0 Consensus size: 79
21389518 CAGCTTAACT
*
21389528 AAATTTCATTAATAAAGTATTAGTTTCATCATATTT-TTTTAATAAAGGATTAACTAAGCTAAAA
1 AAATTTCATTAATAAAGTATTAGTTTCATCATATTTCCTTT-ATAAAGGATTAACTAAGCTAAAA
*
21389592 GAAATTAGTTTGGCC
65 GAAATCAGTTTGGCC
* * * * * *
21389607 AAATTTTATTGATAAAGTATTAGCTTT-GTCATATTTCCTTTATAAGGGATTAGCTAGGCTAAAA
1 AAATTTCATTAATAAAGTATTAG-TTTCATCATATTTCCTTTATAAAGGATTAACTAAGCTAAAA
* *
21389671 GAGATCAGTTTGGTC
65 GAAATCAGTTTGGCC
21389686 AAA
1 AAA
21389689 AAAGCTCAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 64 0.91
80 6 0.09
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (79 bp):
AAATTTCATTAATAAAGTATTAGTTTCATCATATTTCCTTTATAAAGGATTAACTAAGCTAAAAG
AAATCAGTTTGGCC
Found at i:21389709 original size:177 final size:177
Alignment explanation
Indices: 21389313--21389730 Score: 486
Period size: 177 Copynumber: 2.4 Consensus size: 177
21389303 TACCTTAGTC
* **
21389313 AAAAGAGATCAGTTTGGCCAAAAGAGTTCAA-TAAGGCTAAATTTTC-TTGGTAAAGTATTAGCT
1 AAAAGAGATCAGTTTGGCCAAAAGAGTTCAACTTA-GCTAAA-TTTCATTAATAAAGTATTAGCT
* *
21389376 TCACCATATTTTTTTAATAAAGGATTAGCTTGACCAAAAGAAATTAGCTTAGCCAAATTTTATTG
64 TCACCATATTTTTTTAATAAAGGATTAACTAGACCAAAAGAAATTAGCTTAGCCAAATTTTATTG
* * *
21389441 ATAAAATATCAGTTTTATCTTATTTCTTTAATAAAAGATTAGCTTGGCT
129 ATAAAATATCAGCTTTATCATATTTCTTTAATAAAAGATTAGCTAGGCT
* * * * * * * *
21389490 AAAACAAATAAACTCT-GCCAAAAGAGTTCAGCTTAACTAAATTTCATTAATAAAGTATTAGTTT
1 AAAAGAGAT-CAGTTTGGCCAAAAGAGTTCAACTTAGCTAAATTTCATTAATAAAGTATTAGCTT
* * * *
21389554 CATCATATTTTTTTAATAAAGGATTAACTA-AGCTAAAAGAAATTAGTTTGGCCAAATTTTATTG
65 CACCATATTTTTTTAATAAAGGATTAACTAGA-CCAAAAGAAATTAGCTTAGCCAAATTTTATTG
* * * **
21389618 ATAAAGTATTAGCTTTGTCATATTTCCTTT-ATAAGGGATTAGCTAGGCT
129 ATAAAATATCAGCTTTATCATATTT-CTTTAATAAAAGATTAGCTAGGCT
* * * * *
21389667 AAAAGAGATCAGTTTGGTCAAAAAAGCTCAACTTAGCTAAATTTGATTAATAAAATATTAGCTT
1 AAAAGAGATCAGTTTGGCCAAAAGAGTTCAACTTAGCTAAATTTCATTAATAAAGTATTAGCTT
21389731 TTTCATATGT
Statistics
Matches: 197, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
176 8 0.04
177 180 0.91
178 9 0.05
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (177 bp):
AAAAGAGATCAGTTTGGCCAAAAGAGTTCAACTTAGCTAAATTTCATTAATAAAGTATTAGCTTC
ACCATATTTTTTTAATAAAGGATTAACTAGACCAAAAGAAATTAGCTTAGCCAAATTTTATTGAT
AAAATATCAGCTTTATCATATTTCTTTAATAAAAGATTAGCTAGGCT
Found at i:21389885 original size:98 final size:97
Alignment explanation
Indices: 21389609--21389915 Score: 307
Period size: 98 Copynumber: 3.1 Consensus size: 97
21389599 GTTTGGCCAA
* * * * * *
21389609 ATTTTATTGATAAAGTATTAGCTTTGTCATATTTCCTTTATAAGGGATTAGC-TAGGCTAAAAGA
1 ATTTCATTGATAAAATATTAGCTTTATCATATTTCCTTAATAAAGGATTAGCTTA-GCCAAAAGA
* * *
21389673 GATCAGTT-TGGTCAAAAAAGCTCAACTTAGCTAA
65 GATC--TTCTGGTCAAAAGAGCTTAACTTAGCTAG
* * * * * * **
21389707 ATTTGATTAATAAAATATTAGCTTTTTCATATGTCATTAATAAAAGATTAAATTAGCCAAAAGAG
1 ATTTCATTGATAAAATATTAGCTTTATCATATTTCCTTAATAAAGGATTAGCTTAGCCAAAAGAG
** *
21389772 ATCAACTTGGTCAAAAGAGCTTAGC-TATGCTAG
66 ATCTTC-TGGTCAAAAGAGCTTAACTTA-GCTAG
*
21389805 ATTTCATTGATAAAATATTAGCTTTATCATATTTCCTTAATAAAGGATTAGCTTAGCCAAAATAG
1 ATTTCATTGATAAAATATTAGCTTTATCATATTTCCTTAATAAAGGATTAGCTTAGCCAAAAGAG
* ** *
21389870 ATTTTCTCGACCAAAAGAGC-TAACTTAGTTAG
66 ATCTTCT-GGTCAAAAGAGCTTAACTTAGCTAG
21389902 ATTTCATTGATAAA
1 ATTTCATTGATAAA
21389916 TTACTATGTT
Statistics
Matches: 169, Mismatches: 34, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
97 24 0.14
98 143 0.85
99 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (97 bp):
ATTTCATTGATAAAATATTAGCTTTATCATATTTCCTTAATAAAGGATTAGCTTAGCCAAAAGAG
ATCTTCTGGTCAAAAGAGCTTAACTTAGCTAG
Found at i:21390508 original size:45 final size:44
Alignment explanation
Indices: 21390459--21390559 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 44
21390449 ATATCTTTTC
* *
21390459 TTTTTAATTTCTAAAATTTTCA-CAATTTGGGTCTATTTAGAAATT
1 TTTTTTATTTCTAAAATTTTCATC-ATTTGAGTCTATTTAG-AATT
*
21390504 TTTTTTATTTCTAAATTTTTCATCATTTGAGTCTATTTAGAATT
1 TTTTTTATTTCTAAAATTTTCATCATTTGAGTCTATTTAGAATT
21390548 TTTTTTATTTCT
1 TTTTTTATTTCT
21390560 CTTTGGAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 16 0.31
45 35 0.67
46 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.58
Consensus pattern (44 bp):
TTTTTTATTTCTAAAATTTTCATCATTTGAGTCTATTTAGAATT
Found at i:21391003 original size:14 final size:14
Alignment explanation
Indices: 21390986--21391016 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
21390976 TAATACCAAA
21390986 AAAATGGCTTGGCT
1 AAAATGGCTTGGCT
21391000 AAAATGGCTTGGCT
1 AAAATGGCTTGGCT
21391014 AAA
1 AAA
21391017 GACATAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (14 bp):
AAAATGGCTTGGCT
Found at i:21392054 original size:43 final size:43
Alignment explanation
Indices: 21391958--21392300 Score: 287
Period size: 43 Copynumber: 7.9 Consensus size: 43
21391948 ACATAAAAAT
* * * *
21391958 TCCTCTAAACAGAGGCTTC-ACAACTTTTAAGAAATAAATAAGGC
1 TCCTCTAAACAGAGGC-TCAACGACTTTGAA-AAATAAACAAAGC
* * * *
21392002 TACTTTAAGCAGAGGCTCAACGACTTTGAAAAATAAGCAAAGC
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGC
* * * * * *
21392045 TCCTCTAAGCAAAGGTTCAATGCCTTTTAAAAAATAAACAAAGC
1 TCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAATAAACAAAGC
** *
21392089 TTTTCTAAACAGAGGCTCAATC-ACGTTGAAAAATAAACAAAGC
1 TCCTCTAAACAGAGGCTCAA-CGACTTTGAAAAATAAACAAAGC
* ** * * * * *
21392132 TCTTCTAAGTAGAGGCTCAATGATTTTTAAAAAAAATAAATAAGGC
1 TCCTCTAAACAGAGGCTCAACGA-CTTT--GAAAAATAAACAAAGC
* *
21392178 TCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAA-TAAGAC
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAG-C
* * * * *
21392221 TCTTCTAAACAGAGGCTCAACAACTTTAAAAAATAAATAAAAC
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGC
* *
21392264 TCCTATAAACAGAGGCTCAACAACTTTGAAAAATAAA
1 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
21392301 GCTCCTTGAT
Statistics
Matches: 240, Mismatches: 50, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
42 2 0.01
43 143 0.60
44 59 0.25
45 3 0.01
46 33 0.14
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (43 bp):
TCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGC
Found at i:21392211 original size:89 final size:87
Alignment explanation
Indices: 21391982--21392300 Score: 347
Period size: 87 Copynumber: 3.7 Consensus size: 87
21391972 GCTTCACAAC
* * * * * *
21391982 TTTTAAGAAATAAATAAGGCTACTTTAAGCAGAGGCTCAACGACTTTGAAAAATAAGCAAAGCTC
1 TTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTC
* * * **
21392047 CTCTAAGCAAAGGTTCAATGCC
66 TTCTAAGCAGAGGCTCAATGAA
* ** *
21392069 TTTTAAAAAATAAACAAAGCTTTTCTAAACAGAGGCTCAATC-ACGTTGAAAAATAAACAAAGCT
1 TTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAA-CGACTTTGAAAAATAAACAAAGCT
* *
21392133 CTTCTAAGTAGAGGCTCAATGAT
65 CTTCTAAGCAGAGGCTCAATGAA
* * *
21392156 TTTTAAAAAAAATAAATAAGGCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAA-TAAGA
1 TTTT--AAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAG-
* *
21392220 CTCTTCTAAACAGAGGCTCAA-CAA
63 CTCTTCTAAGCAGAGGCTCAATGAA
* * * *
21392244 CTTTAAAAAATAAATAAAACTCCTATAAACAGAGGCTCAACAACTTTGAAAAATAAA
1 TTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
21392301 GCTCCTTGAT
Statistics
Matches: 195, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
86 48 0.25
87 74 0.38
88 8 0.04
89 65 0.33
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.24
Consensus pattern (87 bp):
TTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTC
TTCTAAGCAGAGGCTCAATGAA
Found at i:21393778 original size:26 final size:26
Alignment explanation
Indices: 21393749--21393814 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
21393739 AATTTGAGTC
*
21393749 TTTATTTTCTC-TTTATTTATATTTTT
1 TTTATTTTCTCATTT-TGTATATTTTT
*
21393775 TTTATTTTCTCATTTTGTCTATTTTT
1 TTTATTTTCTCATTTTGTATATTTTT
21393801 TTT-TTTTC-CATTTT
1 TTTATTTTCTCATTTT
21393815 TTCATTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 6 0.16
25 5 0.14
26 23 0.62
27 3 0.08
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTATTTTCTCATTTTGTATATTTTT
Found at i:21393798 original size:32 final size:32
Alignment explanation
Indices: 21393762--21393838 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
21393752 ATTTTCTCTT
21393762 TATTTATATTTTTTTT-ATTTTCTCATTTTGTC
1 TATTTATATTTTTTTTCATTTTCTCATTTT-TC
*
21393794 TATTT-T-TTTTTTTTCCATTTTTTCATTTTTC
1 TATTTATATTTTTTTT-CATTTTCTCATTTTTC
21393825 T-TTCTA-ATTTTTTT
1 TATT-TATATTTTTTT
21393839 CATCCATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
30 10 0.26
31 5 0.13
32 24 0.62
ACGTcount: A:0.13, C:0.10, G:0.01, T:0.75
Consensus pattern (32 bp):
TATTTATATTTTTTTTCATTTTCTCATTTTTC
Found at i:21393806 original size:24 final size:24
Alignment explanation
Indices: 21393771--21393823 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
21393761 TTATTTATAT
21393771 TTTTTTTA-TTTTCTCATTTTGTCTA
1 TTTTTTTATTTTTC-CATTTTGTC-A
*
21393796 TTTTTTT-TTTTTCCATTTTTTCA
1 TTTTTTTATTTTTCCATTTTGTCA
21393819 TTTTT
1 TTTTT
21393824 CTTTCTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.23
24 8 0.31
25 12 0.46
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTTTTTATTTTTCCATTTTGTCA
Found at i:21394538 original size:31 final size:32
Alignment explanation
Indices: 21394467--21394531 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
21394457 AACAAAGATA
*
21394467 AACTCATGGATCTTTATAAAGGACTGCATATCT
1 AACTCATTGATCTTTATAAAGGAC-GCATATCT
21394500 AACTCATTGATCTTTATAAAGGAC-CATATCT
1 AACTCATTGATCTTTATAAAGGACGCATATCT
21394531 A
1 A
21394532 TTTCATTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 8 0.26
33 23 0.74
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
AACTCATTGATCTTTATAAAGGACGCATATCT
Found at i:21400055 original size:46 final size:44
Alignment explanation
Indices: 21400005--21400104 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 44
21399995 ATATCTTCTC
* * *
21400005 TTTTTAATTTCTAAATTTTTCA-CATTTTGGGCCTATTTAGAAAAT
1 TTTTTTATTTCTAAAATTTTCACCA-TTTAGGCCTATTTAG-AAAT
**
21400050 TTTTTTATTTCTAAAATTTTCACCATTTAGGTTTATTTAGAAA-
1 TTTTTTATTTCTAAAATTTTCACCATTTAGGCCTATTTAGAAAT
21400093 TTTTTTATTTCT
1 TTTTTTATTTCT
21400105 CTTTGGAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 12 0.24
44 3 0.06
45 32 0.65
46 2 0.04
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (44 bp):
TTTTTTATTTCTAAAATTTTCACCATTTAGGCCTATTTAGAAAT
Found at i:21400666 original size:29 final size:29
Alignment explanation
Indices: 21400631--21400712 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
21400621 ACTTGGCTAA
* *
21400631 ACTCGGTTCGGTTGAAGGCCTTGGCTGTG
1 ACTCGGTTCGGCTAAAGGCCTTGGCTGTG
*
21400660 ACTCGGTTTGGCTAAAGGCCTTGGCTGTG
1 ACTCGGTTCGGCTAAAGGCCTTGGCTGTG
** *
21400689 ACTCGGTTTAGCTCAAGGCCTTGG
1 ACTCGGTTCGGCTAAAGGCCTTGG
21400713 TTGGAACACG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.13, C:0.22, G:0.34, T:0.30
Consensus pattern (29 bp):
ACTCGGTTCGGCTAAAGGCCTTGGCTGTG
Found at i:21401341 original size:19 final size:17
Alignment explanation
Indices: 21401317--21401351 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
21401307 TCTTTTAAAC
21401317 TTCAACTTCAAACCTCAAG
1 TTCAAC-TCAAA-CTCAAG
21401336 TTCAACTCAAACTCAA
1 TTCAACTCAAACTCAA
21401352 ACAAGTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.40, C:0.31, G:0.03, T:0.26
Consensus pattern (17 bp):
TTCAACTCAAACTCAAG
Found at i:21401610 original size:20 final size:20
Alignment explanation
Indices: 21401552--21401612 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
21401542 TTTCTTTAAC
21401552 AAAAGATTAGCTC-AACAAA
1 AAAAGATTAGCTCGAACAAA
* *
21401571 AAATAGATTAGCTTG-GCAAA
1 AAA-AGATTAGCTCGAACAAA
* *
21401591 AAAATATTAGCTCGACCAAA
1 AAAAGATTAGCTCGAACAAA
21401611 AA
1 AA
21401613 CATTCAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 12 0.35
20 22 0.65
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (20 bp):
AAAAGATTAGCTCGAACAAA
Found at i:21401611 original size:19 final size:19
Alignment explanation
Indices: 21401552--21401612 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
21401542 TTTCTTTAAC
* *
21401552 AAAAGATTAGCTC-AACAA
1 AAAATATTAGCTCGACCAA
* * *
21401570 AAAATAGATTAGCTTGGCAAA
1 AAAAT--ATTAGCTCGACCAA
21401591 AAAATATTAGCTCGACCAA
1 AAAATATTAGCTCGACCAA
21401610 AAA
1 AAA
21401613 CATTCAGTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
18 4 0.12
19 14 0.44
20 7 0.22
21 7 0.22
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (19 bp):
AAAATATTAGCTCGACCAA
Found at i:21402193 original size:30 final size:30
Alignment explanation
Indices: 21402123--21402198 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
21402113 AATTTTTTTC
*
21402123 ATAAAGGCTTAGCTCAAGAAAAATGCTTTA
1 ATAAAGGCTTAGCTCGAGAAAAATGCTTTA
* * * *
21402153 AAAAAAGCTTAGCTCGATAAAATTGCCTTT-
1 ATAAAGGCTTAGCTCGAGAAAAATG-CTTTA
*
21402183 ATAAAGGCTTAACTCG
1 ATAAAGGCTTAGCTCG
21402199 GCAATGAGCT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 33 0.89
31 4 0.11
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (30 bp):
ATAAAGGCTTAGCTCGAGAAAAATGCTTTA
Found at i:21403975 original size:21 final size:22
Alignment explanation
Indices: 21403927--21403975 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
21403917 TTTAATTTTC
*
21403927 ATTTT-GATAACTTTTGATAAA
1 ATTTTGGATAACTTTCGATAAA
*
21403948 ATTTTGGA-AACTTTCGATACA
1 ATTTTGGATAACTTTCGATAAA
21403969 ATTTTGG
1 ATTTTGG
21403976 TAATCTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (22 bp):
ATTTTGGATAACTTTCGATAAA
Found at i:21404169 original size:16 final size:17
Alignment explanation
Indices: 21404140--21404172 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
21404130 TAAAATTTAG
21404140 AATTTAATTATAAAATA
1 AATTTAATTATAAAATA
21404157 AATTTAA-TATAAAATA
1 AATTTAATTATAAAATA
21404173 TCTTATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAATTATAAAATA
Found at i:21405901 original size:4 final size:4
Alignment explanation
Indices: 21405892--21405933 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
21405882 TGAACTCAAG
* *
21405892 ATAC ATAC ATAT ATAC ATAC ATAC ATAC AAAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
21405934 GGATACATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:21406664 original size:22 final size:22
Alignment explanation
Indices: 21406645--21406828 Score: 128
Period size: 22 Copynumber: 8.4 Consensus size: 22
21406635 GGTATACTGT
21406645 TAAATTATGAATGATTTACTAC
1 TAAATTATGAATGATTTACTAC
** * *
21406667 TAAATTACCATTGATTTAGTAC
1 TAAATTATGAATGATTTACTAC
* * *
21406689 TCATTTATAAATGATTTACTA-
1 TAAATTATGAATGATTTACTAC
**
21406710 TAAAGTTATGAACAATTTACTAC
1 TAAA-TTATGAATGATTTACTAC
*
21406733 TAAATTATTAATGATTTACTAC
1 TAAATTATGAATGATTTACTAC
* *
21406755 TAAGTTAATG-ATGATTTATTA-
1 TAAATT-ATGAATGATTTACTAC
* * *
21406776 TATTATTAT-AACTGATTTATTAT
1 TA-AATTATGAA-TGATTTACTAC
*
21406799 TAATTTATTG-ATGATTTACTAC
1 TAAATTA-TGAATGATTTACTAC
21406821 -AAAGTTAT
1 TAAA-TTAT
21406829 CAATTACTAA
Statistics
Matches: 124, Mismatches: 28, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
21 10 0.08
22 104 0.84
23 10 0.08
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (22 bp):
TAAATTATGAATGATTTACTAC
Found at i:21406769 original size:66 final size:66
Alignment explanation
Indices: 21406614--21406939 Score: 187
Period size: 66 Copynumber: 4.8 Consensus size: 66
21406604 GTTATCGAGT
* * * * * * ** *
21406614 ATTTACTACTAGGTT-ATCAATGGTATACTGTTAAATTATGAATGATTTACTACTAAATTACCAT
1 ATTTACTACTAAGTTAATAAATGATTTACT-ATAAATTATGAACGATTTACTACTAAATTATTAA
21406678 TG
65 TG
* * * *
21406680 ATTTAGTACTCA-TTTATAAATGATTTACTATAAAGTTATGAACAATTTACTACTAAATTATTAA
1 ATTTACTACTAAGTTAATAAATGATTTACTATAAA-TTATGAACGATTTACTACTAAATTATTAA
21406744 TG
65 TG
* * * * * * *
21406746 ATTTACTACTAAGTTAAT-GATGATTTATTATATTATTAT-AACTGATTTATTATTAATTTATTG
1 ATTTACTACTAAGTTAATAAATGATTTACTATA-AATTATGAAC-GATTTACTACTAAATTATTA
21406809 ATG
64 ATG
* * * * *
21406812 ATTTACTACAAAGTTATCAATTACTAACTAATTTACTACTAAATTAT-AAGTGATTTACAATTAA
1 ATTTACTACTAAG-T-T-AA-TA--AA-TGATTTACTA-TAAATTATGAA-CGATTTACTACTAA
*
21406876 GTTATTAATG
57 ATTATTAATG
* * * * * **
21406886 ATTTACTACTAAATT-ATCAATAATTTACATCTAAATTATCATTGATTTACTACT
1 ATTTACTACTAAGTTAATAAATGATTTAC-TATAAATTATGAACGATTTACTACT
21406940 TAGTTTTTTT
Statistics
Matches: 203, Mismatches: 40, Indels: 34
0.73 0.14 0.12
Matches are distributed among these distances:
65 9 0.04
66 128 0.63
67 10 0.05
68 1 0.00
69 3 0.01
70 2 0.01
72 1 0.00
73 2 0.01
74 45 0.22
75 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (66 bp):
ATTTACTACTAAGTTAATAAATGATTTACTATAAATTATGAACGATTTACTACTAAATTATTAAT
G
Found at i:21406772 original size:44 final size:43
Alignment explanation
Indices: 21406645--21406939 Score: 175
Period size: 44 Copynumber: 6.5 Consensus size: 43
21406635 GGTATACTGT
* ** *
21406645 TAAATTATGAATGATTTACTACTAAATTACCATTGATTTAGTAC
1 TAAATTATTAATGATTTACTACTAAATTATGA-TGATTTACTAC
* * * **
21406689 TCATTTATAAATGATTTACTA-TAAAGTTATGAACAATTTACTAC
1 TAAATTATTAATGATTTACTACTAAA-TTATG-ATGATTTACTAC
* *
21406733 TAAATTATTAATGATTTACTACTAAGTTAATGATGATTTATTA-
1 TAAATTATTAATGATTTACTACTAAATT-ATGATGATTTACTAC
* * * *
21406776 TATTATTA-TAACTGATTTATTATTAATTTATTGATGATTTACTAC
1 TA-AATTATTAA-TGATTTACTACTAAATTA-TGATGATTTACTAC
* * * * *
21406821 AAAGTTATCAATTACTAACTAATTTACTACTAAATTATAAGTGATTTACAAT
1 -----TA--AATTATTAA-TGATTTACTACTAAATTATGA-TGATTTACTAC
* * *
21406873 TAAGTTATTAATGATTTACTACTAAATTATCAATAATTTAC-ATC
1 TAAATTATTAATGATTTACTACTAAATTAT-GATGATTTACTA-C
* *
21406917 TAAATTATCATTGATTTACTACT
1 TAAATTATTAATGATTTACTACT
21406940 TAGTTTTTTT
Statistics
Matches: 196, Mismatches: 37, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
43 11 0.06
44 132 0.67
45 16 0.08
47 2 0.01
50 2 0.01
51 6 0.03
52 27 0.14
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (43 bp):
TAAATTATTAATGATTTACTACTAAATTATGATGATTTACTAC
Found at i:21406868 original size:22 final size:21
Alignment explanation
Indices: 21406842--21406939 Score: 99
Period size: 22 Copynumber: 4.5 Consensus size: 21
21406832 TTACTAACTA
21406842 ATTTACTACTAAATTATAAGTG
1 ATTTACTACTAAATTATAA-TG
* * *
21406864 ATTTACAATTAAGTTATTAATG
1 ATTTACTACTAAATTA-TAATG
*
21406886 ATTTACTACTAAATTATCAATA
1 ATTTACTACTAAATTAT-AATG
*
21406908 ATTTAC-ATCTAAATTATCATTG
1 ATTTACTA-CTAAATTAT-AATG
21406930 ATTTACTACT
1 ATTTACTACT
21406940 TAGTTTTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
21 2 0.03
22 57 0.90
23 4 0.06
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTACTACTAAATTATAATG
Found at i:21406932 original size:118 final size:118
Alignment explanation
Indices: 21406723--21406938 Score: 262
Period size: 118 Copynumber: 1.8 Consensus size: 118
21406713 AGTTATGAAC
* * * *
21406723 AATTTACTACTAAATTATTAATGATTTACTACTAAGTTAATGATGATTTATTATATTATTATAAC
1 AATTTACTACTAAATTATTAATGATTTACAACTAAGTTAATAATGATTTACTATATAATTATAAC
* * * *
21406788 TGATTTATTATTAATTTATTGATGATTTACTACAAAGTTATCAATTACTAACT
66 TAATTTATCATTAAATTATTCATGATTTACTACAAAGTTATCAATTACTAACT
* *
21406841 AATTTACTACTAAATTA-TAAGTGATTTACAATTAAGTTATTAATGATTTACTACTA-AATTATC
1 AATTTACTACTAAATTATTAA-TGATTTACAACTAAGTTAATAATGATTTACTA-TATAATTAT-
21406904 AA-TAATTTA-CATCTAAATTA-TCATTGATTTACTAC
63 AACTAATTTATCAT-TAAATTATTCA-TGATTTACTAC
21406939 TTAGTTTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
117 7 0.08
118 72 0.87
119 4 0.05
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (118 bp):
AATTTACTACTAAATTATTAATGATTTACAACTAAGTTAATAATGATTTACTATATAATTATAAC
TAATTTATCATTAAATTATTCATGATTTACTACAAAGTTATCAATTACTAACT
Found at i:21407020 original size:22 final size:22
Alignment explanation
Indices: 21406953--21407077 Score: 107
Period size: 22 Copynumber: 5.8 Consensus size: 22
21406943 TTTTTTTATT
* *
21406953 ATTTATTATAAAATCAT-CACA
1 ATTTATTATTAAATTATCCACA
*
21406974 TATTTATTACTT-AATTAACCACA
1 -ATTTATTA-TTAAATTATCCACA
*
21406997 ATTTATTATTAAGTTAT-CACCA
1 ATTTATTATTAAATTATCCA-CA
*
21407019 ATTTA-TATTAAATTATCCATA
1 ATTTATTATTAAATTATCCACA
* *
21407040 ATTTA-CATTAAATTATCCATA
1 ATTTATTATTAAATTATCCACA
* *
21407061 ATTTACTATTAAGTTAT
1 ATTTATTATTAAATTAT
21407078 TTAACTATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
21 40 0.46
22 42 0.48
23 5 0.06
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTATTATTAAATTATCCACA
Found at i:21407027 original size:21 final size:22
Alignment explanation
Indices: 21406986--21407077 Score: 100
Period size: 21 Copynumber: 4.3 Consensus size: 22
21406976 TTTATTACTT
* *
21406986 AATTAACCACAATTTATTATTA
1 AATTATCCACAATTTACTATTA
*
21407008 AGTTAT-CACCAATTTA-TATTA
1 AATTATCCA-CAATTTACTATTA
*
21407029 AATTATCCATAATTTAC-ATTA
1 AATTATCCACAATTTACTATTA
*
21407050 AATTATCCATAATTTACTATTA
1 AATTATCCACAATTTACTATTA
*
21407072 AGTTAT
1 AATTAT
21407078 TTAACTATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
21 39 0.64
22 22 0.36
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTATCCACAATTTACTATTA
Found at i:21407086 original size:16 final size:15
Alignment explanation
Indices: 21407061--21407094 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
21407051 ATTATCCATA
*
21407061 ATTTACTATTAAGTT
1 ATTTACTATTAAGCT
21407076 ATTTAACTATTAAGCT
1 ATTT-ACTATTAAGCT
21407092 ATT
1 ATT
21407095 GATGATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (15 bp):
ATTTACTATTAAGCT
Found at i:21407179 original size:21 final size:22
Alignment explanation
Indices: 21407142--21407196 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
21407132 TACGTTTTTA
* *
21407142 ATGATTAACTACT-AAATTATTT
1 ATGATTTACTA-TAAAATAATTT
21407164 -TGATTTACTATAAAATAATTT
1 ATGATTTACTATAAAATAATTT
*
21407185 ATGATTTGCTAT
1 ATGATTTACTAT
21407197 TGCTAAACGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
ATGATTTACTATAAAATAATTT
Found at i:21407196 original size:22 final size:21
Alignment explanation
Indices: 21407155--21407196 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
21407145 ATTAACTACT
*
21407155 AAATTATTTTGATTTACTATA
1 AAATAATTTTGATTTACTATA
*
21407176 AAATAATTTATGATTTGCTAT
1 AAATAATTT-TGATTTACTAT
21407197 TGCTAAACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
AAATAATTTTGATTTACTATA
Found at i:21407288 original size:22 final size:22
Alignment explanation
Indices: 21407219--21407290 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
21407209 ACTAATTTAC
* *
21407219 TATTAAGATATCATTGACTTATT
1 TATTAAGTTATCATTTA-TTATT
* * **
21407242 T-TTAAGTTATTAATTATTAAC
1 TATTAAGTTATCATTTATTATT
*
21407263 TATTAAGTTATCATTTATTTTT
1 TATTAAGTTATCATTTATTATT
21407285 TATTAA
1 TATTAA
21407291 CTTGTAATTG
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
21 4 0.11
22 32 0.86
23 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (22 bp):
TATTAAGTTATCATTTATTATT
Found at i:21407767 original size:22 final size:22
Alignment explanation
Indices: 21407742--21407795 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
21407732 AATGATTAAT
*
21407742 TAATTTACTACTAAATTATCAC
1 TAATTTACTACTAAATTATCAA
* *
21407764 TAATTTACAACTAAATTATTAA
1 TAATTTACTACTAAATTATCAA
21407786 TAATTTACTA
1 TAATTTACTA
21407796 TTAGGTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTTACTACTAAATTATCAA
Found at i:21407900 original size:22 final size:22
Alignment explanation
Indices: 21407853--21407904 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
21407843 TATCACTGAT
* * *
21407853 TTACTATTATATTTTTATACAT
1 TTACTATTATATTATCATACAA
21407875 TTACTATTATATTATCATTA-AA
1 TTACTATTATATTATCA-TACAA
21407897 TTACTATT
1 TTACTATT
21407905 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.56
Consensus pattern (22 bp):
TTACTATTATATTATCATACAA
Found at i:21408060 original size:22 final size:22
Alignment explanation
Indices: 21407937--21408127 Score: 90
Period size: 22 Copynumber: 8.9 Consensus size: 22
21407927 AAATTGTCAC
*
21407937 GATTTACCACTAAATTATCT-AT
1 GATTTACTACTAAATTAT-TAAT
* * * *
21407959 GATTCACTACTGAGTTATTACT
1 GATTTACTACTAAATTATTAAT
* *
21407981 GATTTA-T-TTAAATT-TTGCAT
1 GATTTACTACTAAATTATT-AAT
* * * * *
21408001 GATTTATTATTAAGTTATCACT
1 GATTTACTACTAAATTATTAAT
* *
21408023 GA-TTACT-CATACATTATTGAT
1 GATTTACTAC-TAAATTATTAAT
* *
21408044 AATTTACTACTAAATTA-TATT
1 GATTTACTACTAAATTATTAAT
** * *
21408065 GATTTACTTTTAAGTTTTTAAT
1 GATTTACTACTAAATTATTAAT
* *
21408087 GATTAACTACTAAATTATCAAT
1 GATTTACTACTAAATTATTAAT
* *
21408109 TATTTACTACTAATTTATT
1 GATTTACTACTAAATTATT
21408128 TTTTATTTAC
Statistics
Matches: 118, Mismatches: 42, Indels: 18
0.66 0.24 0.10
Matches are distributed among these distances:
19 2 0.02
20 11 0.09
21 29 0.25
22 74 0.63
23 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.48
Consensus pattern (22 bp):
GATTTACTACTAAATTATTAAT
Found at i:21408154 original size:19 final size:19
Alignment explanation
Indices: 21408116--21408154 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21408106 AATTATTTAC
* * *
21408116 TACTAATTTATTTTTTATT
1 TACTAAGTTATTTATGATT
21408135 TACTAAGTTATTTATGATT
1 TACTAAGTTATTTATGATT
21408154 T
1 T
21408155 GTTACTTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TACTAAGTTATTTATGATT
Found at i:21408233 original size:22 final size:22
Alignment explanation
Indices: 21408188--21408485 Score: 94
Period size: 22 Copynumber: 13.7 Consensus size: 22
21408178 AAACTGAAAA
* *
21408188 TTACTATTTAA-TTATTAATAAT
1 TTACTA-TTAAGTTATTATTGAT
*
21408210 TTACTATTAAATTATTATTGAT
1 TTACTATTAAGTTATTATTGAT
* ** *
21408232 TTATTGCTAAGTTATTAATGAT
1 TTACTATTAAGTTATTATTGAT
* ** * * *
21408254 TAACTGCTAACTTATCATTTAT
1 TTACTATTAAGTTATTATTGAT
** *
21408276 TTTTTATTAAGTTATCT-TTAAT
1 TTACTATTAAGTTAT-TATTGAT
* * *
21408298 TTAATACTATGTTATTA-TGTAT
1 TTACTATTAAGTTATTATTG-AT
* * *
21408320 TTACAACTATA-TTATAATTGAT
1 TTACTATTA-AGTTATTATTGAT
* * **
21408342 TTACCATTAAGGTATTATACAT
1 TTACTATTAAGTTATTATTGAT
* * *
21408364 ATATTATTATA-TTATTACTGAT
1 TTACTATTA-AGTTATTATTGAT
* * *
21408386 TTATTA-AAAATT-TTAATT-AT
1 TTACTATTAAGTTATT-ATTGAT
* * * *
21408406 TTACAATTAAATTATCATTCAT
1 TTACTATTAAGTTATTATTGAT
** * *
21408428 TTGTTATTAAGTTATCATTAAT
1 TTACTATTAAGTTATTATTGAT
*
21408450 TTACTAATAAGTTATTGA-TGA-
1 TTACTATTAAGTTATT-ATTGAT
21408471 TTACTATTAAGTTAT
1 TTACTATTAAGTTAT
21408486 ACTAATTACA
Statistics
Matches: 201, Mismatches: 61, Indels: 29
0.69 0.21 0.10
Matches are distributed among these distances:
20 9 0.04
21 34 0.17
22 154 0.77
23 4 0.02
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (22 bp):
TTACTATTAAGTTATTATTGAT
Found at i:21409566 original size:52 final size:50
Alignment explanation
Indices: 21409474--21409619 Score: 114
Period size: 52 Copynumber: 2.9 Consensus size: 50
21409464 AATTGTAATT
* * ** **
21409474 GAGAGATTTTTTAGATTTAATTCTAGAATCAACTGGCATTAACAATGATGTG
1 GAGAGA-TTGTTAGATTTAATTCCAGAATCAACTCACATTAA-AATGATAAG
* * *
21409526 GAGAGATTGTTAGAATTTAATTCCATAATCAATTCACATTAAATTGATAAG
1 GAGAGATTGTTAG-ATTTAATTCCAGAATCAACTCACATTAAAATGATAAG
* * ** * *
21409577 GAGAGATT-TTGGGAATTAATTTTAGAATCAATTCTCATTAAAA
1 GAGAGATTGTT-AGATTTAATTCCAGAATCAACTCACATTAAAA
21409620 CAGAAATAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
50 26 0.34
51 21 0.28
52 29 0.38
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (50 bp):
GAGAGATTGTTAGATTTAATTCCAGAATCAACTCACATTAAAATGATAAG
Found at i:21410086 original size:24 final size:22
Alignment explanation
Indices: 21410044--21410087 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
21410034 TGTTTTGACT
21410044 TTATTTTTTTATTTTATTTATG
1 TTATTTTTTTATTTTATTTATG
21410066 TTATTTTGTTTATTTTTATTTA
1 TTATTTT-TTTA-TTTTATTTA
21410088 CTCTTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (22 bp):
TTATTTTTTTATTTTATTTATG
Found at i:21410196 original size:6 final size:6
Alignment explanation
Indices: 21410185--21410210 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21410175 ACAAAAGAAT
21410185 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
21410211 TCTTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:21411115 original size:45 final size:44
Alignment explanation
Indices: 21411020--21411115 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 44
21411010 TTTTTTTCTT
* * *
21411020 TTCATTGTCTATATTTGATTAATTATTTATTTATTTTCACTTCT
1 TTCATTGTCTATATTTGATTAATTATTTATTTATTATCACGTCA
* *
21411064 TCTCATTGTTTATATTTGTTTAATTATTTATTATATATATCA-GTCA
1 T-TCATTGTCTATATTTGATTAATTATTTATT-TAT-TATCACGTCA
21411110 TTCATT
1 TTCATT
21411116 TGCATGTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 33 0.75
46 6 0.14
47 4 0.09
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.59
Consensus pattern (44 bp):
TTCATTGTCTATATTTGATTAATTATTTATTTATTATCACGTCA
Found at i:21411608 original size:16 final size:16
Alignment explanation
Indices: 21411587--21411622 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
21411577 CTTCTTTTTA
21411587 TTATGTATGCA-TACAT
1 TTATGTAT-CACTACAT
21411603 TTATGTATCACTACAT
1 TTATGTATCACTACAT
21411619 TTAT
1 TTAT
21411623 CCTCATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (16 bp):
TTATGTATCACTACAT
Found at i:21412576 original size:14 final size:14
Alignment explanation
Indices: 21412557--21412590 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
21412547 GATGGTGGGA
21412557 TGTAGCTGTTCAAG
1 TGTAGCTGTTCAAG
21412571 TGTAGCTGTTCAAG
1 TGTAGCTGTTCAAG
21412585 TGTAGC
1 TGTAGC
21412591 CACCCTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (14 bp):
TGTAGCTGTTCAAG
Found at i:21414337 original size:10 final size:11
Alignment explanation
Indices: 21414325--21414391 Score: 75
Period size: 11 Copynumber: 5.9 Consensus size: 11
21414315 GAAAGAGAAA
21414325 TAAAAAAAAA-
1 TAAAAAAAAAG
21414335 TAAGAAAAAATATG
1 TAA-AAAAAA-A-G
21414349 TAAAAAAAAAG
1 TAAAAAAAAAG
21414360 TAAAAAAAAAGG
1 TAAAAAAAAA-G
*
21414372 T-AAAAAAAAT
1 TAAAAAAAAAG
21414382 TAAAAAAAAA
1 TAAAAAAAAA
21414392 AGAAAGAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
10 4 0.08
11 33 0.66
12 4 0.08
13 6 0.12
14 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.13
Consensus pattern (11 bp):
TAAAAAAAAAG
Found at i:21414340 original size:17 final size:17
Alignment explanation
Indices: 21414306--21414442 Score: 50
Period size: 17 Copynumber: 7.5 Consensus size: 17
21414296 GTCATTAATG
*
21414306 AATAAAAAAGAAAGAGA
1 AATAAAAAAGAAAAAGA
21414323 AATAAAAAA-AAATAAGA
1 AATAAAAAAGAAA-AAGA
* *
21414340 AAAAATATGTAAAAAAAAAGTA
1 AATAA-A---AAAGAAAAAG-A
21414362 AA-AAAAAAGGTAAAAA-A
1 AATAAAAAA-G-AAAAAGA
*
21414379 AATTAAAAA-AAAAAGA
1 AATAAAAAAGAAAAAGA
*
21414395 AAGAAAAGCAAATGAAAAAAGA
1 AA-TAAA--AAA-G-AAAAAGA
*
21414417 AAGAAAAAGAGACAAAAGA
1 AATAAAAA-AGA-AAAAGA
21414436 AA-AAAAA
1 AATAAAAA
21414443 GGAAGACTTA
Statistics
Matches: 94, Mismatches: 7, Indels: 37
0.68 0.05 0.27
Matches are distributed among these distances:
15 5 0.05
16 6 0.06
17 24 0.26
18 12 0.13
19 19 0.20
20 2 0.02
21 11 0.12
22 15 0.16
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.08
Consensus pattern (17 bp):
AATAAAAAAGAAAAAGA
Found at i:21414344 original size:11 final size:10
Alignment explanation
Indices: 21414309--21414442 Score: 69
Period size: 11 Copynumber: 12.8 Consensus size: 10
21414299 ATTAATGAAT
21414309 AAAAAAGAAAG
1 AAAAAA-AAAG
* *
21414320 AGAAATAAA-
1 AAAAAAAAAG
*
21414329 AAAAAATAAG
1 AAAAAAAAAG
* *
21414339 AAAAAATATG
1 AAAAAAAAAG
21414349 TAAAAAAAAAG
1 -AAAAAAAAAG
21414360 TAAAAAAAAAGG
1 -AAAAAAAAA-G
21414372 TAAAAAAAATTA-
1 -AAAAAAAA--AG
21414384 AAAAAAAAAG
1 AAAAAAAAAG
*
21414394 -AAAGAAAAG
1 AAAAAAAAAG
21414403 CAAATGAAAAAAG
1 -AAA--AAAAAAG
*
21414416 AAAGAAAAAG
1 AAAAAAAAAG
* *
21414426 -AGACAAAAG
1 AAAAAAAAAG
21414435 AAAAAAAA
1 AAAAAAAA
21414443 GGAAGACTTA
Statistics
Matches: 96, Mismatches: 16, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
9 21 0.22
10 23 0.24
11 32 0.33
12 13 0.14
13 6 0.06
14 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:21414353 original size:23 final size:23
Alignment explanation
Indices: 21414325--21414391 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 23
21414315 GAAAGAGAAA
*
21414325 TAAAAAAAAA-TAAGAAAAAATATG
1 TAAAAAAAAAGTAA-AAAAAA-AGG
21414349 TAAAAAAAAAGTAAAAAAAAAGG
1 TAAAAAAAAAGTAAAAAAAAAGG
*
21414372 T-AAAAAAAATTAAAAAAAAA
1 TAAAAAAAAAGTAAAAAAAAA
21414392 AGAAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.45
23 3 0.08
24 16 0.40
25 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.13
Consensus pattern (23 bp):
TAAAAAAAAAGTAAAAAAAAAGG
Found at i:21414392 original size:23 final size:23
Alignment explanation
Indices: 21414325--21414393 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
21414315 GAAAGAGAAA
* *
21414325 TAAAAAAAAATAAGAAAAAATATG
1 TAAAAAAAAATAA-AAAAAAAAGG
21414349 TAAAAAAAAAGT-AAAAAAAAAGG
1 TAAAAAAAAA-TAAAAAAAAAAGG
*
21414372 TAAAAAAAATTAAAAAAAAAAG
1 TAAAAAAAAATAAAAAAAAAAG
21414394 AAAGAAAAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
22 1 0.03
23 27 0.68
24 11 0.28
25 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (23 bp):
TAAAAAAAAATAAAAAAAAAAGG
Found at i:21414401 original size:22 final size:22
Alignment explanation
Indices: 21414354--21414425 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
21414344 ATATGTAAAA
*
21414354 AAAAAGTAAAAAAAAAGGTAAA-
1 AAAAAGTAAAAAAAAAAG-AAAG
*
21414376 AAAAATTAAAAAAAAAAGAAAG
1 AAAAAGTAAAAAAAAAAGAAAG
* *
21414398 -AAAAGCAAATGAAAAAAGAAAG
1 AAAAAGTAAA-AAAAAAAGAAAG
21414420 AAAAAG
1 AAAAAG
21414426 AGACAAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
21 10 0.24
22 27 0.64
23 5 0.12
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (22 bp):
AAAAAGTAAAAAAAAAAGAAAG
Found at i:21414432 original size:26 final size:26
Alignment explanation
Indices: 21414378--21414442 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
21414368 AAGGTAAAAA
*
21414378 AAATTAAAAAAAAAAGAAAGAAAAGC
1 AAATGAAAAAAAAAAGAAAGAAAAGC
* *
21414404 AAATGAAAAAAGAAAGAAA-AAGAGAC
1 AAATGAAAAAAAAAAGAAAGAAAAG-C
*
21414430 AAAAGAAAAAAAA
1 AAATGAAAAAAAA
21414443 GGAAGACTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 4 0.12
26 29 0.88
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (26 bp):
AAATGAAAAAAAAAAGAAAGAAAAGC
Found at i:21415495 original size:115 final size:115
Alignment explanation
Indices: 21415364--21415677 Score: 335
Period size: 115 Copynumber: 2.7 Consensus size: 115
21415354 CAATCTCGAT
* * * * *
21415364 TCAATCCATATTATTTTTTTAACTTGTGGCATCATC-CTGGTCATTCATCTTCGACCTCGACTCG
1 TCAATCCAGATCATTTTTTTAACTTGTGGCATCATCTC-GATCATTCATCTTTGACTTCGACTCG
* *
21415428 GTCTTGATCATTTTTAGACTC-TCGGCATCATCCTAATCATTTGATCTTTGC
65 GTCTTGATCACTTTTAGACTCAT-GGCATCATCCTAATCATTTGATCTTGGC
* * * ** * * * * * *
21415479 TCAGTCCAGATCATTTTCTTGACTTGTGGCATTGTCTCGATTATTCATTTTTTACTTGGACTTGA
1 TCAATCCAGATCATTTTTTTAACTTGTGGCATCATCTCGATCATTCATCTTTGACTTCGACTCGG
* * *
21415544 TCTTGATCGCTTTCAGACTCATGGCATCATCCTGATCATTTGATCTTGGC
66 TCTTGATCACTTTTAGACTCATGGCATCATCCTAATCATTTGATCTTGGC
* * * * * * *
21415594 TTAATCCAGATCATTTTTTTTATTTGCGACATCATCTCGATCATTCATCTTTGACTTTGACTCAG
1 TCAATCCAGATCATTTTTTTAACTTGTGGCATCATCTCGATCATTCATCTTTGACTTCGACTCGG
*
21415659 TCTTGGTCACTTTTAGACT
66 TCTTGATCACTTTTAGACT
21415678 TACGACATCG
Statistics
Matches: 157, Mismatches: 40, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
115 155 0.99
116 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (115 bp):
TCAATCCAGATCATTTTTTTAACTTGTGGCATCATCTCGATCATTCATCTTTGACTTCGACTCGG
TCTTGATCACTTTTAGACTCATGGCATCATCCTAATCATTTGATCTTGGC
Found at i:21415990 original size:17 final size:17
Alignment explanation
Indices: 21415947--21415996 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
21415937 TCTTTCTTAC
21415947 GAATCTAAAAGTCTTTGT
1 GAATCTAAAA-TCTTTGT
*
21415965 -AAACTTAAAATCTTTGT
1 GAATC-TAAAATCTTTGT
*
21415982 GAATCTAAAACCTTT
1 GAATCTAAAATCTTT
21415997 ACGAAACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (17 bp):
GAATCTAAAATCTTTGT
Found at i:21416100 original size:69 final size:69
Alignment explanation
Indices: 21415978--21416176 Score: 179
Period size: 69 Copynumber: 2.9 Consensus size: 69
21415968 CTTAAAATCT
* * * * * ****
21415978 TTGTGAATCTAAAACCTTTACGAAACTTAGAAT-CTTATGAATCTTTTTTTCTTGTGAATCTGAA
1 TTGTGAACCTAAAATCTTTACGAATC-TAGAATCCTTGTGAAACTTAAAATCTTGTGAATCTGAA
21416042 AGTCC
65 AGTCC
* * *
21416047 TTGTGAACCTAAAATCTTTATGAATCTAGAA-CCTT-TACGAAACTTAAAATCTTGCGAATTTGA
1 TTGTGAACCTAAAATCTTTACGAATCTAGAATCCTTGT--GAAACTTAAAATCTTGTGAATCTGA
*
21416110 AAGTTC
64 AAGTCC
** * * * *
21416116 TTGTGAACCTGGAATTTTTGCGAATCTAGAATCCTTGTGAAACTTGAAATCATGTGAATCT
1 TTGTGAACCTAAAATCTTTACGAATCTAGAATCCTTGTGAAACTTAAAATCTTGTGAATCT
21416177 TTTTTTCTTG
Statistics
Matches: 104, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
67 1 0.01
68 8 0.08
69 90 0.87
70 4 0.04
71 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (69 bp):
TTGTGAACCTAAAATCTTTACGAATCTAGAATCCTTGTGAAACTTAAAATCTTGTGAATCTGAAA
GTCC
Found at i:21416297 original size:155 final size:155
Alignment explanation
Indices: 21416015--21416302 Score: 400
Period size: 155 Copynumber: 1.9 Consensus size: 155
21416005 TAGAATCTTA
* * * **
21416015 TGAATCTTTTTTTCTTGTGAATCTGAAAGTCCTTGTGAACCTAAAATCTTTATGAATCTAGAACC
1 TGAATCTTTTTTTCTTGCGAATCTAAAAATCCTTGCAAACCTAAAATCTTTATGAATCTAGAACC
* * ** *
21416080 TTTACGAAACTTAAAATCTTGCGAATTTGAAAGTTCTTGTGAACCTGGAATTTTTGCGAATCTAG
66 TTTACGAAACTTAAAATCTTGCAAATTTGAAAGTTCTTGTGAACCTGAAAGCTTTGCAAATCTAG
21416145 AATCCTTGTGAAACTTGAAATCATG
131 AATCCTTGTGAAACTTGAAATCATG
*
21416170 TGAATCTTTTTTTCTTGCGAATCTAAAAATCCTTGCAAACCTGAAATCTTTATGAATCTAGAACC
1 TGAATCTTTTTTTCTTGCGAATCTAAAAATCCTTGCAAACCTAAAATCTTTATGAATCTAGAACC
* * * *
21416235 TTTACGAAACTTGAAATCTTGCAAATCTT-CAA-TTCTTGTGAATCTGAAAAGCTTTGTAAATCT
66 TTTACGAAACTTAAAATCTTGCAAAT-TTGAAAGTTCTTGTGAACCTG-AAAGCTTTGCAAATCT
*
21416298 TGAAT
129 AGAAT
21416303 ATTTGCGATT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
154 13 0.11
155 100 0.87
156 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (155 bp):
TGAATCTTTTTTTCTTGCGAATCTAAAAATCCTTGCAAACCTAAAATCTTTATGAATCTAGAACC
TTTACGAAACTTAAAATCTTGCAAATTTGAAAGTTCTTGTGAACCTGAAAGCTTTGCAAATCTAG
AATCCTTGTGAAACTTGAAATCATG
Found at i:21421318 original size:16 final size:15
Alignment explanation
Indices: 21421293--21421328 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
21421283 AATTTTTAGG
*
21421293 AAAAATAAAAAAAACT
1 AAAAAGAAAAAAAA-T
21421309 AAAAAGAAAAAAAAT
1 AAAAAGAAAAAAAAT
21421324 AAAAA
1 AAAAA
21421329 TTGATGGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (15 bp):
AAAAAGAAAAAAAAT
Found at i:21421642 original size:41 final size:41
Alignment explanation
Indices: 21421592--21421670 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
21421582 GAGAAATGAA
**
21421592 AAAATAAGAAAAAAGTGTGTAAAAAAAAGCAAAAAAAAAGGT
1 AAAATAAGAAAAAAGTGTAAAAAAAAAAG-AAAAAAAAAGGT
*
21421634 AAAA-AAGAAAAAATTGTAAAAAAAAAAGAAAAAAAAA
1 AAAATAAGAAAAAAGTGTAAAAAAAAAAGAAAAAAAAA
21421671 CAAATGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 9 0.26
41 21 0.62
42 4 0.12
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (41 bp):
AAAATAAGAAAAAAGTGTAAAAAAAAAAGAAAAAAAAAGGT
Found at i:21421646 original size:16 final size:16
Alignment explanation
Indices: 21421622--21421660 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21421612 AAAAAAAAGC
21421622 AAAAAAAAA-GGTAAA
1 AAAAAAAAATGGTAAA
*
21421637 AAAGAAAAAATTGTAAA
1 AAA-AAAAAATGGTAAA
21421654 AAAAAAA
1 AAAAAAA
21421661 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 10 0.48
17 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAAAATGGTAAA
Found at i:21421646 original size:17 final size:16
Alignment explanation
Indices: 21421622--21421660 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
21421612 AAAAAAAAGC
21421622 AAAAAAAAAGGTAAAA
1 AAAAAAAAAGGTAAAA
**
21421638 AAGAAAAAATTGTAAAA
1 AA-AAAAAAAGGTAAAA
21421655 AAAAAA
1 AAAAAA
21421661 GAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAAAAGGTAAAA
Found at i:21421665 original size:10 final size:10
Alignment explanation
Indices: 21421612--21421697 Score: 50
Period size: 10 Copynumber: 8.3 Consensus size: 10
21421602 AAAAGTGTGT
21421612 AAAAAAAAGCA
1 AAAAAAAAG-A
21421623 AAAAAAAAG-
1 AAAAAAAAGA
**
21421632 GTAAAAAAG-
1 AAAAAAAAGA
**
21421641 AAAAAATTGTAA
1 AAAAAAAAG--A
21421653 AAAAAAAAGA
1 AAAAAAAAGA
*
21421663 AAAAAAAACA
1 AAAAAAAAGA
21421673 AATGAAAAAAGA
1 AA--AAAAAAGA
**
21421685 AGCAAAAAGA
1 AAAAAAAAGA
21421695 AAA
1 AAA
21421698 GAGACAAAGG
Statistics
Matches: 56, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
9 12 0.21
10 20 0.36
11 9 0.16
12 15 0.27
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:21421665 original size:28 final size:26
Alignment explanation
Indices: 21421613--21421697 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 26
21421603 AAAGTGTGTA
* *
21421613 AAAAAAAGCAAAAAAAAAGGTAAAAAAG
1 AAAAAATG-AAAAAAAAAAG-AAAAAAG
21421641 AAAAAATTGTAAAAAAAAAAGAAAAAA-
1 AAAAAA-TG-AAAAAAAAAAGAAAAAAG
* *
21421668 AAACAAATG-AAAAAAGAAGCAAAAAG
1 AAA-AAATGAAAAAAAAAAGAAAAAAG
21421694 AAAA
1 AAAA
21421698 GAGACAAAGG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
25 15 0.31
26 3 0.06
27 5 0.10
28 15 0.31
29 11 0.22
ACGTcount: A:0.79, C:0.04, G:0.12, T:0.06
Consensus pattern (26 bp):
AAAAAATGAAAAAAAAAAGAAAAAAG
Found at i:21422715 original size:114 final size:115
Alignment explanation
Indices: 21422515--21423006 Score: 333
Period size: 114 Copynumber: 4.3 Consensus size: 115
21422505 AGATTATTTA
* * * * *
21422515 ATCTTGACTCAATCCAAATCATTTTCTTGAC-T-C-ACACCATCGTCTTAGTCACTCATCTTCAA
1 ATCTTGACTCAGTTCAAATCATTTTCTTGACTTGCGACATCATC--CTTA-TCATTCATCTTCGA
* * * *
21422577 TCTTGACTCAGTCGTGATCACTTTTAGACTCACGGTATCATCTCGA-CATTCG
63 CCTCGACTCAGTCCTGATCACTTTTAGACTCACGGTATCATCTCAATCATTCG
* *
21422629 ATCTTGATTCAGTTCAAATCATTTTCTTAACTTGCGACATCATCCTTATCATTCATCTTCGACCT
1 ATCTTGACTCAGTTCAAATCATTTTCTTGACTTGCGACATCATCCTTATCATTCATCTTCGACCT
* * *
21422694 CGACTCAGTCCTGATCACTTTTAGACTCGCGGTATCATCTTAATTATTCG
66 CGACTCAGTCCTGATCACTTTTAGACTCACGGTATCATCTCAATCATTCG
* * * * * *
21422744 ATCTTGGCTCAG-TCTAAATTATTTTCTTGACTTGTGGCATTAT-CTCGATCATTCATCTTCGAC
1 ATCTTGACTCAGTTC-AAATCATTTTCTTGACTTGCGACATCATCCT-TATCATTCATCTTCGAC
* * * ** * ** * *
21422807 CTGGACTC-GATCTTGGTTGCTTTTAAACTCGTGGCT-TCATCCCGATCATTCG
64 CTCGACTCAG-TCCTGATCACTTTTAGACTCACGG-TATCATCTCAATCATTCG
* * * * * * * * * * * *
21422859 ATCTCGACTCAATTTAGATCATTTT-TTAACTTACGGCATCAT-TTTGATTATTTATTTTTGACC
1 ATCTTGACTCAGTTCAAATCATTTTCTTGACTTGCGACATCATCCTT-ATCATTCATCTTCGACC
* ** ** * *
21422922 TCGACTC-GATCCT-AGTCGCTTTTAGACTTGCAATATCATCTCGATTATTCG
65 TCGACTCAG-TCCTGA-TCACTTTTAGACTCACGGTATCATCTCAATCATTCG
* * * *
21422973 ATCTCGACTCAATCCAAATCATTTTTTTGACTTG
1 ATCTTGACTCAGTTCAAATCATTTTCTTGACTTG
21423007 TGATGTCAGC
Statistics
Matches: 300, Mismatches: 65, Indels: 25
0.77 0.17 0.06
Matches are distributed among these distances:
113 1 0.00
114 170 0.57
115 119 0.40
116 3 0.01
117 7 0.02
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (115 bp):
ATCTTGACTCAGTTCAAATCATTTTCTTGACTTGCGACATCATCCTTATCATTCATCTTCGACCT
CGACTCAGTCCTGATCACTTTTAGACTCACGGTATCATCTCAATCATTCG
Found at i:21423321 original size:86 final size:86
Alignment explanation
Indices: 21423185--21423370 Score: 273
Period size: 86 Copynumber: 2.2 Consensus size: 86
21423175 GACCTTTGCA
* * * *
21423185 AAACTTAAAATCTTATGAATCTTTTTTTCTTACGAATCTGAAAGTTCTTGTAAACCTAAAATCTT
1 AAACTTGAAATCTTACGAATCTTTCTTTCTTACGAATCTGAAAGTCCTTGTAAACCTAAAATCTT
*
21423250 TGCGAATTTAGAACCTTTATG
66 TGCGAATCTAGAACCTTTATG
** *
21423271 AAACTTGAAATCTTACGAATCTTTCTTTCTTGTGAATCTGAAAGTCCTTGTGAACCTAAAATCTT
1 AAACTTGAAATCTTACGAATCTTTCTTTCTTACGAATCTGAAAGTCCTTGTAAACCTAAAATCTT
* *
21423336 TGCGAATCTATAACCTTTGTG
66 TGCGAATCTAGAACCTTTATG
*
21423357 AAACTTGGAATCTT
1 AAACTTGAAATCTT
21423371 GTGAATTTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (86 bp):
AAACTTGAAATCTTACGAATCTTTCTTTCTTACGAATCTGAAAGTCCTTGTAAACCTAAAATCTT
TGCGAATCTAGAACCTTTATG
Found at i:21424082 original size:52 final size:52
Alignment explanation
Indices: 21424025--21424170 Score: 145
Period size: 52 Copynumber: 2.8 Consensus size: 52
21424015 AACCGAAATT
** *
21424025 GAGAGATTTTTTAGATTTAATTCTAGAATCAATTGGCATTAAAAATGATATG
1 GAGAGATTTTTTAGATTTAATTCTAGAATCAATTCACATTAAAAATGATAAG
* ** * * *
21424077 GAGAGATTGTTGGGATTTAATTCCATAATCAATTCACATT-AAATTGATAAG
1 GAGAGATTTTTTAGATTTAATTCTAGAATCAATTCACATTAAAAATGATAAG
* * * *
21424128 GAAAGA--TTTTAGGATTTAATTTTAGAGTCAATTCTCATTAAAA
1 GAGAGATTTTTTA-GATTTAATTCTAGAATCAATTCACATTAAAA
21424171 TGAAAATCAA
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
49 2 0.03
50 22 0.30
51 17 0.23
52 33 0.45
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (52 bp):
GAGAGATTTTTTAGATTTAATTCTAGAATCAATTCACATTAAAAATGATAAG
Found at i:21424159 original size:50 final size:50
Alignment explanation
Indices: 21424033--21424173 Score: 158
Period size: 50 Copynumber: 2.8 Consensus size: 50
21424023 TTGAGAGATT
** * *
21424033 TTTTA-GATTTAATTCTAGAATCAATTGGCATTAAAAATGATATGGAGAGA
1 TTTTAGGATTTAATTCTAGAATCAATTCACATT-AAAATGATAAGGAAAGA
* * * *
21424083 TTGTTGGGATTTAATTCCATAATCAATTCACATTAAATTGATAAGGAAAGA
1 TT-TTAGGATTTAATTCTAGAATCAATTCACATTAAAATGATAAGGAAAGA
* * *
21424134 TTTTAGGATTTAATTTTAGAGTCAATTCTCATTAAAATGA
1 TTTTAGGATTTAATTCTAGAATCAATTCACATTAAAATGA
21424174 AAATCAAATA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 33 0.45
51 18 0.24
52 23 0.31
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (50 bp):
TTTTAGGATTTAATTCTAGAATCAATTCACATTAAAATGATAAGGAAAGA
Found at i:21424717 original size:23 final size:23
Alignment explanation
Indices: 21424668--21424718 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
21424658 TGTTTTGACT
* *
21424668 TTATTTTACTTATTTTATTTTTG
1 TTATTTTACTTATTTTATTTCTC
*
21424691 TTATTTT-GTTATTTTATTTACTC
1 TTATTTTACTTATTTTATTT-CTC
21424714 TTATT
1 TTATT
21424719 ATTTCTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (23 bp):
TTATTTTACTTATTTTATTTCTC
Found at i:21427846 original size:15 final size:15
Alignment explanation
Indices: 21427808--21427846 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
21427798 TTAATATATT
*
21427808 AAAACAAAAAATTGA
1 AAAACAAAAAATAGA
*
21427823 AAGACAAAAAATAGA
1 AAAACAAAAAATAGA
21427838 AAAA-AAAAA
1 AAAACAAAAA
21427847 CAAATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (15 bp):
AAAACAAAAAATAGA
Found at i:21430038 original size:35 final size:35
Alignment explanation
Indices: 21429999--21430148 Score: 205
Period size: 35 Copynumber: 4.3 Consensus size: 35
21429989 GTAAGTTTAG
* *
21429999 AAATAAAGATGATTATGA-GAAAATCACAAGTCAAA
1 AAATAAAGATGACTAAGATG-AAATCACAAGTCAAA
* *
21430034 AAATAAATATGACTAAGATGAAATTACAAGTCAAA
1 AAATAAAGATGACTAAGATGAAATCACAAGTCAAA
*
21430069 AAATAAATATGACTAAGATGAAATCACAAGTCAAA
1 AAATAAAGATGACTAAGATGAAATCACAAGTCAAA
* * *
21430104 AAATAAAAATGACTATGATGAAACCACAAGTCAAA
1 AAATAAAGATGACTAAGATGAAATCACAAGTCAAA
21430139 AAAT-AAGATG
1 AAATAAAGATG
21430149 GTCGAGATGA
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
34 5 0.05
35 99 0.94
36 1 0.01
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (35 bp):
AAATAAAGATGACTAAGATGAAATCACAAGTCAAA
Found at i:21430168 original size:34 final size:34
Alignment explanation
Indices: 21430023--21430168 Score: 150
Period size: 35 Copynumber: 4.2 Consensus size: 34
21430013 ATGAGAAAAT
* * *
21430023 CACAAGTCAAAAAATAAATATGACTAAGATGAAAT
1 CACAAGTCAAAAAATAAAAATGAC-GAGATGAAAC
* * * *
21430058 TACAAGTCAAAAAATAAATATGACTAAGATGAAAT
1 CACAAGTCAAAAAATAAAAATGAC-GAGATGAAAC
*
21430093 CACAAGTCAAAAAATAAAAATGACTATGATGAAAC
1 CACAAGTCAAAAAATAAAAATGACGA-GATGAAAC
* *
21430128 CACAAGTCAAAAAAT-AAGATGGTCGAGATGAAAC
1 CACAAGTCAAAAAATAAAAAT-GACGAGATGAAAC
*
21430162 CTCAAGT
1 CACAAGT
21430169 TGAGAAATAA
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
34 19 0.19
35 81 0.81
ACGTcount: A:0.54, C:0.13, G:0.14, T:0.19
Consensus pattern (34 bp):
CACAAGTCAAAAAATAAAAATGACGAGATGAAAC
Found at i:21430398 original size:35 final size:36
Alignment explanation
Indices: 21430331--21430433 Score: 88
Period size: 35 Copynumber: 2.9 Consensus size: 36
21430321 GATCAAGATG
* * * ** *
21430331 AAGCTTCAAGTCAG-GAACAAAGATGACCAGGATTG
1 AAGCTACAAGTCAGAAAATAAAGATGATTAGGATTA
* *
21430366 AA-CTATAGGTCAG-AAATAAAAGATGATTAGGA-TA
1 AAGCTACAAGTCAGAAAAT-AAAGATGATTAGGATTA
*
21430400 AAGCTACAAGTTAGAAAATAAAGATGATTAGGAT
1 AAGCTACAAGTCAGAAAATAAAGATGATTAGGAT
21430434 GAAGCCGTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
34 13 0.25
35 36 0.68
36 4 0.08
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21
Consensus pattern (36 bp):
AAGCTACAAGTCAGAAAATAAAGATGATTAGGATTA
Found at i:21430446 original size:35 final size:36
Alignment explanation
Indices: 21430379--21430448 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
21430369 TATAGGTCAG
*
21430379 AAATAAAAGATGATTAGGATAAAGCTACAAGTTAGA
1 AAATAAAAGATGATTAGGATAAAGCCACAAGTTAGA
* **
21430415 AAAT-AAAGATGATTAGGATGAAGCCGTAAGTTAG
1 AAATAAAAGATGATTAGGATAAAGCCACAAGTTAG
21430449 GAACAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 26 0.87
36 4 0.13
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (36 bp):
AAATAAAAGATGATTAGGATAAAGCCACAAGTTAGA
Found at i:21430962 original size:35 final size:35
Alignment explanation
Indices: 21430872--21430964 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 35
21430862 AGGAACAAAG
* * *
21430872 ATGATC-AGGATGAAACTGTAAGTCAAGAAATAAAT
1 ATGATCGA-GATGAAACCGCAAGTCAAAAAATAAAT
* * * *
21430907 ACGATCGGGAT-AAAGTCGCAAGTGAAAAAATAAAT
1 ATGATCGAGATGAAA-CCGCAAGTCAAAAAATAAAT
21430942 ATGATCGAGATGAAACCGCAAGT
1 ATGATCGAGATGAAACCGCAAGT
21430965 TGAGAACAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
34 3 0.07
35 39 0.87
36 3 0.07
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (35 bp):
ATGATCGAGATGAAACCGCAAGTCAAAAAATAAAT
Found at i:21431168 original size:35 final size:34
Alignment explanation
Indices: 21430997--21431210 Score: 117
Period size: 35 Copynumber: 6.1 Consensus size: 34
21430987 TAAACTGTAG
* * * *
21430997 GTCAAAAAATAAAGATGATTAAGACGAAGTCACAA
1 GTCAAAAAATAAAGATGATTAGGATG-AGCCATAA
* ** * * * * *
21431032 GTCAAAAAATAAAAATGGCTGGGGTAAAACCGTAA
1 GTCAAAAAATAAAGATGATTAGGAT-GAGCCATAA
* * * * *
21431067 GTTAAGAAATAAAGATGACTAGAGATGAATCCGTAA
1 GTCAAAAAATAAAGATGATTAG-GATG-AGCCATAA
** * * *
21431103 GTC-ATGAACAAAGATGATCAGGATTGAGCCATAG
1 GTCAAAAAATAAAGATGATTAGGA-TGAGCCATAA
*
21431137 GTCAAGAAATAAA-AGTGATTAGGATGAAGCCATAA
1 GTCAAAAAATAAAGA-TGATTAGGATG-AGCCATAA
* *
21431172 GTCAAAAAATAAAGATGACTAGGATGGAGCCACAA
1 GTCAAAAAATAAAGATGATTAGGAT-GAGCCATAA
21431207 GTCA
1 GTCA
21431211 GGAATAAGGT
Statistics
Matches: 133, Mismatches: 37, Indels: 18
0.71 0.20 0.10
Matches are distributed among these distances:
34 13 0.10
35 107 0.80
36 13 0.10
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (34 bp):
GTCAAAAAATAAAGATGATTAGGATGAGCCATAA
Found at i:21431718 original size:18 final size:18
Alignment explanation
Indices: 21431692--21431739 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
21431682 CCATCAAATG
* *
21431692 ATGCAAATGTAAATGTCA
1 ATGCGAATGCAAATGTCA
21431710 ATGCGAATGCAAATGTCA
1 ATGCGAATGCAAATGTCA
*
21431728 ATACGAATGCAA
1 ATGCGAATGCAA
21431740 GTATGCGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (18 bp):
ATGCGAATGCAAATGTCA
Found at i:21432015 original size:32 final size:32
Alignment explanation
Indices: 21431969--21432037 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
21431959 AGTAAATGCA
* * * *
21431969 AATGTCTTTTTCATGATATAGATGTGAATATG
1 AATGTCTTTCTCATGATACACATGTCAATATG
*
21432001 AATGTCTTTCTCATGATGCACATGTCAATATG
1 AATGTCTTTCTCATGATACACATGTCAATATG
21432033 AATGT
1 AATGT
21432038 AAGTGATACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (32 bp):
AATGTCTTTCTCATGATACACATGTCAATATG
Found at i:21432055 original size:85 final size:84
Alignment explanation
Indices: 21431962--21432140 Score: 272
Period size: 85 Copynumber: 2.1 Consensus size: 84
21431952 TAAATGAAGT
*
21431962 AAATGCAAATGT-CTTTTTCATGATATAGATGTGAATATGAATGTCTTTCTCATGATGCACATGT
1 AAATGCAAATGTCCCTTTT-ATGATATAGATGTGAATATGAATGTCTTTCTCATGATGCACATG-
21432026 CAATATG-AATGTAAGTGATAC
64 CAA-ATGCAATGTAAGTGATAC
* *
21432047 AAATGCAAATGTCCCTTTTATGATGTAGATGTGAATATGAATGTCTTTCTCATGATGCATATGCA
1 AAATGCAAATGTCCCTTTTATGATATAGATGTGAATATGAATGTCTTTCTCATGATGCACATGCA
* *
21432112 AGTGCAATGTAAGTTATAC
66 AATGCAATGTAAGTGATAC
21432131 AAATGCAAAT
1 AAATGCAAAT
21432141 TTTTTTTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
83 2 0.02
84 26 0.30
85 54 0.62
86 5 0.06
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (84 bp):
AAATGCAAATGTCCCTTTTATGATATAGATGTGAATATGAATGTCTTTCTCATGATGCACATGCA
AATGCAATGTAAGTGATAC
Found at i:21434413 original size:6 final size:6
Alignment explanation
Indices: 21434399--21434440 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
21434389 AAAAGAAAAC
*
21434399 TTCTTT TTCTCT TTCTTT TTC-TT TTC-TT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
21434441 TGTGAAACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:21434431 original size:16 final size:17
Alignment explanation
Indices: 21434403--21434439 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
21434393 GAAAACTTCT
21434403 TTTTCTCTTTCTTTTTC
1 TTTTCTCTTTCTTTTTC
21434420 TTTTCT-TTTCTTTTTC
1 TTTTCTCTTTCTTTTTC
21434436 TTTT
1 TTTT
21434440 TTGTGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTCTTTCTTTTTC
Found at i:21447632 original size:8 final size:7
Alignment explanation
Indices: 21447608--21447669 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 7
21447598 TTTATTTAGA
21447608 ATATATT
1 ATATATT
*
21447615 CATAT-GT
1 -ATATATT
21447622 ATATAGTT
1 ATATA-TT
21447630 ATATATT
1 ATATATT
21447637 ATTATATT
1 A-TATATT
21447645 AT-TATT
1 ATATATT
*
21447651 ATTTATT
1 ATATATT
21447658 AT-TATT
1 ATATATT
21447664 AT-TATT
1 ATATATT
21447670 TTTTTTTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
6 20 0.42
7 11 0.23
8 17 0.35
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (7 bp):
ATATATT
Found at i:21447641 original size:3 final size:3
Alignment explanation
Indices: 21447628--21447669 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
21447618 ATGTATATAG
21447628 TTA TATA TTA TTA -TA TTA TTA TTA TTTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
21447670 TTTTTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21447659 original size:13 final size:14
Alignment explanation
Indices: 21447623--21447668 Score: 67
Period size: 13 Copynumber: 3.2 Consensus size: 14
21447613 TTCATATGTA
21447623 TATAGTTATATATTAT
1 TATA-TTAT-TATTAT
21447639 TATATTATTATTAT
1 TATATTATTATTAT
21447653 T-TATTATTATTAT
1 TATATTATTATTAT
21447666 TAT
1 TAT
21447669 TTTTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.45
14 8 0.28
15 4 0.14
16 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TATATTATTATTAT
Found at i:21447669 original size:16 final size:15
Alignment explanation
Indices: 21447623--21447670 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
21447613 TTCATATGTA
21447623 TATAGTTATATATTA-T
1 TATA-TTAT-TATTATT
21447639 TATATTATTATTATT
1 TATATTATTATTATT
21447654 TATTATTATTATTATT
1 TA-TATTATTATTATT
21447670 T
1 T
21447671 TTTTTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TATATTATTATTATT
Found at i:21448127 original size:26 final size:24
Alignment explanation
Indices: 21448086--21448134 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
21448076 TGGGAGTGAG
21448086 AAAAAATTTTTAGAAATTTTTGGC
1 AAAAAATTTTTAGAAATTTTTGGC
*
21448110 AAAAAATTTTTCTGGAAATTTTTGG
1 AAAAAA-TTTT-TAGAAATTTTTGG
21448135 GAAATTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (24 bp):
AAAAAATTTTTAGAAATTTTTGGC
Found at i:21448185 original size:31 final size:31
Alignment explanation
Indices: 21448150--21448215 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
21448140 TTCCAGATTC
*
21448150 CGACGAAAATTCCGGC-AAAATTTGAATTTTT
1 CGACGAAAATTCCGGCGAAAA-TTGAAGTTTT
* *
21448181 CGACGACAATTCCGGCGAACATTGAAGTTTT
1 CGACGAAAATTCCGGCGAAAATTGAAGTTTT
21448212 CGAC
1 CGAC
21448216 AACTTGCCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (31 bp):
CGACGAAAATTCCGGCGAAAATTGAAGTTTT
Found at i:21448606 original size:19 final size:19
Alignment explanation
Indices: 21448584--21448620 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21448574 CTTTGAATGT
21448584 TTTTTTATTTGTTTATTTG
1 TTTTTTATTTGTTTATTTG
*
21448603 TTTTTTATTTTTTTATTT
1 TTTTTTATTTGTTTATTT
21448621 ATTATGTTAG
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:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (19 bp):
TTTTTTATTTGTTTATTTG
Found at i:21448668 original size:17 final size:18
Alignment explanation
Indices: 21448645--21448684 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
21448635 ATTTAATATT
21448645 CTTTTTATCTTAGTTTTA
1 CTTTTTATCTTAGTTTTA
* *
21448663 -TTTTTATTTTTGTTTTA
1 CTTTTTATCTTAGTTTTA
21448680 CTTTT
1 CTTTT
21448685 CTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
CTTTTTATCTTAGTTTTA
Found at i:21448821 original size:59 final size:57
Alignment explanation
Indices: 21448735--21449189 Score: 599
Period size: 57 Copynumber: 7.7 Consensus size: 57
21448725 AATTTTCCAA
* *
21448735 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATACATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATA-AATTTC
* *
21448793 AAAAAAGAGATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
1 AAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* * *
21448851 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
* *
21448909 AAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTC
1 ---AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAA-TTTC
*
21448971 AAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
* * *
21449029 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAATTTCAC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT--C
21449087 AAAAAAATATTTTT-AGGGAAAAGTTGAAATTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
1 AAAAAAATATTTTTGA-GGAAAA---G---TTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* *
21449150 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
21449190 TCCTACACAA
Statistics
Matches: 352, Mismatches: 28, Indels: 35
0.85 0.07 0.08
Matches are distributed among these distances:
56 3 0.01
57 108 0.31
58 28 0.08
59 108 0.31
60 1 0.00
61 45 0.13
62 8 0.02
63 20 0.06
65 31 0.09
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (57 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
Found at i:21449013 original size:177 final size:173
Alignment explanation
Indices: 21448716--21449189 Score: 680
Period size: 177 Copynumber: 2.7 Consensus size: 173
21448706 TTTCTTCAAA
21448716 TAAAAATCAAATTTTCCAAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAG
1 TAAAAAT-AAATTTT-CAAAAAAAAATATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* * *
21448781 AAATACATTTTCAAAAAAGAGATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAGAAATAA
63 AAATA-AATTTCAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAA
21448846 ATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
126 ATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* *
21448894 TAAAAATAAATTTTCAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGA
1 TAAAAATAAATTTTC-AAAAAAAAATATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTAGA
*
21448959 AATCAAAGTTTCAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
64 AAT-AAA-TTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
* *
21449024 TTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCT
127 TTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
21449071 CAGAAATAAA-TTTCACAAAAAAATATTTTTAGGGAAAAGTTGAAATTGAAAGTATCAATTTTCC
1 TAAAAATAAATTTTCAAAAAAAAATATTTTTA-GGAAAA---G---TTGAAAGTATCAATTTTCC
* *
21449135 TTAGAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
59 TTAGAAATAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
21449190 TCCTACACAA
Statistics
Matches: 269, Mismatches: 17, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
174 1 0.00
175 20 0.07
176 5 0.02
177 154 0.57
178 19 0.07
179 41 0.15
180 3 0.01
181 26 0.10
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (173 bp):
TAAAAATAAATTTTCAAAAAAAAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA
TAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:21449238 original size:12 final size:12
Alignment explanation
Indices: 21449221--21449259 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
21449211 CTTTCCTTCC
*
21449221 TTTCTATTCTGA
1 TTTCTATTTTGA
21449233 TTTCTATTTTGA
1 TTTCTATTTTGA
*
21449245 TTTTTATTTTGA
1 TTTCTATTTTGA
21449257 TTT
1 TTT
21449260 TTCTTTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTCTATTTTGA
Found at i:21453804 original size:18 final size:18
Alignment explanation
Indices: 21453781--21453816 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21453771 ACTCAATTAG
21453781 ACTCGGATTAGACCCCTA
1 ACTCGGATTAGACCCCTA
21453799 ACTCGGATTAGACCCCTA
1 ACTCGGATTAGACCCCTA
21453817 GACTTCTACC
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:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (18 bp):
ACTCGGATTAGACCCCTA
Found at i:21457963 original size:19 final size:20
Alignment explanation
Indices: 21457922--21457968 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
21457912 TACAAAAATA
*
21457922 TTAATATTCATTATTTATCT
1 TTAATATTCATTATATATCT
21457942 TTAAT-TTCATTAATATAT-T
1 TTAATATTCATT-ATATATCT
21457961 TTAATATT
1 TTAATATT
21457969 TTACTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATATTCATTATATATCT
Found at i:21458230 original size:16 final size:16
Alignment explanation
Indices: 21458204--21458246 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
21458194 TAGGATAAAA
*
21458204 AATTATTTAAATTATTT
1 AATT-TTTAAAATATTT
21458221 AATTTTTAAAATATTT
1 AATTTTTAAAATATTT
21458237 ATATTTTTAA
1 A-ATTTTTAA
21458247 TTGATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTTAAAATATTT
Found at i:21458232 original size:17 final size:17
Alignment explanation
Indices: 21458209--21458246 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
21458199 TAAAAAATTA
*
21458209 TTTAAATTATTTA-ATT
1 TTTAAAATATTTATATT
21458225 TTTAAAATATTTATATT
1 TTTAAAATATTTATATT
21458242 TTTAA
1 TTTAA
21458247 TTGATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAAATATTTATATT
Found at i:21471285 original size:357 final size:359
Alignment explanation
Indices: 21470662--21471380 Score: 1101
Period size: 358 Copynumber: 2.0 Consensus size: 359
21470652 TGTAACTCAT
* * * ***
21470662 TAGGATTCAACATAGTAAAAAATTAATTTCAAATTCGTTCCCAATCAGTGTAGTTAATTCTTGCA
1 TAGGATTCAACATAGTAAAAAATTAATTTCAAATTCATTCCCAATCAATATAGTTAATTCTAAAA
* * * * *
21470727 TTTGAAGGTTGAAATCTTGGAGGTAGTGAATATCAGGTGTGCAATTTAAGTTGGAACTTGGTTCT
66 TTTGAAGGTTGAAATCTTGGAGGCAGTGAAAATCAGATGTGCAATTCAAGTTGAAACTTGGTTCT
* * * *
21470792 TCTCTCCTTTAGGAGATTTGGTTTGCTCTTTTAAACCTTTGATCTCTTAGATTTACTTGTTACCT
131 TCTCTCCTCTAGGAGATTTGGTTTGCTCCTTTAAACCTTCGATCTCTCAGATTTACTTGTTACCT
* * * *
21470857 TGCTTATTTTTATTTTGTTACAATTTATTTCATGTTTTTGGTGGCTATTTAGATTAATTTTGTTG
196 TACTTATTTTTATTTTGTTACAATTTATTTCATGTCTTTGATGGCTATTTAGATTAATTTTGTTA
* *
21470922 ATCATGCTTTGTTTTCTACTTATTTGCACACTGTTTGGAATCTTAGTTTGTTGAGCTA-TTTTTT
261 ATCATGCTTTGTTTTCTACTTATTTGCACACTATTTAGAATCTTAGTTTGTTGAGCTATTTTTTT
21470986 TCTTATTTTGCTACAAATTTTTTGTTAGATTTTG
326 TCTTATTTTGCTACAAATTTTTTGTTAGATTTTG
* *
21471020 TAGGATTCAACATAGTGAAAAATT-ATTATCAAATTCATTCTCAATCAATATAGTTAATTCTCAA
1 TAGGATTCAACATAGTAAAAAATTAATT-TCAAATTCATTCCCAATCAATATAGTTAATTCT-AA
*
21471084 AATTT-AAGGTTGAAATTTTGGAGGCAGTGAAAATCAGATGTGCAATTCAAGTT-AAACCTTGGT
64 AATTTGAAGGTTGAAATCTTGGAGGCAGTGAAAATCAGATGTGCAATTCAAGTTGAAA-CTTGGT
21471147 TCTTCTCTCCTCTAGGCA-ATTT-GTTTGCTCCTTTAAACCTTCGATCTCTCAGATTTACTTGTT
128 TCTTCTCTCCTCTAGG-AGATTTGGTTTGCTCCTTTAAACCTTCGATCTCTCAGATTTACTTGTT
* * *
21471210 ATCTTACTTGTTTTTATTTTGTTACAATTTATTTTATGTCTTTGATGG-TCATTTAGATTAATTT
192 ACCTTACTTATTTTTATTTTGTTACAATTTATTTCATGTCTTTGATGGCT-ATTTAGATTAATTT
21471274 TGTTAATCATGCTTTGTTTTCTACTTATTTGCACACTATTTAGAATCTTAGTTTGTTGAGCTATT
256 TGTTAATCATGCTTTGTTTTCTACTTATTTGCACACTATTTAGAATCTTAGTTTGTTGAGCTATT
21471339 TTTTTTCTTATTTTGCTACAAATTTTTTGTTAGATTTTG
321 TTTTTTCTTATTTTGCTACAAATTTTTTGTTAGATTTTG
21471378 TAG
1 TAG
21471381 TAAACTCGTT
Statistics
Matches: 328, Mismatches: 27, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
356 1 0.00
357 159 0.48
358 163 0.50
359 5 0.02
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (359 bp):
TAGGATTCAACATAGTAAAAAATTAATTTCAAATTCATTCCCAATCAATATAGTTAATTCTAAAA
TTTGAAGGTTGAAATCTTGGAGGCAGTGAAAATCAGATGTGCAATTCAAGTTGAAACTTGGTTCT
TCTCTCCTCTAGGAGATTTGGTTTGCTCCTTTAAACCTTCGATCTCTCAGATTTACTTGTTACCT
TACTTATTTTTATTTTGTTACAATTTATTTCATGTCTTTGATGGCTATTTAGATTAATTTTGTTA
ATCATGCTTTGTTTTCTACTTATTTGCACACTATTTAGAATCTTAGTTTGTTGAGCTATTTTTTT
TCTTATTTTGCTACAAATTTTTTGTTAGATTTTG
Found at i:21492002 original size:63 final size:61
Alignment explanation
Indices: 21491825--21492073 Score: 153
Period size: 62 Copynumber: 4.0 Consensus size: 61
21491815 ATTACAAAAA
* * * * * * * *
21491825 TTGAATGGGGTTATTCAAGGTATTTTTGCTT-AAAATACTTTCAATAAT-TCTCTTCAATTT
1 TTGAATGAGATTATTCAAGGCATTTCTGGTTAAAAATACCTTAAATAATCTCT-TTTAATTT
* * * * * ** * *
21491885 TTGTAA-GAAGATTATTCAAGACGTTTTTAGTCAAAAACGCTTTGAATAATCTCTTTTAATTT
1 TTG-AATG-AGATTATTCAAGGCATTTCTGGTTAAAAATACCTTAAATAATCTCTTTTAATTT
* * * * ** ***
21491947 TTTATTAGAGATTATTCAAGGCATTTTTGTTTAAAAAATACCTTAAATAATCTCTTACAAAAAA
1 TTGAAT-GAGATTATTCAAGGCATTTCTGGTT-AAAAATACCTTAAATAATCTCTT-TTAATTT
* * * *
21492011 TTGAATGAGATTATTCAAGGTATTTCTGGTTAAAAGTACCTTCAATAATTTCTTTTAATTT
1 TTGAATGAGATTATTCAAGGCATTTCTGGTTAAAAATACCTTAAATAATCTCTTTTAATTT
21492072 TT
1 TT
21492074 ATGAGAACAT
Statistics
Matches: 140, Mismatches: 41, Indels: 15
0.71 0.21 0.08
Matches are distributed among these distances:
60 4 0.03
61 23 0.16
62 62 0.44
63 45 0.32
64 6 0.04
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.44
Consensus pattern (61 bp):
TTGAATGAGATTATTCAAGGCATTTCTGGTTAAAAATACCTTAAATAATCTCTTTTAATTT
Found at i:21493037 original size:25 final size:25
Alignment explanation
Indices: 21493003--21493053 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
21492993 TGATGACCCT
*
21493003 TTAGGGTAAGCCGTTTTTTAACCAA
1 TTAGGGTAAGCCGGTTTTTAACCAA
21493028 TTAGGGTAAGCCGGTTTTTAACCAA
1 TTAGGGTAAGCCGGTTTTTAACCAA
21493053 T
1 T
21493054 GACCAGCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (25 bp):
TTAGGGTAAGCCGGTTTTTAACCAA
Found at i:21493747 original size:10 final size:11
Alignment explanation
Indices: 21493726--21493754 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
21493716 GATAATTAAG
21493726 TTAAATTATTA
1 TTAAATTATTA
21493737 TTAAATT-TTA
1 TTAAATTATTA
21493747 TTAAATTA
1 TTAAATTA
21493755 ATTAAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAATTATTA
Found at i:21497317 original size:26 final size:27
Alignment explanation
Indices: 21497276--21497349 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
21497266 AATAATTACA
* *
21497276 CCAATAATTCATTGAATCATTGA-TTCT
1 CCAA-AATTCATTGAATCATTAACTACT
* * *
21497303 TCAAAATTCATTGAAACTTTAACTACT
1 CCAAAATTCATTGAATCATTAACTACT
*
21497330 CCAAAATTCATCGAATCATT
1 CCAAAATTCATTGAATCATT
21497350 TACTTATACT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 15 0.41
27 22 0.59
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (27 bp):
CCAAAATTCATTGAATCATTAACTACT
Found at i:21497577 original size:32 final size:32
Alignment explanation
Indices: 21497541--21497612 Score: 76
Period size: 32 Copynumber: 2.2 Consensus size: 32
21497531 TAATCTAATT
*
21497541 ATCATAATC-TAACTTCTT-ATAAATCTTCAAA
1 ATCATAATCGT-ACTTCTTAAAAAATCTTCAAA
* * *
21497572 GATCATTATCGTAGTTCTTAAAAAATCTTTAAA
1 -ATCATAATCGTACTTCTTAAAAAATCTTCAAA
21497605 ATCATAAT
1 ATCATAAT
21497613 ATAAGCTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (32 bp):
ATCATAATCGTACTTCTTAAAAAATCTTCAAA
Found at i:21511910 original size:18 final size:18
Alignment explanation
Indices: 21511887--21511928 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
21511877 GCCTCCCCTT
21511887 CTTACTTTTTCTT-GGAAC
1 CTTACTTTTT-TTCGGAAC
21511905 CTTACTTTTTTTCGGAAC
1 CTTACTTTTTTTCGGAAC
*
21511923 CATACT
1 CTTACT
21511929 CATCATTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.48
Consensus pattern (18 bp):
CTTACTTTTTTTCGGAAC
Found at i:21516212 original size:4 final size:4
Alignment explanation
Indices: 21516199--21516274 Score: 53
Period size: 4 Copynumber: 18.2 Consensus size: 4
21516189 ATATTTATTC
* * **
21516199 ATAA ATTAA ATAA ATAA ATAA TATCAA TTTA ACCA ATAA ATAA ATAA ATAA
1 ATAA A-TAA ATAA ATAA ATAA -AT-AA ATAA ATAA ATAA ATAA ATAA ATAA
** * *
21516250 GCAA AAAA ATAA ATAA ATGA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
21516275 AAACTTAGCT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
4 46 0.84
5 7 0.13
6 2 0.04
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Done.