Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 100 of 126
Found at i:19640552 original size:14 final size:16
Alignment explanation
Indices: 19640517--19640572 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
19640507 TTTTAATTTA
*
19640517 TATATATTTATATAAT
1 TATATATTTAAATAAT
19640533 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
19640548 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
* *
19640563 AATATTTTTA
1 TATATATTTA
19640573 TTAATTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
14 10 0.29
15 5 0.15
16 19 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:19647917 original size:31 final size:30
Alignment explanation
Indices: 19647853--19647924 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
19647843 TTTTTTAAAA
*
19647853 AATTTACTAATTAATGAAATAATATAATCT
1 AATTTACTAATTAATAAAATAATATAATCT
* * * *
19647883 AATTTACCTTATTAATAAAATGATATCATTT
1 AATTTA-CTAATTAATAAAATAATATAATCT
*
19647914 AATTTATTAAT
1 AATTTACTAAT
19647925 GATATATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (30 bp):
AATTTACTAATTAATAAAATAATATAATCT
Found at i:19649911 original size:9 final size:9
Alignment explanation
Indices: 19649883--19649932 Score: 59
Period size: 10 Copynumber: 5.4 Consensus size: 9
19649873 ATTCCAAAAA
19649883 TTTTA-TAT
1 TTTTATTAT
19649891 TTTTATGT-T
1 TTTTAT-TAT
19649900 TTTTATTAT
1 TTTTATTAT
19649909 TTTTAATTAT
1 TTTT-ATTAT
19649919 TTTTAATTAT
1 TTTT-ATTAT
19649929 TTTT
1 TTTT
19649933 GGTTTGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
8 6 0.16
9 12 0.32
10 20 0.53
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:19649911 original size:10 final size:10
Alignment explanation
Indices: 19649898--19649932 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
19649888 TATTTTTATG
*
19649898 TTTTTTATTA
1 TTTTTAATTA
19649908 TTTTTAATTA
1 TTTTTAATTA
19649918 TTTTTAATTA
1 TTTTTAATTA
19649928 TTTTT
1 TTTTT
19649933 GGTTTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTAATTA
Found at i:19650027 original size:26 final size:25
Alignment explanation
Indices: 19649998--19650054 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
19649988 CATTTGGGAT
19649998 AAATTT-AAACAAAATTTCTCACTTAG
1 AAATTTCAAA-AAAATTTCTCA-TTAG
* * *
19650024 AAATTTCATAAAAATTTGTCATTTG
1 AAATTTCAAAAAAATTTCTCATTAG
19650049 AAATTT
1 AAATTT
19650055 TTATAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 16 0.59
27 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (25 bp):
AAATTTCAAAAAAATTTCTCATTAG
Found at i:19650180 original size:32 final size:32
Alignment explanation
Indices: 19650143--19650204 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
19650133 TAATGAAAAC
***
19650143 CATAAAACAAAGTGAATAAATAAACAATTATG
1 CATAAAACAAAACAAATAAATAAACAATTATG
* *
19650175 CATAAAATAAAACAAATGAATAAACAATTA
1 CATAAAACAAAACAAATAAATAAACAATTA
19650205 AATAAAGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.63, C:0.10, G:0.06, T:0.21
Consensus pattern (32 bp):
CATAAAACAAAACAAATAAATAAACAATTATG
Found at i:19650197 original size:18 final size:18
Alignment explanation
Indices: 19650144--19650198 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
19650134 AATGAAAACC
19650144 ATAAAACAAAGTGAAT-AA
1 ATAAAACAAA-TGAATAAA
*
19650162 AT-AAACAATTATGCATAAA
1 ATAAAACAA--ATGAATAAA
19650181 ATAAAACAAATGAATAAA
1 ATAAAACAAATGAATAAA
19650199 CAATTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 6 0.19
18 14 0.45
19 5 0.16
20 6 0.19
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.20
Consensus pattern (18 bp):
ATAAAACAAATGAATAAA
Found at i:19650707 original size:9 final size:8
Alignment explanation
Indices: 19650688--19650727 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
19650678 CTCAAACACC
19650688 TTTTTTAT
1 TTTTTTAT
*
19650696 TTTTTCAT
1 TTTTTTAT
19650704 TTTTATTAT
1 TTTT-TTAT
*
19650713 TTTTTTAA
1 TTTTTTAT
19650721 TTTTTTA
1 TTTTTTA
19650728 ATTGTCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTAT
Found at i:19650724 original size:17 final size:16
Alignment explanation
Indices: 19650688--19650727 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
19650678 CTCAAACACC
*
19650688 TTTTTTATTTTTTCAT
1 TTTTTTATTTTTTCAA
*
19650704 TTTTATTATTTTTTTAA
1 TTTT-TTATTTTTTCAA
19650721 TTTTTTA
1 TTTTTTA
19650728 ATTGTCAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTTTCAA
Found at i:19650948 original size:42 final size:42
Alignment explanation
Indices: 19650864--19651053 Score: 251
Period size: 42 Copynumber: 4.5 Consensus size: 42
19650854 TTTTAAAGAA
* * * * *
19650864 AAAAT-AACAAAGCTTCTCTAAATAGAGGCTCAATGGCTTTTG
1 AAAATAAATAAAGCTCCTCTAAATAAAGGCTCAACGAC-TTTG
19650906 AAAATAAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTG
1 AAAATAAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTG
*
19650948 AAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGACTTTG
1 AAAATAAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTG
* * *
19650990 AAAATAAACAAAGCTCCTCTAAACAAAGGCTCAATGACTTTG
1 AAAATAAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTG
*
19651032 AAAAGTAAAT--TGCTCCTCTAAA
1 AAAA-TAAATAAAGCTCCTCTAAA
19651054 CAGAGGCACC
Statistics
Matches: 134, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
41 11 0.08
42 92 0.69
43 31 0.23
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (42 bp):
AAAATAAATAAAGCTCCTCTAAATAAAGGCTCAACGACTTTG
Found at i:19651208 original size:42 final size:42
Alignment explanation
Indices: 19651002--19651201 Score: 250
Period size: 41 Copynumber: 4.8 Consensus size: 42
19650992 AATAAACAAA
* * * *
19651002 GCTCCTCTAAACAAAGGCTCAATGAC-TTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATT
19651043 GCTCCTCTAAACAGAGGCACC-TCAACTTTT-AAAATGTAAATT
1 GCTCCTCTAAACAGAGGCACCAT-AACTTTTGAAAA-GTAAATT
* *
19651085 GCT-CTCTAAATAGAGGCACCACAACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATT
* * *
19651125 GCTCCTCTAAATAGAAGCAACCATAAC-TTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGC-ACCATAACTTTTGAAAAGTAAATT
19651167 GCTCCTCTAAACAGAGGCACCATAACTTTTGAAAA
1 GCTCCTCTAAACAGAGGCACCATAACTTTTGAAAA
19651202 AAAAATTACT
Statistics
Matches: 139, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
40 11 0.08
41 75 0.54
42 53 0.38
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCATAACTTTTGAAAAGTAAATT
Found at i:19651828 original size:22 final size:22
Alignment explanation
Indices: 19651779--19651819 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19651769 GGTTTCATTC
*
19651779 CTCAAAGATTCTCATTTTGAAA
1 CTCAAAGATTCTCAATTTGAAA
19651801 CTCAAAGATTCT-AATTTGA
1 CTCAAAGATTCTCAATTTGA
19651820 GTTCTCAAAA
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:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
CTCAAAGATTCTCAATTTGAAA
Found at i:19661398 original size:27 final size:27
Alignment explanation
Indices: 19661361--19661427 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
19661351 TTTTGATTTG
*
19661361 AATTTAAATAATTATCTAAACATATTA
1 AATTTAAATAATTATCCAAACATATTA
* *
19661388 AATTTACATAATTATCCAAGCATATTA
1 AATTTAAATAATTATCCAAACATATTA
19661415 AATTTAAATAATT
1 AATTTAAATAATT
19661428 TATTAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.40
Consensus pattern (27 bp):
AATTTAAATAATTATCCAAACATATTA
Found at i:19662200 original size:2 final size:2
Alignment explanation
Indices: 19662193--19662225 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19662183 ATTTGTTATG
19662193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19662226 AAGATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19674066 original size:20 final size:20
Alignment explanation
Indices: 19674043--19674085 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19674033 ATTTTTCTTA
19674043 TTTTTCTCAATTTTCTAAA-T
1 TTTTTCTCAA-TTTCTAAAGT
* *
19674063 TTTTTTTCTATTTCTAAAGT
1 TTTTTCTCAATTTCTAAAGT
19674083 TTT
1 TTT
19674086 CTATAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTCTCAATTTCTAAAGT
Found at i:19678381 original size:31 final size:33
Alignment explanation
Indices: 19678338--19678399 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
19678328 TTTCTTGATT
*
19678338 TTTCTTATTTTTATCAATTTT-C-TAAATTTTTC
1 TTTCTTATTTTTAAC-ATTTTCCATAAATTTTTC
19678370 TTTC-TATTTTTAACATTTTCCATAAATTTT
1 TTTCTTATTTTTAACATTTTCCATAAATTTT
19678400 AATTTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 5 0.19
31 10 0.37
32 12 0.44
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (33 bp):
TTTCTTATTTTTAACATTTTCCATAAATTTTTC
Found at i:19678688 original size:23 final size:23
Alignment explanation
Indices: 19678662--19678710 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
19678652 TTGAAAAGTA
* *
19678662 AAAAAATCATAAA-TAATAATTTT
1 AAAAAAT-AAAAAGTAAGAATTTT
*
19678685 AAAATATAAAAAGTAAGAATTTT
1 AAAAAATAAAAAGTAAGAATTTT
19678708 AAA
1 AAA
19678711 TGTAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
AAAAAATAAAAAGTAAGAATTTT
Found at i:19679070 original size:46 final size:46
Alignment explanation
Indices: 19679000--19679087 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
19678990 ATTGGGGTAC
* *
19679000 AATCCAAGAAAAAAAGTTGAAACGCTAGAAGGAGGGCTTGAAATAA
1 AATCCAAGAAAAAAAATCGAAACGCTAGAAGGAGGGCTTGAAATAA
*
19679046 AATCCAAGAAAAAAAATCGGAACGCTAGAAGGAGGGCTTGAA
1 AATCCAAGAAAAAAAATCGAAACGCTAGAAGGAGGGCTTGAA
19679088 CCTCCGACCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.49, C:0.12, G:0.25, T:0.14
Consensus pattern (46 bp):
AATCCAAGAAAAAAAATCGAAACGCTAGAAGGAGGGCTTGAAATAA
Found at i:19681821 original size:3 final size:3
Alignment explanation
Indices: 19681813--19681840 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19681803 TTTTAAACTA
19681813 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19681841 TAGTTTCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:19682090 original size:16 final size:17
Alignment explanation
Indices: 19682071--19682103 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19682061 ATAATGTTTT
*
19682071 ATAA-AAAAAGGGAGAA
1 ATAATAAAAAGGAAGAA
19682087 ATAATAAAAAGGAAGAA
1 ATAATAAAAAGGAAGAA
19682104 TGACTCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (17 bp):
ATAATAAAAAGGAAGAA
Found at i:19682216 original size:25 final size:26
Alignment explanation
Indices: 19682172--19682233 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
19682162 TTTATCTTTC
* *
19682172 AAAAAA-ATAAAATAGTAATAATAAT
1 AAAAAATAAAAAATAGTAATAAAAAT
* *
19682197 AATAATTAAAAAATAG-AATAAAAAT
1 AAAAAATAAAAAATAGTAATAAAAAT
19682222 AAAAAATAAAAA
1 AAAAAATAAAAA
19682234 TTTTCGAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 22 0.73
26 8 0.27
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (26 bp):
AAAAAATAAAAAATAGTAATAAAAAT
Found at i:19682223 original size:31 final size:29
Alignment explanation
Indices: 19682173--19682230 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
19682163 TTATCTTTCA
**
19682173 AAAAAATAAAATAGTAATAATAATAATAATT
1 AAAAAATAAAATAAAAATAA-AA-AATAATT
*
19682204 AAAAAATAGAATAAAAATAAAAAATAA
1 AAAAAATAAAATAAAAATAAAAAATAA
19682231 AAATTTTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 2 0.08
31 17 0.71
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (29 bp):
AAAAAATAAAATAAAAATAAAAAATAATT
Found at i:19682618 original size:24 final size:23
Alignment explanation
Indices: 19682573--19682617 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19682563 GTAATATGAT
19682573 TTTGATAGTGAAATTTTAAAAAG
1 TTTGATAGTGAAATTTTAAAAAG
*
19682596 TTTGAATAGT-AATTTTTAAAAA
1 TTTG-ATAGTGAAATTTTAAAAA
19682618 ATCTTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (23 bp):
TTTGATAGTGAAATTTTAAAAAG
Found at i:19683029 original size:19 final size:20
Alignment explanation
Indices: 19683007--19683049 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
19682997 ATATGCATGG
*
19683007 TAAACATGAA-TATTAAAAA
1 TAAACATGAACTATCAAAAA
* *
19683026 TAAATATGAACTATCGAAAA
1 TAAACATGAACTATCAAAAA
19683046 TAAA
1 TAAA
19683050 ATTTTTGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAACATGAACTATCAAAAA
Found at i:19694641 original size:19 final size:19
Alignment explanation
Indices: 19694617--19694656 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
19694607 GAAATAATAT
19694617 TATCTATTTACTTCATTAA
1 TATCTATTTACTTCATTAA
19694636 TATCTATTTACTTCATTAA
1 TATCTATTTACTTCATTAA
19694655 TA
1 TA
19694657 AAGTGACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (19 bp):
TATCTATTTACTTCATTAA
Found at i:19700178 original size:10 final size:10
Alignment explanation
Indices: 19700163--19700187 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19700153 CCAGCAATCT
19700163 TTAAATTTCC
1 TTAAATTTCC
19700173 TTAAATTTCC
1 TTAAATTTCC
19700183 TTAAA
1 TTAAA
19700188 AGAAAATAAT
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (10 bp):
TTAAATTTCC
Found at i:19701207 original size:21 final size:22
Alignment explanation
Indices: 19701175--19701221 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
19701165 TAAGTTGATA
*
19701175 TAAAAATCAGTACTTAAATAAG
1 TAAAAATCAGTAATTAAATAAG
* *
19701197 TAAAAAT-AGTAATTAATTGAG
1 TAAAAATCAGTAATTAAATAAG
19701218 TAAA
1 TAAA
19701222 TATTAAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (22 bp):
TAAAAATCAGTAATTAAATAAG
Found at i:19710488 original size:23 final size:24
Alignment explanation
Indices: 19710443--19710497 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
19710433 AAAAAATTAT
*
19710443 AAATAATAATTTTAAAATAT-AAA
1 AAATAAGAATTTTAAAATATAAAA
*
19710466 AAATAAGAATTTT-AAATGTTAAAA
1 AAATAAGAATTTTAAAAT-ATAAAA
19710490 AAATAAGA
1 AAATAAGA
19710498 CATAATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 13 0.46
24 11 0.39
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (24 bp):
AAATAAGAATTTTAAAATATAAAA
Found at i:19710834 original size:46 final size:46
Alignment explanation
Indices: 19710764--19710851 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
19710754 ATTGGGGTAC
* *
19710764 AATCCAAGAAAAAAAGTTGAAACGCTAGAAGGAGGGCTTGAAGTAA
1 AATCCAAGAAAAAAAATCGAAACGCTAGAAGGAGGGCTTGAAGTAA
*
19710810 AATCCAAGAAAAAAAATCGGAACGCTAGAAGGAGGGCTTGAA
1 AATCCAAGAAAAAAAATCGAAACGCTAGAAGGAGGGCTTGAA
19710852 CCTCCGACCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.48, C:0.12, G:0.26, T:0.14
Consensus pattern (46 bp):
AATCCAAGAAAAAAAATCGAAACGCTAGAAGGAGGGCTTGAAGTAA
Found at i:19713626 original size:3 final size:3
Alignment explanation
Indices: 19713618--19713658 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
19713608 TTCCCTTTCA
19713618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19713659 ATTTTCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19713750 original size:18 final size:18
Alignment explanation
Indices: 19713729--19713769 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
19713719 AAATATTTTT
19713729 ATAA-AAAATATTATTAAA
1 ATAATAAAATATT-TTAAA
*
19713747 ATAATGAAATATTTTAAA
1 ATAATAAAATATTTTAAA
19713765 A-AATA
1 ATAATA
19713770 TTCAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 10 0.50
19 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
ATAATAAAATATTTTAAA
Found at i:19713855 original size:16 final size:17
Alignment explanation
Indices: 19713836--19713868 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19713826 ATAATATTTT
*
19713836 ATAA-AAAAAGGGAGAA
1 ATAATAAAAAGGAAGAA
19713852 ATAATAAAAAGGAAGAA
1 ATAATAAAAAGGAAGAA
19713869 TGACTCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (17 bp):
ATAATAAAAAGGAAGAA
Found at i:19714001 original size:15 final size:15
Alignment explanation
Indices: 19713981--19714012 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19713971 AAAATAGAAT
19713981 AAAAATAAAAACAAA
1 AAAAATAAAAACAAA
*
19713996 AAAAATAAAAATAAA
1 AAAAATAAAAACAAA
19714011 AA
1 AA
19714013 TTTTAGAGAA
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:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAATAAAAACAAA
Found at i:19714307 original size:16 final size:15
Alignment explanation
Indices: 19714263--19714313 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
19714253 ATGTCTTTTT
*
19714263 TAAAATAAT-AATAA
1 TAAAAAAATAAATAA
**
19714277 TAAAAAAATGTATAA
1 TAAAAAAATAAATAA
19714292 TGAAAAAAATAAATAA
1 T-AAAAAAATAAATAA
19714308 -AAAAAA
1 TAAAAAA
19714314 TTGTATATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
16 12 0.39
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (15 bp):
TAAAAAAATAAATAA
Found at i:19714312 original size:30 final size:30
Alignment explanation
Indices: 19714264--19714320 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19714254 TGTCTTTTTT
*
19714264 AAAATAATAATAATAAAAAAATGTATAATG
1 AAAAAAATAATAATAAAAAAATGTATAATG
*
19714294 AAAAAAATAAATAA-AAAAAATTGTATA
1 AAAAAAAT-AATAATAAAAAAATGTATA
19714321 TGCATATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAAAAATAATAATAAAAAAATGTATAATG
Found at i:19720147 original size:27 final size:26
Alignment explanation
Indices: 19720115--19720171 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
19720105 ATAAAATAAA
*
19720115 ATAATATTATTTAATTTTATTTTATCT
1 ATAATATTATTTAATTTTATCTTAT-T
*
19720142 ATAATATTATTTTATTTTATCTTATT
1 ATAATATTATTTAATTTTATCTTATT
19720168 ATAA
1 ATAA
19720172 ACTTATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
ATAATATTATTTAATTTTATCTTATT
Found at i:19722020 original size:15 final size:16
Alignment explanation
Indices: 19721994--19722023 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19721984 ATTATATCAT
19721994 AAAATTATATTATTAA
1 AAAATTATATTATTAA
19722010 AAAATTA-ATTATTA
1 AAAATTATATTATTA
19722024 TTTTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTATATTATTAA
Found at i:19722112 original size:42 final size:42
Alignment explanation
Indices: 19722040--19722122 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
19722030 AAATTAAAAA
* **
19722040 ATATATTAAAATAAATATTTATTATTTAATA-ATCATATATG
1 ATATATAAAAATAAATATTTATTAAATAATATATCATATATG
* *
19722081 ATATATAATAAATAATTATTTTTTAAATAATATTATCATATA
1 ATATATAA-AAATAAATATTTATTAAATAATA-TATCATATA
19722123 ATATGATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 7 0.21
42 19 0.56
44 8 0.24
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (42 bp):
ATATATAAAAATAAATATTTATTAAATAATATATCATATATG
Found at i:19729500 original size:16 final size:15
Alignment explanation
Indices: 19729470--19729505 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
19729460 ATTTTATAAA
19729470 AAAATTAATATTTAT
1 AAAATTAATATTTAT
*
19729485 TAAATTAATAATTTAT
1 AAAATTAAT-ATTTAT
19729501 AAAAT
1 AAAAT
19729506 AATGATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATTAATATTTAT
Found at i:19730277 original size:2 final size:2
Alignment explanation
Indices: 19730270--19730299 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19730260 TGAATTTTAC
19730270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19730300 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19730506 original size:81 final size:81
Alignment explanation
Indices: 19730383--19730557 Score: 278
Period size: 81 Copynumber: 2.2 Consensus size: 81
19730373 AGTTAGTATG
* *
19730383 AATCAATTAAATCGACGAAAATTGAGTAAATCCAATTAATTTGATTTGATTTATTCGATTTTAAT
1 AATCAATTAAATTGACGAAAATTGAGCAAATCCAATTAATTTGATTTGATTTATTCGATTTTAAT
19730448 TATAATTAATTTTTTA
66 TATAATTAATTTTTTA
* * ** *
19730464 AATTAATTAAATTGATGAAAATTGAGCAAATTTAATTGATTTGATTTGATTTATTCGATTTTAAT
1 AATCAATTAAATTGACGAAAATTGAGCAAATCCAATTAATTTGATTTGATTTATTCGATTTTAAT
19730529 TATAATTAATTTTTTA
66 TATAATTAATTTTTTA
*
19730545 AATCAATAAAATT
1 AATCAATTAAATT
19730558 AATTAACTAG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (81 bp):
AATCAATTAAATTGACGAAAATTGAGCAAATCCAATTAATTTGATTTGATTTATTCGATTTTAAT
TATAATTAATTTTTTA
Found at i:19730834 original size:15 final size:15
Alignment explanation
Indices: 19730814--19730844 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19730804 CAAATTGATC
*
19730814 TAACCAAATCAATTT
1 TAACCAAAGCAATTT
19730829 TAACCAAAGCAATTT
1 TAACCAAAGCAATTT
19730844 T
1 T
19730845 GGTAGATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (15 bp):
TAACCAAAGCAATTT
Found at i:19731157 original size:16 final size:17
Alignment explanation
Indices: 19731117--19731158 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
19731107 TAAGTAAAGG
19731117 AATTTG-TATCCATAAA
1 AATTTGTTATCCATAAA
* *
19731133 AAGTAGTTA-CCATAAA
1 AATTTGTTATCCATAAA
19731149 AATTTGTTAT
1 AATTTGTTAT
19731159 TACTAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (17 bp):
AATTTGTTATCCATAAA
Found at i:19736110 original size:18 final size:17
Alignment explanation
Indices: 19736089--19736134 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
19736079 TTTTAAACAT
19736089 ATTTTTCTATATTTCATA
1 ATTTTT-TATATTTCATA
* *
19736107 ATTTTTTTTTATTTCGTA
1 A-TTTTTTATATTTCATA
19736125 ATTTTTTATA
1 ATTTTTTATA
19736135 ATTCGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 11 0.46
19 5 0.21
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTTTTATATTTCATA
Found at i:19736139 original size:17 final size:17
Alignment explanation
Indices: 19736089--19736142 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
19736079 TTTTAAACAT
*
19736089 ATTTTTCTATATTTCATA
1 ATTTTT-TATATTTCGTA
*
19736107 ATTTTTTTTTATTTCGTA
1 A-TTTTTTATATTTCGTA
*
19736125 ATTTTTTATAATTCGTA
1 ATTTTTTATATTTCGTA
19736142 A
1 A
19736143 AAAAGTAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 15 0.48
18 11 0.35
19 5 0.16
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (17 bp):
ATTTTTTATATTTCGTA
Found at i:19737398 original size:9 final size:9
Alignment explanation
Indices: 19737380--19737413 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19737370 GGTAGCAAGT
*
19737380 AAAAGGAAA
1 AAAAGAAAA
19737389 AAAAGAAAA
1 AAAAGAAAA
19737398 AAAAGAAAA
1 AAAAGAAAA
19737407 GAAAAGA
1 -AAAAGA
19737414 TGATGTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:19746870 original size:20 final size:20
Alignment explanation
Indices: 19746832--19746871 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19746822 TTATTTATCA
*
19746832 TGAAGTTAAATGACAGATTC
1 TGAAGTTAAATCACAGATTC
*
19746852 TGAAGTTAAATCACTGATTC
1 TGAAGTTAAATCACAGATTC
19746872 AGTTTACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
TGAAGTTAAATCACAGATTC
Found at i:19753324 original size:29 final size:31
Alignment explanation
Indices: 19753247--19753324 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 31
19753237 TAATGAAAAT
* *
19753247 AAATTTTTAAGAGTTCAATTGATTCAAAATAA
1 AAATATTT-AGAGTTTAATTGATTCAAAATAA
* * *
19753279 AAATATTTAAAGCTTAATTGA-TCATAAT-A
1 AAATATTTAGAGTTTAATTGATTCAAAATAA
19753308 AAATA-TTAGGAGTTTAA
1 AAATATTTA-GAGTTTAA
19753325 ACGATTATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.08
29 12 0.32
30 6 0.16
31 10 0.26
32 7 0.18
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (31 bp):
AAATATTTAGAGTTTAATTGATTCAAAATAA
Found at i:19756315 original size:14 final size:14
Alignment explanation
Indices: 19756283--19756316 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19756273 AGTAATTTTA
*
19756283 AATTTTAAAATTTT
1 AATTTTAAAATTAT
*
19756297 TATTTTAAAATTAT
1 AATTTTAAAATTAT
19756311 AATTTT
1 AATTTT
19756317 TATATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTTTAAAATTAT
Found at i:19756316 original size:20 final size:20
Alignment explanation
Indices: 19756277--19756333 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
19756267 ATATTTAGTA
* *
19756277 ATTTTAAATTTTAAAATTTTT
1 ATTTTAAA-ATTATAATTTTT
19756298 ATTTTAAAATTATAATTTTT
1 ATTTTAAAATTATAATTTTT
* * *
19756318 ATATAAAAATAATAAT
1 ATTTTAAAATTATAAT
19756334 AATAAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTAAAATTATAATTTTT
Found at i:19758056 original size:19 final size:20
Alignment explanation
Indices: 19758034--19758082 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19758024 CCGTCAATTA
*
19758034 TAATAATTAATAA-AAACTT
1 TAATAATAAATAATAAACTT
* *
19758053 TAATAAAAAATAATAAAGTT
1 TAATAATAAATAATAAACTT
19758073 TAATAATAAA
1 TAATAATAAA
19758083 ATTCAATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAATAATAAATAATAAACTT
Found at i:19759296 original size:10 final size:10
Alignment explanation
Indices: 19759275--19759307 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
19759265 ATATAATGAT
19759275 AAAATA-ATA
1 AAAATATATA
19759284 AAAATATATA
1 AAAATATATA
19759294 AAAATATA-A
1 AAAATATATA
19759303 AAAAT
1 AAAAT
19759308 TTGATTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 12 0.52
10 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATATATA
Found at i:19760206 original size:20 final size:21
Alignment explanation
Indices: 19760181--19760226 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
19760171 TTAAGGTTCG
* *
19760181 TTTATGTTTGTTTGA-ATTTA
1 TTTATGTTCGTTTAAGATTTA
19760201 TTTATGTTCGTTTAAGATTTA
1 TTTATGTTCGTTTAAGATTTA
19760222 TTTAT
1 TTTAT
19760227 TTAAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.63
Consensus pattern (21 bp):
TTTATGTTCGTTTAAGATTTA
Found at i:19760238 original size:25 final size:25
Alignment explanation
Indices: 19760195--19760254 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
19760185 TGTTTGTTTG
**
19760195 AATTTATTTATGTTCGTTTAAGATT-T
1 AATTTATTTAAATTCGTTT--GATTAT
*
19760221 -ATTTATTTAAATTTGTTTGATTAT
1 AATTTATTTAAATTCGTTTGATTAT
19760245 AATTTATTTA
1 AATTTATTTA
19760255 TTGTTCATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 4 0.14
24 1 0.03
25 24 0.83
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (25 bp):
AATTTATTTAAATTCGTTTGATTAT
Found at i:19760932 original size:21 final size:22
Alignment explanation
Indices: 19760902--19760944 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
19760892 ATCTTCGTAC
19760902 TTACAATTTTTTTATTTT-TAAA
1 TTACAATTTTTTT-TTTTGTAAA
19760924 TTAC-ATTTTTTTTTTTGTAAA
1 TTACAATTTTTTTTTTTGTAAA
19760945 AAATAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
TTACAATTTTTTTTTTTGTAAA
Found at i:19760952 original size:27 final size:27
Alignment explanation
Indices: 19760922--19760973 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
19760912 TTTATTTTTA
* *
19760922 AATTACATTTTT-TTTTTTGTAAAAAAT
1 AATTA-ATTTTTCTATTTTATAAAAAAT
19760949 AATTAATTTTTCTATTTTATAAAAA
1 AATTAATTTTTCTATTTTATAAAAA
19760974 CAAAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (27 bp):
AATTAATTTTTCTATTTTATAAAAAAT
Found at i:19767698 original size:24 final size:24
Alignment explanation
Indices: 19767670--19767715 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
19767660 GCATGCACAG
19767670 GTGGATCCACATGTATAGGTAGAA
1 GTGGATCCACATGTATAGGTAGAA
19767694 GTGGATCCACATGTATAGGTAG
1 GTGGATCCACATGTATAGGTAG
19767716 GGTGTCCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.26
Consensus pattern (24 bp):
GTGGATCCACATGTATAGGTAGAA
Found at i:19768776 original size:121 final size:122
Alignment explanation
Indices: 19768540--19768783 Score: 384
Period size: 121 Copynumber: 2.0 Consensus size: 122
19768530 ATGCGATGGG
19768540 TGGAAATGGTAATAATTATTTTTTTAATGAAGCTAGTCCTTGGTAACTTGTCTTCTTCTAGTGAT
1 TGGAAATGGTAATAATTATTTTTTTAATGAAGCTAGTCCTTGGTAACTTGTCTTCTTCTAGTGAT
* * * **
19768605 TGTAGTATGAGTCTTATTGTTTTGGAGTGGTTTGTTGAAGCAACGGAACACTAGCTA
66 TGTAGTATGAGTCTTAATGTTTTAGAGTGGTTTATTGAAGCAAAAGAACACTAGCTA
**
19768662 TGGAAATGGTAATAATTA-TTTTTTCGTGAAGCTAGTCCTTGGTAAACTTGTCTTCTTCTAGTGA
1 TGGAAATGGTAATAATTATTTTTTTAATGAAGCTAGTCCTTGGT-AACTTGTCTTCTTCTAGTGA
* *
19768726 TTGTAGTATGGGTTTTAAT-TTTTAGAGTGGTTTATTGAAGCAAAAGAACACTAGCTA
65 TTGTAGTATGAGTCTTAATGTTTTAGAGTGGTTTATTGAAGCAAAAGAACACTAGCTA
19768783 T
1 T
19768784 CTTACGTGAG
Statistics
Matches: 112, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
121 58 0.52
122 54 0.48
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (122 bp):
TGGAAATGGTAATAATTATTTTTTTAATGAAGCTAGTCCTTGGTAACTTGTCTTCTTCTAGTGAT
TGTAGTATGAGTCTTAATGTTTTAGAGTGGTTTATTGAAGCAAAAGAACACTAGCTA
Found at i:19775379 original size:147 final size:146
Alignment explanation
Indices: 19775109--19775396 Score: 400
Period size: 147 Copynumber: 2.0 Consensus size: 146
19775099 TTTAATTTTC
* * *
19775109 AAATTTATCGTAATTTTGTGTGTTTGGGATTGGATTGGGCTATGTTGCATTGGTAGAAAGGGCAT
1 AAATTTATCGTAATTTTGTGCGTTTGAGATTGGATTGGGCTATGTTGCATTGGTAGAAAGGGCAG
* *
19775174 GAGTTACTGGGACTTAAAATGAGAGACAAGAGATGATAATAAGACTTGAGATTGACAAAAATGAG
66 GAGTTACTGGGACTTAAAATGAGAGACAAGAGATAACAATAAGACTTGAGATTGACAAAAATGAG
* *
19775239 CAGATATCACATATCG
131 CAAATAGCACATATCG
* *
19775255 AAATTTGTCGTGATTTTGTGCGTTTGAGATTGGATTGGGCTATGTTGCATTGGTA-AAAGGGGGC
1 AAATTTATCGTAATTTTGTGCGTTTGAGATTGGATTGGGCTATGTTGCATTGGTAGAAA--GGGC
* * * * * *
19775319 AGGAGTT-GTCGTGACTTAAAATGAGAGACAAGAGATAACAGTGAGATTTGAGGTTGACAAAAAT
64 AGGAGTTACT-GGGACTTAAAATGAGAGACAAGAGATAACAATAAGACTTGAGATTGACAAAAAT
19775383 GAGCAAATAGCACA
128 GAGCAAATAGCACA
19775397 CATTAGAAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
145 3 0.02
146 52 0.42
147 69 0.56
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.29
Consensus pattern (146 bp):
AAATTTATCGTAATTTTGTGCGTTTGAGATTGGATTGGGCTATGTTGCATTGGTAGAAAGGGCAG
GAGTTACTGGGACTTAAAATGAGAGACAAGAGATAACAATAAGACTTGAGATTGACAAAAATGAG
CAAATAGCACATATCG
Found at i:19775617 original size:22 final size:23
Alignment explanation
Indices: 19775592--19775637 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
19775582 ATTTACTTTA
*
19775592 AGCC-ATAAAAAGCAATTCTCTT
1 AGCCAATAAAAAGCAATACTCTT
* *
19775614 AGCCAATAAATAGTAATACTCTT
1 AGCCAATAAAAAGCAATACTCTT
19775637 A
1 A
19775638 CTTAATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (23 bp):
AGCCAATAAAAAGCAATACTCTT
Found at i:19797605 original size:18 final size:18
Alignment explanation
Indices: 19797579--19797615 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19797569 TAATAAAATG
*
19797579 ATACGAAAAAAAAATGAT
1 ATACCAAAAAAAAATGAT
19797597 ATACCAAAAAAAAATGAT
1 ATACCAAAAAAAAATGAT
19797615 A
1 A
19797616 AGGAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (18 bp):
ATACCAAAAAAAAATGAT
Found at i:19797625 original size:18 final size:17
Alignment explanation
Indices: 19797573--19797616 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
19797563 TTATGATAAT
19797573 AAAATGAT-ACGAAAAA
1 AAAATGATAACGAAAAA
*
19797589 AAAATGATATACCAAAAA
1 AAAATGATA-ACGAAAAA
19797607 AAAATGATAA
1 AAAATGATAA
19797617 GGAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 16 0.64
ACGTcount: A:0.68, C:0.07, G:0.09, T:0.16
Consensus pattern (17 bp):
AAAATGATAACGAAAAA
Found at i:19801064 original size:2 final size:2
Alignment explanation
Indices: 19801057--19801088 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19801047 CGATCCACAA
19801057 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19801089 CTTCAACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19801077 original size:15 final size:15
Alignment explanation
Indices: 19801057--19801085 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19801047 CGATCCACAA
19801057 ATATATATATATATT
1 ATATATATATATATT
19801072 ATATATATATATAT
1 ATATATATATATAT
19801086 ATACTTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:19809034 original size:2 final size:2
Alignment explanation
Indices: 19809029--19809070 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
19809019 ACACACACAC
* *
19809029 AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19809071 TTATTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:19809061 original size:20 final size:20
Alignment explanation
Indices: 19809036--19809078 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
19809026 CACATATATA
19809036 TATATATATATATATTTATT
1 TATATATATATATATTTATT
19809056 TATATATATATATATTTATT
1 TATATATATATATATTTATT
19809076 TAT
1 TAT
19809079 TTATTGACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATATATATATATTTATT
Found at i:19815929 original size:25 final size:24
Alignment explanation
Indices: 19815901--19815951 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
19815891 CAAAAAAAGT
19815901 TTTAAGATTAAAAAAAATAAAATAA
1 TTTAAGATTAAAAAAAA-AAAATAA
* * * *
19815926 TTTATGTTTAAAATAAAAAACTAA
1 TTTAAGATTAAAAAAAAAAAATAA
19815950 TT
1 TT
19815952 AAAAATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (24 bp):
TTTAAGATTAAAAAAAAAAAATAA
Found at i:19819464 original size:23 final size:23
Alignment explanation
Indices: 19819434--19819480 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
19819424 GCTATCATTT
*
19819434 TCTTTTACATTAGACATTGTATC
1 TCTTTTACATTAAACATTGTATC
19819457 TCTTTTACATTAAACATTGTATC
1 TCTTTTACATTAAACATTGTATC
19819480 T
1 T
19819481 TGAGGACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (23 bp):
TCTTTTACATTAAACATTGTATC
Found at i:19824021 original size:19 final size:19
Alignment explanation
Indices: 19823984--19824026 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
19823974 GAAACTACAA
*
19823984 AAATATAAATATTCATTTAT
1 AAATAAAAATATT-ATTTAT
19824004 CAAATAAAAATATT-TTTAT
1 -AAATAAAAATATTATTTAT
19824023 AAAT
1 AAAT
19824027 TACATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
21 12 0.57
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAAAAATATTATTTAT
Found at i:19826920 original size:655 final size:648
Alignment explanation
Indices: 19825836--19827187 Score: 2077
Period size: 655 Copynumber: 2.1 Consensus size: 648
19825826 TGACATATGC
19825836 ATTAGTATATCCATGTATTTAATTTCCCTAAATTCAATTATCCATTGATGTTGATGCATACATGA
1 ATTAGTATATCCATGTATTTAATTTCCCTAAATTCAATTATCCATTGATGTTGATGCATACATGA
*
19825901 AGGCTATGTATTCTCTTTTTTTTTTTTTTAACATTTAAGATCAGAAAAAACCACAAGTTTCAAAG
66 AGGCTATGTA--------TTTTTTTTTTTAACATTTAAGATCAGAAAAAACCACAAGCTTCAAAG
19825966 AAGATTTATATTAAATTTATAAATTATCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTA
123 AAGATTTATATTAAATTTATAAATTATCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTA
*
19826031 AGAAAGACTATATATTCATACAATATTATGGAATTTTTTTCTAAAGAAAAGAATATATAGAACTA
188 AGAAAGACTATATATCCATACAATATTATGGAATTTTTTTCTAAAGAAAAGAATATATAGAACTA
* *
19826096 GAAAATTTTTGTTCCTTTAAAATTTCTTTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATAC
253 GAAAACTTTTGTTCCTTTAAAA-TTCTTTTTTTATACAGTTACATTGAAGAGAGTTGGTTCATAC
* * *
19826161 TTTTCTTTTTTAAATGTATATATCACTAGAGTACTATTCACATTAAGCTTGATAATTATGCATTG
317 TTTTCTTTTTTAAATGTAAATATCACTAGAGCACTATTCACATGAAGCTTGATAATTATGCATTG
*
19826226 AATAAGATAAGTAATTAATTTTGTATAAACTCAAAAAATAGCTTATAAAACTTAAAATAATATAT
382 AATAAGATAAGTAATTAATTTTGTATAAACTCAAAAAATAGCATATAAAACTTAAAATAATATAT
* * *
19826291 TTAGAATTTAGGATTTAGTTTAGTTAATTCATACAATTTTTTTTTTAATAATTGTATTTATGACC
447 ATAGAATTTAAGATTTAGTTTAGTTAATTCATACAA---TTTTTCTAATAATTGTATTTATGACC
* * * *
19826356 ATTGGCCCTTTCTGAGTAATTGTCCTAATCTTTCTTCAATGGTGTTTGGTACACTTACCTTTTTA
509 ATTGGCCCTTTCCGAGAAATTGTCCTAATCCTTCTTCAATGGTGTTTGGTACACTTACCTTTTCA
* ** *
19826421 ATTTATAGATTTTTCCTTTCTTTCCTTTTC-AGAAATATTAACTTGTCTATTTCATTTCTGGTTG
574 ATTTATAGATTTTT-CTTTCTTTCCTTCTCGA-AAATACAAACTTGTCTATTTCATTTCTGGTAG
19826485 GTATATATAAGA
637 GTATATATAAGA
* *
19826497 ATTAGTATATCCATGTATTTAATTTCCCTAAATTCAATTATCCATTTGATGTTGATGTATATATG
1 ATTAGTATATCCATGTATTTAATTTCCCTAAATTCAATTATCCA-TTGATGTTGATGCATACATG
*
19826562 AAGGCTATGTA-TTTTTTTTTTAACGTTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTT
65 AAGGCTATGTATTTTTTTTTTTAACATTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTT
* * *
19826626 ATATTAAATTTATATATTATCTATCAAGAGAAATTGTAGATAGTGGAAATTGAATCTAAGAAAGA
130 ATATTAAATTTATAAATTATCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGA
* * *
19826691 CTATATGTCCATACTACAATATTATGGCATTTTTTTTTTAAAGAAAAG-A-ATATAGAACTAGAA
195 CTATATATCC--A-TACAATATTATGG-AATTTTTTTCTAAAGAAAAGAATATATAGAACTAGAA
* *
19826754 AACTTTTGTTCCTTTAGAA-T-TTTTTTTATACAGTTACATTGAAGAGAGTTGGTTCATCCTTTT
256 AACTTTTGTTCCTTTAAAATTCTTTTTTTATACAGTTACATTGAAGAGAGTTGGTTCATAC---T
*
19826817 TTTTTTTTTTAAATGTAAATATCACTAGAGCACTATTCACATGAAGCTTGATAATTATGCATTGA
318 TTTCTTTTTTAAATGTAAATATCACTAGAGCACTATTCACATGAAGCTTGATAATTATGCATTGA
*
19826882 ATAAGATAAGTAATTAATTTTGTATAAGCTCAAAAAATAGCATATAAAACTTAAAATAATATATA
383 ATAAGATAAGTAATTAATTTTGTATAAACTCAAAAAATAGCATATAAAACTTAAAATAATATATA
* * *
19826947 TAGAATTTAAGATTTAGTTTAGTTAATTTATATAATTTTTCTACTAATTGTATTTATGACCATTG
448 TAGAATTTAAGATTTAGTTTAGTTAATTCATACAATTTTTCTAATAATTGTATTTATGACCATTG
* *
19827012 GCCCTTTCCGAGAAATTGTCCTTATCCTTCTTCAATGGTGTTTGGTACACTTAGCTTTTCAATTT
513 GCCCTTTCCGAGAAATTGTCCTAATCCTTCTTCAATGGTGTTTGGTACACTTACCTTTTCAATTT
* *
19827077 GTAGATTTTTTTTTCTTTCCTTCTCGAAAATACAAACTTGTCTATTTCATTTCTGGTAGGTATAT
578 ATAGATTTTTCTTTCTTTCCTTCTCGAAAATACAAACTTGTCTATTTCATTTCTGGTAGGTATAT
* *
19827142 ATATGT
643 ATAAGA
*
19827148 ATTAGTACATCCATGTATGTTAATTTCCCTAAATTCAATT
1 ATTAGTATATCCATGTAT-TTAATTTCCCTAAATTCAATT
19827188 TTTTTTGGGA
Statistics
Matches: 639, Mismatches: 42, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
651 69 0.11
652 155 0.24
653 122 0.19
655 188 0.29
656 14 0.02
657 18 0.03
661 44 0.07
662 29 0.05
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (648 bp):
ATTAGTATATCCATGTATTTAATTTCCCTAAATTCAATTATCCATTGATGTTGATGCATACATGA
AGGCTATGTATTTTTTTTTTTAACATTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTA
TATTAAATTTATAAATTATCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGAC
TATATATCCATACAATATTATGGAATTTTTTTCTAAAGAAAAGAATATATAGAACTAGAAAACTT
TTGTTCCTTTAAAATTCTTTTTTTATACAGTTACATTGAAGAGAGTTGGTTCATACTTTTCTTTT
TTAAATGTAAATATCACTAGAGCACTATTCACATGAAGCTTGATAATTATGCATTGAATAAGATA
AGTAATTAATTTTGTATAAACTCAAAAAATAGCATATAAAACTTAAAATAATATATATAGAATTT
AAGATTTAGTTTAGTTAATTCATACAATTTTTCTAATAATTGTATTTATGACCATTGGCCCTTTC
CGAGAAATTGTCCTAATCCTTCTTCAATGGTGTTTGGTACACTTACCTTTTCAATTTATAGATTT
TTCTTTCTTTCCTTCTCGAAAATACAAACTTGTCTATTTCATTTCTGGTAGGTATATATAAGA
Found at i:19828776 original size:661 final size:657
Alignment explanation
Indices: 19827400--19830509 Score: 5135
Period size: 656 Copynumber: 4.7 Consensus size: 657
19827390 TTGATAGTCA
**
19827400 CTAAATTCAATTATTTATTTGATGTTGATGTATACATGAAGGCTATGTATTC-TTTTTTTTTTTT
1 CTAAATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATTCTTTTTTTTTTTTT
* * * *
19827464 TTTAACATTTAAGATCAGAAAAAACCACAACCTTCAAAGAAGATTTATATAAAATTTACAAATTA
66 TTTAACGTTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTATATTAAATTTATAAATTA
*
19827529 TCTATCAAGAGAAATTGTAGATAGCGAAAATCGAATCTAAGAAAGACTATATATTCATACTACAA
131 TCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGACTATATATTCATACTACAA
19827594 TATTATGCAATTTTTTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAATT
196 TATTATGCAATTTTTTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAATT
19827659 TTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATATCAC
261 TTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATATCAC
* * * *
19827724 TAGAGTACTATGCACATTAAGCTTGATAATTAAGAATTGAATAAGATAAGTAATTAGTTTTGTAT
326 TAGAGTACTATTCACATTAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTGTAT
19827789 AAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTAGTTA
391 AAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTAGTTA
* * *
19827854 AATCATACAATATTTTTAATAATTGTATTTATGACCATTGACCCTTTCTGAGTAATTGTCCTAAT
456 ATTCATACAATTTTTTTAATAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCTAAT
* *
19827919 CTTTCTTCAATGGTGTTTGGTACACTTACCTTTTCAATTTGTAGA-TTTTTTTTTCTTTCCTTTT
521 CTTTCTTCAATGGTGTTTGGTACACATACCTTTTCAATTTGTAGACTTTTCTTTTCTTTCCTTTT
** * **
19827983 TGAAAATATTAACTTGTCTATTTCATTTCTGGTAGGTATATATATCTATTAGTATGTCCATGCGT
586 CAAAAATATTAACTTGTCTATTTCATTTCTGGTAGGTATATATATGTATTAGTACATCCAT--GT
*
19828048 TTAATTTCC
649 TTAATTACC
* * * *
19828057 CTAAATTTAATTATCCATTTGATGTTGGTGTATACATGAAGGCTACGTACTCTTTTTTTTTTTTT
1 CTAAATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATTCTTTTTTTTTTTTT
* * * *
19828122 CCTTTAACGCTTAAGATAAAAAAAAACCACAAGCTTCAAAGAAGATTTATATCAAATTTATAAAT
66 --TTTAACGTTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTATATTAAATTTATAAAT
* * * * *
19828187 TATCTATCAATAGAAATTGTAGATAGCGCAAATCAAATCTAAGAAAGACCATATATTTATACTAC
129 TATCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGACTATATATTCATACTAC
19828252 AATATTATGCAATTTTTTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAA
194 AATATTATGCAATTTTTTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAA
*
19828317 TTTTTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATAC
259 -TTTTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATAT
*
19828382 CACTAGAGTACTATTCACATTAAGCTTGATAATTATACATTGAATAAGATAAGTAATTAATTTTG
323 CACTAGAGTACTATTCACATTAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTG
*
19828447 TATAAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTTG
388 TATAAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTAG
*
19828512 TTAATTCATACAATTTTTTTAACAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCT
453 TTAATTCATACAATTTTTTTAATAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCT
*
19828577 AATCTTTCTTCAATGGTGTTTGGTACACATAGCTTTTCAATTTGTAGACTTTTCTTTTCTTTCCT
518 AATCTTTCTTCAATGGTGTTTGGTACACATACCTTTTCAATTTGTAGACTTTTCTTTTCTTTCCT
* *
19828642 TTTCAAAAATATTGACTTGTCTATTTCATTTCTGGTTGGTATATATATGTATTAGTACATCCATG
583 TTTCAAAAATATTAACTTGTCTATTTCATTTCTGGTAGGTATATATATGTATTAGTACATCCATG
19828707 TTTAATTACC
648 TTTAATTACC
*
19828717 CTATATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATTCTTTTTTTTTTTTT
1 CTAAATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATTCTTTTTTTTTTTTT
* *
19828782 TTTAACGTTTAAGATCAGAAAAAACCCCAAGCTTCAAAGAAGATTTATATTAAATTTATAAATTG
66 TTTAACGTTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTATATTAAATTTATAAATTA
*
19828847 TCTATCAAGAGAAATTGTAGATAGCGGAAATTGAATCTAAGAAAGACTATATATTCATACTACAA
131 TCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGACTATATATTCATACTACAA
19828912 TATTATGGC-ATTTTTTTAAAAGAAAAG-A-ATATAGAACTAGAAAATTTTTGTTCCTTTAGAAT
196 TATTAT-GCAATTTTTTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAAT
* * *
19828974 TTTTTTTATATAGTTGCACTGAAGAGAGTTGGTTCATACTTTTTTTTTTTTAAATGTAAATATCA
260 TTTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATATCA
* *
19829039 CTAGAGTACTATTGACATTAAGCTTGATAATTATGCATTGAATAAGATATGTAATTAATTTTGTA
325 CTAGAGTACTATTCACATTAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTGTA
* *
19829104 TAAACTCAAAAAATAGCGTAGAAAACTTAAAATAATATATTTAGAATTTAGG-TTTAGTTTAGTT
390 TAAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTAGTT
19829168 AATTCATACAATTTTTTTTAATAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCTA
455 AATTCATACAA-TTTTTTTAATAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCTA
*
19829233 ATCTTTCTTCAATGGTGTTTGGTACACATAGCTTTTCAATTTGTAGACTTTTCTTTTCTTTCCTT
519 ATCTTTCTTCAATGGTGTTTGGTACACATACCTTTTCAATTTGTAGACTTTTCTTTTCTTTCCTT
*
19829298 TTCAAAAATATTAACTTGTCTATTTCATTTCTGGTTGGTATATATATGTATTAGTACATCCATGT
584 TTCAAAAATATTAACTTGTCTATTTCATTTCTGGTAGGTATATATATGTATTAGTACATCCATGT
19829363 TTAATTACC
649 TTAATTACC
* *
19829372 CTATATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATCCTTTTTTTTTTTTT
1 CTAAATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATTC-TTTTTTTTTTTT
*
19829437 TTTTAACGTTTAAGATCAGAAAAAACCCCAAGCTTCAAAGAAGATTTATATTAAATTTATAAATT
65 TTTTAACGTTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTATATTAAATTTATAAATT
* **
19829502 GTCTATCAAGAGAAATTGTAGATAGTAGAAATCGAATCTAAGAAAGACTATATATTCATACTACA
130 ATCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGACTATATATTCATACTACA
* * *
19829567 ATATTATGGAATTTTGTTT-AAAGAAAAGAATATATAGAACCAGAAAATTTTTGTTCCTTCAGAA
195 ATATTATGCAATTTT-TTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAA
* * *
19829631 ATTTTTTTATATAGTTACATTGAAGAGAATTGGTTCATAC-TCTTTTTTTT-AAATGTAAATATC
259 TTTTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATATC
*
19829694 ACTAGAGTACTGTTCACATTAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTGT
324 ACTAGAGTACTATTCACATTAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTGT
* *
19829759 ATAAACTCAAAAAATAGCATATCAAACTTAAAATAATATATTTAGAATTTAGGATTTCGTTTAGT
389 ATAAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTAGT
19829824 TAATTCATACAATTTTTTTAATAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCTA
454 TAATTCATACAATTTTTTTAATAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCTA
* *
19829889 ATCTTTCTTCAATGGTGTTTGGTACACTTACCTTTTCAATTTGTAGATTTTTCTTTTCTTTCCTT
519 ATCTTTCTTCAATGGTGTTTGGTACACATACCTTTTCAATTTGTAGACTTTTCTTTTCTTTCCTT
* * *
19829954 TTCCAAAATATTAACTTGTCTATTTCATTTCTGGTAGGTATATATATGAATTAGTATATCCATGT
584 TTCAAAAATATTAACTTGTCTATTTCATTTCTGGTAGGTATATATATGTATTAGTACATCCATG-
*
19830019 ATTTAATTTCC
648 -TTTAATTACC
* * *
19830030 CTAAATTCAATTATCCATTTGATTTTGATGTATTCATGAAAGCTATGTATTC--TTTTTTTTTTT
1 CTAAATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATTCTTTTTTTTTTTTT
*
19830093 TTTAACATTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTATATTAAA-TTATAAATTA
66 TTTAACGTTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTATATTAAATTTATAAATTA
* * *
19830157 TCTATCAAGAGCAATTCTAGATAGCGGAAATCGAATCT----AAGACTATATATTCATACTAAAA
131 TCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGACTATATATTCATACTACAA
* * *
19830218 TATTATGGAATATTTTTT-AAATAAAAGAATATGTAGAACTAGAAAATTTTTGTTCCTTTAGAAT
196 TATTATGCAAT-TTTTTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAAT
* *
19830282 TTTTTTTATATATTTACATTGAAGAGAGTTGGTTGATAC---TTTTTTTTAAAATGTAAATATCA
260 TTTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATATCA
*
19830344 CTAGAGTACTATTCACAATAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTGTA
325 CTAGAGTACTATTCACATTAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTGTA
* * *
19830409 TAAACTCAAAAAATAGCGTATAAAACTTAAAATAATATATTTAAAATTTAGGATCTAGTTTAGTT
390 TAAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTAGTT
19830474 AATTCATACAAATTTTTTTAATAATTGTATTTATGA
455 AATTCATAC-AATTTTTTTAATAATTGTATTTATGA
19830510 TAAACAATGT
Statistics
Matches: 2311, Mismatches: 124, Indels: 43
0.93 0.05 0.02
Matches are distributed among these distances:
648 8 0.00
649 146 0.06
650 139 0.06
651 3 0.00
654 65 0.03
655 479 0.21
656 493 0.21
657 82 0.04
658 277 0.12
659 2 0.00
660 251 0.11
661 294 0.13
662 72 0.03
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (657 bp):
CTAAATTCAATTATCCATTTGATGTTGATGTATACATGAAGGCTATGTATTCTTTTTTTTTTTTT
TTTAACGTTTAAGATCAGAAAAAACCACAAGCTTCAAAGAAGATTTATATTAAATTTATAAATTA
TCTATCAAGAGAAATTGTAGATAGCGGAAATCGAATCTAAGAAAGACTATATATTCATACTACAA
TATTATGCAATTTTTTTAAAAGAAAAGAATATATAGAACTAGAAAATTTTTGTTCCTTTAGAATT
TTTTTTATATAGTTACATTGAAGAGAGTTGGTTCATACTTTTTTTTTTTAAAATGTAAATATCAC
TAGAGTACTATTCACATTAAGCTTGATAATTATGCATTGAATAAGATAAGTAATTAATTTTGTAT
AAACTCAAAAAATAGCATATAAAACTTAAAATAATATATTTAGAATTTAGGATTTAGTTTAGTTA
ATTCATACAATTTTTTTAATAATTGTATTTATGACCATTGGCCCTTTCTGAGTAATTGTCCTAAT
CTTTCTTCAATGGTGTTTGGTACACATACCTTTTCAATTTGTAGACTTTTCTTTTCTTTCCTTTT
CAAAAATATTAACTTGTCTATTTCATTTCTGGTAGGTATATATATGTATTAGTACATCCATGTTT
AATTACC
Found at i:19830440 original size:21 final size:21
Alignment explanation
Indices: 19830406--19830445 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19830396 AATTAATTTT
19830406 GTATAAACTCAAAA-AATAGC
1 GTATAAACTCAAAATAATAGC
*
19830426 GTATAAAACTTAAAATAATA
1 GTAT-AAACTCAAAATAATA
19830446 TATTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (21 bp):
GTATAAACTCAAAATAATAGC
Found at i:19833811 original size:15 final size:14
Alignment explanation
Indices: 19833767--19833827 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
19833757 TAGGGTTTCG
19833767 AGGGTTTATGATTTT
1 AGGGTTTA-GATTTT
* *
19833782 TGGGTTTGGAGTTTT
1 AGGGTTTAGA-TTTT
19833797 AGGGTTTTAGATTTT
1 AGGG-TTTAGATTTT
*
19833812 AAGGTTTTAGATTTT
1 -AGGGTTTAGATTTT
19833827 A
1 A
19833828 AGCTTAGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.08
15 27 0.71
16 8 0.21
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (14 bp):
AGGGTTTAGATTTT
Found at i:19833828 original size:15 final size:15
Alignment explanation
Indices: 19833793--19833829 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
19833783 GGGTTTGGAG
*
19833793 TTTTAGGGTTTTAGA
1 TTTTAAGGTTTTAGA
19833808 TTTTAAGGTTTTAGA
1 TTTTAAGGTTTTAGA
19833823 TTTTAAG
1 TTTTAAG
19833830 CTTAGGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (15 bp):
TTTTAAGGTTTTAGA
Found at i:19834566 original size:35 final size:35
Alignment explanation
Indices: 19834544--19834620 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
19834534 TCGTGTGTCT
19834544 GAAAATAAAGATGATCGAGATTGAATAGTAAGTTA
1 GAAAATAAAGATGATCGAGATTGAATAGTAAGTTA
* * *
19834579 GAGAATAAAGATGACCGAGATTGAATAGTAAGTAA
1 GAAAATAAAGATGATCGAGATTGAATAGTAAGTTA
19834614 GAGAAAT
1 GA-AAAT
19834621 GAAAACAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 34 0.92
36 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.25, T:0.22
Consensus pattern (35 bp):
GAAAATAAAGATGATCGAGATTGAATAGTAAGTTA
Found at i:19834985 original size:33 final size:33
Alignment explanation
Indices: 19834948--19835099 Score: 107
Period size: 33 Copynumber: 4.7 Consensus size: 33
19834938 ATTGGGTTCA
* *
19834948 AGATAATCTAGATTTAAATCTTTCTTTGGTGCC
1 AGATAAACTAGACTTAAATCTTTCTTTGGTGCC
* * * **
19834981 AGATAAACTGGGCTT-AA--GTT-TGGGGTGCC
1 AGATAAACTAGACTTAAATCTTTCTTTGGTGCC
* * *
19835010 AAATAATCTA-AGCTTAAATCTTTCTTTTGTGCC
1 AGATAAACTAGA-CTTAAATCTTTCTTTGGTGCC
* * *
19835043 AGATAAACTAGGCTTAAATCATTCTTTGATGCC
1 AGATAAACTAGACTTAAATCTTTCTTTGGTGCC
** *
19835076 AGATAAGTTAGGCTTAAAATCTTT
1 AGATAAACTAGACTT-AAATCTTT
19835100 TCATGGTATG
Statistics
Matches: 88, Mismatches: 24, Indels: 13
0.70 0.19 0.10
Matches are distributed among these distances:
29 17 0.19
30 4 0.05
32 4 0.05
33 56 0.64
34 7 0.08
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (33 bp):
AGATAAACTAGACTTAAATCTTTCTTTGGTGCC
Found at i:19835160 original size:102 final size:98
Alignment explanation
Indices: 19835021--19835237 Score: 249
Period size: 98 Copynumber: 2.2 Consensus size: 98
19835011 AATAATCTAA
* * * ** *
19835021 GCTTAAATCTTTCTTTTGTGCCAGATAAACTAGGCTTAAATCATTCTTTGATGCCAGATAAGTTA
1 GCTTAAGTATTTCTTTTGTACCAGATAAACTAGGCTT-AA--ATT-TAGGATGCCAGAGAAGTTA
* **
19835086 GGCTTAAAATCTTTTCATGGTATGCTAGATAATTTGG
62 GGCTTAAAATCTTTTCATGGTATGCCAGATAATCAGG
* * *
19835123 GCTTAAGTATTTCTTTTGTACTAGATAAACT-GTGCTTAAATTTAGGGTGCCAGAGAAGTTGGGC
1 GCTTAAGTATTTCTTTTGTACCAGATAAACTAG-GCTTAAATTTAGGATGCCAGAGAAGTTAGGC
*
19835187 TTAAAATCTTTTCATGGTGTGCCAGATAATCAGG
65 TTAAAATCTTTTCATGGTATGCCAGATAATCAGG
19835221 GCTT-AGATATTTCTTTT
1 GCTTAAG-TATTTCTTTT
19835238 ACGCCAGTTA
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
97 2 0.02
98 61 0.61
99 3 0.03
101 3 0.03
102 31 0.31
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (98 bp):
GCTTAAGTATTTCTTTTGTACCAGATAAACTAGGCTTAAATTTAGGATGCCAGAGAAGTTAGGCT
TAAAATCTTTTCATGGTATGCCAGATAATCAGG
Found at i:19835250 original size:98 final size:98
Alignment explanation
Indices: 19835072--19835259 Score: 252
Period size: 98 Copynumber: 1.9 Consensus size: 98
19835062 CATTCTTTGA
* * **
19835072 TGCCAGATAAGTTAGGCTTAAAATCTTTTCATGGTATGCTAGATAATTTGGGCTTAAGTATTTCT
1 TGCCAGAGAAGTTAGGCTTAAAATCTTTTCATGGTATGCCAGATAATCAGGGCTTAAGTATTTCT
** * *
19835137 TTTGTACTAGATAAACTGTGCTTAAATTTAGGG
66 TTTACACCAGATAAACTGAGCTTAAATTTAGGG
* *
19835170 TGCCAGAGAAGTTGGGCTTAAAATCTTTTCATGGTGTGCCAGATAATCAGGGCTT-AGATATTTC
1 TGCCAGAGAAGTTAGGCTTAAAATCTTTTCATGGTATGCCAGATAATCAGGGCTTAAG-TATTTC
* *
19835234 TTTTACGCCAGTTAAACTGAGCTTAA
65 TTTTACACCAGATAAACTGAGCTTAA
19835260 GACTTTGTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 2 0.03
98 75 0.97
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (98 bp):
TGCCAGAGAAGTTAGGCTTAAAATCTTTTCATGGTATGCCAGATAATCAGGGCTTAAGTATTTCT
TTTACACCAGATAAACTGAGCTTAAATTTAGGG
Found at i:19835463 original size:22 final size:22
Alignment explanation
Indices: 19835438--19835532 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 22
19835428 GATAATCTGG
* *
19835438 GCTTATGTGCTAGTTAATTTAA
1 GCTTATGTGCTAGCTAATCTAA
* ** * *
19835460 GCTTATGTGCCATTTAAACT-G
1 GCTTATGTGCTAGCTAATCTAA
*
19835481 GACTTATATGCTAGCTAATCTAA
1 G-CTTATGTGCTAGCTAATCTAA
* *
19835504 GCTTATGTTCTAGCTAATCTAG
1 GCTTATGTGCTAGCTAATCTAA
19835526 GCTTATG
1 GCTTATG
19835533 GCTTTTCGAT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 1 0.02
22 55 0.96
23 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (22 bp):
GCTTATGTGCTAGCTAATCTAA
Found at i:19835531 original size:44 final size:43
Alignment explanation
Indices: 19835430--19835531 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 43
19835420 CTTTTTTAGA
* * * **
19835430 TAATCTGGGCTTATGTGCTAGTTAATTTAAGCTTATGTGCCATT
1 TAATCT-GGCTTATATGCTAGCTAATCTAAGCTTATGTGCCAGC
* * *
19835474 TAAACTGGACTTATATGCTAGCTAATCTAAGCTTATGTTCTAGC
1 TAATCTGG-CTTATATGCTAGCTAATCTAAGCTTATGTGCCAGC
19835518 TAATCTAGGCTTAT
1 TAATCT-GGCTTAT
19835532 GGCTTTTCGA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
43 2 0.04
44 43 0.91
45 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (43 bp):
TAATCTGGCTTATATGCTAGCTAATCTAAGCTTATGTGCCAGC
Found at i:19836175 original size:12 final size:11
Alignment explanation
Indices: 19836159--19836211 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
19836149 TAGAGCCACA
19836159 TTTATTTTTCT
1 TTTATTTTTCT
19836170 ATTTATTTTTCT
1 -TTTATTTTTCT
19836182 TTCT-TTCTTTCT
1 TT-TATT-TTTCT
*
19836194 TTTATTTTACT
1 TTTATTTTTCT
19836205 TTT-TTTT
1 TTTATTTT
19836212 ACCTTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 4 0.11
11 12 0.32
12 21 0.57
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTTTTCT
Found at i:19839827 original size:20 final size:20
Alignment explanation
Indices: 19839802--19839840 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19839792 CAGGTCCGGG
19839802 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
*
19839822 CCCGGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
19839841 GCCCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:19840167 original size:12 final size:12
Alignment explanation
Indices: 19840140--19840172 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
19840130 AATTATCTAG
19840140 ATTTTT-TTTTA
1 ATTTTTATTTTA
19840151 A-TTTTATTTTA
1 ATTTTTATTTTA
19840162 ATTTTTATTTT
1 ATTTTTATTTT
19840173 GGAGGGCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 7 0.35
12 9 0.45
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:19840552 original size:31 final size:31
Alignment explanation
Indices: 19840487--19840553 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
19840477 AATTTCCAGA
* *
19840487 TTCCGGCGAAAATTCCGGCGACTTTTAAATT
1 TTCCGGCGAAAATTCCGACGACTTTTAAAGT
* *
19840518 TTCCGGCGATAATTCCGACGAAC-TTTGAAGT
1 TTCCGGCGAAAATTCCGACG-ACTTTTAAAGT
19840549 TTCCG
1 TTCCG
19840554 ACGACAGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (31 bp):
TTCCGGCGAAAATTCCGACGACTTTTAAAGT
Found at i:19840645 original size:19 final size:19
Alignment explanation
Indices: 19840621--19840665 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
19840611 TCCGGCCAAT
19840621 TTCCGGCGAAATTCCCAGA
1 TTCCGGCGAAATTCCCAGA
* * *
19840640 TTCCGGTGAATTTTCCAGA
1 TTCCGGCGAAATTCCCAGA
*
19840659 ATCCGGC
1 TTCCGGC
19840666 ACCGGCGTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (19 bp):
TTCCGGCGAAATTCCCAGA
Found at i:19841625 original size:156 final size:156
Alignment explanation
Indices: 19841010--19841607 Score: 1097
Period size: 156 Copynumber: 3.8 Consensus size: 156
19841000 TTTTTCCTTA
* *
19841010 TTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACTCCT
19841075 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
* * *
19841140 AATTAATTACTTGGCTGATTTTGATTTTTT
130 AATTAATTAATTGGTTGATCTTGA---TTT
19841170 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
19841235 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
19841300 ATTAATTAATTGGTTGATCTTGATTT
131 ATTAATTAATTGGTTGATCTTGATTT
19841326 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
19841391 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
19841456 ATTAATTAATTGGTTGATCTTGATTT
131 ATTAATTAATTGGTTGATCTTGATTT
* *
19841482 TTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCTTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
19841547 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
19841608 AACAACTAAC
Statistics
Matches: 431, Mismatches: 7, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
156 283 0.66
159 113 0.26
160 35 0.08
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (156 bp):
TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
ATTAATTAATTGGTTGATCTTGATTT
Found at i:19843570 original size:9 final size:9
Alignment explanation
Indices: 19843556--19843629 Score: 80
Period size: 9 Copynumber: 8.0 Consensus size: 9
19843546 CAATAATGGG
19843556 TGAAAAAAA
1 TGAAAAAAA
19843565 TGAAAAAAAA
1 TG-AAAAAAA
*
19843575 T-ATAAAATA
1 TGA-AAAAAA
19843584 TGAAAAAAAA
1 TG-AAAAAAA
*
19843594 AGAGAAAAAA
1 TGA-AAAAAA
19843604 TGAAAAAAA
1 TGAAAAAAA
19843613 TG-AAAAAA
1 TGAAAAAAA
19843621 TGAAAAAAA
1 TGAAAAAAA
19843630 GATGAAAATG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
8 9 0.16
9 23 0.42
10 22 0.40
11 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (9 bp):
TGAAAAAAA
Found at i:19843590 original size:20 final size:20
Alignment explanation
Indices: 19843559--19843629 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
19843549 TAATGGGTGA
* *
19843559 AAAAAATG-AAAAAAAATAT
1 AAAAAATGAAAAAAAAAGAG
*
19843578 AAAATATGAAAAAAAAAGAG
1 AAAAAATGAAAAAAAAAGAG
*
19843598 AAAAAATG--AAAAAAA-TG
1 AAAAAATGAAAAAAAAAGAG
19843615 AAAAAATGAAAAAAA
1 AAAAAATGAAAAAAA
19843630 GATGAAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.20
18 7 0.16
19 12 0.27
20 16 0.36
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (20 bp):
AAAAAATGAAAAAAAAAGAG
Found at i:19843601 original size:29 final size:29
Alignment explanation
Indices: 19843558--19843637 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
19843548 ATAATGGGTG
* *
19843558 AAAAAAATGAAAAAAAAT-ATAAAATATGA
1 AAAAAAAAGAAAAAAAATGA-AAAAAATGA
*
19843587 AAAAAAAAGAGAAAAAATGAAAAAAATG-
1 AAAAAAAAGAAAAAAAATGAAAAAAATGA
*
19843615 -AAAAAATGAAAAAAAGATGAAAA
1 AAAAAAAAGAAAAAAA-ATGAAAA
19843638 TGAGAGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 13 0.30
28 7 0.16
29 23 0.52
30 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (29 bp):
AAAAAAAAGAAAAAAAATGAAAAAAATGA
Found at i:19843634 original size:19 final size:18
Alignment explanation
Indices: 19843559--19843637 Score: 90
Period size: 18 Copynumber: 4.2 Consensus size: 18
19843549 TAATGGGTGA
19843559 AAAAAATGAAAAAAAAT-
1 AAAAAATGAAAAAAAATG
*
19843576 ATAAAATATGAAAAAAAAAGAG
1 A-AAAA-ATG-AAAAAAAA-TG
19843598 AAAAAATG-AAAAAAATG
1 AAAAAATGAAAAAAAATG
19843615 AAAAAATGAAAAAAAGATG
1 AAAAAATGAAAAAAA-ATG
19843634 AAAA
1 AAAA
19843638 TGAGAGAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.19
18 17 0.32
19 10 0.19
20 11 0.21
21 4 0.08
22 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAAATGAAAAAAAATG
Found at i:19843637 original size:9 final size:8
Alignment explanation
Indices: 19843597--19843628 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
19843587 AAAAAAAAGA
19843597 GAAAAAAT
1 GAAAAAAT
19843605 GAAAAAAAT
1 G-AAAAAAT
19843614 GAAAAAAT
1 GAAAAAAT
19843622 GAAAAAA
1 GAAAAAA
19843629 AGATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (8 bp):
GAAAAAAT
Found at i:19843640 original size:17 final size:17
Alignment explanation
Indices: 19843559--19843629 Score: 72
Period size: 17 Copynumber: 3.9 Consensus size: 17
19843549 TAATGGGTGA
19843559 AAAAAATGAAAAAAAAT-
1 AAAAAATG-AAAAAAATG
*
19843576 ATAAAATATGAAAAAAAAAGAG
1 A-AAAA-ATG--AAAAAAA-TG
19843598 AAAAAATGAAAAAAATG
1 AAAAAATGAAAAAAATG
19843615 AAAAAATGAAAAAAA
1 AAAAAATGAAAAAAA
19843630 GATGAAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
17 17 0.36
18 11 0.23
19 3 0.06
20 11 0.23
21 4 0.09
22 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (17 bp):
AAAAAATGAAAAAAATG
Found at i:19844832 original size:25 final size:25
Alignment explanation
Indices: 19844804--19844894 Score: 100
Period size: 25 Copynumber: 3.8 Consensus size: 25
19844794 CATAAATGAG
**
19844804 AATCTTTAAGATGTTTTCAAATAAA
1 AATCTTTAAGACATTTTCAAATAAA
* * * *
19844829 AATCTTT--GA-GTCTT-AAATGAG
1 AATCTTTAAGACATTTTCAAATAAA
19844850 AATCTTTAAGACATTTTCAAATAAA
1 AATCTTTAAGACATTTTCAAATAAA
19844875 AATCTTTAAGACATTTTCAA
1 AATCTTTAAGACATTTTCAA
19844895 CCGAGAATCT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
21 12 0.22
22 4 0.07
23 4 0.07
24 3 0.05
25 32 0.58
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (25 bp):
AATCTTTAAGACATTTTCAAATAAA
Found at i:19844853 original size:21 final size:22
Alignment explanation
Indices: 19844791--19844926 Score: 69
Period size: 25 Copynumber: 5.9 Consensus size: 22
19844781 ATTTTGATGA
*
19844791 AGTCATAAATGAGAATCTTTAAG
1 AGTCTTAAATGAGAATCTTT-AG
* * *
19844814 ATGTTTTCAAATAAAAATCTTT-G
1 A-GTCTT-AAATGAGAATCTTTAG
19844837 AGTCTTAAATGAGAATCTTTAAG
1 AGTCTTAAATGAGAATCTTT-AG
* * * *
19844860 ACATTTTCAAATAAAAATCTTTAAG
1 A-GTCTT-AAATGAGAATCTTT-AG
* * **
19844885 ACATTTTCAACCGAGAATCTTTA-
1 A-GTCTT-AAATGAGAATCTTTAG
19844908 AGTCTTAAATGAGAATCTT
1 AGTCTTAAATGAGAATCTT
19844927 CAAATGAAAA
Statistics
Matches: 88, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
21 23 0.26
22 7 0.08
23 6 0.07
24 7 0.08
25 45 0.51
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (22 bp):
AGTCTTAAATGAGAATCTTTAG
Found at i:19844854 original size:46 final size:46
Alignment explanation
Indices: 19844791--19844881 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
19844781 ATTTTGATGA
**
19844791 AGTCATAAATGAGAATCTTTAAGATGTTTTCAAATAAAAATCTTTG
1 AGTCATAAATGAGAATCTTTAAGACATTTTCAAATAAAAATCTTTG
*
19844837 AGTCTTAAATGAGAATCTTTAAGACATTTTCAAATAAAAATCTTT
1 AGTCATAAATGAGAATCTTTAAGACATTTTCAAATAAAAATCTTT
19844882 AAGACATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (46 bp):
AGTCATAAATGAGAATCTTTAAGACATTTTCAAATAAAAATCTTTG
Found at i:19844903 original size:25 final size:25
Alignment explanation
Indices: 19844847--19844909 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
19844837 AGTCTTAAAT
*
19844847 GAGAATCTTTAAGACATTTTCAAAT
1 GAGAATCTTTAAGACATTTTCAAAC
* * *
19844872 AAAAATCTTTAAGACATTTTCAACC
1 GAGAATCTTTAAGACATTTTCAAAC
19844897 GAGAATCTTTAAG
1 GAGAATCTTTAAG
19844910 TCTTAAATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (25 bp):
GAGAATCTTTAAGACATTTTCAAAC
Found at i:19844925 original size:46 final size:46
Alignment explanation
Indices: 19844875--19845123 Score: 238
Period size: 45 Copynumber: 5.7 Consensus size: 46
19844865 TTCAAATAAA
* *
19844875 AATCTTTAAGACATTTTCAACCGAGAATCTTTAAGTCTTAAATGAG
1 AATCTTTAAGACATTTTCAACTGAGAATCTTTGAGTCTTAAATGAG
* *
19844921 AATC-TT----CA-----AA-TGAAAATCTTTGAGTTTTAAATGAG
1 AATCTTTAAGACATTTTCAACTGAGAATCTTTGAGTCTTAAATGAG
* * * *
19844956 AATCTTTAAGACGTTTTCAAATGA-AATCTTTGAGTTTTAAATGAA
1 AATCTTTAAGACATTTTCAACTGAGAATCTTTGAGTCTTAAATGAG
* * * * *
19845001 AATATTTGAGACATTTTTAAATGAGAATCTTTGAG-CTTTAAATAAG
1 AATCTTTAAGACATTTTCAACTGAGAATCTTTGAGTC-TTAAATGAG
* * *
19845047 AAT-GTTAAGATATTTTCAACTGAGAATCTTTGAGTCATAAATGAG
1 AATCTTTAAGACATTTTCAACTGAGAATCTTTGAGTCTTAAATGAG
*
19845092 AATCTTTAAGACATTTTCAACTAAGAATCTTT
1 AATCTTTAAGACATTTTCAACTGAGAATCTTT
19845124 ACGACGTTTA
Statistics
Matches: 165, Mismatches: 23, Indels: 30
0.76 0.11 0.14
Matches are distributed among these distances:
35 25 0.15
36 4 0.02
40 1 0.01
41 2 0.01
45 80 0.48
46 53 0.32
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (46 bp):
AATCTTTAAGACATTTTCAACTGAGAATCTTTGAGTCTTAAATGAG
Found at i:19844989 original size:45 final size:46
Alignment explanation
Indices: 19844925--19845169 Score: 259
Period size: 45 Copynumber: 5.4 Consensus size: 46
19844915 AATGAGAATC
* *
19844925 TTCAAATGAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGACGTT
1 TTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGACATT
* * *
19844971 TTCAAATGA-AATCTTTGAGTTTTAAATGAAAATATTTGAGACATT
1 TTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGACATT
* * * * *
19845016 TTTAAATGAGAATCTTTGAGCTTTAAATAAGAAT-GTTAAGATATT
1 TTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGACATT
* **
19845061 TTCAACTGAGAATCTTTGAGTCATAAATGAGAATCTTTAAGACATT
1 TTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGACATT
* * * *
19845107 TTCAACTAAGAATCTTTACGACGTTTACAAATGAGAATCTTTGAGAC---
1 TTCAAATGAGAATCTTT--GA-GTTT-TAAATGAGAATCTTTAAGACATT
19845154 TT-AAATGAGAATCTTT
1 TTCAAATGAGAATCTTT
19845170 AAGATGTTTT
Statistics
Matches: 167, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
45 76 0.46
46 67 0.40
47 2 0.01
48 2 0.01
49 2 0.01
50 18 0.11
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (46 bp):
TTCAAATGAGAATCTTTGAGTTTTAAATGAGAATCTTTAAGACATT
Found at i:19845048 original size:21 final size:21
Alignment explanation
Indices: 19844928--19845308 Score: 188
Period size: 21 Copynumber: 16.7 Consensus size: 21
19844918 GAGAATCTTC
*
19844928 AAATGAAAATCTTTGAGTTTT
1 AAATGAGAATCTTTGAGTTTT
19844949 AAATGAGAATCTTTAAGACGTTTT
1 AAATGAGAATCTTT--GA-GTTTT
19844973 CAAATGA-AATCTTTGAGTTTT
1 -AAATGAGAATCTTTGAGTTTT
* *
19844994 AAATGAAAATATTTGAGACATTTTT
1 AAATGAGAATCTTTGAG----TTTT
*
19845019 AAATGAGAATCTTTGAGCTTT
1 AAATGAGAATCTTTGAGTTTT
* * * *
19845040 AAATAAGAATGTTAAGATATTTT
1 AAATGAGAATCTT-TGA-GTTTT
* **
19845063 CAACTGAGAATCTTTGAGTCAT
1 -AAATGAGAATCTTTGAGTTTT
*
19845085 AAATGAGAATCTTTAAGACATTTT
1 AAATGAGAATCTTT--GA-GTTTT
* * *
19845109 CAACTAAGAATCTTTACGACGTTTAC
1 -AAATGAGAATCTTT--GA-GTTT-T
**
19845135 AAATGAGAATCTTTGAGACTT
1 AAATGAGAATCTTTGAGTTTT
19845156 AAATGAGAATCTTTAAGATGTTTT
1 AAATGAGAATCTTT--GA-GTTTT
* *
19845180 CAAAATAAGAATCTTTGAGTCTT
1 --AAATGAGAATCTTTGAGTTTT
* *
19845203 AAATGAGAATCATTAAGACTTTTT
1 AAATGAGAATC-TT-TGA-GTTTT
* * * *
19845227 CAAATAAGGACCTTTGAGTCTT
1 -AAATGAGAATCTTTGAGTTTT
*
19845249 AAATGAGAATTTTTAAGATGTTTT
1 AAATGAGAATCTTT--GA-GTTTT
* * * * *
19845273 CAAATAAGGACCTTTGAATCTT
1 -AAATGAGAATCTTTGAGTTTT
19845295 AAATGAGAATCTTT
1 AAATGAGAATCTTT
19845309 TAGACATTTT
Statistics
Matches: 271, Mismatches: 59, Indels: 60
0.69 0.15 0.15
Matches are distributed among these distances:
20 6 0.02
21 99 0.37
22 16 0.06
23 25 0.09
24 38 0.14
25 74 0.27
26 13 0.05
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTTTT
Found at i:19845075 original size:91 final size:91
Alignment explanation
Indices: 19844925--19845123 Score: 247
Period size: 91 Copynumber: 2.2 Consensus size: 91
19844915 AATGAGAATC
* * * * *
19844925 TTCAAATGAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGACGTTTTCAAATGAAATCTTTGAG
1 TTCAAATGAGAATCTTTGAGCTTTAAATAAGAATCGTTAAGACATTTTCAAATGAAATCTTTGAG
** *
19844990 TTTTAAATGAAAATATTTGAGACATT
66 TCATAAATGAAAATATTTAAGACATT
* * *
19845016 TTTAAATGAGAATCTTTGAGCTTTAAATAAGAAT-GTTAAGATATTTTCAACTGAGAATCTTTGA
1 TTCAAATGAGAATCTTTGAGCTTTAAATAAGAATCGTTAAGACATTTTCAAATGA-AATCTTTGA
* *
19845080 GTCATAAATGAGAATCTTTAAGACATT
65 GTCATAAATGAAAATATTTAAGACATT
* *
19845107 TTCAACTAAGAATCTTT
1 TTCAAATGAGAATCTTT
19845124 ACGACGTTTA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
90 16 0.18
91 75 0.82
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (91 bp):
TTCAAATGAGAATCTTTGAGCTTTAAATAAGAATCGTTAAGACATTTTCAAATGAAATCTTTGAG
TCATAAATGAAAATATTTAAGACATT
Found at i:19845165 original size:46 final size:46
Alignment explanation
Indices: 19845115--19845323 Score: 249
Period size: 46 Copynumber: 4.5 Consensus size: 46
19845105 TTTTCAACTA
* * * *
19845115 AGAATCTTTACGACGTTTACAAATGAGAATCTTTGAGACTTAAATG
1 AGAATCTTTAAGACGTTTTCAAATAAGAACCTTTGAGACTTAAATG
* * *
19845161 AGAATCTTTAAGATGTTTTCAAAATAAGAATCTTTGAGTCTTAAATG
1 AGAATCTTTAAGACGTTTTC-AAATAAGAACCTTTGAGACTTAAATG
* * * *
19845208 AGAATCATTAAGACTTTTTCAAATAAGGACCTTTGAGTCTTAAATG
1 AGAATCTTTAAGACGTTTTCAAATAAGAACCTTTGAGACTTAAATG
* * *
19845254 AGAATTTTTAAGATGTTTTCAAATAAGGACCTTTGA-ATCTTAAATG
1 AGAATCTTTAAGACGTTTTCAAATAAGAACCTTTGAGA-CTTAAATG
* *
19845300 AGAATCTTTTAGACATTTTCAAAT
1 AGAATCTTTAAGACGTTTTCAAAT
19845324 CTTTGAGATG
Statistics
Matches: 142, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
46 101 0.71
47 41 0.29
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (46 bp):
AGAATCTTTAAGACGTTTTCAAATAAGAACCTTTGAGACTTAAATG
Found at i:19845227 original size:118 final size:116
Alignment explanation
Indices: 19845019--19845234 Score: 317
Period size: 118 Copynumber: 1.8 Consensus size: 116
19845009 AGACATTTTT
* *
19845019 AAATGAGAATCTTTGAGCTTTAAATAAGAATGTTAAGATATTTTCAACTGAGAATCTTTGAGTCA
1 AAATGAGAATCTTTGAGCTTTAAATAAGAATGTTAAGATATTTTCAAATAAGAATCTTTGAGTCA
* *
19845084 TAAATGAGAATCTTTAAGACATTTTCAACTAAGAATCTTTACGACGTTTAC
66 TAAATGAGAATCATTAAGACATTTTCAAATAAGAATCTTTACGACGTTTAC
* * *
19845135 AAATGAGAATCTTTGAGAC-TTAAATGAGAATCTTTAAGATGTTTTCAAAATAAGAATCTTTGAG
1 AAATGAGAATCTTTGAG-CTTTAAATAAGAAT-GTTAAGATATTTTC-AAATAAGAATCTTTGAG
* *
19845199 TCTTAAATGAGAATCATTAAGACTTTTTCAAATAAG
63 TCATAAATGAGAATCATTAAGACATTTTCAAATAAG
19845235 GACCTTTGAG
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
116 28 0.32
117 13 0.15
118 47 0.53
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (116 bp):
AAATGAGAATCTTTGAGCTTTAAATAAGAATGTTAAGATATTTTCAAATAAGAATCTTTGAGTCA
TAAATGAGAATCATTAAGACATTTTCAAATAAGAATCTTTACGACGTTTAC
Found at i:19845231 original size:93 final size:92
Alignment explanation
Indices: 19845115--19845323 Score: 283
Period size: 93 Copynumber: 2.3 Consensus size: 92
19845105 TTTTCAACTA
* * * * *
19845115 AGAATCTTTACGACGTTTACAAATGAGAATCTTTGAGACTTAAATGAGAATCTTTAAGATGTTTT
1 AGAATCTTTAAGACATTTTCAAATAAGAACCTTTGAGACTTAAATGAGAATCTTTAAGATGTTTT
* *
19845180 CAAAATAAGAATCTTTGAGTCTTAAATG
66 C-AAATAAGAACCTTTGAATCTTAAATG
* * * * *
19845208 AGAATCATTAAGACTTTTTCAAATAAGGACCTTTGAGTCTTAAATGAGAATTTTTAAGATGTTTT
1 AGAATCTTTAAGACATTTTCAAATAAGAACCTTTGAGACTTAAATGAGAATCTTTAAGATGTTTT
*
19845273 CAAATAAGGACCTTTGAATCTTAAATG
66 CAAATAAGAACCTTTGAATCTTAAATG
*
19845300 AGAATCTTTTAGACATTTTCAAAT
1 AGAATCTTTAAGACATTTTCAAAT
19845324 CTTTGAGATG
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
92 44 0.44
93 57 0.56
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (92 bp):
AGAATCTTTAAGACATTTTCAAATAAGAACCTTTGAGACTTAAATGAGAATCTTTAAGATGTTTT
CAAATAAGAACCTTTGAATCTTAAATG
Found at i:19845872 original size:42 final size:41
Alignment explanation
Indices: 19845796--19846253 Score: 492
Period size: 41 Copynumber: 11.1 Consensus size: 41
19845786 GATTGTCGAT
19845796 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* *
19845837 GAACAATTTATTTTTCAAAAGTTGTGGTGCTTCTGTTTAGAG
1 GAGCAATTTATTTTTC-AAAGTTGTGGTGCCTCTGTTTAGAG
* * *
19845879 TAGCAATTTA-TTTTCAAAGTTATGATGCCTCTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * *
19845919 GAGTAATTTATTTTTTCAAAAGTTATGGTGCCTCTATTTAGAG
1 GAGCAATTTA-TTTTTC-AAAGTTGTGGTGCCTCTGTTTAGAG
*
19845962 GAGCATTTTAGTTTTT-AAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * *
19846003 AAGCAATTTTATTTTCCAAAGTTGTGGTGCTTCTATTTAGAG
1 GAGCAA-TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * *
19846045 GAGCATTTTAATTTTCAAAGTTGTGGTGCCTTTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* *
19846086 GAGCATTTTATTTTTTCAAAGTTGTGGCGCCTCTGTTTAGAG
1 GAGCAATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
*** * * * * *
19846128 GAGTTTTTTATTTTTTAAAGTCGTTGAGCCTCTGTTTAGAA
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * * * *
19846169 GAGC-CTTTCATTTTTCAAAATCGTTGAGCCTATGTTTAGAG
1 GAGCAATTT-ATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* ** *
19846210 GAGC-ACTTATTTTTTCAAAGTTGCAGAGCCTCTGTTTAGAG
1 GAGCAATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
19846251 GAG
1 GAG
19846254 TTTTTAAAAA
Statistics
Matches: 357, Mismatches: 51, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
40 34 0.10
41 183 0.51
42 104 0.29
43 36 0.10
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (41 bp):
GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
Found at i:19845948 original size:83 final size:84
Alignment explanation
Indices: 19845796--19846253 Score: 473
Period size: 83 Copynumber: 5.5 Consensus size: 84
19845786 GATTGTCGAT
* *
19845796 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAACAATTTA-TTTTTCAAAAGTT
1 GAGCAATTTAGTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAAGTT
* *
19845860 GTGGTGCTTCTGTTTAGAG
66 GTGGTGCCTCTATTTAGAG
* * * *
19845879 TAGCAATTTA-TTTTCAAAGTTATGATGCCTCTGTTTAGAGGAGTAATTTATTTTTTCAAAAGTT
1 GAGCAATTTAGTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAAGTT
*
19845943 ATGGTGCCTCTATTTAGAG
66 GTGGTGCCTCTATTTAGAG
* * * * *
19845962 GAGCATTTTAGTTTTTAAAGTTGTGGTGCCTCTGTTTAGAGAAGCAATTT-TATTTTCCAAAGTT
1 GAGCAATTTAGTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAAGTT
*
19846026 GTGGTGCTTCTATTTAGAG
66 GTGGTGCCTCTATTTAGAG
* * * *
19846045 GAGCATTTTAATTTTCAAAGTTGTGGTGCCTTTGTTTAGAGGAGCATTTTATTTTTTC-AAAGTT
1 GAGCAATTTAGTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAAGTT
* *
19846109 GTGGCGCCTCTGTTTAGAG
66 GTGGTGCCTCTATTTAGAG
*** * * * * * * *
19846128 GAGTTTTTTATTTTTTAAAGTCGTTGAGCCTCTGTTTAGAAGAGC-CTTTCA-TTTTTCAAAA-T
1 GAGCAATTTAGTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTT-ATTTTTTCAAAAGT
* * * * *
19846190 CGTTGAGCCTATGTTTAGAG
65 TGTGGTGCCTCTATTTAGAG
* * ** *
19846210 GAGC-ACTTATTTTTTCAAAGTTGCAGAGCCTCTGTTTAGAGGAG
1 GAGCAATTTA-GTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAG
19846254 TTTTTAAAAA
Statistics
Matches: 319, Mismatches: 50, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
81 3 0.01
82 94 0.29
83 182 0.57
84 40 0.13
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (84 bp):
GAGCAATTTAGTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAAGTT
GTGGTGCCTCTATTTAGAG
Found at i:19846730 original size:306 final size:295
Alignment explanation
Indices: 19846177--19846781 Score: 958
Period size: 306 Copynumber: 2.0 Consensus size: 295
19846167 AAGAGCCTTT
* *
19846177 CATTTTTCAAAATCGTTGAGCCTATGTTTAGAGGAGCACTTATTTTTTCAAAGTTGCAGAGCCTC
1 CATTTTTCAAAATCGTTGAGCCTATATTTAGAGGAGCACTTATTTTTCCAAAGTTGCAGAGCCTC
19846242 TGTTTAGAGGAGTTTTTAAAAAGTGTGAGTATGTTTAAAAAAAAAAGGCATCAAGTTGAGTTTGA
66 TGTTTAGAGGAGTTTTTAAAAAGTGTGAGTATGTTTAAAAAAAAAAGGCATCAAGTTGAGTTTGA
* * **
19846307 TTGGGTTATCTATATCTTTGCATAATTTCTGTTTCACAGAAAATGTGTAAAGAGGTGCAGCTGTA
131 TTGGGTTATCTATATCTTTGCACAATTTCTGTTTCACAGAAAATGTGTAAAGAGGGGCAGCAATA
* * * *
19846372 GACACCCTAATCTATCCAGGAGTCTGTTTTTTATTTTTGCTAATAAAAAAACAAAAAAATGAAAA
196 AACACCCTAATCTATCCAAGAGTCTGCTTTTGATTTTTGCTAATAAAAAAAC----------AAA
19846437 AAACAGGTAGTTGAGTTTGTGTGAAATTGTTGGAATTGGTTTGTAA
251 AAA-AGGTAGTTGAGTTTGTGTGAAATTGTTGGAATTGGTTTGTAA
* * *
19846483 CATTTTTCAAAATCGTTGAGCCTCTATTTAGAGGAGCATTTATTTTTCCAAAGTTGCGGAGCCTC
1 CATTTTTCAAAATCGTTGAGCCTATATTTAGAGGAGCACTTATTTTTCCAAAGTTGCAGAGCCTC
* *
19846548 TGTTTAGAGGAGTTTTTAGAAAGTGTGAGTATGTTTAAAAAAAAAAGGCGTCAAGTTGAGTTTGA
66 TGTTTAGAGGAGTTTTTAAAAAGTGTGAGTATGTTTAAAAAAAAAAGGCATCAAGTTGAGTTTGA
* *
19846613 TTGGGTTGTCTATGTCTTTGCACAATTTCTGTTTCACAGAAAATGTGTAAAGAGGGGCAGCAATA
131 TTGGGTTATCTATATCTTTGCACAATTTCTGTTTCACAGAAAATGTGTAAAGAGGGGCAGCAATA
19846678 AACACCCTAATCTATCCAAGAGTCTGCTTTTGATTTTTGCTAATAAAAAAACAAAAAAAGGTAGT
196 AACACCCTAATCTATCCAAGAGTCTGCTTTTGATTTTTGCTAATAAAAAAACAAAAAAAGGTAGT
19846743 TGAGTTTGTGTGAAATTGTTGGAATTGGTTTGTAA
261 TGAGTTTGTGTGAAATTGTTGGAATTGGTTTGTAA
19846778 CATT
1 CATT
19846782 AGAGTTAGGT
Statistics
Matches: 282, Mismatches: 17, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
295 46 0.16
296 6 0.02
306 230 0.82
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (295 bp):
CATTTTTCAAAATCGTTGAGCCTATATTTAGAGGAGCACTTATTTTTCCAAAGTTGCAGAGCCTC
TGTTTAGAGGAGTTTTTAAAAAGTGTGAGTATGTTTAAAAAAAAAAGGCATCAAGTTGAGTTTGA
TTGGGTTATCTATATCTTTGCACAATTTCTGTTTCACAGAAAATGTGTAAAGAGGGGCAGCAATA
AACACCCTAATCTATCCAAGAGTCTGCTTTTGATTTTTGCTAATAAAAAAACAAAAAAAGGTAGT
TGAGTTTGTGTGAAATTGTTGGAATTGGTTTGTAA
Found at i:19847957 original size:51 final size:51
Alignment explanation
Indices: 19847893--19848072 Score: 180
Period size: 51 Copynumber: 3.4 Consensus size: 51
19847883 AAATAGGCCC
* *
19847893 AAATGGTAGAAAATTTAAAAATTTCAAAAAAAAATATTTCTAAATTGACTT
1 AAATGATAAAAAATTTAAAAATTTCAAAAAAAAATATTTCTAAATTGACTT
* * * * * * **
19847944 AAATGATAAAAAATTTAGAAATCTAACAAAAAAAGAGAGAAATTCTAAATAGGCCC
1 AAATGATAAAAAATTTAAAAAT-T-TCAAAAAAA-A-A-TATTTCTAAATTGACTT
* * **
19848000 AAATGGTAGAAAATTTAAAAATTTTGAAAAAAAATATTTCTAAATTGACTT
1 AAATGATAAAAAATTTAAAAATTTCAAAAAAAAATATTTCTAAATTGACTT
*
19848051 AAATGATAAAAAATTTAGAAAT
1 AAATGATAAAAAATTTAAAAAT
19848073 CCAACAAAAA
Statistics
Matches: 99, Mismatches: 25, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
51 49 0.49
52 2 0.02
53 9 0.09
54 7 0.07
55 2 0.02
56 30 0.30
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (51 bp):
AAATGATAAAAAATTTAAAAATTTCAAAAAAAAATATTTCTAAATTGACTT
Found at i:19848108 original size:106 final size:107
Alignment explanation
Indices: 19847814--19848149 Score: 509
Period size: 107 Copynumber: 3.1 Consensus size: 107
19847804 TAAAATAAAT
* ** * *
19847814 AAAATATATTTCTAAATTGACCCAAATTG-TGAAAAATTTAGAAATCCAACAAAAAAAGAAAGAA
1 AAAAAATATTTCTAAATTGACTTAAA-TGATAAAAAATTTAGAAATCCAACAAAAAAAGAGAGAA
*
19847878 TTTCTAAATAGGCCCAAATGGTAGAAAATTTAAAAATTTCAAA
65 ATTCTAAATAGGCCCAAATGGTAGAAAATTTAAAAATTTCAAA
*
19847921 AAAAAATATTTCTAAATTGACTTAAATGATAAAAAATTTAGAAATCTAACAAAAAAAGAGAGAAA
1 AAAAAATATTTCTAAATTGACTTAAATGATAAAAAATTTAGAAATCCAACAAAAAAAGAGAGAAA
**
19847986 TTCTAAATAGGCCCAAATGGTAGAAAATTTAAAAATTTTGAA
66 TTCTAAATAGGCCCAAATGGTAGAAAATTTAAAAATTTCAAA
19848028 AAAAAATATTTCTAAATTGACTTAAATGATAAAAAATTTAGAAATCCAACAAAAAAA-AGAGAAA
1 AAAAAATATTTCTAAATTGACTTAAATGATAAAAAATTTAGAAATCCAACAAAAAAAGAGAGAAA
* *
19848092 TTCTAAATAGGCCCAAATGGT-GAAAAATTTAGAAA-CTCAAA
66 TTCTAAATAGGCCCAAATGGTAG-AAAATTTAAAAATTTCAAA
19848133 AGAGAAAATATTTCTAA
1 A-A-AAAATATTTCTAA
19848150 TTTGGCCCAA
Statistics
Matches: 211, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
105 5 0.02
106 42 0.20
107 164 0.78
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.26
Consensus pattern (107 bp):
AAAAAATATTTCTAAATTGACTTAAATGATAAAAAATTTAGAAATCCAACAAAAAAAGAGAGAAA
TTCTAAATAGGCCCAAATGGTAGAAAATTTAAAAATTTCAAA
Found at i:19848773 original size:17 final size:16
Alignment explanation
Indices: 19848741--19848786 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
19848731 TTTCCACCGA
*
19848741 TTCATTTCTTTTATTT
1 TTCATTTCTTTCATTT
19848757 TTCATTTCCTTTCATTT
1 TTCATTT-CTTTCATTT
* *
19848774 TTCCTTTTTTTCA
1 TTCATTTCTTTCA
19848787 CCTTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCATTTCTTTCATTT
Found at i:19851722 original size:16 final size:16
Alignment explanation
Indices: 19851697--19851740 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
19851687 TATTGAGTGT
*
19851697 ATACATAAATGGATGA
1 ATACATAAATGAATGA
19851713 ATGA-ATAAATGAATGA
1 AT-ACATAAATGAATGA
19851729 ATACATAAATGA
1 ATACATAAATGA
19851741 CAAAGCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.25
Consensus pattern (16 bp):
ATACATAAATGAATGA
Found at i:19855212 original size:16 final size:15
Alignment explanation
Indices: 19855185--19855273 Score: 72
Period size: 16 Copynumber: 5.7 Consensus size: 15
19855175 TTGGGTCTCA
19855185 TTTTAGGATTTTAAGG
1 TTTTAGG-TTTTAAGG
19855201 TTTTAAGGTTTTAAGG
1 TTTT-AGGTTTTAAGG
* *
19855217 TTTTGGGTTTTAGGG
1 TTTTAGGTTTTAAGG
* **
19855232 TTTT-GATTTTAAAA
1 TTTTAGGTTTTAAGG
**
19855246 TTTTAGGGTTTCGAGG
1 TTTTA-GGTTTTAAGG
19855262 TTTTATGGTTTT
1 TTTTA-GGTTTT
19855274 GGTGTTTCAA
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
14 10 0.18
15 13 0.23
16 31 0.54
17 3 0.05
ACGTcount: A:0.19, C:0.01, G:0.26, T:0.54
Consensus pattern (15 bp):
TTTTAGGTTTTAAGG
Found at i:19855227 original size:15 final size:15
Alignment explanation
Indices: 19855193--19855236 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
19855183 CATTTTAGGA
*
19855193 TTTTAAGGTTTTAAGG
1 TTTTAAGGTTTT-GGG
19855209 TTTTAAGGTTTTGGG
1 TTTTAAGGTTTTGGG
*
19855224 TTTTAGGGTTTTG
1 TTTTAAGGTTTTG
19855237 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.55
Consensus pattern (15 bp):
TTTTAAGGTTTTGGG
Found at i:19855346 original size:15 final size:15
Alignment explanation
Indices: 19855323--19855367 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
19855313 AAATTTAAGA
*
19855323 TTTAAGGTTTCAAAT
1 TTTAGGGTTTCAAAT
*
19855338 TTTAGGGTTTTAAAAT
1 TTTAGGG-TTTCAAAT
*
19855354 TTTAGAGTTTCAAA
1 TTTAGGGTTTCAAA
19855368 AGTTTGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (15 bp):
TTTAGGGTTTCAAAT
Found at i:19855355 original size:16 final size:15
Alignment explanation
Indices: 19855323--19855516 Score: 63
Period size: 15 Copynumber: 12.7 Consensus size: 15
19855313 AAATTTAAGA
* *
19855323 TTTAAGGTTTCAAAT
1 TTTAGGGTTTTAAAT
19855338 TTTAGGGTTTTAAAAT
1 TTTAGGGTTTT-AAAT
* *
19855354 TTTAGAGTTTCAAAAGT
1 TTTAGGGTTT-TAAA-T
* * * *
19855371 TTGAAGAGTTTTGAGT
1 TT-TAGGGTTTTAAAT
* *
19855387 TTTAAGGTTTTAGAT
1 TTTAGGGTTTTAAAT
19855402 TTTAGGGTTTTGAAA-
1 TTTAGGGTTTT-AAAT
* * *
19855417 TTTAAGG-TTTGAGT
1 TTTAGGGTTTTAAAT
* * *
19855431 TTTTGAGTTTTTAAAG
1 TTTAG-GGTTTTAAAT
* *
19855447 TTTAGGGTTTCAAAGG
1 TTTAGGGTTTTAAA-T
* *
19855463 TTTAGAGTTTT-GAT
1 TTTAGGGTTTTAAAT
* *
19855477 TTTAAGGTTTCT-ATT
1 TTTAGGGTTT-TAAAT
**
19855492 TTTAGGGTTTTGGAT
1 TTTAGGGTTTTAAAT
*
19855507 TTTAGAGTTT
1 TTTAGGGTTT
19855517 GGATTTTAGG
Statistics
Matches: 128, Mismatches: 40, Indels: 22
0.67 0.21 0.12
Matches are distributed among these distances:
13 1 0.01
14 15 0.12
15 62 0.48
16 39 0.30
17 4 0.03
18 7 0.05
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.50
Consensus pattern (15 bp):
TTTAGGGTTTTAAAT
Found at i:19855486 original size:14 final size:13
Alignment explanation
Indices: 19855463--19855554 Score: 78
Period size: 14 Copynumber: 6.5 Consensus size: 13
19855453 GTTTCAAAGG
19855463 TTTAGAGTTTTGAT
1 TTTAG-GTTTTGAT
19855477 TTTAAGGTTTCT-ATT
1 TTT-AGGTTT-TGA-T
19855492 TTTAGGGTTTTGGAT
1 TTTA-GGTTTT-GAT
*
19855507 TTTAGAGTTTGGAT
1 TTTAG-GTTTTGAT
*
19855521 TTTAGGATTTGCAT
1 TTTAGGTTTTG-AT
19855535 TTTAGAGTTTTGAT
1 TTTAG-GTTTTGAT
19855549 TTTAGG
1 TTTAGG
19855555 GTTTAAAGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
13 5 0.08
14 33 0.51
15 26 0.40
16 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (13 bp):
TTTAGGTTTTGAT
Found at i:19855540 original size:28 final size:28
Alignment explanation
Indices: 19855491--19855554 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
19855481 AGGTTTCTAT
* *
19855491 TTTTAGGGTTTTGGATTTTAGAGTTTGGA
1 TTTTA-GGATTTGCATTTTAGAGTTTGGA
*
19855520 TTTTAGGATTTGCATTTTAGAGTTTTGA
1 TTTTAGGATTTGCATTTTAGAGTTTGGA
19855548 TTTTAGG
1 TTTTAGG
19855555 GTTTAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.19, C:0.02, G:0.27, T:0.53
Consensus pattern (28 bp):
TTTTAGGATTTGCATTTTAGAGTTTGGA
Found at i:19855558 original size:14 final size:14
Alignment explanation
Indices: 19855378--19855558 Score: 89
Period size: 15 Copynumber: 12.3 Consensus size: 14
19855368 AGTTTGAAGA
*
19855378 GTTTTGAGTTTTAAG
1 GTTTTGA-TTTTAGG
19855393 GTTTTAGATTTTAGG
1 GTTTT-GATTTTAGG
* *
19855408 GTTTTGAAATTTAAG
1 GTTTTG-ATTTTAGG
*
19855423 G-TTTGAGTTTTTGAG
1 GTTTTGA-TTTTAG-G
* * *
19855438 TTTTTAAAGTTTAGG
1 GTTTT-GATTTTAGG
** * *
19855453 GTTTCAAAGGTTTAGA
1 GTTT-TGA-TTTTAGG
*
19855469 GTTTTGATTTTAAG
1 GTTTTGATTTTAGG
19855483 GTTTCT-ATTTTTAGG
1 GTTT-TGA-TTTTAGG
*
19855498 GTTTTGGATTTTAGA
1 GTTTT-GATTTTAGG
*
19855513 GTTTGGATTTTA-G
1 GTTTTGATTTTAGG
* *
19855526 GATTTGCATTTTAGA
1 GTTTTG-ATTTTAGG
19855541 GTTTTGATTTTAGG
1 GTTTTGATTTTAGG
19855555 GTTT
1 GTTT
19855559 AAAGTTTCAA
Statistics
Matches: 125, Mismatches: 27, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
13 5 0.04
14 42 0.34
15 57 0.46
16 20 0.16
17 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.25, T:0.52
Consensus pattern (14 bp):
GTTTTGATTTTAGG
Found at i:19855877 original size:3 final size:3
Alignment explanation
Indices: 19855863--19855898 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
19855853 AATTATTTAT
19855863 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19855899 TTAAAAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19856031 original size:31 final size:31
Alignment explanation
Indices: 19855953--19856033 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
19855943 AATCTCTTTC
* *
19855953 ATTATTTTATTTTCATTATCACTTTTTTTTAT
1 ATTATTTT-TTTTTATTATCACTTTTTTGTAT
*
19855985 ATTTTTTATTCTTTTATTCATCA-TTTTTTGGT-T
1 ATTATTT-TT-TTTTATT-ATCACTTTTTT-GTAT
19856018 ATTATTTTTTTTTATT
1 ATTATTTTTTTTTATT
19856034 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
31 7 0.17
32 9 0.22
33 20 0.49
34 5 0.12
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (31 bp):
ATTATTTTTTTTTATTATCACTTTTTTGTAT
Found at i:19856082 original size:3 final size:3
Alignment explanation
Indices: 19856074--19856166 Score: 109
Period size: 3 Copynumber: 31.0 Consensus size: 3
19856064 ATCATTTTCA
19856074 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
19856122 TGT TAT TGT TGT TGT TGT TAT TATT TAGT TAT T-T TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT
19856167 AATTTTATAA
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
2 4 0.05
3 72 0.88
4 6 0.07
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (3 bp):
TAT
Done.