Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 26
Found at i:382132 original size:37 final size:37
Alignment explanation
Indices: 382038--382251 Score: 187
Period size: 36 Copynumber: 5.9 Consensus size: 37
382028 AATATTTTCA
* * *
382038 AAAAATATCTTTTTAAAAACAATATAATATATATGTTTTT
1 AAAAA-ATGTTTTCAAAAACTATAT-ATATATATG-TTTT
* * *
382078 TAAAAATGTTTTAAAAAACCATATA-ATATATGTTTT
1 AAAAAATGTTTTCAAAAACTATATATATATATGTTTT
382114 AAAAAATGTTTTCCAAAAACTATATA-ATATAT-TTTT
1 AAAAAATGTTTT-CAAAAACTATATATATATATGTTTT
*
382150 CAAAAATGTTTTCAAAAACTATATATATATATGTTTT
1 AAAAAATGTTTTCAAAAACTATATATATATATGTTTT
* * *
382187 --CAAAT-TTTTC-CAAACTATATAATACATATATATTTT
1 AAAAAATGTTTTCAAAAACTATAT-AT--ATATATGTTTT
* *
382223 --GAAATATTTTC-AAAACTATATATATATAT
1 AAAAAATGTTTTCAAAAACTATATATATATAT
382252 ATATATATAT
Statistics
Matches: 154, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
33 9 0.06
34 13 0.08
35 17 0.11
36 52 0.34
37 42 0.27
38 1 0.01
39 16 0.10
40 4 0.03
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (37 bp):
AAAAAATGTTTTCAAAAACTATATATATATATGTTTT
Found at i:382216 original size:36 final size:36
Alignment explanation
Indices: 382137--382279 Score: 125
Period size: 37 Copynumber: 3.9 Consensus size: 36
382127 CAAAAACTAT
*
382137 ATAATATAT-TTTTCAAAAATGTTTTCAAAAACTATAT-
1 ATAATATATATTTTC--AAATATTTTC-AAAACTATATA
* *
382174 AT-ATATATGTTTTCAAAT-TTTTCCAAACTATATA
1 ATAATATATATTTTCAAATATTTTCAAAACTATATA
*
382208 ATACATATATATTTTGAAATATTTTCAAAACTATATA
1 ATA-ATATATATTTTCAAATATTTTCAAAACTATATA
*
382245 TATATATATATATATATAT-ATATATTTTCAAAACT
1 -ATA-ATATATAT-T-T-TCAAATATTTTCAAAACT
382280 TGTTTTCTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
33 9 0.10
34 7 0.08
35 4 0.04
36 20 0.22
37 22 0.24
38 11 0.12
39 1 0.01
40 16 0.18
41 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (36 bp):
ATAATATATATTTTCAAATATTTTCAAAACTATATA
Found at i:382219 original size:38 final size:39
Alignment explanation
Indices: 382169--382279 Score: 113
Period size: 38 Copynumber: 2.9 Consensus size: 39
382159 TTTCAAAAAC
* *
382169 TATATATATATATGTTTTCAAAT-TTTTCCAAACTATATA
1 TATACATATATAT-TTTTCAAATATTTTCAAAACTATATA
*
382208 -ATACATATATA-TTTTGAAATATTTTCAAAACTATATA
1 TATACATATATATTTTTCAAATATTTTCAAAACTATATA
* * *
382245 TATATATATATATATATAT-ATATATTTTCAAAACT
1 TATACATATATAT-T-TTTCAAATATTTTCAAAACT
382280 TGTTTTCTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
36 8 0.13
37 15 0.25
38 20 0.33
40 16 0.26
41 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (39 bp):
TATACATATATATTTTTCAAATATTTTCAAAACTATATA
Found at i:382246 original size:2 final size:2
Alignment explanation
Indices: 382239--382269 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
382229 TTTTCAAAAC
382239 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
382270 TTTCAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:387532 original size:23 final size:23
Alignment explanation
Indices: 387506--387590 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
387496 GAGTCGAGGG
* *
387506 TTCTATGTGGTCCTTCGGAATAA
1 TTCTACGTGGTCCTTCGGGATAA
* * *
387529 TTCTACGTGGTCCTTAGGGACAT
1 TTCTACGTGGTCCTTCGGGATAA
*
387552 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGATAA
* *
387575 TACTATGTGGTCCTTC
1 TTCTACGTGGTCCTTC
387591 AGGACGTTTC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGATAA
Found at i:387603 original size:23 final size:23
Alignment explanation
Indices: 387506--387607 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
387496 GAGTCGAGGG
387506 TTCTATGTGGTCCTTC-GGA-AT
1 TTCTATGTGGTCCTTCAGGACAT
*
387527 AATTCTACGTGGTCCTT-AGGGACAT
1 --TTCTATGTGGTCCTTCA-GGACAT
* * * * *
387552 TTCTACGCGGTCCTTCGGGATAA
1 TTCTATGTGGTCCTTCAGGACAT
* *
387575 TACTATGTGGTCCTTCAGGACGT
1 TTCTATGTGGTCCTTCAGGACAT
387598 TTCTATGTGG
1 TTCTATGTGG
387608 CACTTCGGTG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
23 57 0.92
24 3 0.05
25 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCAGGACAT
Found at i:387614 original size:46 final size:46
Alignment explanation
Indices: 387506--387615 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 46
387496 GAGTCGAGGG
*
387506 TTCTATGTGGTCCTTCGGAATAATTCTACGTGGTCCTTAGGGACAT
1 TTCTATGTGGTCCTTCGGAATAATACTACGTGGTCCTTAGGGACAT
* * * * *
387552 TTCTACGCGGTCCTTCGGGATAATACTATGTGGTCCTTCA-GGACGT
1 TTCTATGTGGTCCTTCGGAATAATACTACGTGGTCCTT-AGGGACAT
387598 TTCTATGTGG-CACTTCGG
1 TTCTATGTGGTC-CTTCGG
387616 TGCTGTAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
45 1 0.02
46 52 0.96
47 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.35
Consensus pattern (46 bp):
TTCTATGTGGTCCTTCGGAATAATACTACGTGGTCCTTAGGGACAT
Found at i:391935 original size:21 final size:21
Alignment explanation
Indices: 391909--391968 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
391899 GCGTAGAATT
391909 TGTCCCGAAGGACCACGTAGA
1 TGTCCCGAAGGACCACGTAGA
*
391930 TGTCCCGAATGACCAC-T--A
1 TGTCCCGAAGGACCACGTAGA
* *
391948 TGTCCCAAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
391969 CCCTCGACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 14 0.44
19 1 0.03
20 1 0.03
21 16 0.50
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACGTAGA
Found at i:396737 original size:21 final size:21
Alignment explanation
Indices: 396707--396753 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
396697 GTGTAAACGA
*
396707 GCCGAGTCGAGCTCGAGTATT
1 GCCGAATCGAGCTCGAGTATT
*
396728 GCCGAATCGAGTTCGAGTATT
1 GCCGAATCGAGCTCGAGTATT
396749 GCCGA
1 GCCGA
396754 GCTCAACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (21 bp):
GCCGAATCGAGCTCGAGTATT
Found at i:396887 original size:16 final size:16
Alignment explanation
Indices: 396862--396893 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
396852 ATTGAAACTC
396862 GACTCGAACTCAAAAA
1 GACTCGAACTCAAAAA
*
396878 GACTCTAACTCAAAAA
1 GACTCGAACTCAAAAA
396894 ATATTCAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.25, G:0.09, T:0.16
Consensus pattern (16 bp):
GACTCGAACTCAAAAA
Found at i:397903 original size:7 final size:7
Alignment explanation
Indices: 397891--397970 Score: 52
Period size: 7 Copynumber: 11.4 Consensus size: 7
397881 CATATAATCA
397891 GGTTTAG
1 GGTTTAG
397898 GGTTTAG
1 GGTTTAG
* *
397905 GGCTTAT
1 GGTTTAG
*
397912 GATTTAG
1 GGTTTAG
*
397919 GATTTAG
1 GGTTTAG
* *
397926 GATTTAA
1 GGTTTAG
*
397933 GGTTTAT
1 GGTTTAG
*
397940 GGTTTAT
1 GGTTTAG
*
397947 AGTTTAG
1 GGTTTAG
*
397954 AGTTTAG
1 GGTTTAG
**
397961 AATTTAG
1 GGTTTAG
397968 GGT
1 GGT
397971 GCAATCTAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:398052 original size:7 final size:7
Alignment explanation
Indices: 398040--398140 Score: 89
Period size: 7 Copynumber: 14.7 Consensus size: 7
398030 AATTGGATTA
398040 AGGGTTT
1 AGGGTTT
*
398047 AGGGTTA
1 AGGGTTT
* *
398054 AGTGCTT
1 AGGGTTT
*
398061 AAGGTTT
1 AGGGTTT
398068 AGGGTTT
1 AGGGTTT
398075 AGGGTTT
1 AGGGTTT
*
398082 AGAGTTT
1 AGGGTTT
398089 A-GGTTT
1 AGGGTTT
398095 AGGGTTT
1 AGGGTTT
**
398102 AGTATTT
1 AGGGTTT
**
398109 ATAGTTT
1 AGGGTTT
*
398116 AGAGTTT
1 AGGGTTT
398123 A-GGTTT
1 AGGGTTT
*
398129 AGGATTT
1 AGGGTTT
398136 AGGGT
1 AGGGT
398141 GTATTCTAAC
Statistics
Matches: 73, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
6 10 0.14
7 63 0.86
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:398100 original size:27 final size:27
Alignment explanation
Indices: 398062--398137 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
398052 TAAGTGCTTA
*
398062 AGGTTTAGGGTTTAGGGTTTAGAGTTT
1 AGGTTTAGGGTTTAGGATTTAGAGTTT
* *
398089 AGGTTTAGGGTTTAGTATTTATAGTTT
1 AGGTTTAGGGTTTAGGATTTAGAGTTT
398116 AGAGTTTA-GGTTTAGGATTTAG
1 AG-GTTTAGGGTTTAGGATTTAG
398138 GGTGTATTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 38 0.88
28 5 0.12
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (27 bp):
AGGTTTAGGGTTTAGGATTTAGAGTTT
Found at i:398317 original size:14 final size:14
Alignment explanation
Indices: 398298--398338 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
398288 TATAATTATC
398298 AATAATGTATTTTT
1 AATAATGTATTTTT
398312 AATAA--T-TTTTT
1 AATAATGTATTTTT
*
398323 AATAATGTAATTTT
1 AATAATGTATTTTT
398337 AA
1 AA
398339 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:400807 original size:21 final size:20
Alignment explanation
Indices: 400783--400915 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 20
400773 CAGTTCCTAG
400783 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
400803 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
400824 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
400846 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
400866 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
400886 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
400906 TATCGCAACG
1 AATCGCAACG
400916 AGTATCCGTA
Statistics
Matches: 87, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.53
21 35 0.40
22 3 0.03
23 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:400871 original size:20 final size:20
Alignment explanation
Indices: 400846--401121 Score: 227
Period size: 20 Copynumber: 13.7 Consensus size: 20
400836 GATTTTCCAG
** *
400846 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
400866 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
400886 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
400905 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
*
400927 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
400947 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
* *
400968 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* * *
400988 AATTGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
401008 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
401028 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
401048 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
401068 AATCACAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
401089 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
401109 AATCGCAACGCGA
1 AATCGCAACGCGA
401122 TTTTTAAAGC
Statistics
Matches: 203, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.00
20 150 0.74
21 51 0.25
22 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:400936 original size:81 final size:81
Alignment explanation
Indices: 400846--401121 Score: 308
Period size: 81 Copynumber: 3.4 Consensus size: 81
400836 GATTTTCCAG
* ** * * *
400846 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT-A-AAT
* *
400909 CGCAACGAGTATCCGTAA
64 CGCAACGAGAATACGTAA
* * *
400927 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA-AAATCGCAACGTGTATCCGTAAAT
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCCGTAAAT
*
400991 TGCAACGAGAATACGT-A
64 CGCAACGAGAATACGTAA
* * * ** * *
401008 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
*
401073 CAACGACAATACGTAA
66 CAACGAGAATACGTAA
401089 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
401122 TTTTTAAAGC
Statistics
Matches: 163, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.01
80 36 0.22
81 88 0.54
82 29 0.18
83 8 0.05
84 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (81 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
CAACGAGAATACGTAA
Found at i:401023 original size:40 final size:41
Alignment explanation
Indices: 400907--401118 Score: 329
Period size: 41 Copynumber: 5.2 Consensus size: 41
400897 GATTCTGACT
* *
400907 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
400948 ATCGCAACGACAATACGTAAAATCGCAACGTGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
400989 ATTGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
401029 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
401069 ATCACAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
401110 ATCGCAACG
1 ATCGCAACG
401119 CGATTTTTAA
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 73 0.47
41 82 0.53
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:401699 original size:20 final size:20
Alignment explanation
Indices: 401674--401764 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
401664 TTCTAAACTT
* *
401674 AAAATCGCAATATGAAAATG
1 AAAATCGCAACACGAAAATG
401694 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
401714 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
401735 AAAATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
401754 AAAATCGCAAC
1 AAAATCGCAAC
401765 GATATAATCG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
19 16 0.26
20 30 0.48
21 16 0.26
ACGTcount: A:0.52, C:0.19, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:401753 original size:40 final size:41
Alignment explanation
Indices: 401689--401766 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
401679 CGCAATATGA
**
401689 AAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACACGAAAATGAAAATCGCAACGAGAG
401730 AAATGAAAATCGCAACACG-AAATGAAAATCGCAACGA
1 AAATGAAAATCGCAACACGAAAATGAAAATCGCAACGA
401767 TATAATCGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 16 0.46
41 19 0.54
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.12
Consensus pattern (41 bp):
AAATGAAAATCGCAACACGAAAATGAAAATCGCAACGAGAG
Found at i:401869 original size:20 final size:19
Alignment explanation
Indices: 401791--401903 Score: 119
Period size: 20 Copynumber: 6.1 Consensus size: 19
401781 GAAACCAAAA
*
401791 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
401810 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
401824 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
401843 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
401862 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
401882 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
401902 TC
1 TC
401904 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 30 0.39
20 31 0.40
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:403520 original size:94 final size:94
Alignment explanation
Indices: 403359--403738 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
403349 TAGATTGCTT
* *
403359 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
403424 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
403453 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
403518 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
403547 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
403612 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
403641 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
403706 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
403734 AGTAA
1 AGTAA
403739 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 25 0.09
94 249 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:403842 original size:19 final size:17
Alignment explanation
Indices: 403826--403889 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 17
403816 AAAAATGACT
403826 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
403843 ATCGCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
*
403857 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
403876 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
403890 CTATAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.21
15 4 0.11
16 4 0.11
17 8 0.21
19 14 0.37
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:403899 original size:19 final size:19
Alignment explanation
Indices: 403802--403889 Score: 64
Period size: 19 Copynumber: 4.9 Consensus size: 19
403792 CATGAAACTT
*
403802 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
403823 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
403842 --AATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
403854 AGAATCGTAACGCGAAATG
1 AAAATCGCAACGCGAAATG
403873 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
403890 CTATAATCGC
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 7 0.13
15 2 0.04
16 2 0.04
17 7 0.13
18 1 0.02
19 21 0.40
21 11 0.21
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:403918 original size:19 final size:19
Alignment explanation
Indices: 403896--404019 Score: 118
Period size: 19 Copynumber: 6.8 Consensus size: 19
403886 GAAACTATAA
403896 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
403915 TCGCAATGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
403929 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
403948 TCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
403967 TCGCGTTGCGA--TTCATT
1 TCGCGTTGCGATTTTCATT
**
403984 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
404005 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
404020 AAGTTCCAGA
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.09
16 3 0.04
17 20 0.24
19 40 0.47
21 14 0.16
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:403974 original size:38 final size:37
Alignment explanation
Indices: 403896--404019 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 37
403886 GAAACTATAA
**
403896 TCGCGTTGCGATTTTCATTTCGCAATGCGA-TTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCATT
* *
403929 TCTCGTTGCGATTTTCATTTCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGA-TTTCATT
*
403967 TCGCGTTGCGA--TTCATTTCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGAT-TTCA--TT
*
404005 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
404020 AAGTTCCAGA
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
33 26 0.36
35 4 0.05
36 19 0.26
38 22 0.30
40 2 0.03
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (37 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTCATT
Found at i:403977 original size:52 final size:54
Alignment explanation
Indices: 403899--404019 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 54
403889 ACTATAATCG
* **
403899 CGTTGCGATTTTCATTTCGCAATGCGATTC-TCTCGTTGCGATTTTCA-TTTCA
1 CGTTGCGATTTTCATTTCGCAATGCGATTCTTCGCGTTGCGATAGTCATTTTCA
**
403951 CGTTGCGATTTTCATTTCGCGTTGCGATTCATTTCGCGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCATTTCGCAATGCGATTC--TTCGCGTTGCGATAGTCA-TTTTCA
404008 CGTTGCGATTTT
1 CGTTGCGATTTT
404020 AAGTTCCAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
52 28 0.47
55 14 0.24
57 17 0.29
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (54 bp):
CGTTGCGATTTTCATTTCGCAATGCGATTCTTCGCGTTGCGATAGTCATTTTCA
Found at i:404496 original size:21 final size:21
Alignment explanation
Indices: 404472--404538 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
404462 TCATTCCTCG
404472 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
404493 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
404514 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
404535 AGAG
1 AGAG
404539 CCCGATTCAT
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:404496 original size:42 final size:42
Alignment explanation
Indices: 404420--404538 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
404410 GACTCGCCTG
* * * * * * *
404420 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
404462 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
404504 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
404539 CCCGATTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:405883 original size:14 final size:14
Alignment explanation
Indices: 405864--405899 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
405854 ATTGTTTAAT
405864 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
405878 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
405892 TGATTTGT
1 TGATTTGT
405900 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:406022 original size:19 final size:17
Alignment explanation
Indices: 406006--406089 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 17
405996 AAAAATGACT
406006 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
406025 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
406039 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
406058 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
406072 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
406089 A
1 A
406090 AATCACAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.30
16 10 0.19
17 12 0.23
19 15 0.28
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:406048 original size:33 final size:33
Alignment explanation
Indices: 406006--406132 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
405996 AAAAATGACT
406006 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
406039 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
406072 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
406105 ATCGCAACGCGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
406133 CGTTGCGATT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 87 0.99
34 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:406206 original size:19 final size:19
Alignment explanation
Indices: 406149--406208 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
406139 GATTCCCTCG
406149 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
406168 TTTCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
406182 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
406201 TTGCGATT
1 TTGCGATT
406209 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.22
17 7 0.22
19 13 0.41
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:406220 original size:14 final size:14
Alignment explanation
Indices: 406133--406221 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
406123 AATCGCAACG
*
406133 CGTTGCGATTCCCT
1 CGTTGCGATTCTCT
*
406147 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
406164 CGCATTTCGATTCTCT
1 CG--TTGCGATTCTCT
*
406180 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
406197 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
406213 CGTTGCGAT
1 CGTTGCGAT
406222 AGTAATTTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 13 0.22
19 11 0.19
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:406230 original size:33 final size:33
Alignment explanation
Indices: 406135--406221 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
406125 TCGCAACGCG
*
406135 TTGCGATTCCCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
406168 TTTCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
406201 TTGCGATTCTCTCGTTGCGAT
1 TTGCGATTCTCTCGTTGCGAT
406222 AGTAATTTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:406287 original size:20 final size:20
Alignment explanation
Indices: 406214--406287 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
406204 CGATTCTCTC
* *
406214 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
406234 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
406254 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
406275 GTTGCGATAGTCA
1 GTTGCGATAGTCA
406288 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:407219 original size:24 final size:24
Alignment explanation
Indices: 407168--407219 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
407158 ATCTGAGTAT
** *
407168 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
407192 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
407216 TGAC
1 TGAC
407220 TAGTACTAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:408105 original size:20 final size:19
Alignment explanation
Indices: 408082--408124 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
408072 ATTTACAGAT
* *
408082 TCGCTATACGATTACGTAAA
1 TCGCAATACGAATACGT-AA
*
408102 TCGCAATGCGAATACGTAA
1 TCGCAATACGAATACGTAA
408121 TCGC
1 TCGC
408125 GTTGCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (19 bp):
TCGCAATACGAATACGTAA
Found at i:408137 original size:20 final size:20
Alignment explanation
Indices: 408117--408275 Score: 264
Period size: 20 Copynumber: 8.0 Consensus size: 20
408107 ATGCGAATAC
*
408117 GTAATCGCGTTGCGATTTAC
1 GTAATCGCGTTGCGATTTAA
* *
408137 GTATTCGCGTTGCGATTTAC
1 GTAATCGCGTTGCGATTTAA
*
408157 GTATTCGCGTTGCGATTTAA
1 GTAATCGCGTTGCGATTTAA
408177 GTAATCGCGTTGCGATTTAA
1 GTAATCGCGTTGCGATTTAA
408197 GTAATCGCGTTGCGATTTAA
1 GTAATCGCGTTGCGATTTAA
408217 GTAATCGCGTTGCGATTTAA
1 GTAATCGCGTTGCGATTTAA
*
408237 GTAATCGCGTTGCGATTTAC
1 GTAATCGCGTTGCGATTTAA
*
408257 GTATTCGCGTTGCGATTTA
1 GTAATCGCGTTGCGATTTA
408276 GGAAAATCGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 134 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTAATCGCGTTGCGATTTAA
Found at i:409584 original size:46 final size:46
Alignment explanation
Indices: 409517--409606 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
409507 GAATATCTTT
409517 GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGCCC
1 GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGCCC
* * * *
409563 GATATTTATATTTTCGGTAGAAAAAATGACATTTTATGTAGCGC
1 GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGC
409607 TCTACCGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (46 bp):
GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGCCC
Found at i:409859 original size:29 final size:29
Alignment explanation
Indices: 409825--409883 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
409815 CCTAAATTAA
*
409825 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATATCATTACTTACATCAATTTAGT
*
409854 TTTGATATCATTGCTTACATCAATTTAGT
1 TTTGATATCATTACTTACATCAATTTAGT
409883 T
1 T
409884 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTGATATCATTACTTACATCAATTTAGT
Found at i:413524 original size:26 final size:26
Alignment explanation
Indices: 413488--413540 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
413478 CAAGAGAGTA
413488 CATGGTTAATACAGTTGATGAATAAT
1 CATGGTTAATACAGTTGATGAATAAT
*
413514 CATGGTTAATATAGTTGATGAATAAT
1 CATGGTTAATACAGTTGATGAATAAT
413540 C
1 C
413541 TACATCAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (26 bp):
CATGGTTAATACAGTTGATGAATAAT
Found at i:413902 original size:29 final size:29
Alignment explanation
Indices: 413868--413926 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
413858 CCTAAATTAA
*
413868 TTTGATGTCATTGCTTATATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
413897 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
413926 T
1 T
413927 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:416449 original size:29 final size:29
Alignment explanation
Indices: 416407--416465 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
416397 ATTTTCACCT
416407 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
416436 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
416465 A
1 A
416466 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:421135 original size:29 final size:29
Alignment explanation
Indices: 421093--421151 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
421083 ATTTTCACCT
421093 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
421122 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
421151 A
1 A
421152 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:426876 original size:195 final size:191
Alignment explanation
Indices: 426541--426932 Score: 610
Period size: 195 Copynumber: 2.0 Consensus size: 191
426531 TTTGGTCGGG
** *
426541 CGGGTC-GGTTTTTTTAAGTGTGATATTTGGGTCTGGTCGAGTTCGGATTTAGGGTGAAAAATAC
1 CGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGGTCGAGTTCGGATTTAGGGTGAAAAATAC
*
426605 CCGACCCGAAAATATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCATCTA
66 CCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCATCTA
* * *
426670 TATATAATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATATTTTTTTTATTATTT
131 TATATAATTTTTTTCAATTAAATCAATGTTTTTATTGAATAAAAATA-ATTTTTTATTATTT
*
426732 CGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGGTC-AGGTTCGGGTTTAGGGTGAAAAA-A
1 CGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGGTCGA-GTTCGGATTTAGGGTGAAAAATA
*
426795 CGGACACGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
65 C---C-CGACCCGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCC
*
426860 CTCTATATATAATTTTTTTCAATTAAATCAATGTTTTTATTGAATAAAAATAATTTTTTATTATT
126 ATCTATATATAATTTTTTTCAATTAAATCAATGTTTTTATTGAATAAAAATAATTTTTTATTATT
426925 T
191 T
*
426926 CGTGTCG
1 CGGGTCG
426933 ATGTCGGGTT
Statistics
Matches: 184, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
191 9 0.05
192 49 0.27
194 20 0.11
195 106 0.58
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (191 bp):
CGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGGTCGAGTTCGGATTTAGGGTGAAAAATAC
CCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCATCTA
TATATAATTTTTTTCAATTAAATCAATGTTTTTATTGAATAAAAATAATTTTTTATTATTT
Found at i:427328 original size:92 final size:92
Alignment explanation
Indices: 427171--427354 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
427161 ATATATTACT
427171 ACATGTAAGTTGTAAAACAAACTTAAATAAAGTAAAAAAACAAGAAGAGCAATTCTGTCATTTTA
1 ACATGTAAGTTGTAAAACAAACTTAAATAAAGTAAAAAAACAAGAAGAGCAATTCTGTCATTTTA
427236 CATTACTGAAATCAAATTCATTTGACA
66 CATTACTGAAATCAAATTCATTTGACA
427263 ACATGTAAGTTGTAAAACAAACTTAAATAAAGTAAAAAAACAAGAAGAGCAATTCTGTCATTTTA
1 ACATGTAAGTTGTAAAACAAACTTAAATAAAGTAAAAAAACAAGAAGAGCAATTCTGTCATTTTA
427328 CATTACTGAAATCAAATTCATTTGACA
66 CATTACTGAAATCAAATTCATTTGACA
427355 TGTCTGTAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (92 bp):
ACATGTAAGTTGTAAAACAAACTTAAATAAAGTAAAAAAACAAGAAGAGCAATTCTGTCATTTTA
CATTACTGAAATCAAATTCATTTGACA
Found at i:427408 original size:17 final size:18
Alignment explanation
Indices: 427386--427431 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
427376 ATGAAATTAA
*
427386 ATTCCAATTCC-TGACAG
1 ATTCCAATTCCTTCACAG
427403 ATTCCAATTCCTTCACAG
1 ATTCCAATTCCTTCACAG
*
427421 ATTCTAATTCC
1 ATTCCAATTCC
427432 CTCATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAG
Found at i:437447 original size:22 final size:21
Alignment explanation
Indices: 437421--437464 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
437411 GGTTCACATT
437421 CCTATAATTACAGGGTGTATGA
1 CCTAT-ATTACAGGGTGTATGA
* * *
437443 CCTATGTTATAGGGTTTATGA
1 CCTATATTACAGGGTGTATGA
437464 C
1 C
437465 TAACGGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (21 bp):
CCTATATTACAGGGTGTATGA
Found at i:437547 original size:23 final size:23
Alignment explanation
Indices: 437477--437548 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
437467 ACGGTTTAGA
437477 GTTTAAATTTCTTTATCAATAGG
1 GTTTAAATTTCTTTATCAATAGG
* *
437500 GTTTACGA---C-TTA-CGATTTAGG
1 GTTTA-AATTTCTTTATC-A-ATAGG
437521 GTTTAAATTTCTTTATCAATAGG
1 GTTTAAATTTCTTTATCAATAGG
437544 GTTTA
1 GTTTA
437549 TGACTTACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
19 1 0.03
20 5 0.14
21 10 0.27
23 15 0.41
24 5 0.14
25 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.46
Consensus pattern (23 bp):
GTTTAAATTTCTTTATCAATAGG
Found at i:437566 original size:21 final size:21
Alignment explanation
Indices: 437496--437569 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
437486 TCTTTATCAA
*
437496 TAGGGTTTACGACTTACGATT
1 TAGGGTTTATGACTTACGATT
** *
437517 TAGGGTTTAAATTTCTTTATC-A-A
1 TAGGGTTT--ATGAC-TTA-CGATT
437540 TAGGGTTTATGACTTACGATT
1 TAGGGTTTATGACTTACGATT
437561 TAGGGTTTA
1 TAGGGTTTA
437570 AACCTCTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 1 0.03
20 4 0.10
21 20 0.50
23 10 0.25
24 4 0.10
25 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (21 bp):
TAGGGTTTATGACTTACGATT
Found at i:437578 original size:44 final size:44
Alignment explanation
Indices: 437451--437571 Score: 206
Period size: 44 Copynumber: 2.8 Consensus size: 44
437441 GACCTATGTT
* * *
437451 ATAGGGTTTATGACTAACGGTTTAGAGTTTAAATTTCTTTATCA
1 ATAGGGTTTATGACTTACGATTTAGGGTTTAAATTTCTTTATCA
*
437495 ATAGGGTTTACGACTTACGATTTAGGGTTTAAATTTCTTTATCA
1 ATAGGGTTTATGACTTACGATTTAGGGTTTAAATTTCTTTATCA
437539 ATAGGGTTTATGACTTACGATTTAGGGTTTAAA
1 ATAGGGTTTATGACTTACGATTTAGGGTTTAAA
437572 CCTCTTTTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (44 bp):
ATAGGGTTTATGACTTACGATTTAGGGTTTAAATTTCTTTATCA
Found at i:451623 original size:12 final size:12
Alignment explanation
Indices: 451603--451634 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
451593 TTGAATGAAA
*
451603 TGCTGGATTCCT
1 TGCTAGATTCCT
451615 TGCTAGATTCCT
1 TGCTAGATTCCT
451627 TGCTAGAT
1 TGCTAGAT
451635 GCAAGGCGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (12 bp):
TGCTAGATTCCT
Found at i:462010 original size:15 final size:16
Alignment explanation
Indices: 461990--462020 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
461980 GTTTTCAGTC
461990 GAGAG-AAAAAATAGA
1 GAGAGAAAAAAATAGA
462005 GAGAGAAAAAAATAGA
1 GAGAGAAAAAAATAGA
462021 AAACCAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (16 bp):
GAGAGAAAAAAATAGA
Found at i:462959 original size:29 final size:30
Alignment explanation
Indices: 462927--463001 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
462917 TATGTTAGGG
*
462927 TTTAACTTTCTATTTT-GATATTTTCGTCC
1 TTTAACTTTCTATTTTAGATATTTTAGTCC
* *
462956 TTTAACTTTCTGTTTTAGCTATTTTAGTCC
1 TTTAACTTTCTATTTTAGATATTTTAGTCC
* **
462986 CTTAGGTTTCTATTTT
1 TTTAACTTTCTATTTT
463002 TTCTATTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.59
Consensus pattern (30 bp):
TTTAACTTTCTATTTTAGATATTTTAGTCC
Found at i:463129 original size:22 final size:21
Alignment explanation
Indices: 463104--463147 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
463094 ATGTATGTAC
*
463104 ATGTTGTAAATGTTATTATTTT
1 ATGTTGTAAATATT-TTATTTT
463126 ATGTTGTAAATATTTTATTTT
1 ATGTTGTAAATATTTTATTTT
463147 A
1 A
463148 CATCGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
ATGTTGTAAATATTTTATTTT
Found at i:469874 original size:29 final size:29
Alignment explanation
Indices: 469835--469897 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
469825 CACACTTAAA
469835 TTAA-TTTGATGTCATTGCTTACATCAAT
1 TTAATTTTGATGTCATTGCTTACATCAAT
469863 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAATTTTGATGTCATTGCTTACATCAAT
469892 TTAATT
1 TTAATT
469898 AGGTGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.49
Consensus pattern (29 bp):
TTAATTTTGATGTCATTGCTTACATCAAT
Found at i:474374 original size:29 final size:28
Alignment explanation
Indices: 474335--474394 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
474325 CACACCTAAA
474335 TTAATTTGATGTCATTGCTTACATCAAT
1 TTAATTTGATGTCATTGCTTACATCAAT
474363 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAA-TTTGATGTCATTGCTTACATCAAT
474392 TTA
1 TTA
474395 GTTAGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAATTTGATGTCATTGCTTACATCAAT
Found at i:475085 original size:22 final size:22
Alignment explanation
Indices: 475060--475108 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
475050 AAGTGTATAC
475060 AAGCAGATATGTAGCACAAGAG
1 AAGCAGATATGTAGCACAAGAG
475082 AAGCAGATATGTAGCACAAGAG
1 AAGCAGATATGTAGCACAAGAG
475104 AAGCA
1 AAGCA
475109 AATAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.27, T:0.12
Consensus pattern (22 bp):
AAGCAGATATGTAGCACAAGAG
Found at i:478515 original size:7 final size:8
Alignment explanation
Indices: 478502--478534 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
478492 TTGAATTTAT
*
478502 GATTTTAC
1 GATTTAAC
478510 GATTTAAC
1 GATTTAAC
478518 GATTTAAC
1 GATTTAAC
478526 GATTTAAC
1 GATTTAAC
478534 G
1 G
478535 TCCCTTGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (8 bp):
GATTTAAC
Found at i:479693 original size:29 final size:29
Alignment explanation
Indices: 479661--479717 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
479651 GAAGTGTATC
*
479661 AAATTCTCAATTAT-ATACATAATGTTTTA
1 AAATTCTCAATT-TCATACATAATATTTTA
* *
479690 AAATTTTCAGTTTCATACATAATATTTT
1 AAATTCTCAATTTCATACATAATATTTT
479718 CTTTCGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.47
Consensus pattern (29 bp):
AAATTCTCAATTTCATACATAATATTTTA
Found at i:488738 original size:17 final size:19
Alignment explanation
Indices: 488716--488750 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
488706 TCAAATCATA
488716 ATAAATT-ATA-TAACATG
1 ATAAATTCATACTAACATG
488733 ATAAATTCATACTAACAT
1 ATAAATTCATACTAACAT
488751 TAAATAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.34
Consensus pattern (19 bp):
ATAAATTCATACTAACATG
Found at i:489846 original size:21 final size:21
Alignment explanation
Indices: 489822--489915 Score: 102
Period size: 21 Copynumber: 4.6 Consensus size: 21
489812 ACGTTGCATT
489822 TCGCATTGCGATAGTTGAAAA
1 TCGCATTGCGATAGTTGAAAA
489843 TCGCATTGCGATAGTTGAAAA
1 TCGCATTGCGATAGTTGAAAA
* ** ** **
489864 TCGCGTTGCG-TTTTTTCATT
1 TCGCATTGCGATAGTTGAAAA
*
489884 TCGCGTTGCGATAGTTG-AAA
1 TCGCATTGCGATAGTTGAAAA
489904 TCGCATTGCGAT
1 TCGCATTGCGAT
489916 CTCTTTGAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
20 26 0.44
21 33 0.56
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATAGTTGAAAA
Found at i:491045 original size:24 final size:23
Alignment explanation
Indices: 491018--491090 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
491008 ATCAAAATTT
491018 AAAACATAATTCAGGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
* * *
491042 AAAACAGAGTCCATGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
*
491066 ATATAA-AAATTCAGGTCAAATATC
1 A-A-AACAAATTCAGGTCAAGTATC
491090 A
1 A
491091 TATCGGAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 35 0.90
25 2 0.05
26 2 0.05
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (23 bp):
AAAACAAATTCAGGTCAAGTATC
Found at i:491091 original size:24 final size:24
Alignment explanation
Indices: 491051--491119 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
491041 CAAAACAGAG
* *
491051 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* ***
491075 TTCAGGTCAAATATCATATCGGAA
1 TCCAGGTCAAATATCATATAAAAA
*
491099 TCCAGGTCAAA-ATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
491120 CTATTTATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 6 0.18
24 28 0.82
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:491794 original size:13 final size:13
Alignment explanation
Indices: 491776--491817 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
491766 AACGGTCAAC
491776 GGTCAACGGGTCG
1 GGTCAACGGGTCG
491789 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
491801 GGTAAACGGGTCG
1 GGTCAACGGGTCG
491814 GGTC
1 GGTC
491818 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:491819 original size:18 final size:18
Alignment explanation
Indices: 491796--491849 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
491786 TCGGGTCAAC
491796 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
491814 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
491832 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
491850 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:491849 original size:13 final size:13
Alignment explanation
Indices: 491780--491816 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
491770 GTCAACGGTC
*
491780 AACGGGTCGGGTC
1 AACGGGTCGGGTA
491793 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
491805 AACGGGTCGGGT
1 AACGGGTCGGGT
491817 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:491872 original size:10 final size:10
Alignment explanation
Indices: 491852--491906 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
491842 ACGGGTCGTG
491852 ACCGGTC-AA
1 ACCGGTCAAA
491861 ACCGGTCAAA
1 ACCGGTCAAA
491871 ACCGGTTCAAA
1 ACCGG-TCAAA
*
491882 ACCGGT-TAA
1 ACCGGTCAAA
491891 ACCGGTCAAA
1 ACCGGTCAAA
491901 ACCGGT
1 ACCGGT
491907 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:491907 original size:19 final size:19
Alignment explanation
Indices: 491852--491907 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
491842 ACGGGTCGTG
*
491852 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
491871 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
491891 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
491908 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:498140 original size:24 final size:23
Alignment explanation
Indices: 498113--498178 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
498103 ATCAAAATTT
498113 AAAACATAATTCAGGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
* * *
498137 AAAACAGAGTCCATGTCAAGTATC
1 AAAACA-AATTCAGGTCAAGTATC
498161 ATATAA-AAATTCAGGTCA
1 A-A-AACAAATTCAGGTCA
498179 TATATCATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
24 29 0.88
25 2 0.06
26 2 0.06
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (23 bp):
AAAACAAATTCAGGTCAAGTATC
Found at i:498892 original size:13 final size:13
Alignment explanation
Indices: 498874--498915 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
498864 AACGGTCAAC
498874 GGTCAACGGGTCG
1 GGTCAACGGGTCG
498887 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
498899 GGTAAACGGGTCG
1 GGTCAACGGGTCG
498912 GGTC
1 GGTC
498916 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:498917 original size:18 final size:18
Alignment explanation
Indices: 498894--498947 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
498884 TCGGGTCAAC
498894 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
498912 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
498930 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
498948 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:498947 original size:13 final size:13
Alignment explanation
Indices: 498878--498914 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
498868 GTCAACGGTC
*
498878 AACGGGTCGGGTC
1 AACGGGTCGGGTA
498891 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
498903 AACGGGTCGGGT
1 AACGGGTCGGGT
498915 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:498980 original size:11 final size:10
Alignment explanation
Indices: 498950--499002 Score: 74
Period size: 9 Copynumber: 5.4 Consensus size: 10
498940 ACGGGTCGTG
498950 ACCGGTC-AA
1 ACCGGTCAAA
498959 ACCGGTCAAA
1 ACCGGTCAAA
498969 ACCGGTTCAAA
1 ACCGG-TCAAA
*
498980 ACCGGT-TAA
1 ACCGGTCAAA
498989 ACCGGTCAAA
1 ACCGGTCAAA
498999 ACCG
1 ACCG
499003 ATTTCCAGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 15 0.38
10 14 0.36
11 10 0.26
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:500276 original size:8 final size:8
Alignment explanation
Indices: 500258--500287 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
500248 GATCATTAAG
500258 TTTAA-TT
1 TTTAATTT
500265 TTTAATTT
1 TTTAATTT
500273 TTTAATTT
1 TTTAATTT
500281 TTTAATT
1 TTTAATT
500288 ACTCCTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTAATTT
Found at i:502072 original size:21 final size:21
Alignment explanation
Indices: 502046--502087 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
502036 AATGATCAAG
502046 AAATATTATAAATATACATTA
1 AAATATTATAAATATACATTA
502067 AAATATTATAAATATACATTA
1 AAATATTATAAATATACATTA
502088 CCTTGTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATTATAAATATACATTA
Found at i:502340 original size:17 final size:18
Alignment explanation
Indices: 502318--502355 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
502308 ATTAATTATG
*
502318 TTTTATA-AACAAATTAA
1 TTTTATAGAAAAAATTAA
502335 TTTTATAGGAAAAAATTAA
1 TTTTATA-GAAAAAATTAA
502354 TT
1 TT
502356 AAAATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (18 bp):
TTTTATAGAAAAAATTAA
Found at i:507546 original size:40 final size:40
Alignment explanation
Indices: 507502--507591 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
507492 CAAGTTTTCT
* * *
507502 TTTCGCAACAAGATTTTCT-AAATCGCAATACGAATTTTGA
1 TTTCGCAACAAGATTTT-TGAAATCGCAACACGAATATTAA
** * *
507542 TTTCGCAACTCGATTTTTGGATTCGCAACACGAATATTAA
1 TTTCGCAACAAGATTTTTGAAATCGCAACACGAATATTAA
507582 TTTCGCAACA
1 TTTCGCAACA
507592 GCTTTTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (40 bp):
TTTCGCAACAAGATTTTTGAAATCGCAACACGAATATTAA
Found at i:507547 original size:20 final size:20
Alignment explanation
Indices: 507524--507589 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
507514 ATTTTCTAAA
507524 TCGCAATACGAATTTTGATT
1 TCGCAATACGAATTTTGATT
*
507544 TCGCAACT-CGATTTTTGGA-T
1 TCGCAA-TACGAATTTT-GATT
* * *
507564 TCGCAACACGAATATTAATT
1 TCGCAATACGAATTTTGATT
507584 TCGCAA
1 TCGCAA
507590 CAGCTTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.03
20 33 0.89
21 3 0.08
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
TCGCAATACGAATTTTGATT
Found at i:508399 original size:12 final size:12
Alignment explanation
Indices: 508378--508411 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
508368 ACCACATTTC
*
508378 CAATACCAAACA
1 CAATATCAAACA
508390 CAATATCAAACA
1 CAATATCAAACA
*
508402 CAATCTCAAA
1 CAATATCAAA
508412 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:508588 original size:24 final size:24
Alignment explanation
Indices: 508523--508590 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
508513 GTGAGTACTA
* *
508523 GTCAATATTCAAAATTTGATCTTG
1 GTCAATACTCAGAATTTGATCTTG
* * *
508547 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACTCAGAATTTGATCTTG
*
508571 GTCAATACTCAGATTTTGAT
1 GTCAATACTCAGAATTTGAT
508591 GATGTTCAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GTCAATACTCAGAATTTGATCTTG
Found at i:510885 original size:18 final size:18
Alignment explanation
Indices: 510862--510897 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
510852 AAGTAAAAGG
*
510862 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
510880 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
510898 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:511330 original size:20 final size:20
Alignment explanation
Indices: 511202--511329 Score: 148
Period size: 20 Copynumber: 6.4 Consensus size: 20
511192 ATGTACACTT
511202 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* * ** *
511222 CCACAGTGCGAAAGTTAAAA
1 TCGCAACGCGAAAGTCAAAA
* *
511242 CCACAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* *
511262 CCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAA
511282 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
**
511302 TCGCAACGTAAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
511322 TCACAACG
1 TCGCAACG
511330 TGGAAATATT
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:511401 original size:16 final size:16
Alignment explanation
Indices: 511380--511415 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
511370 TGCAGAGTGA
* *
511380 AATTAAACAACAAATC
1 AATTAAACAAAAAAAC
511396 AATTAAACAAAAAAAC
1 AATTAAACAAAAAAAC
511412 AATT
1 AATT
511416 CTTATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (16 bp):
AATTAAACAAAAAAAC
Found at i:511535 original size:20 final size:20
Alignment explanation
Indices: 511518--511600 Score: 112
Period size: 20 Copynumber: 4.2 Consensus size: 20
511508 TGCGAAAGAT
511518 AAATTCGCAACACGAAAGTC
1 AAATTCGCAACACGAAAGTC
511538 AAATTCGCAACACGAAAGTC
1 AAATTCGCAACACGAAAGTC
* **
511558 AAAATCGCAATGCGAAAGTC
1 AAATTCGCAACACGAAAGTC
* **
511578 ATATTCGCAACGTGAAAGTC
1 AAATTCGCAACACGAAAGTC
511598 AAA
1 AAA
511601 CTCACGTTGC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATTCGCAACACGAAAGTC
Found at i:511782 original size:20 final size:20
Alignment explanation
Indices: 511757--511888 Score: 156
Period size: 20 Copynumber: 6.6 Consensus size: 20
511747 GTTTTCCCTG
*
511757 AATTCGCAACGCGAAAATCA
1 AATTCGCAACGCGAAAGTCA
**
511777 AATTCGCAACAAGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
*
511797 AAATCGCAACGCGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
* *
511817 TATTCGCAACGCAAAAGTCA
1 AATTCGCAACGCGAAAGTCA
* *
511837 AAATAGCAACGCGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
* *
511857 AATTTGCAACGTGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
* *
511877 AAATCACAACGC
1 AATTCGCAACGC
511889 AAAAATCGCA
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 92 1.00
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AATTCGCAACGCGAAAGTCA
Found at i:511895 original size:14 final size:14
Alignment explanation
Indices: 511876--511905 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
511866 CGTGAAAGTC
511876 AAAATCACAACGCA
1 AAAATCACAACGCA
*
511890 AAAATCGCAACGCA
1 AAAATCACAACGCA
511904 AA
1 AA
511906 TTTGATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.27, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAATCACAACGCA
Found at i:511928 original size:292 final size:281
Alignment explanation
Indices: 511377--511958 Score: 658
Period size: 292 Copynumber: 2.0 Consensus size: 281
511367 TAATGCAGAG
511377 TGAAATTAAACAACAAATCAATTAAACAAAAAAACAATTCTTATTTACACTTATCAGATTGTTGC
1 TGAAATTAAACAACAAATCAATTAAACAAAAAAACAATTCTTATTTACACTTAT-AGATTGTT-C
* * **
511442 CTGTTATCTTTTTTAAGGTGTTTTCCTTGATTCGCAACGCGAAAATCAAATTCGCGTTGCGATTG
64 CTGTTATCTTTTTGAAGGTGTTTTCCCTGATTCGCAACGCGAAAATCAAATTCGCG-AACGA---
* * * * *
511507 TTGCGAAAGATAAATTCGCAACACGAAAGTCAAATTCGCAACACGAAAGTCAAAATCGCAATGCG
125 -T-AGAAAGATAAAATCGCAACACGAAAGTCAAATTCGCAACACAAAAGTCAAAATAGCAACGCG
* * * *
511572 AAAGTCATATTCGCAACGTGAAAGTCAAACTCACGTTGCAATTTTGACTTTCGCGTTGCGAAAGT
188 AAAGTCAAATTCGCAACGTGAAAGTCAAACACACGTCGCAAATTTGACTTTCGCGTTGCGAAAGT
* * *
511637 GTACCTTATGGTATTTTTTGTCTTCAACA
253 ATACATTATGGTATTTTTTGCCTTCAACA
511666 TGAAATTAAACAACAAATCAATTAAACAAAAAAAAAACAATTCTTATTTACACTTAT-G-TTG-T
1 TGAAATTAAACAACAAATCAATTAAAC---AAAAAAACAATTCTTATTTACACTTATAGATTGTT
511728 -CTGTTATCTTTTTGAAGGTGTTTTCCCTGAATTCGCAACGCGAAAATCAAATTCGC-AAC-A-A
63 CCTGTTATCTTTTTGAAGGTGTTTTCCCTG-ATTCGCAACGCGAAAATCAAATTCGCGAACGATA
* * *
511789 GAAAG-TCAAAATCGCAACGCGAAAGTCATATTCGCAACGCAAAAGTCAAAATAGCAACGCGAAA
127 GAAAGAT-AAAATCGCAACACGAAAGTCAAATTCGCAACACAAAAGTCAAAATAGCAACGCGAAA
* *
511853 GTCAAATTTGCAACGTGAAAGTCAAAATCACAACGCAAAAATCGCAACGCAAATTTGATTTTCGC
191 GTCAAATTCGCAACGTGAAAGTC-AAA-CAC-ACG------T-----CGCAAATTTGACTTTCGC
* *
511918 GTTGCGAAAGTATACATTCTGGTGTTTTTTGCCTTCAACA
242 GTTGCGAAAGTATACATTATGGTATTTTTTGCCTTCAACA
511958 T
1 T
511959 AATGCAGAGT
Statistics
Matches: 251, Mismatches: 23, Indels: 35
0.81 0.07 0.11
Matches are distributed among these distances:
277 1 0.00
278 76 0.30
279 3 0.01
280 2 0.01
281 3 0.01
284 1 0.00
285 1 0.00
286 27 0.11
287 27 0.11
288 1 0.00
289 30 0.12
290 1 0.00
292 78 0.31
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (281 bp):
TGAAATTAAACAACAAATCAATTAAACAAAAAAACAATTCTTATTTACACTTATAGATTGTTCCT
GTTATCTTTTTGAAGGTGTTTTCCCTGATTCGCAACGCGAAAATCAAATTCGCGAACGATAGAAA
GATAAAATCGCAACACGAAAGTCAAATTCGCAACACAAAAGTCAAAATAGCAACGCGAAAGTCAA
ATTCGCAACGTGAAAGTCAAACACACGTCGCAAATTTGACTTTCGCGTTGCGAAAGTATACATTA
TGGTATTTTTTGCCTTCAACA
Found at i:512016 original size:14 final size:13
Alignment explanation
Indices: 511979--512024 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
511969 GAAATTAAAC
511979 AACAAATCAATTA
1 AACAAATCAATTA
*
511992 AACAAATTCAACTTT
1 AACAAA-TCAA-TTA
*
512007 TACAAATCAATTA
1 AACAAATCAATTA
512020 AACAA
1 AACAA
512025 GTAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 12 0.44
14 8 0.30
15 7 0.26
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (13 bp):
AACAAATCAATTA
Found at i:512110 original size:64 final size:64
Alignment explanation
Indices: 511984--512158 Score: 295
Period size: 63 Copynumber: 2.8 Consensus size: 64
511974 TAAACAACAA
511984 ATCAATTAAACAAATTCAACTTTTACAAATCAATTAAACAAGT-AAAAAATAATTCTTATTCCTC
1 ATCAATTAAACAAA-TCAACTTTTACAAATCAATTAAACAAGTAAAAAAATAATTCTTATTCCTC
512048 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAA-TAAAAAAATAATTCTTATTTCCTC
1 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGTAAAAAAATAATTCTTA-TTCCTC
*
512112 ATCAATTAAACAAATCAAC--TTACAAATCAATTAAACAAGCAAAAAAA
1 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGTAAAAAAA
512159 GTGTACACAG
Statistics
Matches: 107, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
62 20 0.19
63 48 0.45
64 39 0.36
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.29
Consensus pattern (64 bp):
ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGTAAAAAAATAATTCTTATTCCTC
Found at i:513522 original size:21 final size:21
Alignment explanation
Indices: 513498--513585 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
513488 CGGGCTCTCA
*
513498 AACGGTGGGAGGGACCTCTTG
1 AACGGTGGGAGGGGCCTCTTG
* **
513519 AACGATGACAGGGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTG
513540 AACGGTGGGAGGGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTG
* * * *
513561 AACGATAGAAGAGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTG
513582 AACG
1 AACG
513586 ATGACAGGTG
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.24, C:0.20, G:0.38, T:0.18
Consensus pattern (21 bp):
AACGGTGGGAGGGGCCTCTTG
Found at i:513558 original size:42 final size:42
Alignment explanation
Indices: 513498--513585 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
513488 CGGGCTCTCA
*
513498 AACGGTGGGAGGGACCTCTTGAACGAT-GACAGGGGCCTCTTG
1 AACGGTGGGAGGGACCTCTTGAACGATAGA-AGAGGCCTCTTG
*
513540 AACGGTGGGAGGGGCCTCTTGAACGATAGAAGAGGCCTCTTG
1 AACGGTGGGAGGGACCTCTTGAACGATAGAAGAGGCCTCTTG
513582 AACG
1 AACG
513586 ATGACAGGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.38, T:0.18
Consensus pattern (42 bp):
AACGGTGGGAGGGACCTCTTGAACGATAGAAGAGGCCTCTTG
Found at i:513962 original size:21 final size:21
Alignment explanation
Indices: 513938--513980 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
513928 TTGTCATCGA
513938 GTAAA-ACCTCTACCTCACCAC
1 GTAAATACC-CTACCTCACCAC
* *
513959 GTAAATACCGTACCTCATCAC
1 GTAAATACCCTACCTCACCAC
513980 G
1 G
513981 CCATGCACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.37, G:0.09, T:0.21
Consensus pattern (21 bp):
GTAAATACCCTACCTCACCAC
Found at i:514021 original size:21 final size:21
Alignment explanation
Indices: 513997--514046 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
513987 ACCATTGTCG
* *
513997 TCACGTAAAGTACTGACCTCC
1 TCACGTAAAGCACTGACCTCA
*
514018 TCACGTAAAGCATTGACCTCA
1 TCACGTAAAGCACTGACCTCA
514039 TCACGTAA
1 TCACGTAA
514047 CTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (21 bp):
TCACGTAAAGCACTGACCTCA
Found at i:514184 original size:21 final size:21
Alignment explanation
Indices: 514160--514214 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
514150 GTGATGGAAT
*
514160 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCATTGTAG
*
514181 AGGTGATGGCTCTCATTGTGG
1 AGGTGATGGCTCTCATTGTAG
514202 AGGTGATGGCTCT
1 AGGTGATGGCTCT
514215 GGTGTCAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.15, G:0.38, T:0.33
Consensus pattern (21 bp):
AGGTGATGGCTCTCATTGTAG
Found at i:515763 original size:20 final size:20
Alignment explanation
Indices: 515740--515778 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
515730 TTTGAAACTT
*
515740 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACACGAAAATG
*
515760 AAAATTGCAACACGAAAAT
1 AAAATCGCAACACGAAAAT
515779 CGCAACGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:515829 original size:20 final size:20
Alignment explanation
Indices: 515790--515848 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 20
515780 GCAACGCAAA
515790 TTTCATTTTCGCAACGTTGCGAT
1 TTTCATTTTCG---CGTTGCGAT
515813 TTTCATTTTCGCGTTGCGAT
1 TTTCATTTTCGCGTTGCGAT
*
515833 TTTCATTTTCGTGTTG
1 TTTCATTTTCGCGTTG
515849 TGAATTTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 24 0.69
23 11 0.31
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTCATTTTCGCGTTGCGAT
Found at i:516382 original size:20 final size:20
Alignment explanation
Indices: 516357--516572 Score: 106
Period size: 20 Copynumber: 10.8 Consensus size: 20
516347 ATCGAAAATA
516357 ATATTCGCGTTGCGATTTAC
1 ATATTCGCGTTGCGATTTAC
** **
516377 ATATTCGTATTGCGATTTTGG
1 ATATTCGCGTTGCGA-TTTAC
* *
516398 AAAATCGCGTTGCGATTTAC
1 ATATTCGCGTTGCGATTTAC
** * *
516418 ATATTATCATTGCGAATTAC
1 ATATTCGCGTTGCGATTTAC
* * *
516438 CTATTCACGCTGCGAATTTGAC
1 ATATTCGCGTTGCG-ATTT-AC
*
516460 -T-TTAGCGTTGCGAATTTGAC
1 ATATTCGCGTTGCG-ATTT-AC
*
516480 -T-TTCTCGTTGCGATTTTGAC
1 ATATTCGCGTTGCGA-TTT-AC
*
516500 -T-TTCGCGTTGAGATTTTGAC
1 ATATTCGCGTTGCGA-TTT-AC
*
516520 -T-TTCGCGTTACGATTTAC
1 ATATTCGCGTTGCGATTTAC
**
516538 ATATTATCGTTGCGATTTAC
1 ATATTCGCGTTGCGATTTAC
* *
516558 TTATTCGTGTTGCGA
1 ATATTCGCGTTGCGA
516573 ATTTGGAACC
Statistics
Matches: 152, Mismatches: 38, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 125 0.82
21 18 0.12
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
ATATTCGCGTTGCGATTTAC
Found at i:516534 original size:40 final size:40
Alignment explanation
Indices: 516454--516535 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
516444 ACGCTGCGAA
* * *
516454 TTTGACTTTAGCGTTGCGAATTTGACTTTCTCGTTGCGAT
1 TTTGACTTTAGCGTTGAGAATTTGACTTTCGCGTTACGAT
* *
516494 TTTGACTTTCGCGTTGAGATTTTGACTTTCGCGTTACGAT
1 TTTGACTTTAGCGTTGAGAATTTGACTTTCGCGTTACGAT
516534 TT
1 TT
516536 ACATATTATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (40 bp):
TTTGACTTTAGCGTTGAGAATTTGACTTTCGCGTTACGAT
Found at i:521103 original size:19 final size:19
Alignment explanation
Indices: 521079--521116 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
521069 ATTGTTCATA
521079 TTGGTAACAAATGCAGTTG
1 TTGGTAACAAATGCAGTTG
521098 TTGGTAACAAATGCAGTTG
1 TTGGTAACAAATGCAGTTG
521117 ACTAACTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
TTGGTAACAAATGCAGTTG
Found at i:522075 original size:23 final size:23
Alignment explanation
Indices: 522032--522076 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
522022 TAACTTATGT
522032 ATAATAAAACTCAAACATAAATA
1 ATAATAAAACTCAAACATAAATA
* *
522055 ATAA-AAAATTCAAGACCTAAAT
1 ATAATAAAACTCAA-ACATAAAT
522077 CTTGACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.22
Consensus pattern (23 bp):
ATAATAAAACTCAAACATAAATA
Found at i:523977 original size:22 final size:22
Alignment explanation
Indices: 523949--523994 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
523939 TTTTTATGTT
523949 CATGTAATAAACGAATCAAACA
1 CATGTAATAAACGAATCAAACA
*
523971 CATGTAATATACGAATCAAACA
1 CATGTAATAAACGAATCAAACA
523993 CA
1 CA
523995 AATAATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.20, G:0.09, T:0.20
Consensus pattern (22 bp):
CATGTAATAAACGAATCAAACA
Found at i:524000 original size:22 final size:21
Alignment explanation
Indices: 523953--524019 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
523943 TATGTTCATG
**
523953 TAATAAACGAATCAAACACATG
1 TAAT-AACGAATCAAACACAAA
523975 TAATATACGAATCAAACACAAA
1 TAATA-ACGAATCAAACACAAA
*
523997 TAATAATCG-AGCAAACACAAA
1 TAATAA-CGAATCAAACACAAA
524018 TA
1 TA
524020 GAAGTGTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 15 0.38
22 25 0.62
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.18
Consensus pattern (21 bp):
TAATAACGAATCAAACACAAA
Found at i:525971 original size:13 final size:13
Alignment explanation
Indices: 525953--525978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
525943 AAGATTAGAA
525953 AGGTATTCAGCTT
1 AGGTATTCAGCTT
525966 AGGTATTCAGCTT
1 AGGTATTCAGCTT
525979 CACACCCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
AGGTATTCAGCTT
Found at i:528612 original size:5 final size:5
Alignment explanation
Indices: 528602--528654 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
528592 AACGGTCAAC
* *
528602 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
528651 GGTC
1 GGTC
528655 AGACCGATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:528617 original size:17 final size:17
Alignment explanation
Indices: 528595--528655 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
528585 AACGGTCAAC
528595 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
528612 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
528634 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
528651 GGTCA
1 GGTCA
528656 GACCGATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:528622 original size:7 final size:7
Alignment explanation
Indices: 528575--528605 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
528565 GTCAAAGAAA
*
528575 GTCAATG
1 GTCAACG
528582 GTCAACG
1 GTCAACG
528589 GTCAACG
1 GTCAACG
528596 GTCAACG
1 GTCAACG
528603 GTC
1 GTC
528606 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:528630 original size:22 final size:22
Alignment explanation
Indices: 528588--528654 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
528578 AATGGTCAAC
*
528588 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
528612 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
528634 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
528655 AGACCGATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:528689 original size:9 final size:9
Alignment explanation
Indices: 528651--528749 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
528641 GGTCGGGTCG
*
528651 GGTCAGACC
1 GGTCAAACC
*
528660 GATCAAACC
1 GGTCAAACC
* *
528669 GATTCAGACC
1 G-GTCAAACC
528679 GGTCAAACC
1 GGTCAAACC
*
528688 GGTTCGAACC
1 GG-TCAAACC
*
528698 GGTTGAAACC
1 GG-TCAAACC
528708 GGTCAAACC
1 GGTCAAACC
528717 GGTCAGAACC
1 GGTCA-AACC
*
528727 GGTTGAAAACC
1 GG-T-CAAACC
*
528738 GGTTAAACC
1 GGTCAAACC
528747 GGT
1 GGT
528750 TTCCAGCAGC
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
9 35 0.48
10 30 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:528698 original size:19 final size:19
Alignment explanation
Indices: 528657--528750 Score: 77
Period size: 19 Copynumber: 4.8 Consensus size: 19
528647 GTCGGGTCAG
* *
528657 ACCGATCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
528675 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* *
528695 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
528714 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
*
528735 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
528751 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 34 0.55
20 18 0.29
21 8 0.13
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:528708 original size:29 final size:31
Alignment explanation
Indices: 528676--528750 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
528666 ACCGATTCAG
528676 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
528705 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
528735 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
528751 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:535930 original size:5 final size:5
Alignment explanation
Indices: 535920--535972 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
535910 AACGGTCAAC
* *
535920 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
535969 GGTC
1 GGTC
535973 AGACCGATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:535935 original size:17 final size:17
Alignment explanation
Indices: 535913--535973 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
535903 AATGGTCAAC
535913 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
535930 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
535952 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
535969 GGTCA
1 GGTCA
535974 GACCGATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:535948 original size:22 final size:22
Alignment explanation
Indices: 535906--535972 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
535896 GAAAGTCAAT
*
535906 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
535930 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
535952 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
535973 AGACCGATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:536007 original size:9 final size:9
Alignment explanation
Indices: 535969--536067 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
535959 GGTCGGGTCG
*
535969 GGTCAGACC
1 GGTCAAACC
*
535978 GATCAAACC
1 GGTCAAACC
* *
535987 GATTCAGACC
1 G-GTCAAACC
535997 GGTCAAACC
1 GGTCAAACC
*
536006 GGTTCGAACC
1 GG-TCAAACC
*
536016 GGTTGAAACC
1 GG-TCAAACC
536026 GGTCAAACC
1 GGTCAAACC
536035 GGTCAGAACC
1 GGTCA-AACC
*
536045 GGTTGAAAACC
1 GG-T-CAAACC
*
536056 GGTTAAACC
1 GGTCAAACC
536065 GGT
1 GGT
536068 TTCCAGCAGC
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
9 35 0.48
10 30 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:536016 original size:19 final size:19
Alignment explanation
Indices: 535975--536068 Score: 77
Period size: 19 Copynumber: 4.8 Consensus size: 19
535965 GTCGGGTCAG
* *
535975 ACCGATCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
535993 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* *
536013 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
536032 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
*
536053 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
536069 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 34 0.55
20 18 0.29
21 8 0.13
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:536026 original size:29 final size:31
Alignment explanation
Indices: 535994--536068 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
535984 ACCGATTCAG
535994 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
536023 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
536053 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
536069 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:541977 original size:33 final size:34
Alignment explanation
Indices: 541940--542046 Score: 89
Period size: 33 Copynumber: 3.2 Consensus size: 34
541930 GGTAAGAAAT
* * *
541940 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
541973 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
* * *
542007 -T-TTTTTAT-TAAAATAATATTTATATAATTATTA
1 TTATTTTTATAT-TAAT-ATATTTATGTAAATATTA
542040 TTTATTT
1 -TTATTT
542047 AGAATTATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
31 1 0.02
32 10 0.16
33 33 0.54
34 6 0.10
35 8 0.13
36 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:542024 original size:35 final size:33
Alignment explanation
Indices: 541971--542047 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
541961 TTTAAATAGT
*
541971 TATTATTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTT-TATTAAAATAATATTTATATAAA
*
542002 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
542035 TATTATTTATTTA
1 TATTATTT-TTTA
542048 GAATTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 4 0.10
31 10 0.25
32 3 0.08
33 19 0.47
34 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Done.