Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 4 of 19
Found at i:991203 original size:21 final size:21
Alignment explanation
Indices: 991174--991228 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
991164 GAGCATGTAG
991174 TTCTCTGCTTCAATCCCATCGA
1 TTCT-TGCTTCAATCCCATCGA
991196 TTCTTGCTTCAATCCCATCGA
1 TTCTTGCTTCAATCCCATCGA
*
991217 TTCTTACTTCAA
1 TTCTTGCTTCAA
991229 GTGTGCACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCTTGCTTCAATCCCATCGA
Found at i:997786 original size:2 final size:2
Alignment explanation
Indices: 997779--997810 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
997769 AATCTATGTA
997779 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
997811 GTTACACCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:998609 original size:23 final size:22
Alignment explanation
Indices: 998575--998622 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
998565 TATGTTGAGC
998575 TTTGTACAGGTCATGCTTTTCTT
1 TTTGTACAGGTCAT-CTTTTCTT
* *
998598 TTTGT-CAGGGTCCTCTTTTGTT
1 TTTGTACA-GGTCATCTTTTCTT
998620 TTT
1 TTT
998623 AAGATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.08, C:0.17, G:0.19, T:0.56
Consensus pattern (22 bp):
TTTGTACAGGTCATCTTTTCTT
Found at i:1003393 original size:11 final size:10
Alignment explanation
Indices: 1003359--1003402 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1003349 TAACAATCTT
*
1003359 TAAAGTAAAT
1 TAAAGTAAAA
*
1003369 TAAAGCAAAA
1 TAAAGTAAAA
1003379 TAAAGTAAAA
1 TAAAGTAAAA
*
1003389 CTAAATTAAAA
1 -TAAAGTAAAA
1003400 TAA
1 TAA
1003403 TTTAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (10 bp):
TAAAGTAAAA
Found at i:1005199 original size:2 final size:2
Alignment explanation
Indices: 1005192--1005228 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1005182 TTCAAGCTGT
1005192 TA TA TA 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 TA TA TA T
1005229 TCTCTAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1011818 original size:2 final size:2
Alignment explanation
Indices: 1011811--1011836 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1011801 CAAGGTAGCT
1011811 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1011837 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1018120 original size:27 final size:28
Alignment explanation
Indices: 1018087--1018149 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
1018077 TTAAATTTTT
*
1018087 TAAATATTAATAATATAA-AATTTAATTA
1 TAAATATTAATAAT-TAATAATTTAAATA
*
1018115 -AAATATTAATAATTAATCATTTAAATA
1 TAAATATTAATAATTAATAATTTAAATA
1018142 TAAATATT
1 TAAATATT
1018150 TTATTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 3 0.10
27 21 0.68
28 7 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAATATTAATAATTAATAATTTAAATA
Found at i:1018171 original size:41 final size:43
Alignment explanation
Indices: 1018093--1018199 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 43
1018083 TTTTTAAATA
*
1018093 TTAATAATATAAA-A-TTTAATTAAAATATTAATAATTAATCA-T
1 TTAA-AATATAAATATTTTATTTAAAATATTAATAATTAAT-ATT
* *
1018135 TT-AAATATAAATATTTTATTTATAAT-TTAATCATTAATATT
1 TTAAAATATAAATATTTTATTTAAAATATTAATAATTAATATT
*
1018176 TTAAAATATTAATATTTTATTTAA
1 TTAAAATATAAATATTTTATTTAA
1018200 TTTAAATATT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
40 9 0.16
41 16 0.29
42 31 0.55
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (43 bp):
TTAAAATATAAATATTTTATTTAAAATATTAATAATTAATATT
Found at i:1018278 original size:18 final size:16
Alignment explanation
Indices: 1018167--1018274 Score: 69
Period size: 16 Copynumber: 6.7 Consensus size: 16
1018157 TAATTTAATC
1018167 ATTAATATTTTAAAAT
1 ATTAATATTTTAAAAT
*
1018183 ATTAATATTTTATTTAAT
1 ATTAATATTTTA--AAAT
* **
1018201 -TTAA-ATATTATTAT
1 ATTAATATTTTAAAAT
* ***
1018215 GATCAATTATTTTATTTT
1 -ATTAA-TATTTTAAAAT
* *
1018233 ATT-TTATTTTCAAAT
1 ATTAATATTTTAAAAT
1018248 ATTAATATTTTAAAAT
1 ATTAATATTTTAAAAT
1018264 ATTAATATTTT
1 ATTAATATTTT
1018275 TTAATTTAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
14 3 0.04
15 10 0.14
16 41 0.58
17 6 0.08
18 11 0.15
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (16 bp):
ATTAATATTTTAAAAT
Found at i:1018319 original size:81 final size:81
Alignment explanation
Indices: 1018146--1018316 Score: 278
Period size: 79 Copynumber: 2.1 Consensus size: 81
1018136 TAAATATAAA
*
1018146 TATTTTATTTATAATTT--AATCATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATAT
1 TATTTTATTT-TATTTTCAAAT-ATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATAT
1018209 TATTATGATCAATTATTT
64 TATTATGATCAATTATTT
1018227 TATTTTATTTTATTTTCAAATATTAATATTTTAAAATATTAATA-TTT-TTTAATTTAAATATTA
1 TATTTTATTTTATTTTCAAATATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATATTA
*
1018290 TTATGATTAATTATTT
66 TTATGATCAATTATTT
1018306 TATTTTATTTT
1 TATTTTATTTT
1018317 TTAAATATTA
Statistics
Matches: 86, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
79 42 0.49
80 8 0.09
81 33 0.38
82 3 0.03
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (81 bp):
TATTTTATTTTATTTTCAAATATTAATATTTTAAAATATTAATATTTTATTTAATTTAAATATTA
TTATGATCAATTATTT
Found at i:1018368 original size:27 final size:25
Alignment explanation
Indices: 1018312--1018399 Score: 71
Period size: 27 Copynumber: 3.6 Consensus size: 25
1018302 ATTTTATTTT
*
1018312 ATTT-TTTAAATATTAATAATTGAT
1 ATTTATTTAAATATTAATAATTGAC
*
1018336 AGTTTATTTAAAATGTTAATAATTGAC
1 A-TTTATTT-AAATATTAATAATTGAC
* *
1018363 ---CATTTAAATATTAAT-ATTTA-
1 ATTTATTTAAATATTAATAATTGAC
1018383 ATTTAATTTAAATATTA
1 ATTT-ATTTAAATATTA
1018400 TTATGATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
21 4 0.08
22 9 0.18
23 4 0.08
24 13 0.25
25 3 0.06
26 3 0.06
27 15 0.29
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (25 bp):
ATTTATTTAAATATTAATAATTGAC
Found at i:1018465 original size:123 final size:126
Alignment explanation
Indices: 1018303--1018529 Score: 338
Period size: 123 Copynumber: 1.8 Consensus size: 126
1018293 TGATTAATTA
*
1018303 TTTTATTTTATTTTTTAAATATTAATAATTGATAGTTTATTTAAAATGTTAATAATTGACCATTT
1 TTTTATTTTATTTTTTAAATATTAATAATTGATAGTTTATTTAAAATATTAATAATTGACCATTT
*
1018368 AAATATTAATA-TTTA-ATTTAATTTAAAT-ATTATTATGATTAACTTTTTATTTTCTTTCT
66 AAATATTAATATTTTATATATAATTTAAATGA-TATTATGATTAACTTTTTATTTTCTTTCT
**
1018427 TTTTATTTTA-TTTTTAAATATTAATAATTGATCA-TTTATTTAAAATATTAATAATTGATGATT
1 TTTTATTTTATTTTTTAAATATTAATAATTGAT-AGTTTATTTAAAATATTAATAATTGACCATT
** *
1018490 TATTTATTAGTATTTTATATATAATTTAAATGATATTATG
65 TAAATATTAATATTTTATATATAATTTAAATGATATTATG
1018530 CTTATTTATT
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
123 57 0.62
124 15 0.16
125 19 0.21
126 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (126 bp):
TTTTATTTTATTTTTTAAATATTAATAATTGATAGTTTATTTAAAATATTAATAATTGACCATTT
AAATATTAATATTTTATATATAATTTAAATGATATTATGATTAACTTTTTATTTTCTTTCT
Found at i:1018475 original size:27 final size:27
Alignment explanation
Indices: 1018433--1018495 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
1018423 TTCTTTTTAT
*
1018433 TTTATTTTTAAATATTAATAATTGATCA
1 TTTA-TTTAAAATATTAATAATTGATCA
*
1018461 TTTATTTAAAATATTAATAATTGATGA
1 TTTATTTAAAATATTAATAATTGATCA
1018488 TTTATTTA
1 TTTATTTA
1018496 TTAGTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (27 bp):
TTTATTTAAAATATTAATAATTGATCA
Found at i:1018553 original size:123 final size:124
Alignment explanation
Indices: 1018296--1018553 Score: 316
Period size: 123 Copynumber: 2.1 Consensus size: 124
1018286 ATTATTATGA
*
1018296 TTAA-TTA-TTTTATTTTATTTTTTAAATATTAATAATTGATAGTTTATTTAAAATGTTAATAAT
1 TTAATTTATTTTTATTTTATTTTTTAAATATTAATAATTGATAGTTTATTTAAAATATTAATAAT
*
1018359 TGACCATTTAAATATTAATATTTAATTTAATTTAAATATTATTATGATTAACTTTTTAT
66 TGACCATTTAAATATTAATATTTAATATAATTTAAATATTATTATGATTAACTTTTTAT
** *
1018418 TTTCTTTCTTTTTATTTTA-TTTTTAAATATTAATAATTGATCA-TTTATTTAAAATATTAATAA
1 TTAATTTATTTTTATTTTATTTTTTAAATATTAATAATTGAT-AGTTTATTTAAAATATTAATAA
** ** * *
1018481 TTGATGATTTATTTATTAGTATTTTATATATAATTTAAATGA-TATTATGCTT-A-TTTATT-T
65 TTGACCATTTAAATATTAATA-TTTA-ATATAATTTAAAT-ATTATTATGATTAACTTT-TTAT
1018541 TTAATTTATTTTT
1 TTAATTTATTTTT
1018554 TAAACAGGAA
Statistics
Matches: 115, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
122 2 0.02
123 73 0.63
124 18 0.16
125 21 0.18
126 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (124 bp):
TTAATTTATTTTTATTTTATTTTTTAAATATTAATAATTGATAGTTTATTTAAAATATTAATAAT
TGACCATTTAAATATTAATATTTAATATAATTTAAATATTATTATGATTAACTTTTTAT
Found at i:1018566 original size:113 final size:108
Alignment explanation
Indices: 1018426--1018627 Score: 251
Period size: 109 Copynumber: 1.8 Consensus size: 108
1018416 ATTTTCTTTC
* * ** * *
1018426 TTTTTATTTTATTTTTAAATATTAATAATTGATCATTTATTTAAAATATTAATAATTGATGATTT
1 TTTTTAATTTATTTTTAAACAGGAATAATTGATAATTTATTT----TATTAATAATTGATAATTT
** *
1018491 ATTTATTAGTATTTTATATATAATTTAAATGATATTATGCTTATTTA
62 AAATATTAATATTTTATATATAATTTAAATGATATTATGCTTATTTA
* *
1018538 TTTTTAATTTATTTTTTAAACAGGAATAATTTATAATTTATTTTATTAATAATTTATAATTTAAA
1 TTTTTAATTTA-TTTTTAAACAGGAATAATTGATAATTTATTTTATTAATAATTGATAATTTAAA
*
1018603 TATTAATATTTTATTTATAATTTAA
65 TATTAATATTTTATATATAATTTAA
1018628 TATTAATATG
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
109 41 0.53
112 10 0.13
113 26 0.34
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (108 bp):
TTTTTAATTTATTTTTAAACAGGAATAATTGATAATTTATTTTATTAATAATTGATAATTTAAAT
ATTAATATTTTATATATAATTTAAATGATATTATGCTTATTTA
Found at i:1018662 original size:19 final size:20
Alignment explanation
Indices: 1018581--1018662 Score: 71
Period size: 19 Copynumber: 4.0 Consensus size: 20
1018571 TAATTTATTT
*
1018581 TATTAATAATTTATAATTTAAA
1 TATTAAT-ATTTAT-ATTAAAA
*
1018603 TATTAATATTT-TATTTATAA
1 TATTAATATTTATA-TTAAAA
*
1018623 T-TTAATATTAATATGTTAAAA
1 TATTAATATT--TATATTAAAA
1018644 TATTAATATTT-TATTAAAA
1 TATTAATATTTATATTAAAA
1018663 GTTGAAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
19 16 0.32
20 7 0.14
21 11 0.22
22 16 0.32
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (20 bp):
TATTAATATTTATATTAAAA
Found at i:1031874 original size:10 final size:10
Alignment explanation
Indices: 1031859--1031897 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
1031849 AAACTAATTA
1031859 TAAAAATAAT
1 TAAAAATAAT
*
1031869 TAAAAATAAA
1 TAAAAATAAT
1031879 TAAAATTATAAT
1 TAAAA--ATAAT
1031891 TAAAAAT
1 TAAAAAT
1031898 TGAGTACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:1048063 original size:64 final size:66
Alignment explanation
Indices: 1047844--1048123 Score: 232
Period size: 64 Copynumber: 4.2 Consensus size: 66
1047834 AGTAAGTAGG
* ** * * * * *
1047844 CTTTATTTCACTATGTTTTATTATTATTATGGATGAGCTTAGGATCTTTGGCTAGTGT-TTTTAT
1 CTTTATTTCTCTATACTTTATGATTATTATGGATGAGTTTAGGCTCTTTGGATAATGTATTTTAT
*
1047908 G
66 A
* * * * *
1047909 CTTTATTTAATTTCTCTAT-GTTTAATGATTATTATGAATGAGTTTTGGGTC-TTGGACTATTGT
1 C----TTT-ATTTCTCTATACTTT-ATGATTATTATGGATGAGTTTAGGCTCTTTGGA-TAATGT
1047972 -TTTTATA
59 ATTTTATA
* * * *
1047979 ATTTATTTCTCTCTATTTTATGATTATTATTGATGAGTTTACGGCT-TTTGGAT-A-GTATTTTA
1 CTTTATTTCTCTATACTTTATGATTATTATGGATGAGTTTA-GGCTCTTTGGATAATGTATTTTA
1048041 TA
65 TA
* * * *
1048043 CTTTATTTCTCTATACTTTATTATTATTATGGATGAGTTTAGGGTCTTTGGCTAATGTTTTTTGA
1 CTTTATTTCTCTATACTTTATGATTATTATGGATGAGTTTAGGCTCTTTGGATAATGTATTTT-A
1048108 TA
65 TA
1048110 CTTTATTTCTCTAT
1 CTTTATTTCTCTAT
1048124 GTTTAGGATT
Statistics
Matches: 174, Mismatches: 26, Indels: 28
0.76 0.11 0.12
Matches are distributed among these distances:
63 5 0.03
64 49 0.28
65 31 0.18
66 20 0.11
67 17 0.10
69 10 0.06
70 42 0.24
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.54
Consensus pattern (66 bp):
CTTTATTTCTCTATACTTTATGATTATTATGGATGAGTTTAGGCTCTTTGGATAATGTATTTTAT
A
Found at i:1052408 original size:28 final size:28
Alignment explanation
Indices: 1052383--1052446 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
1052373 AGGTTCAAGC
* *
1052383 TTCAAGTATAACCATTGCCTTTTCAAAG
1 TTCAAGCATAACCATTGACTTTTCAAAG
*
1052411 ATCAAGCATAACCATTGACTTTTCAAAG
1 TTCAAGCATAACCATTGACTTTTCAAAG
1052439 TTCAAGCA
1 TTCAAGCA
1052447 CACCCTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (28 bp):
TTCAAGCATAACCATTGACTTTTCAAAG
Found at i:1053150 original size:21 final size:21
Alignment explanation
Indices: 1053126--1053186 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1053116 TAATTTTAAC
*
1053126 AAATTTAAAAA-CTATTCAAAT
1 AAATTCAAAAATC-ATTCAAAT
1053147 AAATTCAAAAATCATTCAAAT
1 AAATTCAAAAATCATTCAAAT
* * *
1053168 AAGTTCAAAGATTATTCAA
1 AAATTCAAAAATCATTCAA
1053187 GTAATTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 34 0.97
22 1 0.03
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.31
Consensus pattern (21 bp):
AAATTCAAAAATCATTCAAAT
Found at i:1053323 original size:21 final size:21
Alignment explanation
Indices: 1053281--1053366 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
1053271 TCAAAAACAT
* * *
1053281 ATTCAAACAACTTCAAAAATC
1 ATTCAAACAAGTTTAAAGATC
* *
1053302 ATTCAAACAAATTTAAGGATC
1 ATTCAAACAAGTTTAAAGATC
* *
1053323 ACTCAAACAAGTTTAAGGATC
1 ATTCAAACAAGTTTAAAGATC
*
1053344 ACTCAAACAAGTTTAAAGATC
1 ATTCAAACAAGTTTAAAGATC
1053365 AT
1 AT
1053367 CGAAGCAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.26
Consensus pattern (21 bp):
ATTCAAACAAGTTTAAAGATC
Found at i:1059736 original size:5 final size:5
Alignment explanation
Indices: 1059726--1059755 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1059716 TGACTTTTGT
*
1059726 AAACC AAACC AAACC AAACC ATACC AAACC
1 AAACC AAACC AAACC AAACC AAACC AAACC
1059756 GAGTAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.40, G:0.00, T:0.03
Consensus pattern (5 bp):
AAACC
Found at i:1060419 original size:15 final size:15
Alignment explanation
Indices: 1060375--1060430 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1060365 TTTAAAATTT
*
1060375 AATAATTTAAATTTAA
1 AATAATTTAAA-TTCA
** *
1060391 AATAATTTGCATTCG
1 AATAATTTAAATTCA
*
1060406 AATGATTTAAATTCA
1 AATAATTTAAATTCA
1060421 AATAATTTAA
1 AATAATTTAA
1060431 GTATCAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (15 bp):
AATAATTTAAATTCA
Found at i:1074125 original size:16 final size:14
Alignment explanation
Indices: 1074101--1074141 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
1074091 GAATTTTAAA
1074101 AAAAATAAAAATAC
1 AAAAATAAAAATAC
*
1074115 ACAATAATAAAAATAT
1 A-AA-AATAAAAATAC
1074131 AAAAATAAAAA
1 AAAAATAAAAA
1074142 AGAGATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 9 0.38
15 4 0.17
16 11 0.46
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAAAAATAC
Found at i:1080320 original size:13 final size:13
Alignment explanation
Indices: 1080302--1080327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1080292 AGGAAATTTT
1080302 AAAAAATATAGGC
1 AAAAAATATAGGC
1080315 AAAAAATATAGGC
1 AAAAAATATAGGC
1080328 TTGTTTCTTT
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:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAAATATAGGC
Found at i:1084669 original size:46 final size:44
Alignment explanation
Indices: 1084483--1084864 Score: 340
Period size: 45 Copynumber: 8.5 Consensus size: 44
1084473 TTTTATGTAA
* * * * ** *
1084483 CCTCATTCCAAATAAAGAGCTTATTCTCTTTTTAAACTTATATGG
1 CCTCATTCTAGATAAGGAGCTTATTCT-TTTTTAAAGTTACGTAG
* * * *
1084528 CCTCATTCCAAATAAGGAACTTATTCTTCTTTTAAAGTCACGTAG
1 CCTCATTCTAGATAAGGAGCTTATTCTT-TTTTAAAGTTACGTAG
* * *
1084573 CTTCATTCTAGATAAAGAGCTTATTCCTTTTTTAAAGTTATGTAG
1 CCTCATTCTAGATAAGGAGCTTATT-CTTTTTTAAAGTTACGTAG
* *
1084618 CCTCATTCTAGATAAGGAGCTCATTCATTTTGTTAAAGTTACATAG
1 CCTCATTCTAGATAAGGAGCTTATTC-TTTT-TTAAAGTTACGTAG
* * * * *
1084664 CCTCATTCTGGATGAGGAACTCATTCTTTTTTTTAAAGTTATGTAG
1 CCTCATTCTAGATAAGGAGCTTATTC--TTTTTTAAAGTTACGTAG
* * *
1084710 CCTCATTCCAGATAAGGAGGTTATTTCTTTTTTAAAGTTATGT-G
1 CCTCATTCTAGATAAGGAGCTTA-TTCTTTTTTAAAGTTACGTAG
* *
1084754 ACCTTATTCTAGATGAA-GAGCTTATT-TCTTTTTAAAGTTACATAG
1 -CCTCATTCTAGAT-AAGGAGCTTATTCT-TTTTTAAAGTTACGTAG
* * *
1084799 GCTCATTCTAGATTAGGAG-TTCATTCTTTTTTAAAAGTTACGTAA
1 CCTCATTCTAGATAAGGAGCTT-ATTCTTTTTT-AAAGTTACGTAG
* *
1084844 CCTCATTTTAGATGAGGAGCT
1 CCTCATTCTAGATAAGGAGCT
1084865 CTTTTTTTNN
Statistics
Matches: 278, Mismatches: 44, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
43 4 0.01
44 40 0.14
45 157 0.56
46 70 0.25
47 7 0.03
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (44 bp):
CCTCATTCTAGATAAGGAGCTTATTCTTTTTTAAAGTTACGTAG
Found at i:1087385 original size:15 final size:15
Alignment explanation
Indices: 1087364--1087523 Score: 65
Period size: 15 Copynumber: 9.9 Consensus size: 15
1087354 TTTTAATGTC
1087364 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
1087379 ATTTATTATTATAATATTT
1 ATATATT-TTAT--T-TTT
1087398 -TATATTTTATTTTT
1 ATATATTTTATTTTT
*
1087412 A-ATATATTTATATTT
1 ATATAT-TTTATTTTT
*
1087427 ATAT-TATTAATTTTT
1 ATATAT-TTTATTTTT
* **
1087442 ATATAATATCATATCTTAA
1 ATAT-AT-T-TTAT-TTTT
* * *
1087461 ATATATTTTTAATGTC
1 ATATA-TTTTATTTTT
*
1087477 ATATATTTTATTTTC
1 ATATATTTTATTTTT
* *
1087492 ATTTATTATTATAATCTT
1 ATATATT-TTAT--TTTT
1087510 ATATATTTTATTTT
1 ATATATTTTATTTT
1087524 CATTTTTTAA
Statistics
Matches: 109, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
14 7 0.06
15 45 0.41
16 16 0.15
17 13 0.12
18 18 0.17
19 10 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:1087396 original size:21 final size:22
Alignment explanation
Indices: 1087372--1087445 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
1087362 TCATATATTT
1087372 TATTTT-TATTTATTATTATAA
1 TATTTTATATTTATTATTATAA
1087393 TATTTTATATTTTATT-TT-TAA
1 TATTTTATA-TTTATTATTATAA
1087414 TATATTTATATTTA-TATTATTAA
1 TAT-TTTATATTTATTATTA-TAA
1087437 T-TTTTATAT
1 TATTTTATAT
1087446 AATATCATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.02
21 25 0.53
22 11 0.23
23 10 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTATATTTATTATTATAA
Found at i:1087534 original size:28 final size:30
Alignment explanation
Indices: 1087464--1087531 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 30
1087454 ATCTTAAATA
*
1087464 TATTTTTAATGTCATATATTTTATTTTCATT
1 TATTTTTAATCTCATATATTTTATTTTCA-T
*
1087495 TATTATTATAATCTTATATATTTTATTTTCAT
1 TATT-TT-TAATCTCATATATTTTATTTTCAT
1087527 T-TTTT
1 TATTTT
1087532 AATATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 6 0.18
32 4 0.12
33 21 0.64
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.66
Consensus pattern (30 bp):
TATTTTTAATCTCATATATTTTATTTTCAT
Found at i:1087548 original size:113 final size:113
Alignment explanation
Indices: 1087296--1087523 Score: 402
Period size: 113 Copynumber: 2.0 Consensus size: 113
1087286 AAAATACAAG
* *
1087296 TTTAATATATTTATATTTTTCTTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
* *
1087361 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
66 GTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATT
*
1087409 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
*
1087474 GTCATATATTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
66 GTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATT
1087522 TT
1 TT
1087524 CATTTTTTAA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (113 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
GTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATT
Found at i:1087622 original size:24 final size:25
Alignment explanation
Indices: 1087590--1087637 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1087580 TATATAAATG
*
1087590 TTAATTTTTTATATT-TTATTTTATT
1 TTAATTTTTT-TATTCTTATATTATT
1087615 TTAA-TTTTTTATTCTTATATTAT
1 TTAATTTTTTTATTCTTATATTAT
1087638 ATACTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (25 bp):
TTAATTTTTTTATTCTTATATTATT
Found at i:1087648 original size:33 final size:33
Alignment explanation
Indices: 1087609--1087671 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1087599 TATATTTTAT
1087609 TTTATTTT-A-ATTTTTTATTCTTATATTATATAC
1 TTTATTTTAATATTTTTTATT-TTA-ATTATATAC
1087642 TTTATTTTAATATTTTTTATTTTAATTATA
1 TTTATTTTAATATTTTTTATTTTAATTATA
1087672 ACATTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 14 0.50
34 4 0.14
35 10 0.36
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (33 bp):
TTTATTTTAATATTTTTTATTTTAATTATATAC
Found at i:1089649 original size:15 final size:15
Alignment explanation
Indices: 1089629--1089659 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1089619 GTAAAAATTC
1089629 CACAATCCACAATAT
1 CACAATCCACAATAT
*
1089644 CACAATGCACAATAT
1 CACAATCCACAATAT
1089659 C
1 C
1089660 TCTACAATCA
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:0.32, G:0.03, T:0.19
Consensus pattern (15 bp):
CACAATCCACAATAT
Found at i:1092891 original size:4 final size:4
Alignment explanation
Indices: 1092882--1092912 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1092872 AAAATAAGAA
1092882 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1092913 ACAAGATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1093223 original size:14 final size:14
Alignment explanation
Indices: 1093204--1093230 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1093194 TGGTAAATTT
1093204 TTTTTTATAAGTTC
1 TTTTTTATAAGTTC
1093218 TTTTTTATAAGTT
1 TTTTTTATAAGTT
1093231 ATAATTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTTATAAGTTC
Found at i:1094883 original size:21 final size:20
Alignment explanation
Indices: 1094837--1094883 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
1094827 CATAAAAACT
1094837 AATAAATAGTAACTAAAATAA
1 AATAAATAG-AACTAAAATAA
*
1094858 GATAAATA-AACATAAAATTAA
1 AATAAATAGAAC-TAAAA-TAA
1094879 AATAA
1 AATAA
1094884 CTTAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 5 0.23
21 14 0.64
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (20 bp):
AATAAATAGAACTAAAATAA
Found at i:1131962 original size:2 final size:2
Alignment explanation
Indices: 1131951--1131988 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1131941 GCAGGATTCA
1131951 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1131989 GCAACTCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1135487 original size:21 final size:22
Alignment explanation
Indices: 1135451--1135492 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1135441 ATTTTTATTA
*
1135451 AATAAACATGAGTGAA-GTTAG
1 AATAAACATGAATGAATGTTAG
*
1135472 AATAAACATTAATGAATGTTA
1 AATAAACATGAATGAATGTTA
1135493 TAAAATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (22 bp):
AATAAACATGAATGAATGTTAG
Found at i:1137671 original size:36 final size:35
Alignment explanation
Indices: 1137624--1137691 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
1137614 TTTAGTGGGG
1137624 TTTAGTCTATCAACCACAAAGT-TTTATCAGTAGGGC
1 TTTAGTCTATCAACCACAAA-TCTTTATC-GTAGGGC
1137660 TTTAGTCTATCAACCACAAATCTTTATCGTAG
1 TTTAGTCTATCAACCACAAATCTTTATCGTAG
1137692 CCAATAGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (35 bp):
TTTAGTCTATCAACCACAAATCTTTATCGTAGGGC
Found at i:1142288 original size:2 final size:2
Alignment explanation
Indices: 1142281--1142305 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1142271 AATGGATAAC
1142281 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 A
1142306 GCCTCGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1144405 original size:15 final size:15
Alignment explanation
Indices: 1144382--1144456 Score: 87
Period size: 15 Copynumber: 5.0 Consensus size: 15
1144372 ATTTTACAAT
1144382 GTAATGTGATTACAG
1 GTAATGTGATTACAG
*
1144397 GTAAGGTGATTACAG
1 GTAATGTGATTACAG
* * *
1144412 GTAATGTAATTGCAA
1 GTAATGTGATTACAG
* *
1144427 GTAATGTGATTATAA
1 GTAATGTGATTACAG
*
1144442 GCAATGTGATTACAG
1 GTAATGTGATTACAG
1144457 AGAAAATAAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (15 bp):
GTAATGTGATTACAG
Found at i:1144867 original size:33 final size:33
Alignment explanation
Indices: 1144791--1144853 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
1144781 AAATTTTAAT
1144791 TTCTTATATT-T-TATTTTATTTTAATTTTTGA
1 TTCTTATATTATATATTTTATTTTAATTTTTGA
1144822 TTCTTATATTATATATTTTATTTTAATATTTT
1 TTCTTATATTATATATTTTATTTTAAT-TTTT
1144854 TTGTTCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 10 0.34
32 1 0.03
33 14 0.48
34 4 0.14
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (33 bp):
TTCTTATATTATATATTTTATTTTAATTTTTGA
Found at i:1154829 original size:44 final size:46
Alignment explanation
Indices: 1154723--1154838 Score: 148
Period size: 44 Copynumber: 2.6 Consensus size: 46
1154713 CCTCTAATCT
* *
1154723 CTCACCCTCAAGCTTCACAAAGTCAACGATACTCTAATCTCTCACC
1 CTCACCCTCAAGCTTCACAAAGTCGACGATACTCTAATATCTCACC
* * *
1154769 CTCCCCCTCAAACTTCACAAACTCGACGAT-CT-T-ATAATCTCACC
1 CTCACCCTCAAGCTTCACAAAGTCGACGATACTCTAAT-ATCTCACC
*
1154813 TTCACCCTCAAGCTTCACAAAGTCGA
1 CTCACCCTCAAGCTTCACAAAGTCGA
1154839 AATTTAATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
43 2 0.03
44 30 0.50
45 2 0.03
46 26 0.43
ACGTcount: A:0.30, C:0.39, G:0.07, T:0.24
Consensus pattern (46 bp):
CTCACCCTCAAGCTTCACAAAGTCGACGATACTCTAATATCTCACC
Found at i:1155046 original size:2 final size:2
Alignment explanation
Indices: 1155041--1155083 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1155031 ACCGTAGGGT
*
1155041 TC TC TC TC TC TC TC TC CC TC -C TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1155082 TC
1 TC
1155084 CGTGTGGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1158366 original size:2 final size:2
Alignment explanation
Indices: 1158359--1158386 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1158349 CAGTCCTCAG
1158359 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1158387 ATTATATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1161405 original size:8 final size:8
Alignment explanation
Indices: 1161392--1161430 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1161382 TCAGAGGATT
1161392 TAAAATAA
1 TAAAATAA
1161400 TAAAATAA
1 TAAAATAA
* *
1161408 TCAAAT-T
1 TAAAATAA
1161415 TAAAATAA
1 TAAAATAA
1161423 TAAAATAA
1 TAAAATAA
1161431 AAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAAATAA
Found at i:1168285 original size:16 final size:17
Alignment explanation
Indices: 1168254--1168286 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1168244 ATCATTATAA
*
1168254 ATTTTCAAATTTTTTTC
1 ATTTTCAAATTATTTTC
1168271 ATTTTC-AATTATTTTC
1 ATTTTCAAATTATTTTC
1168287 TACCATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTCAAATTATTTTC
Found at i:1171011 original size:53 final size:52
Alignment explanation
Indices: 1170938--1171265 Score: 219
Period size: 53 Copynumber: 6.2 Consensus size: 52
1170928 GCTTCTATGT
* * * * *
1170938 TTGGAACACCCTAGGTGCTTCTGTACTTAGAACGCCCCTGGGCGCTTTTACGC
1 TTGGAACACCCTGGGCGCTTCTGCACTT-GAACGCCCCTGGGCGCTTCTACAC
* * * * * * *
1170991 TTGGAACGCCTTGGGCGCTTCTACACTTGGAATGCCCCTAGGTGCTTCTATAC
1 TTGGAACACCCTGGGCGCTTCTGCACTT-GAACGCCCCTGGGCGCTTCTACAC
* * *
1171044 TTGAAACACCCTGGGCGCTTCTGCACTTGAAACACCCTTGGGCGCTTCTACAC
1 TTGGAACACCCTGGGCGCTTCTGCACTTG-AACGCCCCTGGGCGCTTCTACAC
* * * ** * * * **
1171097 TTGGAA-AGCCCCTAGGCACTTCTGCACTTGGAATGCCTTTGGGTGATTTTGTAC
1 TTGGAACA--CCCTGGGCGCTTCTGCACTT-GAACGCCCCTGGGCGCTTCTACAC
* * * * * *
1171151 TTGGAACACCCTAGGTGCTTCTACACTTGGAATGCCCCTGGGCGCTTCTGCAG
1 TTGGAACACCCTGGGCGCTTCTGCACTT-GAACGCCCCTGGGCGCTTCTACAC
* * * * * * **
1171204 TTGGAACGCCATGGGCGCTTCTGCGCTTGGAAC-TCCATGGGCGTTTCTGTAC
1 TTGGAACACCCTGGGCGCTTCTGCACTT-GAACGCCCCTGGGCGCTTCTACAC
1171256 TTGGAACACC
1 TTGGAACACC
1171266 TCTAGGAACT
Statistics
Matches: 213, Mismatches: 57, Indels: 11
0.76 0.20 0.04
Matches are distributed among these distances:
52 25 0.12
53 147 0.69
54 39 0.18
55 2 0.01
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.28
Consensus pattern (52 bp):
TTGGAACACCCTGGGCGCTTCTGCACTTGAACGCCCCTGGGCGCTTCTACAC
Found at i:1171019 original size:26 final size:26
Alignment explanation
Indices: 1170938--1171262 Score: 227
Period size: 26 Copynumber: 12.3 Consensus size: 26
1170928 GCTTCTATGT
* * * *
1170938 TTGGAACACCCTAGGTGCTTCTGTAC
1 TTGGAACGCCCTGGGCGCTTCTGCAC
* * * *
1170964 TTAGAACGCCCCTGGGCGCTTTTACGC
1 TTGGAACG-CCCTGGGCGCTTCTGCAC
* *
1170991 TTGGAACGCCTTGGGCGCTTCTACAC
1 TTGGAACGCCCTGGGCGCTTCTGCAC
* * * **
1171017 TTGGAATGCCCCTAGGTGCTTCTATAC
1 TTGGAACG-CCCTGGGCGCTTCTGCAC
* *
1171044 TTGAAACACCCTGGGCGCTTCTGCAC
1 TTGGAACGCCCTGGGCGCTTCTGCAC
* * *
1171070 TTGAAACACCCTTGGGCGCTTCTACAC
1 TTGGAACGCCC-TGGGCGCTTCTGCAC
* * *
1171097 TTGGAAAGCCCCTAGGCACTTCTGCAC
1 TTGGAACG-CCCTGGGCGCTTCTGCAC
* * * * * *
1171124 TTGGAATGCCTTTGGGTGATTTTGTAC
1 TTGGAACGCC-CTGGGCGCTTCTGCAC
* * * *
1171151 TTGGAACACCCTAGGTGCTTCTACAC
1 TTGGAACGCCCTGGGCGCTTCTGCAC
* *
1171177 TTGGAATGCCCCTGGGCGCTTCTGCAG
1 TTGGAACG-CCCTGGGCGCTTCTGCAC
* *
1171204 TTGGAACGCCATGGGCGCTTCTGCGC
1 TTGGAACGCCCTGGGCGCTTCTGCAC
* * * *
1171230 TTGGAACTCCATGGGCGTTTCTGTAC
1 TTGGAACGCCCTGGGCGCTTCTGCAC
1171256 TTGGAAC
1 TTGGAAC
1171263 ACCTCTAGGA
Statistics
Matches: 232, Mismatches: 61, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
26 115 0.50
27 114 0.49
28 3 0.01
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.29
Consensus pattern (26 bp):
TTGGAACGCCCTGGGCGCTTCTGCAC
Found at i:1171084 original size:80 final size:80
Alignment explanation
Indices: 1170946--1171236 Score: 291
Period size: 80 Copynumber: 3.6 Consensus size: 80
1170936 GTTTGGAACA
* * * * * *
1170946 CCCTAGGTGCTTCTGTACTT-AGAACGCCCCTGGGCGCTTTTACGCTTGGAAC-GCCTTGGGCGC
1 CCCTAGGCGCTTCTGCACTTGA-AACG-CCCTGGGCGCTTCTGCACTTGGAACACCCTTGGGCGC
1171009 TTCTACACTTGGAATGC
64 TTCTACACTTGGAATGC
* ** * *
1171026 CCCTAGGTGCTTCTATACTTGAAACACCCTGGGCGCTTCTGCACTTGAAACACCCTTGGGCGCTT
1 CCCTAGGCGCTTCTGCACTTGAAACGCCCTGGGCGCTTCTGCACTTGGAACACCCTTGGGCGCTT
*
1171091 CTACACTTGGAAAGC
66 CTACACTTGGAATGC
* * * * * * * * * *
1171106 CCCTAGGCACTTCTGCACTTGGAATGCCTTTGGGTGATTTTGTACTTGGAACACCC-TAGGTGCT
1 CCCTAGGCGCTTCTGCACTTGAAACGCC-CTGGGCGCTTCTGCACTTGGAACACCCTTGGGCGCT
1171170 TCTACACTTGGAATGC
65 TCTACACTTGGAATGC
* * * * *
1171186 CCCTGGGCGCTTCTGCAGTTGGAACGCCATGGGCGCTTCTGCGCTTGGAAC
1 CCCTAGGCGCTTCTGCACTTGAAACGCCCTGGGCGCTTCTGCACTTGGAAC
1171237 TCCATGGGCG
Statistics
Matches: 174, Mismatches: 34, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
79 38 0.22
80 114 0.66
81 22 0.13
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.28
Consensus pattern (80 bp):
CCCTAGGCGCTTCTGCACTTGAAACGCCCTGGGCGCTTCTGCACTTGGAACACCCTTGGGCGCTT
CTACACTTGGAATGC
Found at i:1173654 original size:36 final size:36
Alignment explanation
Indices: 1173539--1173694 Score: 147
Period size: 36 Copynumber: 4.3 Consensus size: 36
1173529 AGCCAAGCGA
* * *
1173539 AGAACAAATCACAGTCAGTGCTGAAGCAATTGATGG
1 AGAACAAATCACACTCAGTGCTGAAGCAATGGATAG
* * * * *
1173575 AGAATCAAATCACACAT-GGTGTTGAAGCAGTAGATGG
1 AGAA-CAAATCACAC-TCAGTGCTGAAGCAATGGATAG
* *
1173612 ACAACAAATTA-AGCTCAGTGCTGAAGCAACTGG-TAG
1 AGAACAAATCACA-CTCAGTGCTGAAGCAA-TGGATAG
* *
1173648 AGAACAAATCACACTCATTGCTGAAGCAATGGATGG
1 AGAACAAATCACACTCAGTGCTGAAGCAATGGATAG
1173684 AGAACAAATCA
1 AGAACAAATCA
1173695 TGCACAACAC
Statistics
Matches: 97, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
35 5 0.05
36 60 0.62
37 31 0.32
38 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (36 bp):
AGAACAAATCACACTCAGTGCTGAAGCAATGGATAG
Found at i:1173690 original size:72 final size:72
Alignment explanation
Indices: 1173539--1173694 Score: 183
Period size: 72 Copynumber: 2.2 Consensus size: 72
1173529 AGCCAAGCGA
* * *
1173539 AGAACAAATCACAGTCAGTGCTGAAGCAATTGATGGAGAATCAAATCACACATGGTGTTGAAGCA
1 AGAACAAATCACAGTCAGTGCTGAAGCAACTGATAGAGAATCAAATCACACAT-GTGCTGAAGCA
*
1173604 GTAGATGG
65 ATAGATGG
* * *
1173612 ACAACAAATTA-AGCTCAGTGCTGAAGCAACTGGTAGAGAA-CAAATCACACTCAT-TGCTGAAG
1 AGAACAAATCACAG-TCAGTGCTGAAGCAACTGATAGAGAATCAAATCACA--CATGTGCTGAAG
*
1173674 CAATGGATGG
63 CAATAGATGG
1173684 AGAACAAATCA
1 AGAACAAATCA
1173695 TGCACAACAC
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
72 35 0.50
73 32 0.46
74 3 0.04
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (72 bp):
AGAACAAATCACAGTCAGTGCTGAAGCAACTGATAGAGAATCAAATCACACATGTGCTGAAGCAA
TAGATGG
Found at i:1176457 original size:18 final size:18
Alignment explanation
Indices: 1176434--1176468 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1176424 TAAGTCTTTC
1176434 AAACAAAAACATGTTATG
1 AAACAAAAACATGTTATG
*
1176452 AAACAAAAACATTTTAT
1 AAACAAAAACATGTTAT
1176469 ATGGTGACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (18 bp):
AAACAAAAACATGTTATG
Found at i:1181844 original size:29 final size:29
Alignment explanation
Indices: 1181811--1181866 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1181801 GTTGAAGAAA
1181811 ATTCAAAT-AAGCCCTTATACTTTTATTGC
1 ATTC-AATCAAGCCCTTATACTTTTATTGC
1181840 ATTCAATCAAGCCCTTATACTTTTATT
1 ATTCAATCAAGCCCTTATACTTTTATT
1181867 TTAAGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.43
Consensus pattern (29 bp):
ATTCAATCAAGCCCTTATACTTTTATTGC
Found at i:1183582 original size:11 final size:11
Alignment explanation
Indices: 1183566--1183602 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1183556 CTATATGTGT
1183566 AAGAAAAGGAA
1 AAGAAAAGGAA
*
1183577 AAG-AAA-CAA
1 AAGAAAAGGAA
1183586 AAGAAAAGGAA
1 AAGAAAAGGAA
1183597 AAGAAA
1 AAGAAA
1183603 CCAATTCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.23
10 6 0.27
11 11 0.50
ACGTcount: A:0.76, C:0.03, G:0.22, T:0.00
Consensus pattern (11 bp):
AAGAAAAGGAA
Found at i:1183591 original size:20 final size:20
Alignment explanation
Indices: 1183566--1183603 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1183556 CTATATGTGT
1183566 AAGAAAAGGAAAAGAAACAA
1 AAGAAAAGGAAAAGAAACAA
1183586 AAGAAAAGGAAAAGAAAC
1 AAGAAAAGGAAAAGAAAC
1183604 CAATTCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (20 bp):
AAGAAAAGGAAAAGAAACAA
Found at i:1214236 original size:2 final size:2
Alignment explanation
Indices: 1214231--1214256 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1214221 AAAAACGTCA
1214231 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
1214257 CAATTTAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1219756 original size:67 final size:67
Alignment explanation
Indices: 1219648--1219802 Score: 204
Period size: 67 Copynumber: 2.3 Consensus size: 67
1219638 TCAATCAATT
* * * ** *
1219648 AAAACCCAAAATAACTTTTCACAGGCTCAGCCATAACCTTTAATAATGATATTTCAT-GGGATCG
1 AAAACCCAAAATAACTTTTCACAGACTCAGCCACAACCTTTAAAAATGATATTTC-TCAAGATCA
1219712 ACC
65 ACC
** *
1219715 AAAACCCAAAATGGCTTTTCACAGACTCAGCCACAACCTTTAAAAATGATTTTTCTCAAGATCAA
1 AAAACCCAAAATAACTTTTCACAGACTCAGCCACAACCTTTAAAAATGATATTTCTCAAGATCAA
1219780 CC
66 CC
1219782 AAAACCCAAAACTAACTTTTC
1 AAAACCCAAAA-TAACTTTTC
1219803 TAAGGCTTAG
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
66 1 0.01
67 67 0.89
68 7 0.09
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (67 bp):
AAAACCCAAAATAACTTTTCACAGACTCAGCCACAACCTTTAAAAATGATATTTCTCAAGATCAA
CC
Found at i:1220254 original size:74 final size:74
Alignment explanation
Indices: 1220126--1220275 Score: 237
Period size: 74 Copynumber: 2.0 Consensus size: 74
1220116 GTGCTTAATT
* * *
1220126 TCAAATTTTCTGACAGTGAGCTTTTAGTTGGCTAACCATACTACTTAGTTGATTAAGTCTTCTCT
1 TCAAATTCTCTGACAGTGAGCTTTTAGTTGGCTAACCATACTACTTAATGGATTAAGTCTTCTCT
1220191 GTCTTGCAA
66 GTCTTGCAA
* * * *
1220200 TCAAATTCTCTGACTGTGAGCTTTTAGTTGGCTAACCATACTTCTTAATGGATTAAGTCTTTTTT
1 TCAAATTCTCTGACAGTGAGCTTTTAGTTGGCTAACCATACTACTTAATGGATTAAGTCTTCTCT
1220265 GTCTTGCAA
66 GTCTTGCAA
1220274 TC
1 TC
1220276 TACTTTACTC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (74 bp):
TCAAATTCTCTGACAGTGAGCTTTTAGTTGGCTAACCATACTACTTAATGGATTAAGTCTTCTCT
GTCTTGCAA
Found at i:1250827 original size:15 final size:16
Alignment explanation
Indices: 1250807--1250839 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1250797 ATATAGTTTC
*
1250807 TTTCTC-TATTTTGTT
1 TTTCTCTTATTTTCTT
1250822 TTTCTCTTATTTTCTT
1 TTTCTCTTATTTTCTT
1250838 TT
1 TT
1250840 ACTTGAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTCTCTTATTTTCTT
Found at i:1267668 original size:20 final size:21
Alignment explanation
Indices: 1267643--1267682 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1267633 CATTTTCCCA
1267643 ATTTGAAA-TATAAAATTTAT
1 ATTTGAAATTATAAAATTTAT
*
1267663 ATTTGAAATTATTAAATTTA
1 ATTTGAAATTATAAAATTTA
1267683 AACCCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTTGAAATTATAAAATTTAT
Found at i:1269448 original size:10 final size:10
Alignment explanation
Indices: 1269421--1269464 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1269411 TTAATTTAAG
*
1269421 TTATTTTAGT
1 TTATTTTACT
1269431 TTATTTTTACT
1 TTA-TTTTACT
*
1269442 TTATTTTGCT
1 TTATTTTACT
*
1269452 TTAATTTACT
1 TTATTTTACT
1269462 TTA
1 TTA
1269465 AAAAGGGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (10 bp):
TTATTTTACT
Found at i:1274068 original size:14 final size:14
Alignment explanation
Indices: 1274049--1274080 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1274039 ATTTTTGGTT
*
1274049 TTTTTATTAGTTTA
1 TTTTTATTAATTTA
1274063 TTTTTATTAATTTA
1 TTTTTATTAATTTA
1274077 TTTT
1 TTTT
1274081 AATTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTTATTAATTTA
Found at i:1284635 original size:15 final size:15
Alignment explanation
Indices: 1284603--1284645 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1284593 ATTTTTGTAA
1284603 AATTTT-TAAAATAA-
1 AATTTTATAAAA-AAG
1284617 AATTTTATAAAAAAG
1 AATTTTATAAAAAAG
1284632 AATTTTA-AAAAAAG
1 AATTTTATAAAAAAG
1284646 TTTCAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
AATTTTATAAAAAAG
Found at i:1284960 original size:20 final size:18
Alignment explanation
Indices: 1284934--1284980 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
1284924 AAATCTAATA
1284934 TTATTTTAAAAATTGTTTT
1 TTATTTTAAAAATT-TTTT
* *
1284953 GTTTTTTTATAAATTTTTT
1 -TTATTTTAAAAATTTTTT
1284972 TTATTTTAA
1 TTATTTTAA
1284981 CATCTGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.30
19 4 0.17
20 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (18 bp):
TTATTTTAAAAATTTTTT
Found at i:1285798 original size:55 final size:55
Alignment explanation
Indices: 1285739--1285848 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
1285729 TGCCATTGAT
* * *
1285739 GGTTGAGTGTGAAAAATATCAAATAATCATATTATTATATTATATCAGTATGTCA
1 GGTTGAGTGTGAAAAATATCAAAAAACCATATTATTATACTATATCAGTATGTCA
*
1285794 GGTTGAGTGTGAAAAATATCAAAAAACCATATTATTATGCTATATCAGTATGTCA
1 GGTTGAGTGTGAAAAATATCAAAAAACCATATTATTATACTATATCAGTATGTCA
1285849 AGTTAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.35
Consensus pattern (55 bp):
GGTTGAGTGTGAAAAATATCAAAAAACCATATTATTATACTATATCAGTATGTCA
Found at i:1286236 original size:15 final size:17
Alignment explanation
Indices: 1286207--1286238 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1286197 TAAATTGTTG
1286207 CTTGCTTTTTAATTAAT
1 CTTGCTTTTTAATTAAT
1286224 CTTG-TTTTT-ATTAAT
1 CTTGCTTTTTAATTAAT
1286239 AAAGTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.22, C:0.09, G:0.06, T:0.62
Consensus pattern (17 bp):
CTTGCTTTTTAATTAAT
Found at i:1286281 original size:28 final size:28
Alignment explanation
Indices: 1286249--1286305 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1286239 AAAGTTAATT
1286249 TTAGAGACTATTTAATGAAATATTACCC
1 TTAGAGACTATTTAATGAAATATTACCC
1286277 TTAGAGACTATTTAATGAAATATTACCC
1 TTAGAGACTATTTAATGAAATATTACCC
1286305 T
1 T
1286306 AAAAAATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (28 bp):
TTAGAGACTATTTAATGAAATATTACCC
Found at i:1292197 original size:2 final size:2
Alignment explanation
Indices: 1292190--1292216 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1292180 AATTAGCAAC
1292190 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 A
1292217 AACAACCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1299549 original size:189 final size:179
Alignment explanation
Indices: 1299222--1299630 Score: 433
Period size: 189 Copynumber: 2.2 Consensus size: 179
1299212 AATTACACAT
* * * *
1299222 TCACACAATACCTAAAAATTAGTGAAGAAATGCCTCAAAATAAGAAATGCATTGCACAATCACGC
1 TCACGCAATA-CTAAAAAATAGTCAAGAAATGCCTCAAAACAAGAAATGCATTGCACAATCACGC
* * ** * * *
1299287 AGTGCCAGTCTCGTAATATTTAATAATAAGTCACTCAATACTTAATAGCTACTCACGTTATGCCA
65 AGTACCAGTCTCGCAATACCTAACAATAAGTCACTCAATACCTAATAGCCACTCACGTTATGCCA
* * ** *
1299352 AAATAACCAGTCACGTATT-AGCCTAACGTTATGCAATACATAACAACCAG
130 AAATAACCAGTCACGTATTGA-CCCAACGTCACACAATACATAACAACAAG
* *
1299402 TCACGCAATATCTAAAAAATAGTCAAGAAATGTCTCAAAACAAGATATGCATTGCACAATTCACG
1 TCACGCAATA-CTAAAAAATAGTCAAGAAATGCCTCAAAACAAGAAATGCATTGCACAA-TCACG
* * *
1299467 CAATGTCTATAAACCAGTCTCGCAATACCTAACAATAAGTCACTCCATGCCTAATATCCACTCAC
64 C-A-G----T--ACCAGTCTCGCAATACCTAACAATAAGTCACTCAATACCTAATAGCCACTCAC
* *
1299532 GTTATGCCAACATAACCAGTTACGTATTGACCCAACGTCACACAATACATAACAACAAG
121 GTTATGCCAAAATAACCAGTCACGTATTGACCCAACGTCACACAATACATAACAACAAG
* * * * * *
1299591 TCATGGAATACATAAAAACTAGTCACGCAATGCCTAAAAA
1 TCACGCAATAC-TAAAAAATAGTCAAGAAATGCCTCAAAA
1299631 ATAGTCAAGA
Statistics
Matches: 187, Mismatches: 31, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
180 52 0.28
181 6 0.03
182 1 0.01
183 1 0.01
187 1 0.01
188 1 0.01
189 124 0.66
190 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.23
Consensus pattern (179 bp):
TCACGCAATACTAAAAAATAGTCAAGAAATGCCTCAAAACAAGAAATGCATTGCACAATCACGCA
GTACCAGTCTCGCAATACCTAACAATAAGTCACTCAATACCTAATAGCCACTCACGTTATGCCAA
AATAACCAGTCACGTATTGACCCAACGTCACACAATACATAACAACAAG
Found at i:1299593 original size:22 final size:22
Alignment explanation
Indices: 1299568--1299630 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
1299558 TTGACCCAAC
* *
1299568 GTCACACAATACATAACAACAA
1 GTCACGCAATACATAAAAACAA
* * *
1299590 GTCATGGAATACATAAAAACTA
1 GTCACGCAATACATAAAAACAA
* *
1299612 GTCACGCAATGCCTAAAAA
1 GTCACGCAATACATAAAAA
1299631 ATAGTCAAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.17
Consensus pattern (22 bp):
GTCACGCAATACATAAAAACAA
Found at i:1299644 original size:22 final size:22
Alignment explanation
Indices: 1299603--1299644 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1299593 ATGGAATACA
* * *
1299603 TAAAAACTAGTCACGCAATGCC
1 TAAAAAATAGTCAAGAAATGCC
1299625 TAAAAAATAGTCAAGAAATG
1 TAAAAAATAGTCAAGAAATG
1299645 TCTCAAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (22 bp):
TAAAAAATAGTCAAGAAATGCC
Found at i:1299760 original size:211 final size:210
Alignment explanation
Indices: 1299386--1299976 Score: 783
Period size: 211 Copynumber: 2.8 Consensus size: 210
1299376 AACGTTATGC
* * **
1299386 AATACATAACAACCAGTCACGCAATATCTAAAAAATAGTCAAGAAATGTCTCAAAACAAGATATG
1 AATACATAAAAACTAGTCACGCAATGCCTAAAAAATAGTCAAGAAATGTCTCAAAACAAGATATG
* * * * *
1299451 CATTGCACAATTCACGCAATGTCTATAAACCAGTCTCGCAATACCTAACAATAAGTCACTCCATG
66 CATTGCACAATTCACGCAACG-CTATAAGCCAGTCTCGCAATACCTAATAATAACTCACTCAATG
* *
1299516 CCTAATATCCACTCACGTTATGCCAACATAACCAGTTACGTATTGACCCAACGTCACACAATACA
130 CCTAATATCCACTCACGTTATGCCAAAATAACCAGTTACATATTGACCCAACGTCACACAATACA
**
1299581 TAACAACAAGTCATGG
195 TAACAACAAAACATGG
*
1299597 AATACATAAAAACTAGTCACGCAATGCCTAAAAAATAGTCAAGAAATGTCTCAAAACAATATATG
1 AATACATAAAAACTAGTCACGCAATGCCTAAAAAATAGTCAAGAAATGTCTCAAAACAAGATATG
* *
1299662 CATTGCACAATTCACGCAACGCCTATAAGCCAGTCTCACAATACCTAATAATAACTCACTTAATG
66 CATTGCACAATTCACGCAACG-CTATAAGCCAGTCTCGCAATACCTAATAATAACTCACTCAATG
* * * * * * ** *
1299727 CCAAATATCCACTCACATTATGTCAATATAACCAGTCACATATTGGCCCAGTGTCACATAATACA
130 CCTAATATCCACTCACGTTATGCCAAAATAACCAGTTACATATTGACCCAACGTCACACAATACA
1299792 TAACAACAAAACATGG
195 TAACAACAAAACATGG
* *
1299808 AATACATAAAAACCTA-TCACGCAATGCATAAAAAAGTAGTCAAGAAATGTATCAAAACAAGATA
1 AATACATAAAAA-CTAGTCACGCAATGCCTAAAAAA-TAGTCAAGAAATGTCTCAAAACAAGATA
* * * * * * *
1299872 TGCATTACACAATTCATGCAGCGC-ATAAGTCAATCTTGCAATACCTAATAATAAGC-CACGCAA
64 TGCATTGCACAATTCACGCAACGCTATAAGCCAGTCTCGCAATACCTAATAATAA-CTCACTCAA
* * *
1299935 TGCCTAACATCCACTCATGTTATGCCAAAATACCCAGTTACA
128 TGCCTAATATCCACTCACGTTATGCCAAAATAACCAGTTACA
1299977 CCTTGGCTCT
Statistics
Matches: 332, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
210 65 0.20
211 218 0.66
212 49 0.15
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.23
Consensus pattern (210 bp):
AATACATAAAAACTAGTCACGCAATGCCTAAAAAATAGTCAAGAAATGTCTCAAAACAAGATATG
CATTGCACAATTCACGCAACGCTATAAGCCAGTCTCGCAATACCTAATAATAACTCACTCAATGC
CTAATATCCACTCACGTTATGCCAAAATAACCAGTTACATATTGACCCAACGTCACACAATACAT
AACAACAAAACATGG
Found at i:1300110 original size:22 final size:22
Alignment explanation
Indices: 1300046--1300110 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
1300036 ACGCAATGTC
*
1300046 TAATATCTATTCACACAATGCA
1 TAATATCTATTCACATAATGCA
* *
1300068 TAATATCCATTCACATGATGCA
1 TAATATCTATTCACATAATGCA
*
1300090 TAATATCTATTCACTTAATGC
1 TAATATCTATTCACATAATGC
1300111 CTATAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (22 bp):
TAATATCTATTCACATAATGCA
Found at i:1307754 original size:31 final size:30
Alignment explanation
Indices: 1307685--1307756 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
1307675 ACACGAAGCA
* * *
1307685 AGCAAAGAAACCAAACCCAGATCATATTTT
1 AGCAAATAAACAAAACCCAAATCATATTTT
* *
1307715 AGATAAATAAACAAAACCCAAATGATATTTT
1 AG-CAAATAAACAAAACCCAAATCATATTTT
1307746 GAGCAAATAAA
1 -AGCAAATAAA
1307757 TGAAATCCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 2 0.06
31 30 0.88
32 2 0.06
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.21
Consensus pattern (30 bp):
AGCAAATAAACAAAACCCAAATCATATTTT
Found at i:1312832 original size:18 final size:18
Alignment explanation
Indices: 1312797--1312883 Score: 65
Period size: 18 Copynumber: 5.0 Consensus size: 18
1312787 TAATTATTTT
***
1312797 TAAAATAAAATAAAATTA
1 TAAAATAAAATTTTATTA
*
1312815 TAATATAAAATTTTATTA
1 TAAAATAAAATTTTATTA
*
1312833 -AAAAT-TAATTTCT-TT-
1 TAAAATAAAATTT-TATTA
**
1312848 TAAAATAAAATTAAATTA
1 TAAAATAAAATTTTATTA
*
1312866 TAACATAAAATTTTATTA
1 TAAAATAAAATTTTATTA
1312884 ATAATTTAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
16 12 0.23
17 11 0.21
18 29 0.56
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATAAAATTTTATTA
Found at i:1312849 original size:51 final size:51
Alignment explanation
Indices: 1312781--1312889 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 51
1312771 ATTGAAAATA
*
1312781 AAAAATTAATTATTTTTAAAATAAAATAAAATTATAATATAAAATTTTATT
1 AAAAATTAATTATTTTTAAAATAAAATAAAATTATAACATAAAATTTTATT
*
1312832 AAAAATTAATT-TCTTTTAAAATAAAATTAAATTATAACATAAAATTTTATT
1 AAAAATTAATTAT-TTTTAAAATAAAATAAAATTATAACATAAAATTTTATT
*
1312883 AATAATT
1 AAAAATT
1312890 TAAATATAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 1 0.02
51 53 0.98
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (51 bp):
AAAAATTAATTATTTTTAAAATAAAATAAAATTATAACATAAAATTTTATT
Found at i:1314726 original size:35 final size:35
Alignment explanation
Indices: 1314678--1314768 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
1314668 CATTGGAATA
* * *
1314678 AAAGGAAAAGTTATGTTTGTTGGAAATTAGAAAAT
1 AAAGGAAAAGTTATGTCTATTGGAAATAAGAAAAT
*
1314713 AAAGGAAAGGTTATGTCTATTGGAAATAAGAAAAT
1 AAAGGAAAAGTTATGTCTATTGGAAATAAGAAAAT
* * *
1314748 AAAAGAAGAGTCATGTCTATT
1 AAAGGAAAAGTTATGTCTATT
1314769 AAAACATACA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (35 bp):
AAAGGAAAAGTTATGTCTATTGGAAATAAGAAAAT
Found at i:1323486 original size:101 final size:100
Alignment explanation
Indices: 1323288--1323475 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 100
1323278 TTTTTATAAT
* * *
1323288 TTATTATGCTACATATTTTTCATTGGATATCTTGCATATGCTTTCGTCAATAAAGATACATATTT
1 TTATTATGCTACATATTTTTCACTAGATATCTTGCATATGCTTTCATCAATAAAGATACATATTT
*
1323353 GGCTACTTTGTCTCTTTCGTGTTGTCTATGATTTA
66 GGCTAATTTGTCTCTTTCGTGTTGTCTATGATTTA
* *
1323388 TTATTATGCTACATATTTTTTTACTAGATATCTTGCATCTGCTTTCATCAATAAAGATACAT-TT
1 TTATTATGCTACATA-TTTTTCACTAGATATCTTGCATATGCTTTCATCAATAAAGATACATATT
*
1323452 TTGCTTAATTTGTCTCTTTCGTGT
65 TGGC-TAATTTGTCTCTTTCGTGT
1323476 GTTTTATGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 20 0.25
101 59 0.75
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.49
Consensus pattern (100 bp):
TTATTATGCTACATATTTTTCACTAGATATCTTGCATATGCTTTCATCAATAAAGATACATATTT
GGCTAATTTGTCTCTTTCGTGTTGTCTATGATTTA
Found at i:1325683 original size:105 final size:111
Alignment explanation
Indices: 1325515--1325730 Score: 349
Period size: 105 Copynumber: 2.0 Consensus size: 111
1325505 AAAATACAAG
1325515 TTTTAATATATTTATATTTTTTATTATAAATTTTTATATAATATCATCTCTTAAATATATTTTT-
1 TTTTAATATATTTATATTTTTTATTATAAATTTTTATATAATATCATCTCTTAAATATATTTTTA
1325579 ATGTCATATATTTTATTT-TCATTTATTATTATAATCTTATATATTTT
66 ATGTCATATATTTTATTTAT--TTTATTATTATAATCTTATATATTTT
*
1325626 TTTTAA-ATATTTATA-TTTTTATTATTAA-TTTTATAT-A-ATCAT-TCTTAAATATATTTTTA
1 TTTTAATATATTTATATTTTTTATTATAAATTTTTATATAATATCATCTCTTAAATATATTTTTA
1325685 ATGTCATATATTTTATTTATTTTATTATTATAATCTTATATATTTT
66 ATGTCATATATTTTATTTATTTTATTATTATAATCTTATATATTTT
1325731 ATTTCATTTA
Statistics
Matches: 102, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
105 42 0.41
106 23 0.23
107 2 0.02
108 8 0.08
109 12 0.12
110 9 0.09
111 6 0.06
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (111 bp):
TTTTAATATATTTATATTTTTTATTATAAATTTTTATATAATATCATCTCTTAAATATATTTTTA
ATGTCATATATTTTATTTATTTTATTATTATAATCTTATATATTTT
Found at i:1325705 original size:54 final size:55
Alignment explanation
Indices: 1325527--1325705 Score: 158
Period size: 54 Copynumber: 3.3 Consensus size: 55
1325517 TTAATATATT
* *
1325527 TATATTTTTTATTATAAATTTTTATATAATATCATCTCTTAAATATATTTTT-ATGTCA
1 TATATTTTATATTATTAA-TTTTATAT-A-ATCAT-TCTTAAATATATTTTTAATGTCA
* * * * * * * *
1325585 TATATTTTATTTTCATTTATTAT-TATAATC-TT-ATATAT-TTTTTTTAAATAT-T
1 TATATTTTATATT-ATTAATTTTATATAATCATTCTTAAATATATTTTT-AATGTCA
1325637 TATATTTT-TATTATTAATTTTATATAATCATTCTTAAATATATTTTTAATGTCA
1 TATATTTTATATTATTAATTTTATATAATCATTCTTAAATATATTTTTAATGTCA
1325691 TATATTTTAT-TTATT
1 TATATTTTATATTATT
1325706 TTATTATTAT
Statistics
Matches: 94, Mismatches: 18, Indels: 22
0.70 0.13 0.16
Matches are distributed among these distances:
50 7 0.07
51 16 0.17
52 14 0.15
53 12 0.13
54 20 0.21
55 4 0.04
56 1 0.01
57 3 0.03
58 14 0.15
59 3 0.03
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (55 bp):
TATATTTTATATTATTAATTTTATATAATCATTCTTAAATATATTTTTAATGTCA
Found at i:1325726 original size:32 final size:32
Alignment explanation
Indices: 1325690--1325772 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
1325680 TTTTAATGTC
1325690 ATATATTTTATTT-ATTTTATTATTATAATCTT
1 ATATATTTTATTTCA-TTTATTATTATAATCTT
1325722 ATATATTTTATTTCATTTATTATTATAATCTT
1 ATATATTTTATTTCATTTATTATTATAATCTT
1325754 ATATATTTTATTTTCATTT
1 ATATATTTTA-TTTCATTT
1325773 CTTTAATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
32 40 0.82
33 9 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (32 bp):
ATATATTTTATTTCATTTATTATTATAATCTT
Found at i:1325762 original size:105 final size:104
Alignment explanation
Indices: 1325535--1325808 Score: 299
Period size: 105 Copynumber: 2.6 Consensus size: 104
1325525 TTTATATTTT
*
1325535 TTATTATAAATTTTTATATAATATCATCTCTTAAATATATTTTTATGTCATATATTTTATTTTCA
1 TTATTATTAA-TTTTATAT-A-ATCAT-TCTTAAATATATTTTTATGTCATATATTTTATTTT-A
* * *
1325600 TTTATTATTATAATCTTATATATTTTTTTTAAATATTTATATTT
61 TTTATTATTATAATCTTATATATTTTTTTCAAATATTTATAATC
1325644 TTATTATTAATTTTATATAATCATTCTTAAATATATTTTTAATGTCATATATTTTA-TTTATTTT
1 TTATTATTAATTTTATATAATCATTCTTAAATATATTTTT-ATGTCATATATTTTATTTTA-TTT
**
1325708 ATTATTATAATCTTATATATTTTATTTCATTTATTATTATAATC
64 ATTATTATAATCTTATATATTTT-TTTCAAATA-T-TTATAATC
* * * * *
1325752 TTA-TA-T-ATTTTAT-T-TTCATTTCTTTAATATATTTTTTATATTATATGTTTTATTTTA
1 TTATTATTAATTTTATATAATCA-TTCTTAAATATA-TTTTTATGTCATATATTTTATTTTA
1325809 ATTTGTTTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 20
0.82 0.06 0.11
Matches are distributed among these distances:
103 3 0.02
104 25 0.17
105 61 0.42
106 27 0.18
107 4 0.03
108 17 0.12
109 9 0.06
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (104 bp):
TTATTATTAATTTTATATAATCATTCTTAAATATATTTTTATGTCATATATTTTATTTTATTTAT
TATTATAATCTTATATATTTTTTTCAAATATTTATAATC
Found at i:1325793 original size:33 final size:32
Alignment explanation
Indices: 1325690--1325782 Score: 125
Period size: 32 Copynumber: 2.8 Consensus size: 32
1325680 TTTTAATGTC
*
1325690 ATATATTTTATTT-ATTTTATTATTATAATCTT
1 ATATATTTTATTTCA-TTTATTAATATAATCTT
*
1325722 ATATATTTTATTTCATTTATTATTATAATCTT
1 ATATATTTTATTTCATTTATTAATATAATCTT
*
1325754 ATATATTTTATTTTCATTTCTTTAATATA
1 ATATATTTTA-TTTCATTT-ATTAATATA
1325783 TTTTTTATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 40 0.71
33 9 0.16
34 7 0.12
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.63
Consensus pattern (32 bp):
ATATATTTTATTTCATTTATTAATATAATCTT
Found at i:1326635 original size:18 final size:20
Alignment explanation
Indices: 1326595--1326635 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1326585 TAAGCAACTG
1326595 ATTTAT-TTTT-TATCATTT
1 ATTTATATTTTATATCATTT
1326613 ATTTATATTTTATAT-ATTT
1 ATTTATATTTTATATCATTT
1326632 -TTTA
1 ATTTA
1326636 ATTAATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.48
19 8 0.38
20 3 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTATATTTTATATCATTT
Found at i:1327258 original size:19 final size:20
Alignment explanation
Indices: 1327230--1327277 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1327220 CATTTTTATC
* * *
1327230 TTATTCTTTTCTCCTTGT-T
1 TTATTTTTTTATCCTTCTCT
*
1327249 TTATTTTTTTATCTTTCTCT
1 TTATTTTTTTATCCTTCTCT
1327269 TTATTTTTT
1 TTATTTTTT
1327278 GCTATGTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (20 bp):
TTATTTTTTTATCCTTCTCT
Found at i:1329523 original size:30 final size:30
Alignment explanation
Indices: 1329487--1329553 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
1329477 AACATAGTCT
*
1329487 ATTATTTTAAATTTGTATCATAACAAATAA
1 ATTATTTTAAATTTGCATCATAACAAATAA
1329517 ATTA-TTTAAATTTGCATCATAACAAATAA
1 ATTATTTTAAATTTGCATCATAACAAATAA
1329546 ATTATTTT
1 ATTATTTT
1329554 TTTCTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (30 bp):
ATTATTTTAAATTTGCATCATAACAAATAA
Found at i:1330580 original size:351 final size:349
Alignment explanation
Indices: 1329759--1330726 Score: 1338
Period size: 351 Copynumber: 2.8 Consensus size: 349
1329749 ACTTAACTTT
* * * * * *
1329759 TTTTTTTAATTTCTTGTAATTAAGAACAAATTCATAAAGTTAATTAAATTAATTTATGAAACCAT
1 TTTTTTTAATTTCATGTAATTAAGGACAAACTCATATAGTTAATTAAATTAATTAATGAAACTAT
** * *
1329824 GATTATTAATTAACTTGTAATGTCTTTTAATATATAT-GGTTTATATATTGTGTTAATTTATAAG
66 GATTATTAATTAACTTGTAATGTCTTTTAATATATATACCTTTATATATTGGGTTCATTTATAAG
* ** * * * *
1329888 AAATATAATTGTTATTATATTTATACCAAAATACTTTTAGTATATATATATATATATATTAAATA
131 GAATATAATTACTATTATATATATACTAAAATACTTTTAG--TGTATATATATA-CT-TTAAATA
* * *
1329953 TAAATATATTTACTTTCTATTTTGTGTTAACATTATAAAATTGTAATTTATAAAATTATTAATTA
192 TAAATATATTTACTTTCTATTTTGTATTAACATTAAAAAATTATAATTTATAAAATTATTAATTA
* * * *
1330018 T-A-ATATATATATATCTTTTGCTTATATAAACTTACAATATATAAACCTACAGAGAAGTTGTAA
257 TAATATATATATATATCCTTTGCTTACATAAACTTACAATATATAAACCTAAAGAGAAATTGTAA
** *
1330081 AATTAGAATAGTTTTTGAACCTTAGTTT
322 AATTAGAATAGTTTTAAAACCTTAGTTA
* * * *
1330109 TTTTTTTAATTTCATATAATTAAGGACAAACTCATATAATTAATTAAATTAATTCATGAAAATAT
1 TTTTTTTAATTTCATGTAATTAAGGACAAACTCATATAGTTAATTAAATTAATTAATGAAACTAT
* *
1330174 GATTATTAATTAACTTATAATGTCTTTTAATATATATACCTTATATATGTTGGGTTCATTTATAA
66 GATTATTAATTAACTTGTAATGTCTTTTAATATATATACCTT-TATATATTGGGTTCATTTATAA
* *
1330239 GGAATATAATTACTATTATATACATACTAAAATATTTTTAGTGTATATATATACTTTAAATATAA
130 GGAATATAATTACTATTATATATATACTAAAATACTTTTAGTGTATATATATACTTTAAATATAA
*
1330304 ACATATTTACTTTCTATTTTGTATTAACATTACAAAAATTATAATTTATAAAATTATTAATTATA
195 ATATATTTACTTTCTATTTTGTATTAACATTA-AAAAATTATAATTTATAAAATTATTAATTATA
* * * * *
1330369 ATATATATATATATACCTTTGTTTACATAAACTTATAATATATAAATCTAAAGAGAAATTGTGAG
259 ATATATATATATAT-CCTTTGCTTACATAAACTTACAATATATAAACCTAAAGAGAAATTGTAAA
1330434 ATTAGAATAGTTTTAAAACC-TAGTTA
323 ATTAGAATAGTTTTAAAACCTTAGTTA
1330460 TTTTTTTAATTTCATGTAATTAAGGACAAAC-CTATATAGTTAATTAAATTAATTAATGAAACTA
1 TTTTTTTAATTTCATGTAATTAAGGACAAACTC-ATATAGTTAATTAAATTAATTAATGAAACTA
* * * * * *
1330524 TGGTCAATAATTAACATGTAATGTTTTTTAATATATATACTTTGTATATATTGGGTTCATTTATA
65 TGATTATTAATTAACTTGTAATGTCTTTTAATATATATACCTT-TATATATTGGGTTCATTTATA
* *
1330589 AGGATTATAATTACTATTTTATATATACTAAAATACTTTTA--GTATATATATACTTTAAATATA
129 AGGAATATAATTACTATTATATATATACTAAAATACTTTTAGTGTATATATATACTTTAAATATA
* *
1330652 AATATATTTACTTTTTATTTTTTATTAACATTATAAAAATTATAATTTATAAAATTATTAATTAT
194 AATATATTTACTTTCTATTTTGTATTAACATTA-AAAAATTATAATTTATAAAATTATTAATTAT
1330717 AATATATATA
258 AATATATATA
1330727 CACACTTTAT
Statistics
Matches: 550, Mismatches: 61, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
348 40 0.07
349 123 0.22
350 105 0.19
351 170 0.31
352 112 0.20
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (349 bp):
TTTTTTTAATTTCATGTAATTAAGGACAAACTCATATAGTTAATTAAATTAATTAATGAAACTAT
GATTATTAATTAACTTGTAATGTCTTTTAATATATATACCTTTATATATTGGGTTCATTTATAAG
GAATATAATTACTATTATATATATACTAAAATACTTTTAGTGTATATATATACTTTAAATATAAA
TATATTTACTTTCTATTTTGTATTAACATTAAAAAATTATAATTTATAAAATTATTAATTATAAT
ATATATATATATCCTTTGCTTACATAAACTTACAATATATAAACCTAAAGAGAAATTGTAAAATT
AGAATAGTTTTAAAACCTTAGTTA
Found at i:1330701 original size:16 final size:16
Alignment explanation
Indices: 1330681--1330718 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1330671 TTTTATTAAC
1330681 ATTATAAAAATTA-TA
1 ATTATAAAAATTATTA
1330696 ATT-TATAAAATTATTA
1 ATTATA-AAAATTATTA
1330712 ATTATAA
1 ATTATAA
1330719 TATATATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.10
15 10 0.50
16 6 0.30
17 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATAAAAATTATTA
Found at i:1331331 original size:40 final size:40
Alignment explanation
Indices: 1331287--1331406 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
1331277 TGTTTAAGAA
*
1331287 GTTGTTTGAATATTTGTTTTTGGTTATTTAAGTTTATGTT
1 GTTGTTTGAATATTTGTTTTTAGTTATTTAAGTTTATGTT
* *
1331327 GTTGTTTGAATATTTGGTTTTAGTTATTTAATTTTATG-T
1 GTTGTTTGAATATTTGTTTTTAGTTATTTAAGTTTATGTT
* * *
1331366 GACTATTTGAGTATATT-TTTTTAGTTATTTAAGTTTATGTT
1 G-TTGTTTGAATAT-TTGTTTTTAGTTATTTAAGTTTATGTT
1331407 TGAGATATTG
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.03
40 64 0.93
41 3 0.04
ACGTcount: A:0.21, C:0.01, G:0.17, T:0.61
Consensus pattern (40 bp):
GTTGTTTGAATATTTGTTTTTAGTTATTTAAGTTTATGTT
Found at i:1347738 original size:3 final size:3
Alignment explanation
Indices: 1347730--1347771 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1347720 AATAAATTTT
1347730 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1347772 CCCAACCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1349934 original size:22 final size:22
Alignment explanation
Indices: 1349892--1349934 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1349882 GGGTAAATGA
*
1349892 TAAAAATACCTTTTATTAAAATT
1 TAAAAATA-CTTTTATGAAAATT
1349915 TAAAAAT-CTTTTAATGAAAA
1 TAAAAATACTTTT-ATGAAAA
1349935 AACAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAAATACTTTTATGAAAATT
Found at i:1350246 original size:45 final size:45
Alignment explanation
Indices: 1350186--1350279 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
1350176 ATTAAATTTA
* *
1350186 AATAATACTAAATAATATTCTTTATTATATTTACTATA-TTCAAAT
1 AATAATACTAAATAATACTCTTTATAATATTTACTATAGTT-AAAT
* **
1350231 AATAATATTAAATAATACTCTTTATAATATTTTTTATAGTTAAAT
1 AATAATACTAAATAATACTCTTTATAATATTTACTATAGTTAAAT
1350276 AATA
1 AATA
1350280 TTAATATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (45 bp):
AATAATACTAAATAATACTCTTTATAATATTTACTATAGTTAAAT
Found at i:1350944 original size:25 final size:25
Alignment explanation
Indices: 1350903--1350994 Score: 59
Period size: 25 Copynumber: 3.8 Consensus size: 25
1350893 TATTATAATT
*
1350903 AAAA-TAAATATATAATATAAGAATA
1 AAAATTAAA-ATAAAATATAAGAATA
* *
1350928 AAAATTAAAATAAAATAAAAAAAT-
1 AAAATTAAAATAAAATATAAGAATA
* ** *
1350952 TAAATT-TTATATAATAT-AG-ATAA
1 AAAATTAAAATAAAATATAAGAAT-A
1350975 ACAAATTAAAATAAAATATA
1 A-AAATTAAAATAAAATATA
1350995 TAATATAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 11
0.67 0.18 0.15
Matches are distributed among these distances:
21 2 0.04
22 1 0.02
23 7 0.15
24 10 0.21
25 24 0.50
26 4 0.08
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATTAAAATAAAATATAAGAATA
Found at i:1351011 original size:48 final size:48
Alignment explanation
Indices: 1350891--1351011 Score: 115
Period size: 48 Copynumber: 2.5 Consensus size: 48
1350881 ACTATTTTAT
1350891 AATATTATAAT-TAAAATAAATATATAATATAAGAATAAAAATTAAAATAA
1 AATA-TATAATAT-AAA-AAATATATAATATAAGAATAAAAATTAAAATAA
* * ***
1350941 AATA-AAAAAATTAAATTTTATATAATAT-AG-ATAAACAAATTAAAATAA
1 AATATATAATA-TAAAAAATATATAATATAAGAAT-AA-AAATTAAAATAA
1350989 AATATATAATATAAAAAATATAT
1 AATATATAATATAAAAAATATAT
1351012 TAAAGAAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
46 2 0.04
47 4 0.07
48 38 0.68
49 7 0.12
50 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (48 bp):
AATATATAATATAAAAAATATATAATATAAGAATAAAAATTAAAATAA
Found at i:1351076 original size:70 final size:68
Alignment explanation
Indices: 1350977--1351126 Score: 185
Period size: 70 Copynumber: 2.2 Consensus size: 68
1350967 ATAGATAAAC
* *
1350977 AAATTAAAATAAAATATATAATATAAAAAATATATTAAAGAAATGAATAAAATATAGAAAATT-A
1 AAATAAAAAT-AAATATATAACATAAAAAATATATTAAAGAAATG-ATAAAATATA-AAAATTAA
1351041 TAATAAT
63 TAAT-AT
* * * **
1351048 AAATAAAAATAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAATTAATAA
1 AAATAAAAATAAATATATAACATAAAAAATATATTAAAGAAATGATAAAATATAAAAATTAATAA
1351113 TAT
66 TAT
*
1351116 AAATATAAATA
1 AAATAAAAATA
1351127 TATTAAAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
68 18 0.26
69 13 0.19
70 30 0.43
71 9 0.13
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (68 bp):
AAATAAAAATAAATATATAACATAAAAAATATATTAAAGAAATGATAAAATATAAAAATTAATAA
TAT
Found at i:1351103 original size:29 final size:28
Alignment explanation
Indices: 1351071--1351223 Score: 95
Period size: 28 Copynumber: 5.4 Consensus size: 28
1351061 TATATGACAT
*
1351071 TAAAAATATATTTAAGAAATGATATTATA
1 TAAAAATATAATTAAGAAAT-ATATTATA
* * *
1351100 TAAAAAT-TAATAATATAAATATAAATATA
1 TAAAAATATAATTA-AGAAATAT-ATTATA
* *
1351129 TTAAAAATA-AAAT-ATAAA-ATATTATAA
1 -TAAAAATATAATTAAGAAATATATTAT-A
* * *
1351156 TAATAAATAAAAAT-A-AAATATATGATA
1 TAA-AAATATAATTAAGAAATATATTATA
*
1351183 TTAAAAATATATTTAAGAAATGATATTATA
1 -TAAAAATATAATTAAGAAAT-ATATTATA
1351213 TAAAAAT-TAAT
1 TAAAAATATAAT
1351224 AATAAAAAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 25
0.72 0.09 0.18
Matches are distributed among these distances:
26 7 0.07
27 19 0.19
28 29 0.29
29 28 0.28
30 16 0.16
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (28 bp):
TAAAAATATAATTAAGAAATATATTATA
Found at i:1351117 original size:15 final size:15
Alignment explanation
Indices: 1351097--1351162 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
1351087 AAATGATATT
1351097 ATATAAAAATTAATA
1 ATATAAAAATTAATA
* *
1351112 ATATAAATATAAAT-
1 ATATAAAAATTAATA
1351126 ATATTAAAAA-TAA-A
1 ATA-TAAAAATTAATA
1351140 ATATAAAATATT-ATA
1 ATATAAAA-ATTAATA
1351155 ATAATAAA
1 AT-ATAAA
1351163 TAAAAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 5 0.12
14 10 0.24
15 21 0.51
16 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATAAAAATTAATA
Found at i:1351121 original size:21 final size:22
Alignment explanation
Indices: 1351097--1351170 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
1351087 AAATGATATT
1351097 ATATAAAA-ATTAATAATATAA
1 ATATAAAATATTAATAATATAA
*
1351118 ATATAAATATATTAAAAATA-AA
1 ATATAAA-ATATTAATAATATAA
1351140 ATATAAAATATT-ATAATAATAA
1 ATATAAAATATTAATAAT-ATAA
1351162 ATA-AAAATA
1 ATATAAAATA
1351171 AAATATATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.09
21 19 0.40
22 15 0.32
23 9 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATATAA
Found at i:1351122 original size:6 final size:6
Alignment explanation
Indices: 1351111--1351177 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
1351101 AAAAATTAAT
* *
1351111 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
1351161 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
1351178 TGATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:1351157 original size:112 final size:114
Alignment explanation
Indices: 1351022--1351247 Score: 395
Period size: 113 Copynumber: 2.0 Consensus size: 114
1351012 TAAAGAAATG
1351022 AATAAAATATAGAAAATTATAATAATAAATAAAAAT-AAATATATGACATTAAAAATATATTTAA
1 AATAAAATATAGAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAA
*
1351086 GAAATGATATTATATAAAAATTAATAAT-ATAAATATAAATATATTAAA
66 GAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAAA
*
1351134 AATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTA
1 AATAAAATATAGAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTA
*
1351198 AGAAATGATATTATATAAAAATTAATAATAAAAAATGTAAATATATTAAA
65 AGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAAA
1351248 CTTATATTTT
Statistics
Matches: 108, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
111 3 0.03
112 32 0.30
113 55 0.51
114 18 0.17
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (114 bp):
AATAAAATATAGAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAA
GAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAAA
Found at i:1351175 original size:15 final size:16
Alignment explanation
Indices: 1351109--1351177 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
1351099 ATAAAAATTA
*
1351109 ATAATATAAATATAAAT
1 ATAATAAAAATA-AAAT
*
1351126 ATATTAAAAATAAAAT
1 ATAATAAAAATAAAAT
*
1351142 ATAA-AATATTATAATAAT
1 ATAATAA-A-AATAA-AAT
1351160 A-AATAAAAATAAAAT
1 ATAATAAAAATAAAAT
1351175 ATA
1 ATA
1351178 TGATATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
15 6 0.14
16 13 0.31
17 17 0.40
18 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAAAAATAAAAT
Found at i:1351446 original size:15 final size:15
Alignment explanation
Indices: 1351397--1351436 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1351387 TTTTCCCTGT
*
1351397 AATCACATTGCTTGC
1 AATCACATTACTTGC
1351412 AATCACATTACTTGC
1 AATCACATTACTTGC
1351427 AATCACATTA
1 AATCACATTA
1351437 TCTGTAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:1353307 original size:28 final size:28
Alignment explanation
Indices: 1353275--1353330 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1353265 TTAGTGAATT
1353275 GCAAATTTAAAATGAACATTAAAATACA
1 GCAAATTTAAAATGAACATTAAAATACA
*
1353303 GCAAATTTGAAATGAACATTAAAATACA
1 GCAAATTTAAAATGAACATTAAAATACA
1353331 AACTTACAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (28 bp):
GCAAATTTAAAATGAACATTAAAATACA
Found at i:1353995 original size:3 final size:3
Alignment explanation
Indices: 1353989--1354014 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1353979 TTTTCAACAA
1353989 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
1354015 TGTTTTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:1357382 original size:2 final size:2
Alignment explanation
Indices: 1357375--1357404 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1357365 AGATTAAAAT
*
1357375 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1357405 CATAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1359163 original size:20 final size:20
Alignment explanation
Indices: 1359135--1359178 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1359125 TTTATCCATA
1359135 AAATGTTTTACATTTAAAAT
1 AAATGTTTTACATTTAAAAT
* * *
1359155 AAATTTTTTACCTTTCAAAT
1 AAATGTTTTACATTTAAAAT
1359175 AAAT
1 AAAT
1359179 ATAAGTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATGTTTTACATTTAAAAT
Found at i:1359320 original size:2 final size:2
Alignment explanation
Indices: 1359313--1359364 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1359303 ACTAGTCAAC
*
1359313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1359355 CA TA CA TA TA
1 TA TA TA TA TA
1359365 ATCAAACGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1359506 original size:35 final size:35
Alignment explanation
Indices: 1359456--1359525 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1359446 AGGATTTCAT
1359456 CTTCGACCTTAGGCATCAATTCAACAATATAACTA
1 CTTCGACCTTAGGCATCAATTCAACAATATAACTA
* *
1359491 CTTCGACCTTGGGCATCAATTCAATAATATAACTA
1 CTTCGACCTTAGGCATCAATTCAACAATATAACTA
1359526 TCTATCCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (35 bp):
CTTCGACCTTAGGCATCAATTCAACAATATAACTA
Found at i:1362577 original size:137 final size:141
Alignment explanation
Indices: 1362316--1362588 Score: 403
Period size: 147 Copynumber: 1.9 Consensus size: 141
1362306 CCACTAACTA
*
1362316 ATACTTTTGGGTTCACCACTGATTGCTCTCAGGCCAAAAAATGGCAATTTCAACCGTGCTATGAC
1 ATACTTTTGGGTTCACCACTGATTGCTATCAGGCCAAAAAATGGCAATTTCAACCGTGCTATGAC
1362381 TACTCATGCCATGCAAGATTGAGGTAGGTTTCTTAAGGTAGGGGCAGGAAAGATATATTTTTAAA
66 TACTCATGCCATGCAAGA-T-A-GT--GTTTCTTAAGGTAGGGGCAGGAAAGATATA-TTTTAAA
1362446 AACAATTCTATATAGTT
125 AACAATTCTATATAGTT
* * *
1362463 ATACTTTTGGTTTCACCACTGATTGCTATCAGGCCAAAAAATGGCAATTTCAACTGTGCTATGGC
1 ATACTTTTGGGTTCACCACTGATTGCTATCAGGCCAAAAAATGGCAATTTCAACCGTGCTATGAC
* *
1362528 TACTCATGCCATGC-A-A-A-T-TTTCTTGAGGTAGGGGCAGGAAAGATATATTTTCAAAACAAT
66 TACTCATGCCATGCAAGATAGTGTTTCTTAAGGTAGGGGCAGGAAAGATATATTTTAAAAACAAT
1362588 T
131 T
1362589 TTTCTCTATA
Statistics
Matches: 120, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
136 13 0.11
137 28 0.23
140 1 0.01
142 1 0.01
145 1 0.01
146 1 0.01
147 75 0.62
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (141 bp):
ATACTTTTGGGTTCACCACTGATTGCTATCAGGCCAAAAAATGGCAATTTCAACCGTGCTATGAC
TACTCATGCCATGCAAGATAGTGTTTCTTAAGGTAGGGGCAGGAAAGATATATTTTAAAAACAAT
TCTATATAGTT
Found at i:1368160 original size:2 final size:2
Alignment explanation
Indices: 1368153--1368178 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1368143 GTATTTAACA
1368153 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
1368179 TAATGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1375673 original size:16 final size:16
Alignment explanation
Indices: 1375625--1375673 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
1375615 ATCTATTTAA
1375625 ATATTAATATATTTA-TG
1 ATATTAA-AT-TTTATTG
*
1375642 ATAATTAAAATTTATTG
1 AT-ATTAAATTTTATTG
1375659 ATATTAAATTTTATT
1 ATATTAAATTTTATT
1375674 TTATTTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 16 0.57
17 7 0.25
18 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
ATATTAAATTTTATTG
Found at i:1382626 original size:16 final size:16
Alignment explanation
Indices: 1382602--1382647 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
1382592 TCTTGGGCCG
*
1382602 TGCTTCATGCTTCATC
1 TGCTGCATGCTTCATC
1382618 TGCTGCATGCTTCATC
1 TGCTGCATGCTTCATC
1382634 TGCTGCATGCTTCA
1 TGCTGCATGCTTCA
1382648 CCTATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.39
Consensus pattern (16 bp):
TGCTGCATGCTTCATC
Found at i:1384702 original size:285 final size:283
Alignment explanation
Indices: 1384181--1384839 Score: 1016
Period size: 285 Copynumber: 2.3 Consensus size: 283
1384171 AAGCCATGAG
* * *
1384181 AATAGTTTCACCGATGAGGTAGAAAGCTTGGTTCATTATGCAATAACATCTGTTGATTGTCATTG
1 AATAGTCTCACCAATGAGGTAGAAAGCTTGGTTCATTATGCAATAACATGTGTTGATTGTCATTG
* * * * * *
1384246 TTTGAAAGCCATGTAACAGGCTATGCAATAAAACATTTGAGATAAAAACAAAATGGCATTTATAT
66 TTTGGAAGCCACGTAACAGGCTGTGCAACAAAACATTTGAAATAAAAACAAAATGGCATTAATAT
* * * *
1384311 GCTACTTCTGCAATAAAACATTTGAGATAAAAACAACCATGTGTCTTCTGGCCGGCCATGAGACT
131 GCTACTTCTGCAATAAAACATTTGAGATAAAAACAACCATCTGTCTGCTAGCAGGCCATGAGACT
* * *
1384376 CAAGGTTATTTTCAAGCAGAAATTTATCTTTGAAAAGTTGAATATCCCAGCAGACTAATGGGAAT
196 CAAGGTTATTTTCAAGCAAAAATTTATCTTTCAAAAGTTGAATATCCCAGCAGACTAACGGGAAT
1384441 TGAATTTGAAGGTATATGTCCAC
261 TGAATTTGAAGGTATATGTCCAC
* *
1384464 AATAGTCTGACCAATGAGGTAGAAAGCTTGGTTCATTATGCAATAACATGTGTTGATTGTCACTG
1 AATAGTCTCACCAATGAGGTAGAAAGCTTGGTTCATTATGCAATAACATGTGTTGATTGTCATTG
* *
1384529 TTTGGAAGCCACGTAAAAGGTTGTGCAACAAAACATTTGAAATAAAAAACAAAATGGCATTCAAT
66 TTTGGAAGCCACGTAACAGGCTGTGCAACAAAACATTTGAAAT-AAAAACAAAATGGCATT-AAT
*
1384594 TTGCTACTTCTGCAATAAAACATTTGAGATAAAAACAACCATCTGTCTGC-AGCTAGGCCATGAG
129 ATGCTACTTCTGCAATAAAACATTTGAGATAAAAACAACCATCTGTCTGCTAGC-AGGCCATGAG
* *
1384658 ACTCAAGGTTATTTTCAAGTAAAAATTTATC-TTCATTAAGTTGAATATCCCAGCAGACTAACGG
193 ACTCAAGGTTATTTTCAAGCAAAAATTTATCTTTCA-AAAGTTGAATATCCCAGCAGACTAACGG
* *
1384722 GAGTTGAATTTGAAGGTATATGTCCAT
257 GAATTGAATTTGAAGGTATATGTCCAC
* * *
1384749 AATAGTCTCACCGATGAGATAGAAAGCTAGGTTCATTATGCAATAACATGTGTTGATTGTCATTG
1 AATAGTCTCACCAATGAGGTAGAAAGCTTGGTTCATTATGCAATAACATGTGTTGATTGTCATTG
1384814 TTTGGAAGCCACGTAACAGGCTGTGC
66 TTTGGAAGCCACGTAACAGGCTGTGC
1384840 TTCTTGCACC
Statistics
Matches: 340, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
283 96 0.28
284 22 0.06
285 222 0.65
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (283 bp):
AATAGTCTCACCAATGAGGTAGAAAGCTTGGTTCATTATGCAATAACATGTGTTGATTGTCATTG
TTTGGAAGCCACGTAACAGGCTGTGCAACAAAACATTTGAAATAAAAACAAAATGGCATTAATAT
GCTACTTCTGCAATAAAACATTTGAGATAAAAACAACCATCTGTCTGCTAGCAGGCCATGAGACT
CAAGGTTATTTTCAAGCAAAAATTTATCTTTCAAAAGTTGAATATCCCAGCAGACTAACGGGAAT
TGAATTTGAAGGTATATGTCCAC
Found at i:1388836 original size:3 final size:3
Alignment explanation
Indices: 1388828--1388866 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1388818 CTTGTTGGAC
1388828 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
1388867 GTAGTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1390563 original size:19 final size:20
Alignment explanation
Indices: 1390522--1390563 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1390512 TTGAACTAAG
*
1390522 ATAACTTTTCATTTTATAAA
1 ATAACTTTTCATTTTAGAAA
*
1390542 ATAACTTTTTATTTT-GAAA
1 ATAACTTTTCATTTTAGAAA
1390561 ATA
1 ATA
1390564 CATCGACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAACTTTTCATTTTAGAAA
Found at i:1392551 original size:78 final size:77
Alignment explanation
Indices: 1392438--1392725 Score: 283
Period size: 78 Copynumber: 3.7 Consensus size: 77
1392428 AAGATGATAA
* * * ** *
1392438 ATTTACATATTGGCACCATTGTACCTTCCTATATAATAGGAATGCCACTTGCCCACCTATCACAT
1 ATTTACATATTGACATCATTATACCTTAATATATAATAGGAATGCCACATGCCCACCTATCACAT
*
1392503 GGAACTTAATAGT
66 GGAACATAAT-GT
* * *
1392516 ATTTACATATTGGCATCATTATACCTTAATGTATAAAAGGAATGCCACATGCCCACCTATCACAT
1 ATTTACATATTGACATCATTATACCTTAATATATAATAGGAATGCCACATGCCCACCTATCACAT
* * *
1392581 GTACCATGATGGT
66 GGAACATAAT-GT
* * * * * * * *
1392594 ATTTATATGTTCACATCATTATACCTTCATATAAAATAGAAATGCCACATACCCACCTATGACAT
1 ATTTACATATTGACATCATTATACCTTAATATATAATAGGAATGCCACATGCCCACCTATCACAT
* * *
1392659 AGAACATAGTGAC
66 GGAACATAATG-T
* * *
1392672 ATTTATATATTGACATCATTATA-C-TATATGTATAATAAGAATGCCACATGCCCA
1 ATTTACATATTGACATCATTATACCTTA-ATATATAATAGGAATGCCACATGCCCA
1392726 TGCCTTGTGT
Statistics
Matches: 171, Mismatches: 37, Indels: 5
0.80 0.17 0.02
Matches are distributed among these distances:
76 1 0.01
77 24 0.14
78 146 0.85
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (77 bp):
ATTTACATATTGACATCATTATACCTTAATATATAATAGGAATGCCACATGCCCACCTATCACAT
GGAACATAATGT
Found at i:1397975 original size:24 final size:23
Alignment explanation
Indices: 1397935--1397979 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1397925 ATTTTTTGTT
*
1397935 TATATATTTTATATATATTAATA
1 TATATATATTATATATATTAATA
*
1397958 TATATAATATTATGTATATTAA
1 TATAT-ATATTATATATATTAA
1397980 GAAGAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATATATTATATATATTAATA
Found at i:1400375 original size:15 final size:15
Alignment explanation
Indices: 1400348--1400388 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1400338 AATTTTATGT
1400348 ATGTTATTTATATTAA
1 ATGTTA-TTATATTAA
* *
1400364 ATTTTATTATATTTA
1 ATGTTATTATATTAA
1400379 ATGTTATTAT
1 ATGTTATTAT
1400389 TATTTTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
ATGTTATTATATTAA
Found at i:1404708 original size:18 final size:19
Alignment explanation
Indices: 1404662--1404706 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1404652 TTTTCTTTTC
* *
1404662 CTTTCTTTT-TCTTTTTGA
1 CTTTATTTTATCTTTTGGA
1404680 CTTTATTTTATCTTTTGGA
1 CTTTATTTTATCTTTTGGA
*
1404699 TTTTATTT
1 CTTTATTT
1404707 ATTGTTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (19 bp):
CTTTATTTTATCTTTTGGA
Done.