Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 137 of 143
Found at i:40743088 original size:19 final size:19
Alignment explanation
Indices: 40743049--40743089 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40743039 TAATAACTTT
*
40743049 TAATAATAATAACTAATAA
1 TAATAATAATAACTAAAAA
40743068 TAATAATAATAA-TATAAAA
1 TAATAATAATAACTA-AAAA
40743087 TAA
1 TAA
40743090 AAAAAGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAATAATAACTAAAAA
Found at i:40744145 original size:30 final size:30
Alignment explanation
Indices: 40744099--40744398 Score: 476
Period size: 30 Copynumber: 10.0 Consensus size: 30
40744089 CCCTAAATTA
* *
40744099 TCCAGAAATTATATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
40744130 TCCAAAATTAAATTTTGA-CCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
40744159 TCCTAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
40744189 TCTAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
40744219 TCCAAAAATTATATTTTGACCCTAAAACTTT
1 TCC-AAAATTACATTTTGACCCCAAAACTTT
*
40744250 ACCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
40744280 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
40744310 TCCATAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
40744340 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
40744370 TCCATAGTTACATTTTGACCCCAAAACTT
1 TCCAAAATTACATTTTGACCCCAAAACTT
40744399 CCTTAAATCC
Statistics
Matches: 250, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
29 26 0.10
30 193 0.77
31 31 0.12
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:40744365 original size:19 final size:19
Alignment explanation
Indices: 40744251--40744305 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 19
40744241 TAAAACTTTA
40744251 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
40744270 CC-AAA--AC-TTTT----
1 CCAAAATTACATTTTGACC
40744281 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
40744300 CCAAAA
1 CCAAAA
40744306 CTTTTCCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
14 2 0.07
15 8 0.29
16 2 0.07
18 3 0.11
19 8 0.29
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (19 bp):
CCAAAATTACATTTTGACC
Found at i:40751967 original size:29 final size:29
Alignment explanation
Indices: 40751934--40752117 Score: 146
Period size: 29 Copynumber: 6.3 Consensus size: 29
40751924 CAAAATTTCG
*
40751934 ATTTTTGGATGCTT-GAGGGTAAAATGGTG
1 ATTTTTGGA-GCTTCGAGGGTAAAATGGTA
* * *
40751963 ATTTTTGGAGGTTCAAGGGTAAAACGGTA
1 ATTTTTGGAGCTTCGAGGGTAAAATGGTA
* *
40751992 ATTTTTGGA-CACTCGGGGGTAAAAAT-GTA
1 ATTTTTGGAGC-TTCGAGGGT-AAAATGGTA
40752021 ATTTTTGGA-CATTCGAGGGTAAAATGGTA
1 ATTTTTGGAGC-TTCGAGGGTAAAATGGTA
** *
40752050 ATTTTTGGAAATTTTG-GGGTCAAAAATGG-A
1 ATTTTTGG-AGCTTCGAGGGT--AAAATGGTA
** *
40752080 ATTTTTGGATATTCGAGGGTAAAATGGCA
1 ATTTTTGGAGCTTCGAGGGTAAAATGGTA
*
40752109 ACTTTTGGA
1 ATTTTTGGA
40752118 AAATTTAGGG
Statistics
Matches: 128, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
28 15 0.12
29 85 0.66
30 21 0.16
31 7 0.05
ACGTcount: A:0.30, C:0.07, G:0.29, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAGCTTCGAGGGTAAAATGGTA
Found at i:40752085 original size:30 final size:29
Alignment explanation
Indices: 40752007--40752299 Score: 188
Period size: 29 Copynumber: 10.0 Consensus size: 29
40751997 TGGACACTCG
* *
40752007 GGGGTAAAAATGTAATTTTTGGACA-TTC
1 GGGGTAAAAATGGAATTTTTGGAAAGTTC
* *
40752035 GAGGGT-AAAATGGTAATTTTTGGAAATTTT
1 G-GGGTAAAAATGG-AATTTTTGGAAAGTTC
*
40752065 GGGGTCAAAAATGGAATTTTTGGATA-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAAGTTC
* * *
40752094 GAGGGT-AAAATGGCAACTTTTGGAAAATTTA
1 G-GGGTAAAAATGG-AATTTTTGG-AAAGTTC
* * *
40752125 GGGTTAAAAATGGAA-TTTT-CAAACATTC
1 GGGGTAAAAATGGAATTTTTGGAAA-GTTC
* *
40752153 AGGGGT-AAAATGGTAATTTTTGAAAAGTTT
1 -GGGGTAAAAATGG-AATTTTTGGAAAGTTC
* *
40752183 GAGGGTAAAAATGTAATTTTTGAAAAGTTC
1 G-GGGTAAAAATGGAATTTTTGGAAAGTTC
* ** * * *
40752213 GGGGCAAAAATTTAATTTTTGTAAACTTTA
1 GGGGTAAAAATGGAATTTTTGGAAA-GTTC
* *
40752243 AGGG-AAAAATGTAATTTTTGGAAAGTTC
1 GGGGTAAAAATGGAATTTTTGGAAAGTTC
* * *
40752271 GAGGGTCAAAATGTAATTTTTAGAAAGTT
1 G-GGGTAAAAATGGAATTTTTGGAAAGTT
40752300 TGACGGTCAA
Statistics
Matches: 214, Mismatches: 31, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.01
28 25 0.12
29 83 0.39
30 77 0.36
31 26 0.12
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAAGTTC
Found at i:40752099 original size:59 final size:58
Alignment explanation
Indices: 40751950--40752301 Score: 295
Period size: 59 Copynumber: 6.0 Consensus size: 58
40751940 GGATGCTTGA
* ** * * * * **
40751950 GGGT-AAAATGGTGATTTTTGGAGGTTCAAGGGTAAAACGGTAATTTTTGGACACTCGG
1 GGGTAAAAATGG-AATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTG
* * *
40752008 GGGTAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAATTTTG
1 GGGTAAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTG
* * * *
40752066 GGGTCAAAAATGGAATTTTTGGATATTCGAGGGTAAAATGGCAACTTTTGGAAAATTTAG
1 GGGT-AAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTT-G
* ** *
40752126 GGTTAAAAATGGAA-TTTTCAAACATTC-AGGGGTAAAATGGTAATTTTTGAAAAGTTTG
1 GGGTAAAAATGGAATTTTTGGAA-ATTCGA-GGGTAAAATGGTAATTTTTGGAAAGTTTG
* * * * * * *
40752184 AGGGTAAAAATGTAATTTTTGAAAAGTTCG-GGGCAAAAAT-TTAATTTTTGTAAACTTTAA
1 -GGGTAAAAATGGAATTTTTGGAAA-TTCGAGGG-TAAAATGGTAATTTTTGGAAAGTTT-G
* *
40752244 GGG-AAAAATGTAATTTTTGGAAAGTTCGAGGGTCAAAAT-GTAATTTTTAGAAAGTTTG
1 GGGTAAAAATGGAATTTTTGGAAA-TTCGAGGGT-AAAATGGTAATTTTTGGAAAGTTTG
40752302 ACGGTCAAAA
Statistics
Matches: 243, Mismatches: 38, Indels: 26
0.79 0.12 0.08
Matches are distributed among these distances:
58 76 0.31
59 148 0.61
60 19 0.08
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (58 bp):
GGGTAAAAATGGAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTTG
Found at i:40752233 original size:118 final size:119
Alignment explanation
Indices: 40752008--40752335 Score: 316
Period size: 118 Copynumber: 2.8 Consensus size: 119
40751998 GGACACTCGG
*** * *
40752008 GGGTAAAAATGTAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAATTTTG-GGGTCA
1 GGGTAAAAATGTAATTTTCAAACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTTGAGGGT-A
* * *
40752072 AAAATGGAATTTTTGGATA-TTCGAGGGTAAAATGGCAACTTTTGGAAAATTT-A
65 AAAATGTAATTTTTGAATAGTTCGAGGGAAAAATGGCAACTTTTGGAAAATTTAA
*
40752125 GGGTTAAAAATGGAATTTTCAAACATTC-AGGGGTAAAATGGTAATTTTTGAAAAGTTTGAGGGT
1 GGG-TAAAAATGTAATTTTCAAACATTCGA-GGGTAAAATGGTAATTTTTGAAAAGTTTGAGGGT
* ** * * *
40752189 AAAAATGTAATTTTTGAAAAGTTCG-GGGCAAAAAT-TTAATTTTTGTAAACTTTAA
64 AAAAATGTAATTTTTGAATAGTTCGAGGG-AAAAATGGCAACTTTTGGAAAATTTAA
* * *
40752244 GGG-AAAAATGTAATTTTTGGAAA-GTTCGAGGGTCAAAAT-GTAATTTTT-AGAAAGTTTGACG
1 GGGTAAAAATGTAA-TTTT-CAAACATTCGAGGGT-AAAATGGTAATTTTTGA-AAAGTTTGAGG
* * * *
40752305 GTCAAAATATGATTTTTGAATAGTTCAAGGG
62 GTAAAAATGTAATTTTTGAATAGTTCGAGGG
40752336 TCAAAATATG
Statistics
Matches: 175, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
117 14 0.08
118 132 0.75
119 29 0.17
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (119 bp):
GGGTAAAAATGTAATTTTCAAACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTTGAGGGTAA
AAATGTAATTTTTGAATAGTTCGAGGGAAAAATGGCAACTTTTGGAAAATTTAA
Found at i:40752308 original size:30 final size:30
Alignment explanation
Indices: 40752008--40752342 Score: 196
Period size: 30 Copynumber: 11.3 Consensus size: 30
40751998 GGACACTCGG
* * * *
40752008 GGGTAAAAATGTAATTTTTGGACA-TTCGA
1 GGGTCAAAATGTAATTTTTGAAAAGTTTGA
* *
40752037 GGGT-AAAATGGTAATTTTTGGAAATTTTG-
1 GGGTCAAAAT-GTAATTTTTGAAAAGTTTGA
* * * *
40752066 GGGTCAAAAATGGAATTTTTGGATA-TTCGA
1 GGGTC-AAAATGTAATTTTTGAAAAGTTTGA
* *
40752096 GGGT-AAAATGGCAACTTTTGGAAAA-TTT-A
1 GGGTCAAAAT-GTAA-TTTTTGAAAAGTTTGA
* * * *
40752125 GGGTTAAAAATGGAA-TTTTCAAACA--TTCA
1 GGG-TCAAAATGTAATTTTTGAAA-AGTTTGA
40752154 GGGGT-AAAATGGTAATTTTTGAAAAGTTTGA
1 -GGGTCAAAAT-GTAATTTTTGAAAAGTTTGA
* *
40752185 GGGTAAAAATGTAATTTTTGAAAAGTTCG-
1 GGGTCAAAATGTAATTTTTGAAAAGTTTGA
* * * *
40752214 GGG-CAAAAATTTAATTTTTGTAAACTTTAA
1 GGGTC-AAAATGTAATTTTTGAAAAGTTTGA
* * *
40752244 GGG-AAAAATGTAATTTTTGGAAAGTTCGA
1 GGGTCAAAATGTAATTTTTGAAAAGTTTGA
40752273 GGGTCAAAATGTAATTTTT-AGAAAGTTTGA
1 GGGTCAAAATGTAATTTTTGA-AAAGTTTGA
* * * * **
40752303 CGGTCAAAATATGATTTTTGAATAGTTCAA
1 GGGTCAAAATGTAATTTTTGAAAAGTTTGA
40752333 GGGTCAAAAT
1 GGGTCAAAAT
40752343 ATGATTTCTG
Statistics
Matches: 245, Mismatches: 39, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
28 23 0.09
29 83 0.34
30 120 0.49
31 19 0.08
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGAAAAGTTTGA
Found at i:40753155 original size:20 final size:21
Alignment explanation
Indices: 40753132--40753170 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40753122 AAAACTTCTC
40753132 TTTTCATTTCC-TTAAAACAG
1 TTTTCATTTCCTTTAAAACAG
*
40753152 TTTTGATTTCCTTTAAAAC
1 TTTTCATTTCCTTTAAAAC
40753171 TTTTCCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTTCATTTCCTTTAAAACAG
Found at i:40753488 original size:3 final size:3
Alignment explanation
Indices: 40753475--40753537 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
40753465 ATTTCCTTTT
* * *
40753475 TTA TTA TTTA TTA TTA TTA ATG TTA TTA ATA TTA -TA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
40753521 TTA TTA TATA TTTA TTA
1 TTA TTA T-TA -TTA TTA
40753538 CTATATTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
2 2 0.04
3 37 0.76
4 9 0.18
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:40753500 original size:15 final size:15
Alignment explanation
Indices: 40753479--40753546 Score: 75
Period size: 15 Copynumber: 4.4 Consensus size: 15
40753469 CCTTTTTTAT
40753479 TATTTATTATTATTA
1 TATTTATTATTATTA
*
40753494 -ATGTTATTAATATTA
1 TAT-TTATTATTATTA
40753509 TATTTATTATTATTA
1 TATTTATTATTATTA
* *
40753524 TTATATATTTATTACTA
1 -TATTTA-TTATTATTA
40753541 TATTTA
1 TATTTA
40753547 CTAAATGCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.05
15 22 0.50
16 12 0.27
17 8 0.18
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (15 bp):
TATTTATTATTATTA
Found at i:40754215 original size:17 final size:17
Alignment explanation
Indices: 40754193--40754270 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
40754183 TAATTTTTTT
40754193 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
*
40754210 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTTA
* * *
40754227 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTTA
*
40754244 AATTTAAAATAAATTAA
1 AATTTAAAATAAATTTA
*
40754261 AATTAAAAAT
1 AATTTAAAAT
40754271 TAAAAGTTGG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:40756665 original size:57 final size:57
Alignment explanation
Indices: 40756555--40756691 Score: 170
Period size: 57 Copynumber: 2.4 Consensus size: 57
40756545 AGACATTCAA
* *
40756555 GGGTAAAACGTTAATTTTTAGAAAAATCGGGATCAAAAATAGAATTTTTGGACACCGG
1 GGGTAAAATGGTAATTTTT-GAAAAATCGGGATCAAAAATAGAATTTTTGGACACCGG
** * * *
40756613 GGGTAAAATGGTAATTTTTGAAAGTTTCGGG-TCAAAAATAGAGTTTTTGGACATCTG
1 GGGTAAAATGGTAATTTTTGAAA-AATCGGGATCAAAAATAGAATTTTTGGACACCGG
*
40756670 GGGCAAAATGGTAA-TTTTGAAA
1 GGGTAAAATGGTAATTTTTGAAA
40756692 TTTTTAAGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
56 8 0.11
57 40 0.57
58 22 0.31
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGAAAAATCGGGATCAAAAATAGAATTTTTGGACACCGG
Found at i:40756730 original size:58 final size:56
Alignment explanation
Indices: 40756612--40756864 Score: 172
Period size: 58 Copynumber: 4.3 Consensus size: 56
40756602 TTGGACACCG
* * * * * *
40756612 GGGGTAAAATGGTAATTTTTGAAAGTTTCGGGTCAAAAATAGAGTTTTTGGACA-TCT
1 GGGGTAAAATGGTAA-TTTTGAAATTTTAGGGTCAAAAATGGAATTTTT-GAAAGTTT
* *
40756669 GGGGCAAAATGGTAATTTTGAAATTTTTAAGGGACAAAAATGGAATTTTTGAAAGTTT
1 GGGGTAAAATGGTAATTTTGAAA-TTTT-AGGGTCAAAAATGGAATTTTTGAAAGTTT
* * * *
40756727 GGGGTTAAAAAT-GTAATTTTAAAAGTTTTAGGGTTAAAATTGGAATTTTAGAGAAGTTT
1 GGGG-T-AAAATGGTAATTTTGAAA-TTTTAGGGTCAAAAATGGAATTTTTGA-AAGTTT
*** * * * * *
40756786 GAGGGTAAAAACTTAATTTTTGGAAGTTTT-GAGGTTAAAATTGAAATTTTTGAAAGTTC
1 G-GGGTAAAATGGTAA-TTTT-GAAATTTTAG-GGTCAAAAATGGAATTTTTGAAAGTTT
40756845 GAGGGTAAAAAT-GTAATTTT
1 G-GGGT-AAAATGGTAATTTT
40756865 TGGATGTTTC
Statistics
Matches: 160, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
56 8 0.05
57 20 0.12
58 50 0.31
59 41 0.26
60 39 0.24
61 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (56 bp):
GGGGTAAAATGGTAATTTTGAAATTTTAGGGTCAAAAATGGAATTTTTGAAAGTTT
Found at i:40756744 original size:29 final size:29
Alignment explanation
Indices: 40756704--40756866 Score: 145
Period size: 29 Copynumber: 5.6 Consensus size: 29
40756694 TTTAAGGGAC
*
40756704 AAAAATGGAATTTTTGAAAGTTTGGGGTT
1 AAAAATGTAATTTTTGAAAGTTTGGGGTT
* *
40756733 AAAAATGTAA-TTTTAAAAGTTTTAGGGTT
1 AAAAATGTAATTTTTGAAAG-TTTGGGGTT
* * *
40756762 AAAATTGGAATTTTAGAGAAGTTTGAGGG-T
1 AAAAATGTAATTTTTGA-AAGTTTG-GGGTT
* *
40756792 AAAAACT-TAATTTTTGGAAGTTTTGAGGTT
1 AAAAA-TGTAATTTTTGAAAG-TTTGGGGTT
* * *
40756822 AAAATTGAAATTTTTGAAAGTTCGAGGG-T
1 AAAAATGTAATTTTTGAAAGTTTG-GGGTT
40756851 AAAAATGTAATTTTTG
1 AAAAATGTAATTTTTG
40756867 GATGTTTCGG
Statistics
Matches: 105, Mismatches: 20, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
28 8 0.08
29 49 0.47
30 41 0.39
31 7 0.07
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.39
Consensus pattern (29 bp):
AAAAATGTAATTTTTGAAAGTTTGGGGTT
Found at i:40756784 original size:59 final size:58
Alignment explanation
Indices: 40756674--40756864 Score: 217
Period size: 59 Copynumber: 3.2 Consensus size: 58
40756664 CATCTGGGGC
* ** *
40756674 AAAATGGTAATTTTGAAATTTTTAAGGGACAAAAATGGAATTTTTGAAAGTTTG-GGGTTA
1 AAAAT-GTAATTTTGAAAGTTTT-AGGGTTAAAATTGGAATTTTTGAAAGTTTGAGGG-TA
* *
40756734 AAAATGTAATTTTAAAAGTTTTAGGGTTAAAATTGGAATTTTAGAGAAGTTTGAGGGTA
1 AAAATGTAATTTTGAAAGTTTTAGGGTTAAAATTGGAATTTTTGA-AAGTTTGAGGGTA
* * *
40756793 AAAACT-TAATTTTTGGAAGTTTT-GAGGTTAAAATTGAAATTTTTGAAAGTTCGAGGGTA
1 AAAA-TGTAA-TTTTGAAAGTTTTAG-GGTTAAAATTGGAATTTTTGAAAGTTTGAGGGTA
40756852 AAAATGTAATTTT
1 AAAATGTAATTTT
40756865 TGGATGTTTC
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
58 24 0.21
59 51 0.45
60 39 0.34
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTGAAAGTTTTAGGGTTAAAATTGGAATTTTTGAAAGTTTGAGGGTA
Found at i:40756804 original size:30 final size:28
Alignment explanation
Indices: 40756712--40756866 Score: 136
Period size: 30 Copynumber: 5.3 Consensus size: 28
40756702 ACAAAAATGG
40756712 AATTTTTGAAAGTTTG-GGGTTAAAAATGT
1 AATTTTTGAAAGTTTGAGGG-TAAAAAT-T
* * *
40756741 AA-TTTTAAAAGTTTTAGGGTTAAAATT
1 AATTTTTGAAAGTTTGAGGGTAAAAATT
*
40756768 GGAATTTTAGAGAAGTTTGAGGGTAAAAACTT
1 --AATTTTTGA-AAGTTTGAGGGTAAAAA-TT
* *
40756800 AATTTTTGGAAGTTTTGA-GGTTAAAATT
1 AATTTTTGAAAG-TTTGAGGGTAAAAATT
*
40756828 GAAATTTTTGAAAGTTCGAGGGTAAAAATGT
1 --AATTTTTGAAAGTTTGAGGGTAAAAAT-T
40756859 AATTTTTG
1 AATTTTTG
40756867 GATGTTTCGG
Statistics
Matches: 102, Mismatches: 13, Indels: 22
0.74 0.09 0.16
Matches are distributed among these distances:
27 1 0.01
28 19 0.19
29 29 0.28
30 35 0.34
31 16 0.16
32 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.40
Consensus pattern (28 bp):
AATTTTTGAAAGTTTGAGGGTAAAAATT
Found at i:40758352 original size:23 final size:24
Alignment explanation
Indices: 40758298--40758353 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
40758288 GTTGGAGTCC
* *
40758298 AATTTTAATTGAGCCCAACATTTA
1 AATTTAAATTGAACCCAACATTTA
* *
40758322 AA-TCAAATTGAACCCAA-TTTTA
1 AATTTAAATTGAACCCAACATTTA
40758344 AATTTAAATT
1 AATTTAAATT
40758354 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 6 0.23
23 18 0.69
24 2 0.08
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (24 bp):
AATTTAAATTGAACCCAACATTTA
Found at i:40759360 original size:16 final size:16
Alignment explanation
Indices: 40759342--40759376 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
40759332 ATTTTCGAAA
40759342 TTTCTCCAGATCTGGAT
1 TTTC-CCAGATCTGGAT
40759359 TTTCCCAGATCTGGAT
1 TTTCCCAGATCTGGAT
40759375 TT
1 TT
40759377 GGTTTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (16 bp):
TTTCCCAGATCTGGAT
Found at i:40760231 original size:29 final size:29
Alignment explanation
Indices: 40760199--40760353 Score: 106
Period size: 29 Copynumber: 5.3 Consensus size: 29
40760189 AAAATTATCA
40760199 TTTACCCCTAAACTTTCCAAAATTCCATT
1 TTTACCCCTAAACTTTCCAAAATTCCATT
* ** *
40760228 TTTA-ACCTCGA-TTTCACCAAAAATTAC-TAT
1 TTTACCCCTAAACTTT--CC-AAAATTCCAT-T
** *
40760258 TTTACCCCCGAACCTTCCAAAATTCCATT
1 TTTACCCCTAAACTTTCCAAAATTCCATT
*
40760287 TTTAACCCT-AA-TTTCACCAAAAATTACCA-T
1 TTTACCCCTAAACTTT--CC-AAAATT-CCATT
*
40760317 TTTACCCCTAAACTTTCCAAAATGCCATT
1 TTTACCCCTAAACTTTCCAAAATTCCATT
*
40760346 TTAACCCC
1 TTTACCCC
40760354 GATTTAACCA
Statistics
Matches: 96, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
27 5 0.05
28 9 0.09
29 37 0.39
30 32 0.33
31 8 0.08
32 5 0.05
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (29 bp):
TTTACCCCTAAACTTTCCAAAATTCCATT
Found at i:40760248 original size:58 final size:58
Alignment explanation
Indices: 40760186--40760382 Score: 272
Period size: 59 Copynumber: 3.4 Consensus size: 58
40760176 CCTAGACTGT
*
40760186 CCAAAAATTATCA-TTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACC-CGATTTCA
* ** * *
40760244 CCAAAAATTACTATTTTACCCCCGAACCTTCCAAAATTCCATTTTTAACCCTAATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCC-GATTTCA
* *
40760303 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATGCCA-TTTTAACCCCGATTTAA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAA-CCCGATTTCA
*
40760361 CCAAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
40760383 GAGCGTCCAA
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
58 44 0.36
59 78 0.64
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCGATTTCA
Found at i:40760320 original size:30 final size:29
Alignment explanation
Indices: 40760186--40760377 Score: 100
Period size: 30 Copynumber: 6.6 Consensus size: 29
40760176 CCTAGACTGT
* *
40760186 CCAAAAATTATCA-TTTACCCCTAAACTTT-
1 CCAAAAATTACCATTTTAACCCT-AA-TTTA
*
40760215 CC-AAAATT-CCATTTTTAA-CCTCGATTTCA
1 CCAAAAATTACCA-TTTTAACCCT-AATTT-A
* * * *
40760244 CCAAAAATTACTATTTTACCCCCGAACCTT-
1 CCAAAAATTACCATTTTA-ACCCTAA-TTTA
40760274 CC-AAAATT-CCATTTTTAACCCTAATTTCA
1 CCAAAAATTACCA-TTTTAACCCTAATTT-A
*
40760303 CCAAAAATTACCATTTTACCCCTAAACTTT-
1 CCAAAAATTACCATTTTAACCCT-AA-TTTA
* **
40760333 CC-AAAA-TGCCATTTTAACCCCGATTTAA
1 CCAAAAATTACCATTTTAACCCTAATTT-A
40760361 CCAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
40760378 GCCCCGAGCG
Statistics
Matches: 124, Mismatches: 19, Indels: 39
0.68 0.10 0.21
Matches are distributed among these distances:
26 3 0.02
27 8 0.06
28 31 0.25
29 29 0.23
30 38 0.31
31 8 0.06
32 7 0.06
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (29 bp):
CCAAAAATTACCATTTTAACCCTAATTTA
Found at i:40770266 original size:2 final size:2
Alignment explanation
Indices: 40770261--40770285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40770251 ATAAAAATTA
40770261 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
40770286 AAGAAAATCG
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:40771350 original size:17 final size:17
Alignment explanation
Indices: 40771328--40771415 Score: 104
Period size: 17 Copynumber: 4.9 Consensus size: 17
40771318 CCATTTCAAG
*
40771328 TTTATTTTAAAATTAAA
1 TTTATTTTAAATTTAAA
40771345 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
*
40771362 TTTACTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
40771379 TTTATTGAATTTAAATTTAAA
1 TTTA-T---TTTAAATTTAAA
* *
40771400 ATTATTATAAATTTAA
1 TTTATTTTAAATTTAA
40771416 TAAAATGTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
17 46 0.74
20 1 0.02
21 15 0.24
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:40771359 original size:6 final size:6
Alignment explanation
Indices: 40771333--40771399 Score: 66
Period size: 6 Copynumber: 11.0 Consensus size: 6
40771323 TCAAGTTTAT
* * *
40771333 TTTAAA ATTAAA TTT-AT TTTAAA TTTAAA TTT-AC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40771379 TTTATTGAA TTTAAA TTTAAA
1 TTTA---AA TTTAAA TTTAAA
40771400 ATTATTATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 8 0.16
6 36 0.72
9 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:40773392 original size:30 final size:30
Alignment explanation
Indices: 40773351--40773598 Score: 240
Period size: 30 Copynumber: 8.4 Consensus size: 30
40773341 GTCCTCAAAC
* *
40773351 TTTTTC-AAAATTACATTTTGACCATAAAT
1 TTTTTCTAAAATTACATTTTGACCCTAAAA
* *
40773380 TTTTTCTAAAATTATATTTTGACCCCAAAA
1 TTTTTCTAAAATTACATTTTGACCCTAAAA
* *
40773410 CTTCTT-AAAAATTACATTTTGA-CCTCAAAA
1 -TTTTTCTAAAATTACATTTTGACCCT-AAAA
* * *
40773440 CTTTTCCAAAATTACATTTTAACCCTAAAA
1 TTTTTCTAAAATTACATTTTGACCCTAAAA
* * *
40773470 CTTTTCTAAAATTATATTTTGACCCCAAAA
1 TTTTTCTAAAATTACATTTTGACCCTAAAA
* *
40773500 CTTTTT-GAAAATTACAATTTGACTCCT-AAA
1 -TTTTTCTAAAATTACATTTTGAC-CCTAAAA
* *
40773530 TTTTTCCAAAATTATATTTTGACCCTAAAA
1 TTTTTCTAAAATTACATTTTGACCCTAAAA
*
40773560 CTTTT-TAAAATTACA-TTTGACCCTAAAA
1 TTTTTCTAAAATTACATTTTGACCCTAAAA
* *
40773588 CTTTTCCAAAA
1 TTTTTCTAAAA
40773599 ACCCTAAATT
Statistics
Matches: 181, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
28 18 0.10
29 31 0.17
30 119 0.66
31 13 0.07
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTTTCTAAAATTACATTTTGACCCTAAAA
Found at i:40773450 original size:90 final size:89
Alignment explanation
Indices: 40773343--40773590 Score: 340
Period size: 90 Copynumber: 2.8 Consensus size: 89
40773333 CTCTGGAGGT
* * **
40773343 CCTCAAACTTTTTCAAAATTACATTTTGACCATAAATTTTTTCTAAAATTATATTTTGACCCCAA
1 CCTCAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCTAAAATTATATTTTGACCCCAA
*
40773408 AACTTCTTAAAAATTACATTTTGA
66 AACTTCTTAAAAATTACAATTTGA
*
40773432 CCTCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCTAAAATTATATTTTGACCCCA
1 CCTC-AAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCTAAAATTATATTTTGACCCCA
* *
40773497 AAACTTTTTGAAAATTACAATTTGA
65 AAACTTCTTAAAAATTACAATTTGA
* * * *
40773522 -CTCCTAAATTTTTCCAAAATTATATTTTGACCCTAAAACTTTT-TAAAATTACA-TTTGACCCT
1 CCT-C-AAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCTAAAATTATATTTTGACCCC
40773584 AAAACTT
64 AAAACTT
40773591 TTCCAAAAAC
Statistics
Matches: 143, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
88 15 0.10
89 15 0.10
90 113 0.79
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (89 bp):
CCTCAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCTAAAATTATATTTTGACCCCAA
AACTTCTTAAAAATTACAATTTGA
Found at i:40773618 original size:19 final size:20
Alignment explanation
Indices: 40773579--40773618 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40773569 ATTACATTTG
40773579 ACCCTAAAACTTTTCCAAAA
1 ACCCTAAAACTTTTCCAAAA
**
40773599 ACCCTAAATTTTTTCCAAAA
1 ACCCTAAAACTTTTCCAAAA
40773619 TTACATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCCTAAAACTTTTCCAAAA
Found at i:40773643 original size:30 final size:30
Alignment explanation
Indices: 40773609--40773715 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 30
40773599 ACCCTAAATT
40773609 TTTTCCAAAATTACATTTTAACCCTCTAAA
1 TTTTCCAAAATTACATTTTAACCCTCTAAA
*
40773639 TTTTCCAAAATTTCATTTTTAACCC-C--AA
1 TTTTCCAAAATTACA-TTTTAACCCTCTAAA
* *
40773667 -TTTCAACAAAATTACCCTTTTGA-CCT-TAAA
1 TTTTC--CAAAATTA-CATTTTAACCCTCTAAA
*
40773697 TTTTCCAAAATTCCATTTT
1 TTTTCCAAAATTACATTTT
40773716 TTAACCCCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
27 4 0.06
28 9 0.14
29 19 0.30
30 18 0.29
31 13 0.21
ACGTcount: A:0.34, C:0.23, G:0.01, T:0.42
Consensus pattern (30 bp):
TTTTCCAAAATTACATTTTAACCCTCTAAA
Found at i:40773678 original size:59 final size:61
Alignment explanation
Indices: 40773614--40773781 Score: 188
Period size: 59 Copynumber: 2.8 Consensus size: 61
40773604 AAATTTTTTC
*
40773614 CAAAATTA-CATTTTAACCCTCTAAATTTTCCAAAATTTCATTTTTAACCCCAATTTCA-A
1 CAAAATTACCATTTTAACCCTCTAAATTTTCCAAAATTCCATTTTTAACCCCAATTTCATA
* * *
40773673 CAAAATTACCCTTTTGA-CCT-TAAATTTTCCAAAATTCCATTTTTTAACCCCTATTTCATTA
1 CAAAATTACCATTTTAACCCTCTAAATTTTCCAAAATTCCA-TTTTTAACCCCAATTTCA-TA
* * **
40773734 -AAAATTACCATTTTGATCCC-C-GAATTTTTTAAAATTCCATTTTTAACC
1 CAAAATTACCATTTT-AACCCTCTAAATTTTCCAAAATTCCATTTTTAACC
40773782 TCGATTTTGC
Statistics
Matches: 92, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
58 18 0.20
59 28 0.30
60 28 0.30
61 16 0.17
62 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (61 bp):
CAAAATTACCATTTTAACCCTCTAAATTTTCCAAAATTCCATTTTTAACCCCAATTTCATA
Found at i:40773716 original size:29 final size:29
Alignment explanation
Indices: 40773609--40773721 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 29
40773599 ACCCTAAATT
*
40773609 TTTTCCAAAATTACA-TTTTAACCCTCTAAA
1 TTTTCCAAAATTCCATTTTTAA-CCT-TAAA
* **
40773639 TTTTCCAAAATTTCATTTTTAACC-CCAA
1 TTTTCCAAAATTCCATTTTTAACCTTAAA
* *
40773667 -TTTCAACAAAATTACC-CTTTTGACCTTAAA
1 TTTTC--CAAAATT-CCATTTTTAACCTTAAA
40773697 TTTTCCAAAATTCCATTTTTTAACC
1 TTTTCCAAAATTCCA-TTTTTAACC
40773722 CCTATTTCAT
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
27 4 0.06
28 4 0.06
29 21 0.32
30 26 0.40
31 10 0.15
ACGTcount: A:0.34, C:0.24, G:0.01, T:0.42
Consensus pattern (29 bp):
TTTTCCAAAATTCCATTTTTAACCTTAAA
Found at i:40773777 original size:60 final size:58
Alignment explanation
Indices: 40773614--40773781 Score: 187
Period size: 60 Copynumber: 2.8 Consensus size: 58
40773604 AAATTTTTTC
* *
40773614 CAAAATTA-CATTTTAACCCTCTAAATTTTCCAAAATTTCATTTTTAACCCCAATTTCAA
1 CAAAATTACCATTTTGACCC-C-AAATTTTCCAAAATTCCATTTTTAACCCCAATTTCAA
* ** *
40773673 CAAAATTACCCTTTTGACCTTAAATTTTCCAAAATTCCATTTTTTAACCCCTATTTCATTA
1 CAAAATTACCATTTTGACCCCAAATTTTCCAAAATTCCA-TTTTTAACCCCAATTTCA--A
* **
40773734 -AAAATTACCATTTTGATCCCCGAATTTTTTAAAATTCCATTTTTAACC
1 CAAAATTACCATTTTGA-CCCCAAATTTTCCAAAATTCCATTTTTAACC
40773782 TCGATTTTGC
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 17 0.18
59 25 0.27
60 32 0.35
61 18 0.20
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (58 bp):
CAAAATTACCATTTTGACCCCAAATTTTCCAAAATTCCATTTTTAACCCCAATTTCAA
Found at i:40774198 original size:95 final size:96
Alignment explanation
Indices: 40774033--40774218 Score: 225
Period size: 95 Copynumber: 1.9 Consensus size: 96
40774023 AAAACTTTAA
* * * * * *
40774033 AATCGAGGCAATATTCTTTAATTTCGAGTTTTGAAATTTTGCGCCTTAACTTACTAGGTGCGATT
1 AATCAAGGCAATATTCTTTAATTTCGAGTTCTGAAAATTTGCGCCTTAACTCACTAGATGCAATT
* *
40774098 TTTCTTCAAACCGAAATAATCGAATACCCTT
66 CTTCTTCAAACCGAAATAATCAAATACCCTT
*
40774129 AATCAAGGCAATATT-TGTT-ATCTTCGA-TTCTGAAAATTTGCTCCTTAACTCACTAGATGCAA
1 AATCAAGGCAATATTCT-TTAAT-TTCGAGTTCTGAAAATTTGCGCCTTAACTCACTAGATGCAA
* * *
40774191 TTCTTCTTTAAATCGAGATAATCAAATA
64 TTCTTCTTCAAACCGAAATAATCAAATA
40774219 TCTTTTTTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
95 55 0.72
96 21 0.28
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (96 bp):
AATCAAGGCAATATTCTTTAATTTCGAGTTCTGAAAATTTGCGCCTTAACTCACTAGATGCAATT
CTTCTTCAAACCGAAATAATCAAATACCCTT
Found at i:40774929 original size:17 final size:17
Alignment explanation
Indices: 40774907--40774965 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
40774897 AAGAATATGA
40774907 AAGGTTAAGGTAGATGG
1 AAGGTTAAGGTAGATGG
40774924 AAGGTTAAAGGTCA-A-GG
1 AAGGTT-AAGGT-AGATGG
* * *
40774941 GAGGTTATGGAAGATGG
1 AAGGTTAAGGTAGATGG
40774958 AAGGTTAA
1 AAGGTTAA
40774966 AAGTCAAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.03
16 4 0.12
17 21 0.64
18 6 0.18
19 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.39, T:0.22
Consensus pattern (17 bp):
AAGGTTAAGGTAGATGG
Found at i:40774956 original size:34 final size:34
Alignment explanation
Indices: 40774908--40774977 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
40774898 AGAATATGAA
* * *
40774908 AGGTTAAGGTAGATGGAAGGTTAAAGGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAAGG
*
40774942 AGGTTATGGAAGATGGAAGGTTAAAAGTCAAAGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAAGG
40774976 AG
1 AG
40774978 ATGAAAGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.39, T:0.20
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAAGG
Found at i:40781654 original size:29 final size:29
Alignment explanation
Indices: 40781622--40781679 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
40781612 AAGAACGGGA
40781622 TCAAAAATGAAATTTTGGAAAGTTTAGGG
1 TCAAAAATGAAATTTTGGAAAGTTTAGGG
* *
40781651 TCAAATATGAATTTTTGGAAAGTTTAGGG
1 TCAAAAATGAAATTTTGGAAAGTTTAGGG
40781680 GTTAAATCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
TCAAAAATGAAATTTTGGAAAGTTTAGGG
Found at i:40781698 original size:30 final size:30
Alignment explanation
Indices: 40781629--40781830 Score: 169
Period size: 30 Copynumber: 6.7 Consensus size: 30
40781619 GGATCAAAAA
* * *
40781629 TGAAATTTTGGAAAGTTTA-GGGTCAAATA
1 TGAATTTTTGGAAAGTTTAGGGGTTAAATC
40781658 TGAATTTTTGGAAAGTTTAGGGGTTAAATC
1 TGAATTTTTGGAAAGTTTAGGGGTTAAATC
* *
40781688 TGAATGTTTGGAAAG-TTCGAGGGTTAAATC
1 TGAATTTTTGGAAAGTTTAG-GGGTTAAATC
* * * *
40781718 TGAATGTTTGGAAAG-TTCGTGGGTCAAATT
1 TGAATTTTTGGAAAGTTTAG-GGGTTAAATC
* * *
40781748 TGAATTTTTGGTAAGTTCAGGGATTAAATC
1 TGAATTTTTGGAAAGTTTAGGGGTTAAATC
** * * *
40781778 CAAATTTTTGAAAAG-TTCGGGGTTCAAATT
1 TGAATTTTTGGAAAGTTTAGGGGTT-AAATC
* *
40781808 TGAATTCTTAGAAAGTTTGAGGG
1 TGAATTTTTGGAAAGTTT-AGGG
40781831 TCAAAACATA
Statistics
Matches: 138, Mismatches: 29, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
29 27 0.20
30 104 0.75
31 4 0.03
32 3 0.02
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (30 bp):
TGAATTTTTGGAAAGTTTAGGGGTTAAATC
Found at i:40781728 original size:60 final size:58
Alignment explanation
Indices: 40781632--40781849 Score: 208
Period size: 60 Copynumber: 3.7 Consensus size: 58
40781622 TCAAAAATGA
* * * * *
40781632 AATTTTGGAAAGTT-TAGGGTCAAATATGAATTTTTGGAAAGTTTAGGGGTTAAATCTG
1 AATTTTGGAAAGTTCGAGGGTTAAATCTGAATTTTTGGAAAG-TTCGGGGTTAAATTTG
* *
40781690 AATGTTTGGAAAGTTCGAGGGTTAAATCTGAATGTTTGGAAAGTTCGTGGGTCAAATTTG
1 AAT-TTTGGAAAGTTCGAGGGTTAAATCTGAATTTTTGGAAAGTTCG-GGGTTAAATTTG
* ** *
40781750 AATTTTTGGTAAGTTC-AGGGATTAAATCCAAATTTTTGAAAAGTTCGGGGTTCAAATTTG
1 AA-TTTTGGAAAGTTCGAGGG-TTAAATCTGAATTTTTGGAAAGTTCGGGGTT-AAATTTG
* * * *
40781810 AATTCTTAGAAAGTTTGAGGGTCAAAACAT-AATTTTTGGA
1 AATT-TTGGAAAGTTCGAGGGTTAAATC-TGAATTTTTGGA
40781850 TAATTTGGGG
Statistics
Matches: 131, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
58 3 0.02
59 24 0.18
60 99 0.76
61 5 0.04
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (58 bp):
AATTTTGGAAAGTTCGAGGGTTAAATCTGAATTTTTGGAAAGTTCGGGGTTAAATTTG
Found at i:40781793 original size:90 final size:88
Alignment explanation
Indices: 40781632--40781849 Score: 244
Period size: 90 Copynumber: 2.4 Consensus size: 88
40781622 TCAAAAATGA
* * **
40781632 AATTTTGGAAAGTT-TAGGGTCAAATATGAATTTTTGGAAAGTTTAGGGGTTAAATCTGAATGTT
1 AATTTTGGAAAGTTGT-GGGTCAAATATGAATTTTTGGAAAGTTCAGGGATTAAATCCAAATGTT
*
40781696 TGGAAAGTTCGAGGGTT-AAATCTG
65 TGAAAAGTTCG-GGGTTCAAATCTG
* * *
40781720 AATGTTTGGAAAGTTCGTGGGTCAAATTTGAATTTTTGGTAAGTTCAGGGATTAAATCCAAATTT
1 AAT-TTTGGAAAGTT-GTGGGTCAAATATGAATTTTTGGAAAGTTCAGGGATTAAATCCAAATGT
*
40781785 TTGAAAAGTTCGGGGTTCAAATTTG
64 TTGAAAAGTTCGGGGTTCAAATCTG
* * *
40781810 AATTCTTAGAAAGTTTGAGGGTCAAAACAT-AATTTTTGGA
1 AATT-TTGGAAAG-TTGTGGGTC-AAATATGAATTTTTGGA
40781850 TAATTTGGGG
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
88 3 0.03
89 17 0.16
90 82 0.75
91 7 0.06
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (88 bp):
AATTTTGGAAAGTTGTGGGTCAAATATGAATTTTTGGAAAGTTCAGGGATTAAATCCAAATGTTT
GAAAAGTTCGGGGTTCAAATCTG
Found at i:40785986 original size:30 final size:30
Alignment explanation
Indices: 40785918--40786088 Score: 107
Period size: 30 Copynumber: 5.8 Consensus size: 30
40785908 AAAATAAAAT
** *
40785918 TTTGGAAAGTTT-GGGGTCAAATATGAATT
1 TTTGGAAAGTTTAGGGGTCAAATCCGAATG
* *
40785947 TTTGAAAAGTTTAGGGGTTAAATCCGAATG
1 TTTGGAAAGTTTAGGGGTCAAATCCGAATG
* ** *
40785977 TTTGGAAAGTTTAAGGGTCAAATCTAAATT
1 TTTGGAAAGTTTAGGGGTCAAATCCGAATG
* * ** *
40786007 TTTGGGAAG-TTCGTGGGTCAAATCTAAATT
1 TTTGGAAAGTTTAG-GGGTCAAATCCGAATG
* * * * *
40786037 TTTGGTAAG-TTCGGGGATTAAATCCAAATT
1 TTTGGAAAGTTTAGGGG-TCAAATCCGAATG
* *
40786067 TTTGGAATG-TTCGGGGTCAAAT
1 TTTGGAAAGTTTAGGGGTCAAAT
40786089 TTGAATTCTT
Statistics
Matches: 119, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
29 21 0.18
30 98 0.82
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTGGAAAGTTTAGGGGTCAAATCCGAATG
Found at i:40786030 original size:60 final size:58
Alignment explanation
Indices: 40785914--40786088 Score: 165
Period size: 60 Copynumber: 3.0 Consensus size: 58
40785904 GTCAAAAATA
* * ** * *
40785914 AAAT-TTTGGAAAGTTTGGGGTCAAATATGAATTTTTGAAAAGTTTAGGGGTTAAATCC
1 AAATGTTTGGAAAGTTTGGGGTCAAATCTAAATTTTTGGGAAG-TTCGGGGTCAAATCC
* * *
40785972 GAATGTTTGGAAAGTTTAAGGGTCAAATCTAAATTTTTGGGAAGTTCGTGGGTCAAATCT
1 AAATGTTTGGAAAGTTT-GGGGTCAAATCTAAATTTTTGGGAAGTTCG-GGGTCAAATCC
* * * * *
40786032 AAATTTTTGGTAAGTTCGGGGATTAAATCCAAATTTTT-GGAATGTTCGGGGTCAAAT
1 AAATGTTTGGAAAGTTTGGGG-TCAAATCTAAATTTTTGGGAA-GTTCGGGGTCAAAT
40786089 TTGAATTCTT
Statistics
Matches: 96, Mismatches: 16, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
58 3 0.03
59 31 0.32
60 62 0.65
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (58 bp):
AAATGTTTGGAAAGTTTGGGGTCAAATCTAAATTTTTGGGAAGTTCGGGGTCAAATCC
Found at i:40786058 original size:90 final size:89
Alignment explanation
Indices: 40785903--40786073 Score: 209
Period size: 90 Copynumber: 1.9 Consensus size: 89
40785893 GGAAAAACGA
* *
40785903 GGTCAAAAATAAAATTTTGGAAAGTTTGGGGTCAAATATGAATTTTTGAAAAGTTTAGGGGTTAA
1 GGTCAAAAATAAAATTTTGGAAAGTTCGGGGTCAAATATAAATTTTTGAAAAGTTTAGGGGTTAA
*
40785968 ATCCGAATGTTTGGAAAGTTTAAG
66 ATCCAAATGTTTGGAAAGTTTAAG
** * * * ** *
40785992 GGTCAAATCTAAATTTTTGGGAAGTTCGTGGGTCAAATCTAAATTTTTGGTAAG-TTCGGGGATT
1 GGTCAAAAATAAAATTTTGGAAAGTTCG-GGGTCAAATATAAATTTTTGAAAAGTTTAGGGG-TT
*
40786056 AAATCCAAATTTTTGGAA
64 AAATCCAAATGTTTGGAA
40786074 TGTTCGGGGT
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
89 29 0.43
90 39 0.57
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (89 bp):
GGTCAAAAATAAAATTTTGGAAAGTTCGGGGTCAAATATAAATTTTTGAAAAGTTTAGGGGTTAA
ATCCAAATGTTTGGAAAGTTTAAG
Found at i:40790675 original size:28 final size:28
Alignment explanation
Indices: 40790636--40790692 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
40790626 AATGCCATCT
40790636 AGAAGAAAATATGTTGATATCATTACCA
1 AGAAGAAAATATGTTGATATCATTACCA
40790664 AGAAGAAAATATGTTGATATCATTACCA
1 AGAAGAAAATATGTTGATATCATTACCA
40790692 A
1 A
40790693 AAAATTATCT
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:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (28 bp):
AGAAGAAAATATGTTGATATCATTACCA
Found at i:40790884 original size:37 final size:38
Alignment explanation
Indices: 40790838--40790922 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 38
40790828 CTAATTTTTT
*
40790838 TAATATTTTAGG-TTTTTCATAT-TTTTAAAAAT-TATTA
1 TAATTTTTTAGGATTTTT-ATATGTTTTAAAAATAT-TTA
*
40790875 TAATTTTTTAGGATTTTTATATGTTTTAATAATATTTA
1 TAATTTTTTAGGATTTTTATATGTTTTAAAAATATTTA
40790913 TAAGTTTTTT
1 TAA-TTTTTT
40790923 TTATATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
37 15 0.36
38 20 0.48
39 7 0.17
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.60
Consensus pattern (38 bp):
TAATTTTTTAGGATTTTTATATGTTTTAAAAATATTTA
Found at i:40790922 original size:21 final size:23
Alignment explanation
Indices: 40790898--40790944 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
40790888 TTTTTATATG
40790898 TTTTAATA-ATATTTATAAGTTT
1 TTTTAATATATATTTATAAGTTT
* *
40790920 TTTTTATATATTTTTATAAGTTT
1 TTTTAATATATATTTATAAGTTT
40790943 TT
1 TT
40790945 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTTAATATATATTTATAAGTTT
Found at i:40793026 original size:14 final size:14
Alignment explanation
Indices: 40793009--40793050 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
40792999 TTTCTGTCTC
40793009 TTTCTCTTTTTCTT
1 TTTCTCTTTTTCTT
40793023 TTTCTCTATTTTC-T
1 TTTCTCT-TTTTCTT
*
40793037 TCTCTCTTTTTCTT
1 TTTCTCTTTTTCTT
40793051 GCCTTTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 5 0.20
14 15 0.60
15 5 0.20
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTCTTTTTCTT
Found at i:40795772 original size:110 final size:111
Alignment explanation
Indices: 40795569--40795798 Score: 408
Period size: 110 Copynumber: 2.1 Consensus size: 111
40795559 CTTCGAGATC
* *
40795569 TAAAATATTGAATGACCTATTAAAATTGATAATGATCCTTCTATTTACAAAATCGTCTGCCTTTA
1 TAAAAT-TTGAATGACCTATTAAAATTAATAATGATCCTTCTATTTACAAAATCGTCTACCTTTA
40795634 CTCACACCTTTGCCAGATTTCTAAAACTTATCATTTTTCAAGGTATA
65 CTCACACCTTTGCCAGATTTCTAAAACTTATCATTTTTCAAGGTATA
*
40795681 TAAAATTT-AATGACCTATTAAAATTAATAATGATCCTTCTATTTACAAAATCGTCTATCTTTAC
1 TAAAATTTGAATGACCTATTAAAATTAATAATGATCCTTCTATTTACAAAATCGTCTACCTTTAC
*
40795745 TCACTCCTTTGCCAGATTTCTAAAACTTATCATTTTTCAAGGTATA
66 TCACACCTTTGCCAGATTTCTAAAACTTATCATTTTTCAAGGTATA
40795791 TAAAATTT
1 TAAAATTT
40795799 TCCAATTTAA
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
110 106 0.93
111 2 0.02
112 6 0.05
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (111 bp):
TAAAATTTGAATGACCTATTAAAATTAATAATGATCCTTCTATTTACAAAATCGTCTACCTTTAC
TCACACCTTTGCCAGATTTCTAAAACTTATCATTTTTCAAGGTATA
Found at i:40796643 original size:24 final size:24
Alignment explanation
Indices: 40796616--40796661 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40796606 TTCAATTTCA
40796616 ATGAGTAGGC-ATCTTATTGAATCC
1 ATGA-TAGGCAATCTTATTGAATCC
**
40796640 ATGATCTGCAATCTTATTGAAT
1 ATGATAGGCAATCTTATTGAAT
40796662 TCATACACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (24 bp):
ATGATAGGCAATCTTATTGAATCC
Found at i:40798806 original size:16 final size:17
Alignment explanation
Indices: 40798770--40798802 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
40798760 TAAATGAATT
40798770 ATTAACAAATTATAAAA
1 ATTAACAAATTATAAAA
40798787 ATTAA-AAA-TATAAAA
1 ATTAACAAATTATAAAA
40798802 A
1 A
40798803 ATTAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
ATTAACAAATTATAAAA
Found at i:40799824 original size:10 final size:9
Alignment explanation
Indices: 40799758--40799917 Score: 74
Period size: 10 Copynumber: 16.8 Consensus size: 9
40799748 ATATTTTTCC
40799758 ATAAAAATT
1 ATAAAAATT
*
40799767 ATTAAAATT
1 ATAAAAATT
*
40799776 CATTAGAGAATT
1 -A-TA-AAAATT
*
40799788 ATAAAAAAT
1 ATAAAAATT
40799797 ATAAAAAATGT
1 AT-AAAAAT-T
*
40799808 AAAAAAAATT
1 -ATAAAAATT
*
40799818 ATCAAAATAT
1 ATAAAAAT-T
40799828 ATAAAAATT
1 ATAAAAATT
***
40799837 -TGTTAATT
1 ATAAAAATT
40799845 ATTAAAAATAT
1 A-TAAAAAT-T
*
40799856 ATGAAAATT
1 ATAAAAATT
*
40799865 AATATAAACTT
1 -ATA-AAAATT
*
40799876 ATAAATATT
1 ATAAAAATT
40799885 ATAAAAA-T
1 ATAAAAATT
*
40799893 AT-AAGATT
1 ATAAAAATT
*
40799901 CTAATAAATT
1 ATAA-AAATT
40799911 ATAAAAA
1 ATAAAAA
40799918 AATCTTTAAA
Statistics
Matches: 110, Mismatches: 26, Indels: 30
0.66 0.16 0.18
Matches are distributed among these distances:
7 3 0.03
8 10 0.09
9 36 0.33
10 39 0.35
11 16 0.15
12 6 0.05
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:40799938 original size:20 final size:20
Alignment explanation
Indices: 40799916--40799953 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40799906 AAATTATAAA
40799916 AAAATCT-TTAAAATTTTAT
1 AAAATCTATTAAAATTTTAT
*
40799935 AAAATGTATTAAAATTTTA
1 AAAATCTATTAAAATTTTA
40799954 GTAATACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATCTATTAAAATTTTAT
Found at i:40807776 original size:3 final size:3
Alignment explanation
Indices: 40807768--40807797 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
40807758 TCATCAGTTA
40807768 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40807798 GAGAAAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40810246 original size:59 final size:59
Alignment explanation
Indices: 40810185--40810673 Score: 689
Period size: 59 Copynumber: 8.3 Consensus size: 59
40810175 TGGATACCCG
* * * * * *
40810185 GGGGGCAAAATGGTAATTTT-GGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
40810243 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAA-TTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * ** *
40810301 GAGGGTAAAATGGTAATTTTCAGTGAAATCGGGGTCAAAAACAGAATTTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* ** * *
40810360 GAGGGTAAAATGGTAATTTTCGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
*
40810419 GGGGATAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40810477 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40810536 GGGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
40810595 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
*
40810654 GGGGGTTAAAAT-ATAATTTT
1 GGGGG-TAAAATGGTAATTTT
40810674 GGAAAAGTTT
Statistics
Matches: 385, Mismatches: 42, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
58 123 0.32
59 256 0.66
60 6 0.02
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
Found at i:40810356 original size:117 final size:119
Alignment explanation
Indices: 40810191--40810673 Score: 683
Period size: 117 Copynumber: 4.1 Consensus size: 119
40810181 CCCGGGGGGC
* * * *
40810191 AAAATGGTAATTTT-GGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTCGGGGGTAAAATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATG
* * ** * *
40810255 GTAATTTTTGGTGAAATCGGGGTTAAAAATAGAA-TTTAGAAGCTTCGAGGG-T
66 GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGAT
* * ** *
40810307 AAAATGGTAATTTTCAGTGAAATCGGGGTCAAAAACAGAATTTTAAAAGATTCGAGGGTAAAATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATG
** * * * *
40810372 GTAATTTTCGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTTC-GGGGAT
66 GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGAT
40810425 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT-AAAGATTCGGGGGTAAAATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATG
40810489 GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGG-T
66 GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGAT
* * *
40810542 AAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATG
1 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATG
*
40810607 GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGTT
66 GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGAT
*
40810661 AAAAT-ATAATTTT
1 AAAATGGTAATTTT
40810674 GGAAAAGTTT
Statistics
Matches: 330, Mismatches: 31, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
116 14 0.04
117 177 0.54
118 133 0.40
119 6 0.02
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (119 bp):
AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATG
GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGAT
Found at i:40810446 original size:176 final size:176
Alignment explanation
Indices: 40810191--40810673 Score: 720
Period size: 176 Copynumber: 2.7 Consensus size: 176
40810181 CCCGGGGGGC
* * * * *
40810191 AAAATGGTAATTTTGGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTCGGGGGTAAAATGG
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGG
* * * *
40810256 TAATTTTTGGTGAAATCGGGGTTAAAAATAGAA-TTTAGAAGCTTCGAGGGTAAAATGGTAATTT
66 TAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTT
40810320 TCAGTGAAATCGGGGTCAAAAACAGAATTTTAAAAGATTCGAGGGT
131 TCAGTGAAATCGGGGTCAAAAACAGAATTTTAAAAGATTCGAGGGT
** * * *
40810366 AAAATGGTAATTTTCGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTTCGGGGATAAAATG
1 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATG
40810431 GTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAGATTCGGGGGTAAAATGGTAATT
65 GTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATT
* * * *
40810495 TTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGT
130 TTCAGTGAAATCGGGGTCAAAAACAGAATTTTAAAAGATTCGAGGGT
*
40810542 AAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATG
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATG
* * *
40810607 GTAATTTTCGGTGAAATCGGGGTCAAAAACGGAATTTTAGAAGATTCGGGGGTTAAAAT-ATAAT
65 GTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGG-TAAAATGGTAAT
40810671 TTT
129 TTT
40810674 GGAAAAGTTT
Statistics
Matches: 276, Mismatches: 27, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
175 14 0.05
176 229 0.83
177 27 0.10
178 6 0.02
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (176 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGG
TAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTT
TCAGTGAAATCGGGGTCAAAAACAGAATTTTAAAAGATTCGAGGGT
Found at i:40810655 original size:29 final size:28
Alignment explanation
Indices: 40810224--40810657 Score: 190
Period size: 29 Copynumber: 14.8 Consensus size: 28
40810214 GGGGTTGAAG
* *
40810224 ATGGAATCTTAAAAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTC-GGGGTAAAA
* ** *
40810252 ATGGTAATTTTTGGTGAAATCGGGGTTAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGG-TAAAA
* *
40810283 ATAGAA-TTTAGAAGCTTCGAGGGT-AAA
1 ATGGAATTTTAGAAGATTCG-GGGTAAAA
40810310 ATGGTAATTTTCAGTGAA-A-TCGGGGTCAAAA
1 ATGG-AATTTT-A--GAAGATTCGGGGT-AAAA
** *
40810341 ACAGAATTTTAAAAGATTCGAGGGT-AAA
1 ATGGAATTTTAGAAGATTCG-GGGTAAAA
* * *
40810369 ATGGTAATTTTCGGTGAA-ATTAGGGTTAAAA
1 ATGG-AATTTT---AGAAGATTCGGGGTAAAA
* *
40810400 ATGGAATTTTGGAAGTTTCGGGG-ATAAA
1 ATGGAATTTTAGAAGATTCGGGGTA-AAA
* ** *
40810428 ATGGTAATTTTCGGTGAAATCGGGGTTAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGG-TAAAA
40810459 ATGGAATTTTA-AAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTC-GGGGTAAAA
* ** *
40810486 ATGGTAATTTTCGGTGAAATCGGGGTCAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGGT-AAAA
*
40810517 ACGGAATTTTAGAAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTC-GGGGTAAAA
* * ** *
40810545 ATAGTAATTTTTGGTGAAATCGGGGTTAAAA
1 AT-GGAATTTTAGAAG-ATTCGGGG-TAAAA
40810576 ATGGAATTTTAGAAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTC-GGGGTAAAA
* ** *
40810604 ATGGTAATTTTCGGTGAAATCGGGGTCAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGGT-AAAA
*
40810635 ACGGAATTTTAGAAGATTCGGGG
1 ATGGAATTTTAGAAGATTCGGGG
40810658 GTTAAAATAT
Statistics
Matches: 299, Mismatches: 65, Indels: 83
0.67 0.15 0.19
Matches are distributed among these distances:
27 19 0.06
28 49 0.16
29 94 0.31
30 85 0.28
31 46 0.15
32 6 0.02
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (28 bp):
ATGGAATTTTAGAAGATTCGGGGTAAAA
Found at i:40810659 original size:30 final size:29
Alignment explanation
Indices: 40810224--40810665 Score: 205
Period size: 30 Copynumber: 15.1 Consensus size: 29
40810214 GGGGTTGAAG
* *
40810224 ATGGAATCTTAAAAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
* ** * *
40810252 ATGGTAATTTTTGGTGAAATCGGGGTTAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGGGTAAAA
* * *
40810283 ATAGAA-TTTAGAAGCTTCGAGGGT-AAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
40810310 ATGGTAATTTTCAGTGAA-A-TC-GGGGTCAAAA
1 ATGG-AATTTT-A--GAAGATTCGGGGGT-AAAA
** * *
40810341 ACAGAATTTTAAAAGATTCGAGGGT-AAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
* * *
40810369 ATGGTAATTTTCGGTGAA-ATT-AGGGTTAAAA
1 ATGG-AATTTT---AGAAGATTCGGGGGTAAAA
* * *
40810400 ATGGAATTTTGGAAGTTTCGGGGAT-AAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
* ** * *
40810428 ATGGTAATTTTCGGTGAAATCGGGGTTAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGGGTAAAA
40810459 ATGGAATTTTA-AAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
* ** *
40810486 ATGGTAATTTTCGGTGAAATC-GGGGTCAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGGGT-AAAA
*
40810517 ACGGAATTTTAGAAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
* * ** * *
40810545 ATAGTAATTTTTGGTGAAATCGGGGTTAAAA
1 AT-GGAATTTTAGAAG-ATTCGGGGGTAAAA
40810576 ATGGAATTTTAGAAGATTCGGGGGT-AAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
* ** *
40810604 ATGGTAATTTTCGGTGAAATC-GGGGTCAAAA
1 ATGG-AATTTTAGAAG-ATTCGGGGGT-AAAA
* *
40810635 ACGGAATTTTAGAAGATTCGGGGGTTAAA
1 ATGGAATTTTAGAAGATTCGGGGGTAAAA
40810664 AT
1 AT
40810666 ATAATTTTGG
Statistics
Matches: 300, Mismatches: 77, Indels: 73
0.67 0.17 0.16
Matches are distributed among these distances:
27 18 0.06
28 52 0.17
29 86 0.29
30 94 0.31
31 45 0.15
32 5 0.02
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (29 bp):
ATGGAATTTTAGAAGATTCGGGGGTAAAA
Found at i:40810671 original size:29 final size:29
Alignment explanation
Indices: 40810521--40810702 Score: 106
Period size: 30 Copynumber: 6.2 Consensus size: 29
40810511 TCAAAAACGG
40810521 AATTTTAGAAGATTCGGGGG-TAAAATAGT
1 AATTTTAGAAGATTCGGGGGTTAAAATA-T
* ** *
40810550 AATTTTTGGTGAAATC-GGGGTTAAAA-AT
1 AATTTTAGAAG-ATTCGGGGGTTAAAATAT
*
40810578 GGAATTTTAGAAGATTCGGGGG-TAAAATGGT
1 --AATTTTAGAAGATTCGGGGGTTAAAAT-AT
* ** * * *
40810609 AATTTTCGGTGAAATC-GGGGTCAAAA-ACGG
1 AATTTTAGAAG-ATTCGGGGGTTAAAATA--T
40810639 AATTTTAGAAGATTCGGGGGTTAAAATAT
1 AATTTTAGAAGATTCGGGGGTTAAAATAT
* * **
40810668 AATTTTGGAAAAGTTTTGGGGTTAAAATAT
1 AATTTTAGAAGA-TTCGGGGGTTAAAATAT
40810698 AATTT
1 AATTT
40810703 CTGGATTACT
Statistics
Matches: 113, Mismatches: 26, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
28 1 0.01
29 46 0.41
30 64 0.57
31 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
AATTTTAGAAGATTCGGGGGTTAAAATAT
Found at i:40811101 original size:161 final size:163
Alignment explanation
Indices: 40810796--40811113 Score: 518
Period size: 161 Copynumber: 2.0 Consensus size: 163
40810786 ACCCATTTGA
*
40810796 AAACCTTGAAAAATTTTAGGGCCAATTTTGTAATTAAATAATAGTTGATTTAAGGATTAAATTAA
1 AAACCTTGAAAAATTTTAGGGCCAATTTCGTAATTAAATAATAGTTGATTTAAGGATTAAATTAA
* *
40810861 AACAAATTAGAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGACACGTGGTAACCTC
66 AACAAATTAAAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACCTC
*
40810926 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
131 TGGTGCAATCAAACAGTCAAAGGACTAGTTTAT
*
40810959 AAACCTTGAAAAATTATT-GGGCCAATTTCGTAATTAAA-ACTAAGTTGATTT-AGGATTAAATT
1 AAACCTTGAAAAATT-TTAGGGCCAATTTCGTAATTAAATAAT-AGTTGATTTAAGGATTAAATT
* *
40811021 AAAACAAATTAAAAAT-AAAAGGACTAAATACAGAAATAATCCAAAAAGATGACACGTGGCAACC
64 AAAACAAATTAAAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACC
*
40811085 TTTGGTGCAATCAAACAGTCAAAGGACTA
129 TCTGGTGCAATCAAACAGTCAAAGGACTA
40811114 AAGTATAAAC
Statistics
Matches: 145, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
161 72 0.50
162 28 0.19
163 43 0.30
164 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (163 bp):
AAACCTTGAAAAATTTTAGGGCCAATTTCGTAATTAAATAATAGTTGATTTAAGGATTAAATTAA
AACAAATTAAAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACCTC
TGGTGCAATCAAACAGTCAAAGGACTAGTTTAT
Found at i:40811197 original size:161 final size:160
Alignment explanation
Indices: 40810847--40811197 Score: 415
Period size: 161 Copynumber: 2.2 Consensus size: 160
40810837 TAGTTGATTT
*
40810847 AAGGATTAAATTAAAACAAATTAGAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGA
1 AAGGATTAAATTAAAACAAATTAAAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGA
* * *** **
40810912 CACGTGGTAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATT
66 CACGTGGCAACCTCTGGTGCAATCAAACAGTCAAAGGACTAAAGTATAAACCTT-AAAAATTACA
* * * **
40810977 GGGCCAATTTCGTAATTAAAACTAAGTTGATT
130 GGGCAAATTTCATAATTAAAAC-AAGATGAAA
* * *
40811009 TAGGATTAAATTAAAACAAATTAAAAAT-AAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
1 AAGGATTAAATTAAAACAAATTAAAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGA
*
40811073 CACGTGGCAACCTTTGGTGCAATCAAACAGTCAAAGGACTAAAGTATAAACCAATT-AAAATTAC
66 CACGTGGCAACCTCTGGTGCAATCAAACAGTCAAAGGACTAAAGTATAAACC--TTAAAAATTAC
40811137 AGGGCAAATTTGCAAATAATT-AAA-AAGATGCAAA
129 AGGGCAAATTT-C--ATAATTAAAACAAGATG-AAA
* * *
40811171 AAGGACTAAATTGAAGCAAA-TAAAAAT
1 AAGGATTAAATTAAAACAAATTAAAAAT
40811198 GCGGGAGGAC
Statistics
Matches: 162, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
161 108 0.67
162 44 0.27
163 5 0.03
164 5 0.03
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.23
Consensus pattern (160 bp):
AAGGATTAAATTAAAACAAATTAAAAATAAAAAAGACTAAATACAGAAATAATCCAAAAACATGA
CACGTGGCAACCTCTGGTGCAATCAAACAGTCAAAGGACTAAAGTATAAACCTTAAAAATTACAG
GGCAAATTTCATAATTAAAACAAGATGAAA
Found at i:40811907 original size:10 final size:10
Alignment explanation
Indices: 40811891--40811937 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
40811881 CTTAAAAGAT
40811891 TTATTAATTA
1 TTATTAATTA
*
40811901 ATATTAATTA
1 TTATTAATTA
40811911 TTATTAATTA
1 TTATTAATTA
40811921 TTATT-ATTA
1 TTATTAATTA
*
40811930 TCATTAAT
1 TTATTAAT
40811938 GTCATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
TTATTAATTA
Found at i:40812398 original size:20 final size:20
Alignment explanation
Indices: 40812373--40812411 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40812363 AGCTGGTGGG
* *
40812373 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCGGGTGGCCAGCAGA
40812393 TGGAGCGGGTGGCCAGCAG
1 TGGAGCGGGTGGCCAGCAG
40812412 CAGTAGGCAC
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:0.18, C:0.18, G:0.49, T:0.15
Consensus pattern (20 bp):
TGGAGCGGGTGGCCAGCAGA
Found at i:40812474 original size:12 final size:12
Alignment explanation
Indices: 40812457--40812482 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40812447 TGGACTATTG
40812457 TAATTGGGCCCT
1 TAATTGGGCCCT
40812469 TAATTGGGCCCT
1 TAATTGGGCCCT
40812481 TA
1 TA
40812483 TAAATGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (12 bp):
TAATTGGGCCCT
Found at i:40812492 original size:14 final size:13
Alignment explanation
Indices: 40812457--40812506 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
40812447 TGGACTATTG
40812457 TAATTGGGCCC-T
1 TAATTGGGCCCTT
40812469 TAATTGGGCCCTT
1 TAATTGGGCCCTT
* *
40812482 ATAAATGGGCCATT
1 -TAATTGGGCCCTT
40812496 GTAATTGGGCC
1 -TAATTGGGCC
40812507 GTGGGCCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 11 0.34
13 1 0.03
14 20 0.62
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (13 bp):
TAATTGGGCCCTT
Found at i:40812565 original size:6 final size:6
Alignment explanation
Indices: 40812529--40812624 Score: 85
Period size: 6 Copynumber: 16.0 Consensus size: 6
40812519 CATTTGGACT
* *
40812529 TTTAAA TTTAATA TTTTAATA TTT-TA TTTAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA TTTAA-A -TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
40812578 TTTAGATA TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTA-A-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40812625 ATCAATTTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
4 4 0.05
5 12 0.16
6 41 0.55
7 6 0.08
8 12 0.16
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:40812591 original size:25 final size:23
Alignment explanation
Indices: 40812554--40812615 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 23
40812544 TTAATATTTT
*
40812554 ATTTAAATTTAAATTCAAATTAA
1 ATTTAAATTTAAATTCAAAATAA
*
40812577 ATTTAGATATTTAAATTTAAAATAA
1 ATTTA-A-ATTTAAATTCAAAATAA
40812602 ATTTAAATTTAAAT
1 ATTTAAATTTAAAT
40812616 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 13 0.37
24 2 0.06
25 20 0.57
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTTAAATTTAAATTCAAAATAA
Found at i:40812591 original size:31 final size:31
Alignment explanation
Indices: 40812553--40812634 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
40812543 TTTAATATTT
*
40812553 TATTTAAATTTAAATTCAAA-TTAAATTTAGA
1 TATTTAAATTTAAAAT-AAATTTAAATTTAGA
40812584 TATTTAAATTTAAAATAAATTTAAATTTA-A
1 TATTTAAATTTAAAATAAATTTAAATTTAGA
*
40812614 -A--TAAATTTAAAATCAATTTAA
1 TATTTAAATTTAAAATAAATTTAA
40812635 CTCAAAAGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
27 19 0.40
29 1 0.02
30 4 0.08
31 24 0.50
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATTTAAATTTAGA
Found at i:40812626 original size:17 final size:17
Alignment explanation
Indices: 40812554--40812624 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
40812544 TTAATATTTT
*
40812554 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
*
40812572 A-TTAAATTT-AGAT--
1 ATTTAAATTTAAAATAA
40812585 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
40812602 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
40812618 ATTTAAA
1 ATTTAAA
40812625 ATCAATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 3 0.07
16 15 0.33
17 18 0.39
18 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:40816249 original size:43 final size:43
Alignment explanation
Indices: 40816183--40816268 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
40816173 CATTAAAGTA
* *
40816183 GAAGTGGAAGTAACCTCGGAATATGATA-AGATTCTTGAATTGT
1 GAAGTGAAAGTAACCTCGAAATATGATAGA-ATTCTTGAATTGT
*
40816226 GAAGTGAAAGTAACCTCGAAATATGATAGAATTCTTGAGTTGT
1 GAAGTGAAAGTAACCTCGAAATATGATAGAATTCTTGAATTGT
40816269 CTTCACTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (43 bp):
GAAGTGAAAGTAACCTCGAAATATGATAGAATTCTTGAATTGT
Found at i:40816657 original size:27 final size:28
Alignment explanation
Indices: 40816614--40816682 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
40816604 AGCCGCCACA
* *
40816614 TGCCACGTCACCCCATG-CCACATCAGC
1 TGCCACGTCACCACATGTCCACATAAGC
* *
40816641 TGCCACGTCATCACATGTCCACGTAAGC
1 TGCCACGTCACCACATGTCCACATAAGC
40816669 -GCCACGTCAGCCAC
1 TGCCACGTCA-CCAC
40816683 GTGACCCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.23, C:0.43, G:0.17, T:0.16
Consensus pattern (28 bp):
TGCCACGTCACCACATGTCCACATAAGC
Found at i:40819579 original size:29 final size:29
Alignment explanation
Indices: 40819547--40819677 Score: 144
Period size: 29 Copynumber: 4.5 Consensus size: 29
40819537 GACAAGGAAA
40819547 AAAATGGTAATTTTAGAAAGTTCG-GTGGT
1 AAAATGGTAATTTTAGAAAGTTCGAG-GGT
* *
40819576 AAAATGGTAATTTTGGAAAGTTTTG-GGGT
1 AAAATGGTAATTTTAGAAAG-TTCGAGGGT
* *
40819605 AAAATGGTAAATTTTAGTAAA-ATCGAGGTT
1 AAAATGGT-AATTTTAG-AAAGTTCGAGGGT
*
40819635 AAAAATGG-AATTTTGGAAAGTTCGAGGGT
1 -AAAATGGTAATTTTAGAAAGTTCGAGGGT
40819664 AAAATGGTAATTTT
1 AAAATGGTAATTTT
40819678 TGGTAAAATT
Statistics
Matches: 86, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
28 10 0.12
29 52 0.60
30 14 0.16
31 10 0.12
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTAGAAAGTTCGAGGGT
Found at i:40819638 original size:59 final size:57
Alignment explanation
Indices: 40819575--40819913 Score: 208
Period size: 59 Copynumber: 5.8 Consensus size: 57
40819565 AGTTCGGTGG
* *
40819575 TAAAATGGTAATTTTGGAAAGTTTTGGGGTAAAATGGTAAATTTTAGTAAAATCGAGGT
1 TAAAATGG-AATTTTGGAAAGTTTAGGGGTAAAAT-GTAAATTTTAGTAAAATTGAGGT
* * * *
40819634 TAAAAATGGAATTTTGGAAAG-TTCGAGGGTAAAATGGTAATTTTTGGTAAAATTAAGGT
1 T-AAAATGGAATTTTGGAAAGTTTAG-GGGTAAAAT-GTAAATTTTAGTAAAATTGAGGT
* ** * * *
40819693 TAAAATGGAATTATGGAAAACTTGGGGGTAAAAATGT-AATTTTAG-AAAGTTTTGGGGT
1 TAAAATGGAATTTTGGAAAGTTTAGGGGT-AAAATGTAAATTTTAGTAAA--ATTGAGGT
** * * * *
40819751 TAAAATATAATTTTGGAAAAGTTTAGGGATTAAAATGTAATTTTTAG-AAAGTTTTGGGGT
1 TAAAATGGAATTTTGG-AAAGTTTAGGG-GTAAAATGTAAATTTTAGTAAA--ATTGAGGT
** ** *
40819811 TAAAATATAATTTTGGAAAAGTTTAGGATTCAAAATGT-AATTTTA--AAAAGTTTTAAGGT
1 TAAAATGGAATTTTGG-AAAGTTTAGGGGT-AAAATGTAAATTTTAGTAAAA---TTGAGGT
** * *
40819870 TAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATAT-AATTTT
1 TAAAATGGAATTTTGG-AAAGTTT-AGGGGTAAAATGTAAATTTT
40819914 CAAAAAGTTT
Statistics
Matches: 238, Mismatches: 28, Indels: 28
0.81 0.10 0.10
Matches are distributed among these distances:
56 3 0.01
57 6 0.03
58 47 0.20
59 115 0.48
60 67 0.28
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (57 bp):
TAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGTAAATTTTAGTAAAATTGAGGT
Found at i:40819704 original size:29 final size:30
Alignment explanation
Indices: 40819575--40819704 Score: 103
Period size: 29 Copynumber: 4.4 Consensus size: 30
40819565 AGTTCGGTGG
* *
40819575 TAAAATGGTAA-TTTTGG-AAAGTTTTG-GGG
1 TAAAATGGTAATTTTTGGTAAA--ATTGAGGT
* * *
40819604 TAAAATGGTAAATTTTAGTAAAATCGAGGT
1 TAAAATGGTAATTTTTGGTAAAATTGAGGT
* *
40819634 TAAAAATGG-AA-TTTTGG-AAAGTTCGAGGG
1 T-AAAATGGTAATTTTTGGTAAAATT-GAGGT
*
40819663 TAAAATGGTAATTTTTGGTAAAATTAAGGT
1 TAAAATGGTAATTTTTGGTAAAATTGAGGT
40819693 TAAAATGG-AATT
1 TAAAATGGTAATT
40819705 ATGGAAAACT
Statistics
Matches: 82, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
28 11 0.13
29 29 0.35
30 27 0.33
31 15 0.18
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGTAAAATTGAGGT
Found at i:40819740 original size:29 final size:29
Alignment explanation
Indices: 40819575--40819935 Score: 225
Period size: 30 Copynumber: 12.2 Consensus size: 29
40819565 AGTTCGGTGG
*
40819575 TAAAATGGTAATTTTGGAAAGTTTTGGGG-
1 TAAAAT-GTAATTTTGGAAAATTTTGGGGT
* * *
40819604 TAAAATGGTAAATTTTAGTAAAA--TCGAGGT
1 TAAAAT-GT-AATTTT-GGAAAATTTTGGGGT
* * *
40819634 TAAAAATGGAATTTTGG-AAAGTTCGAGGG-
1 T-AAAATGTAATTTTGGAAAATTTTG-GGGT
**
40819663 TAAAATGGTAATTTTTGGTAAAA--TTAAGGT
1 TAAAAT-GTAA-TTTTGG-AAAATTTTGGGGT
* * * *
40819693 TAAAATGGAATTATGGAAAACTTGGGGGT
1 TAAAATGTAATTTTGGAAAATTTTGGGGT
* * *
40819722 AAAAATGTAATTTTAGAAAGTTTTGGGGT
1 TAAAATGTAATTTTGGAAAATTTTGGGGT
* * *
40819751 TAAAATATAATTTTGGAAAAGTTTAGGGAT
1 TAAAATGTAATTTTGGAAAA-TTTTGGGGT
* *
40819781 TAAAATGTAATTTTTAGAAAGTTTTGGGGT
1 TAAAATGTAA-TTTTGGAAAATTTTGGGGT
* * * *
40819811 TAAAATATAATTTTGGAAAAGTTTAGGAT
1 TAAAATGTAATTTTGGAAAATTTTGGGGT
* **
40819840 TCAAAATGTAATTTT-AAAAAGTTTTAAGGT
1 T-AAAATGTAATTTTGGAAAA-TTTTGGGGT
* **
40819870 TAAAATATAATTTTGGAAAAGTTTAAGGGT
1 TAAAATGTAATTTTGGAAAA-TTTTGGGGT
* **
40819900 TAAAATATAATTTTCAAAAAGTTTTGGGGT
1 TAAAATGTAATTTTGGAAAA-TTTTGGGGT
40819930 TAAAAT
1 TAAAAT
40819936 ATACTTTTTT
Statistics
Matches: 260, Mismatches: 53, Indels: 37
0.74 0.15 0.11
Matches are distributed among these distances:
27 7 0.03
28 11 0.04
29 104 0.40
30 118 0.45
31 17 0.07
32 3 0.01
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (29 bp):
TAAAATGTAATTTTGGAAAATTTTGGGGT
Found at i:40819755 original size:30 final size:29
Alignment explanation
Indices: 40819717--40819943 Score: 231
Period size: 30 Copynumber: 7.7 Consensus size: 29
40819707 GGAAAACTTG
* *
40819717 GGGGTAAAAATGTAATTTTAGAAAGTTTT
1 GGGGTTAAAATATAATTTTAGAAAGTTTT
* *
40819746 GGGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAG-AAAGTTTT
* *
40819776 GGGATTAAAATGTAATTTTTAGAAAGTTTT
1 GGGGTTAAAATATAA-TTTTAGAAAGTTTT
*
40819806 GGGGTTAAAATATAATTTTGGAAAAG-TTT
1 GGGGTTAAAATATAATTTTAG-AAAGTTTT
* * * *
40819835 AGGATTCAAAATGTAATTTTAAAAAGTTTT
1 GGGGTT-AAAATATAATTTTAGAAAGTTTT
** * *
40819865 AAGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAG-AAAGTTTT
* *
40819895 AGGGTTAAAATATAATTTTCAAAAAGTTTT
1 GGGGTTAAAATATAATTTT-AGAAAGTTTT
*
40819925 GGGGTTAAAATATACTTTT
1 GGGGTTAAAATATAATTTT
40819944 TTAGATAGTT
Statistics
Matches: 163, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
29 46 0.28
30 112 0.69
31 5 0.03
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.39
Consensus pattern (29 bp):
GGGGTTAAAATATAATTTTAGAAAGTTTT
Found at i:40819802 original size:60 final size:59
Alignment explanation
Indices: 40819723--40819943 Score: 338
Period size: 60 Copynumber: 3.7 Consensus size: 59
40819713 CTTGGGGGTA
*
40819723 AAAATGTAATTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGGATT
1 AAAATGTAATTTTAAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGGATT
*
40819782 AAAATGTAATTTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTA-GGATT
1 AAAATGTAA-TTTTAAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGGATT
**
40819841 CAAAATGTAATTTTAAAAAGTTTTAAGGTTAAAATATAATTTTGGAAAAGTTTAAGGG-TT
1 -AAAATGTAATTTTAAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTT-AGGGATT
* *
40819901 AAAATATAATTTTCAAAAAGTTTTGGGGTTAAAATATACTTTT
1 AAAATGTAATTTT-AAAAAGTTTTGGGGTTAAAATATAATTTT
40819944 TTAGATAGTT
Statistics
Matches: 150, Mismatches: 7, Indels: 9
0.90 0.04 0.05
Matches are distributed among these distances:
59 66 0.44
60 82 0.55
61 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.40
Consensus pattern (59 bp):
AAAATGTAATTTTAAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGGATT
Found at i:40819871 original size:119 final size:119
Alignment explanation
Indices: 40819723--40819943 Score: 363
Period size: 119 Copynumber: 1.9 Consensus size: 119
40819713 CTTGGGGGTA
* **
40819723 AAAATGTAATTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTT-AGGGATTAAAAT
1 AAAATGTAATTTTAAAAAGTTTTAAGGTTAAAATATAATTTTGGAAAAGTTTAAGGG-TTAAAAT
* * *
40819787 GTAATTTTTAGAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGATTC
65 ATAATTTTCAAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGATTC
40819842 AAAATGTAATTTTAAAAAGTTTTAAGGTTAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATA
1 AAAATGTAATTTTAAAAAGTTTTAAGGTTAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATA
*
40819907 TAATTTTCAAAAAGTTTTGGGGTTAAAATATACTTTT
66 TAATTTTCAAAAAGTTTTGGGGTTAAAATATAATTTT
40819944 TTAGATAGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
119 90 0.96
120 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.40
Consensus pattern (119 bp):
AAAATGTAATTTTAAAAAGTTTTAAGGTTAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATA
TAATTTTCAAAAAGTTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGATTC
Found at i:40822550 original size:50 final size:49
Alignment explanation
Indices: 40822491--40823235 Score: 365
Period size: 50 Copynumber: 14.9 Consensus size: 49
40822481 CTTTTGTATC
* * * * *
40822491 TTTGTGGTACTAGATCTGCCATTGCGGTATTAGATCTTCCCCTTCATGCT
1 TTTGAGGTACTAGATCTGCCGTTGC-GTATTAGATCTTTCCCTTCGTGTT
* * *
40822541 TCTGAGGTAC-ACGATCCGCCGTTGCG-ACTTAGACCTTTCCCTTTCGTGTT
1 TTTGAGGTACTA-GATCTGCCGTTGCGTA-TTAGATCTTTCCC-TTCGTGTT
* * * * *
40822591 TTGGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTTCATGTT
1 TTTGAGGTACTAGATCTGCCGTTGC-GTATTAGATCTTTCCC-TTCGTGTT
* * * *
40822642 TTTGAGGTAC-ATGATCCGCCGTTGCG-ACTTAAACCTTTCCCTGTTGTGTTT
1 TTTGAGGTACTA-GATCTGCCGTTGCGTA-TTAGATCTTTCCCT-TCGTG-TT
* * * * * * * *
40822693 TTTGCGGTACTGGATCTGCCATTACGGTCTTAGATATTTCCCTTCATGCT
1 TTTGAGGTACTAGATCTGCCGTTGC-GTATTAGATCTTTCCCTTCGTGTT
* * * * * *
40822743 TCTGAGGTAC-ACGGTCCGCCGTTGTG-ACTTAGACCTTTCCCTATTGTGTT
1 TTTGAGGTACTA-GATCTGCCGTTGCGTA-TTAGATCTTTCCCT-TCGTGTT
* * * * * *
40822793 TTTGCGGTACTGGATCTACCGTTGCGTCTTAGATCTTTCCCTTCATGCT
1 TTTGAGGTACTAGATCTGCCGTTGCGTATTAGATCTTTCCCTTCGTGTT
* * * * * *
40822842 TCTGAGGTAC-ACGGTCCGCCGTTGTG-ACTTAGACCTTTCCCTGTTGTGTT
1 TTTGAGGTACTA-GATCTGCCGTTGCGTA-TTAGATCTTTCCCT-TCGTGTT
* * * * * *
40822892 TTTGCGGTACTGGATCTGCCGTTGCATCTTAGATCTTTCCCTTCATGCT
1 TTTGAGGTACTAGATCTGCCGTTGCGTATTAGATCTTTCCCTTCGTGTT
* * * * *
40822941 TCTGAGGTAC-ACGGTCCGCCGTTGCG-ACTTAGACCTTTCCCTATTGTGTT
1 TTTGAGGTACTA-GATCTGCCGTTGCGTA-TTAGATCTTTCCCT-TCGTGTT
* * * * *
40822991 TTT-ACGGTACT-GAATCTACCATTGCGGTCTTAGATCTTTCTCTTTCATGTT
1 TTTGA-GGTACTAG-ATCTGCCGTTGC-GTATTAGATCTTTC-CCTTCGTGTT
* * * * * *
40823042 TCTGAGGTAC-ACGGTCTGCCATTGTG-ACTTAGACCTTTCCCTTTTGTGTT
1 TTTGAGGTACTA-GATCTGCCGTTGCGTA-TTAGATCTTTCCC-TTCGTGTT
* * * *
40823092 TTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTTGTGCT
1 TTTGAGGTACTAGATCTGCCGTTGC-GTATTAGATCTTTCCCTTCGTGTT
* * * * *
40823142 TCTGAGGTAC-ACGGT-TCGCCGTTGTG-ACTTAGACCTTTCCCTATTGTGTT
1 TTTGAGGTACTA-GATCT-GCCGTTGCGTA-TTAGATCTTTCCCT-TCGTGTT
* * *
40823192 TTTGCGGTACT-GAATCTGCCATTGCAGTCTTAGATCTTTCCCTT
1 TTTGAGGTACTAG-ATCTGCCGTTGC-GTATTAGATCTTTCCCTT
40823236 TCATGTTTCA
Statistics
Matches: 507, Mismatches: 139, Indels: 98
0.68 0.19 0.13
Matches are distributed among these distances:
48 1 0.00
49 118 0.23
50 246 0.49
51 126 0.25
52 16 0.03
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (49 bp):
TTTGAGGTACTAGATCTGCCGTTGCGTATTAGATCTTTCCCTTCGTGTT
Found at i:40822681 original size:101 final size:101
Alignment explanation
Indices: 40822460--40823240 Score: 1110
Period size: 101 Copynumber: 7.8 Consensus size: 101
40822450 TCGGGTTCGT
* * * * * * *
40822460 CGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCTGCCATTGCGGTATTAGA
1 CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
* *
40822525 TC-TTCCCCTTCATGCTTCTGAGGTACACGATCCGC
66 TCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
* *
40822560 CGTTGCGACTTAGACCTTTCCCT-TTCGTGTTTTGGCGGTACTGGATCTGCCGTTGCGGTCTTAG
1 CGTTGCGACTTAGACCTTTCCCTATT-GTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAG
* * * *
40822624 ATCTTTCCCTTTCATGTTTTTGAGGTACATGATCCGC
65 ATCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
* * *
40822661 CGTTGCGACTTAAACCTTTCCCTGTTGTGTTTTTTGCGGTACTGGATCTGCCATTACGGTCTTAG
1 CGTTGCGACTTAGACCTTTCCCTATTGTG-TTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAG
*
40822726 ATATTTCCC-TTCATGCTTCTGAGGTACACGGTCCGC
65 ATCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
* * *
40822762 CGTTGTGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTACCGTTGC-GTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
40822826 TCTTTCCC-TTCATGCTTCTGAGGTACACGGTCCGC
66 TCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
* * * *
40822861 CGTTGTGACTTAGACCTTTCCCTGTTGTGTTTTTGCGGTACTGGATCTGCCGTTGC-ATCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
40822925 TCTTTCCC-TTCATGCTTCTGAGGTACACGGTCCGC
66 TCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
* * *
40822960 CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTACGGTACTGAATCTACCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
* * *
40823025 TCTTTCTCTTTCATGTTTCTGAGGTACACGGTCTGC
66 TCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
* * * * *
40823061 CATTGTGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
* *
40823126 TCTTTCCCTTT-GTGCTTCTGAGGTACACGGTTCGC
66 TCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
* * *
40823161 CGTTGTGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGAATCTGCCATTGCAGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
40823226 TCTTTCCCTTTCATG
66 TCTTTCCCTTTCATG
40823241 TTTCATGATA
Statistics
Matches: 613, Mismatches: 61, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
99 190 0.31
100 184 0.30
101 197 0.32
102 42 0.07
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (101 bp):
CGTTGCGACTTAGACCTTTCCCTATTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
TCTTTCCCTTTCATGCTTCTGAGGTACACGGTCCGC
Found at i:40832859 original size:58 final size:58
Alignment explanation
Indices: 40832791--40832923 Score: 169
Period size: 59 Copynumber: 2.3 Consensus size: 58
40832781 ACCCGAGGCC
* * * * *
40832791 AAAATAGTAATTTTGGTTAAAAT-TGGATCAAAAATGAGATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGG-TAAAATCGGGATCAAAAATGAAATTTTAGAAAGTTCGAGGGT
* * *
40832849 AAAATGGTAATTTTTGGTAAAATCGGGGTGAAAGATGAAATTTTAGAAAGTTCGAGGGT
1 AAAATGGTAA-TTTTGGTAAAATCGGGATCAAAAATGAAATTTTAGAAAGTTCGAGGGT
40832908 AAAATGGTAATTTTGG
1 AAAATGGTAATTTTGG
40832924 AAAGTTCGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
58 21 0.32
59 44 0.68
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTAAAATCGGGATCAAAAATGAAATTTTAGAAAGTTCGAGGGT
Found at i:40832861 original size:29 final size:29
Alignment explanation
Indices: 40832821--40833224 Score: 197
Period size: 30 Copynumber: 13.8 Consensus size: 29
40832811 AATTGGATCA
40832821 AAAATG-AGATTTTGGAAAGTTTGAGGGT-
1 AAAATGTA-ATTTTGGAAAGTTTGAGGGTC
* * *
40832849 AAAATGGTAATTTTTGGTAAA-ATCG-GGGTG
1 AAAAT-GTAA-TTTTGG-AAAGTTTGAGGGTC
* * *
40832879 AAAGATGAAATTTTAGAAAGTTCGAGGGT-
1 AAA-ATGTAATTTTGGAAAGTTTGAGGGTC
*
40832908 AAAATGGTAATTTTGGAAAGTTCG-GGGT-
1 AAAAT-GTAATTTTGGAAAGTTTGAGGGTC
* *
40832936 AAAATGGTAATTTTCGGTAAA-ATTGA-GGTA
1 AAAAT-GTAATTTT-GG-AAAGTTTGAGGGTC
* * * *
40832966 AAAATGGAATTATGGAAAACTTTG-GGGTG
1 AAAATGTAATTTTGG-AAAGTTTGAGGGTC
** *
40832995 AAAATGTAATTTTAAAAAGTTTTGA-GGTT
1 AAAATGTAATTTTGGAAAG-TTTGAGGGTC
* **
40833024 AAAATATAATTTTAAAAAAGTTT-AGGGGTC
1 AAAATGTAATTTT-GGAAAGTTTGA-GGGTC
** * * *
40833054 AAAATGTAATTTTCAAAAAGTTTTAGGTTT
1 AAAATGTAATTTT-GGAAAGTTTGAGGGTC
* *
40833084 AAAATATAATTTTGGAAAAGTTTG-GGATTC
1 AAAATGTAATTTTGG-AAAGTTTGAGG-GTC
** * *
40833114 AAAATGTAATTTTAAAAAGTTTTAGGGTT
1 AAAATGTAATTTTGGAAAGTTTGAGGGTC
* *
40833143 AAAATATAA-TTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGG-AAAGTTTGAGGGTC
* * * *
40833172 AAAATGTAATTTTTAGAAAGTTTTAGAGTT
1 AAAATGTAA-TTTTGGAAAGTTTGAGGGTC
* *
40833202 AAAATATAATTTTTGGATAGTTT
1 AAAATGTAA-TTTTGGAAAGTTT
40833225 AAGGCCTTCT
Statistics
Matches: 299, Mismatches: 50, Indels: 52
0.75 0.12 0.13
Matches are distributed among these distances:
28 40 0.13
29 123 0.41
30 126 0.42
31 10 0.03
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTTGAGGGTC
Found at i:40833058 original size:59 final size:57
Alignment explanation
Indices: 40832873--40833214 Score: 325
Period size: 58 Copynumber: 5.8 Consensus size: 57
40832863 TGGTAAAATC
* * * ** * * *
40832873 GGGGTGAAAGATGAAATTTTAGAAAGTTCGAGGGTAAAATGGTAATTTTGG-AAAGTTC
1 GGGGTCAAA-ATGTAATTTTAAAAAGTTTTAGGTTAAAAT-ATAATTTTGGAAAAGTTT
* * * ** * *
40832931 GGGGT-AAAATGGTAATTTTCGGTAAAA--TTGAGGTAAAAATGGAATTATGGAAAACTTT
1 GGGGTCAAAAT-GTAATTTT---AAAAAGTTTTAGGTTAAAATATAATTTTGGAAAAGTTT
* **
40832989 GGGGTGAAAATGTAATTTTAAAAAGTTTTGAGGTTAAAATATAATTTTAAAAAAGTTT
1 GGGGTCAAAATGTAATTTTAAAAAGTTTT-AGGTTAAAATATAATTTTGGAAAAGTTT
40833047 AGGGGTCAAAATGTAATTTTCAAAAAGTTTTAGGTTTAAAATATAATTTTGGAAAAGTTT
1 -GGGGTCAAAATGTAATTTT-AAAAAGTTTTAGG-TTAAAATATAATTTTGGAAAAGTTT
*
40833107 GGGATTCAAAATGTAATTTTAAAAAGTTTTAGGGTTAAAATATAA-TTTGGAAAAGTTT
1 GGG-GTCAAAATGTAATTTTAAAAAGTTTTA-GGTTAAAATATAATTTTGGAAAAGTTT
* *
40833165 AAGGGTCAAAATGTAATTTTTAGAAAGTTTTAGAGTTAAAATATAATTTT
1 -GGGGTCAAAATGTAA-TTTTAAAAAGTTTTAG-GTTAAAATATAATTTT
40833215 TGGATAGTTT
Statistics
Matches: 240, Mismatches: 26, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
55 4 0.02
56 2 0.01
57 20 0.08
58 79 0.33
59 79 0.33
60 56 0.23
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (57 bp):
GGGGTCAAAATGTAATTTTAAAAAGTTTTAGGTTAAAATATAATTTTGGAAAAGTTT
Found at i:40833970 original size:15 final size:15
Alignment explanation
Indices: 40833947--40833981 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40833937 CTTTTAAATC
*
40833947 AAAACCCAGATCTGG
1 AAAATCCAGATCTGG
40833962 AAAATCCAGATCTGG
1 AAAATCCAGATCTGG
40833977 AAAAT
1 AAAAT
40833982 TTTCCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (15 bp):
AAAATCCAGATCTGG
Found at i:40835035 original size:15 final size:15
Alignment explanation
Indices: 40835012--40835041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40835002 TTGATTAAAT
*
40835012 TAAATTTAAATTTAA
1 TAAACTTAAATTTAA
40835027 TAAACTTAAATTTAA
1 TAAACTTAAATTTAA
40835042 AATAGATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAACTTAAATTTAA
Found at i:40835045 original size:17 final size:17
Alignment explanation
Indices: 40835006--40835070 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
40834996 TGGACATTGA
*
40835006 TTAAATTAAATTTAAAT
1 TTAAAATAAATTTAAAT
*
40835023 TT--AATAAACTTAAAT
1 TTAAAATAAATTTAAAT
* *
40835038 TTAAAATAGATTTAAAA
1 TTAAAATAAATTTAAAT
40835055 TTAAAATAAATTTAAA
1 TTAAAATAAATTTAAA
40835071 ATGGTTTGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.32
17 27 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAAATAAATTTAAAT
Found at i:40839175 original size:91 final size:91
Alignment explanation
Indices: 40839020--40839201 Score: 292
Period size: 91 Copynumber: 2.0 Consensus size: 91
40839010 AAACGAAGTG
* * * * *
40839020 TCAAATTGCAGCAAACACTTAAACCATAATTCATCTATCAAACAATTGCATCGTAACTCAAACTA
1 TCAAATTGCAACAAACACTTAAACCATAATCCACCTATCAAACAACTGCATCGTAACCCAAACTA
40839085 ACAACACCTAATAAAAAAACTCACTA
66 ACAACACCTAATAAAAAAACTCACTA
* *
40839111 TCAAATTGCAACAAACACTTAAATCATAATCCACCTATCAAACAACTGCATCTTAACCCAAACTA
1 TCAAATTGCAACAAACACTTAAACCATAATCCACCTATCAAACAACTGCATCGTAACCCAAACTA
*
40839176 ACAACACCTAATAAAAAATCTCACTA
66 ACAACACCTAATAAAAAAACTCACTA
40839202 CCAAGCTATT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (91 bp):
TCAAATTGCAACAAACACTTAAACCATAATCCACCTATCAAACAACTGCATCGTAACCCAAACTA
ACAACACCTAATAAAAAAACTCACTA
Found at i:40840410 original size:144 final size:144
Alignment explanation
Indices: 40840150--40840436 Score: 495
Period size: 144 Copynumber: 2.0 Consensus size: 144
40840140 TTTATAGCTT
* ** *
40840150 GTAAATTAACATCTCTGTCAATTTTTTATGACACTTTTGATTTTACGTGTGGTTTTAAATGTACA
1 GTAAATTAACATCTCTATCAATTTTTTATGACACTTTTGATTTTACGTGTACTTTTAAATCTACA
*
40840215 AATAATTAAATTATTTGTATAGTTGGCATTCAACTGTTATATTGAATTAAGGATGAAAATCTATT
66 AATAATTAAATTATTTGTATAGTTGGCATTCAACTGTTATATTGAATTAAGGATGAAAACCTATT
40840280 TAATTACCTATAAG
131 TAATTACCTATAAG
40840294 GTAAATTAACATCTCTATCAATTTTTTATGACACTTTTGATTTTACGTGTACTTTTAAATCTACA
1 GTAAATTAACATCTCTATCAATTTTTTATGACACTTTTGATTTTACGTGTACTTTTAAATCTACA
*
40840359 AATAATTAAATTATTTGTATCGTTGGCATTCAACTGTTATATT-ATATTAAGGATGAAAACCTAT
66 AATAATTAAATTATTTGTATAGTTGGCATTCAACTGTTATATTGA-ATTAAGGATGAAAACCTAT
*
40840423 TTAATTACTTATAA
130 TTAATTACCTATAA
40840437 ATAAGAATGC
Statistics
Matches: 135, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
143 1 0.01
144 134 0.99
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (144 bp):
GTAAATTAACATCTCTATCAATTTTTTATGACACTTTTGATTTTACGTGTACTTTTAAATCTACA
AATAATTAAATTATTTGTATAGTTGGCATTCAACTGTTATATTGAATTAAGGATGAAAACCTATT
TAATTACCTATAAG
Found at i:40841157 original size:3 final size:3
Alignment explanation
Indices: 40841149--40841197 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
40841139 AATGAGAAAT
40841149 TAA TAA 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 TAA TAA
40841197 T
1 T
40841198 CGGTTTTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40843487 original size:59 final size:59
Alignment explanation
Indices: 40843302--40843558 Score: 335
Period size: 59 Copynumber: 4.4 Consensus size: 59
40843292 TGTGGATACC
* * * * * *
40843302 CGGGGGCAAAATGGTGA-TTTTAGTGAAATCGGGGTTAAAAATGAAATTTTAAAAGATA
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
40843360 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTA-AAGGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAA-GATT
* * *
40843418 CGAGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* *
40843477 CGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGA-TTTAGGGAAG-TT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA--GAAGATT
**
40843536 TAGGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
40843559 AAAGTTTTGG
Statistics
Matches: 178, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
57 2 0.01
58 69 0.39
59 101 0.57
60 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
Found at i:40843751 original size:30 final size:30
Alignment explanation
Indices: 40843531--40843735 Score: 333
Period size: 30 Copynumber: 6.9 Consensus size: 30
40843521 GGATTTAGGG
* *
40843531 AAGTTTAGGGGT-AAAATGGTAATTTTTG-A
1 AAGTTTCGGGGTCAAAAT-GTAATTTTGGAA
*
40843560 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
40843590 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
40843620 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
*
40843650 AAGTTTCGAGGTCAAAATGTAATTTTGGAA
1 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
*
40843680 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTCGGGGTCAAAATGTAATTTTGGAA
*
40843710 AAGTTTCGGGGTCAAAATATAATTTT
1 AAGTTTCGGGGTCAAAATGTAATTTT
40843736 TGGACAATTT
Statistics
Matches: 166, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
29 20 0.12
30 146 0.88
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
AAGTTTCGGGGTCAAAATGTAATTTTGGAA
Found at i:40844018 original size:162 final size:161
Alignment explanation
Indices: 40843812--40844152 Score: 425
Period size: 161 Copynumber: 2.1 Consensus size: 161
40843802 CATCCAGAGG
* * *
40843812 TCAAGGGACTAATTTGA-AAACCTTGAAAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTTA
1 TCAAAGGACTAATTT-ATAAACCTTGAAAAATTTTAGGACCAATTTCGTAATTAAATAAAAGTTA
* *** * *
40843876 ATTTAAGGACTAAATTAAAATAAATTAAAAATGTCAGGGACTAAATGCATAAATAAGTCAAAAAG
65 ATTTAAGGACTAAATTAAAACAAATT-AAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAG
* * *
40843941 TGACACGTGGCAGTCTCTGGTGCAGCCACACAA
129 TGACACGTGGCAGCCTCTGGTACAGCCAAACAA
** *
40843974 TCAAAGGACTAATTTATAAATTTTGAAAAATTATTAGG-CCAATTTCGTAATTAAATAAAAGTTG
1 TCAAAGGACTAATTTATAAACCTTGAAAAATT-TTAGGACCAATTTCGTAATTAAATAAAAGTTA
** * *
40844038 ATTTGGGGATTAAATTAAAACAAATTAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAATT
65 ATTTAAGGACTAAATTAAAACAAATTAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGT
** * *
40844103 GACACGTGGTTGCCTCTGGTACAGTCAAACAG
130 GACACGTGGCAGCCTCTGGTACAGCCAAACAA
*
40844135 TCAAAGGACTAAATTATA
1 TCAAAGGACTAATTTATA
40844153 GACCAATTAA
Statistics
Matches: 153, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
161 76 0.50
162 73 0.48
163 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (161 bp):
TCAAAGGACTAATTTATAAACCTTGAAAAATTTTAGGACCAATTTCGTAATTAAATAAAAGTTAA
TTTAAGGACTAAATTAAAACAAATTAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTG
ACACGTGGCAGCCTCTGGTACAGCCAAACAA
Found at i:40844792 original size:15 final size:15
Alignment explanation
Indices: 40844759--40844789 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
40844749 TTGGTTTTTC
40844759 GAAACCCAGATCTGG
1 GAAACCCAGATCTGG
40844774 GAAAGCCCAGATCTGG
1 GAAA-CCCAGATCTGG
40844790 AAATATTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.26, G:0.29, T:0.13
Consensus pattern (15 bp):
GAAACCCAGATCTGG
Found at i:40845757 original size:6 final size:6
Alignment explanation
Indices: 40845738--40845816 Score: 92
Period size: 6 Copynumber: 13.2 Consensus size: 6
40845728 ATGTTTAGTG
* *
40845738 TTTAAA TTTTAA TTTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
40845787 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA T
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
40845817 CAATTTAACT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 48 0.76
7 1 0.02
8 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:40845772 original size:11 final size:11
Alignment explanation
Indices: 40845748--40845809 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
40845738 TTTAAATTTT
*
40845748 AATTTAAATTTA
1 AATTTAAA-GTA
40845760 AATTTAAAGTA
1 AATTTAAAGTA
40845771 AATTTAAA-T-
1 AATTTAAAGTA
*
40845780 AA-TTAAATTTA
1 AATTTAAA-GTA
40845791 AATTT-AAGATA
1 AATTTAAAG-TA
40845802 AATTTAAA
1 AATTTAAA
40845810 TTTAAATCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 2 0.05
11 21 0.50
12 12 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
AATTTAAAGTA
Found at i:40845772 original size:17 final size:17
Alignment explanation
Indices: 40845738--40845824 Score: 85
Period size: 17 Copynumber: 5.3 Consensus size: 17
40845728 ATGTTTAGTG
**
40845738 TTTAAATTTTAATTTAAA
1 TTTAAA-TTTAAAGTAAA
40845756 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAAGTAAA
*
40845773 TTTAAA--T-AATTAAA
1 TTTAAATTTAAAGTAAA
40845787 TTTAAATTT-AAGATAAA
1 TTTAAATTTAAAG-TAAA
*
40845804 TTTAAATTTAAA-TCAA
1 TTTAAATTTAAAGTAAA
40845820 TTTAA
1 TTTAA
40845825 CTCCAAATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
14 12 0.20
15 1 0.02
16 11 0.18
17 28 0.47
18 8 0.13
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAGTAAA
Found at i:40845788 original size:31 final size:31
Alignment explanation
Indices: 40845751--40845810 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
40845741 AAATTTTAAT
40845751 TTAAATTTAAATTTAA-AGTAAATTTAAATAA
1 TTAAATTTAAATTTAAGA-TAAATTTAAATAA
40845782 TTAAATTTAAATTTAAGATAAATTTAAAT
1 TTAAATTTAAATTTAAGATAAATTTAAAT
40845811 TTAAATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
TTAAATTTAAATTTAAGATAAATTTAAATAA
Found at i:40845810 original size:37 final size:37
Alignment explanation
Indices: 40845748--40845821 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
40845738 TTTAAATTTT
40845748 AATTTAAATTTAAATTTAAAGTAAATTTAAAT-AATTA
1 AATTTAAATTTAAA-TTAAAGTAAATTTAAATCAATTA
*
40845785 AATTTAAATTTAAGA-TAAATTTAAATTTAAATCAATT
1 AATTTAAATTTAA-ATTAAA-GTAAATTTAAATCAATT
40845822 TAACTCCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 24 0.73
38 5 0.15
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (37 bp):
AATTTAAATTTAAATTAAAGTAAATTTAAATCAATTA
Found at i:40846218 original size:38 final size:37
Alignment explanation
Indices: 40846176--40846749 Score: 105
Period size: 31 Copynumber: 16.5 Consensus size: 37
40846166 ATCTTGCCCT
40846176 TACTTCAATTTCAGAGATGAAGGTGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAAGG-GTGTTATCCAACTC
* ** **
40846214 TACTTCAATTTCA-AG--G--GGATGACAT--TGCTC
1 TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
* *
40846244 TTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTC
1 -TACTTCAATTTCAGAGATGAAG-GGTGTTATCCAACTC
* * ** * *
40846283 TACTTCAATTTCA-AGA-GGATGACG-T-TGC-TCT-
1 TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
* ** *
40846314 TACTTCAATTTCAGAGATAAAGACTTGATATCCAACTC
1 TACTTCAATTTCAGAGATGAAG-GGTGTTATCCAACTC
* ** **
40846352 TACTTCAATTTCA-AG--G--GGATGACAT--TGCTC
1 TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
* * * * *
40846382 TTACTTCAATTTCA-AGA-GGATGATG-T-TGC-TCT-
1 -TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
** *
40846414 TACTTCAATTTCAGAGATGAAGACTTGATATCCAACTC
1 TACTTCAATTTCAGAGATGAAG-GGTGTTATCCAACTC
* * ** * *
40846452 TACTTCAATTTCA-AGA-GGATGACG-T-TGC-TCT-
1 TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
* * * *
40846483 TACTTCGATTTCAGAGATAAAGACGTGATATCCAACTC
1 TACTTCAATTTCAGAGATGAAG-GGTGTTATCCAACTC
* * * ** *
40846521 TACTTCGATTTCA-AGA-GGATGACGTTA--C-TCT-
1 TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
* *
40846552 TACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAAG-GGTGTTATCCAACTC
* * ** * *
40846590 TACTTCAATTTCA-AGA-GGATGACG-T-TGC-TCT-
1 TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
* * *
40846621 TACTTCAATTTCAGAGATAAAGACGTGATATCCAACTC
1 TACTTCAATTTCAGAGATGAAG-GGTGTTATCCAACTC
* * ** * *
40846659 TACTTCAATTTCA-AGA-GGATGACG-T-TGC-TCT-
1 TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
* *
40846690 TACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAAG-GGTGTTATCCAACTC
40846728 TACTTCAATTTCAAGAGGATGA
1 TACTTCAATTTC-AGA-GATGA
40846750 CGTTGCTCTT
Statistics
Matches: 374, Mismatches: 103, Indels: 116
0.63 0.17 0.20
Matches are distributed among these distances:
30 6 0.02
31 104 0.28
32 41 0.11
33 23 0.06
34 19 0.05
35 13 0.03
36 20 0.05
37 35 0.09
38 103 0.28
39 6 0.02
40 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (37 bp):
TACTTCAATTTCAGAGATGAAGGGTGTTATCCAACTC
Found at i:40846285 original size:69 final size:69
Alignment explanation
Indices: 40846169--40846404 Score: 373
Period size: 69 Copynumber: 3.4 Consensus size: 69
40846159 GAAAATGATC
* **
40846169 TTGCCCTTACTTCAATTTCAGAGATGAAGGTGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
40846234 GACA
66 GACA
* *
40846238 TTGCTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
*
40846303 GACG
66 GACA
* * *
40846307 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
40846372 GACA
66 GACA
40846376 TTGCTCTTACTTCAATTTCAAGAGGATGA
1 TTGCTCTTACTTCAATTTC-AGA-GATGA
40846405 TGTTGCTCTT
Statistics
Matches: 152, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
69 145 0.95
70 3 0.02
71 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
GACA
Found at i:40846395 original size:100 final size:100
Alignment explanation
Indices: 40846283--40846702 Score: 471
Period size: 100 Copynumber: 4.1 Consensus size: 100
40846273 TATCCAACTC
40846283 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCA
* *
40846348 ACTCTACTTCAATTTCAAGGGGATGACATTGCTCT
66 ACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
* *
40846383 TACTTCAATTTCAAGAGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCA
40846448 ACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
66 ACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
* ** * * * * ** *
40846483 TACTTCGATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCGATTTCA-AGAGGATGAC--G
1 TACTTCAATTTCA-AGAGGATGAC--G-T-TGC-TCT-TACTTCAATTTCAGAGATAAAGACTTG
* * *
40846545 -T-T---ACTCTTACTTCAATTTCAGAGATG-TAGACGTGTTATCCAACT
59 ATATCCAACTC-TACTTCAATTTCA-AGAGGAT-GAC--G-T-TGC-TCT
*
40846589 CTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCC
1 -TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCC
40846654 AACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
65 AACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
40846690 TACTTCAATTTCA
1 TACTTCAATTTCA
40846703 GAGATGTAGA
Statistics
Matches: 265, Mismatches: 30, Indels: 50
0.77 0.09 0.14
Matches are distributed among these distances:
99 4 0.02
100 147 0.55
101 24 0.09
102 5 0.02
103 6 0.02
104 6 0.02
105 5 0.02
106 26 0.10
107 38 0.14
108 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (100 bp):
TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCA
ACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
Found at i:40846423 original size:169 final size:169
Alignment explanation
Indices: 40846210--40846564 Score: 595
Period size: 169 Copynumber: 2.1 Consensus size: 169
40846200 GTGTTATCCA
* * *
40846210 ACTC-TACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGTAGACGTGTT
1 ACTCTTACTTCAATTTCAAGAGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGAT
*
40846274 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACT
66 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACG
*
40846339 TGATATCCAACTCTACTTCAATTTCAAGGGGATGACATT
131 TGATATCCAACTCTACTTCAATTTCAAGAGGATGACATT
* ** *
40846378 GCTCTTACTTCAATTTCAAGAGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGAT
1 ACTCTTACTTCAATTTCAAGAGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGAT
*
40846443 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCGATTTCAGAGATAAAGACG
66 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACG
* *
40846508 TGATATCCAACTCTACTTCGATTTCAAGAGGATGACGTT
131 TGATATCCAACTCTACTTCAATTTCAAGAGGATGACATT
40846547 ACTCTTACTTCAATTTCA
1 ACTCTTACTTCAATTTCA
40846565 GAGATGTAGA
Statistics
Matches: 173, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
168 3 0.02
169 170 0.98
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (169 bp):
ACTCTTACTTCAATTTCAAGAGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACGTGAT
ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACG
TGATATCCAACTCTACTTCAATTTCAAGAGGATGACATT
Found at i:40846456 original size:69 final size:69
Alignment explanation
Indices: 40846383--40846816 Score: 742
Period size: 69 Copynumber: 6.3 Consensus size: 69
40846373 ACATTGCTCT
* * *
40846383 TACTTCAATTTCAAGAGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
40846448 ACTC
66 ACTC
*
40846452 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCGATTTCAGAGATAAAGACGTGATATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
40846517 ACTC
66 ACTC
* * ** *
40846521 TACTTCGATTTCAAGAGGATGACGTTACTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
40846586 ACTC
66 ACTC
40846590 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
40846655 ACTC
66 ACTC
** *
40846659 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
40846724 ACTC
66 ACTC
*
40846728 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCA
1 TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
40846793 ACTC
66 ACTC
*
40846797 TACTTCAATTTCAAGCGGAT
1 TACTTCAATTTCAAGAGGAT
40846817 TGGCATTGAT
Statistics
Matches: 342, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 342 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (69 bp):
TACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCA
ACTC
Found at i:40846592 original size:238 final size:238
Alignment explanation
Indices: 40846163--40846633 Score: 764
Period size: 238 Copynumber: 2.0 Consensus size: 238
40846153 AGGATAGAAA
* *
40846163 ATGATCTTGCCCTTACTTCAATTTCAGAGATGAAGGTGTGTTATCCAACTCTACTTCAATTTCAA
1 ATGATCTTGCCCTTACTTCAATTTCAGAGATGAAGCTGTGATATCCAACTCTACTTCAATTTCAA
* ** *
40846228 GGGGATGACATTGCTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTTCAATT
66 GAGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATT
* *
40846293 TCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTC
131 TCAAGAGGATGACGTTACTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTC
*
40846358 AATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAAGAGG
196 AATTTCAAGAGGATGACATTGCTCTTACTTCAATTTCAAGAGG
* *
40846401 ATGATGTTGCTCTTACTTCAATTTCAGAGATGAAGACT-TGATATCCAACTCTACTTCAATTTCA
1 ATGATCTTGCCCTTACTTCAATTTCAGAGATGAAG-CTGTGATATCCAACTCTACTTCAATTTCA
* * *
40846465 AGAGGATGACGTTGCTCTTACTTCGATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCGAT
65 AGAGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAAT
** *
40846530 TTCAAGAGGATGACGTTACTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTT
130 TTCAAGAGGATGACGTTACTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTT
*
40846595 CAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
195 CAATTTCAAGAGGATGACATTGCTCTTACTTCAATTTCA
40846634 GAGATAAAGA
Statistics
Matches: 214, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
238 213 1.00
239 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (238 bp):
ATGATCTTGCCCTTACTTCAATTTCAGAGATGAAGCTGTGATATCCAACTCTACTTCAATTTCAA
GAGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATT
TCAAGAGGATGACGTTACTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTC
AATTTCAAGAGGATGACATTGCTCTTACTTCAATTTCAAGAGG
Found at i:40846633 original size:169 final size:168
Alignment explanation
Indices: 40846210--40846608 Score: 516
Period size: 169 Copynumber: 2.3 Consensus size: 168
40846200 GTGTTATCCA
* * ** * * * * *
40846210 ACTC-TACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGTAGACGTGTT
1 ACTCTTACTTCAATTTCAAGAGGACGATGTTCCACTTACTTCAATTTCAGAGAGGAAGAC-TGAT
*
40846274 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACT
65 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACG
*
40846339 TGATATCCAACTCTACTTCAATTTCAAGGGGATGACATT
130 TGATATCCAACTCTACTTCAATTTCAAGAGGATGACATT
* * * * *
40846378 GCTCTTACTTCAATTTCAAGAGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGAT
1 ACTCTTACTTCAATTTCAAGAGGACGATGTTCCACTTACTTCAATTTCAGAGAGGAAGAC-TGAT
*
40846443 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCGATTTCAGAGATAAAGACG
65 ATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACG
* *
40846508 TGATATCCAACTCTACTTCGATTTCAAGAGGATGACGTT
130 TGATATCCAACTCTACTTCAATTTCAAGAGGATGACATT
40846547 ACTCTTACTTCAATTTCAGAGATGTAGACG-TGTTATCCAACTCTACTTCAATTTCA-AGAGGA
1 ACTCTTACTTCAATTTCA-AGA-G--GACGATG-T-TCC-ACT-TACTTCAATTTCAGAGAGGA
40846609 TGACGTTGCT
Statistics
Matches: 205, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
168 3 0.01
169 170 0.83
170 3 0.01
171 1 0.00
172 2 0.01
173 4 0.02
174 2 0.01
175 7 0.03
176 13 0.06
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (168 bp):
ACTCTTACTTCAATTTCAAGAGGACGATGTTCCACTTACTTCAATTTCAGAGAGGAAGACTGATA
TCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGT
GATATCCAACTCTACTTCAATTTCAAGAGGATGACATT
Found at i:40846771 original size:307 final size:306
Alignment explanation
Indices: 40846169--40846746 Score: 908
Period size: 307 Copynumber: 1.9 Consensus size: 306
40846159 GAAAATGATC
* ** * *
40846169 TTGCCCTTACTTCAATTTCAGAGATGAAGGTGTGTTATCCAACTCTACTTCAATTTCAAGGGGAT
1 TTGCCCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
*
40846234 GACATTGCTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTTCAATTTCAAGA
66 GACATTACTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTTCAATTTCAAGA
*
40846299 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTC
131 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTC
* * * *
40846364 AAGGGGATGACATTGCTCTTACTTCAATTTCAAGAGGATGATGTTGCTCTTACTTCAATTTCAGA
196 AAGAGGATGACATTGCTCTTACTTCAATTTCAAGAGGACGATGTTCCACTTACTTCAATTTCAGA
*
40846429 GATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATGACG
261 GAGGAAGAC-TGATATCCAACTCTACTTCAATTTCAAGAGGATGACG
* * *
40846476 TTGCTCTTACTTCGATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCGATTTCAAGAGGAT
1 TTGCCCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
*
40846541 GACGTTACTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTTCAATTTCAAGA
66 GACATTACTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTTCAATTTCAAGA
40846606 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTC
131 GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTC
*
40846671 AAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGTAGACG-TGTTATCCAACTCTACTTCA
196 AAGAGGATGACATTGCTCTTACTTCAATTTCA-AGA-G--GACGATG-T-TCC-ACT-TACTTCA
40846735 ATTTCA-AGAGGA
253 ATTTCAGAGAGGA
40846747 TGACGTTGCT
Statistics
Matches: 246, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
307 214 0.87
308 3 0.01
309 1 0.00
310 2 0.01
311 4 0.02
312 2 0.01
313 7 0.03
314 13 0.05
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (306 bp):
TTGCCCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
GACATTACTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCAACTCTACTTCAATTTCAAGA
GGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTC
AAGAGGATGACATTGCTCTTACTTCAATTTCAAGAGGACGATGTTCCACTTACTTCAATTTCAGA
GAGGAAGACTGATATCCAACTCTACTTCAATTTCAAGAGGATGACG
Found at i:40858984 original size:29 final size:29
Alignment explanation
Indices: 40858942--40859151 Score: 121
Period size: 30 Copynumber: 7.1 Consensus size: 29
40858932 ACCCGGGGGC
*
40858942 AAAATGGTGATTTTGGTGAAATCGAGGTT
1 AAAATGGTAATTTTGGTGAAATCGAGGTT
** * *
40858971 AAAAATGG-AATTTT--AAAAGATACAGGGGGT
1 -AAAATGGTAATTTTGGTGAA-AT-C-GAGGTT
40859001 AAAATGGTAATTTTTGGTGAAATC-AGGGTT
1 AAAATGGTAA-TTTTGGTGAAATCGA-GGTT
*** * * * *
40859031 AAAATGG-AATTTTAAAGGATTCGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTT
40859059 AAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGTT
* *
40859089 AAAAATGG-AATTTT--AGAAGATTCGAGGGT
1 -AAAATGGTAATTTTGGTGAA-A-TCGAGGTT
* *
40859118 AAAATGGTAATTTTTGATGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGTT
40859148 AAAA
1 AAAA
40859152 ATGGGATTTA
Statistics
Matches: 134, Mismatches: 28, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
27 5 0.04
28 28 0.21
29 30 0.22
30 51 0.38
31 13 0.10
32 5 0.04
33 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGAGGTT
Found at i:40859008 original size:59 final size:59
Alignment explanation
Indices: 40858935--40859160 Score: 332
Period size: 59 Copynumber: 3.8 Consensus size: 59
40858925 TATGGATACC
* * *
40858935 CGGGGGCAAAATGGTGA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATA
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
*
40858993 CAGGGGGTAAAATGGTAATTTTTGGTGAAATC-AGGGTT-AAAATGGAATTTTAAAGGATT
1 C-GGGGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTAAAAGATT
*
40859052 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
* * * *
40859111 CGAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGGATTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTT
40859161 AGGGTAGTTT
Statistics
Matches: 153, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
58 35 0.23
59 101 0.66
60 17 0.11
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
Found at i:40859081 original size:118 final size:118
Alignment explanation
Indices: 40858935--40859192 Score: 362
Period size: 118 Copynumber: 2.2 Consensus size: 118
40858925 TATGGATACC
* * *
40858935 CGGGGGCAAAATGGTGA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATACAGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATAC-GAGG
*
40858999 GTAAAATGGTAATTTTTGGTGAAATCAGGGTT-AAAATGGAATTTTAAAGG-A-TT
65 GTAAAATGGTAATTTTTGATGAAATCAGGGTTAAAAATGGAA-TTT-AAGGTAGTT
* *
40859052 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATTCGAGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATACGAGGG
* * *
40859117 TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGGATTTAGGGTAGTT
66 TAAAATGGTAATTTTTGATGAAATCAGGGTTAAAAATGGAATTTAAGGTAGTT
**
40859170 TAGGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
40859193 AAAGTTTTGG
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
116 3 0.02
117 52 0.41
118 71 0.56
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (118 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATACGAGGG
TAAAATGGTAATTTTTGATGAAATCAGGGTTAAAAATGGAATTTAAGGTAGTT
Found at i:40859177 original size:59 final size:58
Alignment explanation
Indices: 40858937--40859193 Score: 261
Period size: 59 Copynumber: 4.4 Consensus size: 58
40858927 TGGATACCCG
* * * * ** **
40858937 GGGGCAAAATGGTGA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATACA
1 GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGGAG-TTTA
* * **
40858995 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTT-AAAATGGAATTTTAAAGGA-TTCG
1 -GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTT--AGGAGTTTA
* * * * *
40859054 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGGAGTTTA
*
40859112 GAGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGGA-TTTAGGGTAGTTTA
1 G-GGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTA-GG-AGTTTA
40859172 GGGGTAAAATGGTAATTTTTGA
1 GGGGTAAAATGGTAATTTTTGA
40859194 AAGTTTTGGG
Statistics
Matches: 170, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
57 3 0.02
58 39 0.23
59 104 0.61
60 22 0.13
61 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGGAGTTTA
Found at i:40859205 original size:59 final size:58
Alignment explanation
Indices: 40859157--40859368 Score: 250
Period size: 59 Copynumber: 3.6 Consensus size: 58
40859147 TAAAAATGGG
** *
40859157 ATTTAGGGTAGTTTAGGGGTAAAATGGTAATTTTTG-AAAGTTTTGGGGTCAAAATGTA
1 ATTTAGGAAAGTTTAGGGGTAAAAT-GTAATTTTGGAAAAGTTTTGGGGTCAAAATGTA
*
40859215 ATTTTAGAAAAGTTTTA-GGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTA
1 A-TTTAGGAAAG-TTTAGGGGT-AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTA
* *
40859275 ATTTTGGAAAAGTTTCGGGGTTAAAATGTAATTTTGGAAAAGTTTT-GGGTCAAAATGTA
1 ATTTAGG-AAAGTTTAGGGG-TAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTA
* * *
40859334 ATTTTGGAAAAGTTTCAAGGTTAAAATGTAATTTT
1 ATTTAGG-AAAGTTT-AGGGGTAAAATGTAATTTT
40859369 TGGACAATTT
Statistics
Matches: 136, Mismatches: 10, Indels: 15
0.84 0.06 0.09
Matches are distributed among these distances:
58 1 0.01
59 69 0.51
60 65 0.48
61 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (58 bp):
ATTTAGGAAAGTTTAGGGGTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTA
Found at i:40859227 original size:30 final size:30
Alignment explanation
Indices: 40859166--40859368 Score: 286
Period size: 30 Copynumber: 6.8 Consensus size: 30
40859156 GATTTAGGGT
* *
40859166 AGTTTAGGGGT-AAAATGGTAATTTTTG-AA
1 AGTTTTGGGGTCAAAAT-GTAATTTTGGAAA
*
40859195 AGTTTTGGGGTCAAAATGTAATTTTAGAAA
1 AGTTTTGGGGTCAAAATGTAATTTTGGAAA
*
40859225 AGTTTTAGGGTCAAAATGTAATTTTGGAAA
1 AGTTTTGGGGTCAAAATGTAATTTTGGAAA
40859255 AGTTTTGGGGTCAAAATGTAATTTTGGAAA
1 AGTTTTGGGGTCAAAATGTAATTTTGGAAA
* *
40859285 AGTTTCGGGGTTAAAATGTAATTTTGGAAA
1 AGTTTTGGGGTCAAAATGTAATTTTGGAAA
40859315 AGTTTT-GGGTCAAAATGTAATTTTGGAAA
1 AGTTTTGGGGTCAAAATGTAATTTTGGAAA
*** *
40859344 AGTTTCAAGGTTAAAATGTAATTTT
1 AGTTTTGGGGTCAAAATGTAATTTT
40859369 TGGACAATTT
Statistics
Matches: 159, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
29 46 0.29
30 113 0.71
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
AGTTTTGGGGTCAAAATGTAATTTTGGAAA
Found at i:40859738 original size:159 final size:160
Alignment explanation
Indices: 40859488--40859782 Score: 430
Period size: 159 Copynumber: 1.9 Consensus size: 160
40859478 TGGACTAATT
* *** *
40859488 TTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAATAAATTAAAAATGTTAGGGACTAAA
1 TTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAA
* * * * *
40859553 TGCATAAATAAGTCAAAAAGTGACACGTGGCAGTCTCTGGTGCAGCCACACAGTCAAAGGACTAA
66 TGCATAAATAAGCCAAAAAGTGACACGTGGCAGCCTCTGATACAGCCAAACAGTCAAAGGACTAA
*
40859618 TTTATAAATTTTGAAAAATTATTGGGCCAA
131 ATTATAAATTTTGAAAAATTATTGGGCCAA
** * *
40859648 TTGTAATTAAATAAAAGTTGGTTTGAGGATTAAATTAAAACAAATT-AAAATAAAAAGGACTAAA
1 TTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAA
* *
40859712 TGCATAAATAAGCCAAAAATTGACACGTGGCAGCCTCTGATACAGTCAAACAGTCAAAGGACTAA
66 TGCATAAATAAGCCAAAAAGTGACACGTGGCAGCCTCTGATACAGCCAAACAGTCAAAGGACTAA
40859777 ATTATA
131 ATTATA
40859783 GACCAATTAA
Statistics
Matches: 118, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
159 77 0.65
160 41 0.35
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (160 bp):
TTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAA
TGCATAAATAAGCCAAAAAGTGACACGTGGCAGCCTCTGATACAGCCAAACAGTCAAAGGACTAA
ATTATAAATTTTGAAAAATTATTGGGCCAA
Found at i:40860405 original size:15 final size:15
Alignment explanation
Indices: 40860372--40860402 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
40860362 TTGGTTTTTC
40860372 GAAACCCAGATCTGG
1 GAAACCCAGATCTGG
40860387 GAAAGCCCAGATCTGG
1 GAAA-CCCAGATCTGG
40860403 AAATATTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.26, G:0.29, T:0.13
Consensus pattern (15 bp):
GAAACCCAGATCTGG
Found at i:40861384 original size:6 final size:6
Alignment explanation
Indices: 40861357--40861435 Score: 83
Period size: 6 Copynumber: 13.2 Consensus size: 6
40861347 ATGTTTAGTG
* * *
40861357 TTTAAA TTTTAA TTTTAA TTTAAA TTTAAA -GTAAA TTTAAA TAATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
40861406 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA T
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA T
40861436 CAATTTAACT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 48 0.76
7 1 0.02
8 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:40861393 original size:17 final size:16
Alignment explanation
Indices: 40861373--40861443 Score: 83
Period size: 17 Copynumber: 4.4 Consensus size: 16
40861363 TTTTAATTTT
40861373 AATTTAAATTTAAAGTA
1 AATTTAAATTT-AAGTA
*
40861390 AATTTAAA--TAATTA
1 AATTTAAATTTAAGTA
40861404 AATTTAAATTTAAGATA
1 AATTTAAATTTAAG-TA
* *
40861421 AATTTAAATTTAAATC
1 AATTTAAATTTAAGTA
40861437 AATTTAA
1 AATTTAA
40861444 CTCCAAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
14 12 0.26
15 1 0.02
16 11 0.23
17 23 0.49
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAAGTA
Found at i:40864864 original size:3 final size:3
Alignment explanation
Indices: 40864856--40864883 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40864846 AATCGGAAAT
40864856 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40864884 CGGCTTTACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40867600 original size:14 final size:14
Alignment explanation
Indices: 40867558--40867602 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
40867548 ATATATATTA
40867558 TATTTT-TTTTTC-
1 TATTTTATTTTTCT
*
40867570 TATCTTATTTTAT-T
1 TATTTTATTTT-TCT
40867584 TATTTTATTTTTCT
1 TATTTTATTTTTCT
40867598 TATTT
1 TATTT
40867603 CGAATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 17 0.63
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (14 bp):
TATTTTATTTTTCT
Found at i:40868590 original size:3 final size:3
Alignment explanation
Indices: 40868582--40868609 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40868572 TGTAACCCTT
40868582 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40868610 ACTAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40878251 original size:6 final size:6
Alignment explanation
Indices: 40878215--40878318 Score: 69
Period size: 6 Copynumber: 18.0 Consensus size: 6
40878205 AACTTTGATT
* * * * *
40878215 TTTAAG TTTAAA -TTAAT TTTAAG TTT-TA TTTAGA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40878259 TCTTAAA TTTAAA TTTATTTA TTTAAA TTT-AC TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40878308 -TTAAA TTTAAA
1 TTTAAA TTTAAA
40878319 AATAATATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.05
5 17 0.22
6 49 0.64
7 2 0.03
8 5 0.06
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:40878252 original size:17 final size:16
Alignment explanation
Indices: 40878239--40878318 Score: 110
Period size: 17 Copynumber: 5.0 Consensus size: 16
40878229 AATTTTAAGT
*
40878239 TTTATTTAGATTTAAA
1 TTTATTTAAATTTAAA
40878255 TTTATCTTAAATTTAAA
1 TTTAT-TTAAATTTAAA
40878272 TTTATTT--ATTTAAA
1 TTTATTTAAATTTAAA
40878286 TTTACTTTAAATTTAAA
1 TTTA-TTTAAATTTAAA
*
40878303 TTTAATTAAATTTAAA
1 TTTATTTAAATTTAAA
40878319 AATAATATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.19
15 3 0.05
16 18 0.31
17 26 0.45
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTATTTAAATTTAAA
Done.