Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 54 of 276
Found at i:16822282 original size:19 final size:18
Alignment explanation
Indices: 16822241--16822311 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
16822231 AAACATATTT
* *
16822241 AAAATAATTAAAATTGTATA
1 AAAATATTTAAAA-TATA-A
16822261 AAAATATTTAAAATCATAA
1 AAAATATTTAAAAT-ATAA
* **
16822280 AAATTATAAAAAATATAA
1 AAAATATTTAAAATATAA
16822298 AAAAGTA-TTAAAAT
1 AAAA-TATTTAAAAT
16822312 TGATATCAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 12 0.29
19 15 0.37
20 14 0.34
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATATTTAAAATATAA
Found at i:16826438 original size:18 final size:19
Alignment explanation
Indices: 16826401--16826439 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
16826391 AAACCAATTT
*
16826401 TTTTAATATATTTTTTTAA
1 TTTTAATATATTTGTTTAA
*
16826420 TTTTAATGT-TTTGTTTAA
1 TTTTAATATATTTGTTTAA
16826438 TT
1 TT
16826440 GAACTAGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTAATATATTTGTTTAA
Found at i:16826867 original size:17 final size:15
Alignment explanation
Indices: 16826836--16826875 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
16826826 TCATTAGATT
16826836 TTTTATATTTTATAA
1 TTTTATATTTTATAA
16826851 TTTTATAGTTTTAATAA
1 TTTTATA-TTTT-ATAA
*
16826868 GTTTATAT
1 TTTTATAT
16826876 CAATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 5 0.23
17 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTATATTTTATAA
Found at i:16830308 original size:131 final size:131
Alignment explanation
Indices: 16830070--16830315 Score: 377
Period size: 131 Copynumber: 1.9 Consensus size: 131
16830060 TCGGTTAAGA
* * * * *
16830070 ATTCTTTAAAATGAAGATGAGATTCGATCTTTAGCAATTCGCGAAATAGTGCCCTAATGTGTTGG
1 ATTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGAAATAGTGCCCTAACGTGTTGG
**
16830135 GTTGCAATTTTGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAA
66 GTTGCAATTTCACGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAA
16830200 T
131 T
* *
16830201 ATTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCA-TGCGCTAACGTGTTG
1 ATTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGAAAT-AGTGCCCTAACGTGTTG
* *
16830265 GGTTGCAATTTCACGTTTGCTCAAAATAATCGAGTATCCCTTCAAAATTTC
65 GGTTGCAATTTCACGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTC
16830316 CTTTCATATC
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
131 102 0.99
132 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (131 bp):
ATTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGAAATAGTGCCCTAACGTGTTGG
GTTGCAATTTCACGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTTTTAA
T
Found at i:16841947 original size:24 final size:24
Alignment explanation
Indices: 16841920--16841973 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
16841910 GCTAACAAGC
*
16841920 AGAAAAGCCTGTTAAAAGACAGAG
1 AGAAAAGCCTGTCAAAAGACAGAG
* *
16841944 AGAAGAGCGTGTCAAAAGACAGAG
1 AGAAAAGCCTGTCAAAAGACAGAG
*
16841968 AAAAAA
1 AGAAAA
16841974 ATATTACTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.11, G:0.26, T:0.09
Consensus pattern (24 bp):
AGAAAAGCCTGTCAAAAGACAGAG
Found at i:16842900 original size:9 final size:9
Alignment explanation
Indices: 16842848--16842960 Score: 66
Period size: 9 Copynumber: 11.7 Consensus size: 9
16842838 TATAATACGA
16842848 TTTTATAATT
1 TTTTATAA-T
*
16842858 TTTTCTATAT
1 TTTTATA-AT
*
16842868 TTCTAT-AT
1 TTTTATAAT
16842876 ATTTTATCAATTT
1 -TTTTAT-AA--T
16842889 TTTTATAAT
1 TTTTATAAT
*
16842898 TTTTACAAT
1 TTTTATAAT
16842907 TTTTAATAAT
1 TTTT-ATAAT
* **
16842917 TTATACGAT
1 TTTTATAAT
*
16842926 TTTTATTAAAA
1 TTTTA-T-AAT
*
16842937 TTTAATAAT
1 TTTTATAAT
16842946 TTTTATAAT
1 TTTTATAAT
16842955 TTTTAT
1 TTTTAT
16842961 TTGTTTTATC
Statistics
Matches: 78, Mismatches: 16, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
8 2 0.03
9 41 0.53
10 19 0.24
11 9 0.12
12 6 0.08
13 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:16842908 original size:29 final size:29
Alignment explanation
Indices: 16842847--16842913 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
16842837 TTATAATACG
*
16842847 ATTTTATAATTTTTTCTATATTTCTATAT
1 ATTTTATAATTTTTTCTATATTTCTACAT
*
16842876 ATTTTATCAATTTTTT-TATAATTTTTACA-
1 ATTTTAT-AATTTTTTCTAT-ATTTCTACAT
16842905 ATTTT-TAAT
1 ATTTTATAAT
16842914 AATTTATACG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 15 0.44
30 15 0.44
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (29 bp):
ATTTTATAATTTTTTCTATATTTCTACAT
Found at i:16842915 original size:19 final size:19
Alignment explanation
Indices: 16842877--16842959 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
16842867 TTTCTATATA
*
16842877 TTTTATCAATTTTTTTATAAT
1 TTTTA-CAA-TTTTTAATAAT
16842898 TTTTACAATTTTTAATAAT
1 TTTTACAATTTTTAATAAT
* * * *
16842917 TTATACGATTTTTATTAAAA
1 TTTTACAATTTTTAAT-AAT
* *
16842937 TTTAATAATTTTT-ATAAT
1 TTTTACAATTTTTAATAAT
16842955 TTTTA
1 TTTTA
16842960 TTTGTTTTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.12
19 24 0.49
20 14 0.29
21 5 0.10
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTTACAATTTTTAATAAT
Found at i:16843417 original size:55 final size:55
Alignment explanation
Indices: 16843328--16843438 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
16843318 GGAACACTTA
*
16843328 ATTTGTAAAATTAAACAAATCTAGACATCGGTGATTAGCTCGCTTTGGTGATTAT
1 ATTTATAAAATTAAACAAATCTAGACATCGGTGATTAGCTCGCTTTGGTGATTAT
*
16843383 ATTTATAAAATTAATCAAATCTAGACATCGGTGATTAGCTCGCTTTGGTGATTAT
1 ATTTATAAAATTAAACAAATCTAGACATCGGTGATTAGCTCGCTTTGGTGATTAT
16843438 A
1 A
16843439 ACAAATTCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (55 bp):
ATTTATAAAATTAAACAAATCTAGACATCGGTGATTAGCTCGCTTTGGTGATTAT
Found at i:16844565 original size:20 final size:20
Alignment explanation
Indices: 16844542--16844585 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
16844532 GCCGTTAACT
16844542 TTAATAGTCAATTGTTAAAG
1 TTAATAGTCAATTGTTAAAG
*
16844562 TTAATAGTCAATTGTTAAGG
1 TTAATAGTCAATTGTTAAAG
16844582 TTAA
1 TTAA
16844586 AGGCCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (20 bp):
TTAATAGTCAATTGTTAAAG
Found at i:16844884 original size:19 final size:20
Alignment explanation
Indices: 16844851--16844895 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
16844841 CCAAAAAATA
16844851 TTTTCTGGAAAATGATTTAC
1 TTTTCTGGAAAATGATTTAC
16844871 TTTTCTGG-AAATGATTTAC
1 TTTTCTGGAAAATGATTTAC
16844890 TTTTCT
1 TTTTCT
16844896 AGTGTTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTTCTGGAAAATGATTTAC
Found at i:16848166 original size:34 final size:34
Alignment explanation
Indices: 16848126--16848197 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
16848116 GACCCTATGA
* * *
16848126 AGAGGAATGAGATTTGTCTGGGAAAGAGAGAAAG
1 AGAGGAATGAGATTTGCCTGAGAAAGAAAGAAAG
16848160 AGAGGAATGAGATTTGCCTGAGAAAGAAAGAAAG
1 AGAGGAATGAGATTTGCCTGAGAAAGAAAGAAAG
16848194 AGAG
1 AGAG
16848198 AAAGAAGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.44, C:0.04, G:0.36, T:0.15
Consensus pattern (34 bp):
AGAGGAATGAGATTTGCCTGAGAAAGAAAGAAAG
Found at i:16848682 original size:81 final size:80
Alignment explanation
Indices: 16848595--16848744 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 80
16848585 TTGTTTTTTG
* * * * * * *
16848595 TTTTTTTTTAAGTTT-GGGGCTTTTTTTTATGTATTTTGGCAGTTCAAGTATCTAATTGAGTTCC
1 TTTTTTTTTAAGTTTAAGGG--TCTTTTTATGCATTTTGGCAGTTCAAGTACCCAATTGAGTGCA
16848659 AAAAAAGCAGGGTTTAA
64 AAAAAAGCAGGGTTTAA
*
16848676 TTTTTTTTTAAGTTTAAGGGTCTTTTTATGCATTTTGGCAGTTTAAGTACCCAATTGAGTGCAAA
1 TTTTTTTTTAAGTTTAAGGGTCTTTTTATGCATTTTGGCAGTTCAAGTACCCAATTGAGTGCAAA
16848741 AAAA
66 AAAA
16848745 AAATAGGGGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 42 0.70
81 15 0.25
82 3 0.05
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (80 bp):
TTTTTTTTTAAGTTTAAGGGTCTTTTTATGCATTTTGGCAGTTCAAGTACCCAATTGAGTGCAAA
AAAAGCAGGGTTTAA
Found at i:16850900 original size:16 final size:16
Alignment explanation
Indices: 16850876--16850910 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16850866 TAATAGCTAC
* *
16850876 GCCCGAGCCTAACCCA
1 GCCCAAGCCCAACCCA
16850892 GCCCAAGCCCAACCCA
1 GCCCAAGCCCAACCCA
16850908 GCC
1 GCC
16850911 TGTATCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.54, G:0.17, T:0.03
Consensus pattern (16 bp):
GCCCAAGCCCAACCCA
Found at i:16852630 original size:25 final size:25
Alignment explanation
Indices: 16852572--16852634 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
16852562 AAGGGAATAG
*
16852572 GAGAAGAGAATGA-AGAAAAATAGAA
1 GAGAAGTGAA-GAGAGAAAAATAGAA
*
16852597 GGGAA-TGAAGAGAGAAAAAT-GAGA
1 GAGAAGTGAAGAGAGAAAAATAGA-A
16852621 GAGAAGTGAAGAGA
1 GAGAAGTGAAGAGA
16852635 TGAGAAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 4 0.12
24 16 0.50
25 12 0.38
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.08
Consensus pattern (25 bp):
GAGAAGTGAAGAGAGAAAAATAGAA
Found at i:16853925 original size:22 final size:23
Alignment explanation
Indices: 16853900--16853945 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
16853890 ACATATGCTC
*
16853900 TCTTTTGTTGTTCTT-TTTCTTT
1 TCTTTTCTTGTTCTTCTTTCTTT
*
16853922 TCTTTTCTTGTTCTTCTTTTTTT
1 TCTTTTCTTGTTCTTCTTTCTTT
16853945 T
1 T
16853946 TTCATGAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (23 bp):
TCTTTTCTTGTTCTTCTTTCTTT
Found at i:16856852 original size:30 final size:30
Alignment explanation
Indices: 16856795--16856853 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16856785 TATATTTGAA
* *
16856795 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
16856825 AATATTTACAAAAAGA-GCAACCAAATTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTT
16856854 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:16877258 original size:25 final size:25
Alignment explanation
Indices: 16877173--16877259 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 25
16877163 CTCTAGATAA
16877173 CCATATATCGAGAAG-TTCAAATGAG
1 CCATATATCGAGAAGCTTCAAA-GAG
* * *
16877198 CCA-ATATTGGGAAGCTCATAAAAGAG
1 CCATATATCGAGAAGCT--TCAAAGAG
*
16877224 CC-TTTAATCGAGAAGCTTCAAAGAG
1 CCATAT-ATCGAGAAGCTTCAAAGAG
16877249 CCATATATCGA
1 CCATATATCGA
16877260 TACGCTTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
24 9 0.19
25 18 0.38
26 8 0.17
27 13 0.27
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (25 bp):
CCATATATCGAGAAGCTTCAAAGAG
Found at i:16879505 original size:40 final size:40
Alignment explanation
Indices: 16879461--16879590 Score: 197
Period size: 40 Copynumber: 3.2 Consensus size: 40
16879451 GCTCTCGATA
*
16879461 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
1 TAATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG
* *
16879501 TAATATATATCCGGGTTAAATCCTGCAGGCTTTGTGCTGG
1 TAATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG
*
16879541 TAATATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGG
1 T-A-ATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG
*
16879583 TACTATAT
1 TAATATAT
16879591 CCGGACTTAA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 44 0.54
41 2 0.02
42 36 0.44
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (40 bp):
TAATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG
Found at i:16879549 original size:42 final size:42
Alignment explanation
Indices: 16879463--16879590 Score: 197
Period size: 42 Copynumber: 3.1 Consensus size: 42
16879453 TCTCGATATA
*
16879463 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT-A-
1 ATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAAT
* *
16879503 ATATATATCCGGGTTAAATCCTGCAGGCTTTGTGCTGGTAAT
1 ATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAAT
* *
16879545 ATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTACT
1 ATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAAT
16879587 ATAT
1 ATAT
16879591 CCGGACTTAA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 37 0.46
41 1 0.01
42 42 0.52
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (42 bp):
ATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAAT
Found at i:16879611 original size:82 final size:82
Alignment explanation
Indices: 16879463--16879625 Score: 224
Period size: 82 Copynumber: 2.0 Consensus size: 82
16879453 TCTCGATATA
* * *
16879463 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATATATCCGGGTTAAATCCTGCA
1 ATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTAATATATATCCGGCTTAAATCCTGCA
* *
16879528 GGCTTTGTGCTGGTAAT
66 GGCTTTGAGCTAGTAAT
*
16879545 ATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGT-A-CTATATCCGGACTTAAAGTTCC-
1 ATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTAATATATATCCGG-CTTAAA--TCCT
16879607 GCAGGCTTTGAGCTAGTAA
63 GCAGGCTTTGAGCTAGTAA
16879626 CTGGATTCGG
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
80 9 0.12
81 6 0.08
82 54 0.75
83 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (82 bp):
ATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTAATATATATCCGGCTTAAATCCTGCA
GGCTTTGAGCTAGTAAT
Found at i:16887157 original size:42 final size:42
Alignment explanation
Indices: 16887110--16887241 Score: 198
Period size: 42 Copynumber: 3.2 Consensus size: 42
16887100 GCTCTCGATA
* *
16887110 TAATATATATATCCGGGTTAAATCCCGCAGGCTTCGTTCTGG
1 TAATATATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGG
16887152 T-A-ATATATATCCTA-GTTAAATCCCGCAGGCTTCGTGCTGG
1 TAATATATATATCC-AGGTTAAATCCCGCAGGCTTCGTGCTGG
*
16887192 TAATATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGG
1 TAATATATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGG
*
16887234 TACTATAT
1 TAATATAT
16887242 CCGGACTTAA
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
40 36 0.44
41 3 0.04
42 43 0.52
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (42 bp):
TAATATATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGG
Found at i:16887158 original size:40 final size:40
Alignment explanation
Indices: 16887114--16887241 Score: 186
Period size: 40 Copynumber: 3.1 Consensus size: 40
16887104 TCGATATAAT
* *
16887114 ATATATATCCGGGTTAAATCCCGCAGGCTTCGTTCTGGTA
1 ATATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTA
16887154 ATATATATCCTA-GTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 ATATATATCC-AGGTTAAATCCCGCAGGCTTCGTGCTGGT-A
*
16887195 TATATATATCCAGGTTAAATCCCGCAGGCTTAGTGCTGGTA
1 -ATATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTA
*
16887236 CTATAT
1 ATATAT
16887242 CCGGACTTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
40 41 0.51
41 3 0.04
42 36 0.45
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (40 bp):
ATATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTA
Found at i:16888265 original size:21 final size:21
Alignment explanation
Indices: 16888241--16888282 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16888231 GAATTTAATA
*
16888241 TCAATTTAATACAATTCACAT
1 TCAATTCAATACAATTCACAT
* *
16888262 TCAATTCAATCCATTTCACAT
1 TCAATTCAATACAATTCACAT
16888283 GTTAGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:16889218 original size:34 final size:35
Alignment explanation
Indices: 16889180--16889246 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16889170 ATATCAATTT
*
16889180 GGCCTTAGCTCATCTCAGTAACAG-TAAGCAGTGG
1 GGCCTTAGCCCATCTCAGTAACAGATAAGCAGTGG
* *
16889214 GGCCTTAGCCCATCTTAGTAACAGATATGCAGT
1 GGCCTTAGCCCATCTCAGTAACAGATAAGCAGT
16889247 CACAAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (35 bp):
GGCCTTAGCCCATCTCAGTAACAGATAAGCAGTGG
Found at i:16892459 original size:27 final size:28
Alignment explanation
Indices: 16892413--16892465 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
16892403 TACATAATAT
* * *
16892413 ATATAAAAATATGATGTTAAGAGTATAC
1 ATATAAAAATATAATATTAAAAGTATAC
16892441 ATAT-AAAATATAATATTAAAAGTAT
1 ATATAAAAATATAATATTAAAAGTAT
16892466 GTATACATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (28 bp):
ATATAAAAATATAATATTAAAAGTATAC
Found at i:16892604 original size:15 final size:17
Alignment explanation
Indices: 16892577--16892629 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 17
16892567 ATACTTCATA
16892577 AATATATATATACATACT
1 AATA-ATATATACATACT
*
16892595 AA-AA-ATATACATAAT
1 AATAATATATACATACT
16892610 AATAATATATACATAC-
1 AATAATATATACATACT
16892626 AATA
1 AATA
16892630 GTAAGACGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 12 0.39
16 7 0.23
17 10 0.32
18 2 0.06
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATATATACATACT
Found at i:16892794 original size:22 final size:22
Alignment explanation
Indices: 16892769--16892810 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16892759 AAAAACGTAC
*
16892769 AAATATATA-TAAGTACTAATTA
1 AAATAGATACTAAG-ACTAATTA
16892791 AAATAGATACTAAGACTAAT
1 AAATAGATACTAAGACTAAT
16892811 AATAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
AAATAGATACTAAGACTAATTA
Found at i:16899552 original size:17 final size:18
Alignment explanation
Indices: 16899519--16899553 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16899509 CCATGTTGTC
*
16899519 TGCCCGTGTGGGCCCACA
1 TGCCCGTGTGAGCCCACA
16899537 TGCCCGTGT-AGCCCACA
1 TGCCCGTGTGAGCCCACA
16899554 CGGTCCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.40, G:0.29, T:0.17
Consensus pattern (18 bp):
TGCCCGTGTGAGCCCACA
Found at i:16903225 original size:47 final size:45
Alignment explanation
Indices: 16903068--16903236 Score: 171
Period size: 44 Copynumber: 3.6 Consensus size: 45
16903058 GGGATACATT
* * *
16903068 GCCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGT
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATC-T-T-TGCGA
* * * *
16903118 GCTGATGCATGTCCCAGACATGTCTTACACTAGCATAAC--TCCTA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TATCTTTGCGA
* *
16903162 GCCGATGCGTGTCCCAGACACGTCTTACACTAGCTATCTTTGTCGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTATCTTTG-CGA
16903208 GGCCGATGCATGTCCCAGACATGTCTTAC
1 -GCCGATGCATGTCCCAGACATGTCTTAC
16903237 TTTGGCACTC
Statistics
Matches: 99, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
43 3 0.03
44 33 0.33
45 1 0.01
46 2 0.02
47 26 0.26
48 12 0.12
49 16 0.16
50 6 0.06
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTATCTTTGCGA
Found at i:16903327 original size:94 final size:92
Alignment explanation
Indices: 16903067--16903333 Score: 288
Period size: 94 Copynumber: 2.9 Consensus size: 92
16903057 TGGGATACAT
*
16903067 TGCCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGCTGATGCATGTCC
1 TGCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGAG-GCTGATGCATGTCC
16903132 CAGACATGTCTTACACTAGCATAACTCCTA
63 CAGACATGTCTTACACTAGCATAACTCCTA
* * * * * ** *
16903162 -GCCGATGCGTGTCCCAGACA-CGTCTTACACTAGCTATCTTTGTCGAGGCCGATGCATGTCCCA
1 TGCCGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GAGGCTGATGCATGTCCCA
** * *
16903225 GACATGTCTTACTTTGGCACTCA-TCTCTA
65 GACATGTCTTACACTAGCA-TAACTC-CTA
* * * * *
16903254 TGCCGATGCCATGTCCCTGACATGGTCTTACGCTGGCTCTCATAATGTGGCTAAAGCATGTCCCA
1 TGCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGCTGATGCATGTCCCA
16903319 GACATGTCTTACACT
65 GACATGTCTTACACT
16903334 GGCGCACAAA
Statistics
Matches: 138, Mismatches: 28, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
91 34 0.25
92 23 0.17
93 19 0.14
94 46 0.33
95 16 0.12
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.29
Consensus pattern (92 bp):
TGCCGATGCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGCTGATGCATGTCCCAG
ACATGTCTTACACTAGCATAACTCCTA
Found at i:16922059 original size:33 final size:35
Alignment explanation
Indices: 16922004--16922069 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
16921994 GTCTATTGAT
*
16922004 ATTTTATATATTTTTAAAATTT-AATTTAATTTTA
1 ATTTTATATATTTTTAAAATTTAAATTGAATTTTA
* *
16922038 ATTTTA-ATTTTTTTAATATTTAAATTGAATTT
1 ATTTTATATATTTTTAAAATTTAAATTGAATTT
16922070 AAACAAAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (35 bp):
ATTTTATATATTTTTAAAATTTAAATTGAATTTTA
Found at i:16922063 original size:17 final size:16
Alignment explanation
Indices: 16922014--16922060 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
16922004 ATTTTATATA
*
16922014 TTTTTAAAATTTAATT
1 TTTTTAATATTTAATT
16922030 TAATTTTAAT-TTTAATT
1 T--TTTTAATATTTAATT
16922047 TTTTTAATATTTAA
1 TTTTTAATATTTAA
16922061 ATTGAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 8 0.30
18 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAATATTTAATT
Found at i:16926621 original size:54 final size:54
Alignment explanation
Indices: 16926539--16926664 Score: 227
Period size: 54 Copynumber: 2.3 Consensus size: 54
16926529 CTTATCACCA
16926539 TGGTCC-AGTTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
1 TGGTCCTA-TTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
*
16926593 TGGTCCTATTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCT
1 TGGTCCTATTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
16926647 TGGTCCTATTGCAAAGCC
1 TGGTCCTATTGCAAAGCC
16926665 TCCTACAGCA
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
54 69 0.99
55 1 0.01
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.26
Consensus pattern (54 bp):
TGGTCCTATTGCAAAGCCACCCACAGGATCATCTCCGGTTCCTGCTCTGGCTCC
Found at i:16932693 original size:10 final size:10
Alignment explanation
Indices: 16932671--16932713 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
16932661 ACAAGTAATT
16932671 TAAAAAT-TA
1 TAAAAATATA
*
16932680 TAAAAATATT
1 TAAAAATATA
*
16932690 TAAATATATA
1 TAAAAATATA
16932700 TAAAAATATA
1 TAAAAATATA
16932710 -AAAA
1 TAAAA
16932714 GTTAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 11 0.38
10 18 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAATATA
Found at i:16932703 original size:20 final size:19
Alignment explanation
Indices: 16932668--16932708 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
16932658 GTTACAAGTA
16932668 ATTTAAAAATTATAAAAAT
1 ATTTAAAAATTATAAAAAT
*
16932687 ATTTAAATATATATAAAAAT
1 ATTTAAAAAT-TATAAAAAT
16932707 AT
1 AT
16932709 AAAAAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTAAAAATTATAAAAAT
Found at i:16932713 original size:8 final size:8
Alignment explanation
Indices: 16932671--16932748 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 8
16932661 ACAAGTAATT
16932671 TAAAAATTA
1 TAAAAA-TA
16932680 TAAAAATA
1 TAAAAATA
16932688 TTTAAATATATA
1 --TAAA-A-ATA
16932700 TAAAAATA
1 TAAAAATA
16932708 TAAAAAGTTAA
1 TAAAAA--T-A
16932719 TAAAAA-A
1 TAAAAATA
16932726 TCAAAAATA
1 T-AAAAATA
16932735 -AAAAATA
1 TAAAAATA
16932742 -AAAAATA
1 TAAAAATA
16932749 AGCATGAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
7 16 0.27
8 16 0.27
9 8 0.13
10 9 0.15
11 8 0.13
12 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (8 bp):
TAAAAATA
Found at i:16932737 original size:6 final size:7
Alignment explanation
Indices: 16932717--16932749 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
16932707 ATAAAAAGTT
16932717 AATAAAA
1 AATAAAA
*
16932724 AATCAAA
1 AATAAAA
16932731 AATAAAA
1 AATAAAA
16932738 AATAAAA
1 AATAAAA
16932745 AATAA
1 AATAA
16932750 GCATGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:16933135 original size:30 final size:30
Alignment explanation
Indices: 16933079--16933135 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
16933069 AATTTGATTT
* *
16933079 TTTTTTTTAAAGATTGATGGACAAATTAAA
1 TTTTTTTAAAAGATTGATGGAAAAATTAAA
*
16933109 TTTTTTTAAAAGGTTGA-GGATAAAATT
1 TTTTTTTAAAAGATTGATGGA-AAAATT
16933136 TAACTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (30 bp):
TTTTTTTAAAAGATTGATGGAAAAATTAAA
Found at i:16938001 original size:18 final size:18
Alignment explanation
Indices: 16937978--16938013 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16937968 TTCCATGCAG
16937978 TTCTTAGTTAAGAGAATA
1 TTCTTAGTTAAGAGAATA
16937996 TTCTTAGTTAAGAGAATA
1 TTCTTAGTTAAGAGAATA
16938014 CGTAAAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
TTCTTAGTTAAGAGAATA
Found at i:16955612 original size:56 final size:55
Alignment explanation
Indices: 16955547--16955654 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 55
16955537 TTATAGATTG
* *
16955547 CAAATTAATTATTCATGAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
1 CAAATTAATTATTAATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
16955602 CAAATTTAATTATTAATAAGCACTATTCAAATTAAAAGTGATGATTTATCATC
1 CAAA-TTAATTATTAATAAGCACTATTCAAATTAAAAGTGATGATTTATCATC
16955655 CAATAGATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 4 0.08
56 46 0.92
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (55 bp):
CAAATTAATTATTAATAAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
Found at i:16963582 original size:27 final size:27
Alignment explanation
Indices: 16963552--16963616 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
16963542 TTAAACATGA
**
16963552 GATAATCTGACAGGACGTTAAATACAG
1 GATAATCCAACAGGACGTTAAATACAG
*
16963579 GATAGTCCAACAGGACGTTAAATACAG
1 GATAATCCAACAGGACGTTAAATACAG
*
16963606 GATAACCCAAC
1 GATAATCCAAC
16963617 GGAACATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (27 bp):
GATAATCCAACAGGACGTTAAATACAG
Found at i:16963626 original size:27 final size:27
Alignment explanation
Indices: 16963561--16963627 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
16963551 AGATAATCTG
* **
16963561 ACAGGACGTTAAATACAGGATAGTCCA
1 ACAGGACATTAAATACAGGATAACCCA
*
16963588 ACAGGACGTTAAATACAGGATAACCCA
1 ACAGGACATTAAATACAGGATAACCCA
16963615 AC-GGAACATTAAA
1 ACAGG-ACATTAAA
16963628 CACTGGGTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (27 bp):
ACAGGACATTAAATACAGGATAACCCA
Found at i:16965603 original size:87 final size:86
Alignment explanation
Indices: 16965494--16965657 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 86
16965484 TTTAAATTCA
* *
16965494 GTGAATTCATCAAGCCCGTCTCAATAGGACCACCCAAA-CTCTGAGATATGAACTCATTAAGATT
1 GTGAATTCATCAAGCCCATCTCAATAGGACCACCCAAACCT-TGAGATATGAACTCATTAAGAGT
16965558 AAGAAACTCAACCTCACATGTCG
65 AAGAAA-TCAACCTCACATGTCG
** * * * * *
16965581 GTGAATTCATCAAGTTCATCTCAGTAGGACTATCCAAACCTTGGGATATGAATTCATTAAGAGTA
1 GTGAATTCATCAAGCCCATCTCAATAGGACCACCCAAACCTTGAGATATGAACTCATTAAGAGTA
16965646 AGAAATCAACCT
66 AGAAATCAACCT
16965658 TATGCATGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 7 0.10
87 58 0.87
88 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (86 bp):
GTGAATTCATCAAGCCCATCTCAATAGGACCACCCAAACCTTGAGATATGAACTCATTAAGAGTA
AGAAATCAACCTCACATGTCG
Found at i:16969545 original size:90 final size:89
Alignment explanation
Indices: 16969442--16969720 Score: 360
Period size: 90 Copynumber: 3.1 Consensus size: 89
16969432 GCATATTGAA
* * ** *
16969442 TTGTATAAATATTTTCTTGATTTCCGATAGTGTATCGTAACTTATACTAATTGAATTTGTTTGGT
1 TTGTATAAATATTTTCTTGATTTCCGATAGTATATCGTAACTTATACTGATTGAATTCATTTGAT
16969507 TGAGAAGATTATGCAACTTGTATAT
66 TGAG-AGATTATGCAACTTGTATAT
* * * * *
16969532 TTGTATAAATATTTGCTTGATTTTCGATAGTATATAGTAACTTATACTGATTAAATTCATTTGAC
1 TTGTATAAATATTTTCTTGATTTCCGATAGTATATCGTAACTTATACTGATTGAATTCATTTGAT
** *
16969597 TGTTCAGATTATGTAACTTGTATAT
66 TG-AGAGATTATGCAACTTGTATAT
* *
16969622 TTGTATAAATATTTTCTTGATTTCCGATAGTATATCGTAACTTGATATTGATTGAATTCATATGA
1 TTGTATAAATATTTTCTTGATTTCCGATAGTATATCGTAACTT-ATACTGATTGAATTCATTTGA
* *
16969687 TTGAGTGAATTATGCAAATTGTATAT
65 TTGAGAG-ATTATGCAACTTGTATAT
*
16969713 TTATATAA
1 TTGTATAA
16969721 CTCACTATTG
Statistics
Matches: 160, Mismatches: 26, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
90 117 0.73
91 43 0.27
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (89 bp):
TTGTATAAATATTTTCTTGATTTCCGATAGTATATCGTAACTTATACTGATTGAATTCATTTGAT
TGAGAGATTATGCAACTTGTATAT
Found at i:16978619 original size:12 final size:11
Alignment explanation
Indices: 16978597--16978637 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
16978587 AATTTCCTTG
16978597 AGCTTCTTTTC
1 AGCTTCTTTTC
16978608 AGCTTCCTTTTC
1 AGCTT-CTTTTC
16978620 AGC-TCTTTT-
1 AGCTTCTTTTC
*
16978629 AGCTGCTTT
1 AGCTTCTTT
16978638 GGCTGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 3 0.11
10 9 0.33
11 6 0.22
12 9 0.33
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (11 bp):
AGCTTCTTTTC
Found at i:16980237 original size:27 final size:30
Alignment explanation
Indices: 16980184--16980240 Score: 93
Period size: 27 Copynumber: 2.0 Consensus size: 30
16980174 ATTTCCGGCG
16980184 AGTGACAAAAAGAGAAGCAAAGACTTGACT
1 AGTGACAAAAAGAGAAGCAAAGACTTGACT
16980214 AGTGAC-AAAA-AG-AGCAAAGACTTGACT
1 AGTGACAAAAAGAGAAGCAAAGACTTGACT
16980241 GCAGCGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 15 0.56
28 2 0.07
29 4 0.15
30 6 0.22
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (30 bp):
AGTGACAAAAAGAGAAGCAAAGACTTGACT
Found at i:16991194 original size:23 final size:23
Alignment explanation
Indices: 16991151--16991194 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
16991141 TAACTTTGGA
*
16991151 ATATTATTTTTTTATAAATAAGT
1 ATATTATTTTTTAATAAATAAGT
16991174 ATATTA-TTTTTAATAATATAA
1 ATATTATTTTTTAATAA-ATAA
16991195 AGCATGGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATTATTTTTTAATAAATAAGT
Found at i:16992154 original size:25 final size:25
Alignment explanation
Indices: 16992126--16992266 Score: 133
Period size: 25 Copynumber: 5.7 Consensus size: 25
16992116 GACACACCAC
16992126 AGCTCTCATGAGCTTCCTGATATCT
1 AGCTCTCATGAGCTTCCTGATATCT
* *
16992151 AGCTATTATGAGCTTCCTGATATCT
1 AGCTCTCATGAGCTTCCTGATATCT
* *
16992176 AGCTCTTATGAGCTTCCTGAT-TTT
1 AGCTCTCATGAGCTTCCTGATATCT
* * * *
16992200 AGCTTTTATGAGCTTCTTGATAAAC-
1 AGCTCTCATGAGCTTCCTGAT-ATCT
* * * * *
16992225 AACTCGCATGAGCTTCCCGTTATTT
1 AGCTCTCATGAGCTTCCTGATATCT
*
16992250 AGCTCACATGAGCTTCC
1 AGCTCTCATGAGCTTCC
16992267 CATTATATAG
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
24 22 0.23
25 72 0.77
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (25 bp):
AGCTCTCATGAGCTTCCTGATATCT
Found at i:16992208 original size:24 final size:25
Alignment explanation
Indices: 16992133--16992221 Score: 135
Period size: 25 Copynumber: 3.6 Consensus size: 25
16992123 CACAGCTCTC
16992133 ATGAGCTTCCTGATATCTAGCTATT
1 ATGAGCTTCCTGATATCTAGCTATT
*
16992158 ATGAGCTTCCTGATATCTAGCTCTT
1 ATGAGCTTCCTGATATCTAGCTATT
* *
16992183 ATGAGCTTCCTGAT-TTTAGCTTTT
1 ATGAGCTTCCTGATATCTAGCTATT
*
16992207 ATGAGCTTCTTGATA
1 ATGAGCTTCCTGATA
16992222 AACAACTCGC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 21 0.36
25 38 0.64
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (25 bp):
ATGAGCTTCCTGATATCTAGCTATT
Found at i:16992221 original size:49 final size:50
Alignment explanation
Indices: 16992126--16992221 Score: 149
Period size: 49 Copynumber: 1.9 Consensus size: 50
16992116 GACACACCAC
16992126 AGCTCTCATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGATATCT
1 AGCTCTCATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGATATCT
* * * *
16992176 AGCTCTTATGAGCTTCCTGAT-TTTAGCTTTTATGAGCTTCTTGATA
1 AGCTCTCATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGATA
16992222 AACAACTCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 22 0.52
50 20 0.48
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (50 bp):
AGCTCTCATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGATATCT
Found at i:16992236 original size:49 final size:50
Alignment explanation
Indices: 16992132--16992241 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 50
16992122 CCACAGCTCT
* * *
16992132 CATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGATATCTAGCTCT
1 CATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGATAACTAACTCG
* * * *
16992182 TATGAGCTTCCTGAT-TTTAGCTTTTATGAGCTTCTTGATAAAC-AACTCG
1 CATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGAT-AACTAACTCG
16992231 CATGAGCTTCC
1 CATGAGCTTCC
16992242 CGTTATTTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 35 0.69
50 16 0.31
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (50 bp):
CATGAGCTTCCTGATATCTAGCTATTATGAGCTTCCTGATAACTAACTCG
Found at i:16992267 original size:25 final size:25
Alignment explanation
Indices: 16992231--16992291 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
16992221 AAACAACTCG
* *
16992231 CATGAGCTTCCCGTTATTTAGCTCA
1 CATGAGCTTCCCATTATATAGCTCA
16992256 CATGAGCTTCCCATTATATAGCTCA
1 CATGAGCTTCCCATTATATAGCTCA
* *
16992281 AAAGAGCTTCC
1 CATGAGCTTCC
16992292 TGTTTACATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (25 bp):
CATGAGCTTCCCATTATATAGCTCA
Found at i:17010909 original size:22 final size:22
Alignment explanation
Indices: 17010883--17010925 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17010873 ATCTGGTTAG
*
17010883 GAGCCAATTGAGCTGATGGTTT
1 GAGCCAATTAAGCTGATGGTTT
*
17010905 GAGCCAATTAAGTTGATGGTT
1 GAGCCAATTAAGCTGATGGTT
17010926 CTTTTTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (22 bp):
GAGCCAATTAAGCTGATGGTTT
Found at i:17018311 original size:51 final size:51
Alignment explanation
Indices: 17018230--17018404 Score: 235
Period size: 51 Copynumber: 3.3 Consensus size: 51
17018220 ACTTCTGATC
* * *
17018230 AGTGACAAGTGATAAGTGGTAG-TCTCAGCTATACTTTTCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCT-TTAGCTACACTTATCTGATCAGTGACA
17018281 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG---A-T--C-AGTGACA
17018339 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
17018390 ATTGACAAGTGATAA
1 AGTGACAAGTGATAA
17018405 ATGTGATCTG
Statistics
Matches: 112, Mismatches: 4, Indels: 16
0.85 0.03 0.12
Matches are distributed among these distances:
51 57 0.51
52 2 0.02
54 2 0.02
55 2 0.02
57 1 0.01
58 48 0.43
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:17018337 original size:7 final size:7
Alignment explanation
Indices: 17018325--17018356 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
17018315 TTATCTGATT
17018325 AGTGACA
1 AGTGACA
17018332 AGTGACA
1 AGTGACA
17018339 AGTGACA
1 AGTGACA
*
17018346 AGTGATA
1 AGTGACA
17018353 AGTG
1 AGTG
17018357 GTAGCTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (7 bp):
AGTGACA
Found at i:17018339 original size:58 final size:58
Alignment explanation
Indices: 17018274--17018401 Score: 238
Period size: 58 Copynumber: 2.2 Consensus size: 58
17018264 TTTTCTGATC
*
17018274 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
17018332 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
17018390 ATTGACAAGTGA
1 AGTGACAAGTGA
17018402 TAAATGTGAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 68 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (58 bp):
AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:17037629 original size:26 final size:26
Alignment explanation
Indices: 17037593--17037648 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
17037583 TGAAATTCCA
17037593 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17037619 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17037645 ATCA
1 ATCA
17037649 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:17043167 original size:32 final size:33
Alignment explanation
Indices: 17043123--17043186 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
17043113 TGAGTGAATT
* *
17043123 TTCTTTTTAGTTTTA-TTTTGCTATT-TATTTTC
1 TTCTATTTAGTTTTAGTTTAG-TATTATATTTTC
17043155 TTCTATTTAGTTTTAGTTTAGTATTATATTTT
1 TTCTATTTAGTTTTAGTTTAGTATTATATTTT
17043187 TATTATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (33 bp):
TTCTATTTAGTTTTAGTTTAGTATTATATTTTC
Found at i:17044855 original size:22 final size:21
Alignment explanation
Indices: 17044819--17044869 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
17044809 TATTATGATG
17044819 AAATAAAGAAAAT-AAATAAAT
1 AAATAAAGAAAATAAAAT-AAT
*
17044840 AAATAACGAGAAATAAAATAAT
1 AAATAAAGA-AAATAAAATAAT
17044862 AAAATAAA
1 -AAATAAA
17044870 TCAAATCTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 8 0.32
22 7 0.28
23 10 0.40
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (21 bp):
AAATAAAGAAAATAAAATAAT
Found at i:17047140 original size:21 final size:21
Alignment explanation
Indices: 17047108--17047148 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17047098 TCGTGTGAGA
17047108 AATCTACTTATG-CTATGGATG
1 AATCTACTTATGTC-ATGGATG
17047129 AATCTA-TCTATGTCATGGAT
1 AATCTACT-TATGTCATGGAT
17047149 AAATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.06
21 16 0.89
22 1 0.06
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (21 bp):
AATCTACTTATGTCATGGATG
Found at i:17057033 original size:27 final size:27
Alignment explanation
Indices: 17057003--17057057 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17056993 AGCCGTTTAG
17057003 TAGCTGGTAAGTTTCTATTATGTTTCT
1 TAGCTGGTAAGTTTCTATTATGTTTCT
17057030 TAGCTGGTAAGTTTCTATTATGTTTCT
1 TAGCTGGTAAGTTTCTATTATGTTTCT
17057057 T
1 T
17057058 CACCCTCGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (27 bp):
TAGCTGGTAAGTTTCTATTATGTTTCT
Found at i:17061984 original size:42 final size:41
Alignment explanation
Indices: 17061891--17062032 Score: 110
Period size: 44 Copynumber: 3.3 Consensus size: 41
17061881 GACGTCCCAA
* * *
17061891 ACGTGGCCTTACATGTAATCAAATATCGATGCC-ACTGTTCTAG
1 ACGTGGTCTTACATGAAATCAAATA-CGATGCCAACT-CTC-AG
**
17061934 ACAAGGTCTTACATGAAATCAAATACGATGCCAACATCTCAG
1 ACGTGGTCTTACATGAAATCAAATACGATGCCAAC-TCTCAG
* * *
17061976 ACGTGGTCTTACACAT-ACATACCAAAT-TGATGCCAACTTCCCAG
1 ACGTGGTCTT--ACATGA-A-ATCAAATACGATGCCAAC-TCTCAG
17062020 ACGTGGTCTTACA
1 ACGTGGTCTTACA
17062033 CGACATCACA
Statistics
Matches: 82, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
42 20 0.24
43 26 0.32
44 30 0.37
45 6 0.07
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (41 bp):
ACGTGGTCTTACATGAAATCAAATACGATGCCAACTCTCAG
Found at i:17065857 original size:28 final size:28
Alignment explanation
Indices: 17065825--17065882 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
17065815 CTTGGGCTCG
17065825 AGCTGTGTGTAATTTTGAGTTGGTTTCT
1 AGCTGTGTGTAATTTTGAGTTGGTTTCT
17065853 AGCTGTGTGTAATTTTGAGTTGGTTTCT
1 AGCTGTGTGTAATTTTGAGTTGGTTTCT
17065881 AG
1 AG
17065883 TTGACACGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.16, C:0.07, G:0.29, T:0.48
Consensus pattern (28 bp):
AGCTGTGTGTAATTTTGAGTTGGTTTCT
Found at i:17066454 original size:13 final size:13
Alignment explanation
Indices: 17066436--17066463 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17066426 GGAGCACGAC
17066436 TCACACGGGCGTG
1 TCACACGGGCGTG
17066449 TCACACGGGCGTG
1 TCACACGGGCGTG
17066462 TC
1 TC
17066464 CCTGCCGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (13 bp):
TCACACGGGCGTG
Found at i:17067019 original size:15 final size:15
Alignment explanation
Indices: 17066999--17067030 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17066989 GGGTGAAACC
17066999 TAACAAGAGGATCCA
1 TAACAAGAGGATCCA
17067014 TAACAAGAGGATCCA
1 TAACAAGAGGATCCA
17067029 TA
1 TA
17067031 GGTCGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (15 bp):
TAACAAGAGGATCCA
Found at i:17073076 original size:13 final size:13
Alignment explanation
Indices: 17073058--17073085 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17073048 GGAGCACAAC
17073058 TCACACGGGCGTG
1 TCACACGGGCGTG
17073071 TCACACGGGCGTG
1 TCACACGGGCGTG
17073084 TC
1 TC
17073086 CCTGCCGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (13 bp):
TCACACGGGCGTG
Found at i:17075631 original size:43 final size:43
Alignment explanation
Indices: 17075582--17075733 Score: 216
Period size: 43 Copynumber: 3.6 Consensus size: 43
17075572 GGGCATTGGC
17075582 CCTAGCAGGCTATAATGCCGGTGAGATAATATCAGGCTTCGGG
1 CCTAGCAGGCTATAATGCCGGTGAGATAATATCAGGCTTCGGG
*
17075625 CCTAGCAGGCTATAATGCCGGTGAGATAATATCGGGCTTCGGG
1 CCTAGCAGGCTATAATGCCGGTGAGATAATATCAGGCTTCGGG
* ** * * **
17075668 CCTAGCAGGCTATAATGCTGGCAAAATGATATCAGGCTTCAAG
1 CCTAGCAGGCTATAATGCCGGTGAGATAATATCAGGCTTCGGG
*
17075711 CCTAGCAGGCGA-AATGCCGGTGA
1 CCTAGCAGGCTATAATGCCGGTGA
17075734 ATGAATTCAA
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 8 0.08
43 88 0.92
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (43 bp):
CCTAGCAGGCTATAATGCCGGTGAGATAATATCAGGCTTCGGG
Found at i:17075757 original size:41 final size:41
Alignment explanation
Indices: 17075711--17075814 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 41
17075701 AGGCTTCAAG
* *
17075711 CCTAGCAGGCGAAATGCCGGTGAATGAATTCAAACTTAAAG
1 CCTAGCAGGCTAAATGCCGGTGAATGAATTCAAACTTAAAA
* ** ****
17075752 TCTAGCAGGCTTCATGCCGGTG-ATGAATTCGGGTTTAAAA
1 CCTAGCAGGCTAAATGCCGGTGAATGAATTCAAACTTAAAA
17075792 CCTAGCAGGCTAAATGCCGGTGA
1 CCTAGCAGGCTAAATGCCGGTGA
17075815 TTTGATAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 32 0.64
41 18 0.36
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAATGCCGGTGAATGAATTCAAACTTAAAA
Found at i:17082024 original size:9 final size:9
Alignment explanation
Indices: 17082010--17082037 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
17082000 TCACACACCA
17082010 AAACTTACC
1 AAACTTACC
17082019 AAACTTACC
1 AAACTTACC
17082028 AAACTTACC
1 AAACTTACC
17082037 A
1 A
17082038 TTTCTCTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.21
Consensus pattern (9 bp):
AAACTTACC
Found at i:17082740 original size:43 final size:42
Alignment explanation
Indices: 17082675--17082833 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 42
17082665 AGCTCGTACA
* * * *
17082675 ATGCCGACGTCCCAGATATGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGACCCAGACATGGTCTTACACGTAATCAAATAT-G
* * * * * * *
17082718 ATGCCAATGTCTCAGACATGGTCTTATAGGAAATTAAATATG
1 ATGCCAACGACCCAGACATGGTCTTACACGTAATCAAATATG
*
17082760 ATGCCAACGACCCAAACATGGTCTTACACGTAAATACCAAATCA--
1 ATGCCAACGACCCAGACATGGTCTTACACGT-AAT--CAAAT-ATG
* * *
17082804 ATGCCAACGTCCCAGACCTGTTCTTACACG
1 ATGCCAACGACCCAGACATGGTCTTACACG
17082834 ATATCACATA
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
42 25 0.27
43 36 0.39
44 26 0.28
45 4 0.04
46 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (42 bp):
ATGCCAACGACCCAGACATGGTCTTACACGTAATCAAATATG
Found at i:17087951 original size:12 final size:12
Alignment explanation
Indices: 17087928--17087960 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17087918 AAAGAATATT
17087928 AGAAATGAAAAGA
1 AGAAA-GAAAAGA
17087941 AGAAAGAAAAGA
1 AGAAAGAAAAGA
17087953 A-AAAGAAA
1 AGAAAGAAA
17087961 TGGAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 8 0.40
13 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (12 bp):
AGAAAGAAAAGA
Found at i:17087961 original size:28 final size:27
Alignment explanation
Indices: 17087928--17087983 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
17087918 AAAGAATATT
17087928 AGAAATGAAAAGAAGAA-AGAAAAGAAAA
1 AGAAATGAAAAGAA-AATAGAAAA-AAAA
* *
17087956 AGAAATGGAATGAAAATAGAAAAAAAA
1 AGAAATGAAAAGAAAATAGAAAAAAAA
17087983 A
1 A
17087984 TCTAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (27 bp):
AGAAATGAAAAGAAAATAGAAAAAAAA
Found at i:17089569 original size:57 final size:56
Alignment explanation
Indices: 17089503--17089619 Score: 146
Period size: 57 Copynumber: 2.1 Consensus size: 56
17089493 AGATAAATAA
* *
17089503 GAAATATTTGAAAATGATTAAGATTTTCTACAAAATGAAAAT-GAAAATGGAGAAAT
1 GAAATATTTGAAAATGACTAAGATTTTCTACAAAATGAAAATGGAAAAT-GAAAAAT
* ** * *
17089559 GAAATCATTTGGAAATGACTGTGGTTTTCTCCAAAATGAAAATGGAAAATGAAAAAT
1 GAAAT-ATTTGAAAATGACTAAGATTTTCTACAAAATGAAAATGGAAAATGAAAAAT
17089616 GAAA
1 GAAA
17089620 ATGACTTGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 5 0.10
57 41 0.79
58 6 0.12
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (56 bp):
GAAATATTTGAAAATGACTAAGATTTTCTACAAAATGAAAATGGAAAATGAAAAAT
Found at i:17097537 original size:20 final size:20
Alignment explanation
Indices: 17097512--17097552 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
17097502 CTGCTTTTTC
17097512 TATCTCTTGAAATTTAGTTT
1 TATCTCTTGAAATTTAGTTT
17097532 TATCTCTTGAAATTTAGTTT
1 TATCTCTTGAAATTTAGTTT
17097552 T
1 T
17097553 CTTTTATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
TATCTCTTGAAATTTAGTTT
Found at i:17100357 original size:22 final size:22
Alignment explanation
Indices: 17100332--17100374 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17100322 AAATGATGAG
17100332 AATATAAGCTTTAAATTGTTTA
1 AATATAAGCTTTAAATTGTTTA
17100354 AATATAAGCTTTAAATTGTTT
1 AATATAAGCTTTAAATTGTTT
17100375 TTCTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (22 bp):
AATATAAGCTTTAAATTGTTTA
Found at i:17103443 original size:11 final size:11
Alignment explanation
Indices: 17103424--17103456 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
17103414 TTGAAACTTA
*
17103424 TCTTGAATATC
1 TCTTAAATATC
17103435 TCTTAAATATC
1 TCTTAAATATC
17103446 TCTTAAATATC
1 TCTTAAATATC
17103457 CTGGACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.45
Consensus pattern (11 bp):
TCTTAAATATC
Found at i:17110209 original size:16 final size:16
Alignment explanation
Indices: 17110184--17110226 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
17110174 TTATTTATAT
*
17110184 TTATTCATATAATAAA
1 TTATTAATATAATAAA
17110200 TTATTAATATAATAAA
1 TTATTAATATAATAAA
17110216 TTATTTAATAT
1 TTA-TTAATAT
17110227 TTTAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATTAATATAATAAA
Found at i:17110318 original size:15 final size:15
Alignment explanation
Indices: 17110298--17110354 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
17110288 ATTCAATATT
17110298 AATATTTTAATAATA
1 AATATTTTAATAATA
*
17110313 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
17110332 AATATATTAATAATA
1 AATATTTTAATAATA
*
17110347 AATGTTTT
1 AATATTTT
17110355 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:17115587 original size:21 final size:22
Alignment explanation
Indices: 17115547--17115588 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
17115537 GATTTCGATT
17115547 TTCTCATTATTCCTTCTCCCAC
1 TTCTCATTATTCCTTCTCCCAC
17115569 TTCT-ATTCATTCC-TCTCCCA
1 TTCTCATT-ATTCCTTCTCCCA
17115589 TCAATCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.45
Consensus pattern (22 bp):
TTCTCATTATTCCTTCTCCCAC
Found at i:17118669 original size:27 final size:27
Alignment explanation
Indices: 17118631--17118687 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
17118621 AATAGACTCT
17118631 TTCGTATATCCATTATCAGAATCCACA
1 TTCGTATATCCATTATCAGAATCCACA
*
17118658 TTCGTATATCCATTATCGGAATCCACA
1 TTCGTATATCCATTATCAGAATCCACA
17118685 TTC
1 TTC
17118688 CTACACTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (27 bp):
TTCGTATATCCATTATCAGAATCCACA
Found at i:17118880 original size:14 final size:14
Alignment explanation
Indices: 17118863--17118889 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17118853 AAAATATAAT
17118863 AAATTAAATTTTAA
1 AAATTAAATTTTAA
17118877 AAATTAAATTTTA
1 AAATTAAATTTTA
17118890 GAAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTAAATTTTAA
Found at i:17124669 original size:12 final size:13
Alignment explanation
Indices: 17124640--17124666 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17124630 ACTGAACAAT
17124640 TTATTGAAAAATC
1 TTATTGAAAAATC
17124653 TTATTGAAAAATC
1 TTATTGAAAAATC
17124666 T
1 T
17124667 ATTAAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTATTGAAAAATC
Found at i:17125757 original size:13 final size:13
Alignment explanation
Indices: 17125716--17125765 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
17125706 TGTCATGAAA
17125716 AAATATAATAAATT
1 AAATATAAT-AATT
* *
17125730 ATAATTTTAAAAATT
1 A-AA-TATAATAATT
17125745 AAATATAATAATT
1 AAATATAATAATT
17125758 AAATATAA
1 AAATATAA
17125766 AAAATATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 16 0.53
14 3 0.10
15 7 0.23
16 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAATAATT
Found at i:17125774 original size:29 final size:29
Alignment explanation
Indices: 17125716--17125774 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
17125706 TGTCATGAAA
**
17125716 AAATATAATAAATTATAATTTTAAAAATT
1 AAATATAATAAATTATAATTAAAAAAATT
17125745 AAATATAAT-AATTA-AATATAAAAAATATT
1 AAATATAATAAATTATAAT-TAAAAAA-ATT
17125774 A
1 A
17125775 TAAAAATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 3 0.12
28 10 0.38
29 13 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATATAATAAATTATAATTAAAAAAATT
Found at i:17134596 original size:165 final size:165
Alignment explanation
Indices: 17134324--17134653 Score: 660
Period size: 165 Copynumber: 2.0 Consensus size: 165
17134314 AAGCAATTGA
17134324 ATTGTAAATTAAGAGATATAATGAATTTTGTGAGACAAGGTCAGAATAAATTCGGATTCTCCTAT
1 ATTGTAAATTAAGAGATATAATGAATTTTGTGAGACAAGGTCAGAATAAATTCGGATTCTCCTAT
17134389 TCTGACTTTGAAAAATCACAAAAAATTGAAGAAAAATAATTAGAGGCTTAAAGTTATATGTTTAA
66 TCTGACTTTGAAAAATCACAAAAAATTGAAGAAAAATAATTAGAGGCTTAAAGTTATATGTTTAA
17134454 AATCCTTAATTGGTCTATTTTTAAGAGAAATCAAT
131 AATCCTTAATTGGTCTATTTTTAAGAGAAATCAAT
17134489 ATTGTAAATTAAGAGATATAATGAATTTTGTGAGACAAGGTCAGAATAAATTCGGATTCTCCTAT
1 ATTGTAAATTAAGAGATATAATGAATTTTGTGAGACAAGGTCAGAATAAATTCGGATTCTCCTAT
17134554 TCTGACTTTGAAAAATCACAAAAAATTGAAGAAAAATAATTAGAGGCTTAAAGTTATATGTTTAA
66 TCTGACTTTGAAAAATCACAAAAAATTGAAGAAAAATAATTAGAGGCTTAAAGTTATATGTTTAA
17134619 AATCCTTAATTGGTCTATTTTTAAGAGAAATCAAT
131 AATCCTTAATTGGTCTATTTTTAAGAGAAATCAAT
17134654 GGGAATATTA
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 165 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (165 bp):
ATTGTAAATTAAGAGATATAATGAATTTTGTGAGACAAGGTCAGAATAAATTCGGATTCTCCTAT
TCTGACTTTGAAAAATCACAAAAAATTGAAGAAAAATAATTAGAGGCTTAAAGTTATATGTTTAA
AATCCTTAATTGGTCTATTTTTAAGAGAAATCAAT
Found at i:17135323 original size:14 final size:14
Alignment explanation
Indices: 17135304--17135332 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17135294 AATGAAAGTG
17135304 AATTGAGAATTGAA
1 AATTGAGAATTGAA
17135318 AATTGAGAATTGAA
1 AATTGAGAATTGAA
17135332 A
1 A
17135333 TACCCTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.28
Consensus pattern (14 bp):
AATTGAGAATTGAA
Found at i:17135441 original size:23 final size:23
Alignment explanation
Indices: 17135411--17135495 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 23
17135401 TTTACTGATC
*
17135411 AGGCACTTTATGTGTCGTATTTT
1 AGGCACTTCATGTGTCGTATTTT
* *
17135434 AGGCACTTCGTGTGTCGTA--TC
1 AGGCACTTCATGTGTCGTATTTT
* *
17135455 AGGCACCTCGTGTGTCG--TTTT
1 AGGCACTTCATGTGTCGTATTTT
* *
17135476 AGGCACTTTATGTGTTGTAT
1 AGGCACTTCATGTGTCGTAT
17135496 ATTGATCAGG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
21 31 0.63
23 18 0.37
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.41
Consensus pattern (23 bp):
AGGCACTTCATGTGTCGTATTTT
Found at i:17135458 original size:21 final size:21
Alignment explanation
Indices: 17135408--17135483 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
17135398 GGCTTTACTG
**
17135408 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTCGTGTGTCGT
*
17135429 ATTTTAGGCACTTCGTGTGTCGT
1 A--TCAGGCACTTCGTGTGTCGT
*
17135452 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTCGTGTGTCGT
* *
17135473 TTTAGGCACTT
1 ATCAGGCACTT
17135484 TATGTGTTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 27 0.60
23 18 0.40
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (21 bp):
ATCAGGCACTTCGTGTGTCGT
Found at i:17143280 original size:25 final size:25
Alignment explanation
Indices: 17143252--17143303 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
17143242 TTTGGCTTGA
**
17143252 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
17143277 CATTTATTATGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
17143302 CA
1 CA
17143304 AATTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:17145900 original size:36 final size:35
Alignment explanation
Indices: 17145798--17145900 Score: 93
Period size: 35 Copynumber: 2.9 Consensus size: 35
17145788 CGATTAACGA
* * *
17145798 TGGGCTTAAATCTTTGTCGATTTATTCGATTAGTAC
1 TGGGC-TAAATCTTTGTCGGTTTATTCGACTAGCAC
** * *
17145834 AAGGC-ACATCTACTGTCGGTTTA-TCTGACTAGCAC
1 TGGGCTAAATCT-TTGTCGGTTTATTC-GACTAGCAC
17145869 TGGGCATAAATCTTTGTCGGTTTATTCGACTA
1 TGGGC-TAAATCTTTGTCGGTTTATTCGACTA
17145901 CTGCTGGGCA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
34 7 0.14
35 19 0.37
36 18 0.35
37 7 0.14
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (35 bp):
TGGGCTAAATCTTTGTCGGTTTATTCGACTAGCAC
Found at i:17148185 original size:95 final size:94
Alignment explanation
Indices: 17148013--17148294 Score: 287
Period size: 95 Copynumber: 3.0 Consensus size: 94
17148003 TATCTTACTG
* ** *
17148013 ATGGATAAGATCTTGCATATATTGCGGATT-TTGCACAGCTAGTGTGAGTAATATCATGTACCGG
1 ATGGATAAGATCCTGCATATATTGCGGATTCTT-CACAGCTAGTGTGAGTAGCATCA-GTAACGG
* *
17148077 TTAATGTCCCGATTTACTAGATACCTTATCA
64 TTAATGTCTCGATTTACTAGATACCTTACCA
* * * *
17148108 ATGGCTAAGATCCTGCATATATTGTGGATTCTTCACAACTAGTGTGAGCAGCATCAGATAACGGT
1 ATGGATAAGATCCTGCATATATTGCGGATTCTTCACAGCTAGTGTGAGTAGCATCAG-TAACGGT
* * * * * *
17148173 TAATGTATCGATTTATTGGATATCTTGCCG
65 TAATGTCTCGATTTACTAGATACCTTACCA
* * * * ** ** * *
17148203 ATGGATAAGATTCTGCTTGTGTTGCATATTCTTCACAGCTCCTGTCAGTAGCATCGTGTAACGGT
1 ATGGATAAGATCCTGCATATATTGCGGATTCTTCACAGCTAGTGTGAGTAGCATC-AGTAACGGT
17148268 TAATGTCTCGATTTACTAGATACCTTA
65 TAATGTCTCGATTTACTAGATACCTTA
17148295 AATGCTCGAG
Statistics
Matches: 149, Mismatches: 35, Indels: 6
0.78 0.18 0.03
Matches are distributed among these distances:
94 1 0.01
95 145 0.97
96 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (94 bp):
ATGGATAAGATCCTGCATATATTGCGGATTCTTCACAGCTAGTGTGAGTAGCATCAGTAACGGTT
AATGTCTCGATTTACTAGATACCTTACCA
Found at i:17150117 original size:20 final size:20
Alignment explanation
Indices: 17150089--17150133 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
17150079 AACCGTCTTC
*
17150089 AAGGTTATGTCGCGACATTA
1 AAGGCTATGTCGCGACATTA
*
17150109 AAGGCTATGTCGCGACATTC
1 AAGGCTATGTCGCGACATTA
17150129 AAGGC
1 AAGGC
17150134 AGTTTCCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
AAGGCTATGTCGCGACATTA
Found at i:17152101 original size:22 final size:22
Alignment explanation
Indices: 17152071--17152115 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17152061 CTTTAGCCAT
17152071 TTTTATTTTTATTGCAATTTAC
1 TTTTATTTTTATTGCAATTTAC
* **
17152093 TTTTGTTTTTATTTTAATTTAC
1 TTTTATTTTTATTGCAATTTAC
17152115 T
1 T
17152116 AATTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATTTTTATTGCAATTTAC
Found at i:17160514 original size:16 final size:18
Alignment explanation
Indices: 17160495--17160527 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
17160485 CTCCCTATCT
17160495 TATTAT-ATTT-TATTTC
1 TATTATGATTTATATTTC
17160511 TATTATGATTTATATTT
1 TATTATGATTTATATTT
17160528 ATTTGTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTATGATTTATATTTC
Found at i:17166121 original size:44 final size:44
Alignment explanation
Indices: 17166058--17166173 Score: 189
Period size: 44 Copynumber: 2.6 Consensus size: 44
17166048 GGATCACATT
17166058 TATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGC
* *
17166102 TATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGC
1 TATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGC
*
17166146 TA-CTACTTATCACTTGTCACTGATCAGA
1 TATC-ACTTGTCACTTGTCACTGATCAGA
17166174 AGTACTCAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 1 0.01
44 67 0.99
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (44 bp):
TATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGC
Found at i:17166979 original size:28 final size:28
Alignment explanation
Indices: 17166947--17167003 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
17166937 ATGATTTACA
17166947 ATTCCATTACTTACACTGTTTCTTCTAT
1 ATTCCATTACTTACACTGTTTCTTCTAT
* *
17166975 ATTCCGTTACTTACATTGTTTCTTCTAT
1 ATTCCATTACTTACACTGTTTCTTCTAT
17167003 A
1 A
17167004 AGAAACTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (28 bp):
ATTCCATTACTTACACTGTTTCTTCTAT
Found at i:17168496 original size:20 final size:20
Alignment explanation
Indices: 17168471--17168521 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
17168461 AAATTGAATG
17168471 AAATGTAAAATTTTAGGGTA
1 AAATGTAAAATTTTAGGGTA
17168491 AAATGTAAAATTTTAGGGTA
1 AAATGTAAAATTTTAGGGTA
17168511 AAATGTAAAAT
1 AAATGTAAAAT
17168522 GTTGATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (20 bp):
AAATGTAAAATTTTAGGGTA
Found at i:17169354 original size:14 final size:16
Alignment explanation
Indices: 17169330--17169361 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17169320 AAGATGATAT
17169330 GTTGAATTATAT-TTG
1 GTTGAATTATATCTTG
17169345 GTTG-ATTATATCTTG
1 GTTGAATTATATCTTG
17169360 GT
1 GT
17169362 ATGTGAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.53
Consensus pattern (16 bp):
GTTGAATTATATCTTG
Found at i:17171669 original size:15 final size:15
Alignment explanation
Indices: 17171651--17171680 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17171641 AAATTTTAAT
*
17171651 TTTTTATAGTTTATA
1 TTTTTATAATTTATA
17171666 TTTTTATAATTTATA
1 TTTTTATAATTTATA
17171681 AAGGATTAAA
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:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTATA
Found at i:17173933 original size:20 final size:21
Alignment explanation
Indices: 17173910--17173960 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
17173900 GTGATTTAGG
*
17173910 AGTTTTTTTTATA-TATTTAA
1 AGTTTTTTATATATTATTTAA
*
17173930 AGTTTTTTATATATTCTTTAA
1 AGTTTTTTATATATTATTTAA
17173951 A-TTTTTTATA
1 AGTTTTTTATA
17173961 ATTTTTTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
AGTTTTTTATATATTATTTAA
Found at i:17178548 original size:52 final size:52
Alignment explanation
Indices: 17178469--17178737 Score: 502
Period size: 52 Copynumber: 5.1 Consensus size: 52
17178459 TACTTCTGAT
17178469 CAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
17178522 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
17178574 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
17178626 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
17178678 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
17178730 CAAAGTGA
1 C-AAGTGA
17178738 TAGGTGGCTA
Statistics
Matches: 213, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
52 200 0.94
53 13 0.06
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
Found at i:17178753 original size:37 final size:35
Alignment explanation
Indices: 17178706--17178774 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
17178696 TGATAGCTTC
*
17178706 GGCTATACTTATCTGATCAAGAGACAAAGTGATAGGT
1 GGCTACACTTATCTGATC-AGAGAC-AAGTGATAGGT
*
17178743 GGCTACACTTATCTGATCAGGGACAAGTGATA
1 GGCTACACTTATCTGATCAGAGACAAGTGATA
17178775 AGTGATCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 8 0.27
36 5 0.17
37 17 0.57
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (35 bp):
GGCTACACTTATCTGATCAGAGACAAGTGATAGGT
Found at i:17182370 original size:28 final size:28
Alignment explanation
Indices: 17182319--17182372 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
17182309 TGCCCACTTA
* ***
17182319 TCCCAGATTGGTACCTATTGTTTTTTTG
1 TCCCAGATTAGTACCTAAACTTTTTTTG
17182347 TCCCAGATTAGTACCTAAACTTTTTT
1 TCCCAGATTAGTACCTAAACTTTTTT
17182373 CCATCCACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.46
Consensus pattern (28 bp):
TCCCAGATTAGTACCTAAACTTTTTTTG
Found at i:17183448 original size:6 final size:6
Alignment explanation
Indices: 17183437--17183488 Score: 61
Period size: 6 Copynumber: 8.3 Consensus size: 6
17183427 AAGTAATGTG
*
17183437 AGAAAA AGAAAAA AGAAATTA AAAAAA AG-AAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AG-AAAA AGAAA--A AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
17183487 AG
1 AG
17183489 CTACAAATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.12
6 24 0.60
7 6 0.15
8 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AGAAAA
Found at i:17199821 original size:177 final size:176
Alignment explanation
Indices: 17199525--17200130 Score: 808
Period size: 177 Copynumber: 3.4 Consensus size: 176
17199515 TTCGACTAGC
* * * *
17199525 CTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCTATGTACCAGCTA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATC-GCTA
* * * * *
17199590 TGGAGTAGATCAAAGATGACGAGTCTTATCTCCATGTATTGGCTATGGAGCAGATTTTAGCCAAC
65 TGGAGCAGATCAAAGATGGCAAGTCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCAAC
*
17199655 AGTCTTATCTCTCTGAGGTGGCAAGAGAGCAGGTTGAAGATACAAGT
130 AGTCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAAGT
*
17199702 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTTCATGTATCGCCTA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCG-CTA
*
17199767 TGGAGCAGATTAGAA-ATGGCAAGTCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCC-A
65 TGGAGCAGATCA-AAGATGGCAAGTCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCAA
*
17199830 CTAGTCTTATCTCTCTGAGGTAGCAAGATAGCAGGTTGAAGATACAAGT
129 C-AGTCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAAGT
* * ** * ** * * * * *
17199879 TTTATCTTCCTGAGCTAACA-AGAAAGCAGACTGGAAATTATAGATCTTATCTCCATGTATCGAC
1 CTTAACCCCCTAAGC-AGTAGGGTAA-CAGGCTGAAAATTACAGATCTTATCTCCATGTATCG-C
*
17199943 TATGGAGCAGATCAAAGATGGCAAGTCTTATCTCTATGTATCGGCTATGGAGTAGATTTTAGCCA
63 TATGGAGCAGATCAAAGATGGCAAGTCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCA
* * * *
17200008 AC-GACCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATACGATT
128 ACAG-TCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAAGT
* *
17200057 CTTAA-CCCCTAAGTAGTAAGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGGCTA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATC-GCTA
17200121 TGGAGCAGAT
65 TGGAGCAGAT
17200131 TTTAGCCACC
Statistics
Matches: 372, Mismatches: 47, Indels: 21
0.85 0.11 0.05
Matches are distributed among these distances:
176 50 0.13
177 181 0.49
178 139 0.37
179 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (176 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCATGTATCGCTAT
GGAGCAGATCAAAGATGGCAAGTCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCAACA
GTCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACAAGT
Found at i:17200133 original size:131 final size:133
Alignment explanation
Indices: 17199968--17200250 Score: 462
Period size: 131 Copynumber: 2.1 Consensus size: 133
17199958 AGATGGCAAG
* *
17199968 TCTTATCTCTATGTATCGGCTATGGAGTAGATTTTAGCCAACGACCTTATCTCTCTAAGGTAGCA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAACGACCTTATCTCTCTAAGGTAGCA
* * * *
17200033 AGAGAGCAGGTTGAAGATACGATTCTTAA-CCCCTAAGTAGTAAGGTAACAGGCT-GAAAATTAC
66 AGAGAGCAGGTTAAAGATACGAGTCTTAACCCCCTAAGCAGTAAGGTAACAAGCTGGAAAATTAC
17200096 AGA
131 AGA
* *
17200099 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCGACCTTATCTCTCTGAGGTAGCA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAACGACCTTATCTCTCTAAGGTAGCA
* *
17200164 AGAGAGCAGGTTAAAGATACGAGTCTTAACCCCCTAAGCAGTAGGGTAACAAGCTGGAAAATTTC
66 AGAGAGCAGGTTAAAGATACGAGTCTTAACCCCCTAAGCAGTAAGGTAACAAGCTGGAAAATTAC
17200229 AGA
131 AGA
17200232 TCTTATCTCCATGTATCGG
1 TCTTATCTCCATGTATCGG
17200251 TTATAGAGTA
Statistics
Matches: 140, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 88 0.63
132 22 0.16
133 30 0.21
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (133 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAACGACCTTATCTCTCTAAGGTAGCA
AGAGAGCAGGTTAAAGATACGAGTCTTAACCCCCTAAGCAGTAAGGTAACAAGCTGGAAAATTAC
AGA
Found at i:17200277 original size:45 final size:45
Alignment explanation
Indices: 17200221--17200353 Score: 178
Period size: 45 Copynumber: 3.0 Consensus size: 45
17200211 AACAAGCTGG
* *
17200221 AAAATTTCAGATCTTATCTCCATGTATCGGTTATAGAGTAGATCA
1 AAAATTACAGATCTTATCTCCATGTATCGGTTATAGAGCAGATCA
17200266 AAAATTACAGATCTTATCTCCATGTATCGGTTATAGAGCAGATCA
1 AAAATTACAGATCTTATCTCCATGTATCGGTTATAGAGCAGATCA
* ** * * *
17200311 AAGA-TGGAGAGTCTTATCTCTATGTATCGGCTATGGAGCAGAT
1 AAAATTACAGA-TCTTATCTCCATGTATCGGTTATAGAGCAGAT
17200354 TTTAGCCACC
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.05
45 75 0.95
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (45 bp):
AAAATTACAGATCTTATCTCCATGTATCGGTTATAGAGCAGATCA
Found at i:17201956 original size:3 final size:3
Alignment explanation
Indices: 17201950--17202014 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
17201940 TTTTTTTAAA
* * *
17201950 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT -TCT GTT A-T AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
* *
17201994 ATT ATT ATC ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
17202015 TTTCTATTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.06
3 49 0.92
4 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17205092 original size:18 final size:16
Alignment explanation
Indices: 17205069--17205105 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
17205059 AAACTTATTA
17205069 AAATTATAAAAATCTAAT
1 AAATTAT-AAAAT-TAAT
17205087 AAATTATAAAATTAAT
1 AAATTATAAAATTAAT
17205103 AAA
1 AAA
17205106 ACTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 5 0.26
18 7 0.37
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAATTAAT
Found at i:17205118 original size:20 final size:20
Alignment explanation
Indices: 17205045--17205118 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 20
17205035 ATAGTAAAAT
*
17205045 ATTAAAATTAACAGAAACTT-
1 ATTAAAATTAATA-AAACTTA
17205065 ATTAAAATT-ATAAAAATCTAATAA
1 ATTAAAATTAAT-AAAA-CT--T-A
17205089 ATTATAAAATTAATAAAACTTA
1 A-T-TAAAATTAATAAAACTTA
17205111 ATTAAAAT
1 ATTAAAAT
17205119 ATTTAAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 18
0.70 0.02 0.29
Matches are distributed among these distances:
19 4 0.09
20 18 0.41
21 1 0.02
22 3 0.07
23 1 0.02
24 1 0.02
25 3 0.07
26 11 0.25
27 2 0.05
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (20 bp):
ATTAAAATTAATAAAACTTA
Found at i:17205136 original size:45 final size:46
Alignment explanation
Indices: 17205047--17205138 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 46
17205037 AGTAAAATAT
*
17205047 TAAAATTAACAGAAACTTATTAAAATTATAAAAATCTAATAAATTA
1 TAAAATTAACAGAAACTTATTAAAATTATAAAAATCTAAAAAATTA
* *
17205093 TAAAATTAATA-AAACTTAATTAAAA-TATTTAAAAT-TAAAAAATTA
1 TAAAATTAACAGAAACTT-ATTAAAATTA-TAAAAATCTAAAAAATTA
17205138 T
1 T
17205139 TAGAATTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
45 18 0.44
46 23 0.56
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (46 bp):
TAAAATTAACAGAAACTTATTAAAATTATAAAAATCTAAAAAATTA
Found at i:17205140 original size:26 final size:25
Alignment explanation
Indices: 17205066--17205172 Score: 74
Period size: 26 Copynumber: 4.0 Consensus size: 25
17205056 CAGAAACTTA
*
17205066 TTAAAATTATAAAAATCTAAT-AAATT
1 TTAAAATTA-AAAAAT-TATTAAAATT
*
17205092 ATAAAATTAATAAAACTTAATTAAAATAT
1 TTAAAATTAA-AAAA-TT-ATTAAAAT-T
*
17205121 TTAAAATTAAAAAATTATTAGAATT
1 TTAAAATTAAAAAATTATTAAAATT
* *
17205146 CTTCAAATTATGAAAAA-TACTAAAATT
1 -TTAAAATTA--AAAAATTATTAAAATT
17205173 GGTATAAACT
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
25 2 0.03
26 28 0.42
27 13 0.20
28 13 0.20
29 10 0.15
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (25 bp):
TTAAAATTAAAAAATTATTAAAATT
Found at i:17206208 original size:10 final size:10
Alignment explanation
Indices: 17206115--17206210 Score: 54
Period size: 10 Copynumber: 9.5 Consensus size: 10
17206105 TTTATGTTTT
*
17206115 TTTTTTCTAA
1 TTTTTTATAA
17206125 -TTTTTATAA
1 TTTTTTATAA
* *
17206134 GTTTATATCAA
1 TTTTTTAT-AA
*
17206145 -TTTTCAT-A
1 TTTTTTATAA
*
17206153 TTTTTAAATATA
1 TTTTT-TATA-A
* *
17206165 TTTTTTGTAT
1 TTTTTTATAA
17206175 TTTTTTATAA
1 TTTTTTATAA
* *
17206185 TGTTTTTCTGA
1 T-TTTTTATAA
17206196 TTTTTTATAA
1 TTTTTTATAA
17206206 TTTTT
1 TTTTT
17206211 AATATTTTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
8 1 0.02
9 12 0.18
10 34 0.52
11 12 0.18
12 6 0.09
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:17214718 original size:41 final size:38
Alignment explanation
Indices: 17214673--17214808 Score: 137
Period size: 38 Copynumber: 3.5 Consensus size: 38
17214663 TAATGTTCAC
* *
17214673 TTGAGCAATACTCAGTATAATCAGTGAATTATTTTGCTCGA
1 TTGAGCAACACTCAGTATAATCAGT--A-GATTTTGCTCGA
* * *
17214714 TTGAGCGACATTCAGTATATTCAGTAGATTTTGCTCGA
1 TTGAGCAACACTCAGTATAATCAGTAGATTTTGCTCGA
* ** * * *
17214752 TTGAGAAACGTTCAGTATATTCAGTAGATTTTACTTGA
1 TTGAGCAACACTCAGTATAATCAGTAGATTTTGCTCGA
*
17214790 TTGAGCAACATTCAGTATA
1 TTGAGCAACACTCAGTATA
17214809 TTTGGTATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
38 61 0.73
39 1 0.01
41 21 0.25
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (38 bp):
TTGAGCAACACTCAGTATAATCAGTAGATTTTGCTCGA
Found at i:17214754 original size:38 final size:38
Alignment explanation
Indices: 17214703--17214810 Score: 171
Period size: 38 Copynumber: 2.8 Consensus size: 38
17214693 TCAGTGAATT
*
17214703 ATTTTGCTCGATTGAGCGACATTCAGTATATTCAGTAG
1 ATTTTGCTCGATTGAGCAACATTCAGTATATTCAGTAG
* *
17214741 ATTTTGCTCGATTGAGAAACGTTCAGTATATTCAGTAG
1 ATTTTGCTCGATTGAGCAACATTCAGTATATTCAGTAG
* *
17214779 ATTTTACTTGATTGAGCAACATTCAGTATATT
1 ATTTTGCTCGATTGAGCAACATTCAGTATATT
17214811 TGGTATTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (38 bp):
ATTTTGCTCGATTGAGCAACATTCAGTATATTCAGTAG
Found at i:17216551 original size:27 final size:27
Alignment explanation
Indices: 17216513--17216577 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
17216503 CACATATTAT
* *
17216513 TACTTTACAGACTAGCTCAAACTTAAA
1 TACTTTATAGACCAGCTCAAACTTAAA
** *
17216540 TACTTTATAGACCAGCTCGCACTTAGA
1 TACTTTATAGACCAGCTCAAACTTAAA
17216567 TACTTTATAGA
1 TACTTTATAGA
17216578 GAGCCCACAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (27 bp):
TACTTTATAGACCAGCTCAAACTTAAA
Found at i:17216779 original size:17 final size:17
Alignment explanation
Indices: 17216759--17216872 Score: 140
Period size: 17 Copynumber: 6.8 Consensus size: 17
17216749 ACAGTTCACT
* *
17216759 TATAAACACAGCTTGTA
1 TATAAACACAGCTAGCA
* *
17216776 TATAAACACAACTCGCA
1 TATAAACACAGCTAGCA
* *
17216793 TAT-AACACAACTAACA
1 TATAAACACAGCTAGCA
*
17216809 TATAAACACAGCTCGCA
1 TATAAACACAGCTAGCA
17216826 TATAAACACAGCTAGCA
1 TATAAACACAGCTAGCA
*
17216843 TATAAACAGAGCTAGCA
1 TATAAACACAGCTAGCA
*
17216860 TATAAACAGAGCT
1 TATAAACACAGCT
17216873 CGTACATTGT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
16 14 0.16
17 72 0.84
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (17 bp):
TATAAACACAGCTAGCA
Found at i:17216829 original size:50 final size:51
Alignment explanation
Indices: 17216759--17216874 Score: 155
Period size: 50 Copynumber: 2.3 Consensus size: 51
17216749 ACAGTTCACT
* * *
17216759 TATAAACACAGCTTGTATATAAACACAACTCGCATATAACACA-A-CTAACA
1 TATAAACACAGCTCGCATATAAACACAACTAGCATATAA-ACAGAGCTAACA
* *
17216809 TATAAACACAGCTCGCATATAAACACAGCTAGCATATAAACAGAGCTAGCA
1 TATAAACACAGCTCGCATATAAACACAACTAGCATATAAACAGAGCTAACA
*
17216860 TATAAACAGAGCTCG
1 TATAAACACAGCTCG
17216875 TACATTGTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 3 0.05
50 36 0.62
51 19 0.33
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (51 bp):
TATAAACACAGCTCGCATATAAACACAACTAGCATATAAACAGAGCTAACA
Found at i:17226148 original size:51 final size:51
Alignment explanation
Indices: 17226067--17226234 Score: 273
Period size: 51 Copynumber: 3.3 Consensus size: 51
17226057 CGGATCACAT
** * *
17226067 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTTGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTGAGGCTACCAC
*
17226118 TTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAACTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTGAGGCTACCAC
* *
17226169 TTATCACTTATCACTTGTCACTGATCAGATAAATGTAACTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTGAGGCTACCAC
17226220 TTATCACTTGTCACT
1 TTATCACTTGTCACT
17226235 AATCCGAAGT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 108 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAACTGAGGCTACCAC
Done.