Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 11 of 402
Found at i:2210055 original size:16 final size:16
Alignment explanation
Indices: 2210009--2210061 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
2209999 ATTATTATTA
2210009 TTTTTTATTTATCCTAT
1 TTTTTTATTTAT-CTAT
* *
2210026 CTTTTCTAAATTATCTAT
1 -TTTT-TTATTTATCTAT
*
2210044 TTTTTTATTTATTTAT
1 TTTTTTATTTATCTAT
2210060 TT
1 TT
2210062 GATTTTGGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 11 0.38
17 4 0.14
18 8 0.28
19 6 0.21
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTATTTATCTAT
Found at i:2210442 original size:31 final size:31
Alignment explanation
Indices: 2210383--2210451 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
2210373 AATTTCCAGA
*
2210383 TTCCGGCGAA-AATTCCGACGAAATTTGAATT
1 TTCCGGC-AACAATTCCGACGAAATTTGAAGT
* *
2210414 TTTCGGCAACAATTCCGGCGAACA-TTGAAGT
1 TTCCGGCAACAATTCCGACGAA-ATTTGAAGT
2210445 TTCCGGC
1 TTCCGGC
2210452 GACCTGCCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.06
31 29 0.91
32 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (31 bp):
TTCCGGCAACAATTCCGACGAAATTTGAAGT
Found at i:2210951 original size:10 final size:10
Alignment explanation
Indices: 2210936--2210982 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
2210926 TTTAACATTC
2210936 TTTTTATCTT
1 TTTTTATCTT
*
2210946 TTTTTATTTT
1 TTTTTATCTT
*
2210956 TATTTTGT-TT
1 T-TTTTATCTT
2210966 TTTTTATCTT
1 TTTTTATCTT
*
2210976 TATTTAT
1 TTTTTAT
2210983 TTTCACTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 5 0.16
10 21 0.68
11 5 0.16
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTTTATCTT
Found at i:2210970 original size:30 final size:31
Alignment explanation
Indices: 2210931--2211009 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
2210921 GTTTATTTAA
* * *
2210931 CATTCTTTTTATCTTTTTTTATTTTTA-TTT
1 CATTTTTTTTATCTTTATTTATTTTCACTTT
**
2210961 TGTTTTTTTTATCTTTATTTATTTTCACTTT
1 CATTTTTTTTATCTTTATTTATTTTCACTTT
2210992 CATTTTTTTTAT-TTTATT
1 CATTTTTTTTATCTTTATT
2211010 ATTCTATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 28 0.68
31 13 0.32
ACGTcount: A:0.14, C:0.09, G:0.01, T:0.76
Consensus pattern (31 bp):
CATTTTTTTTATCTTTATTTATTTTCACTTT
Found at i:2211001 original size:16 final size:15
Alignment explanation
Indices: 2210936--2211009 Score: 73
Period size: 15 Copynumber: 4.9 Consensus size: 15
2210926 TTTAACATTC
*
2210936 TTTTTATCTTTTTTT
1 TTTTTATCTTTATTT
*
2210951 ATTTTTAT-TTTGTTT
1 -TTTTTATCTTTATTT
2210966 TTTTTATCTTTATTT
1 TTTTTATCTTTATTT
*
2210981 ATTTTCA-CTTTCATTT
1 -TTTTTATCTTT-ATTT
2210997 TTTTTAT-TTTATT
1 TTTTTATCTTTATT
2211010 ATTCTATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.20
15 24 0.48
16 16 0.32
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTTATCTTTATTT
Found at i:2211116 original size:59 final size:59
Alignment explanation
Indices: 2211027--2211501 Score: 536
Period size: 59 Copynumber: 8.0 Consensus size: 59
2211017 TTTCTTTAAA
* * * *
2211027 TAAAAATCAAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAATCAAAATTTCAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** * *
2211086 TAAAAAT-AAAATTTCAAAAAAAAGGGTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAATCAAAATTTCAAAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* *
2211145 TAAAGATCAAAATTTCCAAAAAAATTATTTTT-ACGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAAATTT-CAAAAAAA-AATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
* * **
2211206 TGAAAATCAAAGTTTTCAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAA-ATTTCAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * * * *
2211266 TGAAAATCGAAGTTTCCAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAAATTTCAAAAAAAAATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCT
*
2211325 TAAAAATCAAAATTTCAAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-
1 TAAAAATCAAAATTTC-AAAAAA-AAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** * *
2211385 TCGAAATTAAAGTTTCAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATCAAAATTTCAAAAAAAA-ATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
* *
2211445 T---AAT-AAATTTTCAAAAAAAATAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATCAAAATTTC--AAAAAA-AAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
2211502 CTGTACAAGA
Statistics
Matches: 363, Mismatches: 35, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
56 7 0.02
57 3 0.01
58 56 0.15
59 138 0.38
60 68 0.19
61 86 0.24
62 5 0.01
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (59 bp):
TAAAAATCAAAATTTCAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:2211184 original size:120 final size:119
Alignment explanation
Indices: 2211029--2211499 Score: 620
Period size: 120 Copynumber: 4.0 Consensus size: 119
2211019 TCTTTAAATA
* *
2211029 AAAATCAAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-
1 AAAATCAAAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC
***
2211093 AAAATTTCAAAAAAA-AGGGTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTT
66 AAAATTTCAAAAAAATAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTT
* *
2211146 AAAGATCAAAATTTCCAAAAAAATTATTTTTACGGAAAAGTTGAAAGTATCAATTTTCCTTGAAA
1 AAA-ATCAAAATTTCC-AAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
* * *
2211211 ATCAAAGTTTTCAAAAAAAGT---TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
63 ATCAAA-ATTTCAAAAAAA-TAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTT
* *
2211267 GAAAATCGAAGTTTCCAAAAAATATTTTT-GGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
1 -AAAATCAAAATTTCCAAAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAA
* *
2211331 TCAAAATTTCAAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTC
64 TCAAAATTTCAAAAAAATAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTT
* * * *
2211387 GAAATTAAAGTTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AAT
1 AAAATCAAAATTTC-CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
*
2211449 -AAATTTTCAAAAAAAATAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTT
65 CAAAATTTC-AAAAAAATAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTT
2211500 CCCTGTACAA
Statistics
Matches: 318, Mismatches: 21, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
116 7 0.02
117 48 0.15
118 25 0.08
119 59 0.19
120 117 0.37
121 48 0.15
122 14 0.04
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (119 bp):
AAAATCAAAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATC
AAAATTTCAAAAAAATAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTT
Found at i:2211365 original size:180 final size:177
Alignment explanation
Indices: 2211029--2211501 Score: 595
Period size: 180 Copynumber: 2.6 Consensus size: 177
2211019 TCTTTAAATA
* * * *
2211029 AAAATCAAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATA
1 AAAATCAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATA
* * * *
2211094 AAATTT-CAAAAAAAAGGGTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTAAAGATCAAAAT
65 AAATTTCCAAAAAATA--TTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAAT
* *
2211158 TTCCAAAAAAATTATTTTTACGGAAAAGTTGAAAGTATCAATTTTCCTTG
128 TTCCAAAAAAATAATTTTTACGGAAAAGTTGAAAGTATCAATTTTCCTCG
2211208 AAAATCAAAGTTTTCAAAAAAAGT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAA
1 AAAATCAAAG-TTTCAAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAA
* * *
2211272 TCGAAGTTTCCAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAA
63 T-AAAATTTCCAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAA
*
2211336 ATTT-CAAAAAAATAAATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTTCTCG
126 ATTTCCAAAAAAAT-AATTTTT-ACGGAAAAGTTGAAAGTATCAATTTTCCTCG
*
2211388 -AAATTAAAGTTTCAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTT--AAT
1 AAAATCAAAGTTTC-AAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAT
* *
2211449 AAATTTTCAAAAAAAATAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCC
64 AAAATTTC-CAAAAAAT--ATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCC
2211502 CTGTACAAGA
Statistics
Matches: 260, Mismatches: 20, Indels: 29
0.84 0.06 0.09
Matches are distributed among these distances:
175 6 0.02
176 10 0.04
178 37 0.14
179 68 0.26
180 124 0.48
181 7 0.03
182 8 0.03
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (177 bp):
AAAATCAAAGTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAA
AATTTCCAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTC
CAAAAAAATAATTTTTACGGAAAAGTTGAAAGTATCAATTTTCCTCG
Found at i:2212186 original size:27 final size:27
Alignment explanation
Indices: 2212132--2212186 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
2212122 TATATGATTT
*
2212132 TATAATTATTTATTTTAAATTATCAGA
1 TATAATTATTTATTTTAAATTATAAGA
2212159 TATAATATATTTTATTTT-AA-TATAAGA
1 TATAAT-TA-TTTATTTTAAATTATAAGA
2212186 T
1 T
2212187 GTTAAACAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 13 0.52
28 4 0.16
29 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
TATAATTATTTATTTTAAATTATAAGA
Found at i:2226455 original size:2 final size:2
Alignment explanation
Indices: 2226448--2226485 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2226438 TAGGAATGCA
2226448 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2226486 GAAGGTGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2232311 original size:33 final size:33
Alignment explanation
Indices: 2232269--2232335 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2232259 GGTCACAGTG
2232269 TTGTACCAACAGCCTAAAACCATGTATGAATGC
1 TTGTACCAACAGCCTAAAACCATGTATGAATGC
*
2232302 TTGTACCAACATCCTAAAACCATGTATGAATGC
1 TTGTACCAACAGCCTAAAACCATGTATGAATGC
2232335 T
1 T
2232336 GCATTAAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (33 bp):
TTGTACCAACAGCCTAAAACCATGTATGAATGC
Found at i:2244443 original size:8 final size:8
Alignment explanation
Indices: 2244430--2244474 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
2244420 TCGTCGAAAT
2244430 ATTTTTTA
1 ATTTTTTA
2244438 ATTTTTTA
1 ATTTTTTA
*
2244446 A-ATTTTA
1 ATTTTTTA
2244453 ATTTTTTAA
1 ATTTTTT-A
2244462 ATTTTTT-
1 ATTTTTTA
2244469 ATTTTT
1 ATTTTT
2244475 CATCAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 12 0.36
8 13 0.39
9 8 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTTTA
Found at i:2244453 original size:15 final size:15
Alignment explanation
Indices: 2244433--2244466 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2244423 TCGAAATATT
2244433 TTTTAATTTTTTAAA
1 TTTTAATTTTTTAAA
2244448 TTTTAATTTTTTAAA
1 TTTTAATTTTTTAAA
2244463 TTTT
1 TTTT
2244467 TTATTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATTTTTTAAA
Found at i:2244473 original size:15 final size:16
Alignment explanation
Indices: 2244430--2244474 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2244420 TCGTCGAAAT
2244430 ATTTTTTAATTTTTTAA
1 ATTTTTT-ATTTTTTAA
*
2244447 A-TTTTAATTTTTTAA
1 ATTTTTTATTTTTTAA
2244462 ATTTTTTATTTTT
1 ATTTTTTATTTTT
2244475 CATCAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 14 0.56
17 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTTATTTTTTAA
Found at i:2253196 original size:14 final size:13
Alignment explanation
Indices: 2253164--2253208 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
2253154 TAATTATGAT
2253164 TTAAAAAAGTTTTA
1 TTAAAAAA-TTTTA
*
2253178 ATAAAAAATTTATA
1 TTAAAAAATTT-TA
2253192 TTAAATAAATTTTA
1 TTAAA-AAATTTTA
2253206 TTA
1 TTA
2253209 TAATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 18 0.67
15 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
TTAAAAAATTTTA
Found at i:2261001 original size:21 final size:21
Alignment explanation
Indices: 2260962--2261005 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2260952 ATGTTGATGC
*
2260962 ACATATTTTATTCTCTTTTTT
1 ACATATTTTATTATCTTTTTT
*
2260983 ACATATTTTATTAATTTTTTTT
1 ACATATTTTATT-ATCTTTTTT
2261005 A
1 A
2261006 TTCTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (21 bp):
ACATATTTTATTATCTTTTTT
Found at i:2262356 original size:15 final size:15
Alignment explanation
Indices: 2262335--2262402 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 15
2262325 CATCAGCCCC
2262335 ATTTTT-TATTTTTT
1 ATTTTTGTATTTTTT
*
2262349 ATTTTT-T-TTATTT
1 ATTTTTGTATTTTTT
2262362 ATATTTTGTATTTTTAT
1 AT-TTTTGTATTTTT-T
*
2262379 ACTTTTTGTATTTTGT
1 A-TTTTTGTATTTTTT
2262395 ATTTTTGT
1 ATTTTTGT
2262403 TTAATTAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
13 7 0.15
14 11 0.24
15 8 0.17
16 6 0.13
17 13 0.28
18 1 0.02
ACGTcount: A:0.16, C:0.01, G:0.06, T:0.76
Consensus pattern (15 bp):
ATTTTTGTATTTTTT
Found at i:2262402 original size:8 final size:7
Alignment explanation
Indices: 2262335--2262400 Score: 62
Period size: 7 Copynumber: 8.9 Consensus size: 7
2262325 CATCAGCCCC
2262335 ATTTTTT
1 ATTTTTT
2262342 ATTTTTT
1 ATTTTTT
2262349 ATTTTTT
1 ATTTTTT
2262356 -TTATTTAT
1 ATT-TTT-T
*
2262364 ATTTTGT
1 ATTTTTT
2262371 ATTTTTAT
1 ATTTTT-T
2262379 ACTTTTTGT
1 A-TTTTT-T
*
2262388 ATTTTGT
1 ATTTTTT
2262395 ATTTTT
1 ATTTTT
2262401 GTTTAATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
6 2 0.04
7 29 0.59
8 9 0.18
9 9 0.18
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.77
Consensus pattern (7 bp):
ATTTTTT
Found at i:2262536 original size:28 final size:28
Alignment explanation
Indices: 2262496--2262560 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
2262486 CTTTTGGCCT
* *
2262496 AGTTAAATTAAAATCGAGCTTGAAGCCC
1 AGTTGAATTAAAATCGAGCCTGAAGCCC
2262524 AGTTGAATTAAAATCGAGCCTGAAGCCC
1 AGTTGAATTAAAATCGAGCCTGAAGCCC
*
2262552 AATTGAATT
1 AGTTGAATT
2262561 GCAATCGGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (28 bp):
AGTTGAATTAAAATCGAGCCTGAAGCCC
Found at i:2262866 original size:51 final size:50
Alignment explanation
Indices: 2262794--2263217 Score: 327
Period size: 48 Copynumber: 8.3 Consensus size: 50
2262784 CATCTAACTT
*
2262794 GAGGCTCGACAA-TTTTAAAAATTTGATATC-TGAAAAAGGCTCCTCTCAGCA
1 GAGGCTCAACAACTTTT-AAAATTT-ATATCTTGAAAAA-GCTCCTCTCAGCA
* * *
2262845 GAGGCTCAACAACTTTTAAAA-TTCTATCTTCAAAAAAGACTCCTCTCAGTA
1 GAGGCTCAACAACTTTTAAAATTTATATCTT-GAAAAAG-CTCCTCTCAGCA
* * *
2262896 GAGGCTCAACAAGCTCAACAACTTTAAAATTTCTCATCTTGAAAAGGGCTCCTCTCAACA
1 GAGGCTCAACAA-CT-------TTTAAAATTTAT-ATCTTGAAAA-AGCTCCTCTCAGCA
* * * *
2262956 GAGGCCCAATAACTTTAAAAATTCTCAT-T-TTG-AAAAGCTCCTCTAAGCA
1 GAGGCTCAACAACTTTTAAAATT-T-ATATCTTGAAAAAGCTCCTCTCAGCA
* * * *
2263005 GAGGCTCAACAACTTTAAAAATCTCATA---TGAAAAAGCTCCTCTAAACA
1 GAGGCTCAACAACTTTTAAAAT-TTATATCTTGAAAAAGCTCCTCTCAGCA
* * * * * *
2263053 GAGGCTTAACAACTTTAAAAATGCTA-ATATTGAAAAAGCTTCTATCAGCA
1 GAGGCTCAACAACTTTTAAAAT-TTATATCTTGAAAAAGCTCCTCTCAGCA
* *
2263103 GAGACTCAACAACTTTTAAAA-TTA-ATCTTGAAAAAACTCCTCTCAGCA
1 GAGGCTCAACAACTTTTAAAATTTATATCTTGAAAAAGCTCCTCTCAGCA
* *
2263151 GAGGCTCAACAAC-TTTAAAATTT-TATCTTGAAAAAAAAACTCCTCTAAGCA
1 GAGGCTCAACAACTTTTAAAATTTATATCTTG---AAAAAGCTCCTCTCAGCA
2263202 GAGGCTCAACAACTTT
1 GAGGCTCAACAACTTT
2263218 AAAGAAATTC
Statistics
Matches: 307, Mismatches: 37, Indels: 57
0.77 0.09 0.14
Matches are distributed among these distances:
47 10 0.03
48 82 0.27
49 35 0.11
50 42 0.14
51 76 0.25
52 17 0.06
53 1 0.00
54 1 0.00
59 9 0.03
60 28 0.09
61 6 0.02
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (50 bp):
GAGGCTCAACAACTTTTAAAATTTATATCTTGAAAAAGCTCCTCTCAGCA
Found at i:2262959 original size:60 final size:58
Alignment explanation
Indices: 2262848--2263016 Score: 146
Period size: 60 Copynumber: 3.0 Consensus size: 58
2262838 CTCAGCAGAG
* * **
2262848 GCTCAACAACTTTTAAAATTCT-ATCTTCAAAAAAGACTCCTCTCAGTAGAGGCTCAACAA
1 GCTCAACAAC-TTTAAAATTCTCATCTT--GAAAAGGCTCCTCTCAACAGAGGCTCAACAA
2262908 GCTCAACAACTTTAAAATTTCTCATCTTGAAAAGGGCTCCTCTCAACAGAGGC-C--CAA
1 GCTCAACAACTTTAAAA-TTCTCATCTTGAAAA-GGCTCCTCTCAACAGAGGCTCAACAA
*
2262965 --T----AACTTTAAAAATTCTCATTTTGAAAA-GCTCCTCT-AAGCAGAGGCTCAACAA
1 GCTCAACAACTTT-AAAATTCTCATCTTGAAAAGGCTCCTCTCAA-CAGAGGCTCAACAA
2263017 CTTTAAAAAT
Statistics
Matches: 96, Mismatches: 5, Indels: 24
0.77 0.04 0.19
Matches are distributed among these distances:
48 2 0.02
49 15 0.16
50 1 0.01
51 20 0.21
52 7 0.07
55 1 0.01
57 3 0.03
59 12 0.12
60 30 0.31
61 5 0.05
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (58 bp):
GCTCAACAACTTTAAAATTCTCATCTTGAAAAGGCTCCTCTCAACAGAGGCTCAACAA
Found at i:2263048 original size:48 final size:49
Alignment explanation
Indices: 2262908--2263220 Score: 330
Period size: 48 Copynumber: 6.3 Consensus size: 49
2262898 GGCTCAACAA
* *
2262908 GCTCAACAACTTTAAAATTTCTCATCTTGAAAAGGGCTCCTCTCAA-CAGAG
1 GCTCAACAACTTTAAAA-ATCTCATCTTGAAAA-AGCTCCTCT-AAGCAGAG
* * *
2262959 GCCCAATAACTTTAAAAATTCTCATTTTG-AAAAGCTCCTCTAAGCAGAG
1 GCTCAACAACTTTAAAAA-TCTCATCTTGAAAAAGCTCCTCTAAGCAGAG
* *
2263008 GCTCAACAACTTTAAAAATCTCAT-ATGAAAAAGCTCCTCTAAACAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTGAAAAAGCTCCTCTAAGCAGAG
* * * * * *
2263056 GCTTAACAACTTTAAAAATGCTAATATTGAAAAAGCTTCTATCAGCAGAG
1 GCTCAACAACTTTAAAAAT-CTCATCTTGAAAAAGCTCCTCTAAGCAGAG
* * * * *
2263106 ACTCAACAACTTTTAAAAT-TAATCTTGAAAAAACTCCTCTCAGCAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTGAAAAAGCTCCTCTAAGCAGAG
* * *
2263154 GCTCAACAACTTT-AAAATTTTATCTTGAAAAAAAAACTCCTCTAAGCAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTG---AAAAAGCTCCTCTAAGCAGAG
2263205 GCTCAACAACTTTAAA
1 GCTCAACAACTTTAAA
2263221 GAAATTCAAT
Statistics
Matches: 226, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
47 7 0.03
48 89 0.39
49 33 0.15
50 38 0.17
51 57 0.25
52 2 0.01
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (49 bp):
GCTCAACAACTTTAAAAATCTCATCTTGAAAAAGCTCCTCTAAGCAGAG
Found at i:2263219 original size:98 final size:97
Alignment explanation
Indices: 2262908--2263220 Score: 337
Period size: 98 Copynumber: 3.2 Consensus size: 97
2262898 GGCTCAACAA
* * *
2262908 GCTCAACAACTTTAAAATTTCTCATCTTGAAAAGGGCTCCTCTCAACAGAGGCCCAATAACTTTA
1 GCTCAACAACTTTAAAA--TCTCATCTTGAAAA-AGCTCCTCTCAACAGAGGCTCAACAACTTTA
* *
2262973 AAAATTCTCATTTTG-AAAAGCTCCTCTAAGCAGAG
63 AAAATT-TAATATTGAAAAAGCTCCTCTAAGCAGAG
* * *
2263008 GCTCAACAACTTTAAAAATCTCAT-ATGAAAAAGCTCCTCTAAACAGAGGCTTAACAACTTTAAA
1 GCTCAACAACTTT-AAAATCTCATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAA
* * * *
2263072 AATGCTAATATTGAAAAAGCTTCTATCAGCAGAG
65 AAT-TTAATATTGAAAAAGCTCCTCTAAGCAGAG
* * * *
2263106 ACTCAACAACTTTTAAAAT-TAATCTTGAAAAAACTCCTCTCAGCAGAGGCTCAACAACTTT-AA
1 GCTCAACAAC-TTTAAAATCTCATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAA
* * *
2263169 AATTTTATCTTGAAAAAAAAACTCCTCTAAGCAGAG
65 AATTTAATATTG---AAAAAGCTCCTCTAAGCAGAG
2263205 GCTCAACAACTTTAAA
1 GCTCAACAACTTTAAA
2263221 GAAATTCAAT
Statistics
Matches: 178, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
96 6 0.03
97 45 0.25
98 75 0.42
99 35 0.20
100 13 0.07
101 4 0.02
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (97 bp):
GCTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAA
ATTTAATATTGAAAAAGCTCCTCTAAGCAGAG
Found at i:2264025 original size:19 final size:19
Alignment explanation
Indices: 2263997--2264041 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2263987 TACATCATTC
* * *
2263997 TTTTTCATTTTTTTTTTGT
1 TTTTTTATTTTATTTTTAT
2264016 TTTTTTATTTTATTTTTAT
1 TTTTTTATTTTATTTTTAT
2264035 TTTTTTA
1 TTTTTTA
2264042 AGAAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTTATTTTATTTTTAT
Found at i:2264031 original size:11 final size:10
Alignment explanation
Indices: 2263997--2264040 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
2263987 TACATCATTC
*
2263997 TTTTTCATTT
1 TTTTTTATTT
*
2264007 TTTTTT-TGT
1 TTTTTTATTT
2264016 TTTTTTATTT
1 TTTTTTATTT
2264026 TATTTTTATTT
1 T-TTTTTATTT
2264037 TTTT
1 TTTT
2264041 AAGAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.28
10 11 0.38
11 10 0.34
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:2276008 original size:9 final size:9
Alignment explanation
Indices: 2275990--2276039 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
2275980 TTAACCTCTC
2275990 TTTTTCTTTA
1 TTTTT-TTTA
2276000 TTTTTTTTA
1 TTTTTTTTA
*
2276009 ATTTTTTTA
1 TTTTTTTTA
2276018 -TTTTTTTA
1 TTTTTTTTA
2276026 TTTTTTTGTA
1 TTTTTTT-TA
2276036 TTTT
1 TTTT
2276040 GTATTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 8 0.22
9 18 0.49
10 11 0.30
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:2276019 original size:18 final size:18
Alignment explanation
Indices: 2275991--2276039 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
2275981 TAACCTCTCT
2275991 TTTTCTTTATTTTTTTTAA
1 TTTT-TTTATTTTTTTTAA
*
2276010 TTTTTTTA-TTTTTTTAT
1 TTTTTTTATTTTTTTTAA
2276027 TTTTTTGTATTTT
1 TTTTTT-TATTTT
2276040 GTATTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 14 0.52
18 6 0.22
19 7 0.26
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (18 bp):
TTTTTTTATTTTTTTTAA
Found at i:2276044 original size:17 final size:16
Alignment explanation
Indices: 2276009--2276056 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2275999 ATTTTTTTTA
*
2276009 ATTTTTTTATTTTTTT
1 ATTTTTTTATTTTTGT
*
2276025 ATTTTTTTGTATTTTGT
1 ATTTTTTTAT-TTTTGT
*
2276042 A-TTTTATATTTTTGT
1 ATTTTTTTATTTTTGT
2276057 TTAATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
ATTTTTTTATTTTTGT
Found at i:2276054 original size:8 final size:8
Alignment explanation
Indices: 2275991--2276046 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
2275981 TAACCTCTCT
2275991 TTTTCTTTA
1 TTTT-TTTA
2276000 TTTTTTTTAA
1 -TTTTTTT-A
2276010 TTTTTTTA
1 TTTTTTTA
2276018 TTTTTTTA
1 TTTTTTTA
*
2276026 TTTTTTTG
1 TTTTTTTA
*
2276034 TATTTTGTA
1 T-TTTTTTA
2276043 TTTT
1 TTTT
2276047 ATATTTTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 20 0.49
9 16 0.39
10 5 0.12
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2284479 original size:3 final size:3
Alignment explanation
Indices: 2284471--2284498 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2284461 GTGACGACAT
2284471 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2284499 CTTTCGCCTT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2286892 original size:3 final size:3
Alignment explanation
Indices: 2286884--2286913 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2286874 AACCCACAAG
2286884 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2286914 GTAGCAGTAC
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:2288315 original size:18 final size:21
Alignment explanation
Indices: 2288274--2288315 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 21
2288264 TATTTGCGTG
*
2288274 AATGACATCCCCGTACTTCTA
1 AATGACATCCCCGTACTTCCA
2288295 AATGACA-CCCC-T-CTTCCA
1 AATGACATCCCCGTACTTCCA
2288313 AAT
1 AAT
2288316 TTGCACCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 4 0.20
21 7 0.35
ACGTcount: A:0.31, C:0.36, G:0.07, T:0.26
Consensus pattern (21 bp):
AATGACATCCCCGTACTTCCA
Found at i:2289934 original size:2 final size:2
Alignment explanation
Indices: 2289927--2289958 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2289917 GTTTTTGTGC
2289927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2289959 GGATATGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2292068 original size:2 final size:2
Alignment explanation
Indices: 2292061--2292097 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2292051 AAATGTTTTG
* *
2292061 TC TC TC TC TC TC GC TC TC TC TC TC TC TC TA TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2292098 GAATGGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.46, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2297365 original size:21 final size:20
Alignment explanation
Indices: 2297339--2297381 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
2297329 AAAGCGTTTG
*
2297339 ATTTAATTTTATATTATATTT
1 ATTTAATTATATATTA-ATTT
*
2297360 ATTTAATTATATGTTAATTT
1 ATTTAATTATATATTAATTT
2297380 AT
1 AT
2297382 CAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTAATTATATATTAATTT
Found at i:2297379 original size:16 final size:16
Alignment explanation
Indices: 2297339--2297396 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
2297329 AAAGCGTTTG
2297339 ATTTAATTTTATATTAT
1 ATTTAA-TTTATATTAT
2297356 ATTT-ATTTA-ATTAT
1 ATTTAATTTATATTAT
*
2297370 ATGTTAATTTATCAATATT
1 AT-TTAATTTAT-ATTA-T
2297389 ATTTAATT
1 ATTTAATT
2297397 CATCAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 7 0.20
15 6 0.17
16 6 0.17
17 4 0.11
18 9 0.26
19 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTAATTTATATTAT
Found at i:2312029 original size:43 final size:43
Alignment explanation
Indices: 2311968--2312056 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
2311958 TTCAATACTT
*
2311968 AACACAGATCTTAACCTTAAAGCCCATAATAAATAATCTCAGG
1 AACACAGATCTTAACCTTAAAGCCCATAATAAACAATCTCAGG
* *
2312011 AACACAGATCTTAACCTTAAAGCCCCTAATAAACCATCTCAGG
1 AACACAGATCTTAACCTTAAAGCCCATAATAAACAATCTCAGG
2312054 AAC
1 AAC
2312057 TCACAAGAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.21
Consensus pattern (43 bp):
AACACAGATCTTAACCTTAAAGCCCATAATAAACAATCTCAGG
Found at i:2321117 original size:29 final size:29
Alignment explanation
Indices: 2321072--2321147 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
2321062 TATTACACTT
**
2321072 AAAT-AAATTATTAAATTTTAATTTTTATTC
1 AAATAAAATT-TT-AATTTTAATTTAGATTC
*
2321102 AAATAAAATTTTAATTTTAATTTAGATTT
1 AAATAAAATTTTAATTTTAATTTAGATTC
2321131 AAATAAAATTTTAATTT
1 AAATAAAATTTTAATTT
2321148 ATTTATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 31 0.74
30 6 0.14
31 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
AAATAAAATTTTAATTTTAATTTAGATTC
Found at i:2321140 original size:23 final size:23
Alignment explanation
Indices: 2321114--2321168 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2321104 ATAAAATTTT
2321114 AATTTTAATTTAGATT-TAAATAA
1 AATTTTAATTTA-ATTATAAATAA
*
2321137 AATTTTAATTTATTTATAAATAA
1 AATTTTAATTTAATTATAAATAA
*
2321160 ACTTTTAAT
1 AATTTTAAT
2321169 ATAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTTTAATTTAATTATAAATAA
Found at i:2321232 original size:29 final size:28
Alignment explanation
Indices: 2321189--2321271 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 28
2321179 TTTTTATTTG
* * *
2321189 AAATAAAAATCTATTTGAATATAAATTAA
1 AAATAAAAATTTATTTAAATAT-AATAAA
2321218 AAATAAAAATTTATTTAAATATAATAAA
1 AAATAAAAATTTATTTAAATATAATAAA
*
2321246 AATATAAAAATTTATTTTAAAAATAA
1 AA-ATAAAAATTTA-TTTAAATATAA
2321272 AATAATTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
28 7 0.15
29 31 0.65
30 10 0.21
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (28 bp):
AAATAAAAATTTATTTAAATATAATAAA
Found at i:2338589 original size:23 final size:23
Alignment explanation
Indices: 2338535--2338589 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2338525 AATATTTAGT
*
2338535 TTTTAATTCACATTTAAATAAAA
1 TTTTAATTTACATTTAAATAAAA
* *
2338558 TTTTAATTTATATTT-AATTAAA
1 TTTTAATTTACATTTAAATAAAA
2338580 TTCTTAATTT
1 TT-TTAATTT
2338590 TCAATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTAATTTACATTTAAATAAAA
Found at i:2338597 original size:30 final size:29
Alignment explanation
Indices: 2338556--2338624 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 29
2338546 ATTTAAATAA
*
2338556 AATTTTAATTTATATTTAATTAAATTCTT
1 AATTTTAATTTATATTTAAATAAATTCTT
*
2338585 AATTTTCAATTTATATTTAAATAAATTTTT
1 AATTTT-AATTTATATTTAAATAAATTCTT
*
2338615 AATTTGAATT
1 AATTTTAATT
2338625 AATCTTTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (29 bp):
AATTTTAATTTATATTTAAATAAATTCTT
Found at i:2338654 original size:17 final size:17
Alignment explanation
Indices: 2338592--2338656 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
2338582 CTTAATTTTC
2338592 AATTTATATTT-AAATAA
1 AATTT-TATTTAAAATAA
* * *
2338609 ATTTTTAATTTGAATTAA
1 AATTTT-ATTTAAAATAA
** *
2338627 TCTTTTGTTTAAAATAA
1 AATTTTATTTAAAATAA
2338644 AATTTTATTTAAA
1 AATTTTATTTAAA
2338657 TACAATAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
16 1 0.03
17 26 0.72
18 9 0.25
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTTATTTAAAATAA
Found at i:2338813 original size:2 final size:2
Alignment explanation
Indices: 2338806--2338837 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2338796 ATAGAATTAA
2338806 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2338838 AAATCAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2340657 original size:34 final size:34
Alignment explanation
Indices: 2340614--2340682 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2340604 TGACAAGGTA
*
2340614 ACTGCTCCTATTTGATTTATGGTGTGTCATGGAC
1 ACTGCTCCTATTTGATTTATGGTGTATCATGGAC
2340648 ACTGCTCCTATTTGATTTATGGTGTATCATGGAC
1 ACTGCTCCTATTTGATTTATGGTGTATCATGGAC
2340682 A
1 A
2340683 ATCATTGCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (34 bp):
ACTGCTCCTATTTGATTTATGGTGTATCATGGAC
Found at i:2345423 original size:13 final size:13
Alignment explanation
Indices: 2345393--2345455 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
2345383 TTTATTTTTT
2345393 AAATTTT-ATATA
1 AAATTTTAATATA
**
2345405 TTATTTTAATATA
1 AAATTTTAATATA
2345418 AAATTTTAATAT-
1 AAATTTTAATATA
2345430 --A-TTTAA-AT-
1 AAATTTTAATATA
2345438 AAATTTTAATATA
1 AAATTTTAATATA
2345451 AAATT
1 AAATT
2345456 ATTATTTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 2 0.05
11 5 0.12
12 7 0.17
13 20 0.49
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AAATTTTAATATA
Found at i:2346212 original size:20 final size:21
Alignment explanation
Indices: 2346189--2346239 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
2346179 AAATTTTTAT
*
2346189 ATTTTTATTATATTTAAA-AA
1 ATTTTTATTATATTCAAATAA
*
2346209 ATTTTTATTTATATTCAAATAT
1 ATTTTTA-TTATATTCAAATAA
2346231 ATTTTTATT
1 ATTTTTATT
2346240 TCAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATTATATTCAAATAA
Found at i:2346214 original size:29 final size:31
Alignment explanation
Indices: 2346151--2346215 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 31
2346141 ACTAACAAAA
2346151 TTTTAAATTTTTATCATATTATTTAAATAAAT
1 TTTTAAATTTTTAT-ATATTATTTAAATAAAT
*
2346183 TTTTATATTTTTAT-TA-TATTTAAA-AAAT
1 TTTTAAATTTTTATATATTATTTAAATAAAT
2346211 TTTTA
1 TTTTA
2346216 TTTATATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 9 0.28
29 8 0.25
30 2 0.06
32 13 0.41
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (31 bp):
TTTTAAATTTTTATATATTATTTAAATAAAT
Found at i:2346220 original size:21 final size:22
Alignment explanation
Indices: 2346189--2346240 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
2346179 AAATTTTTAT
*
2346189 ATTTTTA-TTATATTTAAA-AA
1 ATTTTTATTTATATTCAAATAA
*
2346209 ATTTTTATTTATATTCAAATAT
1 ATTTTTATTTATATTCAAATAA
2346231 ATTTTTATTT
1 ATTTTTATTT
2346241 CAAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 7 0.25
21 10 0.36
22 11 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTTATTTATATTCAAATAA
Found at i:2346244 original size:17 final size:17
Alignment explanation
Indices: 2346216--2346266 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
2346206 AAAATTTTTA
*
2346216 TTTATATTCAAATATATT
1 TTTAT-TTCAAATATAAT
*
2346234 TTTATTTCAAATAAAAAT
1 TTTATTTCAAAT-ATAAT
2346252 TTTATTT-AAATATAA
1 TTTATTTCAAATATAA
2346267 ATTAAAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 3 0.10
17 11 0.38
18 15 0.52
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTATTTCAAATATAAT
Found at i:2346268 original size:17 final size:17
Alignment explanation
Indices: 2346215--2346269 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2346205 AAAAATTTTT
*
2346215 ATTTATATTCAAATAT-A
1 ATTT-TATTTAAATATAA
* *
2346232 TTTTTATTTCAAATAAAA
1 ATTTTATTT-AAATATAA
2346250 ATTTTATTTAAATATAA
1 ATTTTATTTAAATATAA
2346267 ATT
1 ATT
2346270 AAAAGATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 4 0.13
17 18 0.58
18 9 0.29
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTATTTAAATATAA
Found at i:2352259 original size:21 final size:20
Alignment explanation
Indices: 2352234--2352274 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2352224 TATTAAATTT
2352234 AATAAATATTATTTTTTAAAA
1 AATAAATA-TATTTTTTAAAA
*
2352255 AATAATTATATTTTTTAAAA
1 AATAAATATATTTTTTAAAA
2352275 TGTCATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAAATATATTTTTTAAAA
Found at i:2352268 original size:18 final size:17
Alignment explanation
Indices: 2352222--2352268 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2352212 TTGAGATTCG
* *
2352222 AATATTA-AATTTAATA
1 AATATTATATTTTAAAA
*
2352238 AATATTATTTTTTAAAA
1 AATATTATATTTTAAAA
2352255 AATAATTATATTTT
1 AAT-ATTATATTTT
2352269 TTAAAATGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.28
17 9 0.36
18 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTATATTTTAAAA
Found at i:2356060 original size:26 final size:27
Alignment explanation
Indices: 2356017--2356084 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 27
2356007 TTAAATTCAA
2356017 ATAAATATTTAAAAAAATTCAAATATT
1 ATAAATATTTAAAAAAATTCAAATATT
* *
2356044 ATAAATA-TTAAATAAATT-TAA-A-T
1 ATAAATATTTAAAAAAATTCAAATATT
*
2356067 ACAAATATTTAAAAAAAT
1 ATAAATATTTAAAAAAAT
2356085 AATGAATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 7 0.19
24 10 0.28
25 2 0.06
26 10 0.28
27 7 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAAATATTTAAAAAAATTCAAATATT
Found at i:2359040 original size:6 final size:6
Alignment explanation
Indices: 2359029--2359058 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2359019 TCTAACAGAT
*
2359029 ATTTTA ATTTTA ATTTTA ATTTTA TTTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
2359059 CGAATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTA
Found at i:2359236 original size:23 final size:22
Alignment explanation
Indices: 2359193--2359248 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
2359183 ATTTTTAAGA
2359193 AAAATATATTAATTTCAATTAATCT
1 AAAATA-A-TAATTTCAATT-ATCT
*
2359218 AAAATAATAATTT-ATATTATTT
1 AAAATAATAATTTCA-ATTATCT
2359240 AAAA-AATAA
1 AAAATAATAA
2359249 CCTATTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 5 0.17
22 8 0.28
23 9 0.31
24 1 0.03
25 6 0.21
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATAATAATTTCAATTATCT
Found at i:2362079 original size:13 final size:14
Alignment explanation
Indices: 2362050--2362083 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
2362040 TAAAGAAAAT
2362050 AATTGTAAATATTAA
1 AATT-TAAATATTAA
2362065 AATTTAAAT-TTAA
1 AATTTAAATATTAA
2362078 AATTTA
1 AATTTA
2362084 TTAAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 5 0.26
15 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
AATTTAAATATTAA
Found at i:2363112 original size:20 final size:20
Alignment explanation
Indices: 2363079--2363128 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2363069 TCAAACAAAT
2363079 GAATCTTAAATAAACATAAAC
1 GAATCTT-AATAAACATAAAC
* *
2363100 GAATCTTAATAAATATAAAT
1 GAATCTTAATAAACATAAAC
*
2363120 AAATCTTAA
1 GAATCTTAA
2363129 AATACGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.30
Consensus pattern (20 bp):
GAATCTTAATAAACATAAAC
Found at i:2363218 original size:11 final size:11
Alignment explanation
Indices: 2363202--2363231 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2363192 GAATATTAAA
2363202 CAAACAAATTT
1 CAAACAAATTT
2363213 CAAACAAATTT
1 CAAACAAATTT
*
2363224 TAAACAAA
1 CAAACAAA
2363232 CTTGTTCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (11 bp):
CAAACAAATTT
Found at i:2364447 original size:12 final size:12
Alignment explanation
Indices: 2364430--2364458 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2364420 GGGAGGTTAT
2364430 GACAATCAAAGC
1 GACAATCAAAGC
2364442 GACAATCAAAGC
1 GACAATCAAAGC
2364454 -ACAAT
1 GACAAT
2364459 AGTAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10
Consensus pattern (12 bp):
GACAATCAAAGC
Found at i:2373732 original size:31 final size:30
Alignment explanation
Indices: 2373687--2373751 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
2373677 TTTTTTTAAA
*
2373687 AATTTACTCATTAATAAGAA-AATATCATCT
1 AATTTACTAATTAATAA-AATAATATCATCT
*
2373717 AATTTATCTAATTAATAAAATAATATTATCT
1 AATTTA-CTAATTAATAAAATAATATCATCT
2373748 AATT
1 AATT
2373752 CATTGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.42
Consensus pattern (30 bp):
AATTTACTAATTAATAAAATAATATCATCT
Found at i:2376880 original size:20 final size:20
Alignment explanation
Indices: 2376857--2376902 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2376847 AAATAAATTA
*
2376857 TAAAAAATTTTAAAAGTTTT
1 TAAAAAATTTTAAAAGCTTT
*
2376877 TAAAAAGTTTTAAAAGCTTT
1 TAAAAAATTTTAAAAGCTTT
*
2376897 CAAAAA
1 TAAAAA
2376903 TAAATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (20 bp):
TAAAAAATTTTAAAAGCTTT
Found at i:2376970 original size:34 final size:32
Alignment explanation
Indices: 2376873--2376963 Score: 92
Period size: 34 Copynumber: 2.7 Consensus size: 32
2376863 ATTTTAAAAG
*
2376873 TTTTTAAAAAGTTTTAAAAGCTTTCAAAAATAAA
1 TTTTTAAAAA-TTTTAAAA-CTTTCGAAAATAAA
* * **
2376907 TTTATAAAAATTCTTAAAAACTTTGGAAAATTCA
1 TTTTTAAAAATT-TT-AAAACTTTCGAAAATAAA
2376941 TTTTTAAAAACTTTTAAAACTTT
1 TTTTTAAAAA-TTTTAAAACTTT
2376964 TTGAAAAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
33 10 0.21
34 32 0.67
35 6 0.12
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (32 bp):
TTTTTAAAAATTTTAAAACTTTCGAAAATAAA
Found at i:2377235 original size:20 final size:18
Alignment explanation
Indices: 2377210--2377259 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2377200 AAATTTCATG
2377210 TTAAAAAGTTTTGATACAAT
1 TTAAAAAGTTTTGA-A-AAT
**
2377230 TTAAAATTTTTTGAAAAT
1 TTAAAAAGTTTTGAAAAT
*
2377248 TTCAAAAGTTTT
1 TTAAAAAGTTTT
2377260 AAAGGTTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 12 0.48
19 1 0.04
20 12 0.48
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (18 bp):
TTAAAAAGTTTTGAAAAT
Found at i:2377291 original size:24 final size:24
Alignment explanation
Indices: 2377256--2377302 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2377246 ATTTCAAAAG
* *
2377256 TTTTAAAGGTTTTCAAAATTTTAT
1 TTTTAAAAGTTTTCAAAAATTTAT
*
2377280 TTTTAAAAGTTTTTAAAAATTTA
1 TTTTAAAAGTTTTCAAAAATTTA
2377303 AAAAAATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (24 bp):
TTTTAAAAGTTTTCAAAAATTTAT
Found at i:2379009 original size:2 final size:2
Alignment explanation
Indices: 2379002--2379038 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2378992 TCTTTTACAT
2379002 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2379039 TCTTCTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2379044 original size:3 final size:3
Alignment explanation
Indices: 2379036--2379078 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
2379026 TCTCTCTCTC
*
2379036 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2379079 ACTCTTCCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:2379329 original size:30 final size:32
Alignment explanation
Indices: 2379290--2379357 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
2379280 AAAAAATTCA
* *
2379290 TTCTCTCTCTTTTTTGGGTTTTTCTCC-TTTCT
1 TTCTCTCTC-TTTGTGCGTTTTTCTCCTTTTCT
* *
2379322 TTCTCTCTCTTTGTGCTTTTTTTTCCTTTTCT
1 TTCTCTCTCTTTGTGCGTTTTTCTCCTTTTCT
2379354 TTCT
1 TTCT
2379358 TTAGCTGCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (32 bp):
TTCTCTCTCTTTGTGCGTTTTTCTCCTTTTCT
Found at i:2381828 original size:16 final size:16
Alignment explanation
Indices: 2381807--2381837 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2381797 GCTTTCTTAG
2381807 CTTTTCTTAGTTTTAC
1 CTTTTCTTAGTTTTAC
*
2381823 CTTTTCTTGGTTTTA
1 CTTTTCTTAGTTTTA
2381838 AATGATTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.65
Consensus pattern (16 bp):
CTTTTCTTAGTTTTAC
Found at i:2393089 original size:2 final size:2
Alignment explanation
Indices: 2393082--2393112 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2393072 TTGAACAATA
2393082 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2393113 CTCCTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2399763 original size:20 final size:19
Alignment explanation
Indices: 2399704--2399775 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 19
2399694 CAATATAAAT
* *
2399704 TATAACATAT-ATTTTTTA
1 TATAAAATATAATATTTTA
**
2399722 TATAAAATATAATATAAATA
1 TATAAAATATAATAT-TTTA
*
2399742 TATAAATTATTAATATTTTA
1 TATAAAATA-TAATATTTTA
*
2399762 TATAATATA-AATAT
1 TATAAAATATAATAT
2399776 ACAAATTTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
18 14 0.33
19 3 0.07
20 19 0.45
21 6 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAAAATATAATATTTTA
Found at i:2402607 original size:24 final size:24
Alignment explanation
Indices: 2402527--2402609 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 24
2402517 ATGATATTTA
* * *
2402527 TTTAAAGTATTTTTGATAAAAACGT
1 TTTAAAATATTTTTTA-AAAAACAT
*
2402552 TTT-AAATAATTTTTTTAAATAAAAATT
1 TTTAAAAT-A-TTTTTTAAA-AAACA-T
2402579 ATTTAAAATATTTTTTAAAAAACAT
1 -TTTAAAATATTTTTTAAAAAACAT
2402604 TTTAAA
1 TTTAAA
2402610 CAATTTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
24 9 0.19
25 7 0.15
26 13 0.28
27 10 0.21
28 4 0.09
29 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTAAAATATTTTTTAAAAAACAT
Found at i:2402607 original size:52 final size:53
Alignment explanation
Indices: 2402509--2402616 Score: 146
Period size: 53 Copynumber: 2.1 Consensus size: 53
2402499 ATCACTCGTA
* * * * * *
2402509 TTTTTTAAATGATATTTATTTAAAGTATTTTTGATAAAAACGTTTTAAATAAT
1 TTTTTTAAATAAAAATTATTTAAAATATTTTTGATAAAAACATTTTAAACAAT
*
2402562 TTTTTTAAATAAAAATTATTTAAAATATTTTTTA-AAAAACATTTTAAACAAT
1 TTTTTTAAATAAAAATTATTTAAAATATTTTTGATAAAAACATTTTAAACAAT
2402614 TTT
1 TTT
2402617 AAATAATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 19 0.40
53 29 0.60
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (53 bp):
TTTTTTAAATAAAAATTATTTAAAATATTTTTGATAAAAACATTTTAAACAAT
Found at i:2402636 original size:13 final size:14
Alignment explanation
Indices: 2402616--2402649 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2402606 TAAACAATTT
2402616 TAAATAAT-TTTTA
1 TAAATAATATTTTA
*
2402629 TTAATAATATTTTA
1 TAAATAATATTTTA
2402643 TAAATAA
1 TAAATAA
2402650 AAATAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATAATATTTTA
Found at i:2409371 original size:2 final size:2
Alignment explanation
Indices: 2409366--2409404 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2409356 AAAAAAAAAC
2409366 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2409405 AACCTTGTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2416326 original size:27 final size:27
Alignment explanation
Indices: 2416295--2416356 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
2416285 CGCTGCCTAT
*
2416295 CCTCCACAGGCCCCTGCTGCAGGTTAC
1 CCTCCACAGGCCCCTCCTGCAGGTTAC
* * * *
2416322 CCTCCACATGTCCCTCCTGCTGGTTAT
1 CCTCCACAGGCCCCTCCTGCAGGTTAC
2416349 CCTCCACA
1 CCTCCACA
2416357 AACATACCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.15, C:0.45, G:0.16, T:0.24
Consensus pattern (27 bp):
CCTCCACAGGCCCCTCCTGCAGGTTAC
Found at i:2417488 original size:3 final size:3
Alignment explanation
Indices: 2417480--2417510 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2417470 TACTAAAATT
2417480 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2417511 AACTTCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2417857 original size:22 final size:22
Alignment explanation
Indices: 2417824--2417878 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
2417814 AATCGAGTTA
*
2417824 AATTTAAA-TATTT-TTATATTT
1 AATTTAAATTATTTATGA-ATTT
2417845 AATTTAAATTATTTATGAATTT
1 AATTTAAATTATTTATGAATTT
2417867 AATTT-AATTATT
1 AATTTAAATTATT
2417879 ATATTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 15 0.48
22 14 0.45
23 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTAAATTATTTATGAATTT
Found at i:2417956 original size:25 final size:26
Alignment explanation
Indices: 2417903--2417968 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
2417893 TTTAATTAAA
2417903 AAATATATTAAATTTAAATATAAATAT
1 AAATA-ATTAAATTTAAATATAAATAT
**
2417930 AAATAATTAAATTTTTAT-TAAATAT
1 AAATAATTAAATTTAAATATAAATAT
2417955 AAA-AATTAAATTTA
1 AAATAATTAAATTTA
2417969 TTTTTACATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.28
25 10 0.28
26 11 0.31
27 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AAATAATTAAATTTAAATATAAATAT
Found at i:2418114 original size:18 final size:18
Alignment explanation
Indices: 2418067--2418114 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2418057 TTGAATTGAG
*
2418067 TCAAATTTCAAAATTTTAAT
1 TCAAATTT--AAATTTAAAT
* *
2418087 TTAAAATTAAATTTAAAT
1 TCAAATTTAAATTTAAAT
2418105 TCAAATTTAA
1 TCAAATTTAA
2418115 TATAGTATCG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 17 0.74
20 6 0.26
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TCAAATTTAAATTTAAAT
Found at i:2429692 original size:123 final size:122
Alignment explanation
Indices: 2429479--2429702 Score: 333
Period size: 123 Copynumber: 1.8 Consensus size: 122
2429469 TTTTTTGGGT
* *
2429479 CTGAGTAATCTCAAATAAATTATGAGATTTTTGTTTGGTAAGCCTTGGTTTAGAAGAATAAATTA
1 CTGAGTAATCTCAAATAAATTATGAAATTTTTGTTTGGTAAGCCTTGATTTAGAAGAATAAATTA
* *
2429544 CCACTAAATGTAAAGTCATATTCTGATTTTCAAACACTGTTGTATCTTGTTTTGGAC
66 CCACTAAATGTAAAGTCATACTCTGAGTTTCAAACACTGTTGTATCTTGTTTTGGAC
* * * *
2429601 CTGAGTTATCTCAAATAAGTTATGAAATTTTTTGTTTGGTTAGCCTTGATTTGGAAGAATAAATT
1 CTGAGTAATCTCAAATAAATTATGAAA-TTTTTGTTTGGTAAGCCTTGATTTAGAAGAATAAATT
* *
2429666 CCCACTAAATGTAAAGT-ACTGCTCTGAGTTTCAAACA
65 ACCACTAAATGTAAAGTCA-TACTCTGAGTTTCAAACA
2429703 TGGTTCTACC
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
122 25 0.28
123 65 0.72
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (122 bp):
CTGAGTAATCTCAAATAAATTATGAAATTTTTGTTTGGTAAGCCTTGATTTAGAAGAATAAATTA
CCACTAAATGTAAAGTCATACTCTGAGTTTCAAACACTGTTGTATCTTGTTTTGGAC
Found at i:2429727 original size:123 final size:122
Alignment explanation
Indices: 2429474--2429730 Score: 329
Period size: 123 Copynumber: 2.1 Consensus size: 122
2429464 TACCATTTTT
* * * *
2429474 TGGGTCTGAGTAATCTCAAATAAATTATGAGATTTTTGTTTGGTAAGCCTTGGTTTAGAAGAATA
1 TGGGCCTGAGTTATCTCAAATAAATTATGAAATTTTTGTTTGGTAAGCCTTGATTTAGAAGAATA
* * * * * *
2429539 AATTACCACTAAATGTAAAGTCATATTCTGATTTTCAAACACTGTTGTATCTTGTTT
66 AATTACCACTAAATGTAAAGTCATACTCTGAGTTTCAAACACTGTTCTACCGTGTTC
* * * *
2429596 TGGACCTGAGTTATCTCAAATAAGTTATGAAATTTTTTGTTTGGTTAGCCTTGATTTGGAAGAAT
1 TGGGCCTGAGTTATCTCAAATAAATTATGAAA-TTTTTGTTTGGTAAGCCTTGATTTAGAAGAAT
* *
2429661 AAATTCCCACTAAATGTAAAGT-ACTGCTCTGAGTTTCAAACA-TGGTTCTACCGTGTTC
65 AAATTACCACTAAATGTAAAGTCA-TACTCTGAGTTTCAAACACT-GTTCTACCGTGTTC
2429719 TGGGCCTGAGTT
1 TGGGCCTGAGTT
2429731 TCATTTGCTA
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
122 29 0.25
123 86 0.75
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (122 bp):
TGGGCCTGAGTTATCTCAAATAAATTATGAAATTTTTGTTTGGTAAGCCTTGATTTAGAAGAATA
AATTACCACTAAATGTAAAGTCATACTCTGAGTTTCAAACACTGTTCTACCGTGTTC
Found at i:2436807 original size:35 final size:36
Alignment explanation
Indices: 2436739--2436811 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
2436729 TTGGGTTTAT
*
2436739 TTTAAATAAGTATGTTTAAATAAAAAAATATAATTA
1 TTTAAATAAGTATATTTAAATAAAAAAATATAATTA
* *
2436775 TTTAAATAATTTTATTTAAAT-AAAAAATATAATTA
1 TTTAAATAAGTATATTTAAATAAAAAAATATAATTA
2436810 TT
1 TT
2436812 CGTATCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 16 0.47
36 18 0.53
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (36 bp):
TTTAAATAAGTATATTTAAATAAAAAAATATAATTA
Found at i:2436905 original size:18 final size:18
Alignment explanation
Indices: 2436882--2436917 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2436872 TTTATACTTT
2436882 CTAATTTCATTAACTCTA
1 CTAATTTCATTAACTCTA
*
2436900 CTAATTTCATTAATTCTA
1 CTAATTTCATTAACTCTA
2436918 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (18 bp):
CTAATTTCATTAACTCTA
Found at i:2445442 original size:14 final size:14
Alignment explanation
Indices: 2445425--2445453 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2445415 GTCATTTCAA
2445425 TGCATTTAATTCGT
1 TGCATTTAATTCGT
2445439 TGCATTTAATTCGT
1 TGCATTTAATTCGT
2445453 T
1 T
2445454 TCATATGTAT
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:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TGCATTTAATTCGT
Found at i:2446521 original size:1 final size:1
Alignment explanation
Indices: 2446515--2446544 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2446505 CCCTAAAGTG
2446515 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2446545 CAACAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2449315 original size:17 final size:17
Alignment explanation
Indices: 2449262--2449324 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
2449252 AATAAATTTT
*
2449262 TTTATTTATATTTGAAGAAC
1 TTTATTTATA-TT-AA-AAA
* *
2449282 TTTATTTTAAATAAAAAA
1 TTTA-TTTATATTAAAAA
2449300 TTTATTTATATTAAAAA
1 TTTATTTATATTAAAAA
2449317 TTTATTTA
1 TTTATTTA
2449325 ACATAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 19 0.51
18 6 0.16
19 2 0.05
20 5 0.14
21 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTATTTATATTAAAAA
Found at i:2449331 original size:17 final size:16
Alignment explanation
Indices: 2449282--2449331 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
2449272 TTTGAAGAAC
2449282 TTTATTTTAAATAAAAAA
1 TTTA-TTTAAAT-AAAAA
*
2449300 TTTATTTATATTAAAAA
1 TTTATTTA-AATAAAAA
2449317 TTTATTTAACATAAA
1 TTTATTTAA-ATAAA
2449332 TTAAAAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 1 0.04
17 21 0.75
18 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATTTAAATAAAAA
Found at i:2449343 original size:29 final size:29
Alignment explanation
Indices: 2449310--2449438 Score: 104
Period size: 29 Copynumber: 4.4 Consensus size: 29
2449300 TTTATTTATA
2449310 TTAAAAATTTATTTAACATAAATTAAAAG
1 TTAAAAATTTATTTAACATAAATTAAAAG
* * *
2449339 TTAAAAATTTATTCAAATATAAATT-AAAT
1 TTAAAAATTTATT-TAACATAAATTAAAAG
* ** *
2449368 TTAAGTAA-TTATTTTGCTATAAAATAAAAG
1 TTAA-AAATTTATTTAAC-ATAAATTAAAAG
* *
2449398 TTAAAAACTTATTTAA-ATATAA-TAAAAA
1 TTAAAAATTTATTTAACATA-AATTAAAAG
2449426 TATAAAAATTTAT
1 T-TAAAAATTTAT
2449439 CAAAGTAATA
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
28 9 0.12
29 45 0.58
30 24 0.31
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (29 bp):
TTAAAAATTTATTTAACATAAATTAAAAG
Found at i:2452524 original size:14 final size:14
Alignment explanation
Indices: 2452505--2452532 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2452495 CACACATCTT
2452505 TTTTTTATAAGATA
1 TTTTTTATAAGATA
2452519 TTTTTTATAAGATA
1 TTTTTTATAAGATA
2452533 AAATTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTTTATAAGATA
Found at i:2457316 original size:20 final size:20
Alignment explanation
Indices: 2457282--2457319 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2457272 TCTAGAATAG
2457282 GTTGACAAATTGTTGTATAT
1 GTTGACAAATTGTTGTATAT
2457302 GTTGA-AAATTAGTTGTAT
1 GTTGACAAATT-GTTGTAT
2457320 TGTCATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (20 bp):
GTTGACAAATTGTTGTATAT
Found at i:2457945 original size:9 final size:9
Alignment explanation
Indices: 2457926--2457963 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
2457916 TTATTTTAAT
2457926 ATTAA-AAA
1 ATTAATAAA
2457934 ATTAATAAA
1 ATTAATAAA
2457943 ATTAATAAA
1 ATTAATAAA
2457952 ATTAATAAA
1 ATTAATAAA
2457961 ATT
1 ATT
2457964 TAAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
ATTAATAAA
Found at i:2458787 original size:18 final size:16
Alignment explanation
Indices: 2458764--2458797 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
2458754 CGAAAGGAAA
2458764 TATTTTACTTGTTATAAT
1 TATTTTA-TT-TTATAAT
2458782 TATTTTATTTTATAAT
1 TATTTTATTTTATAAT
2458798 ATAATCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (16 bp):
TATTTTATTTTATAAT
Found at i:2460566 original size:16 final size:16
Alignment explanation
Indices: 2460517--2460568 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
2460507 CAAATTCATT
*
2460517 AGTAATTTATCCAATT
1 AGTAATTTATCCAATA
*
2460533 ACTAAATATCTAATCCAATA
1 AGT-AAT-T-T-ATCCAATA
2460553 AGTAATTTATCCAATA
1 AGTAATTTATCCAATA
2460569 TCAATGAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
16 10 0.34
17 4 0.14
18 2 0.07
19 4 0.14
20 9 0.31
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (16 bp):
AGTAATTTATCCAATA
Found at i:2475391 original size:10 final size:10
Alignment explanation
Indices: 2475365--2475429 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 10
2475355 TTATTATTTT
2475365 TAAATATAAATA
1 TAAATAT-AA-A
*
2475377 TAAATTTAAA
1 TAAATATAAA
2475387 TAAATAT-AA
1 TAAATATAAA
*
2475396 -AAATATATA
1 TAAATATAAA
2475405 -AAAT-TAAA
1 TAAATATAAA
2475413 TAAATAATAAA
1 TAAAT-ATAAA
2475424 -AAATAT
1 TAAATAT
2475430 TTTTATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
8 9 0.20
9 13 0.29
10 11 0.24
11 6 0.13
12 6 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAATATAAA
Found at i:2475403 original size:26 final size:26
Alignment explanation
Indices: 2475372--2475429 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
2475362 TTTTAAATAT
*
2475372 AAATATAAATTTAAATAAAT-ATAAA
1 AAATATAAAATTAAATAAATAATAAA
2475397 AATATATAAAATTAAATAAATAATAAA
1 AA-ATATAAAATTAAATAAATAATAAA
2475424 AAATAT
1 AAATAT
2475430 TTTTATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 2 0.07
26 21 0.70
27 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATATAAAATTAAATAAATAATAAA
Found at i:2475405 original size:16 final size:16
Alignment explanation
Indices: 2475368--2475406 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2475358 TTATTTTTAA
**
2475368 ATATAAATATAAATTT
1 ATATAAATATAAAAAT
*
2475384 AAATAAATATAAAAAT
1 ATATAAATATAAAAAT
2475400 ATATAAA
1 ATATAAA
2475407 ATTAAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAATATAAAAAT
Found at i:2476208 original size:21 final size:19
Alignment explanation
Indices: 2476184--2476230 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2476174 TTATGCAAAT
*
2476184 ATTATTTTTATTGTAGAAAAA
1 ATTATTTTT-TTATA-AAAAA
2476205 ATTATATTTTTTATAAAAAA
1 ATTAT-TTTTTTATAAAAAA
2476225 ATTATT
1 ATTATT
2476231 ATACATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 10 0.42
21 9 0.38
22 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
ATTATTTTTTTATAAAAAA
Found at i:2476570 original size:13 final size:13
Alignment explanation
Indices: 2476552--2476579 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2476542 AAGTGCGTTT
2476552 AGTTATGCTGGTA
1 AGTTATGCTGGTA
2476565 AGTTATGCTGGTA
1 AGTTATGCTGGTA
2476578 AG
1 AG
2476580 CCGACGTAAT
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:0.25, C:0.07, G:0.32, T:0.36
Consensus pattern (13 bp):
AGTTATGCTGGTA
Found at i:2480171 original size:13 final size:13
Alignment explanation
Indices: 2480138--2480174 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2480128 ATTATTTTAA
*
2480138 ATTTTATTTATA-
1 ATTTTATATATAT
2480150 ATTTT-TATATAT
1 ATTTTATATATAT
2480162 ATTTTATATATAT
1 ATTTTATATATAT
2480175 TTATTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 5 0.23
12 10 0.45
13 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTATATATAT
Found at i:2480175 original size:11 final size:11
Alignment explanation
Indices: 2480144--2480176 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2480134 TTAAATTTTA
2480144 TTTATA-AT-T
1 TTTATATATAT
2480153 TTTATATATAT
1 TTTATATATAT
2480164 TTTATATATAT
1 TTTATATATAT
2480175 TT
1 TT
2480177 ATTCAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.27
10 2 0.09
11 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATATATAT
Found at i:2486174 original size:12 final size:12
Alignment explanation
Indices: 2486141--2486174 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2486131 GTGTCCTGGA
*
2486141 TTTGTTTTTCAC
1 TTTGTTTTTTAC
*
2486153 TTTGTTTTTTAT
1 TTTGTTTTTTAC
2486165 TTTGTTTTTT
1 TTTGTTTTTT
2486175 TTCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.06, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTGTTTTTTAC
Found at i:2486475 original size:20 final size:22
Alignment explanation
Indices: 2486428--2486475 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
2486418 TAGTAGAATC
2486428 TTAAATTTATAGTTTCAATAAT
1 TTAAATTTATAGTTTCAATAAT
* * *
2486450 TAAAATTTA-A-TTTTAATACT
1 TTAAATTTATAGTTTCAATAAT
2486470 TTAAAT
1 TTAAAT
2486476 ATCAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.59
21 1 0.05
22 8 0.36
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAAATTTATAGTTTCAATAAT
Found at i:2486946 original size:24 final size:26
Alignment explanation
Indices: 2486889--2486948 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
2486879 AAATATAAAA
*
2486889 AATAAAAATAATATGATTTAAAATTT
1 AATAAAATTAATATGATTTAAAATTT
*
2486915 --TAATAATTATTAT-ATTT-AAATTT
1 AATAA-AATTAATATGATTTAAAATTT
2486938 AATAAAATTAA
1 AATAAAATTAA
2486949 AATATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
23 6 0.21
24 12 0.43
25 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AATAAAATTAATATGATTTAAAATTT
Found at i:2498854 original size:14 final size:14
Alignment explanation
Indices: 2498830--2498866 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2498820 TTTTAATATT
2498830 TTTAT-TAAAAATA
1 TTTATCTAAAAATA
2498843 TTTATCTAAAAATA
1 TTTATCTAAAAATA
*
2498857 TATATC-AAAA
1 TTTATCTAAAA
2498867 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTATCTAAAAATA
Found at i:2499374 original size:49 final size:51
Alignment explanation
Indices: 2499320--2499418 Score: 139
Period size: 49 Copynumber: 2.0 Consensus size: 51
2499310 ACTTCAATTG
* * * *
2499320 AATATAAAATATTTAAATTTTAAATTAAAAT-ATCAAATA-ATATTTTATT
1 AATATAAAATATATAAATATAAAATTAAAATAATAAAATATATATTTTATT
*
2499369 AATATAATATATATAAATATAAAATTAAAATAATAAAATATATATTTTAT
1 AATATAAAATATATAAATATAAAATTAAAATAATAAAATATATATTTTAT
2499419 ATTTATTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 27 0.63
50 7 0.16
51 9 0.21
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (51 bp):
AATATAAAATATATAAATATAAAATTAAAATAATAAAATATATATTTTATT
Found at i:2499849 original size:24 final size:24
Alignment explanation
Indices: 2499816--2499890 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
2499806 GATGGATTAC
2499816 ATCTTAATTATA-TATAAATATAAT
1 ATCTTAATTATATTA-AAATATAAT
* *
2499840 ATCTTTATTATATTAAAATATAAA
1 ATCTTAATTATATTAAAATATAAT
** * *
2499864 ATAATAATTCTATTAACATAATAAT
1 ATCTTAATTATATTAAAAT-ATAAT
2499889 AT
1 AT
2499891 ATAAATATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 33 0.80
25 8 0.20
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (24 bp):
ATCTTAATTATATTAAAATATAAT
Found at i:2500447 original size:23 final size:23
Alignment explanation
Indices: 2500415--2500464 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
2500405 CATTTATTCT
*
2500415 ATAGACATAACA-ATTTATTTTGA
1 ATAGACATAA-ATATATATTTTGA
*
2500438 ATAGATATAAATTATATATTTTGA
1 ATAGACATAAA-TATATATTTTGA
2500462 ATA
1 ATA
2500465 ATCAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.04
23 9 0.39
24 13 0.57
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (23 bp):
ATAGACATAAATATATATTTTGA
Found at i:2501810 original size:18 final size:18
Alignment explanation
Indices: 2501756--2501810 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2501746 TTTGATCGAT
* *
2501756 TTTAATTTAATATATATA
1 TTTAATTTTATATTTATA
* *
2501774 -TTATTTTTA-ATTAATTA
1 TTTAATTTTATATTTA-TA
2501791 TTTAATTTTATATTTATA
1 TTTAATTTTATATTTATA
2501809 TT
1 TT
2501811 AAAAATAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 3 0.11
17 9 0.32
18 12 0.43
19 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTTATATTTATA
Found at i:2501837 original size:21 final size:21
Alignment explanation
Indices: 2501802--2501856 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
2501792 TTAATTTTAT
2501802 ATTTATA-TT-AAAAATAATA
1 ATTTATATTTAAAAAATAATA
*
2501821 TTTTATATTTAAAAAATAATA
1 ATTTATATTTAAAAAATAATA
2501842 ATTTATTAATTTAAA
1 ATTTA-T-ATTTAAA
2501857 TTAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.20
20 2 0.07
21 14 0.47
22 1 0.03
23 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTATATTTAAAAAATAATA
Found at i:2501916 original size:27 final size:26
Alignment explanation
Indices: 2501847--2501917 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
2501837 TAATAATTTA
* *
2501847 TTAATTTAAATTAAATTAAATATAAT
1 TTAATATAAAATAAATTAAATATAAT
* * * *
2501873 TTTATATAATATCAAATTTAATCTAAT
1 TTAATATAAAAT-AAATTAAATATAAT
2501900 TTAAATATAAAATAAATT
1 TT-AATATAAAATAAATT
2501918 CTTTAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 8 0.23
27 19 0.54
28 8 0.23
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATATAAAATAAATTAAATATAAT
Found at i:2508497 original size:13 final size:13
Alignment explanation
Indices: 2508479--2508503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2508469 AGATTGATAA
2508479 AATTTATTATGAT
1 AATTTATTATGAT
2508492 AATTTATTATGA
1 AATTTATTATGA
2508504 GAATCAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
AATTTATTATGAT
Found at i:2508578 original size:29 final size:28
Alignment explanation
Indices: 2508535--2508597 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
2508525 AATTATTAAA
** *
2508535 AATA-TTATTTATAATTTAAATTTAATT
1 AATATTTATTTATAATAAAAATTTAATC
*
2508562 AATATTTATTTAATAATAAAAATTTTATC
1 AATATTTATTT-ATAATAAAAATTTAATC
2508591 AATATTT
1 AATATTT
2508598 TTATTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.13
28 6 0.20
29 20 0.67
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
AATATTTATTTATAATAAAAATTTAATC
Found at i:2508619 original size:14 final size:15
Alignment explanation
Indices: 2508591--2508624 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2508581 AAATTTTATC
*
2508591 AATATTTTTATTAAA
1 AATATTTTTACTAAA
2508606 AATATTTTT-CTAAA
1 AATATTTTTACTAAA
2508620 AATAT
1 AATAT
2508625 ATATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTTTTACTAAA
Found at i:2512158 original size:21 final size:21
Alignment explanation
Indices: 2512114--2512154 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2512104 TGAATTTTAA
*
2512114 AATTTGATCTGAATTTGAATT
1 AATTTGATCTGAATTTAAATT
*
2512135 AATTTGATTTGAA-TTAAATT
1 AATTTGATCTGAATTTAAATT
2512155 TAATCGGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (21 bp):
AATTTGATCTGAATTTAAATT
Found at i:2517776 original size:21 final size:21
Alignment explanation
Indices: 2517752--2517793 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2517742 CTAACGATCA
*
2517752 GTTTATTTAAATTTTATTTAT
1 GTTTATTTAAAATTTATTTAT
*
2517773 GTTTGTTTAAAATTTATTTAT
1 GTTTATTTAAAATTTATTTAT
2517794 ATTCGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
GTTTATTTAAAATTTATTTAT
Found at i:2517801 original size:21 final size:21
Alignment explanation
Indices: 2517757--2517804 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2517747 GATCAGTTTA
* * *
2517757 TTTAAATTTTATTTATGTTTG
1 TTTAAAATTTATTTATATTCG
2517778 TTTAAAATTTATTTATATTCG
1 TTTAAAATTTATTTATATTCG
2517799 TTTAAA
1 TTTAAA
2517805 TAACAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTAAAATTTATTTATATTCG
Found at i:2535687 original size:14 final size:15
Alignment explanation
Indices: 2535661--2535689 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2535651 CCTTTCCTTC
2535661 TTTTGCCATTCTACT
1 TTTTGCCATTCTACT
2535676 TTTTGCCA-TCTACT
1 TTTTGCCATTCTACT
2535690 ACCAACTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.14, C:0.28, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTTGCCATTCTACT
Found at i:2544832 original size:25 final size:24
Alignment explanation
Indices: 2544782--2544830 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
2544772 AATTTTTTTT
2544782 TTTTAAATAATACGTGACAATCATA
1 TTTTAAATAATACG-GACAATCATA
*
2544807 TTTTAAATCATAC-GACAATCATA
1 TTTTAAATAATACGGACAATCATA
2544830 T
1 T
2544831 ATCATTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
25 12 0.52
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (24 bp):
TTTTAAATAATACGGACAATCATA
Found at i:2544936 original size:20 final size:20
Alignment explanation
Indices: 2544913--2544958 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2544903 AAATGAAAAT
2544913 AAAATTTAAATATCTGATTA
1 AAAATTTAAATATCTGATTA
2544933 AAAATTTAAATATCTGATTA
1 AAAATTTAAATATCTGATTA
*
2544953 ATAATT
1 AAAATT
2544959 CAGTGTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAATTTAAATATCTGATTA
Done.