Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 61 of 163
Found at i:15529464 original size:71 final size:71
Alignment explanation
Indices: 15529346--15529499 Score: 222
Period size: 71 Copynumber: 2.2 Consensus size: 71
15529336 AATTCTATGC
*
15529346 AGTATCGGTAGTTAGGACTGATGTATCGATAGAAACCTCCAGACTAGTTAGTCTTGCTCACTGTC
1 AGTATCGGTAGTTAGGACTAATGTATCGATAGAAACCTCCAGACTAGTTAGTCTTGCTCACTGTC
15529411 ATTTGA
66 ATTTGA
* * *
15529417 AGTATTGGTAGTTAGGACTAATGTGTC-AGTAGAAACCTCCAGGCTAGTTAGTCTTGCTCACTGT
1 AGTATCGGTAGTTAGGACTAATGTATCGA-TAGAAACCTCCAGACTAGTTAGTCTTGCTCACTGT
* *
15529481 TATAT-A
65 CATTTGA
15529487 AGGTATCGGTAGT
1 A-GTATCGGTAGT
15529500 GAACTGAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
70 3 0.04
71 71 0.96
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (71 bp):
AGTATCGGTAGTTAGGACTAATGTATCGATAGAAACCTCCAGACTAGTTAGTCTTGCTCACTGTC
ATTTGA
Found at i:15531559 original size:3 final size:3
Alignment explanation
Indices: 15531551--15531599 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
15531541 AAAGGCCTAA
* * *
15531551 ATT ATT ATT ATG ATT ACT ATT ATT ATC ATT ATT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
15531597 ATT
1 ATT
15531600 TTTAGGGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:15532362 original size:148 final size:140
Alignment explanation
Indices: 15532031--15532382 Score: 433
Period size: 148 Copynumber: 2.4 Consensus size: 140
15532021 TGGAAAAAAA
*
15532031 TTTTG-TTTTTTAAACAATTTCGAAATAAAAGCTTTT-ATTTTTAAGTAAAATAGTGATTTTCTT
1 TTTTGATTTTTT-AACTATTTCGAAATAAAAG-TTTTGATTTTTAAGTAAAATAGTGATTTTCTT
*
15532094 TAAAAAAAAGAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTTTAGAAAAGTTTAAA
64 T-AAAAAAAGAGAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTTTAGAAAAGTTTAAA
15532159 TTTTTAAACAAAG
128 TTTTTAAACAAAG
* *
15532172 TTTTGATTTTTTTTTAACTATTTCGAAACAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTCT
1 TTTTGA---TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCT
*
15532237 TT-AAAAAA-AGAGAAAGTTTATATTTTTAAAAATAAAAAATATATTTTTAGTTATTTTAAAGAA
63 TTAAAAAAAGAGAGAAAGTTTAGATTTTTAAAAAT-AAAAATATA---TT--TT-TTTT--AG-A
* *
15532300 AAAGTTTAATTTTTTCAACAAAG
118 AAAGTTTAAATTTTTAAACAAAG
* * * *
15532323 TTTTGATTTTTTAACTATTTTGCAATAAAAGTTTTGATTTTGAATTAAAATAGTGATTTT
1 TTTTGATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT
15532383 GTTTTAATCA
Statistics
Matches: 183, Mismatches: 13, Indels: 23
0.84 0.06 0.11
Matches are distributed among these distances:
141 29 0.16
142 14 0.08
143 3 0.02
144 45 0.25
145 8 0.04
147 2 0.01
148 52 0.28
150 2 0.01
151 28 0.15
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (140 bp):
TTTTGATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTTA
AAAAAAGAGAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTTTAGAAAAGTTTAAATTT
TTAAACAAAG
Found at i:15548251 original size:21 final size:22
Alignment explanation
Indices: 15548200--15548251 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
15548190 AATCCCAAGT
* *
15548200 AACATAAAAAAAGATACCAAACT
1 AACA-AAAAAAAGATAACAAACA
* *
15548223 AACGAAAAAAAGATAAGAAA-A
1 AACAAAAAAAAGATAACAAACA
15548244 AACAAAAA
1 AACAAAAA
15548252 GCTACAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.73, C:0.12, G:0.08, T:0.08
Consensus pattern (22 bp):
AACAAAAAAAAGATAACAAACA
Found at i:15559870 original size:21 final size:20
Alignment explanation
Indices: 15559844--15559893 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 20
15559834 ATCAAAATTA
15559844 AAAAAAATATCAAATTAAG-AG
1 AAAAAAATA--AAATTAAGTAG
15559865 AAAAAAATAAAATTAAGTTAG
1 AAAAAAATAAAATTAAG-TAG
15559886 AAAAAAAT
1 AAAAAAAT
15559894 TGAAAGCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.30
21 19 0.70
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (20 bp):
AAAAAAATAAAATTAAGTAG
Found at i:15559877 original size:19 final size:19
Alignment explanation
Indices: 15559837--15559893 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
15559827 ACTATGGATC
*
15559837 AAAATTAA-A-AAAAATAT
1 AAAATTAAGAGAAAAAAAT
*
15559854 CAAATTAAGAGAAAAAAAT
1 AAAATTAAGAGAAAAAAAT
15559873 AAAATTAAGTTAGAAAAAAAT
1 AAAATTAAG--AGAAAAAAAT
15559894 TGAAAGCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 15 0.45
21 10 0.30
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (19 bp):
AAAATTAAGAGAAAAAAAT
Found at i:15565504 original size:19 final size:19
Alignment explanation
Indices: 15565480--15565516 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15565470 TAAAAGATAA
*
15565480 ATTTTAAATTTTAAAATTC
1 ATTTTAAATCTTAAAATTC
15565499 ATTTTAAATCTTAAAATT
1 ATTTTAAATCTTAAAATT
15565517 TTCAAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTAAATCTTAAAATTC
Found at i:15568416 original size:18 final size:17
Alignment explanation
Indices: 15568385--15568418 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15568375 CTATACTTTT
15568385 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
15568402 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
15568419 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:15572191 original size:26 final size:26
Alignment explanation
Indices: 15572155--15572207 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
15572145 CATACCGGAT
15572155 TTTATAGACTATTTATCCAAGACTTC
1 TTTATAGACTATTTATCCAAGACTTC
15572181 TTTATAGACTATTTATCCAAGACTTC
1 TTTATAGACTATTTATCCAAGACTTC
15572207 T
1 T
15572208 CCAAAATAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (26 bp):
TTTATAGACTATTTATCCAAGACTTC
Found at i:15575905 original size:3 final size:3
Alignment explanation
Indices: 15575897--15575955 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
15575887 ATTAAAGCAA
*
15575897 AAG AAG AAG AA- AAG -AG AA- AAG AAG AAG AAA AAG AA- AAG AAG AAAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
15575942 AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AA
15575956 TACGTTGCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
2 8 0.16
3 38 0.78
4 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15575916 original size:7 final size:6
Alignment explanation
Indices: 15575890--15575955 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
15575880 TGAGGGTATT
* * *
15575890 AAAGCA AAAGAA GAAG-A AAAGAGA AAAGAA GAAGAA AAAG-A AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA
* *
15575937 GAAAGAA GAAGAA GAAGAA
1 -AAAGAA AAAGAA AAAGAA
15575956 TACGTTGCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 9 0.18
6 29 0.58
7 12 0.24
ACGTcount: A:0.73, C:0.02, G:0.26, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:15575918 original size:18 final size:17
Alignment explanation
Indices: 15575890--15575955 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 17
15575880 TGAGGGTATT
15575890 AAAGCAAAAGAAGAAGAA
1 AAAG-AAAAGAAGAAGAA
15575908 AAGAGAAAAGAAGAAGAA
1 AA-AGAAAAGAAGAAGAA
15575926 AAAGAAAAGAAGAAAGAA
1 AAAGAAAAGAAG-AAGAA
*
15575944 GAAGAAGAAGAA
1 AAAGAA-AAGAA
15575956 TACGTTGCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 10 0.23
18 27 0.61
19 7 0.16
ACGTcount: A:0.73, C:0.02, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAGAAGAA
Found at i:15575924 original size:24 final size:24
Alignment explanation
Indices: 15575897--15575955 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
15575887 ATTAAAGCAA
15575897 AAGAAGAAGAAAAG-AGAAAAGAAG
1 AAGAAGAAGAAAAGAAG-AAAGAAG
*
15575921 AAGAAAAAGAAAAGAAGAAAGAAG
1 AAGAAGAAGAAAAGAAGAAAGAAG
15575945 AAGAAGAAGAA
1 AAGAAGAAGAA
15575956 TACGTTGCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AAGAAGAAGAAAAGAAGAAAGAAG
Found at i:15576384 original size:17 final size:17
Alignment explanation
Indices: 15576362--15576399 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
15576352 TTTTCTCTAG
*
15576362 TTGTCATTGCATTTTAA
1 TTGTCACTGCATTTTAA
15576379 TTGTCACTGCATTTTAA
1 TTGTCACTGCATTTTAA
15576396 TTGT
1 TTGT
15576400 TCTCACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (17 bp):
TTGTCACTGCATTTTAA
Found at i:15579071 original size:39 final size:39
Alignment explanation
Indices: 15579028--15579148 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 39
15579018 GTACAATACC
* *
15579028 GTATTACGGTGTTTACAGTGTCACCGTCAGTTCAGTGTT
1 GTATTACGGTGTTTACAGTGTCATCGTCAGTTCAGTATT
* * * **
15579067 GTATTGCAGTTTTTACAGTGTC-TC-TACTAGTTCAGTACA
1 GTATTACGGTGTTTACAGTGTCATCGT-C-AGTTCAGTATT
* *
15579106 GAATTACGGTGTTTACAGTGTCATCGTTAGTTCAGTATT
1 GTATTACGGTGTTTACAGTGTCATCGTCAGTTCAGTATT
15579145 GTAT
1 GTAT
15579149 CACAGTCACA
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
37 1 0.02
38 2 0.03
39 57 0.90
40 2 0.03
41 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (39 bp):
GTATTACGGTGTTTACAGTGTCATCGTCAGTTCAGTATT
Found at i:15579075 original size:78 final size:78
Alignment explanation
Indices: 15578950--15579148 Score: 240
Period size: 78 Copynumber: 2.6 Consensus size: 78
15578940 GCTCAGTTCG
* * * * *
15578950 GTATTACGATGTTTATAGTGTCATCGTCAGTTTAATGTTAG-AATGCAGTGTTTACAGTGT-TAC
1 GTATTACGGTGTTTACAGTGTCATCGTCAGTTCAGTGTT-GTATTGCAGTGTTTACAGTGTCT-C
* *
15579013 TGCTAGTACAATACC
64 TACTAGTACAATACA
* *
15579028 GTATTACGGTGTTTACAGTGTCACCGTCAGTTCAGTGTTGTATTGCAGTTTTTACAGTGTCTCTA
1 GTATTACGGTGTTTACAGTGTCATCGTCAGTTCAGTGTTGTATTGCAGTGTTTACAGTGTCTCTA
* *
15579093 CTAGTTCAGTACA
66 CTAGTACAATACA
* * *
15579106 GAATTACGGTGTTTACAGTGTCATCGTTAGTTCAGTATTGTAT
1 GTATTACGGTGTTTACAGTGTCATCGTCAGTTCAGTGTTGTAT
15579149 CACAGTCACA
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 1 0.01
78 102 0.98
79 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (78 bp):
GTATTACGGTGTTTACAGTGTCATCGTCAGTTCAGTGTTGTATTGCAGTGTTTACAGTGTCTCTA
CTAGTACAATACA
Found at i:15579300 original size:42 final size:42
Alignment explanation
Indices: 15579210--15579292 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
15579200 CGTTTATTAG
*
15579210 CCCGTGTGTCTCACACGACCACACCCATGCCCGTGTATTCAA
1 CCCGTGTGTCTCACACGACCACACCCATGCCAGTGTATTCAA
*
15579252 CCCGTGTGTCTCACACGGCCACACCC-TCGCCAGTGTATTCA
1 CCCGTGTGTCTCACACGACCACACCCAT-GCCAGTGTATTCA
15579293 GGCCGTGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.19, C:0.41, G:0.18, T:0.22
Consensus pattern (42 bp):
CCCGTGTGTCTCACACGACCACACCCATGCCAGTGTATTCAA
Found at i:15585701 original size:12 final size:12
Alignment explanation
Indices: 15585684--15585715 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
15585674 AAAATACATT
15585684 ACACACGATCTG
1 ACACACGATCTG
*
15585696 ACACACAATCTG
1 ACACACGATCTG
15585708 ACACACGA
1 ACACACGA
15585716 CCGTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.34, G:0.12, T:0.12
Consensus pattern (12 bp):
ACACACGATCTG
Found at i:15589194 original size:10 final size:10
Alignment explanation
Indices: 15589179--15589254 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 10
15589169 CATGAGTTTA
15589179 ATGTGATTAT
1 ATGTGATTAT
* *
15589189 ATGTGATGAA
1 ATGTGATTAT
* *
15589199 ATGTGACTAA
1 ATGTGATTAT
15589209 ATGTGATTAT
1 ATGTGATTAT
*
15589219 ATGAG-TGTAT
1 ATGTGAT-TAT
* *
15589229 AGGTGATTAA
1 ATGTGATTAT
15589239 ATGTGATTAAT
1 ATGTGATT-AT
15589250 ATGTG
1 ATGTG
15589255 TTGTGTTAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
9 1 0.02
10 43 0.84
11 7 0.14
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.39
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:15589203 original size:20 final size:20
Alignment explanation
Indices: 15589178--15589254 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
15589168 ACATGAGTTT
*
15589178 AATGTGATTATATGTGATGA
1 AATGTGATTATATGTGATTA
* *
15589198 AATGTGACTAAATGTGATTA
1 AATGTGATTATATGTGATTA
* * *
15589218 TATGAG-TGTATAGGTGATTA
1 AATGTGAT-TATATGTGATTA
15589238 AATGTGATTAATATGTG
1 AATGTGATT-ATATGTG
15589255 TTGTGTTAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 36 0.84
21 7 0.16
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.39
Consensus pattern (20 bp):
AATGTGATTATATGTGATTA
Found at i:15589213 original size:30 final size:30
Alignment explanation
Indices: 15589178--15589255 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
15589168 ACATGAGTTT
*
15589178 AATGTGATTATATGTGATG-AAATGTGACTA
1 AATGTGATTATATGTG-TGTAAAGGTGACTA
* * *
15589208 AATGTGATTATATGAGTGTATAGGTGATTA
1 AATGTGATTATATGTGTGTAAAGGTGACTA
15589238 AATGTGATTAATATGTGT
1 AATGTGATT-ATATGTGT
15589256 TGTGTTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.05
30 32 0.78
31 7 0.17
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (30 bp):
AATGTGATTATATGTGTGTAAAGGTGACTA
Found at i:15590466 original size:6 final size:6
Alignment explanation
Indices: 15590456--15590498 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
15590446 ATTTGAATAT
*
15590456 GAAATG AAAATG GAAATG GAAATG GAAATG GAAAT- GAAATG GA
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GA
15590499 TGCTACAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.16
Consensus pattern (6 bp):
GAAATG
Found at i:15591051 original size:21 final size:22
Alignment explanation
Indices: 15591027--15591067 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15591017 TGTGGCTCTC
*
15591027 CCACACGCCCGTGTG-TCCCTT
1 CCACACGCCCATGTGCTCCCTT
*
15591048 CCACATGCCCATGTGCTCCC
1 CCACACGCCCATGTGCTCCC
15591068 CGTGTGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.12, C:0.49, G:0.17, T:0.22
Consensus pattern (22 bp):
CCACACGCCCATGTGCTCCCTT
Found at i:15593034 original size:32 final size:34
Alignment explanation
Indices: 15592963--15593039 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 34
15592953 CCTATTCACT
15592963 TAAAATAA-ATAATTTTAGTCAAAATAAAAATTAA
1 TAAAATAACA-AATTTTAGTCAAAATAAAAATTAA
* *
15592997 GAAAATAACAAA-TTTAGTCAAAA-CAAAATTAA
1 TAAAATAACAAATTTTAGTCAAAATAAAAATTAA
15593029 TAAAATAACAA
1 TAAAATAACAA
15593040 CTTTGAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
32 18 0.46
33 11 0.28
34 9 0.23
35 1 0.03
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (34 bp):
TAAAATAACAAATTTTAGTCAAAATAAAAATTAA
Found at i:15593636 original size:31 final size:28
Alignment explanation
Indices: 15593573--15593641 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
15593563 AAGTATACAT
*
15593573 AATAAAA-AACAATATATACATAAAATAC
1 AATAAAATAA-AATATATACATAAAATAA
*
15593601 AATAAAATAAAATAATATACATATATGATAA
1 AATAAAATAAAAT-ATATACATA-A-AATAA
15593632 AAT-AAATAAA
1 AATAAAATAAA
15593642 TAAATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 10 0.29
29 11 0.31
30 8 0.23
31 6 0.17
ACGTcount: A:0.68, C:0.06, G:0.01, T:0.25
Consensus pattern (28 bp):
AATAAAATAAAATATATACATAAAATAA
Found at i:15593701 original size:30 final size:29
Alignment explanation
Indices: 15593667--15593880 Score: 178
Period size: 30 Copynumber: 7.2 Consensus size: 29
15593657 TTAAAACCGA
*
15593667 GTCAAATTTGAATTTTTGGAAGCTTTAGGG
1 GTCAAATTTGAATTTTTGGAA-ATTTAGGG
** * *
15593697 GTCAAATCAGAAATTTTGGAAAATTTAAGG
1 GTCAAATTTGAATTTTTGG-AAATTTAGGG
*** * * *
15593727 GTCAAATCAAAATTTTTGAAAAGTTCAAGG
1 GTCAAATTTGAATTTTTGGAAA-TTTAGGG
*
15593757 GTCAAATTTGAATTTTTGGAAAATTT-TGG
1 GTCAAATTTGAATTTTTGG-AAATTTAGGG
*
15593786 GTCAAATTTGAATATTTGGAAATTTTAGGG
1 GTCAAATTTGAATTTTTGGAAA-TTTAGGG
** * *
15593816 GTCAAATTCAAATTTTTGGAAAGTTCAGAG
1 GTCAAATTTGAATTTTTGGAAA-TTTAGGG
* * *
15593846 GTCAAATTTGAATTTTAAGAAAATTTGGGG
1 GTCAAATTTGAATTTT-TGGAAATTTAGGG
15593876 GTCAA
1 GTCAA
15593881 GTTATAATTT
Statistics
Matches: 148, Mismatches: 30, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
28 3 0.02
29 26 0.18
30 110 0.74
31 9 0.06
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (29 bp):
GTCAAATTTGAATTTTTGGAAATTTAGGG
Found at i:15593819 original size:89 final size:90
Alignment explanation
Indices: 15593667--15593880 Score: 274
Period size: 89 Copynumber: 2.4 Consensus size: 90
15593657 TTAAAACCGA
**
15593667 GTCAAATTTGAATTTTTGGAAGCTTTAGGGGTCAAATCAGAAATTTTGGAAAATTTAAGGGTCAA
1 GTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATCAGAAATTTTGGAAAATTTAAGGGTCAA
15593732 A-TCAAAATTTTTGAAAAGTTCA-AGG
66 ATTC-AAATTTTTGAAAAGTTCAGA-G
* ** * *
15593757 GTCAAATTTGAATTTTTGGAAAATTT-TGGGTCAAATTTG-AATATTTGGAAATTTTAGGGGTCA
1 GTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATCAGAAAT-TTTGGAAAATTTAAGGGTCA
*
15593820 AATTCAAATTTTTGGAAAGTTCAGAG
65 AATTCAAATTTTTGAAAAGTTCAGAG
** *
15593846 GTCAAATTTGAATTTTAAGAAAATTTGGGGGTCAA
1 GTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAA
15593881 GTTATAATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
88 3 0.03
89 72 0.66
90 34 0.31
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (90 bp):
GTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATCAGAAATTTTGGAAAATTTAAGGGTCAA
ATTCAAATTTTTGAAAAGTTCAGAG
Found at i:15594516 original size:26 final size:27
Alignment explanation
Indices: 15594481--15594532 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
15594471 ATAATATATC
*
15594481 AAATACATTTAAAA-ACATTAAAAAAT
1 AAATAAATTTAAAATACATTAAAAAAT
15594507 AAATAAATTTAAAATACATTAAAAAA
1 AAATAAATTTAAAATACATTAAAAAA
15594533 ATTTTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (27 bp):
AAATAAATTTAAAATACATTAAAAAAT
Found at i:15594533 original size:38 final size:38
Alignment explanation
Indices: 15594460--15594532 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
15594450 TACAACAAAT
* * *
15594460 TTAAAAAATATATAATATATCAAATACATTTAAAAACA
1 TTAAAAAATAAATAATATATAAAATACATTAAAAAACA
*
15594498 TTAAAAAATAAATAA-ATTTAAAATACATTAAAAAA
1 TTAAAAAATAAATAATATATAAAATACATTAAAAAA
15594533 ATTTTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (38 bp):
TTAAAAAATAAATAATATATAAAATACATTAAAAAACA
Found at i:15594737 original size:44 final size:44
Alignment explanation
Indices: 15594660--15594772 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
15594650 AATAGCATCC
* * ** * *
15594660 AAACAACAAAAAATAACAACCAAAATAGCAGCAAAAATAACAGTA
1 AAACAACAATAAA-AACAACAAAAATAATAGCAAAAACAACAGGA
*
15594705 AAACAACATTAAAAACAACAAAAATAATAGCAAAAACAACAGGA
1 AAACAACAATAAAAACAACAAAAATAATAGCAAAAACAACAGGA
* * *
15594749 AAATAACAATCAAAACAATAAAAA
1 AAACAACAATAAAAACAACAAAAA
15594773 AAACACCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 46 0.81
45 11 0.19
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (44 bp):
AAACAACAATAAAAACAACAAAAATAATAGCAAAAACAACAGGA
Found at i:15594777 original size:21 final size:21
Alignment explanation
Indices: 15594748--15594848 Score: 66
Period size: 21 Copynumber: 4.9 Consensus size: 21
15594738 AAACAACAGG
*
15594748 AAAATAACAATCAAAACAATA
1 AAAAAAACAATCAAAACAATA
* * *
15594769 AAAAAAAC-ACCAAAATAGT-
1 AAAAAAACAATCAAAACAATA
* * **
15594788 AAAATAACAAT-AAAATAGCA
1 AAAAAAACAATCAAAACAATA
* *
15594808 AAAAATAACAACCAAATCAATA
1 AAAAA-AACAATCAAAACAATA
15594830 AAAAAAAGC-ATCAAAACAA
1 AAAAAAA-CAATCAAAACAA
15594849 CAATAAAATT
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
19 14 0.23
20 13 0.22
21 22 0.37
22 11 0.18
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (21 bp):
AAAAAAACAATCAAAACAATA
Found at i:15594783 original size:44 final size:44
Alignment explanation
Indices: 15594691--15594783 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
15594681 AAAATAGCAG
* * * * * *
15594691 CAAAAATAACAGTAAAACAACATTAAAAACAACAAAAATAATAG
1 CAAAAACAACAGGAAAACAACAATAAAAACAACAAAAAAAACAC
* * *
15594735 CAAAAACAACAGGAAAATAACAATCAAAACAATAAAAAAAACAC
1 CAAAAACAACAGGAAAACAACAATAAAAACAACAAAAAAAACAC
15594779 CAAAA
1 CAAAA
15594784 TAGTAAAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.70, C:0.16, G:0.04, T:0.10
Consensus pattern (44 bp):
CAAAAACAACAGGAAAACAACAATAAAAACAACAAAAAAAACAC
Found at i:15594796 original size:19 final size:19
Alignment explanation
Indices: 15594769--15594812 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
15594759 CAAAACAATA
* *
15594769 AAAAAAACACCAAAATAGT
1 AAAAAAACAACAAAATAGC
* *
15594788 AAAATAACAATAAAATAGC
1 AAAAAAACAACAAAATAGC
15594807 AAAAAA
1 AAAAAA
15594813 TAACAACCAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.73, C:0.11, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAAACAACAAAATAGC
Found at i:15595707 original size:10 final size:10
Alignment explanation
Indices: 15595694--15595718 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15595684 TGTATTCAAT
15595694 TTTATTTATA
1 TTTATTTATA
15595704 TTTATTTATA
1 TTTATTTATA
15595714 TTTAT
1 TTTAT
15595719 AAAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTTATA
Found at i:15597771 original size:23 final size:22
Alignment explanation
Indices: 15597740--15597783 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
15597730 AAAGAAATAA
*
15597740 AATTAACTCAATTTAATTAATT
1 AATTAACTCAAATTAATTAATT
*
15597762 AATTCAACTCAAATTATTTAAT
1 AATT-AACTCAAATTAATTAAT
15597784 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTAACTCAAATTAATTAATT
Found at i:15598366 original size:40 final size:39
Alignment explanation
Indices: 15598237--15598425 Score: 129
Period size: 39 Copynumber: 4.8 Consensus size: 39
15598227 ATTGGATTGT
* *
15598237 TTCAATATGCCCCATGGTTGGGG-AAGAGATTTGATGGTC
1 TTCAATTTGCCCCATGGTTGGGGTAAGAGA-TTGATGATC
** * *
15598276 TTCAATTTGCCCTTTGGTTAGGGTAAAAGATTGA--ATTGC
1 TTCAATTTGCCCCATGGTTGGGGTAAGAGATTGATGA-T-C
* * *
15598315 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATC
1 TTCAATTTGCCCCATGGTTGGGGTAAGAGAT-TGATGATC
* * *
15598355 TTCAATTTGCCCTC-TGGTTAGGGTAAAATATTGA--ATTGC
1 TTCAATTTGCCC-CATGGTTGGGGTAAGAGATTGATGA-T-C
* * * *
15598394 TTCAATCTGCTCCATGGTCGGGGTAAAAGATT
1 TTCAATTTGCCCCATGGTTGGGGTAAGAGATT
15598426 TGGGGTCGTA
Statistics
Matches: 116, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
37 1 0.01
38 3 0.03
39 77 0.66
40 32 0.28
41 2 0.02
42 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (39 bp):
TTCAATTTGCCCCATGGTTGGGGTAAGAGATTGATGATC
Found at i:15598367 original size:79 final size:79
Alignment explanation
Indices: 15598218--15598424 Score: 308
Period size: 79 Copynumber: 2.6 Consensus size: 79
15598208 ATAGCTTTAG
* * * * ** *
15598218 GGGTAAAAGATTGGATTGTTTCAATATGCCCCATGGTTGGGG-AAGAGATTTGATGGTCTTCAAT
1 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
*
15598282 TTGCCCTTTGGTTA
66 TTGCCCTCTGGTTA
15598296 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
1 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
15598361 TTGCCCTCTGGTTA
66 TTGCCCTCTGGTTA
* * *
15598375 GGGTAAAATATTGAATTGCTTCAATCTGCTCCATGGTCGGGGTAAAAGAT
1 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGAT
15598425 TTGGGGTCGT
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
78 38 0.32
79 79 0.68
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (79 bp):
GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
TTGCCCTCTGGTTA
Found at i:15598567 original size:50 final size:50
Alignment explanation
Indices: 15598513--15598622 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
15598503 CTCTAGATGA
* * *
15598513 ATGAGATTCGCCATTGCGATTTCAATCTGCCCCTCTACAACTTTAGGTGT
1 ATGAGATTCGCCATTGCGACTTCAATCAGCCCCTCTACAACTTTAGGGGT
* * * ** *
15598563 ATGAGATTTGTCATTGCGGCTTCAATCAGTTCCTCTACAGCTTTAGGGGT
1 ATGAGATTCGCCATTGCGACTTCAATCAGCCCCTCTACAACTTTAGGGGT
15598613 AT-AGGATTCG
1 ATGA-GATTCG
15598623 TCGTTCTATC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (50 bp):
ATGAGATTCGCCATTGCGACTTCAATCAGCCCCTCTACAACTTTAGGGGT
Found at i:15605907 original size:32 final size:32
Alignment explanation
Indices: 15605861--15606299 Score: 578
Period size: 32 Copynumber: 13.8 Consensus size: 32
15605851 TGAGACAATT
* *
15605861 TTCACAGATTGATAGCTTTTACGAGCTTATTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* * *
15605893 TTCATAGATTGATAGCTCTTACAAGCTTATTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* *
15605925 TTCACAGATTGATAGCTCTTACGAGCTTATTA
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* *
15605957 TTCATAGA-T--TAGCTCTTGCGAGCTTACTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* *
15605986 TTCACAAATTGATAGCTCTTACGAGCTTACTT
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* *
15606018 TTCACAAATTGATAGCTCTTACAAGCTTACTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
*
15606050 TTCATAGATTGATAGCTCTTACGAGCTTACTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* *
15606082 TTCATAGATTGATAGCTCTTACGAGCTTACTT
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* *
15606114 TTCACAAATTGATAGCTCTTACGAGCTTACTA
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
*
15606146 TTCACAGATTGATAGCTCTTATGAGCTTACTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* * * * *
15606178 TTTACATATTGATAGCTCTTACAAGTTTACTA
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* * *
15606210 TTCATAGATTGATTGCTCTTACGAGCTTATTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
* * *
15606242 TTCATAGATTGATAGCTCTTATGAGCTCACTG
1 TTCACAGATTGATAGCTCTTACGAGCTTACTG
*
15606274 TTCACAGATTGATAGCTCTTATGAGC
1 TTCACAGATTGATAGCTCTTACGAGC
15606300 ATACCATGAA
Statistics
Matches: 359, Mismatches: 45, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
29 23 0.06
30 1 0.00
31 1 0.00
32 334 0.93
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (32 bp):
TTCACAGATTGATAGCTCTTACGAGCTTACTG
Found at i:15607171 original size:65 final size:65
Alignment explanation
Indices: 15607092--15607228 Score: 222
Period size: 65 Copynumber: 2.1 Consensus size: 65
15607082 TTAGAGAGTT
*
15607092 ACACGGTTTGACACACAGGGAGCACATGGGCATGTGGAAGGGCCACAAAAGCATGTAG-GAGAGC
1 ACACGGTTTGACACACAAGGAGCACATGGGCATGTGGAAGGGCCACAAAAGCATGT-GCGAGAGC
15607156 C
65 C
* **
15607157 ACACTGTTTGACACACAAGGAGCACATGGGCATGTGGAAGGGCCACACGAGCATGTGCGAGAGCC
1 ACACGGTTTGACACACAAGGAGCACATGGGCATGTGGAAGGGCCACAAAAGCATGTGCGAGAGCC
15607222 ACACGGT
1 ACACGGT
15607229 CATGTGACCC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 1 0.02
65 65 0.98
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (65 bp):
ACACGGTTTGACACACAAGGAGCACATGGGCATGTGGAAGGGCCACAAAAGCATGTGCGAGAGCC
Found at i:15608892 original size:14 final size:14
Alignment explanation
Indices: 15608873--15608902 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15608863 AGTTCAAATT
15608873 TCGAGTTAATCAAA
1 TCGAGTTAATCAAA
*
15608887 TCGAGTTAATCGAA
1 TCGAGTTAATCAAA
15608901 TC
1 TC
15608903 AATTCGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (14 bp):
TCGAGTTAATCAAA
Found at i:15609098 original size:18 final size:19
Alignment explanation
Indices: 15609064--15609099 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
15609054 TACAAAATAA
*
15609064 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTATAAAAT
15609083 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
15609100 AAAAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAT
Found at i:15609126 original size:2 final size:2
Alignment explanation
Indices: 15609114--15609162 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
15609104 ATTCAAAATT
15609114 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15609155 TA TA TA TA
1 TA TA TA TA
15609163 ATTTTAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15612070 original size:15 final size:17
Alignment explanation
Indices: 15612028--15612074 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 17
15612018 CATTGCTTTA
*
15612028 AAAAATATTTTTGAAAT
1 AAAAATATTATTGAAAT
*
15612045 AAAAATGTTATT-AAAT
1 AAAAATATTATTGAAAT
15612061 -AAAATATTATTGAA
1 AAAAATATTATTGAA
15612075 CTTTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 10 0.38
16 6 0.23
17 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAAAATATTATTGAAAT
Found at i:15613843 original size:15 final size:16
Alignment explanation
Indices: 15613804--15613842 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
15613794 TGGTTTGAAA
* *
15613804 TTTAAAAAGTAAATTG
1 TTTAAAAAGCAAATTC
15613820 TTTAAAAAGCAAATTC
1 TTTAAAAAGCAAATTC
15613836 TTTAAAA
1 TTTAAAA
15613843 GATTGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (16 bp):
TTTAAAAAGCAAATTC
Found at i:15623469 original size:21 final size:21
Alignment explanation
Indices: 15623445--15623484 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15623435 ACAAATCCCA
* *
15623445 CCACCAGCACCAGCAACACCG
1 CCACAAGCACCAACAACACCG
15623466 CCACAAGCACCAACAACAC
1 CCACAAGCACCAACAACAC
15623485 AGTCGCCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.50, G:0.10, T:0.00
Consensus pattern (21 bp):
CCACAAGCACCAACAACACCG
Found at i:15627893 original size:16 final size:16
Alignment explanation
Indices: 15627872--15627903 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15627862 GTTACTACTC
*
15627872 TTTGTAAAATAGGGGT
1 TTTGTAAAATAAGGGT
15627888 TTTGTAAAATAAGGGT
1 TTTGTAAAATAAGGGT
15627904 GGGCAATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (16 bp):
TTTGTAAAATAAGGGT
Found at i:15628248 original size:30 final size:30
Alignment explanation
Indices: 15628214--15628278 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
15628204 CAACTTAACA
*
15628214 AACAAATATCTCTAAAATAATAACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
* * *
15628244 AACAAATGCCTCTAAAATACTGACAAAATT
1 AACAAATACCTCTAAAATAATAACAAAATT
15628274 AACAA
1 AACAA
15628279 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (30 bp):
AACAAATACCTCTAAAATAATAACAAAATT
Found at i:15628841 original size:16 final size:17
Alignment explanation
Indices: 15628810--15628842 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15628800 ATTAATTAAA
15628810 TTAACTAAAGTAATTTT
1 TTAACTAAAGTAATTTT
*
15628827 TTAATTAAA-TAATTTT
1 TTAACTAAAGTAATTTT
15628843 CTCAACCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAACTAAAGTAATTTT
Found at i:15628988 original size:18 final size:18
Alignment explanation
Indices: 15628945--15628997 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
15628935 TTCATAATAA
15628945 TTAATTAA-TTTAATTCCAT
1 TTAATTAATTTTAATT--AT
*
15628964 TT-TTTAATTTTAATTAT
1 TTAATTAATTTTAATTAT
*
15628981 TTAATTAATTATAATTA
1 TTAATTAATTTTAATTA
15628998 AATAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 4 0.14
18 16 0.55
19 9 0.31
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATTAATTTTAATTAT
Found at i:15629817 original size:19 final size:19
Alignment explanation
Indices: 15629765--15629818 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
15629755 TAAGATAACT
*
15629765 ATATAAAAATTTT-CAATA
1 ATATAAAAATTTTAAAATA
*
15629783 A-ATAAAAATATATAAAATA
1 ATATAAAAAT-TTTAAAATA
*
15629802 ATATAAATATTTTAAAA
1 ATATAAAAATTTTAAAA
15629819 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.28
18 3 0.10
19 11 0.38
20 7 0.24
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAAAATTTTAAAATA
Found at i:15631987 original size:16 final size:16
Alignment explanation
Indices: 15631966--15631997 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15631956 AGAAATTTTT
*
15631966 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
15631982 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
15631998 TTTATAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:15632540 original size:52 final size:52
Alignment explanation
Indices: 15632462--15632700 Score: 415
Period size: 52 Copynumber: 4.6 Consensus size: 52
15632452 TAAATGCAAA
*
15632462 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
15632514 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
15632566 AGGTCCGATAACTATGCGTCATCGTGAGTATATGAATCTTTTACGGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
15632618 AGGTCCGTTGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
15632670 AGGTCCGATGACTATATGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
15632701 TAAATGAGAA
Statistics
Matches: 175, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 175 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:15637854 original size:21 final size:22
Alignment explanation
Indices: 15637808--15637847 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15637798 GAAAGAAGAA
*
15637808 AAGAAAAAATGGGGTGACATAG
1 AAGAAAAAATGGGCTGACATAG
15637830 AAGAAAAAA-GGGCT-ACAT
1 AAGAAAAAATGGGCTGACAT
15637848 GATAAGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.53, C:0.07, G:0.28, T:0.12
Consensus pattern (22 bp):
AAGAAAAAATGGGCTGACATAG
Found at i:15639392 original size:24 final size:24
Alignment explanation
Indices: 15639376--15639426 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
15639366 AGTTTGACTT
15639376 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* * *
15639400 AAACAATTAAACACAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
15639424 AAA
1 AAA
15639427 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:15641392 original size:24 final size:24
Alignment explanation
Indices: 15641355--15641419 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
15641345 TAAACTAATA
* *
15641355 AGAGTTTGACTGAAATAAATAAAT
1 AGAGTTTAACTGAAATAAATAAAC
* ** *
15641379 AGAGTTTAATTGAAGCAATTAAAC
1 AGAGTTTAACTGAAATAAATAAAC
15641403 AGAGTTTAACTGAAATA
1 AGAGTTTAACTGAAATA
15641420 TTATTTTTCA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAATAAATAAAC
Found at i:15650778 original size:20 final size:21
Alignment explanation
Indices: 15650744--15650790 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
15650734 CTTCAGGGAA
* *
15650744 AAGAAAAAGGGTGGAGATTTG
1 AAGAGAAAGGATGGAGATTTG
*
15650765 -AGAGAAAGGATGGAGGTTTG
1 AAGAGAAAGGATGGAGATTTG
15650785 AAGAGA
1 AAGAGA
15650791 CCATCCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.40, T:0.17
Consensus pattern (21 bp):
AAGAGAAAGGATGGAGATTTG
Found at i:15652551 original size:18 final size:17
Alignment explanation
Indices: 15652528--15652562 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
15652518 ATAAATAAAC
*
15652528 AAACTGACTAAACCATTA
1 AAACTGACCAAA-CATTA
15652546 AAACTGACCAAACATTA
1 AAACTGACCAAACATTA
15652563 TTCTCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.23, G:0.06, T:0.20
Consensus pattern (17 bp):
AAACTGACCAAACATTA
Found at i:15653917 original size:32 final size:31
Alignment explanation
Indices: 15653878--15653969 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 31
15653868 TTGATCATAT
15653878 TTTTAAATAAGTTTTTCCTTAATTTTTTAAAA
1 TTTTAAATAA-TTTTTCCTTAATTTTTTAAAA
15653910 TTTTAAAT-A-TTTT--TTAA-TTTTT-AAA
1 TTTTAAATAATTTTTCCTTAATTTTTTAAAA
15653935 TTATT-AATAATTTATTCCTTTTAATTTTTTAAAA
1 TT-TTAAATAATTT-TTCC--TTAATTTTTTAAAA
15653969 T
1 T
15653970 GGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
25 8 0.16
26 8 0.16
27 6 0.12
28 2 0.04
29 4 0.08
31 1 0.02
32 12 0.24
33 5 0.10
34 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (31 bp):
TTTTAAATAATTTTTCCTTAATTTTTTAAAA
Found at i:15653939 original size:19 final size:19
Alignment explanation
Indices: 15653899--15653935 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
15653889 TTTTTCCTTA
15653899 ATTTTTTAAAATTTTAAAT
1 ATTTTTTAAAATTTTAAAT
*
15653918 ATTTTTT-AATTTTTAAAT
1 ATTTTTTAAAATTTTAAAT
15653936 TATTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTTAAAATTTTAAAT
Found at i:15654336 original size:6 final size:6
Alignment explanation
Indices: 15654325--15654352 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
15654315 AATAAACAAA
15654325 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
15654353 GTTAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:15655538 original size:29 final size:28
Alignment explanation
Indices: 15655472--15655538 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 28
15655462 GAGTTTCAAG
*
15655472 TGTATAATTGCACCAAATTAAAGTTCACA
1 TGTATAATTGCACCAAATCAAAGTT-ACA
* * *
15655501 TATACAATTGCACATTAAATCAAAGTT-CA
1 TGTATAATTGCAC--CAAATCAAAGTTACA
15655530 TGTATAATT
1 TGTATAATT
15655539 TTGAGATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
29 20 0.67
31 10 0.33
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (28 bp):
TGTATAATTGCACCAAATCAAAGTTACA
Found at i:15661915 original size:20 final size:20
Alignment explanation
Indices: 15661886--15661946 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
15661876 TATTAAAATA
*
15661886 AATTATAATATTAAATAATT
1 AATTAAAATATTAAATAATT
* *
15661906 TATTAAAATAATAAAATAA-T
1 AATTAAAAT-ATTAAATAATT
*
15661926 AATTTAAATA-TAAATAATT
1 AATTAAAATATTAAATAATT
15661945 AA
1 AA
15661947 ATAAGTCTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 15 0.45
21 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAAATATTAAATAATT
Found at i:15661940 original size:26 final size:24
Alignment explanation
Indices: 15661899--15661950 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
15661889 TATAATATTA
*
15661899 AATAATTTATTAAAATAATAAAAT
1 AATAATTTAATAAAATAATAAAAT
*
15661923 AATAATTTAAATATAAATAATTAAAT
1 AATAATTT-AATA-AAATAATAAAAT
15661949 AA
1 AA
15661951 GTCTCTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 3 0.12
26 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATAATTTAATAAAATAATAAAAT
Found at i:15662330 original size:6 final size:6
Alignment explanation
Indices: 15662321--15662391 Score: 106
Period size: 6 Copynumber: 11.8 Consensus size: 6
15662311 ACTGAAACCC
* * * *
15662321 CTCTCC CTCTCC CTCTCC CTCCCT CTCTCT CTCTCT CTCTCT CTCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
15662369 CTCTCT CTCTCT CTCTCT CTCTC
1 CTCTCT CTCTCT CTCTCT CTCTC
15662392 CACTTCCTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (6 bp):
CTCTCT
Found at i:15662350 original size:4 final size:4
Alignment explanation
Indices: 15662321--15662391 Score: 106
Period size: 4 Copynumber: 17.8 Consensus size: 4
15662311 ACTGAAACCC
* * * *
15662321 CTCT CCCT CTCC CTCT CCCT CCCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
15662369 CTCT CTCT CTCT CTCT CTCT CTC
1 CTCT CTCT CTCT CTCT CTCT CTC
15662392 CACTTCCTCT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (4 bp):
CTCT
Found at i:15665372 original size:9 final size:9
Alignment explanation
Indices: 15665355--15665393 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
15665345 GTTGAATTTT
*
15665355 ATAATTTGA
1 ATAACTTGA
15665364 ATAACTTGA
1 ATAACTTGA
*
15665373 ATAATTTGA
1 ATAACTTGA
*
15665382 ATAACTTAA
1 ATAACTTGA
15665391 ATA
1 ATA
15665394 GCATATTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (9 bp):
ATAACTTGA
Found at i:15665378 original size:18 final size:18
Alignment explanation
Indices: 15665355--15665393 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
15665345 GTTGAATTTT
*
15665355 ATAATTTGAATAACTTGA
1 ATAATTTGAATAACTTAA
15665373 ATAATTTGAATAACTTAA
1 ATAATTTGAATAACTTAA
15665391 ATA
1 ATA
15665394 GCATATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
ATAATTTGAATAACTTAA
Found at i:15665536 original size:17 final size:19
Alignment explanation
Indices: 15665502--15665540 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
15665492 AATAATTTTT
15665502 AAAAATCCAAATATTTATA
1 AAAAATCCAAATATTTATA
*
15665521 AAAAATTCAAA-A-TTATA
1 AAAAATCCAAATATTTATA
15665538 AAA
1 AAA
15665541 TTAAAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATCCAAATATTTATA
Found at i:15666976 original size:24 final size:24
Alignment explanation
Indices: 15666925--15666976 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
15666915 TTCATAAGTC
* *
15666925 AAATAAATTATGCTAAGAAATGCA
1 AAATAAATTATACTAAGAAATACA
* * *
15666949 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAAGAAATACA
15666973 AAAT
1 AAAT
15666977 CTTTTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATAAATTATACTAAGAAATACA
Found at i:15668947 original size:24 final size:24
Alignment explanation
Indices: 15668896--15668941 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
15668886 TTCGTAAGTC
*
15668896 AAATAAATTATGCTAATAAATACA
1 AAATAAATTATACTAATAAATACA
*
15668920 AAATATATTATACTAATAAATA
1 AAATAAATTATACTAATAAATA
15668942 TTAAATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:15669291 original size:27 final size:28
Alignment explanation
Indices: 15669243--15669298 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
15669233 ATTATAAGTA
**
15669243 TTTTTATTTCCAAATTTAATAAAATCAT
1 TTTTTATTTCCAAACCTAATAAAATCAT
* *
15669271 TTTTTATTTCC-AACCTGATAAACTCAT
1 TTTTTATTTCCAAACCTAATAAAATCAT
15669298 T
1 T
15669299 ATACCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (28 bp):
TTTTTATTTCCAAACCTAATAAAATCAT
Found at i:15674963 original size:52 final size:53
Alignment explanation
Indices: 15674845--15674966 Score: 126
Period size: 52 Copynumber: 2.3 Consensus size: 53
15674835 ACAAGATCTC
* *
15674845 AAAAATTAATATAAACAAATATTTATATTTATGTATAAAACATTAGATTTAAACA
1 AAAAATT-AT-TAAACAAATATTTATATTTATGTATAAAACATCAGATTGAAACA
* * * *
15674900 AATAACT-TTAAATAAATCTTTATATTTAT-T-TAAAACATCAGATCTGAAA-A
1 AAAAATTATTAAACAAATATTTATATTTATGTATAAAACATCAGAT-TGAAACA
15674950 AACAAATTATTAAACAA
1 AA-AAATTATTAAACAA
15674967 GATTTGAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
50 15 0.27
51 8 0.15
52 26 0.47
53 1 0.02
55 5 0.09
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (53 bp):
AAAAATTATTAAACAAATATTTATATTTATGTATAAAACATCAGATTGAAACA
Found at i:15678943 original size:82 final size:80
Alignment explanation
Indices: 15678829--15679143 Score: 303
Period size: 82 Copynumber: 3.9 Consensus size: 80
15678819 TAAAATCCAA
* * * **
15678829 AAATAGAATATAATATGTTAATCGGCGGGAATAAATCCCGAAACAGATTTAGTCAACTTATTTTA
1 AAATAGAATAAAATATGTTAAACGACGGGAATAAATCCCGAAACAGATTTA-TTTACTTATTTTA
15678894 TTTTGGAAATAAAATC
65 TTTTGGAAATAAAATC
* * * * * *
15678910 AAACTGGAATAAAATATGTTAAATGGCGGGAATAAATTCCGAAATAGATTTATTTACTTA-ATTA
1 AAA-TAGAATAAAATATGTTAAACGACGGGAATAAATCCCGAAACAGATTTATTTACTTATTTTA
*
15678974 TCATTT-GAAACCAAAATC
65 T--TTTGGAAA-TAAAATC
* * * * *
15678992 AAATATAGAATTAAATCTGTTGAACGACGGGAATAATTCCCGAAACATATTTATTTACTTATTCT
1 -AA-ATAGAATAAAATATGTTAAACGACGGGAATAAATCCCGAAACAGATTTATTTACTTATT-T
** *
15679057 CGTTTTGGAAATAACATC
63 TATTTTGGAAATAAAATC
* * * *
15679075 AAATAGAATAAAATCTGTTAAACAACGGGAAATAAATCCCGAAACAGA-TTATTTTCTAATTTTA
1 AAATAGAATAAAATATGTTAAACGACGGG-AATAAATCCCGAAACAGATTTATTTACTTATTTT-
15679139 ATTTT
64 ATTTT
15679144 ATTCCCGAAC
Statistics
Matches: 189, Mismatches: 34, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
80 5 0.03
81 52 0.28
82 69 0.37
83 56 0.30
84 5 0.03
85 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (80 bp):
AAATAGAATAAAATATGTTAAACGACGGGAATAAATCCCGAAACAGATTTATTTACTTATTTTAT
TTTGGAAATAAAATC
Found at i:15679036 original size:165 final size:165
Alignment explanation
Indices: 15678820--15679128 Score: 385
Period size: 165 Copynumber: 1.9 Consensus size: 165
15678810 TAATTAGTAT
*
15678820 AAAATCCAAAAATAGAATATAATATGTTAATCGGCGGGAATAAATCCCGAAACAGATTTAGTCAA
1 AAAATCCAAAAATAGAATATAATATGTTAATCGACGGGAATAAATCCCGAAACAGATTTA-TCAA
* * *** *
15678885 CTTATT-TTATTTTGGAAATAAAATCAAACTGGAATAAAATATGTTAAATGGCGGG-AATAAATT
65 CTTATTCTCATTTTGGAAATAAAATCAAA-TAGAATAAAATATGTTAAACAACGGGAAATAAATC
*
15678948 CCGAAATAGATTTATTTACTTAATTATCATTTGAAACC
129 CCGAAACAGA-TTATTTACTTAATTATCATTTGAAACC
* * * * **
15678986 AAAAT-CAAATATAGAAT-TAAATCTGTTGAA-CGACGGGAATAATTCCCGAAACATATTTATTT
1 AAAATCCAAAAATAGAATAT-AATATGTT-AATCGACGGGAATAAATCCCGAAACAGATTTATCA
* * *
15679048 ACTTATTCTCGTTTTGGAAATAACATCAAATAGAATAAAATCTGTTAAACAACGGGAAATAAATC
64 ACTTATTCTCATTTTGGAAATAAAATCAAATAGAATAAAATATGTTAAACAACGGGAAATAAATC
15679113 CCGAAACAGATTATTT
129 CCGAAACAGATTATTT
15679129 TCTAATTTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
164 36 0.30
165 79 0.65
166 7 0.06
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (165 bp):
AAAATCCAAAAATAGAATATAATATGTTAATCGACGGGAATAAATCCCGAAACAGATTTATCAAC
TTATTCTCATTTTGGAAATAAAATCAAATAGAATAAAATATGTTAAACAACGGGAAATAAATCCC
GAAACAGATTATTTACTTAATTATCATTTGAAACC
Found at i:15679628 original size:6 final size:6
Alignment explanation
Indices: 15679590--15679683 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
15679580 GGCTTGGGCT
* **
15679590 TTTAAA GTTTAAA -TTAAT TTTAAA TTT-GT TTTAAA TTTAAA TTT--A
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
15679635 TCTTAAA TTTAAA TTTACTTA TTTAAA TTT-AT TTTAGA TTTAAA TTTAA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
15679684 TAAAATTCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 39 0.58
7 8 0.12
8 5 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:15679628 original size:17 final size:17
Alignment explanation
Indices: 15679603--15679682 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
15679593 AAAGTTTAAA
* * *
15679603 TTAATTTTAAATTTGTT
1 TTAAATTTAAATTTATC
15679620 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTATC
15679637 TTAAATTTAAATTTA-C
1 TTAAATTTAAATTTATC
*
15679653 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTATC
*
15679668 TTAGATTTAAATTTA
1 TTAAATTTAAATTTA
15679683 ATAAAATTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.20
15 2 0.04
16 3 0.05
17 40 0.71
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTAAATTTATC
Found at i:15679631 original size:28 final size:29
Alignment explanation
Indices: 15679589--15679644 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
15679579 GGGCTTGGGC
*
15679589 TTTTAAAGTTTAAATTAATTTTAAATTTG
1 TTTTAAAGTTTAAATTAATCTTAAATTTG
*
15679618 TTTTAAA-TTTAAATTTATCTTAAATTT
1 TTTTAAAGTTTAAATTAATCTTAAATTT
15679645 AAATTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTAAAGTTTAAATTAATCTTAAATTTG
Found at i:15679662 original size:31 final size:31
Alignment explanation
Indices: 15679624--15679682 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
15679614 TTTGTTTTAA
15679624 ATTTAAATTTATCTTAAATTTAAATTTACTT
1 ATTTAAATTTATCTTAAATTTAAATTTACTT
* *
15679655 ATTTAAATTTATTTTAGATTTAAATTTA
1 ATTTAAATTTATCTTAAATTTAAATTTA
15679683 ATAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTATCTTAAATTTAAATTTACTT
Found at i:15679675 original size:11 final size:11
Alignment explanation
Indices: 15679597--15679676 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
15679587 GCTTTTAAAG
*
15679597 TTTAAATTAAT
1 TTTAAATTTAT
*
15679608 TTTAAATTTGT
1 TTTAAATTTAT
*
15679619 TTTAAATTTAAA
1 TTTAAATTT-AT
** * *
15679631 TTTATCTTAAA
1 TTTAAATTTAT
15679642 TTTAAATTTACTT
1 TTTAAATTTA--T
15679655 ATTTAAATTTAT
1 -TTTAAATTTAT
*
15679667 TTTAGATTTA
1 TTTAAATTTA
15679677 AATTTAATAA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 36 0.68
12 7 0.13
14 10 0.19
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:15680514 original size:16 final size:16
Alignment explanation
Indices: 15680489--15680520 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15680479 AGCATTAAAG
15680489 ATATTATTAATAATAA
1 ATATTATTAATAATAA
*
15680505 ATATTTTTAATAATAA
1 ATATTATTAATAATAA
15680521 TAAATGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTATTAATAATAA
Found at i:15680520 original size:19 final size:19
Alignment explanation
Indices: 15680496--15680560 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
15680486 AAGATATTAT
15680496 TAATAATAAATATTTTTAA
1 TAATAATAAATATTTTTAA
*
15680515 TAATAATAAATGTTTTACTAA
1 TAATAATAAATATTTT--TAA
15680536 TAATAATATTAATA--TTTAA
1 TAATAATA--AATATTTTTAA
15680555 TAATAA
1 TAATAA
15680561 AAAAGAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 24 0.60
21 13 0.32
23 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TAATAATAAATATTTTTAA
Found at i:15680536 original size:18 final size:19
Alignment explanation
Indices: 15680496--15680560 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 19
15680486 AAGATATTAT
*
15680496 TAATAATAAATATTTTTAA
1 TAATAATAAATAGTTTTAA
*
15680515 TAATAATAAAT-GTTTTAC
1 TAATAATAAATAGTTTTAA
*
15680533 TAATAATAATATTAATATTTAA
1 TAATAATAA-A-TAGT-TTTAA
15680555 TAATAA
1 TAATAA
15680561 AAAAGAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 14 0.37
19 12 0.32
20 1 0.03
21 1 0.03
22 10 0.26
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TAATAATAAATAGTTTTAA
Found at i:15680934 original size:21 final size:20
Alignment explanation
Indices: 15680908--15680963 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
15680898 TTAAGTATAA
15680908 AAGAAAATGAAGCAAAAAGA-
1 AAGAAAATGAAG-AAAAAGAG
*
15680928 AAGGAAAATAGATGAAAAAGAG
1 AA-GAAAAT-GAAGAAAAAGAG
15680950 AAGAAAATGGAAGA
1 AAGAAAAT-GAAGA
15680964 TTGTTCTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.07
21 23 0.77
22 5 0.17
ACGTcount: A:0.66, C:0.02, G:0.25, T:0.07
Consensus pattern (20 bp):
AAGAAAATGAAGAAAAAGAG
Found at i:15681698 original size:30 final size:30
Alignment explanation
Indices: 15681654--15681725 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
15681644 AACAGTCCAG
* *
15681654 AAATTGCA-TTTTGACACC-AAAATTTCAAA
1 AAATTCCATTTTTGAC-CCTAAAACTTCAAA
* *
15681683 AAATTCCATTTTTGACCCTGAAACTTCCAA
1 AAATTCCATTTTTGACCCTAAAACTTCAAA
15681713 AAATTACCATTTT
1 AAATT-CCATTTT
15681726 ACCCCCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.25
30 20 0.56
31 7 0.19
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (30 bp):
AAATTCCATTTTTGACCCTAAAACTTCAAA
Found at i:15681839 original size:117 final size:115
Alignment explanation
Indices: 15681682--15682315 Score: 776
Period size: 117 Copynumber: 5.4 Consensus size: 115
15681672 AAAATTTCAA
*
15681682 AAAATTCCATTTTTGACCCTGAAACTT-CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT
1 AAAATTCCATTTTTGACCC--CAACTTACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT
* * *
15681746 TCTATTTTTAACCTCGATTTCACCAAAAGTTACCATTTTACTCCCGAACTTTTC
64 TCTA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTAC-CCCGAACTTTCC
15681800 AAAATTCCA-TTTTGACCCCAAAACTT-CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT
1 AAAATTCCATTTTTGACCCC--AACTTACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT
*
15681863 TCTATTTTTAACCCCGATTTCAACAAAAATTACCATTTTACCCCTGAACTTTCC
64 TCTA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCC-GAACTTTCC
*
15681917 AAAATTCCATTTTTGACCCCAAAACTT-CCAAAAATTACCATTTTACCCCAAAACTTTCCAAAAT
1 AAAATTCCATTTTTGACCCC--AACTTACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAAT
* ** * * *
15681981 TATATTTTAACCCTAATTTTACCAAAAATTACCATTTTACCCCTAAACTATCC
64 TCTATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCC-GAACTTTCC
* * * *
15682034 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATT
1 AAAATTCCATTTTTGACCCCAACTT-ACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATT
* * * *
15682099 CCATTTTAACTCCGATTTCACCAAAAATTACTATTTTACCCCCGAACTCTCC
65 CTATTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCCGAACTTTCC
* * * * *
15682151 AAAATTCCATTTTTAATCCCAATTTCACCAAAAA-TACCATTTTACCCTCGAACTTTCCAAAATT
1 AAAATTCCATTTTTGACCCCAACTT-ACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATT
* * * * *
15682215 CCATTTTAACCCCAATTTCACC-AAAATTACCATTTTACCTCCAAATTTTCT
65 CTATTTTAACCCCGATTTCACCAAAAATTACCATTTTACC-CCGAACTTTCC
* * * *
15682266 AAAATTCCATTTTCGACCCCGATTTCACCAATAATTACCATTTTACCCCC
1 AAAATTCCATTTTTGACCCCAACTT-ACCAAAAATTACCATTTTACCCCC
15682316 GGGTATCCAA
Statistics
Matches: 464, Mismatches: 43, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
114 2 0.00
115 53 0.11
116 66 0.14
117 274 0.59
118 69 0.15
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (115 bp):
AAAATTCCATTTTTGACCCCAACTTACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC
TATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCGAACTTTCC
Found at i:15682064 original size:29 final size:28
Alignment explanation
Indices: 15681739--15682316 Score: 228
Period size: 29 Copynumber: 19.8 Consensus size: 28
15681729 CCCAAACTTT
* *
15681739 CCAAAATTCTATTTTTAACCTCGATTTCA
1 CCAAAATTCCA-TTTTAACCCCGATTTCA
15681768 CCAAAAGTTACCATTTT-ACTCCCGAACTTT--
1 CCAAAA-TT-CCATTTTAAC-CCCG-A-TTTCA
* * * *
15681798 TCAAAATTCCATTTTGACCCCAAAACTTC-
1 CCAAAATTCCATTTTAACCCC--GATTTCA
* * *
15681827 CAAAAATTACCATTTTACCCCCAAACTTT--
1 CCAAAATT-CCATTTTAACCCC-GA-TTTCA
*
15681856 CCAAAATTCTATTTTTAACCCCGATTTCAA
1 CCAAAATTCCA-TTTTAACCCCGATTTC-A
*
15681886 CAAAAATTACCATTTT-ACCCCTGAACTTT--
1 CCAAAATT-CCATTTTAACCCC-G-A-TTTCA
* * *
15681915 CCAAAATTCCATTTTTGACCCCAAAACTTC-
1 CCAAAATTCCA-TTTTAACCCC--GATTTCA
* *
15681945 CAAAAATTACCATTTT-ACCCCAAAACTTT--
1 CCAAAATT-CCATTTTAACCCC--GA-TTTCA
** ** *
15681974 CCAAAATTATATTTTAACCCTAATTTTA
1 CCAAAATTCCATTTTAACCCCGATTTCA
* **
15682002 CCAAAAATTACCATTTT-ACCCCTA-AACTA
1 CC-AAAATT-CCATTTTAACCCCGATTTC-A
15682031 TCCAAAATTCCATTTTTAACCCCGATTTCA
1 -CCAAAATTCCA-TTTTAACCCCGATTTCA
*
15682061 CCAAAAATTACCATTTTACCCCCGAACTTT--
1 CC-AAAATT-CCATTTTAACCCCG-A-TTTCA
*
15682091 CCAAAATTCCATTTTAACTCCGATTTCA
1 CCAAAATTCCATTTTAACCCCGATTTCA
* * ** *
15682119 CCAAAAATTACTATTTTACCCCCGAACTCT
1 CC-AAAATT-CCATTTTAACCCCGATTTCA
* *
15682149 CCAAAATTCCATTTTTAATCCCAATTTCA
1 CCAAAATTCCA-TTTTAACCCCGATTTCA
*
15682178 CCAAAAATACCATTTT-ACCCTCGAACTTT--
1 CC-AAAATTCCATTTTAACCC-CG-A-TTTCA
*
15682207 CCAAAATTCCATTTTAACCCCAATTTCA
1 CCAAAATTCCATTTTAACCCCGATTTCA
* *
15682235 CCAAAATTACCATTTT-ACCTCCAAATTT-T
1 CCAAAATT-CCATTTTAACC-CC-GATTTCA
* *
15682264 CTAAAATTCCATTTTCGACCCCGATTTCA
1 CCAAAATTCCATTTT-AACCCCGATTTCA
*
15682293 CCAATAATTACCATTTTACCCCCG
1 CCAA-AATT-CCATTTTAACCCCG
15682317 GGTATCCAAA
Statistics
Matches: 426, Mismatches: 64, Indels: 117
0.70 0.11 0.19
Matches are distributed among these distances:
26 9 0.02
27 7 0.02
28 82 0.19
29 163 0.38
30 132 0.31
31 24 0.06
32 9 0.02
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (28 bp):
CCAAAATTCCATTTTAACCCCGATTTCA
Found at i:15682338 original size:59 final size:58
Alignment explanation
Indices: 15681709--15682351 Score: 733
Period size: 59 Copynumber: 11.0 Consensus size: 58
15681699 CCTGAAACTT
* * *
15681709 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCA
* * * * * *
15681768 CCAAAAGTTACCATTTTACTCCCGAACTTTTCAAAATTCCATTTTGACCCCAAAACTT--
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAACCCC--GATTTCA
* *
15681826 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCA
* * * * *
15681885 ACAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTGACCCCAAAACTT--
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCC--GATTTCA
** ** ** *
15681944 CCAAAAATTACCATTTTACCCCAAAACTTTCCAAAATTATATTTTAACCCTAATTTTA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
** *
15682002 CCAAAAATTACCATTTTACCCCTAAACTATCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCA
*
15682061 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAACTCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
* * * *
15682119 CCAAAAATTACTATTTTACCCCCGAACTCTCCAAAATTCCATTTTTAATCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCA
* *
15682178 CCAAAAA-TACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
* * * * *
15682235 CC-AAAATTACCATTTTACCTCCAAATTTTCTAAAATTCCATTTTCGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTT-AACCCCGATTTCA
* ** * * *
15682293 CCAATAATTACCATTTTACCCCCG-GGTATCCAAAAGTCCCGTTTTCAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAA-TTCCATTTT-AACCCCGATTTCA
15682352 TCGTTTCTTC
Statistics
Matches: 500, Mismatches: 69, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
56 8 0.02
57 53 0.11
58 194 0.39
59 239 0.48
60 3 0.01
61 3 0.01
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
Found at i:15684568 original size:22 final size:22
Alignment explanation
Indices: 15684540--15684583 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
15684530 AGTCCAAGCC
15684540 GATAAAGCATATTCAAAAGACG
1 GATAAAGCATATTCAAAAGACG
15684562 GATAAAGCATATTCAAAAGACG
1 GATAAAGCATATTCAAAAGACG
15684584 CAAGTGTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (22 bp):
GATAAAGCATATTCAAAAGACG
Found at i:15694490 original size:76 final size:76
Alignment explanation
Indices: 15694189--15694780 Score: 938
Period size: 76 Copynumber: 7.8 Consensus size: 76
15694179 ATCAAACCGC
* * *
15694189 AGCAAGATCATTCCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
15694254 ATTGAAGTAAG
66 ATTGAAGTAAG
* ** * *
15694265 AGCAAGATCTTTTCCTATGATCTTAAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
15694329 ATTGAAGTAAG
66 ATTGAAGTAAG
* * *
15694340 ACCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
*
15694404 ATTAAAGTAAG
66 ATTGAAGTAAG
* *
15694415 AGCAATG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGA
1 AGCAA-GATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
15694479 AATTGAAGTAAG
65 AATTGAAGTAAG
* * *
15694491 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
15694556 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
15694567 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
15694632 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
15694643 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAATTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
15694708 ATTGAAGTAAG
66 ATTGAAGTAAG
* * *
15694719 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCT
15694781 CTGGAGAGCA
Statistics
Matches: 483, Mismatches: 30, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
75 142 0.29
76 341 0.71
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (76 bp):
AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:15695086 original size:6 final size:6
Alignment explanation
Indices: 15695048--15695141 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
15695038 GGCTTGGGCT
* **
15695048 TTTAAA GTTTAAA -TTAAT TTTAAA TTT-GT TTTAAA TTTAAA TTT--A
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
15695093 TCTTAAA TTTAAA TTTACTTA TTTAAA TTT-AT TTTAGA TTTAAA TTTAA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
15695142 TCAAATTCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 39 0.58
7 8 0.12
8 5 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:15695086 original size:17 final size:17
Alignment explanation
Indices: 15695061--15695140 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
15695051 AAAGTTTAAA
* * *
15695061 TTAATTTTAAATTTGTT
1 TTAAATTTAAATTTATC
15695078 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTATC
15695095 TTAAATTTAAATTTA-C
1 TTAAATTTAAATTTATC
*
15695111 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTATC
*
15695126 TTAGATTTAAATTTA
1 TTAAATTTAAATTTA
15695141 ATCAAATTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.20
15 2 0.04
16 3 0.05
17 40 0.71
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTAAATTTATC
Found at i:15695089 original size:28 final size:29
Alignment explanation
Indices: 15695047--15695102 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
15695037 GGGCTTGGGC
*
15695047 TTTTAAAGTTTAAATTAATTTTAAATTTG
1 TTTTAAAGTTTAAATTAATCTTAAATTTG
*
15695076 TTTTAAA-TTTAAATTTATCTTAAATTT
1 TTTTAAAGTTTAAATTAATCTTAAATTT
15695103 AAATTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTAAAGTTTAAATTAATCTTAAATTTG
Found at i:15695120 original size:31 final size:31
Alignment explanation
Indices: 15695082--15695140 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
15695072 TTTGTTTTAA
15695082 ATTTAAATTTATCTTAAATTTAAATTTACTT
1 ATTTAAATTTATCTTAAATTTAAATTTACTT
* *
15695113 ATTTAAATTTATTTTAGATTTAAATTTA
1 ATTTAAATTTATCTTAAATTTAAATTTA
15695141 ATCAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTATCTTAAATTTAAATTTACTT
Found at i:15695133 original size:11 final size:11
Alignment explanation
Indices: 15695055--15695134 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
15695045 GCTTTTAAAG
*
15695055 TTTAAATTAAT
1 TTTAAATTTAT
*
15695066 TTTAAATTTGT
1 TTTAAATTTAT
*
15695077 TTTAAATTTAAA
1 TTTAAATTT-AT
** * *
15695089 TTTATCTTAAA
1 TTTAAATTTAT
15695100 TTTAAATTTACTT
1 TTTAAATTTA--T
15695113 ATTTAAATTTAT
1 -TTTAAATTTAT
*
15695125 TTTAGATTTA
1 TTTAAATTTA
15695135 AATTTAATCA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 36 0.68
12 7 0.13
14 10 0.19
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:15695990 original size:15 final size:16
Alignment explanation
Indices: 15695952--15696015 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 16
15695942 AAACATATTA
15695952 TTAATAATAAATAATT
1 TTAATAATAAATAATT
**
15695968 TTAATAATAAATGTTT
1 TTAATAATAAATAATT
15695984 TACTAATAATAATATTAATAT
1 T--TAATAATAA-A-TAAT-T
15696005 TTAATAATAAA
1 TTAATAATAAA
15696016 AAAAAAACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.38
18 10 0.26
19 10 0.26
20 2 0.05
21 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAATAATAAATAATT
Found at i:15696866 original size:11 final size:11
Alignment explanation
Indices: 15696850--15696875 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
15696840 TTTAGTCCCT
15696850 TTTATTTTTAA
1 TTTATTTTTAA
15696861 TTTATTTTTAA
1 TTTATTTTTAA
15696872 TTTA
1 TTTA
15696876 ATCCCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTTTTAA
Found at i:15696908 original size:23 final size:24
Alignment explanation
Indices: 15696859--15696909 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
15696849 TTTTATTTTT
* * *
15696859 AATTTATTTTTAATTTAATCCCTA
1 AATTAATTTTTAATTTAATCACAA
*
15696883 AATTAATTTTT-ATTTAATTACAA
1 AATTAATTTTTAATTTAATCACAA
15696906 AATT
1 AATT
15696910 GGCCCAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAATTTTTAATTTAATCACAA
Found at i:15697069 original size:30 final size:28
Alignment explanation
Indices: 15697020--15697478 Score: 235
Period size: 30 Copynumber: 15.6 Consensus size: 28
15697010 CCCCAAACAG
*
15697020 TCCAAAAATTGCATTTTGACCCCAAAATT
1 TCCAAAAATTCCATTTT-ACCCCAAAATT
* *
15697049 TCAAAAAATTCCACTTTTGACCCCAAAACT
1 TCCAAAAATTCCA-TTTT-ACCCCAAAATT
* *
15697079 TCCAAAAATTACCATTTTACCACTAAACTT
1 TCCAAAAATT-CCATTTTACC-CCAAAATT
* * **
15697109 TCC-AAAATTCTATTTTTAACCC-TGATT
1 TCCAAAAATTCCA-TTTTACCCCAAAATT
* *
15697136 TCACCAAAAATTATCATTTTACCCCCAAACTT
1 T--CCAAAAATT-CCATTTTA-CCCCAAAATT
* *
15697168 TCC-AAAATTCCATTTTTGACCCCGAAACT
1 TCCAAAAATTCCA-TTTT-ACCCCAAAATT
15697197 TCCAAAAATTACCATTTTACCCCTAAAATT
1 TCCAAAAATT-CCATTTTACCCC-AAAATT
* *
15697227 TCC-AAAATTCTATTTTTAACCCC--GATT
1 TCCAAAAATTCCA-TTTT-ACCCCAAAATT
* *
15697254 TCACCAAAAATTACCATTTTACCCCCGAACTT
1 T--CCAAAAATT-CCATTTTA-CCCCAAAATT
* *
15697286 TCC-AAAATTCTATTTTTAACCCC--GATT
1 TCCAAAAATTCCA-TTTT-ACCCCAAAATT
* *
15697313 TCACCAAAAATTACCATATTACCCCTAAACTT
1 T--CCAAAAATT-CCATTTTACCCC-AAAATT
* *
15697345 TCC-AAAATTCCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCA-TTTT-ACCCCAAAATT
*
15697374 TCCAAAAATTACCATTTTACCCCCAAACTT
1 TCCAAAAATT-CCATTTTA-CCCCAAAATT
** * *
15697404 TCC-AAAATTTTATTTTTAACCTC--GATT
1 TCCAAAAATTCCA-TTTT-ACCCCAAAATT
*
15697431 TCACCAAAAATTACCATTTTACCCCCAAACTT
1 T--CCAAAAATT-CCATTTTA-CCCCAAAATT
15697463 TCC-AAAATTCCATTTT
1 TCCAAAAATTCCATTTT
15697479 TAACCCCGAT
Statistics
Matches: 329, Mismatches: 54, Indels: 95
0.69 0.11 0.20
Matches are distributed among these distances:
27 13 0.04
28 20 0.06
29 126 0.38
30 140 0.43
31 18 0.05
32 12 0.04
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTACCCCAAAATT
Found at i:15697116 original size:59 final size:58
Alignment explanation
Indices: 15697080--15697689 Score: 733
Period size: 59 Copynumber: 10.4 Consensus size: 58
15697070 CCCAAAACTT
* * * *
15697080 CCAAAAATTACCATTTTACCACTAAACTTTCCAAAATTCTATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
* * *
15697139 CCAAAAATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAAACTT-
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCG--ATTTA
* * *
15697198 CCAAAAATTACCATTTTACCCCTAAAATTTCCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
* *
15697257 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
* * * ** *
15697316 CCAAAAATTACCATATTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAAACTT-
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCC--CGATTTA
** *
15697375 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTTATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
15697434 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
* * * * * * *
15697493 CCAAAAATTACTATTTTACCCTCGAACTCTCCAAAATTCTATTTTTAATCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
* * *
15697552 CC-AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAATCCCGTTTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
* * * ** *
15697610 CC-AAAATTACCATTTTACCCTCAAATTTTCTAAAATTCCATTTTCGACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTT-A
* *
15697668 CCAAAAATTATCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
15697690 TGGGTATCCA
Statistics
Matches: 481, Mismatches: 61, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
57 6 0.01
58 101 0.21
59 368 0.77
61 6 0.01
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTA
Found at i:15697316 original size:177 final size:177
Alignment explanation
Indices: 15697080--15697689 Score: 859
Period size: 177 Copynumber: 3.5 Consensus size: 177
15697070 CCCAAAACTT
* * * *
15697080 CCAAAAATTACCATTTTACCACTAAACTTTCCAAAATTCTATTTTTAACCCTGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
15697145 ATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACC
66 ATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACC
* *
15697210 ATTTTACCCCTAAAATTTCCAAAATTCTATTTTTAACCCCGATTTCA
131 ATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
* *
15697257 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * **
15697322 ATTACCATATTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACC
66 ATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACC
* *
15697387 ATTTTACCCCCAAACTTTCCAAAATTTTATTTTTAACCTCGATTTCA
131 ATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
15697434 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * * * * * * *
15697499 ATTA-CTATTTTACCCTCGAACTCTCCAAAATTCTATTTTTAATCTCG--ATTTCACCAAAATTA
66 ATTATC-ATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAAACTTC-CAAAAATTA
* * * *
15697561 CCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAATCCCGTTTTCA
129 CCATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
* * * ** *
15697610 CC-AAAATTACCATTTTACCCTCAAATTTTCTAAAATTCCATTTTCGACCTCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
*
15697674 ATTATCATTTTGCCCC
66 ATTATCATTTTACCCC
15697690 TGGGTATCCA
Statistics
Matches: 388, Mismatches: 42, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
175 72 0.19
176 55 0.14
177 261 0.67
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (177 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
ATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACC
ATTTTACCCCCAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCA
Found at i:15697673 original size:29 final size:28
Alignment explanation
Indices: 15697228--15697673 Score: 152
Period size: 29 Copynumber: 15.2 Consensus size: 28
15697218 CCTAAAATTT
*
15697228 CCAAAATTCTATTTTTAACCC-CGATTTCA
1 CCAAAATTCCA-TTTT-ACCCTCGATTTCA
*
15697257 CCAAAAATTACCATTTTACCCCCGAACTTT--
1 CC-AAAATT-CCATTTTACCCTCG-A-TTTCA
*
15697287 CCAAAATTCTATTTTTAACCC-CGATTTCA
1 CCAAAATTCCA-TTTT-ACCCTCGATTTCA
* **
15697316 CCAAAAATTACCATATTACCCCTAAACTTT--
1 CC-AAAATT-CCATTTTA-CCCTCGA-TTTCA
** *
15697346 CCAAAATTCCATTTTTGACCCTAAAACTTC-
1 CCAAAATTCCA-TTTT-ACCCT-CGATTTCA
* * *
15697376 CAAAAATTACCATTTTACCCCCAAACTTT--
1 CCAAAATT-CCATTTTACCCTC-GA-TTTCA
** *
15697405 CCAAAATTTTATTTTTAACCTCGATTTCA
1 CCAAAATTCCA-TTTTACCCTCGATTTCA
* *
15697434 CCAAAAATTACCATTTTACCCCCAAACTTT--
1 CC-AAAATT-CCATTTTACCCTC-GA-TTTCA
15697464 CCAAAATTCCATTTTTAACCC-CGATTTCA
1 CCAAAATTCCA-TTTT-ACCCTCGATTTCA
* ** *
15697493 CCAAAAATTACTATTTTACCCTCGAACTCT
1 CC-AAAATT-CCATTTTACCCTCGATTTCA
* **
15697523 CCAAAATTCTATTTTTAATCTCGATTTCA
1 CCAAAATTCCA-TTTTACCCTCGATTTCA
* *
15697552 CCAAAATTACCATTTTACCCCCAAACTTT--
1 CCAAAATT-CCATTTTACCCTC-GA-TTTCA
* * *
15697581 CTAAAATTCCATTTTTAATCC-CGTTTTCA
1 CCAAAATTCCA-TTTT-ACCCTCGATTTCA
* *
15697610 CCAAAATTACCATTTTACCCTCAAATTT-T
1 CCAAAATT-CCATTTTACCCTC-GATTTCA
*
15697639 CTAAAATTCCATTTT-CGACCTCGATTTCA
1 CCAAAATTCCATTTTAC--CCTCGATTTCA
15697668 CCAAAA
1 CCAAAA
15697674 ATTATCATTT
Statistics
Matches: 317, Mismatches: 51, Indels: 98
0.68 0.11 0.21
Matches are distributed among these distances:
27 13 0.04
28 32 0.10
29 149 0.47
30 98 0.31
31 16 0.05
32 9 0.03
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.35
Consensus pattern (28 bp):
CCAAAATTCCATTTTACCCTCGATTTCA
Found at i:15702447 original size:13 final size:13
Alignment explanation
Indices: 15702429--15702454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15702419 CAGGACGGCG
15702429 TATATTATATATA
1 TATATTATATATA
15702442 TATATTATATATA
1 TATATTATATATA
15702455 AGTATAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTATATATA
Found at i:15702460 original size:15 final size:14
Alignment explanation
Indices: 15702428--15702460 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
15702418 ACAGGACGGC
15702428 GTATATTATATATA
1 GTATATTATATATA
15702442 -TATATTATATATAA
1 GTATATTATATAT-A
15702456 GTATA
1 GTATA
15702461 AGAAAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
GTATATTATATATA
Found at i:15704174 original size:20 final size:19
Alignment explanation
Indices: 15704146--15704189 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
15704136 CGAATTAAAG
*
15704146 TTATGAATTCGTATATGTAA
1 TTATAAATTCGTAT-TGTAA
**
15704166 TTATAAATTTTTATTGTAA
1 TTATAAATTCGTATTGTAA
15704185 TTATA
1 TTATA
15704190 TCTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (19 bp):
TTATAAATTCGTATTGTAA
Found at i:15708257 original size:25 final size:25
Alignment explanation
Indices: 15708226--15708301 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
15708216 CTAATTCTCA
15708226 CTCGTAAGAGCATAATTCTGTCTGG
1 CTCGTAAGAGCATAATTCTGTCTGG
* *
15708251 CTTGTAAGAGCA-AATTTTCTGTCTAG
1 CTCGTAAGAGCATAA--TTCTGTCTGG
* *
15708277 CTCGTAAGAGCGTAAATCTGTCTGG
1 CTCGTAAGAGCATAATTCTGTCTGG
15708302 GCTCATATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.05
25 19 0.45
26 19 0.45
27 2 0.05
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (25 bp):
CTCGTAAGAGCATAATTCTGTCTGG
Found at i:15708283 original size:26 final size:25
Alignment explanation
Indices: 15708226--15708299 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
15708216 CTAATTCTCA
*
15708226 CTCGTAAGAGCATAATTCTGTCTGG
1 CTCGTAAGAGCATAATTCTGTCTAG
*
15708251 CTTGTAAGAGCA-AATTTTCTGTCTAG
1 CTCGTAAGAGCATAA--TTCTGTCTAG
* *
15708277 CTCGTAAGAGCGTAAATCTGTCT
1 CTCGTAAGAGCATAATTCTGTCT
15708300 GGGCTCATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 2 0.05
25 18 0.44
26 19 0.46
27 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (25 bp):
CTCGTAAGAGCATAATTCTGTCTAG
Found at i:15708305 original size:26 final size:24
Alignment explanation
Indices: 15708226--15708318 Score: 80
Period size: 26 Copynumber: 3.7 Consensus size: 24
15708216 CTAATTCTCA
*
15708226 CTCGTAAGAGCATAATTCTGTCTGG
1 CTCGTAAGAGC-TAAATCTGTCTGG
* *
15708251 CTTGTAAGAGC-AAATTTTCTGTCTAG
1 CTCGTAAGAGCTAAA---TCTGTCTGG
15708277 CTCGTAAGAGCGTAAATCTGTCTGGG
1 CTCGTAAGAGC-TAAATCTGTCT-GG
* *
15708303 CTCATATGAGCTAAAT
1 CTCGTAAGAGCTAAAT
15708319 TCTAGAAGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
23 2 0.04
25 22 0.40
26 28 0.51
28 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (24 bp):
CTCGTAAGAGCTAAATCTGTCTGG
Found at i:15709000 original size:21 final size:21
Alignment explanation
Indices: 15708974--15709026 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
15708964 GAGTTTTTAA
*
15708974 TATCGGTAGAAG-CATGACTTG
1 TATCGGTAGAAGTC-TCACTTG
*
15708995 TATCGGTAGATGTCTCACTTG
1 TATCGGTAGAAGTCTCACTTG
*
15709016 TTTCGGTAGAA
1 TATCGGTAGAA
15709027 CTGTCATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (21 bp):
TATCGGTAGAAGTCTCACTTG
Found at i:15711979 original size:24 final size:24
Alignment explanation
Indices: 15711948--15712054 Score: 178
Period size: 24 Copynumber: 4.5 Consensus size: 24
15711938 TTCAGCCAAC
15711948 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
15711972 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
* *
15711996 ATGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
* *
15712020 ACGAGCCTAGAATGATTATCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
15712044 ACGAGCCCAGA
1 ACGAGCCCAGA
15712055 CAGAGTTTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:15718101 original size:49 final size:49
Alignment explanation
Indices: 15718029--15718139 Score: 141
Period size: 49 Copynumber: 2.3 Consensus size: 49
15718019 ATAAAGCATT
* ** * * *
15718029 GTCAACTAGGGGCCCGAGTTATACTTCAACCTGTGATCGCATAACCGTC
1 GTCAACTAGGAGCCCGAGTTATACTTCAACCCATAACCGCATAACCATC
** *
15718078 GTCAACTAGGAGCCCTTGTTATACTTCAACCCATAACCGTATAACCATC
1 GTCAACTAGGAGCCCGAGTTATACTTCAACCCATAACCGCATAACCATC
15718127 GTCAACTAGGAGC
1 GTCAACTAGGAGC
15718140 TTGAGTTGCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (49 bp):
GTCAACTAGGAGCCCGAGTTATACTTCAACCCATAACCGCATAACCATC
Found at i:15722919 original size:18 final size:17
Alignment explanation
Indices: 15722883--15722923 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
15722873 AAAATAAATA
15722883 AAAACAAAGGAGTGTGG
1 AAAACAAAGGAGTGTGG
15722900 AAAACAAAGGAGTGTGG
1 AAAACAAAGGAGTGTGG
*
15722917 GAAACAA
1 AAAACAA
15722924 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.07, G:0.32, T:0.10
Consensus pattern (17 bp):
AAAACAAAGGAGTGTGG
Found at i:15730420 original size:40 final size:39
Alignment explanation
Indices: 15730305--15730421 Score: 108
Period size: 40 Copynumber: 2.9 Consensus size: 39
15730295 ACTAGTCCAA
* * * *
15730305 TAGTGTTCACAGTGTCACGACTAGTATAGTAACAACATTG
1 TAGTGTTTACAGTGTCACG-CTAGTTTAGTAATAATATTG
* * * ** *
15730345 CAGCGTTTACAGTTTCACTGCCGGTTCAGTAATAATATTG
1 TAGTGTTTACAGTGTCAC-GCTAGTTTAGTAATAATATTG
*
15730385 TAGTGTTTACAGTGTCACAGCTAGTTTAGTGATAATA
1 TAGTGTTTACAGTGTCAC-GCTAGTTTAGTAATAATA
15730422 CACCCAAATG
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (39 bp):
TAGTGTTTACAGTGTCACGCTAGTTTAGTAATAATATTG
Found at i:15731630 original size:20 final size:22
Alignment explanation
Indices: 15731593--15731647 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
15731583 CTCCAGTGAG
*
15731593 ACTTCAACCGGT-CGAACTC-C
1 ACTTCAACCGATACGAACTCTC
15731613 ACTTCAACCGATAC-AACTCTC
1 ACTTCAACCGATACGAACTCTC
15731634 ACTT-ATACCGATAC
1 ACTTCA-ACCGATAC
15731648 CTTGAAGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.31, C:0.36, G:0.09, T:0.24
Consensus pattern (22 bp):
ACTTCAACCGATACGAACTCTC
Found at i:15734212 original size:54 final size:54
Alignment explanation
Indices: 15734153--15734259 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
15734143 TAAGATTTTG
15734153 AAAACTAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTAC
1 AAAACTAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTAC
15734207 AAAACTAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTA
1 AAAACTAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTA
15734260 TGTTTGTAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (54 bp):
AAAACTAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTAC
Found at i:15737303 original size:54 final size:54
Alignment explanation
Indices: 15737238--15737344 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
15737228 TAAGATTTTG
*
15737238 AAAACTAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTAC
1 AAAACCAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTAC
15737292 AAAACCAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTA
1 AAAACCAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTA
15737345 TGTTTGTAGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (54 bp):
AAAACCAATGATTATGGACCCAAAAGACATTGGGTACCAAAAACTTAATTCTAC
Found at i:15740395 original size:30 final size:30
Alignment explanation
Indices: 15740359--15740418 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
15740349 TTAACAGTTC
*
15740359 ACAATACAC-CTACATTGGATTGTCTGTTAT
1 ACAATACACTC-ACATTGGAGTGTCTGTTAT
*
15740389 ACAATACACTCACATTGGAGTGTCTTTTAT
1 ACAATACACTCACATTGGAGTGTCTGTTAT
15740419 TTATAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (30 bp):
ACAATACACTCACATTGGAGTGTCTGTTAT
Found at i:15741611 original size:30 final size:30
Alignment explanation
Indices: 15741564--15741632 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
15741554 AAATTTTTTT
*
15741564 AAAATTTG-GGATTAAAAT-TGAACTTTTGG
1 AAAATTTGAGGATTAAAATGTG-ACTTTTAG
*
15741593 AAAATTTGAGG-TTGAAAATGTGATTTTTAG
1 AAAATTTGAGGATT-AAAATGTGACTTTTAG
15741623 -AAATTTGAGG
1 AAAATTTGAGG
15741633 GCAAAAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 20 0.57
30 13 0.37
31 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (30 bp):
AAAATTTGAGGATTAAAATGTGACTTTTAG
Found at i:15741705 original size:30 final size:30
Alignment explanation
Indices: 15741660--15741773 Score: 117
Period size: 30 Copynumber: 3.8 Consensus size: 30
15741650 TGAGTGTTCG
15741660 AGGG-TAAAATGGTAATTTTTGGAAAAGTTT
1 AGGGTTAAAAT-GTAATTTTTGGAAAAGTTT
* * *
15741690 AGGGTTGAAATGTAA-TTTTCGAGAAGTTT
1 AGGGTTAAAATGTAATTTTTGGAAAAGTTT
* *
15741719 AGGGGTAAAAATATAATTTTTGGAAAAGTTCT
1 A-GGGTTAAAATGTAATTTTTGGAAAAGTT-T
* *
15741751 A-AGTTAAAATGTGATTTTTGGAA
1 AGGGTTAAAATGTAATTTTTGGAA
15741774 CTTAGGGGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
29 13 0.19
30 37 0.54
31 16 0.24
32 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTTGGAAAAGTTT
Found at i:15741761 original size:60 final size:59
Alignment explanation
Indices: 15741672--15741798 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 59
15741662 GGTAAAATGG
* * *
15741672 TAATTTTTGGAAAAGTTTAGGGTTGAAATGTAATTTTCGAGAAGTTTAGGGG-TAAAAATA
1 TAATTTTTGGAAAAGTTTAGAGTTAAAATGTAATTTTCG-GAA-CTTAGGGGCTAAAAATA
* * *
15741732 TAATTTTTGGAAAAGTTCTA-AGTTAAAATGTGATTTTTGGAACTTAGGGGCTAAAAATG
1 TAATTTTTGGAAAAGTT-TAGAGTTAAAATGTAATTTTCGGAACTTAGGGGCTAAAAATA
*
15741791 TGATTTTT
1 TAATTTTT
15741799 AGAAGTTTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 7 0.12
59 17 0.29
60 32 0.55
61 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (59 bp):
TAATTTTTGGAAAAGTTTAGAGTTAAAATGTAATTTTCGGAACTTAGGGGCTAAAAATA
Done.