Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_pilon, 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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 26
Found at i:2216177 original size:18 final size:18
Alignment explanation
Indices: 2216138--2216179 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2216128 TCAAGTATTG
* *
2216138 AGGAGAAAAAGACAGTTG
1 AGGAGAAAAAGACAGCTA
*
2216156 AGGAGAAGAAGACAGCTA
1 AGGAGAAAAAGACAGCTA
2216174 AGGAGA
1 AGGAGA
2216180 TATATGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.36, T:0.07
Consensus pattern (18 bp):
AGGAGAAAAAGACAGCTA
Found at i:2222187 original size:18 final size:18
Alignment explanation
Indices: 2222164--2222198 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2222154 GATTATGAAC
*
2222164 AAAATTACTAAATTATAA
1 AAAATTACCAAATTATAA
2222182 AAAATTACCAAATTATA
1 AAAATTACCAAATTATA
2222199 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTACCAAATTATAA
Found at i:2222863 original size:29 final size:27
Alignment explanation
Indices: 2222800--2222863 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
2222790 TATATTAGGG
* * *
2222800 GGCGAATTTGAACTTTTAAGATTTCAA
1 GGCGAACTTGAACTTATAAAATTTCAA
2222827 GGTACGAACTTGAACTTATAAAATTTCAGA
1 GG--CGAACTTGAACTTATAAAATTTCA-A
2222857 GAGCGAA
1 G-GCGAA
2222864 AACAGATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.07
29 25 0.83
30 2 0.07
31 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (27 bp):
GGCGAACTTGAACTTATAAAATTTCAA
Found at i:2223184 original size:17 final size:18
Alignment explanation
Indices: 2223154--2223187 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2223144 CAAATTTTAA
*
2223154 AATAAAAATCATTAATAG
1 AATAAAAATAATTAATAG
2223172 AATAAAAA-AATTAATA
1 AATAAAAATAATTAATA
2223188 AAAAAAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAAAAATAATTAATAG
Found at i:2232988 original size:21 final size:21
Alignment explanation
Indices: 2232959--2233021 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
2232949 AGTCGAGGGT
* *
2232959 TACAATGGTCCTTCGAGACAA
1 TACAGTGGTCCTTCGGGACAA
2232980 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
2233001 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
2233022 ATTTCATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (21 bp):
TACAGTGGTCCTTCGGGACAA
Found at i:2234043 original size:14 final size:14
Alignment explanation
Indices: 2234024--2234053 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2234014 GGATAATGTT
2234024 TACGGTACTGTTCA
1 TACGGTACTGTTCA
*
2234038 TACGGTATTGTTCA
1 TACGGTACTGTTCA
2234052 TA
1 TA
2234054 AATACGATTT
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:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (14 bp):
TACGGTACTGTTCA
Found at i:2248705 original size:16 final size:18
Alignment explanation
Indices: 2248665--2248708 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2248655 ACTTTAATTG
2248665 CTTTTACTTA-TTTAATCA
1 CTTTTA-TTATTTTAATCA
2248683 CTTTTATTATTTTAAT-A
1 CTTTTATTATTTTAATCA
2248700 -TTTTATTAT
1 CTTTTATTAT
2248709 CAAAATTCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.36
17 4 0.16
18 12 0.48
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTTTATTATTTTAATCA
Found at i:2251129 original size:15 final size:15
Alignment explanation
Indices: 2251109--2251147 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2251099 TGGGTGGGAG
2251109 GATGTGGGGCGGGCA
1 GATGTGGGGCGGGCA
*
2251124 GATGTGGGGCGGGCG
1 GATGTGGGGCGGGCA
*
2251139 GATGCGGGG
1 GATGTGGGG
2251148 AGGGTAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.10, C:0.13, G:0.64, T:0.13
Consensus pattern (15 bp):
GATGTGGGGCGGGCA
Found at i:2252483 original size:15 final size:15
Alignment explanation
Indices: 2252458--2252496 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2252448 TTCAATTCTG
*
2252458 TTACATTTTTTTATTT
1 TTAC-TTTTTTTAATT
2252474 TTACTTTTTTTAATT
1 TTACTTTTTTTAATT
2252489 TTA-TTTTT
1 TTACTTTTT
2252497 ATTCATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 13 0.59
16 4 0.18
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (15 bp):
TTACTTTTTTTAATT
Found at i:2252885 original size:17 final size:17
Alignment explanation
Indices: 2252863--2252897 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2252853 ACTCCCCTTT
2252863 ATTCTAATCAAAACCAA
1 ATTCTAATCAAAACCAA
* *
2252880 ATTCTATTCAAACCCAA
1 ATTCTAATCAAAACCAA
2252897 A
1 A
2252898 CACCCCCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTCTAATCAAAACCAA
Found at i:2255890 original size:18 final size:18
Alignment explanation
Indices: 2255851--2255886 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2255841 ATTTTTACTA
*
2255851 TAATTGCTTTTACTTATT
1 TAATCGCTTTTACTTATT
2255869 TAATCGCTTTTA-TTATT
1 TAATCGCTTTTACTTATT
2255886 T
1 T
2255887 TAATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (18 bp):
TAATCGCTTTTACTTATT
Found at i:2273821 original size:101 final size:98
Alignment explanation
Indices: 2273590--2273824 Score: 328
Period size: 99 Copynumber: 2.4 Consensus size: 98
2273580 ACAAGCTCAA
*
2273590 AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCTGACTTTCTTCACACA
1 AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCAGACTTTCTTCACAC-
*
2273655 AGAAGCCTCCCTACGAGTTTAAGTAAATACAACT
65 AGAAGCCTCCCTACGAGTCTAAGTAAATACAACT
* * *
2273689 AAATCCTACACAAACAAATAGACAACTATTTCAATGAAAAGATCTTTTCAGTCTTTCTTCACGC-
1 AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCAGACTTTCTTCACACA
* * * *
2273753 GAAGCCTCCCTATGAGTCTCATTAAATTATGACATCT
66 GAAGCCTCCCTACGAGTCTAAGT-AA--AT-ACAACT
*
2273790 AAATCCTACACAAACAAATAGACAATTATTTCAAA
1 AAATCCTACACAAACAAATAGACAACTATTTCAAA
2273825 CAATTATTCA
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
97 19 0.16
98 2 0.02
99 60 0.50
100 2 0.02
101 38 0.31
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.28
Consensus pattern (98 bp):
AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCAGACTTTCTTCACACA
GAAGCCTCCCTACGAGTCTAAGTAAATACAACT
Found at i:2275587 original size:17 final size:17
Alignment explanation
Indices: 2275549--2275587 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2275539 TTTAATGCCT
2275549 TTTTTAATTAATTAATA
1 TTTTTAATTAATTAATA
* *
2275566 ATTTTATTTAATTAATA
1 TTTTTAATTAATTAATA
2275583 TTTTT
1 TTTTT
2275588 GTGTCGTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTAATTAATTAATA
Found at i:2276132 original size:25 final size:27
Alignment explanation
Indices: 2276098--2276149 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2276088 ATATATATAC
2276098 ATATATA-T-TATAGTTTTGAAAACAT
1 ATATATATTATATAGTTTTGAAAACAT
2276123 ATATATATTATATAGTTTTGAAAACAT
1 ATATATATTATATAGTTTTGAAAACAT
2276150 TTCGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 7 0.28
26 1 0.04
27 17 0.68
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (27 bp):
ATATATATTATATAGTTTTGAAAACAT
Found at i:2276161 original size:27 final size:27
Alignment explanation
Indices: 2276106--2276163 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2276096 ACATATATAT
* * *
2276106 TATAGTTTTGAAAACATATATATATTA
1 TATAGTTTTGAAAACATATAGAAAATA
* *
2276133 TATAGTTTTGAAAACATTTCGAAAATA
1 TATAGTTTTGAAAACATATAGAAAATA
2276160 TATA
1 TATA
2276164 TATTACAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (27 bp):
TATAGTTTTGAAAACATATAGAAAATA
Found at i:2276161 original size:34 final size:34
Alignment explanation
Indices: 2276123--2276257 Score: 146
Period size: 34 Copynumber: 3.8 Consensus size: 34
2276113 TTGAAAACAT
*
2276123 ATATATATTATATAGTTTTGAAAACATTTCGAAA
1 ATATATATTATATAGTTTTGAAAACATTTTGAAA
* *
2276157 ATATATA-TATTACAGTTTTGAAAAGATTTTGAAAA
1 ATATATATTA-TATAGTTTTGAAAACATTTTG-AAA
*
2276192 CATATATATAATATATAGTTTTTAAAAACATTTTTGAAA
1 -ATATATAT--TATATAG-TTTTGAAAACA-TTTTGAAA
* *
2276231 ATGTATATTATATACTTTTGAAAACAT
1 ATATATATTATATAGTTTTGAAAACAT
2276258 ATATATATAT
Statistics
Matches: 84, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
33 2 0.02
34 26 0.31
35 13 0.15
36 13 0.15
38 11 0.13
39 14 0.17
40 5 0.06
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (34 bp):
ATATATATTATATAGTTTTGAAAACATTTTGAAA
Found at i:2276191 original size:72 final size:70
Alignment explanation
Indices: 2276053--2276254 Score: 232
Period size: 72 Copynumber: 2.8 Consensus size: 70
2276043 ATTCTTGAAA
* *
2276053 ATATATATATAGTTTTGAAAAACATTTTTGAAAATATATATA-TACATATATAT-TATAGTTTTG
1 ATATATATATAGTTTTG-AAAACATTTTTGAAAATATATATATTACAT-T-T-TGAAAAGTTTTG
2276116 AAAACATAT
62 AAAACATAT
*
2276125 ATATATTATATAGTTTTGAAAACA-TTTCGAAAATATATATATTACAGTTTTGAAAAGATTTTGA
1 ATATA-TATATAGTTTTGAAAACATTTTTGAAAATATATATATTACA-TTTTGAAAAG-TTTTGA
2276189 AAACATAT
63 AAACATAT
* *
2276197 ATATAATATATAGTTTTTAAAAACATTTTTGAAAATGTATATTATATAC-TTTTGAAAA
1 ATAT-ATATATAG-TTTTGAAAACATTTTTGAAAATATATA-TAT-TACATTTTGAAAA
2276255 CATATATATA
Statistics
Matches: 114, Mismatches: 6, Indels: 18
0.83 0.04 0.13
Matches are distributed among these distances:
70 1 0.01
71 20 0.18
72 41 0.36
73 24 0.21
74 22 0.19
75 3 0.03
76 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (70 bp):
ATATATATATAGTTTTGAAAACATTTTTGAAAATATATATATTACATTTTGAAAAGTTTTGAAAA
CATAT
Found at i:2276253 original size:23 final size:23
Alignment explanation
Indices: 2276223--2276280 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
2276213 TTAAAAACAT
**
2276223 TTTTGAAAATGTATAT-TATATA
1 TTTTGAAAACATATATATATATA
2276245 CTTTTGAAAACATATATATATATA
1 -TTTTGAAAACATATATATATATA
*
2276269 GTTTGAAAACAT
1 TTTTGAAAACAT
2276281 TTTTGAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (23 bp):
TTTTGAAAACATATATATATATA
Found at i:2276327 original size:57 final size:57
Alignment explanation
Indices: 2276168--2276345 Score: 200
Period size: 57 Copynumber: 3.0 Consensus size: 57
2276158 TATATATATT
*
2276168 ACAGTTTTGAAAAGATTTTGAAAACATATATATAATATATAGTTTTTAAAAACATTTTTGAA
1 ACAGTTTTG-AAATATTTTGAAAA-ATATATAT-ATATATAG--TTTAAAAACATTTTTGAA
* * *
2276230 A-ATGTATATT-ATATACTTTTG-AAAACATATATATATATAGTTTGAAAACATTTTTGAA
1 ACA-GT-T-TTGAAATA-TTTTGAAAAATATATATATATATAGTTTAAAAACATTTTTGAA
* *
2276288 ACAGTTTTGAAATATTTTGAAAAATATATATATATATAGTTTTAAAATATTTTTGAA
1 ACAGTTTTGAAATATTTTGAAAAATATATATATATATAGTTTAAAAACATTTTTGAA
2276345 A
1 A
2276346 ATATATATAT
Statistics
Matches: 101, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
56 7 0.07
57 40 0.40
58 20 0.20
59 1 0.01
60 8 0.08
61 8 0.08
62 9 0.09
63 6 0.06
64 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (57 bp):
ACAGTTTTGAAATATTTTGAAAAATATATATATATATAGTTTAAAAACATTTTTGAA
Found at i:2276336 original size:35 final size:36
Alignment explanation
Indices: 2276290--2276397 Score: 134
Period size: 35 Copynumber: 3.0 Consensus size: 36
2276280 TTTTTGAAAC
2276290 AGTTTTGAAATA-TTTTGAAAAATATATATATATAT
1 AGTTTTGAAATATTTTTGAAAAATATATATATATAT
*
2276325 AGTTTTAAAATATTTTTG-AAAATATATATAT-TAT
1 AGTTTTGAAATATTTTTGAAAAATATATATATATAT
*
2276359 ATGTTTTTGGGAAATATTTTTGAAAAACATATA-ATATAT
1 A-G-TTTT--GAAATATTTTTGAAAAATATATATATATAT
2276398 TATTATTATT
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
34 4 0.06
35 25 0.40
36 9 0.14
38 13 0.21
39 12 0.19
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (36 bp):
AGTTTTGAAATATTTTTGAAAAATATATATATATAT
Found at i:2276391 original size:37 final size:35
Alignment explanation
Indices: 2276290--2276397 Score: 130
Period size: 37 Copynumber: 3.0 Consensus size: 35
2276280 TTTTTGAAAC
2276290 AGTTTTGAAATA-TTTTGAAAAATATATATATATAT
1 AGTTTTGAAATATTTTTGAAAAATATATAT-TATAT
*
2276325 AGTTTTAAAATATTTTTGAAAATATATATATTATAT
1 AGTTTTGAAATATTTTTGAAAA-ATATATATTATAT
* *
2276361 -GTTTTTGGGAAATATTTTTGAAAAACATATAATATAT
1 AG-TTTT--GAAATATTTTTGAAAAATATATATTATAT
2276398 TATTATTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
35 12 0.19
36 18 0.28
37 19 0.30
38 15 0.23
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (35 bp):
AGTTTTGAAATATTTTTGAAAAATATATATTATAT
Found at i:2276397 original size:154 final size:158
Alignment explanation
Indices: 2276096--2276397 Score: 354
Period size: 154 Copynumber: 1.9 Consensus size: 158
2276086 ATATATATAT
* * *
2276096 ACATATATATTATAGTTTTGAAAACATATATATATTATATAGTTTTGAAAACATTTCGAAAATAT
1 ACATATATATTATAGTTTTGAAAACATATATATATGAAACAGTTTTGAAAACATTTCGAAAATAT
2276161 ATATATTACAGTTTTGAAAAGATTTTGAAAACATATATATAATATATAGTTTTTAAAAACATTTT
66 ATATATTACAGTTTTGAAAAGATTTTGAAAACATATATATAATATATAGTTTTTAAAAACATTTT
** *
2276226 TGAAAATGTATATTATATACTTTTGAAA
131 TGAAAACATATAATATATACTTTTGAAA
* *
2276254 ACATATATATATATAG-TTTGAAAACAT-T-T-T-TGAAACAGTTTTG-AAATATTTTGAAAAAT
1 ACATATATAT-TATAGTTTTGAAAACATATATATATGAAACAGTTTTGAAAACATTTCG-AAAAT
* * * ** *
2276313 ATATATATATATAGTTTT-AAAATATTTTTG-AAA-ATATATATATTATAT-GTTTTTGGGAAAT
64 ATATATAT-TACAGTTTTGAAAAGA-TTTTGAAAACATATATATAATATATAGTTTTT-AAAAAC
2276374 ATTTTTGAAAAACATATAATATAT
126 ATTTTTG-AAAACATATAATATAT
2276398 TATTATTATT
Statistics
Matches: 124, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
152 6 0.05
153 32 0.26
154 44 0.35
155 14 0.11
156 1 0.01
157 1 0.01
158 21 0.17
159 5 0.04
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (158 bp):
ACATATATATTATAGTTTTGAAAACATATATATATGAAACAGTTTTGAAAACATTTCGAAAATAT
ATATATTACAGTTTTGAAAAGATTTTGAAAACATATATATAATATATAGTTTTTAAAAACATTTT
TGAAAACATATAATATATACTTTTGAAA
Found at i:2277455 original size:14 final size:14
Alignment explanation
Indices: 2277436--2277464 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2277426 TTAATTCGAA
2277436 TTTTCTTTTAATTT
1 TTTTCTTTTAATTT
2277450 TTTTCTTTTAATTT
1 TTTTCTTTTAATTT
2277464 T
1 T
2277465 ATTTTATTTC
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:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTAATTT
Found at i:2277474 original size:20 final size:21
Alignment explanation
Indices: 2277441--2277479 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2277431 TCGAATTTTC
2277441 TTTTAATTTTTTTC-TTTTAA
1 TTTTAATTTTTTTCATTTTAA
2277461 TTTT-ATTTTATTTCATTTT
1 TTTTAATTTT-TTTCATTTT
2277480 CATTATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTAATTTTTTTCATTTTAA
Found at i:2285145 original size:30 final size:30
Alignment explanation
Indices: 2285104--2285242 Score: 212
Period size: 30 Copynumber: 4.7 Consensus size: 30
2285094 GTCCATAGAT
* *
2285104 TCCGAATAACCTAGGTAAACAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
*
2285134 TCCGAAGAACCTAGGTAAACAGTCCATAT-
1 TCCGAAGAACATAGGTAAACAGTCCATATG
2285163 TCCCGAAGAACATAGGTAAACA-TCCATATG
1 T-CCGAAGAACATAGGTAAACAGTCCATATG
2285193 TCCCGAAGAACATAGGTAAACAGTCC-TATG
1 T-CCGAAGAACATAGGTAAACAGTCCATATG
2285223 TCCGAAGAACATAGGTAAAC
1 TCCGAAGAACATAGGTAAAC
2285243 CCTCGACCCT
Statistics
Matches: 104, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
29 27 0.26
30 74 0.71
31 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (30 bp):
TCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:2286455 original size:3 final size:3
Alignment explanation
Indices: 2286447--2286478 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2286437 TCTCGTACAT
*
2286447 GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2286479 TGATGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:2292680 original size:13 final size:15
Alignment explanation
Indices: 2292650--2292683 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
2292640 AGGTTTAGAG
2292650 TTTAAAATTTATAAT
1 TTTAAAATTTATAAT
2292665 TTTAAAA-TTA-AAT
1 TTTAAAATTTATAAT
2292678 TTTAAA
1 TTTAAA
2292684 TTCTAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 3 0.16
15 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAATTTATAAT
Found at i:2296239 original size:25 final size:26
Alignment explanation
Indices: 2296211--2296259 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
2296201 TTCAATTCGG
* *
2296211 TTAATATTTAAA-AAAATAAGTTTGA
1 TTAATAGTTAAAGAAAAGAAGTTTGA
2296236 TTAATAGTTAAAGAAAAGAAGTTT
1 TTAATAGTTAAAGAAAAGAAGTTT
2296260 AGTTAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (26 bp):
TTAATAGTTAAAGAAAAGAAGTTTGA
Found at i:2296265 original size:26 final size:24
Alignment explanation
Indices: 2296210--2296266 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
2296200 GTTCAATTCG
* *
2296210 GTTAATATTTAAAAAAATAAGTTT
1 GTTAATAGTTAAAAAAAGAAGTTT
2296234 GATTAATAGTTAAAGAAAAGAAGTTT
1 G-TTAATAGTTAAA-AAAAGAAGTTT
2296260 AGTTAAT
1 -GTTAAT
2296267 TCAGTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 11 0.39
26 15 0.54
27 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (24 bp):
GTTAATAGTTAAAAAAAGAAGTTT
Found at i:2303615 original size:228 final size:226
Alignment explanation
Indices: 2303214--2303661 Score: 783
Period size: 228 Copynumber: 2.0 Consensus size: 226
2303204 GTAAATTATC
* *
2303214 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGT
**
2303279 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
65 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
2303344 TGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTG
130 TGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
2303408 AAACATAAATTACATAACTTTCAAAAAAGTATA
195 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
2303441 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTAAATTA-TTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATT--ATTACTTTA
*
2303505 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
63 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
2303570 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
128 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
2303635 TGAAACATAAATTACATAACTTTAAAA
193 TGAAACATAAATTACATAACTTTAAAA
2303662 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
227 36 0.17
228 144 0.68
229 27 0.13
230 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTT
GTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:2303750 original size:20 final size:19
Alignment explanation
Indices: 2303727--2303771 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
2303717 GATATACCAT
2303727 GTAAAAATATGATAAAACCG
1 GTAAAAA-ATGATAAAACCG
2303747 GTAACAAAATGATAAAACCG
1 GTAA-AAAATGATAAAACCG
2303767 GTAAA
1 GTAAA
2303772 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (19 bp):
GTAAAAAATGATAAAACCG
Found at i:2303916 original size:20 final size:19
Alignment explanation
Indices: 2303893--2303938 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2303883 CGATATAACA
2303893 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
2303913 GGTAACAAATGATAAAACC
1 GGTAAAAAATGATAAAACC
2303932 GGTAAAA
1 GGTAAAA
2303939 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2306205 original size:21 final size:21
Alignment explanation
Indices: 2306159--2306222 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
2306149 AAGACAATCA
* *
2306159 AGAGTCGAAGAG-AACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2306180 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2306200 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2306221 AG
1 AG
2306223 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.39, C:0.16, G:0.30, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2306298 original size:33 final size:33
Alignment explanation
Indices: 2306256--2306321 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2306246 AAATAGATGG
*
2306256 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2306289 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2306322 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2306525 original size:15 final size:14
Alignment explanation
Indices: 2306507--2306554 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
2306497 AAAATATGAA
2306507 GAAGAAAAGAGGGAG
1 GAAGAAAAGA-GGAG
2306522 GAAGAAGAAGA-GATG
1 GAAGAA-AAGAGGA-G
*
2306537 GAAGAAATGAGGAG
1 GAAGAAAAGAGGAG
2306551 GAAG
1 GAAG
2306555 GAAGTCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.34
15 15 0.52
16 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.44, T:0.04
Consensus pattern (14 bp):
GAAGAAAAGAGGAG
Found at i:2308132 original size:19 final size:19
Alignment explanation
Indices: 2308108--2308156 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2308098 AATGTCGAGT
2308108 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2308127 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
2308146 TATTTTTGTAT
1 TAATTTTGTAT
2308157 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2308668 original size:199 final size:199
Alignment explanation
Indices: 2308328--2309956 Score: 3160
Period size: 199 Copynumber: 8.2 Consensus size: 199
2308318 GTCAATATTT
2308328 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2308393 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2308458 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2308523 AATA
196 AATA
2308527 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2308592 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2308657 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2308721 AATA
196 AATA
2308725 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2308790 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2308855 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACAGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2308920 AATA
196 AATA
2308924 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
*
2308989 AACAAGGTGCACCCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
2309054 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309119 AATA
196 AATA
2309123 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2309188 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2309253 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATAAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309317 AATA
196 AATA
2309321 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2309386 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2309451 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTT-TGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309514 AATA
196 AATA
2309518 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2309583 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2309648 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309713 AATA
196 AATA
2309717 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2309782 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2309846 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309911 AATA
196 AATA
2309915 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
2309957 CTAATTTAAA
Statistics
Matches: 1414, Mismatches: 12, Indels: 9
0.99 0.01 0.01
Matches are distributed among these distances:
197 193 0.14
198 537 0.38
199 684 0.48
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATA
Found at i:2309061 original size:397 final size:397
Alignment explanation
Indices: 2308328--2309956 Score: 3165
Period size: 397 Copynumber: 4.1 Consensus size: 397
2308318 GTCAATATTT
2308328 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2308393 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2308458 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2308523 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
196 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
2308588 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
261 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
2308653 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGA
326 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGA
2308718 GAGAATA
391 GAGAATA
2308725 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2308790 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2308855 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACAGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2308920 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
196 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
*
2308985 TAAAAACAAGGTGCACCCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAATCATCG
261 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
2309050 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATG
326 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATAC-CGTTTTATG
2309115 AGAGAATA
390 AGAGAATA
2309123 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2309188 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2309253 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATAAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309317 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
196 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
2309382 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
261 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
* *
2309447 AACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT-TGA
326 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGA
2309511 GAGAATA
391 GAGAATA
2309518 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2309583 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2309648 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309713 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
196 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
2309778 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG
261 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
2309842 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
326 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATG
2309907 AGAGAATA
390 AGAGAATA
2309915 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
2309957 CTAATTTAAA
Statistics
Matches: 1216, Mismatches: 12, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
395 258 0.21
396 137 0.11
397 637 0.52
398 184 0.15
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (397 bp):
TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGA
GAGAATA
Found at i:2309460 original size:596 final size:595
Alignment explanation
Indices: 2308328--2309956 Score: 3165
Period size: 596 Copynumber: 2.7 Consensus size: 595
2308318 GTCAATATTT
2308328 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2308393 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2308458 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2308523 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
196 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
2308588 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
261 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
2308653 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATG
326 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
2308717 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
391 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
2308782 GAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
456 GAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
2308847 ATCGAACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACAGGTTT
521 ATCGAACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACAGG-TT
2308912 TATGAGAGAATA
585 T-TGAGAGAATA
2308924 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
*
2308989 AACAAGGTGCACCCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
2309054 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309119 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
196 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
2309184 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
261 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
* *
2309249 AACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATA
326 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
2309313 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
391 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
2309378 GAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
456 GAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
*
2309443 ATCGAACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
521 ATCGAACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACAGGTTT
2309508 TGAGAGAATA
586 TGAGAGAATA
2309518 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
1 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
2309583 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
66 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2309648 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
131 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
2309713 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
196 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
2309778 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG
261 TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
2309842 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
326 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
2309907 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
391 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
2309957 CTAATTTAAA
Statistics
Matches: 1020, Mismatches: 11, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
593 66 0.06
594 377 0.37
595 16 0.02
596 561 0.55
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (595 bp):
TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
TAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAAT
GAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
ATCGAACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACAGGTTT
TGAGAGAATA
Found at i:2311432 original size:18 final size:18
Alignment explanation
Indices: 2311411--2311495 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 18
2311401 AGCGGTCGCA
2311411 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
2311429 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
2311450 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
2311471 GAAGATG-A--TGACGAT
1 GAAGATGAAGCTGACGAT
*
2311486 GATGATGAAG
1 GAAGATGAAG
2311496 ATGATGATCC
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
15 12 0.23
16 1 0.02
17 1 0.02
18 12 0.23
19 1 0.02
20 1 0.02
21 17 0.33
22 1 0.02
23 1 0.02
24 5 0.10
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:2311435 original size:6 final size:6
Alignment explanation
Indices: 2311411--2311499 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
2311401 AGCGGTCGCA
* * * * * *
2311411 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** *
2311459 GAAGCT GGCGAT GAAGAT GATGACGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GA
2311500 TGATCCAAAC
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 58 0.91
8 1 0.02
9 5 0.08
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:2311446 original size:3 final size:3
Alignment explanation
Indices: 2311426--2311503 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
2311416 TGAAGCTGAC
* * * * * ** *
2311426 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
2311474 GAT GAT GAC GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2311504 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:2311461 original size:42 final size:42
Alignment explanation
Indices: 2311414--2311502 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
2311404 GGTCGCAGAA
* *
2311414 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGAAGAC
* * *
2311456 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGAAGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGAAGAC
2311498 GATGA
1 GATGA
2311503 TCCAAACAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGAAGAC
Found at i:2311498 original size:18 final size:18
Alignment explanation
Indices: 2311411--2311503 Score: 69
Period size: 18 Copynumber: 5.0 Consensus size: 18
2311401 AGCGGTCGCA
* *
2311411 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
2311429 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
2311447 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
**
2311465 GGCGATGAAGATGATGACGAT
1 GAAGATGAAGATGAT---GAT
*
2311486 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
2311504 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
18 44 0.75
21 15 0.25
ACGTcount: A:0.37, C:0.08, G:0.34, T:0.22
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:2313279 original size:184 final size:184
Alignment explanation
Indices: 2312970--2313313 Score: 580
Period size: 184 Copynumber: 1.9 Consensus size: 184
2312960 CTTTCAACAT
* *
2312970 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
* *
2313035 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
*
2313100 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTGCACATCGGAACCCATA
131 AATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTGCACATCGGAACCCATA
** * * *
2313154 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
2313219 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
*
2313284 AATGTGTCGATACCATTTACAAAAGTGTCG
131 AATGTGTCGATACCATTTAAAAAAGTGTCG
2313314 GTAATTTGAA
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
184 148 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (184 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTGCACATCGGAACCCATA
Found at i:2315814 original size:25 final size:25
Alignment explanation
Indices: 2315780--2315844 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
2315770 TTATCATTAA
2315780 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
2315805 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
2315830 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
2315845 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:2316163 original size:23 final size:23
Alignment explanation
Indices: 2316132--2316195 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2316122 ATAGGTAAAC
*
2316132 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2316155 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2316178 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2316196 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2316202 original size:23 final size:23
Alignment explanation
Indices: 2316132--2316204 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2316122 ATAGGTAAAC
* **
2316132 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2316155 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2316178 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2316201 ATAT
1 ATAT
2316205 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2316594 original size:23 final size:23
Alignment explanation
Indices: 2316563--2316626 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2316553 ATAGGTAAAC
*
2316563 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2316586 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2316609 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2316627 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2316633 original size:23 final size:23
Alignment explanation
Indices: 2316563--2316635 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2316553 ATAGGTAAAC
* **
2316563 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2316586 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2316609 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2316632 ATAT
1 ATAT
2316636 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2316647 original size:431 final size:430
Alignment explanation
Indices: 2315844--2316903 Score: 2032
Period size: 431 Copynumber: 2.5 Consensus size: 430
2315834 AGGTATATAC
2315844 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
* *
2315909 GTTACGGTATATATTATTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAAT
66 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
* * * *
2315974 CAACTAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGTAGGTGAAAAATATGAAACACTG
131 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
*
2316039 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGT
196 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGT
2316104 ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
261 ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
2316169 GTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGT
326 GTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCC-TTTTATAAAAGT
2316234 GTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
390 GTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
2316275 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
2316340 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
66 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
2316405 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
131 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
2316470 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGT
196 TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGT
2316535 ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
261 ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
2316600 GTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTG
326 GTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTG
2316665 TCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
391 TCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
2316705 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
2316770 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
66 GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
*
2316835 CAAATAATTTTTT-TTCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
131 CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
2316899 TTAAA
196 TTAAA
2316904 GTATCGATCC
Statistics
Matches: 621, Mismatches: 8, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
429 55 0.09
430 196 0.32
431 370 0.60
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (430 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGATATATATTATTATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAAT
CAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTG
TTAAAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGT
ATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAG
GTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTG
TCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
Found at i:2317526 original size:2 final size:2
Alignment explanation
Indices: 2317519--2317566 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2317509 ATTACTACTG
2317519 AT AT AT AT AT 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 AT AT AT AT AT
2317561 AT AT AT
1 AT AT AT
2317567 CCAAAGCTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2317698 original size:50 final size:50
Alignment explanation
Indices: 2317639--2317738 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2317629 CAACTTTGAC
2317639 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
1 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
2317689 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
1 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
2317739 GATACCGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (50 bp):
TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
Found at i:2319295 original size:20 final size:20
Alignment explanation
Indices: 2319270--2319311 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2319260 CCGGTCCGAC
*
2319270 CGGTCGGAAGAACCGGACGA
1 CGGTCGAAAGAACCGGACGA
2319290 CGGTCGAAAGAACCGGACGA
1 CGGTCGAAAGAACCGGACGA
2319310 CG
1 CG
2319312 TCATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.38, T:0.05
Consensus pattern (20 bp):
CGGTCGAAAGAACCGGACGA
Found at i:2331661 original size:2 final size:2
Alignment explanation
Indices: 2331656--2331716 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
2331646 ATCTAAAATA
* * *
2331656 AT AT AT AT AT AT AT AT AT AT AT A- AT TT AA AA AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2331695 AC A- AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
2331717 GGATTAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
1 5 0.10
2 45 0.90
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2331741 original size:37 final size:39
Alignment explanation
Indices: 2331661--2331741 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
2331651 AAATAATATA
* *
2331661 TATATATATATATATATAATTTAAAAATATAATAACAAT
1 TATATATATATATATATAATTTAAAAATAGAATAACAAG
* *
2331700 TATATATATATATATATGGA-TTAAATATAGAA-AA-AAG
1 TATATATATATATATAT-AATTTAAAAATAGAATAACAAG
2331737 TATAT
1 TATAT
2331742 TAATTGTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 7 0.19
38 2 0.05
39 27 0.73
40 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (39 bp):
TATATATATATATATATAATTTAAAAATAGAATAACAAG
Found at i:2333017 original size:82 final size:81
Alignment explanation
Indices: 2332926--2333116 Score: 247
Period size: 81 Copynumber: 2.3 Consensus size: 81
2332916 CAATATGTTT
* * * * * * *
2332926 CATCTATAGTGGCGTTTTGTCGACAAACGGCACAACCGAGTAGTATTTTTGCGGTGTTTTTATAC
1 CATCTATAGTGTCGTTTTTTCAACAAACGCCACAACCGAGTAGT-TTTTAGCAGAGTTTTTATAC
* *
2332991 AAATGCCACAATAGGTA
65 AAACGCCACAATAGGCA
* **
2333008 CATCTATAGTGTCGTTTTTTCAACAAACGCCTCAAGGGAGTAGTTTTTAGCAGAGTTTTTATACA
1 CATCTATAGTGTCGTTTTTTCAACAAACGCCACAACCGAGTAGTTTTTAGCAGAGTTTTTATACA
*
2333073 AACGCCACAATAGGCC
66 AACGCCACAATAGGCA
*
2333089 CATTTATAGTGTCGTTTTTTCAACAAAC
1 CATCTATAGTGTCGTTTTTTCAACAAAC
2333117 ATCGCAAAGG
Statistics
Matches: 95, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 58 0.61
82 37 0.39
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (81 bp):
CATCTATAGTGTCGTTTTTTCAACAAACGCCACAACCGAGTAGTTTTTAGCAGAGTTTTTATACA
AACGCCACAATAGGCA
Found at i:2333206 original size:82 final size:82
Alignment explanation
Indices: 2332908--2333264 Score: 321
Period size: 82 Copynumber: 4.3 Consensus size: 82
2332898 ATTTCTTCAA
* * * * * * * *
2332908 AAACGCCGCAATATGTTTCATCTATAGTGGCGTTTTGTCGACAAACG--GCACAACCGAGTAGTA
1 AAACGCCACAATA-GGTTCACCTATAGTGTCGTTTTTTCAACAAACGCTGCA-AA-GGAGTACTA
* * *
2332971 TTTTTGCGGTGTTTTTATAC
63 CTTTAGCGGCGTTTTTATAC
* * * * * *
2332991 AAATGCCACAATAGGTACATCTATAGTGTCGTTTTTTCAACAAACGCCT-CAAGGGAGTAGT-TT
1 AAACGCCACAATAGGTTCACCTATAGTGTCGTTTTTTCAACAAACG-CTGCAAAGGAGTACTACT
* *
2333054 TTAGCAGAGTTTTTATAC
65 TTAGCGGCGTTTTTATAC
** ** *
2333072 AAACGCCACAATAGGCCCATTTATAGTGTCGTTTTTTCAACAAAC-ATCGCAAAGGAGTACTACT
1 AAACGCCACAATAGGTTCACCTATAGTGTCGTTTTTTCAACAAACGCT-GCAAAGGAGTACTACT
*
2333136 TTAGCGGCGTATTTATAC
65 TTAGCGGCGTTTTTATAC
* * * *
2333154 AAACGCCGCGATATGGTTCACCTATAGTGACGTTTTTT-AATAAACGCTGCAAAGGAGTACTACT
1 AAACGCCACAATA-GGTTCACCTATAGTGTCGTTTTTTCAACAAACGCTGCAAAGGAGTACTACT
2333218 TTAGCGGCGTTTTTATAC
65 TTAGCGGCGTTTTTATAC
* * *
2333236 AAACGTCATAATATGGTTAACCTATAGTG
1 AAACGCCACAATA-GGTTCACCTATAGTG
2333265 GCATTTATGA
Statistics
Matches: 228, Mismatches: 38, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.00
81 68 0.30
82 125 0.55
83 32 0.14
84 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (82 bp):
AAACGCCACAATAGGTTCACCTATAGTGTCGTTTTTTCAACAAACGCTGCAAAGGAGTACTACTT
TAGCGGCGTTTTTATAC
Found at i:2333240 original size:41 final size:41
Alignment explanation
Indices: 2333119--2333240 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 41
2333109 CAACAAACAT
*
2333119 CGCAAAGGAGTACTACTTTAGCGGCGTATTTATACAAACGC
1 CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACGC
* * * * * * *
2333160 CGCGATATG-GTTC-ACCTATAGTGACGTTTTT-TAATAAACGC
1 CGC-AAAGGAGTACTA-CTTTAGCGGCGTTTTTAT-ACAAACGC
*
2333201 TGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACG
1 CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACG
2333241 TCATAATATG
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
40 5 0.08
41 49 0.83
42 5 0.08
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (41 bp):
CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACGC
Found at i:2338303 original size:26 final size:26
Alignment explanation
Indices: 2338254--2338303 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2338244 AATTATTTTT
*
2338254 AAATAAAAATATATAAATTATATTAA
1 AAATAAAAATATATAAAATATATTAA
*
2338280 AAATAAAATTATATTAAAAT-TATT
1 AAATAAAAATATA-TAAAATATATT
2338304 TAGAGAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATAAAAATATATAAAATATATTAA
Found at i:2338912 original size:14 final size:14
Alignment explanation
Indices: 2338893--2338919 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2338883 AAATGAACAT
2338893 AAACGAACATAAAC
1 AAACGAACATAAAC
2338907 AAACGAACATAAA
1 AAACGAACATAAA
2338920 TTTAATTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.19, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACGAACATAAAC
Found at i:2339040 original size:23 final size:23
Alignment explanation
Indices: 2339012--2339055 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2339002 TTATTTGGGT
2339012 TTAAAATATTAATAGGT-TTAAGG
1 TTAAAAT-TTAATAGGTCTTAAGG
*
2339035 TTAAAATTTATTAGGTCTTAA
1 TTAAAATTTAATAGGTCTTAA
2339056 TATTTCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (23 bp):
TTAAAATTTAATAGGTCTTAAGG
Found at i:2339117 original size:10 final size:10
Alignment explanation
Indices: 2339099--2339159 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
2339089 TAAACGAACG
2339099 AACGAACATA
1 AACGAACATA
* *
2339109 TATGAACATA
1 AACGAACATA
2339119 AACGAACATAAA
1 AACGAACAT--A
2339131 TAAGCGAACATA
1 -AA-CGAACATA
*
2339143 AACAAACATA
1 AACGAACATA
*
2339153 TACGAAC
1 AACGAAC
2339160 GAACATTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
10 27 0.68
11 2 0.05
12 2 0.05
13 2 0.05
14 7 0.17
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.15
Consensus pattern (10 bp):
AACGAACATA
Found at i:2339133 original size:14 final size:14
Alignment explanation
Indices: 2339116--2339149 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2339106 ATATATGAAC
2339116 ATAAACGAACATAA
1 ATAAACGAACATAA
*
2339130 ATAAGCGAACATAA
1 ATAAACGAACATAA
*
2339144 ACAAAC
1 ATAAAC
2339150 ATATACGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.12
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:2339162 original size:24 final size:24
Alignment explanation
Indices: 2339112--2339165 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2339102 GAACATATAT
* *
2339112 GAACATAAACGAACATAAATAAGC
1 GAACATAAACAAACATAAAGAAGC
*
2339136 GAACATAAACAAACATATACGAA-C
1 GAACATAAACAAACATA-AAGAAGC
2339160 GAACAT
1 GAACAT
2339166 TAACGAACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.57, C:0.19, G:0.11, T:0.13
Consensus pattern (24 bp):
GAACATAAACAAACATAAAGAAGC
Found at i:2354646 original size:23 final size:23
Alignment explanation
Indices: 2354616--2354661 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2354606 ATGTCATGTC
2354616 TCCAAACCTTGTCATTATTAAAT
1 TCCAAACCTTGTCATTATTAAAT
2354639 TCCAAACCTTGTCATTATTAAAT
1 TCCAAACCTTGTCATTATTAAAT
2354662 AACTAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (23 bp):
TCCAAACCTTGTCATTATTAAAT
Found at i:2355148 original size:28 final size:28
Alignment explanation
Indices: 2355090--2355152 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
2355080 ATTAAGAAAT
* * * *
2355090 AAAATATTAGATACCAAACTAGAATATA
1 AAAAAATTAGACACCAAACTAGAACAAA
2355118 AAAAAATTAGACACCAAACT-GTAACAAA
1 AAAAAATTAGACACCAAACTAG-AACAAA
2355146 AAAAAAT
1 AAAAAAT
2355153 ACGTTTGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.19
Consensus pattern (28 bp):
AAAAAATTAGACACCAAACTAGAACAAA
Found at i:2356271 original size:17 final size:17
Alignment explanation
Indices: 2356249--2356284 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2356239 AATATTTTTT
2356249 ATTTAATAAAAATAATA
1 ATTTAATAAAAATAATA
*
2356266 ATTTAATTAAAATAATA
1 ATTTAATAAAAATAATA
2356283 AT
1 AT
2356285 ATATATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTAATAAAAATAATA
Found at i:2357920 original size:2 final size:2
Alignment explanation
Indices: 2357913--2357980 Score: 72
Period size: 2 Copynumber: 36.0 Consensus size: 2
2357903 TCTAACCATA
*
2357913 AT AT AT AT AT AT -T AT AT AT AT AT AT AT -T AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
2357953 AT AT A- AT CT AT AT A- AT AT CT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2357981 TCACAATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2357933 original size:15 final size:15
Alignment explanation
Indices: 2357913--2357980 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
2357903 TCTAACCATA
2357913 ATATATATATATTAT
1 ATATATATATATTAT
2357928 ATATATATATATTAT
1 ATATATATATATTAT
*
2357943 ATATATATCTA-TAT
1 ATATATATATATTAT
* *
2357957 A-ATCTATATAATAT
1 ATATATATATATTAT
* *
2357971 CTAAATATAT
1 ATATATATAT
2357981 TCACAATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
13 7 0.16
14 7 0.16
15 31 0.69
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATTAT
Found at i:2357935 original size:17 final size:17
Alignment explanation
Indices: 2357913--2357970 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
2357903 TCTAACCATA
2357913 ATATATATATA-T-TAT
1 ATATATATATATTATAT
2357928 ATATATATATATTATAT
1 ATATATATATATTATAT
* * *
2357945 ATATATCTATATAATCT
1 ATATATATATATTATAT
2357962 ATATA-ATAT
1 ATATATATAT
2357971 CTAAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 11 0.30
16 4 0.11
17 22 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATTATAT
Found at i:2358041 original size:27 final size:27
Alignment explanation
Indices: 2358015--2358085 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
2358005 ATATTTTGAG
2358015 GGTAAAT-ATTGATGAGAGTATAATGA
1 GGTAAATAATTGATGAGAGTATAATGA
* *
2358041 -GTCAATGAATTGATGAGGGTATAATGA
1 GGTAAAT-AATTGATGAGAGTATAATGA
*
2358068 -GTTAATGAATTGATGAGA
1 GGTAAAT-AATTGATGAGA
2358086 AGAAAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 5 0.13
27 34 0.87
ACGTcount: A:0.39, C:0.01, G:0.28, T:0.31
Consensus pattern (27 bp):
GGTAAATAATTGATGAGAGTATAATGA
Found at i:2358508 original size:152 final size:155
Alignment explanation
Indices: 2358239--2358582 Score: 387
Period size: 152 Copynumber: 2.2 Consensus size: 155
2358229 GCATGTGATT
* * *
2358239 CAAATTTGGTAAAAAAATTGACTTAAAGTAAATCACAAATTGAAGAAATAAGGAGATTATAATAA
1 CAAATTTGGT--AAAAA-GGACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATAATAA
* *
2358304 GTTGAAGGACTAAATTTAAAAATAAAAAAAATGGTATAAAAAAGAGGAATTGAAAGTACACATGC
63 GTTGAAGGACTAAATTAAAAAATAAAAAAAATGGTATAAAAAAGAGGAATTGAAAATACACATGC
*
2358369 ATTCTACTAATG-TTTAGGAGC-AT-GTCA
128 ATTCTAC-AATGATTTAAGAGCAATAGT-A
* *
2358396 CAAATTTGGTAAAAAGGACTTAAAAATAAATGACGAATTGAATAAATAA-GAGATTATGAA-AA-
1 CAAATTTGGTAAAAAGGACTT-AAAATAAATGACAAATTGAAGAAATAAGGAGATTAT-AATAAG
* * * * * * * *
2358458 TT-AAGGATTAAATTAAAAAATTAAAAAATTGTTATCAAAAAGAGGGATTGAAAATACATATGTA
64 TTGAAGGACTAAATTAAAAAATAAAAAAAATGGTATAAAAAAGAGGAATTGAAAATACACATGCA
* *
2358522 TTCTACGATGATTTAAGAGCATATAGTT
129 TTCTACAATGATTTAAGAGCA-ATAGTA
*
2358550 TAAATTTGGTAAAAAGAGACTTAAAATAAATGA
1 CAAATTTGGTAAAAAG-GACTTAAAATAAATGA
2358583 GGGGTTGAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
151 3 0.02
152 66 0.41
153 2 0.01
154 43 0.27
155 37 0.23
157 10 0.06
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (155 bp):
CAAATTTGGTAAAAAGGACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATAATAAGTT
GAAGGACTAAATTAAAAAATAAAAAAAATGGTATAAAAAAGAGGAATTGAAAATACACATGCATT
CTACAATGATTTAAGAGCAATAGTA
Found at i:2360226 original size:30 final size:31
Alignment explanation
Indices: 2360192--2360259 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
2360182 AAAAGTTTTG
*
2360192 GGTCACTTACGATATC-GTTTCATAGAATT-T
1 GGTCACTTACGATATCAGTTT-ATAAAATTCT
*
2360222 GGTCACTTACGTTATCAGTTTATAAAATTCT
1 GGTCACTTACGATATCAGTTTATAAAATTCT
2360253 GGTCACT
1 GGTCACT
2360260 GAGACATTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 22 0.65
31 12 0.35
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (31 bp):
GGTCACTTACGATATCAGTTTATAAAATTCT
Found at i:2360480 original size:22 final size:22
Alignment explanation
Indices: 2360455--2360504 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
2360445 GTTGCTGGTT
2360455 TGCTCCATCTCAACTTTGCAAC
1 TGCTCCATCTCAACTTTGCAAC
2360477 TGCTCCATCTCAACTTTGCAAC
1 TGCTCCATCTCAACTTTGCAAC
2360499 TGCTCC
1 TGCTCC
2360505 TCTAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.38, G:0.10, T:0.32
Consensus pattern (22 bp):
TGCTCCATCTCAACTTTGCAAC
Found at i:2361246 original size:28 final size:28
Alignment explanation
Indices: 2361198--2361294 Score: 104
Period size: 28 Copynumber: 3.5 Consensus size: 28
2361188 TTTCAGTGAA
* * * *
2361198 CTTAACGAGCAACGAGCTGAGTAACGTG
1 CTTAACGAGCGACTAGCTGAGCAACGAG
* *
2361226 CTTAACGAGCGACTAGTTGAGCAACGGG
1 CTTAACGAGCGACTAGCTGAGCAACGAG
* * *
2361254 GTTAACGAGTGACTAACTGAGCAACGAG
1 CTTAACGAGCGACTAGCTGAGCAACGAG
*
2361282 CTTAATGAGCGAC
1 CTTAACGAGCGAC
2361295 GAGCACGAGT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.19
Consensus pattern (28 bp):
CTTAACGAGCGACTAGCTGAGCAACGAG
Found at i:2363692 original size:22 final size:22
Alignment explanation
Indices: 2363667--2363710 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2363657 TTAATATACA
*
2363667 TATAGTATAATTTTAATAATAT
1 TATAGTATAATATTAATAATAT
* * *
2363689 TATATTTTAATATTATTAATAT
1 TATAGTATAATATTAATAATAT
2363711 ATACTCAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATAGTATAATATTAATAATAT
Found at i:2363695 original size:16 final size:16
Alignment explanation
Indices: 2363676--2363706 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2363666 ATATAGTATA
2363676 ATTTTAATAATATTAT
1 ATTTTAATAATATTAT
*
2363692 ATTTTAATATTATTA
1 ATTTTAATAATATTA
2363707 ATATATACTC
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTAATAATATTAT
Found at i:2364196 original size:30 final size:30
Alignment explanation
Indices: 2364092--2364199 Score: 130
Period size: 30 Copynumber: 3.6 Consensus size: 30
2364082 CCCAGAAAAT
* * *
2364092 GTAATTTATTTTACCTAAAACAGTTTT-AA
1 GTAATTCATTTTACGTAAAACAATTTTCAA
*
2364121 GTAATTCATTTTAAGTAAAACAATTTTCATA
1 GTAATTCATTTTACGTAAAACAATTTTCA-A
2364152 -TAATTCATTTTACGTAAAACAATTTTCAA
1 GTAATTCATTTTACGTAAAACAATTTTCAA
* * *
2364181 GTTATCCATTCTACGTAAA
1 GTAATTCATTTTACGTAAA
2364200 TTATTTTCCA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
29 24 0.35
30 43 0.63
31 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAACAATTTTCAA
Found at i:2383763 original size:223 final size:224
Alignment explanation
Indices: 2383453--2383913 Score: 755
Period size: 223 Copynumber: 2.1 Consensus size: 224
2383443 TGTCAGTTTA
* *
2383453 TGTCGATACTTTATAAAAATATATTGATCCATAATAATATAATAAGTAAAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAAGTAAAAAAATGACAAAACCG
2383518 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATGTCGATACTTTATAAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATGTCGATACTTTATAAAA
* * * *
2383583 ATGTATCTATCCATAATAATATAACAGGTAAAAAAATGACAAAA-TCGGTCTATAAATGTCAAAA
131 ATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAACT-GGTCTATAAATGACAAAA
2383647 CAGGTAAAACGCTACCGGATATATTGAAAG
195 CAGGTAAAACGCTACCGGATATATTGAAAG
* * *
2383677 TGTCAATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGT-AAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAAGTAAAAAAATGACAAAACCG
* * *
2383741 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATGTCGATACTTTATAAAA
*
2383806 ATGTATCGATCTATAACAATAAAACAGGTAAAAAAATGACAAAACTGGTCTATAAATGACAAAAC
131 ATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAACTGGTCTATAAATGACAAAAC
* * *
2383871 AGGTAAAACGCTACCTGATATGTTGATAG
196 AGGTAAAACGCTACCGGATATATTGAAAG
2383900 TGTCGATACTTTAT
1 TGTCGATACTTTAT
2383914 TATAAGTATC
Statistics
Matches: 219, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
223 176 0.80
224 43 0.20
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (224 bp):
TGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAAGTAAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATGTCGATACTTTATAAAA
ATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAACTGGTCTATAAATGACAAAAC
AGGTAAAACGCTACCGGATATATTGAAAG
Found at i:2383925 original size:111 final size:112
Alignment explanation
Indices: 2383453--2383913 Score: 735
Period size: 112 Copynumber: 4.1 Consensus size: 112
2383443 TGTCAGTTTA
* * * *
2383453 TGTCGATACTTTATAAAAATATATTGATCCATAATAATATAATAAGTAAAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
* *
2383518 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAA
66 GTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAG
* *
2383565 TGTCGATACTTTATAAAAATGTATCTATCCATAATAATATAACAGGTAAAAAAATGACAAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
*
2383630 GTCTATAAATGTCAAAACAGGTAAAACGCTACCGGATATATTGAAAG
66 GTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAG
*
2383677 TGTCAATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGT-AAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
* * *
2383741 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAG
66 GTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAG
* * * *
2383788 TGTCGATACTTTATAAAAATGTATCGATCTATAACAATAAAACAGGTAAAAAAATGACAAAACTG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
* * *
2383853 GTCTATAAATGACAAAACAGGTAAAACGCTACCTGATATGTTGATAG
66 GTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAG
2383900 TGTCGATACTTTAT
1 TGTCGATACTTTAT
2383914 TATAAGTATC
Statistics
Matches: 325, Mismatches: 23, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
111 102 0.31
112 223 0.69
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (112 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAG
Found at i:2383992 original size:182 final size:182
Alignment explanation
Indices: 2383786--2384235 Score: 688
Period size: 182 Copynumber: 2.5 Consensus size: 182
2383776 ATATGTTGAT
* * *
2383786 AGTGTCGATACTTTATAAAAATGTATCGATCTATAACAATAAAACAGGTAAAAAAATGACAAAA-
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
* *
2383850 CTGGTCTATAAATGACAAAACAGGTAAA-ACGCTACCTGATATGTTGATAGTGTCGATACTTTAT
66 C-GGTCTAGAAATGACAAAACAGGTAAAGA-GCTACCGGATATGTTGATAGTGTCGATACTTTAT
* * *
2383914 TATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAA
129 TATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
* * *
2383968 AGTGTCGATATTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
* *
2384033 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
66 CGGTCTAGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
2384098 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
131 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
* * *
2384150 AGTGTCGACACTTTATAAAAATGTATCAATCCATAACAATATAATAGGTAAAAATATGACAAAAA
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAC-AAAA
* **
2384215 TCGATCCCGAAATGACAAAAC
65 TCGGTCTAGAAATGACAAAAC
2384236 CGATAGTAAA
Statistics
Matches: 244, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
182 219 0.90
183 25 0.10
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
CGGTCTAGAAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
Found at i:2384888 original size:23 final size:23
Alignment explanation
Indices: 2384859--2384906 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2384849 AAATAGGTCA
*
2384859 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
* *
2384882 ATATAAGCGTTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
2384905 AT
1 AT
2384907 TATACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:2387005 original size:31 final size:32
Alignment explanation
Indices: 2386962--2387054 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 32
2386952 AATTGAATCA
*
2386962 AAAGTGCGGATGCTTCCTTCCGTTCACT-TCG
1 AAAGTGCCGATGCTTCCTTCCGTTCACTATCG
* **
2386993 AAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAATCG
1 AAAGTGCCGATGCTTCCTTCCGTTC--ACT--ATCG
2387029 AAAGTGCCGATGCTTCCTTCCGTTCA
1 AAAGTGCCGATGCTTCCTTCCGTTCA
2387055 TTTTGAATCG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
31 23 0.45
33 1 0.02
36 27 0.53
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (32 bp):
AAAGTGCCGATGCTTCCTTCCGTTCACTATCG
Found at i:2387037 original size:36 final size:36
Alignment explanation
Indices: 2386990--2387091 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
2386980 TCCGTTCACT
2386990 TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
1 TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
* *
2387026 TCGAAAGTGCCGATGCTTCCTTCCGTTCATTTTGAA
1 TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
* *
2387062 TCGAAAGTGCTGATGTTTCCTTTCGTTCTT
1 TCGAAAGTGCCGATGCTTCCTTTCGTTCTT
2387092 CTTATTCACC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (36 bp):
TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
Found at i:2389545 original size:13 final size:13
Alignment explanation
Indices: 2389512--2389538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2389502 AAAACTTCTT
2389512 AATAAACACTTCA
1 AATAAACACTTCA
2389525 AATAAACACTTCA
1 AATAAACACTTCA
2389538 A
1 A
2389539 CAAAACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAACACTTCA
Found at i:2392661 original size:3 final size:3
Alignment explanation
Indices: 2392653--2392708 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
2392643 TACTTATATA
* **
2392653 AAT AAT AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
2392697 AAT AA- AAT AAT A
1 AAT AAT AAT AAT A
2392709 TTGCAAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2393179 original size:9 final size:9
Alignment explanation
Indices: 2393160--2393191 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2393150 CCTTATGGGC
2393160 CATTT-TTT
1 CATTTCTTT
2393168 CATTTCTTT
1 CATTTCTTT
2393177 CATTTCTTT
1 CATTTCTTT
2393186 C-TTTCT
1 CATTTCT
2393192 CTGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 10 0.43
9 13 0.57
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.69
Consensus pattern (9 bp):
CATTTCTTT
Found at i:2393999 original size:3 final size:3
Alignment explanation
Indices: 2393991--2394042 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
2393981 TAAAATTATT
* * * * *
2393991 TAA TAA TAA TAA TAA -AA TAA TTA TAA TTA TAA TTA TTA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2394038 TAA TA
1 TAA TA
2394043 GAACCGGGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2394597 original size:112 final size:111
Alignment explanation
Indices: 2394347--2395016 Score: 817
Period size: 112 Copynumber: 5.9 Consensus size: 111
2394337 AAATTAAGGC
* * *
2394347 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
** * *** ** *
2394411 TGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGA-TAGAGTCAAACA
65 TGAACTTTTCTGG-AA-----ATGTTGATCCATCAAGTGATG-AATTAGAG-C--A-A
* * *
2394468 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * **
2394533 GAACTTTCTCTGGAAAAGTTAATTTATCAAGTGATGAATTCAG-GCAA
66 GAACTTT-TCTGGAAATGTTGATCCATCAAGTGATGAATT-AGAGCAA
* *
2394580 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
*
2394645 GAACTTTCTCTGGAAATGTTGATCTATCAAGTGATGAATTAGAGCAA
66 GAACTTT-TCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
* *
2394692 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
**
2394757 TGAACACTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
65 TGAACTTTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
* * *
2394804 AAGCTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAA-TTCTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGAT-AAGTTCTTCTCATT
** * *
2394868 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAA
64 ATGAACTTTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
*
2394916 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
2394981 GAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATG
66 GAAC-TTTTCTGGAAATGTTGATCCATCAAGTGATG
2395017 GATTTGAATC
Statistics
Matches: 498, Mismatches: 41, Indels: 29
0.88 0.07 0.05
Matches are distributed among these distances:
110 2 0.00
111 28 0.06
112 346 0.69
113 31 0.06
115 2 0.00
116 15 0.03
117 2 0.00
121 65 0.13
122 7 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (111 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
Found at i:2394904 original size:336 final size:340
Alignment explanation
Indices: 2394347--2395016 Score: 917
Period size: 336 Copynumber: 2.0 Consensus size: 340
2394337 AAATTAAGGC
* *
2394347 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* ** ** * * *
2394412 GAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAAACAAAGGTTGAA
66 GAACACTTCTGGAAA---T-ATGTTGATCCATCAACTGATGTAATAGAGTC-AACAAAGCTTAAA
* **
2394477 CAAATTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACTTTCT
126 CAAATTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACACTCT
** *
2394542 CTGGAAAAGTTAATTTATCAAGTGATGAATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTAT
191 CTGGAAAAGTTAATCCATCAAGTGATGAATT-AGAGCAAAAGGTTGAACAAACTCTTCTCATTAT
* * * *
2394606 GAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCTA
255 GAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCA
2394671 TCAAGTGATGAATTAGAGCAA
320 TCAAGTGATGAATTAGAGCAA
*
2394692 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
*
2394757 TGAACACTTCTGG-AA-ATGTTGATCCATCAAGTGATG-AATTAGAG-C-A-AAAGCTTAAACAA
65 TGAACACTTCTGGAAATATGTTGATCCATCAACTGATGTAA-TAGAGTCAACAAAGCTTAAACAA
* *
2394816 GTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAA-TTCTTCTCATTATGAACACT-TC
129 ATTCTTCTCATTATGAACTTCTTCTTC-ATCTTCAGAT-AAGTTCTTCTCATTATGAACACTCTC
* * * * *
2394879 TGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGA
192 TGGAAAAGTTAATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAACTCTTCTCATTATGA
*
2394944 ACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATC
257 ACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATC
2395009 AAGTGATG
322 AAGTGATG
2395017 GATTTGAATC
Statistics
Matches: 290, Mismatches: 30, Indels: 19
0.86 0.09 0.06
Matches are distributed among these distances:
335 1 0.00
336 161 0.56
337 28 0.10
338 2 0.01
339 2 0.01
340 20 0.07
345 35 0.12
346 41 0.14
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (340 bp):
AAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACACTTCTGGAAATATGTTGATCCATCAACTGATGTAATAGAGTCAACAAAGCTTAAACAAAT
TCTTCTCATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACACTCTCTGGA
AAAGTTAATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTT
CTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
GATGAATTAGAGCAA
Found at i:2395478 original size:22 final size:22
Alignment explanation
Indices: 2395423--2395480 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2395413 CATAAAGCTT
* *
2395423 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
2395445 TCATCTTTGAAGAGGGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2395467 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
2395481 TGTAGATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:2395973 original size:54 final size:53
Alignment explanation
Indices: 2395844--2396049 Score: 242
Period size: 54 Copynumber: 3.9 Consensus size: 53
2395834 AGAATAGCAG
* * *
2395844 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG--TCGA
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTTAGA
* *
2395895 GTT-GTAAAACACTTGACAACACATTCATCCTTTT-TTGTGGCTTCTGCTTAGA
1 GTTCGTAAAACATTTGACAACACATTCAT-CTTTTCCTGTGGCTTCTGCTTAGA
* * *
2395947 TGTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGCTCAGA
1 -GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTTAGA
* * *
2396001 CGTTCGTAAAGCGTTTGACAACACATTTATCCTTTT-CTGTGGCTTCTGC
1 -GTTCGTAAAACATTTGACAACACATTCAT-CTTTTCCTGTGGCTTCTGC
2396050 CAAGATTTCT
Statistics
Matches: 132, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
50 33 0.25
51 8 0.06
52 3 0.02
53 8 0.06
54 75 0.57
55 5 0.04
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTTAGA
Found at i:2398162 original size:114 final size:114
Alignment explanation
Indices: 2397962--2398185 Score: 315
Period size: 114 Copynumber: 2.0 Consensus size: 114
2397952 GATCATGCAG
* * * * *
2397962 TTCATCTTTTAATTCCAATGATTGGTTATGTGGTTCCTACCGAACCAGATCAAATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
2398027 AAACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
66 AAACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
* * * *
2398076 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTT-ATACCAAACCAGATTAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTATGGGGTTCATACCAAACCAGATCAAATAACTCAAAG
* * * *
2398140 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
65 AAAACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAG
2398186 AACGTGGCAC
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 88 0.92
115 8 0.08
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTATGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
AAACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
Found at i:2400387 original size:26 final size:25
Alignment explanation
Indices: 2400348--2400398 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
2400338 TCATTTTTTC
2400348 TTTTTTTTTTCTTTATTTATTGGAT
1 TTTTTTTTTTCTTTATTTATTGGAT
* *
2400373 TTTTCTTTTTTCTTTCTTTGTTGGAT
1 TTTT-TTTTTTCTTTATTTATTGGAT
2400399 GAGTATAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.08, C:0.08, G:0.10, T:0.75
Consensus pattern (25 bp):
TTTTTTTTTTCTTTATTTATTGGAT
Found at i:2404008 original size:14 final size:14
Alignment explanation
Indices: 2403970--2404023 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
2403960 CATAAAAATA
* *
2403970 CAAATGCAAAGATG
1 CAAATGTAAATATG
2403984 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
2403999 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
2404013 TAAATGTAAAT
1 CAAATGTAAAT
2404024 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:2405640 original size:14 final size:16
Alignment explanation
Indices: 2405622--2405659 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
2405612 TACATAATAA
*
2405622 AATAAAAATATTAA-T
1 AATAAAAATAATAAGT
2405637 -ATAAAAATAATAAGT
1 AATAAAAATAATAAGT
2405652 AATAAAAA
1 AATAAAAA
2405660 ATTTGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 12 0.60
15 1 0.05
16 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AATAAAAATAATAAGT
Found at i:2405648 original size:17 final size:17
Alignment explanation
Indices: 2405598--2405661 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
2405588 CTAACAGACA
2405598 AATAAAATAATTAATACA-T
1 AATAAAA-AA-TAATA-AGT
* *
2405617 AATAAAATAAAAAT-ATT
1 AATAAAA-AATAATAAGT
2405634 AATATAAAAATAATAAGT
1 AATA-AAAAATAATAAGT
2405652 AATAAAAAAT
1 AATAAAAAAT
2405662 TTGAAAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.03
17 16 0.41
18 12 0.31
19 10 0.26
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
AATAAAAAATAATAAGT
Found at i:2406483 original size:3 final size:3
Alignment explanation
Indices: 2406475--2406525 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
2406465 TACTTATATA
* **
2406475 AAT AAT AAT AAT AAT AAA AAT AAT AATT AA- AGC AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
2406519 AAT AAT A
1 AAT AAT A
2406526 TTGCAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 3 0.08
3 34 0.85
4 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:2406498 original size:15 final size:14
Alignment explanation
Indices: 2406474--2406525 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
2406464 TTACTTATAT
2406474 AAATAATAATAATA
1 AAATAATAATAATA
*
2406488 ATAAAAATAATAATTA
1 A-AATAATAATAA-TA
**
2406504 AAGCAATAATAATA
1 AAATAATAATAATA
2406518 AAATAATA
1 AAATAATA
2406526 TTGCAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 9 0.29
15 19 0.61
16 3 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:2407806 original size:3 final size:3
Alignment explanation
Indices: 2407798--2407849 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
2407788 TAAAATTATT
* * * * *
2407798 TAA TAA TAA TAA TAA -AA TAA TTA TAA TTA TAA TTA TTA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2407845 TAA TA
1 TAA TA
2407850 GAACCGGGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2412925 original size:30 final size:30
Alignment explanation
Indices: 2412889--2412949 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2412879 AATCAATCAT
*
2412889 TAACGTTATAGTTTGTTACAATATGGCCAC
1 TAACGTTATAGTTTGTTACAAAATGGCCAC
*
2412919 TAACGTTATCGTTTGTTACAAAATGGCCAC
1 TAACGTTATAGTTTGTTACAAAATGGCCAC
2412949 T
1 T
2412950 CGACGTTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (30 bp):
TAACGTTATAGTTTGTTACAAAATGGCCAC
Found at i:2414275 original size:30 final size:30
Alignment explanation
Indices: 2414241--2414298 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2414231 AACGAAAATA
*
2414241 TAATCTCATGTAGATGTCAGAACGGGGAAT
1 TAATCCCATGTAGATGTCAGAACGGGGAAT
*
2414271 TAATCCCATGTAGATGTCAGAATGGGGA
1 TAATCCCATGTAGATGTCAGAACGGGGA
2414299 CTAAGCCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.26
Consensus pattern (30 bp):
TAATCCCATGTAGATGTCAGAACGGGGAAT
Found at i:2414387 original size:2 final size:2
Alignment explanation
Indices: 2414380--2414438 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2414370 ATATGTCGCG
2414380 TA TA TA 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
2414422 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2414439 CACGAACATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2416485 original size:22 final size:22
Alignment explanation
Indices: 2416443--2416520 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
2416433 TTCAGTATTT
* *
2416443 GTCCCGAATGACCACTAGATAC
1 GTCCCGAAGGACCACTGGATAC
* **
2416465 GTCTCGAAGGATGACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
2416487 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
2416509 GTCCCGAAGGAC
1 GTCCCGAAGGAC
2416521 TAATATACCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:2417083 original size:24 final size:24
Alignment explanation
Indices: 2417051--2417153 Score: 170
Period size: 24 Copynumber: 4.3 Consensus size: 24
2417041 CACCATGTAT
*
2417051 CGATGCATCCCTTGACGGGTACAC
1 CGATGCATCCCTTGACGGGTGCAC
*
2417075 CGATGCATCCCTTGGCGGGTGCAC
1 CGATGCATCCCTTGACGGGTGCAC
*
2417099 CGATGTATCCCTTGACGGGTGCAC
1 CGATGCATCCCTTGACGGGTGCAC
*
2417123 CGATGCATCCCTTGACGGGTGCAT
1 CGATGCATCCCTTGACGGGTGCAC
2417147 CGATGCA
1 CGATGCA
2417154 CTACCCATGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.22
Consensus pattern (24 bp):
CGATGCATCCCTTGACGGGTGCAC
Found at i:2417249 original size:64 final size:63
Alignment explanation
Indices: 2417140--2417299 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 63
2417130 TCCCTTGACG
* ** *
2417140 GGTGCATCGATGCACTACCCATGCATCGATGCATAAATCTTATTCGATGTT-TGTATTTTAAAT
1 GGTGCATCGATGCACT-CCTATGCATCGATGCATAAATCGCATTCGATGTTATGTATATTAAAT
* *
2417203 AGGTGCATCGATGCACTCCTTATGCATCGATGCACT-AATGGCATTCGATGTTCATTTATATTAA
1 -GGTGCATCGATGCACTCC-TATGCATCGATGCA-TAAATCGCATTCGATGTT-ATGTATATTAA
2417267 AT
62 AT
* * *
2417269 GAGTGTATCGATACACTCCATGTGCATCGAT
1 G-GTGCATCGATGCACTCC-TATGCATCGAT
2417300 TCACCTTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 2 0.02
64 42 0.52
65 2 0.02
66 35 0.43
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (63 bp):
GGTGCATCGATGCACTCCTATGCATCGATGCATAAATCGCATTCGATGTTATGTATATTAAAT
Found at i:2421866 original size:33 final size:31
Alignment explanation
Indices: 2421801--2421942 Score: 151
Period size: 33 Copynumber: 4.5 Consensus size: 31
2421791 AGAGTCGAGG
** *
2421801 GTTTACCTATGTTCTATGGAACTTATGGACA
1 GTTTACCTATGTTCTAAAGAACATATGGACA
*
2421832 GTTTTACCTATGTCTTTAAAGAACATATGGACA
1 G-TTTACCTATGT-TCTAAAGAACATATGGACA
* * *
2421865 GTTTTACTTATGTCTTTCAAG-ACATATGGACA
1 G-TTTACCTATGT-TCTAAAGAACATATGGACA
* *
2421897 GTATACCTATGTTCTAAAGAATATATGGACA
1 GTTTACCTATGTTCTAAAGAACATATGGACA
*
2421928 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
2421943 TTGGGATATA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
30 5 0.05
31 33 0.35
32 23 0.24
33 34 0.36
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAAGAACATATGGACA
Found at i:2421923 original size:31 final size:31
Alignment explanation
Indices: 2421801--2421961 Score: 137
Period size: 31 Copynumber: 5.1 Consensus size: 31
2421791 AGAGTCGAGG
**
2421801 GTTTACCTATGTTCTATGGAACT-TATGGACA
1 GTTTACCTATGTTCTAAAGAA-TATATGGACA
* *
2421832 GTTTTACCTATGTCTTTAAAGAACATATGGACA
1 G-TTTACCTATGT-TCTAAAGAATATATGGACA
* * * *
2421865 GTTTTACTTATGTCTTTCAAG-ACATATGGACA
1 G-TTTACCTATGT-TCTAAAGAATATATGGACA
*
2421897 GTATACCTATGTTCTAAAGAATATATGGACA
1 GTTTACCTATGTTCTAAAGAATATATGGACA
* *** *
2421928 GTTTACCTAGGTTCTTTGGGATATATGGACA
1 GTTTACCTATGTTCTAAAGAATATATGGACA
2421959 GTT
1 GTT
2421962 GCGAGGTTCT
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
30 5 0.05
31 48 0.44
32 23 0.21
33 33 0.30
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAAGAATATATGGACA
Found at i:2421944 original size:63 final size:65
Alignment explanation
Indices: 2421824--2421961 Score: 167
Period size: 63 Copynumber: 2.2 Consensus size: 65
2421814 CTATGGAACT
* * * *
2421824 TATGGACAGTTTTACCTATGTCTTTAAAGAACATATGGACAGTTTTACTTATGTCTTTCAAGACA
1 TATGGACAGTTATACCTATGTCTCTAAAGAACATATGGACAGTTTTACCTAGGTCTTTCAAGACA
* ** *
2421889 TATGGACAG-TATACCTATGT-TCTAAAGAATATATGGACAG-TTTACCTAGGTTCTTT-GGGAT
1 TATGGACAGTTATACCTATGTCTCTAAAGAACATATGGACAGTTTTACCTAGG-TCTTTCAAGAC
2421950 A
65 A
2421951 TATGGACAGTT
1 TATGGACAGTT
2421962 GCGAGGTTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 20 0.32
63 24 0.38
64 10 0.16
65 9 0.14
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (65 bp):
TATGGACAGTTATACCTATGTCTCTAAAGAACATATGGACAGTTTTACCTAGGTCTTTCAAGACA
Found at i:2424305 original size:2 final size:2
Alignment explanation
Indices: 2424298--2424352 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2424288 CATGATATGA
2424298 AT AT AT AT AT 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 AT AT AT AT AT
2424340 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2424353 AAGGAAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2426292 original size:31 final size:32
Alignment explanation
Indices: 2426168--2426308 Score: 153
Period size: 33 Copynumber: 4.4 Consensus size: 32
2426158 GAGTCAAGGG
**
2426168 TTTACCTATGTTCTATGGAACATATGGACAGT
1 TTTACCTATGTTCTAAAGAACATATGGACAGT
* *
2426200 TTTACCTATGTCTTTAAAGAACATATGGATAGT
1 TTTACCTATGT-TCTAAAGAACATATGGACAGT
* * * *
2426233 TTTACTTATGTCTTTCAAG-ACATGTGGACAG-
1 TTTACCTATGT-TCTAAAGAACATATGGACAGT
*
2426264 TATACCTATGTTCTAAAGAACATATGGACAG-
1 TTTACCTATGTTCTAAAGAACATATGGACAGT
*
2426295 TTTACCTAGGTTCT
1 TTTACCTATGTTCT
2426309 TTGGGACCTA
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
30 5 0.05
31 32 0.35
32 21 0.23
33 34 0.37
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (32 bp):
TTTACCTATGTTCTAAAGAACATATGGACAGT
Found at i:2426310 original size:63 final size:65
Alignment explanation
Indices: 2426187--2426327 Score: 164
Period size: 63 Copynumber: 2.2 Consensus size: 65
2426177 GTTCTATGGA
* * * * *
2426187 ACATATGGACAGTTTTACCTATGTCTTTAAAGAACATATGGATAGTTTTACTTATGTCTTTCAAG
1 ACATATGGACAGTTATACCTATGTCTCTAAAGAACATATGGACAGTTTTACCTAGGTCTTTCAAG
* **
2426252 ACATGTGGACAG-TATACCTATGT-TCTAAAGAACATATGGACAG-TTTACCTAGGTTCTTT-GG
1 ACATATGGACAGTTATACCTATGTCTCTAAAGAACATATGGACAGTTTTACCTAGG-TCTTTCAA
2426313 G
65 G
*
2426314 ACCTATGGACAGTT
1 ACATATGGACAGTT
2426328 GCCGAGGTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
62 19 0.30
63 24 0.38
64 10 0.16
65 11 0.17
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (65 bp):
ACATATGGACAGTTATACCTATGTCTCTAAAGAACATATGGACAGTTTTACCTAGGTCTTTCAAG
Found at i:2426338 original size:30 final size:30
Alignment explanation
Indices: 2426286--2426381 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
2426276 CTAAAGAACA
* *
2426286 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
2426317 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
2426347 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
2426376 TCTGGA
1 TATGGA
2426382 TAGGTCATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:2430364 original size:22 final size:22
Alignment explanation
Indices: 2430338--2430413 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
2430328 CAGTATTTGA
* *
2430338 CCCGAAGAACCACTAGATATGT
1 CCCGAAGGACCACTAGATACGT
*
2430360 CCCGAAGGACTACTAGATACGT
1 CCCGAAGGACCACTAGATACGT
*
2430382 CCCGAAGGACCACTGGATACGT
1 CCCGAAGGACCACTAGATACGT
*
2430404 CTCGAAGGAC
1 CCCGAAGGAC
2430414 TAATATACCC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.16
Consensus pattern (22 bp):
CCCGAAGGACCACTAGATACGT
Found at i:2433887 original size:20 final size:19
Alignment explanation
Indices: 2433858--2433897 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
2433848 AGTAATCTTA
*
2433858 TTCCCTGGTAATCTTACAT
1 TTCCCTGGTAATATTACAT
2433877 TTCCACTGGTAATATTACAT
1 TTCC-CTGGTAATATTACAT
2433897 T
1 T
2433898 CCGTGAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (19 bp):
TTCCCTGGTAATATTACAT
Found at i:2434413 original size:7 final size:7
Alignment explanation
Indices: 2434403--2434489 Score: 57
Period size: 7 Copynumber: 11.6 Consensus size: 7
2434393 ATTTATCATC
2434403 ATTTATT
1 ATTTATT
2434410 ATTTATT
1 ATTTATT
2434417 ATTTATT
1 ATTTATT
*
2434424 ATTTTTT
1 ATTTATT
*
2434431 GTTTTATAT
1 -ATTTAT-T
* *
2434440 TTTTATG
1 ATTTATT
2434447 ATTTATT
1 ATTTATT
*
2434454 ATTTTCTT
1 A-TTTATT
*
2434462 CATTTACAT
1 -ATTTA-TT
*
2434471 ATTTAAT
1 ATTTATT
2434478 ATTTTATT
1 A-TTTATT
2434486 ATTT
1 ATTT
2434490 TTGGTAATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
7 32 0.50
8 29 0.45
9 3 0.05
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (7 bp):
ATTTATT
Found at i:2434443 original size:15 final size:16
Alignment explanation
Indices: 2434405--2434458 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
2434395 TTATCATCAT
*
2434405 TTATTATTTATTATTTA
1 TTATT-TTTATGATTTA
*
2434422 TTATTTTT-TGTTTTA
1 TTATTTTTATGATTTA
2434437 -TATTTTTATGATTTA
1 TTATTTTTATGATTTA
2434452 TTATTTT
1 TTATTTT
2434459 CTTCATTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 7 0.22
15 11 0.34
16 9 0.28
17 5 0.16
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
TTATTTTTATGATTTA
Found at i:2435744 original size:21 final size:20
Alignment explanation
Indices: 2435720--2435759 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2435710 AAAATAGGTA
2435720 AAAGCAAAAAAAGTAAAAACG
1 AAAG-AAAAAAAGTAAAAACG
* *
2435741 AAAGAGAAAAATTAAAAAC
1 AAAGAAAAAAAGTAAAAAC
2435760 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.07, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAGAAAAAAAGTAAAAACG
Found at i:2440476 original size:18 final size:18
Alignment explanation
Indices: 2440453--2440495 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2440443 CCTAATTCAT
2440453 TCTCCTCGTCCACACTCA
1 TCTCCTCGTCCACACTCA
*
2440471 TCTCCTCTTCCACACTCA
1 TCTCCTCGTCCACACTCA
2440489 TCTCCTC
1 TCTCCTC
2440496 CAACTGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.51, G:0.02, T:0.33
Consensus pattern (18 bp):
TCTCCTCGTCCACACTCA
Done.