Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 21 of 199
Found at i:6182058 original size:25 final size:26
Alignment explanation
Indices: 6182021--6182078 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
6182011 GAAATAGTGA
*
6182021 TTTTTGTAAATTCACGATGGAGGTT-
1 TTTTTTTAAATTCACGATGGAGGTTG
*
6182046 TTTTTTTAGATTCACGATGGAGGTTG
1 TTTTTTTAAATTCACGATGGAGGTTG
6182072 TTTTTTT
1 TTTTTTT
6182079 TTTAAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.19, C:0.07, G:0.22, T:0.52
Consensus pattern (26 bp):
TTTTTTTAAATTCACGATGGAGGTTG
Found at i:6183245 original size:24 final size:23
Alignment explanation
Indices: 6183218--6183340 Score: 149
Period size: 24 Copynumber: 5.7 Consensus size: 23
6183208 CTTTCCCTAA
6183218 ACCATCATTCCCAAGGCCATCCAT
1 ACCATCATTCCCAA-GCCATCCAT
6183242 ACCATCATT--C---CCATCCAT
1 ACCATCATTCCCAAGCCATCCAT
6183260 ACCATCATTCCCAAAGCCATCCAT
1 ACCATCATTCCC-AAGCCATCCAT
6183284 ACCATCATT--C---CCATCCAT
1 ACCATCATTCCCAAGCCATCCAT
6183302 ACCATCATTCCCAAAGCCATCCAT
1 ACCATCATTCCC-AAGCCATCCAT
6183326 ACCATCATTCCCAAG
1 ACCATCATTCCCAAG
6183341 GCCTGGGGTG
Statistics
Matches: 87, Mismatches: 0, Indels: 25
0.78 0.00 0.22
Matches are distributed among these distances:
18 34 0.39
20 2 0.02
22 2 0.02
23 3 0.03
24 46 0.53
ACGTcount: A:0.31, C:0.42, G:0.04, T:0.23
Consensus pattern (23 bp):
ACCATCATTCCCAAGCCATCCAT
Found at i:6183257 original size:18 final size:18
Alignment explanation
Indices: 6183234--6183314 Score: 108
Period size: 18 Copynumber: 4.2 Consensus size: 18
6183224 ATTCCCAAGG
6183234 CCATCCATACCATCATTC
1 CCATCCATACCATCATTC
6183252 CCATCCATACCATCATTCCC
1 CCATCCATACCATCATT--C
6183272 AAAGCCATCCATACCATCATTC
1 ----CCATCCATACCATCATTC
6183294 CCATCCATACCATCATTC
1 CCATCCATACCATCATTC
6183312 CCA
1 CCA
6183315 AAGCCATCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
18 38 0.67
20 1 0.02
22 1 0.02
24 17 0.30
ACGTcount: A:0.30, C:0.44, G:0.01, T:0.25
Consensus pattern (18 bp):
CCATCCATACCATCATTC
Found at i:6183269 original size:42 final size:42
Alignment explanation
Indices: 6183218--6183338 Score: 233
Period size: 42 Copynumber: 2.9 Consensus size: 42
6183208 CTTTCCCTAA
*
6183218 ACCATCATTCCCAAGGCCATCCATACCATCATTCCCATCCAT
1 ACCATCATTCCCAAAGCCATCCATACCATCATTCCCATCCAT
6183260 ACCATCATTCCCAAAGCCATCCATACCATCATTCCCATCCAT
1 ACCATCATTCCCAAAGCCATCCATACCATCATTCCCATCCAT
6183302 ACCATCATTCCCAAAGCCATCCATACCATCATTCCCA
1 ACCATCATTCCCAAAGCCATCCATACCATCATTCCCA
6183339 AGGCCTGGGG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.31, C:0.43, G:0.03, T:0.23
Consensus pattern (42 bp):
ACCATCATTCCCAAAGCCATCCATACCATCATTCCCATCCAT
Found at i:6184493 original size:30 final size:31
Alignment explanation
Indices: 6184457--6184518 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
6184447 TAAGACATAA
6184457 AGTGGTGCTTA-TTTTTTTATATTGTCTTTG
1 AGTGGTGCTTATTTTTTTTATATTGTCTTTG
*
6184487 AGTGGTGCTTATTTTTTTTATATTGTGTTTG
1 AGTGGTGCTTATTTTTTTTATATTGTCTTTG
6184518 A
1 A
6184519 TTTCATTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.15, C:0.05, G:0.21, T:0.60
Consensus pattern (31 bp):
AGTGGTGCTTATTTTTTTTATATTGTCTTTG
Found at i:6187249 original size:21 final size:20
Alignment explanation
Indices: 6187209--6187249 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6187199 TTAATGGTAT
* *
6187209 GGACGAGAATGATTAAGAAA
1 GGACGAGAAAGATAAAGAAA
6187229 GGACGAGAAAGACTAAAGAAA
1 GGACGAGAAAGA-TAAAGAAA
6187250 AAACTAACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.54, C:0.07, G:0.29, T:0.10
Consensus pattern (20 bp):
GGACGAGAAAGATAAAGAAA
Found at i:6190018 original size:21 final size:21
Alignment explanation
Indices: 6189976--6190018 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
6189966 TCAAATTTAA
6189976 GTCATTTCAAATTATTTTGTTT
1 GTCATTTCAAA-TATTTTGTTT
6189998 GTCATTTCAAA-ATTCTTGTTT
1 GTCATTTCAAATATT-TTGTTT
6190019 AAATCATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 6 0.30
22 11 0.55
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (21 bp):
GTCATTTCAAATATTTTGTTT
Found at i:6192203 original size:14 final size:14
Alignment explanation
Indices: 6192169--6192216 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
6192159 GTGTTTTATA
*
6192169 GTTTAGGGGTTTAGGG
1 GTTTA-GGGTTTA-AG
6192185 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
*
6192199 GTTTAAGGTTTAAG
1 GTTTAGGGTTTAAG
6192213 GTTT
1 GTTT
6192217 TTTTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 18 0.60
15 7 0.23
16 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.44
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:6192232 original size:20 final size:20
Alignment explanation
Indices: 6192207--6192250 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6192197 AGGTTTAAGG
*
6192207 TTTAAGGTTTTTT-TATATTT
1 TTTAA-GTTTTTTCTATATTC
6192227 TTTAAGTTTTTTCTATATTC
1 TTTAAGTTTTTTCTATATTC
6192247 TTTA
1 TTTA
6192251 TACTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTAAGTTTTTTCTATATTC
Found at i:6192236 original size:7 final size:7
Alignment explanation
Indices: 6192184--6192216 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
6192174 GGGGTTTAGG
*
6192184 GGTTTAG
1 GGTTTAA
6192191 GGTTTAA
1 GGTTTAA
6192198 GGTTTAA
1 GGTTTAA
6192205 GGTTTAA
1 GGTTTAA
6192212 GGTTT
1 GGTTT
6192217 TTTTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
GGTTTAA
Found at i:6195450 original size:5 final size:5
Alignment explanation
Indices: 6195440--6195470 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
6195430 TGAGCATTCG
*
6195440 ATCGA ATCGA ATCGA ATCGG ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
6195471 AATTTTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:6197900 original size:25 final size:25
Alignment explanation
Indices: 6197872--6197926 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
6197862 AACTGTCATT
* *
6197872 GATAGTATATCCTGAAACTGCTATA
1 GATAGTATATACTGAAACTACTATA
* *
6197897 GATAGTATATACTGAGACTATTATA
1 GATAGTATATACTGAAACTACTATA
6197922 GATAG
1 GATAG
6197927 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (25 bp):
GATAGTATATACTGAAACTACTATA
Found at i:6207827 original size:22 final size:22
Alignment explanation
Indices: 6207784--6207849 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
6207774 TGCTAGTAAT
* *
6207784 CAGAATGGCTA-AGAGCCGTAAA
1 CAGAATAGCTACA-AGCCATAAA
* * *
6207806 CAGGATAGCTATAAGCTATAAA
1 CAGAATAGCTACAAGCCATAAA
*
6207828 CAGAATGGCTACAAGCCATAAA
1 CAGAATAGCTACAAGCCATAAA
6207850 TATAGCAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (22 bp):
CAGAATAGCTACAAGCCATAAA
Found at i:6207895 original size:32 final size:32
Alignment explanation
Indices: 6207857--6207978 Score: 149
Period size: 32 Copynumber: 3.8 Consensus size: 32
6207847 AAATATAGCA
* * *
6207857 ATATGATTGGCCCAAAGCCATCAGTAGCAGTG
1 ATATGATCGGCACAAAGCCATCAGTAACAGTG
* *
6207889 ATATGATCGGCACACAGCCATCAGTAAC-GATA
1 ATATGATCGGCACAAAGCCATCAGTAACAG-TG
6207921 ATATGATCGG-ATCAAAGCCATCAGTAACAGTG
1 ATATGATCGGCA-CAAAGCCATCAGTAACAGTG
* *
6207953 ATATGATCGGTACACAGCCATCAGTA
1 ATATGATCGGCACAAAGCCATCAGTA
6207979 GTATCGCAGC
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
31 2 0.03
32 74 0.95
33 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (32 bp):
ATATGATCGGCACAAAGCCATCAGTAACAGTG
Found at i:6208215 original size:24 final size:24
Alignment explanation
Indices: 6208149--6208235 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 24
6208139 GCCATGCTCA
** * *
6208149 AAATCAGTCATACAATTCACAGAAA
1 AAATCAGTCATTTAAATCACAG-AC
6208174 AAAT-AGTCATTTAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
** **
6208197 AAATCAGTCATTTTCATCATGGAC
1 AAATCAGTCATTTAAATCACAGAC
*
6208221 AAATCAATCATTTAA
1 AAATCAGTCATTTAA
6208236 CCTCAAGGGG
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
23 5 0.10
24 41 0.82
25 4 0.08
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (24 bp):
AAATCAGTCATTTAAATCACAGAC
Found at i:6210439 original size:16 final size:17
Alignment explanation
Indices: 6210418--6210451 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6210408 TCACATTGAA
6210418 ATGTTTT-TTAAAAACC
1 ATGTTTTATTAAAAACC
6210434 ATGTTTTCATTAAAAACC
1 ATGTTTT-ATTAAAAACC
6210452 CTTCTTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (17 bp):
ATGTTTTATTAAAAACC
Found at i:6211216 original size:22 final size:21
Alignment explanation
Indices: 6211153--6211221 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
6211143 CAGCAAAGCT
*
6211153 GCTAGTAATCAGAATGGCTAAGA
1 GCTA-TAAACAGAATGGCTAA-A
** * *
6211176 GCCGTAAACAGGATAGCTATAA
1 GCTATAAACAGAATGGCTA-AA
6211198 GCTATAAACAGAATGGCTACAA
1 GCTATAAACAGAATGGCTA-AA
6211220 GC
1 GC
6211222 CATACATATA
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
22 32 0.91
23 3 0.09
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (21 bp):
GCTATAAACAGAATGGCTAAA
Found at i:6211273 original size:32 final size:32
Alignment explanation
Indices: 6211247--6211356 Score: 159
Period size: 32 Copynumber: 3.4 Consensus size: 32
6211237 ATGATTGGCC
*
6211247 CAAAGCCATCAGTAGCAGTGATATGATCGGTA
1 CAAAGCCATCAGTAACAGTGATATGATCGGTA
* * *
6211279 CACAGCCATCAGTAACAATAATATGATCGG-A
1 CAAAGCCATCAGTAACAGTGATATGATCGGTA
6211310 TCAAAGCCATCAGTAACAGTGATATGATCGGTA
1 -CAAAGCCATCAGTAACAGTGATATGATCGGTA
*
6211343 CACAGCCATCAGTA
1 CAAAGCCATCAGTA
6211357 GTATCACAGC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
31 1 0.01
32 66 0.97
33 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (32 bp):
CAAAGCCATCAGTAACAGTGATATGATCGGTA
Found at i:6211570 original size:24 final size:24
Alignment explanation
Indices: 6211525--6211613 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
6211515 ATGTCATGCT
** *
6211525 CAAAATTAGTCATACAATTCACAGA
1 CAAAA-TAGTCATTTAAATCACAGA
6211550 CAAAATAGTCATTTAAATCACAGA
1 CAAAATAGTCATTTAAATCACAGA
* ** *
6211574 -TAAATCAGTCATTTTCATCACGGA
1 CAAAAT-AGTCATTTAAATCACAGA
* *
6211598 CAAATTAATCATTTAA
1 CAAAATAGTCATTTAA
6211614 CCTCGAGGGG
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
23 4 0.08
24 38 0.76
25 8 0.16
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (24 bp):
CAAAATAGTCATTTAAATCACAGA
Found at i:6211730 original size:27 final size:27
Alignment explanation
Indices: 6211687--6211748 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
6211677 TATTTTGGTT
6211687 ATTTTACCCTAAGAGGGT-ATCTC-GATC
1 ATTTTACCCTAAGAGGGTAAT-TCAG-TC
*
6211714 ATTTTACCCTTCA-AGGGTAATTCAGTC
1 ATTTTACCC-TAAGAGGGTAATTCAGTC
6211741 ATTTTACC
1 ATTTTACC
6211749 ACGTATCGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (27 bp):
ATTTTACCCTAAGAGGGTAATTCAGTC
Found at i:6215461 original size:15 final size:16
Alignment explanation
Indices: 6215426--6215467 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
6215416 TAATTGATTT
* *
6215426 AATAAAATAACAGGTA
1 AATAAAATAAAAGGGA
6215442 AATAAAA-AAAAGGGA
1 AATAAAATAAAAGGGA
6215457 AATAATAATAA
1 AATAA-AATAA
6215468 TAATGATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 9 0.41
17 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (16 bp):
AATAAAATAAAAGGGA
Found at i:6218777 original size:7 final size:6
Alignment explanation
Indices: 6218761--6218816 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
6218751 TGTTTCCTGC
* *
6218761 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
6218811 AGAAAA
1 A-AAAA
6218817 ATTAAAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
5 5 0.12
6 22 0.52
7 10 0.24
8 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:6222256 original size:12 final size:12
Alignment explanation
Indices: 6222235--6222359 Score: 54
Period size: 12 Copynumber: 9.8 Consensus size: 12
6222225 AAAAACGAAA
*
6222235 TGATTAAAAACT
1 TGATGAAAAACT
* *
6222247 TGATGGAAAATT
1 TGATGAAAAACT
*
6222259 TTATGAAAAGACT
1 TGATGAAAA-ACT
*
6222272 TGATAAAAAACT
1 TGATGAAAAACT
**
6222284 AT-AAAAAAAACT
1 -TGATGAAAAACT
* *
6222296 TGCTGCAAAACT
1 TGATGAAAAACT
*
6222308 TGATTAAAAAAACT
1 TGA-T-GAAAAACT
*
6222322 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
6222337 TGATAAAAGAACT
1 TGATGAAA-AACT
*
6222350 AGATGAAAAA
1 TGATGAAAAA
6222360 TACTTGAAGA
Statistics
Matches: 84, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
11 1 0.01
12 43 0.51
13 21 0.25
14 8 0.10
15 9 0.11
16 1 0.01
17 1 0.01
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:6222319 original size:14 final size:14
Alignment explanation
Indices: 6222302--6222366 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
6222292 AACTTGCTGC
6222302 AAAACTTGATTAAA
1 AAAACTTGATTAAA
*
6222316 AAAACTTG-GTAATTA
1 AAAACTTGATTAA--A
6222331 AAAACTTGA-TAAA
1 AAAACTTGATTAAA
* * *
6222344 AGAACTAGATGAAA
1 AAAACTTGATTAAA
*
6222358 AATACTTGA
1 AAAACTTGA
6222367 AGAAAGAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
13 11 0.28
14 17 0.43
15 12 0.30
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.26
Consensus pattern (14 bp):
AAAACTTGATTAAA
Found at i:6223233 original size:26 final size:26
Alignment explanation
Indices: 6223180--6223234 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
6223170 TAATGTAATG
*
6223180 ATTTTCATTATGATTTAATATAATAT
1 ATTTTCATTATGAGTTAATATAATAT
* *
6223206 ATTTTCATATATTAGTTAATTTAAATAT
1 ATTTTCAT-TATGAGTTAATAT-AATAT
6223234 A
1 A
6223235 ATATAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTTCATTATGAGTTAATATAATAT
Found at i:6223892 original size:40 final size:41
Alignment explanation
Indices: 6223820--6223901 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 41
6223810 ATAAACATTA
* *
6223820 AAAATTATTTTAAAAATAAAAAAATAAAAAAATTTAT-TTT
1 AAAAGTATTTTAAAAATAAAAAAATAAAAAAATATATATTT
* * *
6223860 AAAAGTATTTTAAAATTTAAAATAA-AATAAAATATATATTT
1 AAAAGTATTTTAAAA-ATAAAAAAATAAAAAAATATATATTT
6223901 A
1 A
6223902 TTATATTCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 24 0.69
41 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (41 bp):
AAAAGTATTTTAAAAATAAAAAAATAAAAAAATATATATTT
Found at i:6240168 original size:42 final size:42
Alignment explanation
Indices: 6240105--6240433 Score: 118
Period size: 44 Copynumber: 7.6 Consensus size: 42
6240095 TTACCTCCTG
* *
6240105 TGGTTACAGTGGAGTACATTGAAGCCGTA-ATTCTATCTCCC
1 TGGTTGCAGTGGAGTAGATTGAAGCCGTAGATTCTATCTCCC
* ***
6240146 TGGTTGGCAGTGGAATAGATTGAAGATTTCAGA-TCTTATCTCCC
1 TGGTT-GCAGTGGAGTAGATTGAAGCCGT-AGATTC-TATCTCCC
* * ** * * *
6240190 TAGGCATT--AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCC
1 T-GG--TTGCAGTGGAGTAGATTGAAG-CCGTAGATTCTATCTCCC
* *
6240234 TGTGGTTACAGTGGAGTACATTGAAGCCGTA-ATTCTATCTCCC
1 --TGGTTGCAGTGGAGTAGATTGAAGCCGTAGATTCTATCTCCC
* * *** *
6240277 TGGTTGGCATTGGAATAGATTGAAGATTTCAGA-TCTTATCTCCT
1 TGGTT-GCAGTGGAGTAGATTGAAGCCGT-AGATTC-TATCTCCC
* ** ** * * *
6240321 TAGGCATT--AGTAGAGTAGATCAAAGATGGCAGATTTTACCTCCCC
1 T-GG--TTGCAGTGGAGTAGATTGAAG-CCGTAGATTCTATCT-CCC
* * *
6240366 GAGGTTACAGTGGAGTACATTGAAGCCAGTA-ATTCTATCTCCC
1 -TGGTTGCAGTGGAGTAGATTGAAGCC-GTAGATTCTATCTCCC
*
6240409 TGGTTGGCAGTGGAATAGATTGAAG
1 TGGTT-GCAGTGGAGTAGATTGAAG
6240434 ATTTCAGATC
Statistics
Matches: 203, Mismatches: 57, Indels: 54
0.65 0.18 0.17
Matches are distributed among these distances:
41 10 0.05
42 37 0.18
43 39 0.19
44 71 0.35
45 41 0.20
46 1 0.00
47 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
TGGTTGCAGTGGAGTAGATTGAAGCCGTAGATTCTATCTCCC
Found at i:6240202 original size:44 final size:43
Alignment explanation
Indices: 6240138--6240654 Score: 167
Period size: 44 Copynumber: 11.7 Consensus size: 43
6240128 GCCGTAATTC
* *
6240138 TATCTCCCTGG-TTGGCAGTGGAATAGATTGAAGATTTCAGATCT
1 TATCTCCCTGGATT--CAGTGGAGTAGATTGAAGATGTCAGATCT
* * * *
6240182 TATCTCCCTAGGCATT-AGTGGAGCAGATCGAAGATGGCAGATTT
1 TATCTCCCT-GG-ATTCAGTGGAGTAGATTGAAGATGTCAGATCT
* * * **
6240226 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCGT-A-AT-T
1 TATCTCCCTG-GATT-CAGTGGAGTAGATTGAAGATGTCAGATCT
* * *
6240268 CTATCTCCCTGG-TTGGCATTGGAATAGATTGAAGATTTCAGATCT
1 -TATCTCCCTGGATT--CAGTGGAGTAGATTGAAGATGTCAGATCT
* * ** * *
6240313 TATCTCCTTAGGCATT-AGTAGAGTAGATCAAAGATGGCAGATTT
1 TATCTCCCT-GG-ATTCAGTGGAGTAGATTGAAGATGTCAGATCT
* * * *
6240357 TACCTCCCCGAGGTTACAGTGGAGTACATTGAAGCCA-GT-A-AT-T
1 TATCTCCCTG-GATT-CAGTGGAGTAGATTGAAG--ATGTCAGATCT
* *
6240400 CTATCTCCCTGG-TTGGCAGTGGAATAGATTGAAGATTTCAGATCT
1 -TATCTCCCTGGATT--CAGTGGAGTAGATTGAAGATGTCAGATCT
* * * * * *
6240445 TATCTCCTTAAGCG-GT-AGTGGAGCAGATCGAAGATGGC-GAATTT
1 TATCTCCCT--G-GATTCAGTGGAGTAGATTGAAGATGTCAG-ATCT
* * *
6240489 TACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCA-GT-A-AT-T
1 TATCTCCCT-GGATT-CAGTGGAGTAGATTGAAG--ATGTCAGATCT
* * *
6240532 CTATCCCCCTGG-TTGGCAGTGGAATAGATTGAAGATTTCAGATCT
1 -TATCTCCCTGGATT--CAGTGGAGTAGATTGAAGATGTCAGATCT
* * * * * *
6240577 TATTTCCCTAAGCATT-AGTGGAGCAGATCGAAGATGGCAGATTT
1 TATCTCCCT--GGATTCAGTGGAGTAGATTGAAGATGTCAGATCT
* * *
6240621 TACCTCCCTGGGGTTACAGTGGAGTACATTGAAG
1 TATCTCCCT-GGATT-CAGTGGAGTAGATTGAAG
6240655 CCAGTAATTC
Statistics
Matches: 342, Mismatches: 85, Indels: 91
0.66 0.16 0.18
Matches are distributed among these distances:
41 4 0.01
42 25 0.07
43 63 0.18
44 172 0.50
45 64 0.19
46 4 0.01
47 10 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
TATCTCCCTGGATTCAGTGGAGTAGATTGAAGATGTCAGATCT
Found at i:6240473 original size:132 final size:132
Alignment explanation
Indices: 6240073--6240732 Score: 1042
Period size: 132 Copynumber: 5.0 Consensus size: 132
6240063 NNNNNNNNNN
* *
6240073 GAGCAGATCGAAG-TAGCAGATTTTACCT-CCTGTGGTTACAGTGGAGTACATTGAAGCC-GTAA
1 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTAA
*
6240135 TTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAGGCATTAG
66 TTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCATTAG
6240200 TG
131 TG
*
6240202 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC-GTAA
1 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
6240266 TTCTATCTCCCTGGTTGGCATTGGAATAGATTGAAGATTTCAGATCTTATCTCCTTAGGCATTAG
66 TTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCATTAG
*
6240331 TA
131 TG
* * * *
6240333 GAGTAGATCAAAGATGGCAGATTTTACCTCCCCGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTAA
* **
6240398 TTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCTTAAGCGGTAG
66 TTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCATTAG
6240463 TG
131 TG
6240465 GAGCAGATCGAAGATGGC-GAATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GAGCAGATCGAAGATGGCAG-ATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTA
* *
6240529 ATTCTATCCCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATTTCCCTAAGCATTA
65 ATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCATTA
6240594 GTG
130 GTG
6240597 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * * * * ** *
6240662 TTCTATCTCCTTGGTCGACAGTGGAATCGATCGAAGAATAGCAGATCTTATCTCCCTAAGCAGTA
66 TTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAG-ATTTCAGATCTTATCTCCCTAAGCATTA
6240727 GTG
130 GTG
6240730 GAG
1 GAG
6240733 TAGACTGATG
Statistics
Matches: 493, Mismatches: 32, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
129 13 0.03
130 14 0.03
131 155 0.31
132 280 0.57
133 31 0.06
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (132 bp):
GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTAA
TTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCATTAG
TG
Found at i:6241677 original size:19 final size:19
Alignment explanation
Indices: 6241653--6241710 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
6241643 TTTATTACTA
6241653 TATTATTATTAGCATT-TAT
1 TATTATTATTA-CATTATAT
* *
6241672 TATTATTGTTATATTATAT
1 TATTATTATTACATTATAT
6241691 TATTATTA-TACA-TATAT
1 TATTATTATTACATTATAT
6241708 TAT
1 TAT
6241711 ATGCGCATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 20 0.59
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TATTATTATTACATTATAT
Found at i:6259753 original size:50 final size:50
Alignment explanation
Indices: 6259620--6260464 Score: 497
Period size: 50 Copynumber: 16.9 Consensus size: 50
6259610 ATACCATAGT
** *
6259620 TTGCAATTTAAAAGATT-AAGACCACAACGGCGAATCTTACCTTCTTAGGCGA
1 TTGCAATTTAAAAGATTGAAG-CCACAACGGCGAATCTTA-CTTCCCAGAC-A
**** * * *
6259672 -TGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTACTTCACC-GACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTC-CCAGACA
* *
6259721 TTGCAATTTAAAAGATTGAGGCCACAACGGCGAATCTTACCTTTCCA-AGCGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTA-CTTCCCAGA-C-A
**** * * ** *
6259773 -TGCAGCCGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* * *
6259822 TTACAATTTAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGGCGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGAC-A
**** * * * *
6259873 -TGCAGCAGAATAGATTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* * *
6259922 TTGCAATTTAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* *** * * * * * ** *
6259972 GTGCAACGGAACAGATTGAAGCTACGATGGTGAATCACACTTCCCCGACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
*
6260022 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGAC-A
*** * * * * * **
6260073 -TGCAACAGAACAA-ATTGAAGCTACGATGGTGAATCTCACTTCCCCTACA
1 TTGCAATTTAA-AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* * *
6260122 TTGCAATTTAAAAGATTAAAGCCACAATGGCGAATCTTACTTCCCAGGCA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* * **** * * * * * * *
6260172 ATGTAGCGGAACAGATTGAAGCTACAATGGTGAATATTGCTTCCCTGACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* * * * *
6260222 TTGCAATTTAAAAGATTGAGGCCACAACGGTGGATCTTACTTCCTAGGCGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGAC-A
**** * * * * *
6260273 -TGCAGCGGAACAA-ATTGAAGCTACGACGGCGAATCTCATTTCCCTGACA
1 TTGCAATTTAA-AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* * * * * * *
6260322 TTGCAATTAAAAAGATTGAAGCTACAATGGTGAATCTTACTTTCCAGGCG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* *** * * ** *
6260372 GTGCAACGGAACAGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
* *** * **
6260422 TTAC-GGCTAAATAGATTGAAGCTACAACAACGAATCTTACTTC
1 TTGCAATTTAAA-AGATTGAAGCCACAACGGCGAATCTTACTTC
6260465 TCTGGCGGTG
Statistics
Matches: 578, Mismatches: 195, Indels: 42
0.71 0.24 0.05
Matches are distributed among these distances:
49 11 0.02
50 495 0.86
51 68 0.12
52 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGACA
Found at i:6260474 original size:100 final size:100
Alignment explanation
Indices: 6259620--6260464 Score: 1064
Period size: 100 Copynumber: 8.4 Consensus size: 100
6259610 ATACCATAGT
**
6259620 TTGCAATTTAAAAGATT-AAGACCACAACGGCGAATCTTACCTTCTTAGGCGATGCAGCGGAACA
1 TTGCAATTTAAAAGATTGAAG-CCACAACGGCGAATCTTA-CTTCCCAGGCGATGCAGCGGAACA
* * *
6259684 GATTGAAGCTACGACGGCGAATCTTACTTCACCGACA
64 GATTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * *
6259721 TTGCAATTTAAAAGATTGAGGCCACAACGGCGAATCTTACCTTTCCAAGCGATGCAGCCGAACAG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTA-CTTCCCAGGCGATGCAGCGGAACAG
*
6259786 ATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * *
6259822 TTACAATTTAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCAGAATAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
*
6259887 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * *
6259922 TTGCAATTTAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGGTGCAACGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * *
6259987 TTGAAGCTACGATGGTGAATCACACTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * *
6260022 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAACAGAACAAA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * *
6260087 TTGAAGCTACGATGGTGAATCTCACTTCCCCTACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * *
6260122 TTGCAATTTAAAAGATTAAAGCCACAATGGCGAATCTTACTTCCCAGGCAATGTAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * ** *
6260187 TTGAAGCTACAATGGTGAATATTGCTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * * *
6260222 TTGCAATTTAAAAGATTGAGGCCACAACGGTGGATCTTACTTCCTAGGCGATGCAGCGGAACAAA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * *
6260287 TTGAAGCTACGACGGCGAATCTCATTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * * * * *
6260322 TTGCAATTAAAAAGATTGAAGCTACAATGGTGAATCTTACTTTCCAGGCGGTGCAACGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
***
6260387 TTGAAGCTACAACGGCGAATCTTGTTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* *** * **
6260422 TTAC-GGCTAAATAGATTGAAGCTACAACAACGAATCTTACTTC
1 TTGCAATTTAAA-AGATTGAAGCCACAACGGCGAATCTTACTTC
6260465 TCTGGCGGTG
Statistics
Matches: 652, Mismatches: 90, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
99 3 0.00
100 523 0.80
101 124 0.19
102 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
Found at i:6260705 original size:41 final size:41
Alignment explanation
Indices: 6260629--6260706 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
6260619 CCTGGTTGGT
* ** *
6260629 AGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAATC
1 AGTGGAATAGATCGAAGATGGCAAATCTTACCTCCCTAATC
* *
6260670 AGTGGAATAGATCGAAGATGGCAGATTTTACCTCCCT
1 AGTGGAATAGATCGAAGATGGCAAATCTTACCTCCCT
6260707 GTGACTACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (41 bp):
AGTGGAATAGATCGAAGATGGCAAATCTTACCTCCCTAATC
Found at i:6261516 original size:28 final size:28
Alignment explanation
Indices: 6261476--6261531 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
6261466 AGCCGAAGCA
*
6261476 AATGTAATAGGAGGGGGTTTTTTTCTTT
1 AATGTAATAGGAGGGGGGTTTTTTCTTT
6261504 AATGTAATAGGAGGGGGGTTTTTTCTTT
1 AATGTAATAGGAGGGGGGTTTTTTCTTT
6261532 CTTTCCTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (28 bp):
AATGTAATAGGAGGGGGGTTTTTTCTTT
Found at i:6261720 original size:17 final size:17
Alignment explanation
Indices: 6261697--6261730 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
6261687 GATTTGTAAT
6261697 AATATATAT-AT-TATA
1 AATATATATAATATATA
6261712 AATATATATAATATATA
1 AATATATATAATATATA
6261729 AA
1 AA
6261731 AAAGGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 2 0.12
17 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATATATAATATATA
Found at i:6262528 original size:18 final size:17
Alignment explanation
Indices: 6262507--6262553 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
6262497 CTATTATAAC
6262507 TATTTATATATACCATCT
1 TATTTATATATA-CATCT
* *
6262525 TATTATATATTTATATCT
1 TATT-TATATATACATCT
6262543 TA-TTATATATA
1 TATTTATATATA
6262554 TCTATATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 7 0.28
17 1 0.04
18 10 0.40
19 7 0.28
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTATATATACATCT
Found at i:6271182 original size:18 final size:18
Alignment explanation
Indices: 6271159--6271200 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
6271149 ACAATGTTTT
*
6271159 TAAAAAGTACTTTTGAGA
1 TAAAAAGCACTTTTGAGA
*
6271177 TAAAAAGCGCTTTTGAGA
1 TAAAAAGCACTTTTGAGA
6271195 TAAAAA
1 TAAAAA
6271201 CATTCTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (18 bp):
TAAAAAGCACTTTTGAGA
Found at i:6279835 original size:38 final size:38
Alignment explanation
Indices: 6279758--6279836 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
6279748 TGATATAAGC
* * *
6279758 AATAAATCCTAAATTCAAAGCTTAAACTCGAAACTTGA
1 AATAAATCCTAAATTCAAACCATAAACTCGAAACCTGA
* * *
6279796 AATAAA-CCTAAATTCTATACCATAAACTCTACACCTGA
1 AATAAATCCTAAATTC-AAACCATAAACTCGAAACCTGA
6279834 AAT
1 AAT
6279837 GCAAAACTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 9 0.26
38 25 0.74
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.27
Consensus pattern (38 bp):
AATAAATCCTAAATTCAAACCATAAACTCGAAACCTGA
Found at i:6284361 original size:19 final size:19
Alignment explanation
Indices: 6284326--6284368 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
6284316 CAGAGGTAAT
*
6284326 CTTTTAAAATTTCTTTC-A
1 CTTTTAAAATTTATTTCTA
*
6284344 CTTTCTAAATTTTATTTCTA
1 CTTT-TAAAATTTATTTCTA
6284364 CTTTT
1 CTTTT
6284369 GTTGGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 12 0.57
20 5 0.24
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.60
Consensus pattern (19 bp):
CTTTTAAAATTTATTTCTA
Found at i:6292182 original size:105 final size:105
Alignment explanation
Indices: 6292024--6292376 Score: 458
Period size: 105 Copynumber: 3.4 Consensus size: 105
6292014 CTAGTGCTAG
* * * *
6292024 ATAGGTTGCGATCTTAAATTAGTTAACAC-TTATAAAATCAACTGTGAAAGTAGGTTATCGAGCT
1 ATAGGTTGCAATCTTAAATCAGCTAAC-CTTTATAAAATCAACTGTGAAAGTAGGTCATCGAGCT
* *
6292088 GTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGATGA
65 ATTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGATGA
* * * * * *
6292129 ATAGGTTGCAATATTAAATTAGTTAACCTTTATATAATCAACTATGAATGTAGGTCATCGAGCTA
1 ATAGGTTGCAATCTTAAATCAGCTAACCTTTATAAAATCAACTGTGAAAGTAGGTCATCGAGCTA
* * * * * * *
6292194 TTTAGAAGTTACAATTTTAAATCAGCTAAATAAAAAATGA
66 TTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGATGA
* * *
6292234 ATAGGTTGCAACCTTAAATCAGCTAACCTTTATAAAATCAATTGTGAACA-TAGGTCATTGAGCT
1 ATAGGTTGCAATCTTAAATCAGCTAACCTTTATAAAATCAACTGTGAA-AGTAGGTCATCGAGCT
*
6292298 ATTTAGGAGTTGCGATATTAAATCAACTAACTCAAAGATGA
65 ATTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGATGA
*
6292339 ATAGATTGCAATCTTAAATCAGCTAACCTTTATAAAAT
1 ATAGGTTGCAATCTTAAATCAGCTAACCTTTATAAAAT
6292377 TAGGATCTGT
Statistics
Matches: 213, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
104 1 0.00
105 212 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (105 bp):
ATAGGTTGCAATCTTAAATCAGCTAACCTTTATAAAATCAACTGTGAAAGTAGGTCATCGAGCTA
TTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGATGA
Found at i:6297222 original size:50 final size:50
Alignment explanation
Indices: 6297106--6297298 Score: 278
Period size: 50 Copynumber: 3.8 Consensus size: 50
6297096 GATAATAACA
* ** * *
6297106 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
6297157 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
6297207 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCACTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
6297257 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
6297299 TTACCCAAAT
Statistics
Matches: 126, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 93 0.74
51 33 0.26
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:6298131 original size:13 final size:13
Alignment explanation
Indices: 6298113--6298138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6298103 TGATCAAAAA
6298113 TTGGCTTTTAATT
1 TTGGCTTTTAATT
6298126 TTGGCTTTTAATT
1 TTGGCTTTTAATT
6298139 CATTTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TTGGCTTTTAATT
Found at i:6304926 original size:50 final size:50
Alignment explanation
Indices: 6304633--6304925 Score: 417
Period size: 50 Copynumber: 5.8 Consensus size: 50
6304623 GATAATAACA
* * ** *
6304633 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
6304684 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGTACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGG-ACCTCTCATCTCGG
*
6304734 TGCCAACGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
6304784 TGCCAACGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
6304834 TGCCAACACCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
6304884 TGCCAATGCCATGTCCCAGACATAGTCTTACAGGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
6304926 TTACCCAAAT
Statistics
Matches: 220, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
50 186 0.85
51 34 0.15
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:6305043 original size:13 final size:13
Alignment explanation
Indices: 6305025--6305051 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6305015 AGTCAACATT
6305025 AAATAAATTCATA
1 AAATAAATTCATA
6305038 AAATAAATTCATA
1 AAATAAATTCATA
6305051 A
1 A
6305052 TTTCTGGAAA
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:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTCATA
Found at i:6312221 original size:33 final size:32
Alignment explanation
Indices: 6312148--6312225 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
6312138 ATATATATAT
** * **
6312148 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
1 ATGTAAGACCATAACTGGGCTATGGCATACAA
*
6312180 ATGATAAGACCATAACTGGGTTATGGCACTACAA
1 ATG-TAAGACCATAACTGGGCTATGGCA-TACAA
6312214 ATGTAAGACCAT
1 ATGTAAGACCAT
6312226 GCAAGGTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 30 0.79
34 5 0.13
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGGCATACAA
Found at i:6322189 original size:27 final size:27
Alignment explanation
Indices: 6322167--6322569 Score: 386
Period size: 27 Copynumber: 15.0 Consensus size: 27
6322157 AAGGGTATAA
6322167 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
6322194 TAGTCATTTTACCCTATGGGGTTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
6322221 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
6322248 CGGTTC-TTTTACCCTATGAGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * * *
6322275 -TGATCATTTTACTCTATTGAGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* *
6322302 CAGTCATTCTACCCTATTGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
6322329 C-GATCATTCTACCCCAT-GGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * *
6322355 TAGTCATTTTACCCTATGAGGGTTTTT
1 CAGTCATTTTACCCTATGGGGGTATTT
** *
6322382 TGGTAATTTTACCCTAT-GGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
6322408 CGGTCATTCTACCTTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * * *
6322435 CGGTTATTTTACCTTATTGAGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
** * * *
6322462 TGGTTATTTTACCTTATTGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
6322489 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
6322516 TAGTTATTTTACCCTA-CGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
6322542 CGGTTATTTTATCCTATGGCGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
6322569 C
1 C
6322570 GGTCGCCTCG
Statistics
Matches: 319, Mismatches: 49, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
26 67 0.21
27 249 0.78
28 3 0.01
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:6326551 original size:32 final size:32
Alignment explanation
Indices: 6326515--6326581 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
6326505 TCCCCTTTGC
* *
6326515 TATAGCATTTCCAGTTATTTACTAATTCCATA
1 TATAGCATTTCAAATTATTTACTAATTCCATA
6326547 TATAGCATTTCAAATTATTTACTAATTCCATA
1 TATAGCATTTCAAATTATTTACTAATTCCATA
6326579 TAT
1 TAT
6326582 TACTCATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.45
Consensus pattern (32 bp):
TATAGCATTTCAAATTATTTACTAATTCCATA
Found at i:6328108 original size:43 final size:43
Alignment explanation
Indices: 6327950--6328108 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 43
6327940 AATGTGTTAT
* *
6327950 CGTGTAAGACCACGTCTGGGACGTTGGCATTGAT-TTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGA-TTA
* * * * * * *
6327994 CGTGTAAGAACATGTCTGGGACATTGCCGTCG-TATATGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
* * *
6328036 CGTGTCAGACC-CTATCTGGGACAG-AGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTA
*
6328079 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
6328109 TGTACGAGTT
Statistics
Matches: 86, Mismatches: 23, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
42 25 0.29
43 33 0.38
44 28 0.33
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:6330286 original size:12 final size:13
Alignment explanation
Indices: 6330269--6330297 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6330259 TATTTTTTAA
6330269 TTTTAAAAT-AAT
1 TTTTAAAATAAAT
6330281 TTTTAAAATAAAT
1 TTTTAAAATAAAT
6330294 TTTT
1 TTTT
6330298 TTATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTAAAATAAAT
Found at i:6332387 original size:28 final size:28
Alignment explanation
Indices: 6332355--6332412 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6332345 GCGTTCATAG
6332355 ATGATATCTTGATTTATCCCAATGATGA
1 ATGATATCTTGATTTATCCCAATGATGA
6332383 ATGATATCTTGATTTATCCCAATGATGA
1 ATGATATCTTGATTTATCCCAATGATGA
6332411 AT
1 AT
6332413 CAGAGTATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (28 bp):
ATGATATCTTGATTTATCCCAATGATGA
Found at i:6333218 original size:17 final size:17
Alignment explanation
Indices: 6333196--6333238 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
6333186 AAAGTATATT
6333196 AGCTCACGAGATTAAAG
1 AGCTCACGAGATTAAAG
6333213 AGCTCACGAGATTAAAG
1 AGCTCACGAGATTAAAG
6333230 AGCTCACGA
1 AGCTCACGA
6333239 CGATACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (17 bp):
AGCTCACGAGATTAAAG
Found at i:6339479 original size:16 final size:17
Alignment explanation
Indices: 6339458--6339490 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6339448 GAAAATTTAA
*
6339458 AATTTTT-TTCAAAAGT
1 AATTTTTCTCCAAAAGT
6339474 AATTTTTCTCCAAAAGT
1 AATTTTTCTCCAAAAGT
6339491 GCTTATTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (17 bp):
AATTTTTCTCCAAAAGT
Found at i:6341118 original size:13 final size:14
Alignment explanation
Indices: 6341100--6341148 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
6341090 AACGACATAG
6341100 AAATAATATAAAC-
1 AAATAATATAAACA
6341113 AAATAA-ATAAACA
1 AAATAATATAAACA
*
6341126 AAATGAATATAAAAA
1 AAAT-AATATAAACA
6341141 ACAATAAT
1 A-AATAAT
6341149 CCATGACATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 6 0.19
13 10 0.32
14 2 0.06
15 10 0.32
16 3 0.10
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (14 bp):
AAATAATATAAACA
Found at i:6343320 original size:16 final size:16
Alignment explanation
Indices: 6343287--6343320 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6343277 CTTTAAAGTA
**
6343287 TTTTTAAAATACTTTT
1 TTTTTAAAATACAATT
6343303 TTTTTAAAATACAATT
1 TTTTTAAAATACAATT
6343319 TT
1 TT
6343321 GGTGTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAAAATACAATT
Found at i:6353912 original size:13 final size:13
Alignment explanation
Indices: 6353867--6353912 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
6353857 AAGAATTTAT
*
6353867 TAATTAT-ATATT
1 TAATTATAATATA
6353879 TAATTATAATATA
1 TAATTATAATATA
6353892 TTAA-TATAATATA
1 -TAATTATAATATA
6353905 TAATTATA
1 TAATTATA
6353913 TTTATATTTN
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.33
13 17 0.57
14 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTATAATATA
Found at i:6354436 original size:16 final size:16
Alignment explanation
Indices: 6354394--6354447 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
6354384 TTGATTTGCT
* *
6354394 ATTACATCTCTAATCC
1 ATTACACCTCTATTCC
6354410 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
**
6354426 ATTACGGCTCTATTCC
1 ATTACACCTCTATTCC
*
6354442 AATACA
1 ATTACA
6354448 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.30, C:0.31, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:6360188 original size:28 final size:29
Alignment explanation
Indices: 6360136--6360192 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
6360126 CCTTTTGAGG
6360136 AAATTAATTCTAAAAAGAAAAAAAACAAA
1 AAATTAATTCTAAAAAGAAAAAAAACAAA
6360165 AAATTAATTCTAAAAAG-AAAAAAACAAA
1 AAATTAATTCTAAAAAGAAAAAAAACAAA
6360193 GGAAACTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.72, C:0.07, G:0.04, T:0.18
Consensus pattern (29 bp):
AAATTAATTCTAAAAAGAAAAAAAACAAA
Found at i:6361204 original size:28 final size:27
Alignment explanation
Indices: 6361162--6361226 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
6361152 CAAAACTTTA
*
6361162 AAAAAATAAATTTATTTGA-TTCAAAAT
1 AAAAAATAAATTTATTT-ACTTAAAAAT
*
6361189 AAAAAATGAATCTTATTTACTTAAAAAT
1 AAAAAATAAAT-TTATTTACTTAAAAAT
6361217 AAAAAATAAA
1 AAAAAATAAA
6361227 ATAATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAAAATAAATTTATTTACTTAAAAAT
Found at i:6364185 original size:16 final size:16
Alignment explanation
Indices: 6364164--6364215 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
6364154 TTTGGTTCGC
6364164 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
6364180 TGTATTGGATTAGGGG
1 TGTATTGGATTAGAGG
6364196 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6364212 TGTA
1 TGTA
6364216 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6364472 original size:18 final size:17
Alignment explanation
Indices: 6364451--6364485 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6364441 TTATTATTAA
*
6364451 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6364469 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6364486 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6364622 original size:156 final size:157
Alignment explanation
Indices: 6364338--6364653 Score: 562
Period size: 156 Copynumber: 2.0 Consensus size: 157
6364328 TAGAATACCC
*
6364338 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * ** *
6364403 TTATCAGTAATAAATTTTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
6364468 TATATAATTTAATAAAATTCTT-ATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
6364494 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
6364559 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
6364624 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
6364651 TTA
1 TTA
6364654 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 145 0.95
157 7 0.05
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:6364624 original size:16 final size:16
Alignment explanation
Indices: 6364587--6364628 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6364577 TTAATCATAT
*
6364587 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
6364603 TT-AAATATATTATAA
1 TTAAAATATATTATAA
6364618 TTAAAATATAT
1 TTAAAATATAT
6364629 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:6364635 original size:14 final size:15
Alignment explanation
Indices: 6364596--6364637 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6364586 TTTAAACATA
*
6364596 ATTATTATTAAATAT
1 ATTATAATTAAATAT
6364611 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
6364625 A-TATAATTTAATA
1 ATTATAATTAAATA
6364638 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:6364687 original size:61 final size:60
Alignment explanation
Indices: 6364622--6364809 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 60
6364612 TTATAATTAA
6364622 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAGATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA-ATCAT
* * * * * * * * * *
6364683 AATATATGATACT-GTAAAA-TATAAATTAACATAATTATTATTAAAT--ATATTA-T-AATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGAAT-TTACTCAATCAT
6364742 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTC-AATCAT
6364803 AATATAT
1 AATATAT
6364810 GATACTGTAA
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
57 9 0.09
58 7 0.07
59 23 0.24
60 9 0.09
61 31 0.33
62 7 0.07
63 9 0.09
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAATCAT
Found at i:6364724 original size:120 final size:120
Alignment explanation
Indices: 6364590--6364829 Score: 455
Period size: 120 Copynumber: 2.0 Consensus size: 120
6364580 ATCATATTTA
6364590 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
6364655 TATTCTTATATGAATTTACTCAGATCATAATATATGATACTGTAAAAT-ATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGT-AAATGATAAATT
6364710 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
6364775 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATGATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATGATAAATT
6364830 TTAGTAAAAG
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
119 4 0.03
120 114 0.97
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATGATAAATT
Found at i:6364755 original size:14 final size:15
Alignment explanation
Indices: 6364706--6364757 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
6364696 GTAAAATATA
6364706 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
6364721 TATTAAATATATTAT
1 AATTAAATATATTAT
6364736 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
6364749 AATTTAATA
1 AATTAAATA
6364758 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:6377239 original size:24 final size:24
Alignment explanation
Indices: 6377195--6377322 Score: 154
Period size: 23 Copynumber: 5.5 Consensus size: 24
6377185 TATTATTAAT
6377195 GGATGAATTGAT-GAAAATGTAAA
1 GGATGAATTGATGGAAAATGTAAA
6377218 GGATGAATTGATGGAAAATGTAAA
1 GGATGAATTGATGGAAAATGTAAA
* * *
6377242 GGAGGAACTAATGGAAAATGTAAA
1 GGATGAATTGATGGAAAATGTAAA
* * * *
6377266 GGAGGAACTGACGG-TAATGTAAA
1 GGATGAATTGATGGAAAATGTAAA
* *
6377289 GGATGAATTGACGG-CAATGTAAA
1 GGATGAATTGATGGAAAATGTAAA
6377312 GGATGAATTGA
1 GGATGAATTGA
6377323 CGACAAATTG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
23 51 0.54
24 44 0.46
ACGTcount: A:0.44, C:0.04, G:0.30, T:0.22
Consensus pattern (24 bp):
GGATGAATTGATGGAAAATGTAAA
Found at i:6379807 original size:19 final size:19
Alignment explanation
Indices: 6379783--6379820 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6379773 GGTATGAATT
6379783 CTTGTCTCGTTTTTAGTAA
1 CTTGTCTCGTTTTTAGTAA
6379802 CTTGTCTCGTTTTTAGTAA
1 CTTGTCTCGTTTTTAGTAA
6379821 TTTTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (19 bp):
CTTGTCTCGTTTTTAGTAA
Found at i:6380739 original size:64 final size:64
Alignment explanation
Indices: 6380612--6380740 Score: 161
Period size: 64 Copynumber: 2.0 Consensus size: 64
6380602 CGAGCATCCC
* * * *
6380612 GATCAGTATTGATCCTGCATGTGTTGCGGACATACCACAGCTCTTTATGAGCATCCTATTATAT
1 GATCAGTATTGATCCTGCATATATTGCGGACATACCACAGCTCTTTATAAGCATCCGATTATAT
* *** *
6380676 GATCGGTATTGATCCTGCATATATTGCGGACATATTGCAGCTCTTTATAAGCGTCCCGA-TATAT
1 GATCAGTATTGATCCTGCATATATTGCGGACATACCACAGCTCTTTATAAGCAT-CCGATTATAT
6380740 G
1 G
6380741 GCTCTTAATG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 52 0.95
65 3 0.05
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (64 bp):
GATCAGTATTGATCCTGCATATATTGCGGACATACCACAGCTCTTTATAAGCATCCGATTATAT
Found at i:6383166 original size:25 final size:25
Alignment explanation
Indices: 6383128--6383239 Score: 134
Period size: 25 Copynumber: 4.5 Consensus size: 25
6383118 CACAACTCTT
*
6383128 ATGAGCTTCTCGATATTTAGCTCAC
1 ATGAGCTTCCCGATATTTAGCTCAC
6383153 ATGAGCTTCCCGATATTTAGCTCAC
1 ATGAGCTTCCCGATATTTAGCTCAC
* * **
6383178 ATGAGCTTTCCGATACTTAGCTTGC
1 ATGAGCTTCCCGATATTTAGCTCAC
* * * *
6383203 ATGAGCTTCCTGTTATTCAGCTCAA
1 ATGAGCTTCCCGATATTTAGCTCAC
*
6383228 AGGAGCTTCCCG
1 ATGAGCTTCCCG
6383240 CTTATAGCTC
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 72 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGATATTTAGCTCAC
Found at i:6385036 original size:22 final size:22
Alignment explanation
Indices: 6385011--6385439 Score: 526
Period size: 22 Copynumber: 19.4 Consensus size: 22
6385001 TGCTGACACG
6385011 TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
6385033 TTAGGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGT
*
6385054 TTAGGGTTTTTAAGTTAAGGGG
1 TTAGGGTTTTTAAGTTAAGGGT
*
6385076 TTAGAGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
6385098 TTAGGATTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGT
* *
6385119 TTAGGGTTTTTTAGTTAAGGGG
1 TTAGGGTTTTTAAGTTAAGGGT
**
6385141 TTACAGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
6385163 TTAGAGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
* *
6385185 TTAGGGTTTTTAAGGTAAAAGG-
1 TTAGGGTTTTTAA-GTTAAGGGT
6385207 TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
6385229 TTAGGGTTTTTAAGTTAAGAGT
1 TTAGGGTTTTTAAGTTAAGGGT
* **
6385251 TTAGGGTTTTAAAGTTAAAAG-
1 TTAGGGTTTTTAAGTTAAGGGT
* *
6385272 TTAGGATTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
* *
6385294 TTATGGGTTTTAAAGTTAATGG-
1 TTA-GGGTTTTTAAGTTAAGGGT
* *
6385316 TTAGGGTTTTTAGGTTAAGGGG
1 TTAGGGTTTTTAAGTTAAGGGT
*
6385338 TTAGGGTTTTTAAGTTAAGGGA
1 TTAGGGTTTTTAAGTTAAGGGT
* *
6385360 TTATGGTTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
6385382 TTAGGGTTTTTAATTTAAGGGTT
1 TTAGGGTTTTTAAGTTAAGGG-T
*
6385405 AGAGTTAGGGTTTTTAGGTTAAGGGT
1 ----TTAGGGTTTTTAAGTTAAGGGT
*
6385431 TTAAGGTTT
1 TTAGGGTTT
6385440 GTCAATTAAA
Statistics
Matches: 353, Mismatches: 42, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
21 77 0.22
22 235 0.67
23 21 0.06
26 1 0.00
27 19 0.05
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (22 bp):
TTAGGGTTTTTAAGTTAAGGGT
Found at i:6385086 original size:65 final size:65
Alignment explanation
Indices: 6385010--6385410 Score: 538
Period size: 65 Copynumber: 6.1 Consensus size: 65
6385000 TTGCTGACAC
*
6385010 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
1 GTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
* *
6385075 GTTAGAGTTTTTAAGTTAAGGGTTTAGGATTTTTAAGTTAAGGGTTAGGGTTTTTTAGTTAAGGG
1 GTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
* * * **
6385140 GTTACAGTTTTTAAGTTAAGGGTTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGGTAAAA
1 GTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGG
6385205 G
65 G
* * * *
6385206 GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGAGTTTAGGGTTTTAAAGTTAA-A
1 GTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAAGG
*
6385270 A
65 G
* * * *
6385271 GTTAG-GATTTTTAGGTTAAGGGTTTATGGGTTTTAAAGTTAATGGTTAGGGTTTTTAGGTTAAG
1 GTTAGAG-TTTTTAAGTTAAGGGTTTA-GGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAG
6385335 GG
64 GG
* * * * *
6385337 GTTAGGGTTTTTAAGTTAAGGGATTATGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAATTTAA-G
1 GTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGG
6385401 G
65 G
6385402 GTTAGAGTT
1 GTTAGAGTT
6385411 AGGGTTTTTA
Statistics
Matches: 295, Mismatches: 34, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
64 1 0.00
65 168 0.57
66 124 0.42
67 2 0.01
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (65 bp):
GTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
Found at i:6385706 original size:21 final size:21
Alignment explanation
Indices: 6385682--6385726 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
6385672 CTTTGTCCAG
*
6385682 CTTCTGGCGGCGG-TTGTGGTT
1 CTTCTGGCGG-GGATTCTGGTT
6385703 CTTCTGGCGGGGATTCTGGTT
1 CTTCTGGCGGGGATTCTGGTT
6385724 CTT
1 CTT
6385727 TCAGTAGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.02, C:0.20, G:0.38, T:0.40
Consensus pattern (21 bp):
CTTCTGGCGGGGATTCTGGTT
Found at i:6386010 original size:18 final size:18
Alignment explanation
Indices: 6385984--6386026 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6385974 GACTCGAAAA
* *
6385984 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
6386002 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
6386020 AGGAAAC
1 AGGAAAC
6386027 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:6386862 original size:20 final size:20
Alignment explanation
Indices: 6386825--6386862 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6386815 TTTATTTTTA
*
6386825 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
6386845 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
6386863 TACATCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:6387855 original size:51 final size:51
Alignment explanation
Indices: 6387800--6387897 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
6387790 AATTATTTAA
6387800 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAAAAT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAAAAT
* * * *
6387851 AAATATGGATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
6387898 GAGGAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAAAT
Found at i:6387873 original size:11 final size:11
Alignment explanation
Indices: 6387859--6387935 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
6387849 ATAAATATGG
6387859 ATTTGAGAGAA
1 ATTTGAGAGAA
*
6387870 ATTTTGA-AGGA
1 A-TTTGAGAGAA
6387881 ATTTGAGAGCAA
1 ATTTGAGAG-AA
6387893 A-TTGAGAGGAA
1 ATTTGAGA-GAA
6387904 ATTT-AGAAGAA
1 ATTTGAG-AGAA
6387915 A-TTGAGAGGAA
1 ATTTGAGA-GAA
6387926 ATTTGAGAGA
1 ATTTGAGAGA
6387936 GGATTAGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
10 8 0.15
11 30 0.55
12 17 0.31
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:6387884 original size:22 final size:22
Alignment explanation
Indices: 6387859--6387935 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
6387849 ATAAATATGG
6387859 ATTTGAGAGAAATTTTGA-AGG-A
1 ATTTGAGAGAAA--TTGAGAGGAA
6387881 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
6387904 ATTT-AGAAGAAATTGAGAGGAA
1 ATTTGAG-AGAAATTGAGAGGAA
6387926 ATTTGAGAGA
1 ATTTGAGAGA
6387936 GGATTAGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.08
22 34 0.68
23 12 0.24
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:6387898 original size:33 final size:33
Alignment explanation
Indices: 6387859--6387935 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
6387849 ATAAATATGG
* *
6387859 ATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAA-GAAATTGAGAGCAA
*
6387893 A-TTGAGAGGAAATTTAGAAGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTTAGAAGAAATTGAGAGCAA
6387926 ATTTGAGAGA
1 ATTTGAGAGA
6387936 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.44, C:0.01, G:0.29, T:0.26
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAAGAAATTGAGAGCAA
Found at i:6388885 original size:54 final size:54
Alignment explanation
Indices: 6388826--6388931 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
6388816 TAGATTCATG
*
6388826 TTAGTTCTCAAACTTATTCAAGGTTTAGGGACTAAAATGAATCTAGTTCCCATT
1 TTAGTTCTCAAACTTATTCAAGGTTTAGGGACCAAAATGAATCTAGTTCCCATT
** *
6388880 TTAGTTCTTGAACTTATTTAAGGTTTAGGGACCAAAATGAATCTAGTTCCCA
1 TTAGTTCTCAAACTTATTCAAGGTTTAGGGACCAAAATGAATCTAGTTCCCA
6388932 AGTTCAAGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (54 bp):
TTAGTTCTCAAACTTATTCAAGGTTTAGGGACCAAAATGAATCTAGTTCCCATT
Found at i:6390837 original size:15 final size:16
Alignment explanation
Indices: 6390807--6390838 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6390797 TTATATTATA
6390807 AAAATATTATTAAATT
1 AAAATATTATTAAATT
6390823 AAAATATTA-TAAATT
1 AAAATATTATTAAATT
6390838 A
1 A
6390839 TATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTATTAAATT
Found at i:6390842 original size:25 final size:26
Alignment explanation
Indices: 6390799--6390851 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
6390789 TTCTTGATTT
6390799 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATT-AATTAAA
*
6390826 ATATTAT-AAATTA-TATTAATTAAA
1 ATATTATAAAAATATTATTAATTAAA
6390850 AT
1 AT
6390852 TAAGATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 4 0.16
26 5 0.20
27 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTATAAAAATATTATTAATTAAA
Found at i:6390859 original size:25 final size:22
Alignment explanation
Indices: 6390809--6390866 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
6390799 ATATTATAAA
**
6390809 AATATTATTAAATTAAAATATTAT
1 AATA-TATT-AATTAAAATAAGAT
6390833 AAATTATATTAATTAAAATTAAGAT
1 -AA-TATATTAATTAAAA-TAAGAT
6390858 AATATATTA
1 AATATATTA
6390867 TAGGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.24
24 10 0.34
25 10 0.34
26 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATTAATTAAAATAAGAT
Found at i:6390866 original size:28 final size:27
Alignment explanation
Indices: 6390810--6390868 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
6390800 TATTATAAAA
6390810 ATATTATTAAATTAAAATATTATAAATT
1 ATATTATTAAATTAAAATA-TATAAATT
* *
6390838 ATATTAATTAAAATTAAGATA-ATATATT
1 ATATT-ATT-AAATTAAAATATATAAATT
6390866 ATA
1 ATA
6390869 GGAAACTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.52
29 3 0.11
30 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATTATTAAATTAAAATATATAAATT
Found at i:6392052 original size:23 final size:22
Alignment explanation
Indices: 6392025--6392089 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
6392015 GCTTTGCCGA
*
6392025 TCAGGCACTTTATGTGCCGTAT
1 TCAGGCACTTTATGTGTCGTAT
6392047 CTCAGGCACTTTATGTGTCGT-T
1 -TCAGGCACTTTATGTGTCGTAT
*
6392069 TCAAGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
6392090 ACTAATCAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.28
21 8 0.21
22 1 0.03
23 19 0.49
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:6396420 original size:23 final size:22
Alignment explanation
Indices: 6396381--6396429 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
6396371 TTATGTCAAA
6396381 TCGAGTGAAAATTCTGAGTTAG
1 TCGAGTGAAAATTCTGAGTTAG
* *
6396403 TCGAGATGATAAA-TCTGATTTTG
1 TCGAG-TGA-AAATTCTGAGTTAG
6396426 TCGA
1 TCGA
6396430 CCAAGCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 15 0.65
24 3 0.13
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (22 bp):
TCGAGTGAAAATTCTGAGTTAG
Found at i:6399324 original size:10 final size:9
Alignment explanation
Indices: 6399300--6399447 Score: 66
Period size: 10 Copynumber: 15.6 Consensus size: 9
6399290 AAGATCATAA
6399300 AAAAATTTT
1 AAAAATTTT
6399309 AAAAATCTTT
1 AAAAAT-TTT
*
6399319 AAAAATTAAT
1 AAAAATT-TT
6399329 AAAAATATTT
1 AAAAAT-TTT
**
6399339 -AATTTTTT
1 AAAAATTTT
* *
6399347 ATAAAAATAT
1 A-AAAATTTT
6399357 AAAAATTCTT
1 AAAAATT-TT
*
6399367 AAAAACTTAT
1 AAAAA-TTTT
*
6399377 AAAAATCATT
1 AAAAAT-TTT
*
6399387 AAAAATATT
1 AAAAATTTT
* *
6399396 AGAAATGATT
1 AAAAAT-TTT
*
6399406 AAAAATATT
1 AAAAATTTT
*
6399415 -AAAATTGAT
1 AAAAATT-TT
*
6399424 ATAAAATTAT
1 A-AAAATTTT
*
6399434 AAAAATTAT
1 AAAAATTTT
6399443 AAAAA
1 AAAAA
6399448 ATCATAAAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
8 8 0.07
9 41 0.37
10 52 0.47
11 9 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAAATTTT
Found at i:6399423 original size:19 final size:18
Alignment explanation
Indices: 6399301--6399449 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 18
6399291 AGATCATAAA
*
6399301 AAAATT-TTAAAAATCTTT
1 AAAATTATTAAAAAT-ATT
*
6399319 AAAAATTAATAAAAATATTT
1 -AAAATTATTAAAAATA-TT
** * *
6399339 AATTTTTTATAAAAATATA
1 AAAATTAT-TAAAAATATT
* *
6399358 AAAATTCTTAAAAACTTATA
1 AAAATTATTAAAAA--TATT
*
6399378 AAAATCATTAAAAATATT
1 AAAATTATTAAAAATATT
*
6399396 AGAAATGATTAAAAATATT
1 A-AAATTATTAAAAATATT
* *
6399415 AAAATTGATATAAAATTATA
1 AAAATT-AT-TAAAAATATT
*
6399435 AAAATTATAAAAAAT
1 AAAATTATTAAAAAT
6399450 CATAAAAACT
Statistics
Matches: 103, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
18 19 0.18
19 37 0.36
20 47 0.46
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAAAATATT
Found at i:6399430 original size:11 final size:10
Alignment explanation
Indices: 6399346--6399449 Score: 53
Period size: 9 Copynumber: 10.8 Consensus size: 10
6399336 TTTAATTTTT
*
6399346 TATAAAAATA
1 TATAAAATTA
*
6399356 TA-AAAATTC
1 TATAAAATTA
6399365 T-TAAAAACTTA
1 TAT-AAAA-TTA
*
6399376 TA-AAAATCA
1 TATAAAATTA
*
6399385 T-TAAAAATA
1 TATAAAATTA
*
6399394 T-TAGAAATGA
1 TATA-AAATTA
*
6399404 T-TAAAAATA
1 TATAAAATTA
6399413 T-TAAAATTGA
1 TATAAAATT-A
6399423 TATAAAATTA
1 TATAAAATTA
6399433 TA-AAAATTA
1 TATAAAATTA
*
6399442 TAAAAAAT
1 TATAAAAT
6399450 CATAAAAACT
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
9 37 0.50
10 27 0.36
11 10 0.14
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (10 bp):
TATAAAATTA
Found at i:6399449 original size:10 final size:9
Alignment explanation
Indices: 6399345--6399457 Score: 79
Period size: 10 Copynumber: 12.0 Consensus size: 9
6399335 ATTTAATTTT
6399345 TTATAAAAA
1 TTATAAAAA
6399354 -TATAAAAA
1 TTATAAAAA
*
6399362 TTCTTAAAAA
1 TT-ATAAAAA
6399372 CTTATAAAAA
1 -TTATAAAAA
*
6399382 TCATTAAAAA
1 TTA-TAAAAA
*
6399392 -TATTAGAAA
1 TTA-TAAAAA
*
6399401 TGATTAAAAA
1 TTA-TAAAAA
*
6399411 -TATTAAAA
1 TTATAAAAA
6399419 TTGATATAAAA
1 TT-ATA-AAAA
6399430 TTATAAAAA
1 TTATAAAAA
6399439 TTATAAAAAA
1 TTAT-AAAAA
*
6399449 TCATAAAAA
1 TTATAAAAA
6399458 CTTGAATTGG
Statistics
Matches: 84, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
8 13 0.15
9 25 0.30
10 38 0.45
11 8 0.10
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:6399454 original size:19 final size:18
Alignment explanation
Indices: 6399345--6399457 Score: 84
Period size: 19 Copynumber: 6.0 Consensus size: 18
6399335 ATTTAATTTT
6399345 TTAT-AAAAATATAAAAA
1 TTATAAAAAATATAAAAA
* *
6399362 TTCTTAAAAACTTATAAAAA
1 TT-ATAAAAA-ATATAAAAA
* * *
6399382 TCATTAAAAATATTAGAAA
1 TTATAAAAAATA-TAAAAA
* * *
6399401 TGATTAAAAATATTAAAA
1 TTATAAAAAATATAAAAA
*
6399419 TTGATATAAAATTATAAAAA
1 TT-ATA-AAAAATATAAAAA
6399439 TTATAAAAAATCATAAAAA
1 TTATAAAAAAT-ATAAAAA
6399458 CTTGAATTGG
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
17 2 0.03
18 13 0.18
19 37 0.50
20 22 0.30
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (18 bp):
TTATAAAAAATATAAAAA
Found at i:6400092 original size:10 final size:10
Alignment explanation
Indices: 6399952--6400116 Score: 57
Period size: 10 Copynumber: 16.8 Consensus size: 10
6399942 TTTTTATGAT
*
6399952 TTTTTTATAA
1 TTTTATATAA
6399962 TTTTA-ATAA
1 TTTTATATAA
*
6399971 GTTTATATCAA
1 TTTTATAT-AA
* * *
6399982 ATTTA-ACAT
1 TTTTATATAA
6399991 TTTTAGTA-AA
1 TTTTA-TATAA
6400001 TTTCT-TATAA
1 TTT-TATATAA
6400011 TTTTCA-ATAAA
1 TTTT-ATAT-AA
* *
6400022 TTTTAT-GAG
1 TTTTATATAA
*
6400031 TTTT-TATGA
1 TTTTATATAA
*
6400040 TTTTATAAAA
1 TTTTATATAA
*
6400050 TTTTAAAT-A
1 TTTTATATAA
*
6400059 TTTTAGAT-A
1 TTTTATATAA
6400068 TGTTT-TATCAA
1 T-TTTATAT-AA
6400079 TTTTATATAA
1 TTTTATATAA
6400089 TTTT-TATGAA
1 TTTTATAT-AA
6400099 -TTTATATTAA
1 TTTTATA-TAA
*
6400109 TTTAATAT
1 TTTTATAT
6400117 TTTTGTATGA
Statistics
Matches: 116, Mismatches: 19, Indels: 40
0.66 0.11 0.23
Matches are distributed among these distances:
8 1 0.01
9 43 0.37
10 47 0.41
11 25 0.22
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (10 bp):
TTTTATATAA
Found at i:6407373 original size:24 final size:24
Alignment explanation
Indices: 6407320--6407367 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6407310 GATAGATTAA
6407320 AAATTTTATTACAAATAGACACAT
1 AAATTTTATTACAAATAGACACAT
*
6407344 AAATTTTATTATAAATAGACACAT
1 AAATTTTATTACAAATAGACACAT
6407368 GTATTTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATTTTATTACAAATAGACACAT
Found at i:6410026 original size:94 final size:94
Alignment explanation
Indices: 6409865--6410041 Score: 268
Period size: 94 Copynumber: 1.9 Consensus size: 94
6409855 CTTGGGGTAA
* *
6409865 TTGGCTGCTCATATCAAGATAAGTACTTTGTCACTTATGTCTTGTTGATGGTTAATACTTATTAA
1 TTGGCTGCTCATATCAAGATAAGTACTTGGTCACTTATGTCTTGTTGATGGTTAATACTTAATAA
*
6409930 GGTACTTAGTTGCTTAAGGGAATTTGTGG
66 GGTACTTAGTTACTTAAGGGAATTTGTGG
* *
6409959 TTGGCTGCTCATATCAAGATATA-TACTTGGTTACTTTTGTCGTT-TTGATGGTTAATACTTAAT
1 TTGGCTGCTCATATCAAGATA-AGTACTTGGTCACTTATGTC-TTGTTGATGGTTAATACTTAAT
*
6410022 AAGGTACTTTGTTACTTAAG
64 AAGGTACTTAGTTACTTAAG
6410042 AGACTTTATA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 72 0.96
95 3 0.04
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (94 bp):
TTGGCTGCTCATATCAAGATAAGTACTTGGTCACTTATGTCTTGTTGATGGTTAATACTTAATAA
GGTACTTAGTTACTTAAGGGAATTTGTGG
Found at i:6410137 original size:219 final size:219
Alignment explanation
Indices: 6409758--6410177 Score: 537
Period size: 219 Copynumber: 1.9 Consensus size: 219
6409748 ACATACATAT
*
6409758 ATATATACTTGGTTACTTATTTTCTTTGATGGTTAATACTTAAGAAGGTACGTAGTTAACTGATA
1 ATATATACTTGGTTACTTATTGTCTTTGATGGTTAATACTTAAGAAGGTACGTAGTTAACTGATA
* * ** * * *
6409823 GAAATTTTTGGGTGGTAAAATTGAATCTATTTCTTGGGGTAATTGGCTGCTCATATCAAGATAAG
66 GAAATTTATAGGTGGTAAAATTGAATAAATTTCGTGAGGTAATTGGCTGCTCATATCAAGATAAA
* * * **
6409888 TACTTTGTCACTTATGTCTTGTTGATGGTTAATACTTATTAAGGTACTTAGTTGCTTAAGGGAAT
131 TACTTGGTCACTTATGTCGTGTTGATGGTTAATACTTATTAAGGTACTTAGTTACTTAAGAAAAT
6409953 TTGTGGTTGGCTGCTCATATCAAG
196 TTGTGGTTGGCTGCTCATATCAAG
* * * *
6409977 ATATATACTTGGTTACTT-TTGTCGTTTTGATGGTTAATACTTAATAAGGTACTTTGTT-ACTTA
1 ATATATACTTGGTTACTTATTGTC--TTTGATGGTTAATACTTAAGAAGGTACGTAGTTAACTGA
* * *
6410040 -AGAGACTTTATAGGTGGTAGAATTGAATAAATTT-GT-AGGTAATTTGCTGCTCATATCAAGAT
64 TAGA-AATTTATAGGTGGTAAAATTGAATAAATTTCGTGAGGTAATTGGCTGCTCATATCAAGAT
* * *
6410102 ATATATACTTGGTTACTT-TTTGCGTGTTGATGGTTAATACTTTTTAAGGTACTTAGTTACTTAA
128 A-A-ATACTTGGTCACTTATGT-CGTGTTGATGGTTAATACTTATTAAGGTACTTAGTTACTTAA
6410166 GAAAATTTGTGG
190 GAAAATTTGTGG
6410178 GTGGAATTGG
Statistics
Matches: 172, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
217 25 0.15
218 11 0.06
219 106 0.62
220 30 0.17
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (219 bp):
ATATATACTTGGTTACTTATTGTCTTTGATGGTTAATACTTAAGAAGGTACGTAGTTAACTGATA
GAAATTTATAGGTGGTAAAATTGAATAAATTTCGTGAGGTAATTGGCTGCTCATATCAAGATAAA
TACTTGGTCACTTATGTCGTGTTGATGGTTAATACTTATTAAGGTACTTAGTTACTTAAGAAAAT
TTGTGGTTGGCTGCTCATATCAAG
Found at i:6410206 original size:102 final size:100
Alignment explanation
Indices: 6410068--6410384 Score: 346
Period size: 95 Copynumber: 3.1 Consensus size: 100
6410058 AGAATTGAAT
* * * *
6410068 AAATTTGTAGGT--AATTTGCTGCTCATATCAAGATATATATACTTGGTTACTT-TTTGCGTGTT
1 AAATTTGTGGGTGGAATTGGCTGCTCATATCAAGATATATATA-TTGGTTACTTATGT-CCTGTT
**
6410130 GATGGTTAATACTTTTTAAGGTACTTAGTTACTTAAGA
64 GATGGTTAATACTTCATAAGGTACTTAGTTACTT-AGA
* *
6410168 AAATTTGTGGGTGGAATTGGCTGCTCATACCAATATATATATGTATATGTTATGTTACTTATGTC
1 AAATTTGTGGGTGGAATTGGCTGCTCATATCAAGATATATA--TAT-TG----GTTACTTATGTC
*
6410233 TTGTTGATGGTTAATACTTCATAAGGTACTTAGTTACTT-G-
59 CTGTTGATGGTTAATACTTCATAAGGTACTTAGTTACTTAGA
* *
6410273 -AATTTGTGGGTGG--TTGGCTGCTAATATCAAGATATATAT-TTGGTTTACTTATGTCCTTTTG
1 AAATTTGTGGGTGGAATTGGCTGCTCATATCAAGATATATATATTGG-TTACTTATGTCCTGTTG
*
6410334 ATGGTTAATACTTCATAAGGTAATTAGTTACTTCAGA
65 ATGGTTAATACTTCATAAGGTACTTAGTTACTT-AGA
*
6410371 AAATTTTTGGGTGG
1 AAATTTGTGGGTGG
6410385 TAGAAGTGAA
Statistics
Matches: 187, Mismatches: 15, Indels: 31
0.80 0.06 0.13
Matches are distributed among these distances:
94 1 0.01
95 47 0.25
97 1 0.01
98 2 0.01
99 13 0.07
100 12 0.06
102 46 0.25
103 1 0.01
104 17 0.09
106 1 0.01
108 44 0.24
109 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (100 bp):
AAATTTGTGGGTGGAATTGGCTGCTCATATCAAGATATATATATTGGTTACTTATGTCCTGTTGA
TGGTTAATACTTCATAAGGTACTTAGTTACTTAGA
Found at i:6410536 original size:327 final size:323
Alignment explanation
Indices: 6409897--6410516 Score: 800
Period size: 327 Copynumber: 1.9 Consensus size: 323
6409887 GTACTTTGTC
*
6409897 ACTTATGTCTTGTTGATGGTTAATACTTATTAAGGTACTTAGTTGCTTAAGGGAATTTGTGGTTG
1 ACTTATGTCTTGTTGATGGTTAATACTTATTAAGGTACTTAGTTACTT-A--GAATTTGTGGTTG
* * *
6409962 GCTGCTCATATCAAGATATATACTTGGTTACTTTTGTCGTTTTGATGGTTAATACTTAATAAGGT
63 GCTGCTAATATCAAGATATATACTTGGTTACTTATGTCCTTTTGATGGTTAATACTTAATAAGGT
* * * * * **
6410027 ACTTTGTTACTTAAGAGACTTTATAGGTGGTAGAATTGAATAAATTTGTAGGTAATTTGCTGCTC
128 AATTAGTTACTTAAGAAAATTTATAGGTGGTAGAAGTGAATAAATTTGTAGGTAATCGGCTGCTC
* * * **
6410092 ATATCAAGATATATATACTTGGTTACTTTTTGCGTGTTGATGGTTAATACTTTTTAAGGTACTTA
193 ATATCAAGA-ATATACACTTGGTTACTTTGTGCGTATTGATGGTTAATACTTAATAAGGTACTTA
** * ** *
6410157 GTTACTTAAGAAAATTTGTGGGTGGAATTGGCTGCTCATACCAATATATATATGTATATGTTATG
257 GTTACTTAAGAAAATACGGGGGTGGAATTGAATGCTCATACCAAGATATATATGTATATGTTATG
6410222 TT
322 TT
6410224 ACTTATGTCTTGTTGATGGTTAATACTTCA-TAAGGTACTTAGTTACTT-GAATTTGTGGGTGGT
1 ACTTATGTCTTGTTGATGGTTAATACTT-ATTAAGGTACTTAGTTACTTAGAA-TT-T--GTGGT
* *
6410287 TGGCTGCTAATATCAAGATATATATTTGGTTTACTTATGTCCTTTTGATGGTTAATACTTCATAA
61 TGGCTGCTAATATCAAGATATATACTTGG-TTACTTATGTCCTTTTGATGGTTAATACTTAATAA
* * * *
6410352 GGTAATTAGTTACTTCAGAAAATTTTTGGGTGGTAGAAGTGAAT-AATTTGTGGGTAATCGGCTG
125 GGTAATTAGTTACTTAAGAAAATTTATAGGTGGTAGAAGTGAATAAATTTGTAGGTAATCGGCTG
* * *
6410416 TTCATATCAAG-ATATGCACTTGGTTACTTATGT-CTTATTGATGGTTAATACTTAATAAGGTAC
190 CTCATATCAAGAATATACACTTGGTTACTT-TGTGCGTATTGATGGTTAATACTTAATAAGGTAC
* *
6410479 TTAGTTACTTGAGAGAATACGGGTGGTGGAATTGAATG
254 TTAGTTACTTAAGAAAATACGGG-GGTGGAATTGAATG
6410517 ACTTGTATCG
Statistics
Matches: 253, Mismatches: 32, Indels: 17
0.84 0.11 0.06
Matches are distributed among these distances:
323 3 0.01
324 2 0.01
325 61 0.24
326 14 0.06
327 104 0.41
328 69 0.27
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.42
Consensus pattern (323 bp):
ACTTATGTCTTGTTGATGGTTAATACTTATTAAGGTACTTAGTTACTTAGAATTTGTGGTTGGCT
GCTAATATCAAGATATATACTTGGTTACTTATGTCCTTTTGATGGTTAATACTTAATAAGGTAAT
TAGTTACTTAAGAAAATTTATAGGTGGTAGAAGTGAATAAATTTGTAGGTAATCGGCTGCTCATA
TCAAGAATATACACTTGGTTACTTTGTGCGTATTGATGGTTAATACTTAATAAGGTACTTAGTTA
CTTAAGAAAATACGGGGGTGGAATTGAATGCTCATACCAAGATATATATGTATATGTTATGTT
Found at i:6410596 original size:217 final size:217
Alignment explanation
Indices: 6410221--6410733 Score: 516
Period size: 217 Copynumber: 2.4 Consensus size: 217
6410211 TATATGTTAT
* * * *
6410221 GTTACTTATGTCTTGTTGATGGTTAATACTTCATAAGGTACTTAGTTACTT---GAATTTGTG-G
1 GTTACTTATGTCTTATTGATGGTTAATACTTAATAAGGTACTTAGTTACTTAGAGAATATGGGTG
** *
6410282 GTGG--TTGGCTGCTAATATCAAGATATATATTTGGTTTACTTATGTCCTTTTGATGGTTAATAC
66 GTGGAATTGAATGCTAATATCAAGATATATATTTCGTTTACTTATGTCCTTTTGATGGTTAATA-
* * * *
6410345 TTCATAAGGTAATTAGTTACTTCAGAAAATTTTTGGGTGGTAGAAGT-GAAT-AATTTGTGGGTA
130 --CAT-A-GCAATTAATTACTTAAGAAAATTTTTGGGTGGTAGAA-TCGAATAAATTTCT-GGT-
* *
6410408 ATCGGCTGTTCATATC-A-AGATATGCACTTG
188 -TC-GCTGCTCACATCAACAGATATGCACTTG
*
6410438 GTTACTTATGTCTTATTGATGGTTAATACTTAATAAGGTACTTAGTTACTTGAGAGAATACGGGT
1 GTTACTTATGTCTTATTGATGGTTAATACTTAATAAGGTACTTAGTTACTT-AGAGAATATGGGT
** * **
6410503 GGTGGAATTGAATGACTTGTATCGAGATATATATTTCG-TTACTTATGTTGTTTTGATGGTTAAT
65 GGTGGAATTGAATG-CTAATATCAAGATATATATTTCGTTTACTTATGTCCTTTTGATGGTTAAT
* * *
6410567 A-AT-GCATTTAATTACTTAAGATAATTTTTGGGTGGTAGAATCGAATAAAATTTCTGGTTCGTT
129 ACATAGCAATTAATTACTTAAGAAAATTTTTGGGTGGTAGAATCGAAT-AAATTTCTGGTTCGCT
* *
6410630 GCTCACATCAACATATATGTACTTG
193 GCTCACATCAACAGATATGCACTTG
* ** *
6410655 GTTGCTTATGT-TGCTTCGATGGTTAATACTTAATAAGGTACTTAGTTACTTA-AGAAATTTGTG
1 GTTACTTATGTCTTATT-GATGGTTAATACTTAATAAGGTACTTAGTTACTTAGAG-AA--TATG
6410718 GGTGGTGGAATTGAAT
62 GGTGGTGGAATTGAAT
6410734 AAGTTTTTCA
Statistics
Matches: 250, Mismatches: 29, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
215 11 0.04
216 10 0.04
217 140 0.56
218 21 0.08
219 6 0.02
220 2 0.01
221 6 0.02
222 5 0.02
224 30 0.12
225 19 0.08
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (217 bp):
GTTACTTATGTCTTATTGATGGTTAATACTTAATAAGGTACTTAGTTACTTAGAGAATATGGGTG
GTGGAATTGAATGCTAATATCAAGATATATATTTCGTTTACTTATGTCCTTTTGATGGTTAATAC
ATAGCAATTAATTACTTAAGAAAATTTTTGGGTGGTAGAATCGAATAAATTTCTGGTTCGCTGCT
CACATCAACAGATATGCACTTG
Found at i:6415914 original size:14 final size:15
Alignment explanation
Indices: 6415891--6415920 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6415881 CATAATCAAA
6415891 TAATACGTAATAAAT
1 TAATACGTAATAAAT
6415906 TAATA-GTAATAAAT
1 TAATACGTAATAAAT
6415920 T
1 T
6415921 TACACTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (15 bp):
TAATACGTAATAAAT
Found at i:6417986 original size:7 final size:7
Alignment explanation
Indices: 6417974--6417999 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6417964 TAGTCGATTG
6417974 GTATTTA
1 GTATTTA
6417981 GTATTTA
1 GTATTTA
6417988 GTATTTA
1 GTATTTA
6417995 GTATT
1 GTATT
6418000 ATGTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:6418448 original size:6 final size:7
Alignment explanation
Indices: 6418418--6418450 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
6418408 TTACGTGTCT
6418418 CCCTAAA
1 CCCTAAA
6418425 CCCTAAA
1 CCCTAAA
*
6418432 CTCTAAA
1 CCCTAAA
6418439 CCCT-AA
1 CCCTAAA
6418445 CCCTAA
1 CCCTAA
6418451 TCTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:6418872 original size:6 final size:6
Alignment explanation
Indices: 6418861--6418886 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6418851 AAATACCTTA
6418861 AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AA
6418887 TCTAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:6418879 original size:224 final size:221
Alignment explanation
Indices: 6418418--6419020 Score: 774
Period size: 224 Copynumber: 2.8 Consensus size: 221
6418408 TTACGTGTCT
6418418 CCCTAAACCCTAAACTCTAAACCCTAACCCTAATCTAATTTTTAAATTTTTTTAATTAAATTACT
1 CCCT-AACCCTAAAC-CT-AACCCTAACCCT-ATCTAATTTTTAAATTTTTTTAATTAAATTACT
*
6418483 CAAGTAATCCTAAACCTTAATTTAATTGATTTTTTCTTAAAAATTAATAAACACGAAAACTAATC
62 CAAGTAATCCTAAACCCTAATTTAATTGATTTTTTCTTAAAAATTAATAAACACGAAAACTAATC
6418548 CAATTTTGAAAAATTTATAAATAATTTAATTGACAAACCCTAAACTCTAAACCCTAATTTATTTA
127 CAATTTTGAAAAATTTATAAATAATTTAATTGACAAACCCTAAACTCT--A---TAATTTATTT-
*
6418613 ATTTTTCCTTAAAAATCTTAACTTAAAAACACCCTA
186 ATTTTTCCTTAAAAACCTTAACTTAAAAACACCCTA
6418649 ----AACCCTAAACCTAACCCTAACCCTGATCTAATTTTTAAATTTTTTTAATTAAATTACTCAA
1 CCCTAACCCTAAACCTAACCCTAACCCT-ATCTAATTTTTAAATTTTTTTAATTAAATTACTCAA
*
6418710 GTAACCCTAAACCCTAATTTAATTGATTTTTTCTTAAAAATTAATAAACACGAAAACTAATCCAA
65 GTAATCCTAAACCCTAATTTAATTGATTTTTTCTTAAAAATTAATAAACACGAAAACTAATCCAA
*
6418775 TTTTGAAAAATTTATAAATGATTTAATTGACAAACCCT-AA-T-T-T-ATTTGA-TT-TTTTT-C
130 TTTTGAAAAATTTATAAATAATTTAATTGACAAACCCTAAACTCTATAATTT-ATTTATTTTTCC
* *
6418832 TTAAAAACCCTTAACTTAAAAATACCTTA
194 TTAAAAA-CCTTAACTTAAAAACACCCTA
* *
6418861 ----AACCCTAACCCTAACCCTAACCCTAATCTAATTTTTTAAATTTTTTTAATTAAAGTACTCA
1 CCCTAACCCTAAACCTAACCCTAACCCT-ATCTAA-TTTTTAAATTTTTTTAATTAAATTACTCA
* *
6418922 AGTAATCCTAAACCCTAATTTAATT-ACTTTTTTCTTAAAAAATAATATACAC-AAAA-T--T--
64 AGTAATCCTAAACCCTAATTTAATTGA-TTTTTTCTTAAAAATTAATAAACACGAAAACTAATCC
*
6418980 -A---TGAAAAATTTATAAATAATTTAATTAACAAACCCTAAACT
128 AATTTTGAAAAATTTATAAATAATTTAATTGACAAACCCTAAACT
6419021 AGAGGTGTTC
Statistics
Matches: 351, Mismatches: 15, Indels: 38
0.87 0.04 0.09
Matches are distributed among these distances:
203 33 0.09
204 2 0.01
205 1 0.00
206 1 0.00
209 1 0.00
211 9 0.03
212 57 0.16
213 75 0.21
214 6 0.02
215 2 0.01
221 1 0.00
222 1 0.00
223 2 0.01
224 148 0.42
225 2 0.01
226 10 0.03
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (221 bp):
CCCTAACCCTAAACCTAACCCTAACCCTATCTAATTTTTAAATTTTTTTAATTAAATTACTCAAG
TAATCCTAAACCCTAATTTAATTGATTTTTTCTTAAAAATTAATAAACACGAAAACTAATCCAAT
TTTGAAAAATTTATAAATAATTTAATTGACAAACCCTAAACTCTATAATTTATTTATTTTTCCTT
AAAAACCTTAACTTAAAAACACCCTA
Found at i:6419218 original size:25 final size:27
Alignment explanation
Indices: 6419177--6419249 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
6419167 TCCGGCCCGA
*
6419177 ATATATAATAAATATTTTTTATTC-TTT
1 ATATTTAA-AAATATTTTTTATTCTTTT
*
6419204 A-ATTTTAAAATATTTTTTATTCTTTTT
1 ATATTTAAAAATATTTTTTATTC-TTTT
6419231 ATATTTAAAAATATTTTTT
1 ATATTTAAAAATATTTTTT
6419250 TGGTGTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 15 0.38
26 4 0.10
27 5 0.12
28 16 0.40
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATTTAAAAATATTTTTTATTCTTTT
Found at i:6419258 original size:27 final size:28
Alignment explanation
Indices: 6419177--6419259 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 28
6419167 TCCGGCCCGA
* *
6419177 ATATATAATAAATATTTTTTAT--TCTTT
1 ATATTTAA-AAATATTTTTTATGCTGTTT
* * *
6419204 A-ATTTTAAAATATTTTTTATTCTTTTT
1 ATATTTAAAAATATTTTTTATGCTGTTT
*
6419231 ATATTTAAAAATATTTTTT-TGGTGTTT
1 ATATTTAAAAATATTTTTTATGCTGTTT
6419258 AT
1 AT
6419260 TAAATAATGG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 13 0.28
26 4 0.09
27 13 0.28
28 16 0.35
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (28 bp):
ATATTTAAAAATATTTTTTATGCTGTTT
Found at i:6421065 original size:22 final size:24
Alignment explanation
Indices: 6421030--6421073 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
6421020 TTTTATTTAA
6421030 ATTTAATTATAAAAT-ATATAAAT
1 ATTTAATTATAAAATAATATAAAT
6421053 ATTTAA-TATAAAATAATATAA
1 ATTTAATTATAAAATAATATAA
6421074 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTTAATTATAAAATAATATAAAT
Found at i:6425448 original size:14 final size:14
Alignment explanation
Indices: 6425429--6425463 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6425419 TGACATTTTT
*
6425429 TTCTAATGATACTA
1 TTCTAACGATACTA
6425443 TTCTAACGATACTA
1 TTCTAACGATACTA
6425457 TTCTAAC
1 TTCTAAC
6425464 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:6426691 original size:14 final size:14
Alignment explanation
Indices: 6426668--6426702 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6426658 AAAACTTGTA
*
6426668 ATAAACTTTGTAAT
1 ATAAATTTTGTAAT
6426682 ATAAATTTTGTAAT
1 ATAAATTTTGTAAT
6426696 ATAAATT
1 ATAAATT
6426703 AAATACATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (14 bp):
ATAAATTTTGTAAT
Found at i:6426736 original size:62 final size:62
Alignment explanation
Indices: 6426586--6426812 Score: 305
Period size: 62 Copynumber: 3.6 Consensus size: 62
6426576 AGATTAATTG
* ** ** *
6426586 CAACATTAAAACTTGGAACAAACTTTATGGTCATAAATTAGATTAAT-TGCAACATTACA-ACAT
1 CAACATTAAAACTTGGAACAAACTTTGTAAT-ATAAATTTTA-TAATAT--AA-ATTAAATACAT
6426649 TA
61 TA
* * *
6426651 CAACATTAAAACTTGTAATAAACTTTGTAATATAAATTTTGTAATATAAATTAAATACATTA
1 CAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTATAATATAAATTAAATACATTA
*
6426713 CAACATTAAAACTTGGAACAAACTTTGTATTATAAATTTTATAATATAAATTAAATACATTA
1 CAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTATAATATAAATTAAATACATTA
6426775 CAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
1 CAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
6426813 AGGTACATTG
Statistics
Matches: 146, Mismatches: 14, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
61 5 0.03
62 103 0.71
63 4 0.03
64 8 0.05
65 26 0.18
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (62 bp):
CAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTATAATATAAATTAAATACATTA
Found at i:6434038 original size:34 final size:32
Alignment explanation
Indices: 6433985--6434049 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
6433975 AATTGTTAAA
6433985 TTTATTAAGCTATGCTATTTTCAA-TTAAAAT
1 TTTATTAAGCTATGCTATTTTCAATTTAAAAT
6434016 TTTATTAAAGTCTATTGCTATTTTCAATTTAAAA
1 TTTATT-AAG-CTA-TGCTATTTTCAATTTAAAA
6434050 AAAACAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.20
32 3 0.10
33 3 0.10
34 12 0.40
35 6 0.20
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.49
Consensus pattern (32 bp):
TTTATTAAGCTATGCTATTTTCAATTTAAAAT
Found at i:6434989 original size:26 final size:26
Alignment explanation
Indices: 6434941--6434991 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
6434931 ATATAATTAT
6434941 TATTTTTATATGTAAAATATTTCAAA
1 TATTTTTATATGTAAAATATTTCAAA
*
6434967 TATTTTTATATGTGAAATATTTCAA
1 TATTTTTATATGTAAAATATTTCAA
6434992 TTAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (26 bp):
TATTTTTATATGTAAAATATTTCAAA
Found at i:6443673 original size:21 final size:22
Alignment explanation
Indices: 6443649--6443697 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
6443639 ATTTTAATAA
*
6443649 AATTTAAAATT-TAATCTCTA-T
1 AATTTAAAATTAAAAT-TCTATT
*
6443670 AATTAAAAATTAAAATTCTATT
1 AATTTAAAATTAAAATTCTATT
6443692 AATTTA
1 AATTTA
6443698 TTGTAGCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAAAATTAAAATTCTATT
Found at i:6460530 original size:24 final size:25
Alignment explanation
Indices: 6460503--6460550 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6460493 AGAGGAAAGT
6460503 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
6460527 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
6460551 TATGAGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:6465044 original size:6 final size:6
Alignment explanation
Indices: 6465033--6465085 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
6465023 AATCATTTAA
* * * *
6465033 TTTTGT TTTTGT TTTTGT TTTTTT ATTTTAT TTTTGG GTTTGT CTTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT -TTTTGT TTTTGT TTTTGT -TTTTGT
6465083 TTT
1 TTT
6465086 CAGTAATTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.04, C:0.02, G:0.15, T:0.79
Consensus pattern (6 bp):
TTTTGT
Found at i:6465074 original size:25 final size:25
Alignment explanation
Indices: 6465032--6465080 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
6465022 TAATCATTTA
* ** *
6465032 ATTTTGTTTTTGTTTTTGTTTTTTT
1 ATTTTATTTTTGGGTTTGTCTTTTT
6465057 ATTTTATTTTTGGGTTTGTCTTTT
1 ATTTTATTTTTGGGTTTGTCTTTT
6465081 GTTTTCAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.06, C:0.02, G:0.14, T:0.78
Consensus pattern (25 bp):
ATTTTATTTTTGGGTTTGTCTTTTT
Found at i:6465679 original size:13 final size:14
Alignment explanation
Indices: 6465654--6465695 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
6465644 TTAAGTGGTG
6465654 ATTGAAATATTTCA
1 ATTGAAATATTTCA
*
6465668 ATT-AATTATTTCAA
1 ATTGAAATATTTC-A
6465682 ATTGAAATATTTCA
1 ATTGAAATATTTCA
6465696 CATATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (14 bp):
ATTGAAATATTTCA
Found at i:6465694 original size:15 final size:15
Alignment explanation
Indices: 6465654--6465695 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
6465644 TTAAGTGGTG
6465654 ATTGAAATATTTC-A
1 ATTGAAATATTTCAA
*
6465668 ATT-AATTATTTCAA
1 ATTGAAATATTTCAA
6465682 ATTGAAATATTTCA
1 ATTGAAATATTTCA
6465696 CATATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 7 0.29
15 9 0.38
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (15 bp):
ATTGAAATATTTCAA
Found at i:6469755 original size:4 final size:4
Alignment explanation
Indices: 6469746--6469780 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
6469736 GGCCCAATAA
6469746 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
6469781 CACACAGTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:6469837 original size:16 final size:16
Alignment explanation
Indices: 6469816--6469849 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6469806 CCCAAACATT
6469816 AAAAAAATATGGCCCA
1 AAAAAAATATGGCCCA
6469832 AAAAAAATATGGCCCA
1 AAAAAAATATGGCCCA
6469848 AA
1 AA
6469850 CCCGATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAAAATATGGCCCA
Found at i:6471019 original size:3 final size:3
Alignment explanation
Indices: 6471011--6471074 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
6471001 ACCACTGTTT
* * * *
6471011 TTA TTA TTA CTCA -TA TTA TTA TTT TTA TTC TTA CTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6471056 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
6471075 CATCATCATC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 1 0.02
3 48 0.94
4 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Done.