Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 90 of 226
Found at i:28330189 original size:16 final size:16
Alignment explanation
Indices: 28330163--28330209 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
28330153 CAGCTATTTT
*
28330163 ATTCAAATAATAATAAC
1 ATTC-AATAATAATAAA
*
28330180 ATTCAATAATATTAAA
1 ATTCAATAATAATAAA
*
28330196 ATTCATTAATAATA
1 ATTCAATAATAATA
28330210 TTATAACTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTCAATAATAATAAA
Found at i:28334113 original size:76 final size:75
Alignment explanation
Indices: 28333941--28334120 Score: 245
Period size: 76 Copynumber: 2.4 Consensus size: 75
28333931 GTAAGTATTG
* * * *
28333941 ATATATTATTGATGTAAAATACAGTAGAATACAATATAAATTATTTTTCTTTTTTTCCGTAGATT
1 ATATATTATTGATGTAAAATACAATAGAATACAATACAAATAATTTTTATTTTTTTCCGTAGATT
28334006 GTAAATAAGT
66 GTAAATAAGT
** ** *
28334016 ATATATTATTGACATGGAATACAATAGAATACAATACAAATAATTTCTTAATTTTTTT-CTTAGA
1 ATATATTATTGATGTAAAATACAATAGAATACAATACAAATAATTT-TT-ATTTTTTTCCGTAGA
28334080 TTGTAAATAAGT
64 TTGTAAATAAGT
*
28334092 ATATATTATTTATGTAAAATACAATAGAA
1 ATATATTATTGATGTAAAATACAATAGAA
28334121 CAATTTTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
75 39 0.44
76 43 0.48
77 7 0.08
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (75 bp):
ATATATTATTGATGTAAAATACAATAGAATACAATACAAATAATTTTTATTTTTTTCCGTAGATT
GTAAATAAGT
Found at i:28335216 original size:26 final size:27
Alignment explanation
Indices: 28335181--28335243 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
28335171 ATAAAAAATA
28335181 ACCAAAATATTAT-AATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
*
28335207 ATCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
28335234 ACCAAAATAT
1 ACCAAAATAT
28335244 ACCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:28335783 original size:23 final size:23
Alignment explanation
Indices: 28335757--28335828 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 23
28335747 ACTCTATTTT
28335757 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
*
28335780 AATTACTTAATAACTCTATT-T--T--
1 AA-T--TTAATAA-ACTATTCTCATCA
28335802 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
28335825 AATT
1 AATT
28335829 ACCAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
21 2 0.05
22 2 0.05
23 6 0.16
24 2 0.05
26 8 0.21
27 5 0.13
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:28335791 original size:45 final size:45
Alignment explanation
Indices: 28335742--28335830 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
28335732 TCTAATTAAG
28335742 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
28335787 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
28335831 CAAAATAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (45 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:28335856 original size:15 final size:15
Alignment explanation
Indices: 28335836--28335885 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
28335826 ATTACCAAAA
28335836 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
28335851 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
28335866 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
28335884 TA
1 TA
28335886 AAATAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:28335890 original size:18 final size:18
Alignment explanation
Indices: 28335854--28335891 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28335844 ATTAAATTAG
*
28335854 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
28335872 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
28335890 AG
1 AG
28335892 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:28336176 original size:15 final size:16
Alignment explanation
Indices: 28336156--28336185 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28336146 GCTGCTGCCA
28336156 CAGGTTTTT-TTTTTG
1 CAGGTTTTTATTTTTG
28336171 CAGGTTTTTATTTTT
1 CAGGTTTTTATTTTT
28336186 ATTTTTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.67
Consensus pattern (16 bp):
CAGGTTTTTATTTTTG
Found at i:28336225 original size:26 final size:26
Alignment explanation
Indices: 28336196--28336257 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
28336186 ATTTTTTGGT
*
28336196 ATATTTTGGTAAATAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAATTATA
28336222 ATATTTTGGTAAATAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAATTATA
28336248 ATATTTTGGT
1 ATATTTTGGT
28336258 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.44
Consensus pattern (26 bp):
ATATTTTGGTAAATAAAAAAATTATA
Found at i:28338948 original size:34 final size:35
Alignment explanation
Indices: 28338890--28338956 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28338880 AAAACACCAG
28338890 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
28338925 AAAATATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
28338957 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28340289 original size:48 final size:48
Alignment explanation
Indices: 28340218--28340312 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
28340208 TTCTTTGCTT
*
28340218 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAATGATTCAACAGC
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
* *
28340266 AAAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAG
28340313 AATTCCCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAGC
Found at i:28340569 original size:36 final size:36
Alignment explanation
Indices: 28340517--28340587 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
28340507 ATCAAAGGCT
28340517 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
* * *
28340553 ACAATTAGAAGTTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGA
28340588 TTACATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:28345678 original size:17 final size:17
Alignment explanation
Indices: 28345656--28345716 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
28345646 CATCAAAGGC
28345656 TACAATTAAAAGCTGTA
1 TACAATTAAAAGCTGTA
*
28345673 TACAATTAAAA-CTCTAAGA
1 TACAATTAAAAGCTGT---A
* *
28345692 CACAATTAGAAGCTGTA
1 TACAATTAAAAGCTGTA
28345709 TACAATTA
1 TACAATTA
28345717 GAACTTTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 19 0.54
19 10 0.29
20 3 0.09
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (17 bp):
TACAATTAAAAGCTGTA
Found at i:28345705 original size:36 final size:36
Alignment explanation
Indices: 28345657--28345727 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
28345647 ATCAAAGGCT
28345657 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
* * *
28345693 ACAATTAGAAGCTGTATACAATTAGAACTTTAAGA
1 ACAATTAAAAGCTGTATACAATTAAAACTCTAAGA
28345728 TTACATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:28348356 original size:13 final size:12
Alignment explanation
Indices: 28348338--28348375 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
28348328 TTTTACATAT
28348338 ATATTAATTTTAA
1 ATATTAA-TTTAA
28348351 ATATTAA-TTAA
1 ATATTAATTTAA
28348362 ATATTAATATTAA
1 ATATTAAT-TTAA
28348375 A
1 A
28348376 ATTTCGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
13 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTAATTTAA
Found at i:28348473 original size:30 final size:30
Alignment explanation
Indices: 28348402--28348475 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
28348392 AAAATATAAA
*
28348402 TTACATTTTGACCCTTAAACTTTTCCAAAT
1 TTACATCTTGACCCTTAAACTTTTCCAAAT
* * ***
28348432 TTACATTTTGACCCTTAACCTTTTTTGAAT
1 TTACATCTTGACCCTTAAACTTTTCCAAAT
*
28348462 TTGCATCTTGACCC
1 TTACATCTTGACCC
28348476 ATAATATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (30 bp):
TTACATCTTGACCCTTAAACTTTTCCAAAT
Found at i:28349241 original size:7 final size:7
Alignment explanation
Indices: 28349219--28349290 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
28349209 AGCCCGAAGG
28349219 AGAA-AA
1 AGAAGAA
28349225 AGAA-ATA
1 AGAAGA-A
*
28349232 AGAAGGA
1 AGAAGAA
28349239 AGAAGAA
1 AGAAGAA
*
28349246 AAAAGAA
1 AGAAGAA
28349253 AGAAGAA
1 AGAAGAA
*
28349260 AAAGAGAA
1 AGA-AGAA
*
28349268 AAAAGGAA
1 AGAA-GAA
28349276 AGAA-AA
1 AGAAGAA
28349282 AGAA-AA
1 AGAAGAA
28349288 AGA
1 AGA
28349291 CAGCAACCCA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
6 16 0.29
7 27 0.48
8 13 0.23
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (7 bp):
AGAAGAA
Found at i:28349246 original size:17 final size:17
Alignment explanation
Indices: 28349219--28349259 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28349209 AGCCCGAAGG
* *
28349219 AGAAAAAGAAATAAGAA
1 AGAAGAAGAAAAAAGAA
*
28349236 GGAAGAAGAAAAAAGAA
1 AGAAGAAGAAAAAAGAA
28349253 AGAAGAA
1 AGAAGAA
28349260 AAAGAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (17 bp):
AGAAGAAGAAAAAAGAA
Found at i:28349269 original size:20 final size:19
Alignment explanation
Indices: 28349219--28349290 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
28349209 AGCCCGAAGG
*
28349219 AGAAAAAGAAATAAGAAGGA
1 AGAAAAAGAAA-AAGAAAGA
*
28349239 AG-AAGA-AAAAAGAAAGA
1 AGAAAAAGAAAAAGAAAGA
*
28349256 AGAAAAAGAGAAAA-AAGGAA
1 AGAAAAAGA-AAAAGAAAG-A
28349276 AGAAAAAGAAAAAGA
1 AGAAAAAGAAAAAGA
28349291 CAGCAACCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 9 0.21
18 6 0.14
19 11 0.26
20 17 0.40
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (19 bp):
AGAAAAAGAAAAAGAAAGA
Found at i:28349995 original size:17 final size:17
Alignment explanation
Indices: 28349952--28349999 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
28349942 TTTTAAAAAA
28349952 TCGTGTTTCAAAAGTTT
1 TCGTGTTTCAAAAGTTT
*
28349969 TCATGTTTTCAAAA-TTT
1 TCGTG-TTTCAAAAGTTT
28349986 CTCGTGTTTCAAAA
1 -TCGTGTTTCAAAA
28350000 AATAATAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (17 bp):
TCGTGTTTCAAAAGTTT
Found at i:28350105 original size:18 final size:17
Alignment explanation
Indices: 28350056--28350266 Score: 93
Period size: 18 Copynumber: 12.1 Consensus size: 17
28350046 TTTAAAAAAT
28350056 AATTTTCGTGTTTC--A
1 AATTTTCGTGTTTCAAA
*
28350071 AACTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
28350089 AATTTCTCGTGTTTCAAAA
1 AATTT-TCGTGTTTC-AAA
28350108 AATTTT-G-G---C---
1 AATTTTCGTGTTTCAAA
* *
28350117 -CTTTTCGCGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
28350134 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
* * *
28350152 AATTTCTCCTATTTTAAA
1 AATTT-TCGTGTTTCAAA
28350170 AATTTTCGACTTTTTGCGTTTTCAAA
1 AATTTTCG------T--GT-TTCAAA
* *
28350196 AATTTTCGTGTTTTAGA
1 AATTTTCGTGTTTCAAA
*
28350213 AATTTTCGTGTTTCTAA
1 AATTTTCGTGTTTCAAA
* *
28350230 AATTCTCGTATTTCAAA
1 AATTTTCGTGTTTCAAA
*
28350247 AATTTCCGTGTTCTCAAA
1 AATTTTCGTGTT-TCAAA
28350265 AA
1 AA
28350267 AATTAGTATC
Statistics
Matches: 148, Mismatches: 22, Indels: 49
0.68 0.10 0.22
Matches are distributed among these distances:
8 4 0.03
9 1 0.01
10 1 0.01
13 1 0.01
14 1 0.01
15 9 0.06
16 5 0.03
17 44 0.30
18 50 0.34
19 16 0.11
20 1 0.01
23 1 0.01
25 1 0.01
26 13 0.09
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (17 bp):
AATTTTCGTGTTTCAAA
Found at i:28350107 original size:17 final size:16
Alignment explanation
Indices: 28350056--28350107 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 16
28350046 TTTAAAAAAT
28350056 AATTTTCGTGTTTC-A
1 AATTTTCGTGTTTCAA
*
28350071 AACTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC-AA
28350089 AATTTCTCGTGTTTCAA
1 AATTT-TCGTGTTTCAA
28350106 AA
1 AA
28350108 AATTTTGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 9 0.29
16 4 0.13
17 4 0.13
18 9 0.29
19 5 0.16
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (16 bp):
AATTTTCGTGTTTCAA
Found at i:28350150 original size:63 final size:63
Alignment explanation
Indices: 28350074--28350231 Score: 232
Period size: 62 Copynumber: 2.6 Consensus size: 63
28350064 TGTTTCAAAC
* * *
28350074 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCAAAAAATTTTGGCCTTTTCGCGTTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAAAAAT
* * *
28350137 TTTCGTGTTTTCAAAAATTTCTCCTATTT-TAAAAATTTTCGACTTTTTGCGTTTTCAAAAAT
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAAAAAT
*
28350199 TTTCGTGTTTT-AGAAATTT-TCGTGTTTCTAAAA
1 TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAA
28350232 TTCTCGTATT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
60 6 0.07
61 12 0.14
62 40 0.47
63 27 0.32
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (63 bp):
TTTCGTGTTTTCAAAAATTTCTCGTGTTTCTAAAAATTTTCGACTTTTCGCGTTTTCAAAAAT
Found at i:28350201 original size:17 final size:17
Alignment explanation
Indices: 28350189--28350266 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 17
28350179 CTTTTTGCGT
28350189 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
* *
28350206 TTTTAGAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
* * *
28350223 TTTCTAAAATTCTCGTA
1 TTTCAAAAATTTTCGTG
*
28350240 TTTCAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
28350257 TTCTCAAAAA
1 TT-TCAAAAA
28350267 AATTAGTATC
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 42 0.86
18 7 0.14
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:28351393 original size:25 final size:25
Alignment explanation
Indices: 28351364--28351514 Score: 101
Period size: 25 Copynumber: 6.1 Consensus size: 25
28351354 CTTTCTCTCA
*
28351364 AGCCATATAACGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGAG
* * **
28351389 AGCCATGTAACGGGAAGCTAATTCG
1 AGCCATATAACGGGAAGCTCATGAG
** * *
28351414 AGCTGTATAACGAGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
* * * *
28351439 AGCCATAATTA--GGAAGTTCAAGCG
1 AGCCAT-ATAACGGGAAGCTCATGAG
* **
28351463 AGCCA-ATATCGGGAAGCTCCGGAG
1 AGCCATATAACGGGAAGCTCATGAG
* * *
28351487 AGCCATATATCAGGAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATGAG
28351512 AGC
1 AGC
28351515 TATGGTGTGT
Statistics
Matches: 93, Mismatches: 29, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
22 2 0.02
24 27 0.29
25 61 0.66
26 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGAG
Found at i:28359380 original size:29 final size:32
Alignment explanation
Indices: 28359338--28359396 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
28359328 ATTATTTGTG
*
28359338 AAAATTGAATC-AAATCAAAATTT-TATATTT
1 AAAATCGAATCAAAATCAAAATTTGTATATTT
*
28359368 AAAATCGAA-CAAAATCAAAGTTTGTATAT
1 AAAATCGAATCAAAATCAAAATTTGTATAT
28359397 GATATTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 19 0.76
31 5 0.20
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (32 bp):
AAAATCGAATCAAAATCAAAATTTGTATATTT
Found at i:28359435 original size:43 final size:43
Alignment explanation
Indices: 28359388--28359481 Score: 181
Period size: 43 Copynumber: 2.2 Consensus size: 43
28359378 AAAATCAAAG
28359388 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
1 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
28359431 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
1 TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
28359474 TTT-TATAT
1 TTTGTATAT
28359482 TTATCCTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 5 0.10
43 46 0.90
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (43 bp):
TTTGTATATGATATTACATATTGAATCAAAATTCGTATATAAT
Found at i:28363350 original size:20 final size:20
Alignment explanation
Indices: 28363325--28363379 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
28363315 AAAACCTCTG
*
28363325 GTATCGATATTTTTACACTA
1 GTATCGATATTTTTACAATA
*
28363345 GTATCGATATTTTTATAATA
1 GTATCGATATTTTTACAATA
*
28363365 GTATCAATATTTTTA
1 GTATCGATATTTTTA
28363380 AGTTGGTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
GTATCGATATTTTTACAATA
Found at i:28369701 original size:23 final size:23
Alignment explanation
Indices: 28369675--28369750 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
28369665 TTTAAAAACA
28369675 CTTTTAATTTATTATATCAAAAT
1 CTTTTAATTTATTATATCAAAAT
** * *
28369698 CTTTT-ATCAAAGCTTA-ATTTAACA-
1 CTTTTAAT-TTA--TTATA-TCAAAAT
28369722 CTTTTAATTTATTATATCAAAAT
1 CTTTTAATTTATTATATCAAAAT
28369745 CTTTTA
1 CTTTTA
28369751 TCAAAGCTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 9 0.24
23 13 0.34
24 7 0.18
25 9 0.24
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (23 bp):
CTTTTAATTTATTATATCAAAAT
Found at i:28369723 original size:47 final size:47
Alignment explanation
Indices: 28369671--28369768 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
28369661 TACATTTAAA
28369671 AACACTTTTAATTTATTATATCAAAATCTTTTATCAAAGCTTAATTT
1 AACACTTTTAATTTATTATATCAAAATCTTTTATCAAAGCTTAATTT
28369718 AACACTTTTAATTTATTATATCAAAATCTTTTATCAAAGCTTAATTT
1 AACACTTTTAATTTATTATATCAAAATCTTTTATCAAAGCTTAATTT
28369765 AACA
1 AACA
28369769 ATGGATTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (47 bp):
AACACTTTTAATTTATTATATCAAAATCTTTTATCAAAGCTTAATTT
Found at i:28376521 original size:62 final size:59
Alignment explanation
Indices: 28376413--28376530 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 59
28376403 TATAATCCCT
*
28376413 AGGGTAGCTTAAAGGAGAAGATCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
1 AGGGTAGCTTAAAGGAGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
* *
28376472 AGGGTAGCTTAAAGAAGAAGAAGAGCCTGTTATCATCGTGCCTTGGGGTATTTATAGGG
1 AGGGTAGCTTAAAG--G-AGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGG
28376531 GGAAGGTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 14 0.26
61 1 0.02
62 38 0.72
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (59 bp):
AGGGTAGCTTAAAGGAGAAGAGCCTGTTATCATCATGCCTTAGGGTATTTATAGGGCCC
Found at i:28385134 original size:22 final size:22
Alignment explanation
Indices: 28385095--28385141 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
28385085 ATAATAGTTC
**
28385095 AAAAATTTTCTTTTCATTTATTA
1 AAAAATTTTCTTGACATTTA-TA
28385118 AAAAATTTTC-TGACATTTATA
1 AAAAATTTTCTTGACATTTATA
28385139 AAA
1 AAA
28385142 TCTATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 7 0.32
23 10 0.45
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
AAAAATTTTCTTGACATTTATA
Found at i:28392369 original size:2 final size:2
Alignment explanation
Indices: 28392362--28392387 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28392352 ATGCTACATT
28392362 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
28392388 AAGCTGTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28401003 original size:164 final size:164
Alignment explanation
Indices: 28400732--28401093 Score: 661
Period size: 164 Copynumber: 2.2 Consensus size: 164
28400722 CCTCTGCCGA
* * *
28400732 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTTCCTTGTTGCTGAAGCCTTAGTTGCAGCTTCT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
28400797 TCAAGCTTTCGAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTCT
66 TCAAGCTTTCGAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTCT
28400862 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
131 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
* *
28400896 TTTCCTTATTGGTAAGTTAATCCCCTTTAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
*
28400961 TCAAGCTTTCGAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTTAAGTTTTCT
66 TCAAGCTTTCGAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTCT
28401026 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
131 TCTTTTATGATATTATTGGCATAACTGAGTAGTT
*
28401060 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTT
28401094 GTTTCACTCT
Statistics
Matches: 189, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
164 189 1.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.45
Consensus pattern (164 bp):
TTTCCTTGTTGGTAAGTTAATCCCCTTCAAATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCCTCT
TCAAGCTTTCGAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATGGGTTCTTCAAGTTTTCT
TCTTTTATGATATTATTGGCATAACTGAGTAGTT
Found at i:28412573 original size:47 final size:45
Alignment explanation
Indices: 28412522--28412686 Score: 121
Period size: 47 Copynumber: 3.6 Consensus size: 45
28412512 TATTTAATAT
28412522 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAAATTATTAT-AA
* * **
28412569 TAATT-TTATGAAA-TTATATATT-AT-T-A-AATTA-TATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAAATTAT-T-ATAA
* * * *
28412610 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAAATTATTA-TAA
28412657 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
28412687 TTTTAATTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
40 3 0.03
41 15 0.16
42 6 0.07
43 7 0.08
44 4 0.04
45 8 0.09
46 5 0.05
47 35 0.38
48 8 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAAATTATTATAA
Found at i:28412598 original size:25 final size:24
Alignment explanation
Indices: 28412570--28412627 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28412560 TATTATCAAT
* *
28412570 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
28412595 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
28412621 AATTATA
1 AATTATA
28412628 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:28412608 original size:88 final size:91
Alignment explanation
Indices: 28412448--28412652 Score: 299
Period size: 88 Copynumber: 2.3 Consensus size: 91
28412438 TTGATTTTAG
* *
28412448 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
28412513 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* *
28412540 TAAATTCATATAAGAAAAATTATTATCAATAATTTTATGAAA-T-TATAT-ATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
28412602 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
28412628 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
28412653 GTTATAATTA
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
88 59 0.57
89 5 0.05
90 1 0.01
91 22 0.21
92 16 0.16
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:28412694 original size:47 final size:49
Alignment explanation
Indices: 28412570--28412695 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 49
28412560 TATTATCAAT
* *
28412570 AATTTTATGAAATTATATATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGTAATAATAATTATTTTA
* *** * *
28412621 AATTATA-CAAATTCATATAAGATAATT-TAT-TAGTTATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATATGTAATAATAATTATTTTA
*
28412668 AATTTTATTAAATCATATATTTTAATTA
1 AATTTTATCAAATCATATATTTTAATTA
28412696 AAATATATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
47 33 0.56
48 6 0.10
49 4 0.07
50 4 0.07
51 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (49 bp):
AATTTTATCAAATCATATATTTTAATTATATGTAATAATAATTATTTTA
Found at i:28412823 original size:16 final size:16
Alignment explanation
Indices: 28412802--28412843 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28412792 TTATTAAATT
*
28412802 ATATATTTTAATTATA
1 ATATATTTTAATAATA
28412818 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
28412833 AT-TATGTTTAA
1 ATATAT-TTTAA
28412844 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:28412828 original size:15 final size:15
Alignment explanation
Indices: 28412793--28412834 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28412783 TTAAGAATTT
*
28412793 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28412807 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28412821 TATTTAATAATAAT
1 TATTTAATTATAAT
28412835 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28413078 original size:16 final size:16
Alignment explanation
Indices: 28413057--28413094 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28413047 TTGATTTGCT
*
28413057 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
28413073 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
28413089 AATACA
1 ATTACA
28413095 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:28417188 original size:19 final size:19
Alignment explanation
Indices: 28417164--28417200 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28417154 ATTCAAGCCC
*
28417164 CAAGATTAAATAATAAAAG
1 CAAGATTAAATAAGAAAAG
28417183 CAAGATTAAATAAGAAAA
1 CAAGATTAAATAAGAAAA
28417201 AAATTCACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.19
Consensus pattern (19 bp):
CAAGATTAAATAAGAAAAG
Found at i:28420074 original size:38 final size:39
Alignment explanation
Indices: 28419978--28420099 Score: 112
Period size: 38 Copynumber: 3.2 Consensus size: 39
28419968 CTTTGAATGC
** * *
28419978 ATATATATA-TTATTCAAATACATATGCCAAAAGCAA-AT
1 ATATATATACTTA-TCAACCACATATGCCGAATGCAACAT
* *
28420016 A-AT-TATACTTATCAACCACATGTGCTGAATGC-ACAT
1 ATATATATACTTATCAACCACATATGCCGAATGCAACAT
*
28420052 ATATATATACTTAT-AATTCACATATGCCGAATGCATACAT
1 ATATATATACTTATCAA-CCACATATGCCGAATGCA-ACAT
28420092 ATATATAT
1 ATATATAT
28420100 CCAACAATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
35 1 0.01
36 22 0.32
37 9 0.13
38 24 0.35
40 12 0.18
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (39 bp):
ATATATATACTTATCAACCACATATGCCGAATGCAACAT
Found at i:28426504 original size:21 final size:19
Alignment explanation
Indices: 28426479--28426519 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28426469 AAAATTCAGA
28426479 AAATAAATAAAACAAACAAAG
1 AAATAAA-AAAA-AAACAAAG
*
28426500 AAATAAAAAAAAAACTAAG
1 AAATAAAAAAAAAACAAAG
28426519 A
1 A
28426520 TGAAATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (19 bp):
AAATAAAAAAAAAACAAAG
Found at i:28429197 original size:18 final size:21
Alignment explanation
Indices: 28429144--28429198 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
28429134 TGCGATTGGT
28429144 TATTGTAGTGGTGAGATTAAA
1 TATTGTAGTGGTGAGATTAAA
**
28429165 TATTGTAGTAATGAGATTAAA
1 TATTGTAGTGGTGAGATTAAA
28429186 -A-T-TAGTGGTGAGA
1 TATTGTAGTGGTGAGA
28429199 CATGTGTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 9 0.30
19 1 0.03
20 1 0.03
21 19 0.63
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (21 bp):
TATTGTAGTGGTGAGATTAAA
Found at i:28431819 original size:16 final size:16
Alignment explanation
Indices: 28431800--28431830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28431790 ATTGATGGAA
*
28431800 AATTCACAGATACATG
1 AATTCACACATACATG
28431816 AATTCACACATACAT
1 AATTCACACATACAT
28431831 TGTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (16 bp):
AATTCACACATACATG
Found at i:28443180 original size:39 final size:39
Alignment explanation
Indices: 28443055--28443276 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 39
28443045 TCCTCGTTCA
* * *
28443055 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCACC
*
28443095 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA-C
1 AATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCACC
*
28443134 AATTGCCTTCGGGACTTAACCCGGATTAGTAACTCGCACC
1 AA-TGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCACC
* *
28443174 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCACC
* * * * *
28443213 AATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-C
1 AATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCACC
*
28443253 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28443277 CATCATTCAA
Statistics
Matches: 156, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
38 11 0.07
39 49 0.31
40 88 0.56
41 8 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCACC
Found at i:28443236 original size:118 final size:119
Alignment explanation
Indices: 28443055--28443276 Score: 281
Period size: 118 Copynumber: 1.9 Consensus size: 119
28443045 TCCTCGTTCA
* *
28443055 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
* * *
28443120 TTAGTAAC-TCGCACAATTGCCTTCGGGACTTAACCCGGATTAGTAACTCGCACC
66 ATAGTAACTTAGCACAA-AGCCTTCGGGACTTAACCCGGATTAGTAACTCGCACC
* * **
28443174 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* * *
28443236 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
28443277 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
117 4 0.05
118 65 0.74
119 19 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTAGTAACTCGCACC
Found at i:28454744 original size:6 final size:6
Alignment explanation
Indices: 28454732--28454775 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
28454722 TAATTTTCTC
* *
28454732 AAAATG GAAATG GAAATG AAAATG AAAATG AAAATG AGAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG A
28454776 TTTATTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:28466101 original size:61 final size:58
Alignment explanation
Indices: 28466036--28466151 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 58
28466026 AGTGATTATC
* * *
28466036 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAGATATTCTATTAATTTAATAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAGAT
28466097 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
28466152 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 22 0.42
59 1 0.02
60 1 0.02
61 28 0.54
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAGAT
Found at i:28466170 original size:58 final size:60
Alignment explanation
Indices: 28466038--28466171 Score: 168
Period size: 58 Copynumber: 2.2 Consensus size: 60
28466028 TGATTATCTT
* * * *
28466038 AATATTAAATTTAATTTAATATTTATCTTGTAGATAGATATTCTATTAATTTAATAGATTT
1 AATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATA-ATTA
28466099 AATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAAT-ATTA
1 AATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAATTA
*
28466155 AAGTGATTAAGTTTAAT
1 AA-T-ATTAAATTTAAT
28466172 TATAATTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
56 5 0.08
57 1 0.02
58 32 0.48
59 1 0.02
60 1 0.02
61 26 0.39
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (60 bp):
AATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAATTA
Found at i:28469819 original size:53 final size:53
Alignment explanation
Indices: 28469752--28470012 Score: 276
Period size: 53 Copynumber: 4.9 Consensus size: 53
28469742 AGCACTAAAG
* * * * *
28469752 GACCATATCATGTAAAATCATAATTGGTGGGTTATGACATCATATGGAATGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
* *
28469805 GACCATATCGTGTAAGACCATAACTGGTGAGTTATGGCATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
* * * * *
28469858 AAACATATCATGTAAGACCATAACTGGTGGGTTAAGGCATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
* * * **
28469911 GATCATATTGTGTAAGA-CAGTAACTGATGGGTTAT-AGCAT-ATTATATAAAGAA
1 GACCATATCGTGTAAGACCA-TAACTGGTGGGTTATGA-CATCA-TATGGAAAGAA
* * * * *
28469964 GGCCATATCGTGTAAGACCGTAACTAGTGGGTTATCATATCATATGGAA
1 GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAA
28470013 GAACTTAAGA
Statistics
Matches: 172, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
52 3 0.02
53 166 0.97
54 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCATAACTGGTGGGTTATGACATCATATGGAAAGAA
Found at i:28474599 original size:15 final size:14
Alignment explanation
Indices: 28474568--28474608 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
28474558 TGTTTCATTG
*
28474568 AAAATAATTTTTGA
1 AAAATGATTTTTGA
28474582 AAAATGATTTTTGA
1 AAAATGATTTTTGA
28474596 AAAATGATATTTT
1 AAAATGAT-TTTT
28474609 CTGATGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (14 bp):
AAAATGATTTTTGA
Found at i:28475771 original size:20 final size:19
Alignment explanation
Indices: 28475711--28475817 Score: 81
Period size: 21 Copynumber: 5.3 Consensus size: 19
28475701 AAATTATTAT
* *
28475711 AAAATATGAAAATACAAAA
1 AAAATATAAAAATATAAAA
* * *
28475730 AATGAT-TAAAAATTTATTAA
1 AA-AATATAAAAATATA-AAA
28475750 AAAATCATAAAAATATAGAAA
1 AAAAT-ATAAAAATATA-AAA
*
28475771 AAAATTTAAAAATTATAAAA
1 AAAATATAAAAA-TATAAAA
*
28475791 AAAATAATATAAAAGATAAAA
1 AAAAT-ATA-AAAATATAAAA
28475812 AAAATA
1 AAAATA
28475818 CAGAAAATTA
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
19 11 0.16
20 21 0.30
21 33 0.48
22 4 0.06
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAATATAAAAATATAAAA
Found at i:28475781 original size:41 final size:40
Alignment explanation
Indices: 28475713--28475833 Score: 111
Period size: 41 Copynumber: 2.9 Consensus size: 40
28475703 ATTATTATAA
* *
28475713 AATATGAAA-ATACAAAAAATGATTAAAAATTTATTAAAAAAT
1 AATATAAAAGATAAAAAAAAT--TTAAAAA-TTATTAAAAAAT
* * *
28475755 CATA-AAAATATAGAAAAAAATTTAAAAATTATAAAAAAAAT
1 AATATAAAAGATA-AAAAAAATTTAAAAATTAT-TAAAAAAT
**
28475796 AATATAAAAGATAAAAAAAATACAGAAAATTATTAAAA
1 AATATAAAAGATAAAAAAAATTTA-AAAATTATTAAAA
28475834 TTTTATTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
40 4 0.06
41 33 0.51
42 21 0.32
43 7 0.11
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (40 bp):
AATATAAAAGATAAAAAAAATTTAAAAATTATTAAAAAAT
Found at i:28480147 original size:26 final size:27
Alignment explanation
Indices: 28480097--28480148 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
28480087 TTTTTCTAAT
* *
28480097 TTTTTATCTTTTATAATAAAATTTTAG
1 TTTTTATATTTTATAAGAAAATTTTAG
*
28480124 TTTTTATATTTT-TAAGAAATTTTTA
1 TTTTTATATTTTATAAGAAAATTTTA
28480149 AATTTCTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTTTATATTTTATAAGAAAATTTTAG
Found at i:28480196 original size:18 final size:18
Alignment explanation
Indices: 28480173--28480208 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28480163 TTCTATATGT
28480173 TTTTATAAATTTTGAATA
1 TTTTATAAATTTTGAATA
* *
28480191 TTTTATATATTTTTAATA
1 TTTTATAAATTTTGAATA
28480209 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATAAATTTTGAATA
Found at i:28480215 original size:30 final size:29
Alignment explanation
Indices: 28480147--28480222 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
28480137 AAGAAATTTT
* *
28480147 TAAATTTCTAGAATTTTTCTATATGTTTTTA
1 TAAATTT-T-GAATTTTTATATATGTTTTAA
28480178 TAAATTTTGAATATTTTATATAT-TTTTAA
1 TAAATTTTGAAT-TTTTATATATGTTTTAA
*
28480207 TAATATTTTTAATTTT
1 TAA-ATTTTGAATTTT
28480223 AAATGATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 15 0.38
30 18 0.45
31 7 0.17
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (29 bp):
TAAATTTTGAATTTTTATATATGTTTTAA
Found at i:28480657 original size:29 final size:30
Alignment explanation
Indices: 28480581--28480646 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
28480571 TTAATTTTTA
28480581 TTATTAAAATAA-AAATATAATATTGAATAAT
1 TTATTAAAATAATAAAT-T-ATATTGAATAAT
28480612 TTATTAAAATAATAAATTATATT-AATAAT
1 TTATTAAAATAATAAATTATATTGAATAAT
28480641 TTATTA
1 TTATTA
28480647 TATTATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 12 0.35
30 5 0.15
31 13 0.38
32 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
TTATTAAAATAATAAATTATATTGAATAAT
Found at i:28496922 original size:109 final size:110
Alignment explanation
Indices: 28496672--28496985 Score: 465
Period size: 109 Copynumber: 2.9 Consensus size: 110
28496662 TAAATTCAAG
* * * * * *
28496672 AGGATATTTTGCAATTTGGTTAAACGAG--AAATTGAAACCCAGCACATTAGGGTACG-TTCCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
28496734 GAATTTCCAAACACAAAACATTGCCTTATTTTAAATTTTTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAA-TATTTTTAAA
28496780 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
28496845 GAATTTCCAAACGCAAAACATTGCCTCATTTTAAA-ATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAATATTTTTAAA
* *
28496889 AGGATGTTTAGCTATTTGGTTGAACGAGAAAAATCGAAATCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
28496954 GAATTTCCCAAACGCTAAATATTGCCTTATTT
66 GAATTT-CCAAACGCAAAACATTGCCTTATTT
28496986 AGAAAAACAT
Statistics
Matches: 188, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
108 25 0.13
109 77 0.41
110 48 0.26
111 38 0.20
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (110 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTAAATATTTTTAAA
Found at i:28499238 original size:43 final size:42
Alignment explanation
Indices: 28499177--28499325 Score: 130
Period size: 43 Copynumber: 3.5 Consensus size: 42
28499167 CTTCAACCTA
* * * * *
28499177 CTCCACTGCTTCTCAGGGATATATGATTGGTTTCTTCTGTCTT
1 CTCCACTACTGCTTAGGGAGATA-GATTGGTTTCTTCTGTCTG
* *
28499220 CTCCACTACTGCTTAGGGAGATAAGACTT-G---ATGC-GATCTG
1 CTCCACTACTGCTTAGGGAGAT-AGA-TTGGTTTCTTCTG-TCTG
*
28499260 CTCCACTACTGCTTAGGGAGATCAGATCGGTTTCTT-TCGTCTG
1 CTCCACTACTGCTTAGGGAGAT-AGATTGGTTTCTTCT-GTCTG
28499303 CTCCACTACTGCTTAGGGAGATA
1 CTCCACTACTGCTTAGGGAGATA
28499326 AGACTTGATG
Statistics
Matches: 86, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
39 2 0.02
40 31 0.36
42 1 0.01
43 48 0.56
44 4 0.05
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (42 bp):
CTCCACTACTGCTTAGGGAGATAGATTGGTTTCTTCTGTCTG
Found at i:28499269 original size:40 final size:40
Alignment explanation
Indices: 28499220--28499349 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
28499210 CTTCTGTCTT
28499220 CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTG
* ** *
28499260 CTCCACTACTGCTTAGGGAGATCAGATCGGTTTCTTTCG-TCTG
1 CTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGCGATCTG
*
28499303 CTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTG
28499343 CTCCACT
1 CTCCACT
28499350 GTAATCTCAG
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
39 4 0.05
40 36 0.47
41 1 0.01
42 1 0.01
43 29 0.38
44 5 0.07
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.31
Consensus pattern (40 bp):
CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTG
Found at i:28499457 original size:131 final size:130
Alignment explanation
Indices: 28499314--28499852 Score: 381
Period size: 131 Copynumber: 4.1 Consensus size: 130
28499304 TCCACTACTG
* *
28499314 CTTAGGGAGATAAGA-CTTGATGTGATCTGCTCCACTGTAA-TCTCAGGGAGATAAGATCTCTGG
1 CTTAGGGAGATAAGATCTTGATGTAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTCTGT
*
28499377 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT
65 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTCGATCTACTCCACTGT
28499442 AA
129 AA
* ** * * * *
28499444 CCTTAGGGAGATAAGA-CCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC-CTTT
1 -CTTAGGGAGATAAGATCTTGATGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTCTGT
* * * ** * * * * *
28499507 ATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGA--T-AGTGTCTTCGATCTGCTCCGCTG
65 -CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTCGATCTACTCCACTG
28499569 TAA
128 TAA
* * * * *
28499572 TCTCAGGGAGATAAGATCTCTGGCT-TCAATCTGTTCCACTGTAACCTCGGGGAGATAAGATCTG
1 -CTTAGGGAGATAAGATCT-T-GATGT-AATCTGCTCCACTGTAACTTCAGGGAGATAAGATCT-
* * * * * * *
28499636 AAAT-TCTTCAGTCTGCTCCATTGTAACCTCAGAGAGATAAGACCTG-A---TGCGATCTACTCT
61 --CTGTCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTACTCC
28499696 ACTGTAA
124 ACTGTAA
* * * * * **
28499703 CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGT
1 CTT-AGGGAGATAAGAT-CTTGA-TGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTCT
* * * * * * **
28499767 GTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CTGGCTTCAATCTGTTCCACT
63 GTCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTCGATCTACTCCACT
28499830 GTAA
127 GTAA
*
28499834 CCTCAGGGAGATAAGATCT
1 -CTTAGGGAGATAAGATCT
28499853 AAAATTCTTC
Statistics
Matches: 312, Mismatches: 72, Indels: 49
0.72 0.17 0.11
Matches are distributed among these distances:
127 3 0.01
128 67 0.21
129 2 0.01
130 7 0.02
131 197 0.63
132 6 0.02
133 27 0.09
134 1 0.00
135 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (130 bp):
CTTAGGGAGATAAGATCTTGATGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTCTGTC
TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTACTCCACTGTAA
Found at i:28499479 original size:46 final size:45
Alignment explanation
Indices: 28499343--28499900 Score: 166
Period size: 44 Copynumber: 12.7 Consensus size: 45
28499333 ATGTGATCTG
* ** * *
28499343 CTCCACTGTAATCTCAGGGAGATAAGATCTCTG-GCTTC-A-ATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA-C-CTGAAATTCTACGTCTA
* *
28499387 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTAC-GTCTA
* * *
28499433 CTCCACTGTAACCTTAGGGAGATAAGACCTG--ATGCGA--TCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTACGTCTA
* * * ** * * **
28499474 CTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTA-ATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGA-CCTGAAATTCTACGTCTA
** * * * * *
28499518 CTCCACTACAACTTCAGGGAGATAGGA--T--AGTGTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAAT-TCTACG-TCTA
* * ** * *
28499561 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTG-GCTTC-A-ATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA-C-CTGAAATTCTACGTCTA
* * * * *
28499605 TTCCACTGTAACCTCGGGGAGATAAGATCTGAAATTCTTCAGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTAC-GTCTA
* * * *
28499651 CTCCATTGTAACCTCAGAGAGATAAGACCTG--ATGCGA--TCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTACGTCTA
* * * ** * * **
28499692 CTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTA-ATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGA-CCTGAAATTCTACGTCTA
* * * * *
28499736 CTCCACTGTAACTTCAGGGAGATAGGA--T--AGTGTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAAT-TCTACG-TCTA
* * ** * *
28499779 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTG-GCTTC-A-ATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA-C-CTGAAATTCTACGTCTA
* * * *
28499823 TTCCACTGTAACCTCAGGGAGATAAGATCTAAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTAC-GTCTA
* * *
28499869 CTCCACTGTAACTTTAGAGAGATAAGACCTGA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGA
28499901 TGCGATCTAC
Statistics
Matches: 377, Mismatches: 101, Indels: 70
0.69 0.18 0.13
Matches are distributed among these distances:
40 2 0.01
41 60 0.16
42 14 0.04
43 65 0.17
44 137 0.36
46 91 0.24
47 6 0.02
48 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (45 bp):
CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTACGTCTA
Found at i:28499582 original size:218 final size:218
Alignment explanation
Indices: 28499337--28500028 Score: 1276
Period size: 218 Copynumber: 3.2 Consensus size: 218
28499327 GACTTGATGT
* *
28499337 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
*
28499402 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTTAGGGAGATAAGACCTGATG
66 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTTAGAGAGATAAGACCTGATG
**
28499467 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTACAACTT
131 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
28499532 CAGGGAGATAGGATAGTGTCTTC
196 CAGGGAGATAGGATAGTGTCTTC
28499555 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
* * * * *
28499620 GGGGAGATAAGATCTGAAATTCTTCAGTCTGCTCCATTGTAACCTCAGAGAGATAAGACCTGATG
66 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTTAGAGAGATAAGACCTGATG
28499685 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
131 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
28499750 CAGGGAGATAGGATAGTGTCTTC
196 CAGGGAGATAGGATAGTGTCTTC
28499773 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
* *
28499838 AGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACTGTAACTTTAGAGAGATAAGACCTGATG
66 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTTAGAGAGATAAGACCTGATG
28499903 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
131 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
28499968 CAGGGAGATAGGATAGTGTCTTC
196 CAGGGAGATAGGATAGTGTCTTC
28499991 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
28500029 AACATTCACT
Statistics
Matches: 457, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 457 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (218 bp):
GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTTAGAGAGATAAGACCTGATG
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
CAGGGAGATAGGATAGTGTCTTC
Found at i:28500024 original size:87 final size:86
Alignment explanation
Indices: 28499338--28500025 Score: 400
Period size: 87 Copynumber: 7.9 Consensus size: 86
28499328 ACTTGATGTG
* * *
28499338 ATCTGCTCCACTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTC
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGAT-ACTGTCTTCGATCTGCTCCACTGTAA-CTC
** *
28499402 AGGGAGATAAGAT-CTGAAATTCTTCG
63 AGGGAGATAAGATCCT-TTA-T-TTCA
* * * * * * *
28499428 GTCTACTCCACTGTAACCTT-AGGGAGATAAGA-CCTG-ATGCGATCTACTCTACTGTAACTTCA
1 ATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATACTGTCTTCGATCTGCTCCACTGTAAC-TCA
* *
28499490 GAGAGATAAGATCCTTTATTTTA
64 GGGAGATAAGATCCTTTATTTCA
* ** * * *
28499513 ATCCGCTCCACTACAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTCGATCTGCTCCACTGTAA-CTCAG
***
28499578 GGAGATAAGAT-CTCTGGCTTCA
65 GGAGATAAGATCCT-TTATTTCA
* * * *
28499600 ATCTGTTCCACTGTAACCTCGGGGAGATAAGAT-CTGAAATTCTTC-AGTCTGCTCCATTGTAAC
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTG----TCTTCGA-TCTGCTCCACTGTAA-
* * * *
28499663 CTCAGAGAGATAAGA-CC-TGA-TGCG
60 CTCAGGGAGATAAGATCCTTTATTTCA
* * * * * * ** *
28499687 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGT-CTTCGATCTGCTCCACTGTAAC-TCA
* ** * * *
28499752 GGGAGATAGGATAGTGT-CTTCG
64 GGGAGATAAGATCCTTTATTTCA
* * * * *
28499774 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGAT-ACTGTCTTCGATCTGCTCCACTGTAA-CTC
** *
28499838 AGGGAGATAAGAT-CTAAAATTCTTCG
63 AGGGAGATAAGATCCT-TTA-T-TTCA
* * * * * * * * *
28499864 GTCTACTCCACTGTAACTTTAGAGAGATAAGA-CCTG-ATGCGATCTACTCTACTGTAACTTCAG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTCGATCTGCTCCACTGTAAC-TCAG
* *
28499927 AGAGATAAGATCCTTTATTTTA
65 GGAGATAAGATCCTTTATTTCA
* * * *
28499949 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTCGATCTGCTCCACTGTAA-CTCAG
28500014 GGAGATAAGATC
65 GGAGATAAGATC
28500026 TCTAACATTC
Statistics
Matches: 452, Mismatches: 111, Indels: 73
0.71 0.17 0.11
Matches are distributed among these distances:
84 5 0.01
85 79 0.17
86 15 0.03
87 242 0.54
88 19 0.04
89 1 0.00
90 88 0.19
91 2 0.00
92 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (86 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTCGATCTGCTCCACTGTAACTCAGG
GAGATAAGATCCTTTATTTCA
Found at i:28511760 original size:109 final size:110
Alignment explanation
Indices: 28511527--28511828 Score: 432
Period size: 109 Copynumber: 2.8 Consensus size: 110
28511517 ATATTTTGCA
* * * * *
28511527 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGTACG-TTCCTCGAATTTTCAAACA
1 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
* *
28511589 CAAAACATTGCCTTATTTTAAATTTTTTTTTAAAAGGATATTTAGCT
66 CAAAACATTGCCTTATTTTAAA--TATTTTTAAAAGGATATTTAACT
28511636 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
* *
28511701 CAAAACATTGCCTCATTTTAAA-ATTTTTAAAAGGATGTTTAACT
66 CAAAACATTGCCTTATTTTAAATATTTTTAAAAGGATATTTAACT
* *
28511745 ATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTCAAATTTCCCAAAC
1 ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTT-CCAAAC
* *
28511810 GCTAAATATTGCCTTATTT
65 GCAAAACATTGCCTTATTT
28511829 AGAAAAACAT
Statistics
Matches: 175, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
109 89 0.51
110 22 0.13
111 27 0.15
112 37 0.21
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (110 bp):
ATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
CAAAACATTGCCTTATTTTAAATATTTTTAAAAGGATATTTAACT
Found at i:28526448 original size:37 final size:37
Alignment explanation
Indices: 28526407--28526591 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
28526397 TAGTTTTAGC
28526407 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
28526444 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
*
28526481 TACAATTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
* *
28526518 TACACTTATCTGATCAAAAAACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
****
28526555 TACACTTATCTGATCAAGTGGTAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
28526592 AGCCTAGCTA
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 138 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
Found at i:28531083 original size:5 final size:5
Alignment explanation
Indices: 28531070--28531105 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
28531060 TACAGTATCC
*
28531070 CTCAT CTCAA CTCAA CTCAA CTCAA CTCAA CTCAA C
1 CTCAA CTCAA CTCAA CTCAA CTCAA CTCAA CTCAA C
28531106 AGTCCAGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (5 bp):
CTCAA
Found at i:28536076 original size:45 final size:45
Alignment explanation
Indices: 28536022--28536114 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
28536012 TAACATGAAC
*
28536022 GTGTTTTCATTCACTCTCATTACCCATAATTTATAACACATTGTT
1 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
28536067 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
1 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
28536112 GTG
1 GTG
28536115 AATTAACCCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (45 bp):
GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
Found at i:28539314 original size:123 final size:125
Alignment explanation
Indices: 28539095--28539371 Score: 506
Period size: 123 Copynumber: 2.2 Consensus size: 125
28539085 TTTCGAGTTA
28539095 ACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
1 ACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
*
28539159 ATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAT-ATTTT-TTTTG
65 ATCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
*
28539218 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGATAAGAAATTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
28539283 TCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
66 TCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
28539343 ACGTTTCTGAGCAAATAGTATAAAATCGC
1 ACGTTTCTGAGCAAATAGTATAAAATCGC
28539372 GCCCTCGTGG
Statistics
Matches: 149, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
123 109 0.73
124 6 0.04
125 34 0.23
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (125 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
TCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
Found at i:28546163 original size:73 final size:73
Alignment explanation
Indices: 28546033--28546168 Score: 184
Period size: 73 Copynumber: 1.9 Consensus size: 73
28546023 CTTTGACTTT
* *
28546033 GGTCACACGGCCAAGCCACACACCCGTGTGCTAGACTGTGTGAGCATACTGACTTGCATTAATAA
1 GGTCACACGGCCAAGCCACACACCCGTGTGCTAGACCGTGTGAGCATACTGACTTGCACTAATAA
28546098 GATACAGG
66 GATACAGG
* * * * **
28546106 GGTCACATGGCCAAGCCACACGCTCGTGTGCTATG-CCGTGTGAGCATTCTGTTTTGCACTAAT
1 GGTCACACGGCCAAGCCACACACCCGTGTGCTA-GACCGTGTGAGCATACTGACTTGCACTAAT
28546169 TAAAAGATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
73 53 0.98
74 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (73 bp):
GGTCACACGGCCAAGCCACACACCCGTGTGCTAGACCGTGTGAGCATACTGACTTGCACTAATAA
GATACAGG
Found at i:28547186 original size:15 final size:15
Alignment explanation
Indices: 28547161--28547195 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28547151 TACTTTATTT
*
28547161 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
28547175 TAATTAATATTAAGA
1 TAATTAATATTAAGA
28547190 TAATTA
1 TAATTA
28547196 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:28550058 original size:68 final size:69
Alignment explanation
Indices: 28549948--28550087 Score: 219
Period size: 68 Copynumber: 2.0 Consensus size: 69
28549938 CTCGAAACAT
*
28549948 TTAGGAATGTCGAGATCAACATTCCGCTGTTGGACACCATCAAGAAAATACCACAGTATGCTAAA
1 TTAGGAATGTCGAGATCAACATTCCACTGTTGGACACCATCAAGAAAATACCACAGTATGCTAAA
28550013 TTTC
66 TTTC
* * * * *
28550017 TTAGGAATGTCGAGAT-TACATTCCACTGTTGGACGCCATCAAGCAAATACCGCGGTATGCTAAA
1 TTAGGAATGTCGAGATCAACATTCCACTGTTGGACACCATCAAGAAAATACCACAGTATGCTAAA
28550081 TTTC
66 TTTC
28550085 TTA
1 TTA
28550088 AAGAGCTTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
68 49 0.75
69 16 0.25
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (69 bp):
TTAGGAATGTCGAGATCAACATTCCACTGTTGGACACCATCAAGAAAATACCACAGTATGCTAAA
TTTC
Found at i:28551220 original size:4 final size:4
Alignment explanation
Indices: 28551211--28551275 Score: 62
Period size: 4 Copynumber: 15.5 Consensus size: 4
28551201 AATTTTTATT
*
28551211 TTTA TTTA TTTA TTTA TTTA TTTTC TTTA CTTTA TTTA -TTA CTTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA -TTTA -TTTA
28551262 TTT- TATTA TTTA TT
1 TTTA T-TTA TTTA TT
28551276 ACTTATTCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
3 4 0.08
4 33 0.63
5 15 0.29
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:28551230 original size:22 final size:21
Alignment explanation
Indices: 28551205--28551275 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
28551195 CAACCCAATT
28551205 TTTATTTTTATTTATTTATTTA
1 TTTA-TTTTATTTATTTATTTA
*
28551227 TTTATTTTCTTTACTTTATTTA
1 TTTATTTTATTTA-TTTATTTA
*
28551249 -TTACTTTATTTTATTT-TATTA
1 TTTATTTTA-TTTATTTAT-TTA
28551270 TTTATT
1 TTTATT
28551276 ACTTATTCGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 20 0.49
22 20 0.49
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTATTTATTTATTTA
Found at i:28552757 original size:25 final size:25
Alignment explanation
Indices: 28552729--28552843 Score: 101
Period size: 25 Copynumber: 4.6 Consensus size: 25
28552719 GTATAACAAA
* *
28552729 AAGCTCTTGCGAGCCAATTATCGGG
1 AAGCTCATGAGAGCCAATTATCGGG
* * *
28552754 AAGCTCAT-ACGAG-CTATAAACGGG
1 AAGCTCATGA-GAGCCAATTATCGGG
*
28552778 AAGCTCAAGAGAGCC-ATTAATCGGG
1 AAGCTCATGAGAGCCAATT-ATCGGG
* * *
28552803 AAGCTCTTGAGAGCCAAATATCGAG
1 AAGCTCATGAGAGCCAATTATCGGG
*
28552828 AAGCTCGTGAGAGCCA
1 AAGCTCATGAGAGCCA
28552844 TATAACATAA
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
24 20 0.28
25 50 0.69
26 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (25 bp):
AAGCTCATGAGAGCCAATTATCGGG
Found at i:28559925 original size:25 final size:24
Alignment explanation
Indices: 28559897--28559990 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 24
28559887 AGCTCTTGCA
28559897 AGCCAATTATCGGGAAGCTCATACG
1 AGCCAATTATCGGGAAGCTCATA-G
*
28559922 AGCC-ATAAAT-GGGAAGCTCAATAG
1 AGCCAAT-TATCGGGAAGCTC-ATAG
* *
28559946 AGCCATTTATCAGGAAGCTCATGAG
1 AGCCAATTATCGGGAAGCTCAT-AG
* *
28559971 ATCCAAATATCGGGAAGCTC
1 AGCCAATTATCGGGAAGCTC
28559991 GTGAAAGCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
24 20 0.36
25 36 0.64
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (24 bp):
AGCCAATTATCGGGAAGCTCATAG
Found at i:28560358 original size:59 final size:61
Alignment explanation
Indices: 28560266--28560382 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 61
28560256 CCTCGACAAG
*
28560266 TATACGTAGATTTGTAAGCTACTAGTCCGATACTTTTT-TTTT-CTCGATCCAATTCCGTA
1 TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCCGTA
28560325 TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCC
1 TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCC
28560383 ATATTAGGTC
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 37 0.67
60 4 0.07
61 14 0.25
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (61 bp):
TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCCGTA
Found at i:28564276 original size:24 final size:24
Alignment explanation
Indices: 28564249--28564309 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
28564239 TGGATTATAA
*
28564249 GAAGATGAAAGGTG-GAGAGTTAAG
1 GAAGATGAAAGGTGAAAG-GTTAAG
*
28564273 GAAGATGAAATGTGAAAGGTTAAG
1 GAAGATGAAAGGTGAAAGGTTAAG
*
28564297 AAAGATGAAAGGT
1 GAAGATGAAAGGT
28564310 TGAACATCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (24 bp):
GAAGATGAAAGGTGAAAGGTTAAG
Found at i:28565042 original size:29 final size:29
Alignment explanation
Indices: 28565000--28565057 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28564990 ATTGGATACT
28565000 CAATAGCAATTCTTTATAATATCATTGTG
1 CAATAGCAATTCTTTATAATATCATTGTG
28565029 CAATAGCAATTCTTTATAATATCATTGTG
1 CAATAGCAATTCTTTATAATATCATTGTG
28565058 TAACAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (29 bp):
CAATAGCAATTCTTTATAATATCATTGTG
Found at i:28570388 original size:24 final size:24
Alignment explanation
Indices: 28570356--28570408 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
28570346 ATAAATCATC
**
28570356 AATA-TAATTAAAATTATTATATT
1 AATATTAATTAAAACAATTATATT
28570379 AATATTAATTAAAACAATTATATT
1 AATATTAATTAAAACAATTATATT
28570403 AATATT
1 AATATT
28570409 TAAAAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AATATTAATTAAAACAATTATATT
Found at i:28570413 original size:21 final size:22
Alignment explanation
Indices: 28570356--28570417 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
28570346 ATAAATCATC
* *
28570356 AATATAATTAAAATTATTATATT
1 AATATTATTAAAA-AATTATATT
28570379 AATATTAATTAAAACAATTATATT
1 AATATT-ATTAAAA-AATTATATT
28570403 AATA-T-TTAAAAAATT
1 AATATTATTAAAAAATT
28570418 CCTTCCCCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
23 6 0.17
24 19 0.54
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATTATTAAAAAATTATATT
Found at i:28573591 original size:25 final size:25
Alignment explanation
Indices: 28573563--28573639 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
28573553 GGAATTTTTT
*
28573563 TTAATATTAATA-TAATTATTTTTCA
1 TTAATATTAATATTAA-TATTTTTAA
*
28573588 TTAATATTAATATTGATATTTTTAA
1 TTAATATTAATATTAATATTTTTAA
*
28573613 TTATATATTAATTATTTATAATTTTTA
1 TTA-ATATTAA-TATTAAT-ATTTTTA
28573640 TATAATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
25 23 0.51
26 9 0.20
27 6 0.13
28 7 0.16
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (25 bp):
TTAATATTAATATTAATATTTTTAA
Found at i:28592188 original size:7 final size:7
Alignment explanation
Indices: 28592178--28592202 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28592168 CAATTACAAC
28592178 TAAAATT
1 TAAAATT
28592185 TAAAATT
1 TAAAATT
28592192 TAAAATT
1 TAAAATT
28592199 TAAA
1 TAAA
28592203 GATAAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:28596015 original size:12 final size:12
Alignment explanation
Indices: 28595998--28596031 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28595988 GTTTTTGCCA
28595998 AAATTGACTAAC
1 AAATTGACTAAC
28596010 AAATTGACTAAC
1 AAATTGACTAAC
*
28596022 CAATATGACT
1 AAAT-TGACT
28596032 CATGATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (12 bp):
AAATTGACTAAC
Found at i:28598869 original size:26 final size:25
Alignment explanation
Indices: 28598839--28598887 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28598829 TCAAATGATG
*
28598839 TATGTTTATATGGAAATGAATTATCA
1 TATGTTTA-ATGCAAATGAATTATCA
*
28598865 TATGTTTAATTCAAATGAATTAT
1 TATGTTTAATGCAAATGAATTAT
28598888 GTATGCATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (25 bp):
TATGTTTAATGCAAATGAATTATCA
Found at i:28603943 original size:19 final size:20
Alignment explanation
Indices: 28603906--28603946 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
28603896 TGGGTAGGAC
28603906 TGTTTTCACAAAATCTGCAT
1 TGTTTTCACAAAATCTGCAT
* *
28603926 TGTTTT-ACTAAATGTGCAT
1 TGTTTTCACAAAATCTGCAT
28603945 TG
1 TG
28603947 ACGTGATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTTTTCACAAAATCTGCAT
Found at i:28605841 original size:26 final size:26
Alignment explanation
Indices: 28605808--28605867 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
28605798 TTTACAACAG
* *
28605808 TAAAATTTTGACAATTTTATTCCTGA
1 TAAAATTTTGACAATTTTACTCCTAA
**
28605834 TAAAATTTTGATGATTTTACTCCTAA
1 TAAAATTTTGACAATTTTACTCCTAA
28605860 TAAAATTT
1 TAAAATTT
28605868 CGAGAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (26 bp):
TAAAATTTTGACAATTTTACTCCTAA
Found at i:28617089 original size:3 final size:3
Alignment explanation
Indices: 28617072--28617139 Score: 66
Period size: 3 Copynumber: 23.0 Consensus size: 3
28617062 AGGTTAGATC
* * * * *
28617072 AAT AAA AAT -AT AAT AAT AGT AGT AGT AAT AAT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
28617119 AAC AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
28617140 GAAGCTCAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28617136 original size:21 final size:21
Alignment explanation
Indices: 28617081--28617137 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
28617071 CAATAAAAAT
* *
28617081 ATAATAATAGTAGTAGTAATA
1 ATAATAATAGTAATAGTAACA
* *
28617102 ATAATAATAATAATATTAACA
1 ATAATAATAGTAATAGTAACA
28617123 ATAATAATAGTAATA
1 ATAATAATAGTAATA
28617138 ATGAAGCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAATAATAGTAATAGTAACA
Found at i:28618843 original size:51 final size:51
Alignment explanation
Indices: 28618750--28618864 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
28618740 AGGAGATGTG
* ** * *
28618750 ATTCGTTGCCTTCAACTTTAATCTGTTCCATTAGAACACCAGGGAAATAAT
1 ATTCGCTGCCTTCAACTTTAATCCATTCCACTAGAACACCAGGGAAATAAA
* * *
28618801 ATTTGCTGCCTTCAGCTTTAATCCATTCCACT-GCAACTCCAGGGAAATAAA
1 ATTCGCTGCCTTCAACTTTAATCCATTCCACTAG-AACACCAGGGAAATAAA
*
28618852 ATTCGCTGTCTTC
1 ATTCGCTGCCTTC
28618865 GATCTGCTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (51 bp):
ATTCGCTGCCTTCAACTTTAATCCATTCCACTAGAACACCAGGGAAATAAA
Found at i:28619193 original size:132 final size:132
Alignment explanation
Indices: 28618842--28619866 Score: 1430
Period size: 132 Copynumber: 7.8 Consensus size: 132
28618832 TGCAACTCCA
* * * * * * * * *
28618842 GGGAA-ATAAAATTCGCTGTCTTCGATCTGCTCTACTACTGCTCAAGGAGACATGATCTGCAATC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
* * *
28618906 TTCAACCTACTCCACTACTGCTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTAGC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
28618971 TT
131 TT
* * * ** * *
28618973 GGGAAGATAAGATTCGCCATTTTTTTTATCTACTCCACTACTGCTTAGGGAGACAAGATTTACAT
1 GGGAAGATAAGATTCACC--GTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACAT
* *
28619038 TCTTCAACCTACTCCACTGCTGCTCAGGGAGAT-GAGATTAGTAGCCTAAATCTGCTTCCCTACT
64 TCTTCAACCTACTCCACTGCTGCTCAGGGAGATAG-GATTAGTGGCTTAAATCTGCTTCCCTACT
28619102 ACCTT
128 ACCTT
*
28619107 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
* * * *
28619172 TTCAACCTACTCCACTGCTGCTCAAGGAGAT-GAGATTAATAGCCTAAATCTGCTTGCCC-ACTA
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAG-GATTAGTGGCTTAAATCTGCTT-CCCTACTA
*
28619235 CATT
129 CCTT
* *
28619239 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
* * **
28619304 TTCAACCTACTCCACTGCTACTCAGGGAGATAGGATTAGTGGCTTAAATCTGTTTCCCTACTATT
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
28619369 TT
131 TT
* *
28619371 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTGCTGCTTAGGGAGACCAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
*
28619436 TTCAACCTACTCCACTACTGCTCAGGGAGATAGGATTAG-GAGCTTAAATCTGCTTCCCTACTAC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTG-GCTTAAATCTGCTTCCCTACTAC
28619500 CTT
130 CTT
* * * *
28619503 AGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTGCTGCTTAGGGAGACCAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
* *
28619568 TTCAACCTACTCCACTGTTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTAAC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
28619633 TT
131 TT
* * *
28619635 GGGAAGATAAGATTCATCGTCTTTGATCTGCTCCACTACTGCTTAGGGAAACAAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
* * *
28619700 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTTACTACT
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
28619765 TT
131 TT
* * * * * * * * * *
28619767 GGGAAGATAAGACTCAACATCTTCAATCTACTCCGCTACTGCTTAGAGAGACAGGATCTACAATA
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
*
28619832 TTCAACCTACTCAACTGCTGCTCAGGGAGATAGGA
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGA
28619867 CTTGTTATCT
Statistics
Matches: 809, Mismatches: 76, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
131 9 0.01
132 682 0.84
133 6 0.01
134 112 0.14
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACATTC
TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
TT
Found at i:28620463 original size:12 final size:12
Alignment explanation
Indices: 28620446--28620470 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28620436 TGACAACAAA
28620446 ATCTGAAGGGAT
1 ATCTGAAGGGAT
28620458 ATCTGAAGGGAT
1 ATCTGAAGGGAT
28620470 A
1 A
28620471 GTCTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ATCTGAAGGGAT
Found at i:28628087 original size:11 final size:12
Alignment explanation
Indices: 28628056--28628090 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28628046 CCGGTCAGCC
*
28628056 TATATTACTTTT
1 TATATTAATTTT
28628068 TATATTAATTTT
1 TATATTAATTTT
28628080 TATA-TAATTTT
1 TATATTAATTTT
28628091 AAAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:28628244 original size:30 final size:30
Alignment explanation
Indices: 28628210--28628272 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
28628200 ACTTAACAAG
*
28628210 CAAATATCTCTAACATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
* *
28628240 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
28628270 CAA
1 CAA
28628273 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:28634563 original size:25 final size:26
Alignment explanation
Indices: 28634535--28634601 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
28634525 CATTCGACCC
*
28634535 ACAGCTCATGTGAGCAGA-ACACTTT
1 ACAGCTCGTGTGAGCAGACACACTTT
* * *
28634560 ACAGCTCGTGTAAGCAGACCCATTTT
1 ACAGCTCGTGTGAGCAGACACACTTT
*
28634586 ATAGCTCGTGTGAGCA
1 ACAGCTCGTGTGAGCA
28634602 CTATTGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 16 0.46
26 19 0.54
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (26 bp):
ACAGCTCGTGTGAGCAGACACACTTT
Found at i:28638868 original size:17 final size:17
Alignment explanation
Indices: 28638846--28638879 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28638836 AATAAAGGAA
28638846 GTAATCTTAGAAGATTT
1 GTAATCTTAGAAGATTT
*
28638863 GTAATCTTAGAGGATTT
1 GTAATCTTAGAAGATTT
28638880 TATTCTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (17 bp):
GTAATCTTAGAAGATTT
Found at i:28641062 original size:33 final size:32
Alignment explanation
Indices: 28641024--28641104 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 32
28641014 CCAATAAAAC
28641024 TAAAACTAAAGTCTACCCAATTACCCAACCCAA
1 TAAAACTAAAGTCTACCCAATTA-CCAACCCAA
28641057 TAAAACTAAAATTAAAGTCTACCCAATTACCAACCCAA
1 TAAAAC------TAAAGTCTACCCAATTACCAACCCAA
*
28641095 TAAAAATAAA
1 TAAAACTAAA
28641105 ACTAAAGTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
32 4 0.10
33 6 0.15
38 14 0.34
39 17 0.41
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (32 bp):
TAAAACTAAAGTCTACCCAATTACCAACCCAA
Found at i:28641099 original size:38 final size:38
Alignment explanation
Indices: 28641000--28641115 Score: 187
Period size: 38 Copynumber: 3.0 Consensus size: 38
28640990 TAATTACCCA
* *
28641000 ACCCAGTTACTAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
*
28641038 ACCCAATTACCCAACCCAATAAAACTAAAATTAAAGTCT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
*
28641077 ACCCAATTACCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
28641115 A
1 A
28641116 ACTCTTAAGT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 36 0.50
39 36 0.50
ACGTcount: A:0.50, C:0.27, G:0.03, T:0.20
Consensus pattern (38 bp):
ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:28641272 original size:17 final size:17
Alignment explanation
Indices: 28641252--28641314 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
28641242 TAATTTCAAG
28641252 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
28641269 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
28641287 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
28641306 AATTATGTA
1 AATTATGTA
28641315 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:28641295 original size:37 final size:37
Alignment explanation
Indices: 28641249--28641323 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
28641239 TGTTAATTTC
*
28641249 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
*
28641286 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
28641323 A
1 A
28641324 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:28642217 original size:19 final size:20
Alignment explanation
Indices: 28642193--28642233 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
28642183 TATATTTGGA
*
28642193 AATTATAAATT-TAACTAAT
1 AATTATAAATTATAAATAAT
28642212 AATTATAAATTATAAATAAT
1 AATTATAAATTATAAATAAT
28642232 AA
1 AA
28642234 GATTTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATAAATTATAAATAAT
Found at i:28648644 original size:23 final size:22
Alignment explanation
Indices: 28648582--28648646 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
28648572 AATACGCTGT
* *
28648582 AAAGGCATTATAGATTATGCCAC
1 AAAGGCATT-TAGAATACGCCAC
* * *
28648605 AAAGGTATTTCGAAATACGTCAC
1 AAAGGCATTTAG-AATACGCCAC
28648628 AAAGGCATTCTAGAATACG
1 AAAGGCATT-TAGAATACG
28648647 ACAAAAAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (22 bp):
AAAGGCATTTAGAATACGCCAC
Found at i:28653593 original size:104 final size:106
Alignment explanation
Indices: 28653411--28653620 Score: 379
Period size: 104 Copynumber: 2.0 Consensus size: 106
28653401 GATAATATTG
* *
28653411 AAAAATTCAATACAAGTATGTTGACTAAAATTACTAGAAACCCTTTCCCTAAGGTTAAAAGGAAA
1 AAAAATTCAATACAAGTATATTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
28653476 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
66 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
*
28653517 AAAAATTCAATACATGTATATTGACT-AAA-TACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
1 AAAAATTCAATACAAGTATATTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
28653580 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
66 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
28653621 GCATAATACT
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 74 0.73
105 3 0.03
106 24 0.24
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (106 bp):
AAAAATTCAATACAAGTATATTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
Found at i:28655639 original size:25 final size:25
Alignment explanation
Indices: 28655587--28655644 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
28655577 TCACCACTAT
*
28655587 GGCTTTCCAAATAATATGCCACATA
1 GGCTTTCCAAATAATATGCCACAAA
* *
28655612 GGCTTTTCAAATAACT-TGCTACAAA
1 GGCTTTCCAAATAA-TATGCCACAAA
28655637 GGCTTTCC
1 GGCTTTCC
28655645 TCCTATTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (25 bp):
GGCTTTCCAAATAATATGCCACAAA
Found at i:28656601 original size:118 final size:117
Alignment explanation
Indices: 28656378--28656604 Score: 357
Period size: 118 Copynumber: 1.9 Consensus size: 117
28656368 CCTATTACAG
* * * *
28656378 ATAGTTTACTAATGTTTCCACTATATGTGACCCCCATGCAAGGTCTTCCTCCATATCCTACTGTT
1 ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCTACATAACCTACTGTT
*
28656443 CTTACATATTTTAACATTCTTACTCTTCAACAATTGTAACATACAGAGATAT
66 CTTACATATTTTAACATTCTTACTCTTCAACAATCGTAACATACAGAGATAT
* *
28656495 ATAGTTTACTAATGTTTTAACTATATGTGACCCCCATACAAGGTCTTCC-ACTTACACCTTACTG
1 ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCTACATA-ACC-TACTG
*
28656559 TTCTTACATCTTTTAACATTCTTACTCTTCAACAATCGTAACATAC
64 TTCTTACATATTTTAACATTCTTACTCTTCAACAATCGTAACATAC
28656605 TGACCTATAA
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
116 3 0.03
117 48 0.48
118 49 0.49
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (117 bp):
ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCTACATAACCTACTGTT
CTTACATATTTTAACATTCTTACTCTTCAACAATCGTAACATACAGAGATAT
Found at i:28659791 original size:27 final size:27
Alignment explanation
Indices: 28659740--28659791 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28659730 GGTGTTAATC
*
28659740 AAAAGTTATATCTTTTGGTTATTGATT
1 AAAAGTTATATCTTTTGATTATTGATT
* *
28659767 AAAAGTTATATCTTTTTATTTTTGA
1 AAAAGTTATATCTTTTGATTATTGA
28659792 CAAAGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.54
Consensus pattern (27 bp):
AAAAGTTATATCTTTTGATTATTGATT
Found at i:28660522 original size:15 final size:15
Alignment explanation
Indices: 28660502--28660535 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28660492 GTGATGGATG
28660502 AGATGAGTGATGT-CA
1 AGATGAGTG-TGTGCA
28660517 AGATGAGTGTGTGCA
1 AGATGAGTGTGTGCA
28660532 AGAT
1 AGAT
28660536 AAAGCAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (15 bp):
AGATGAGTGTGTGCA
Found at i:28667721 original size:39 final size:39
Alignment explanation
Indices: 28667678--28667777 Score: 101
Period size: 39 Copynumber: 2.6 Consensus size: 39
28667668 CATGTTTTTG
* *
28667678 AGTATTGTGATATATACTTGAATGTTAAGTGATTATATA
1 AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
* * * * *
28667717 AGTATTGTTATATATGCTTAAATTTTATGTGAATATATG
1 AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
* * * *
28667756 TGTAATGTGATACATGCTTAAA
1 AGTATTGTGATATATACTTAAA
28667778 AGTAAATATG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (39 bp):
AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
Found at i:28669414 original size:32 final size:30
Alignment explanation
Indices: 28669358--28669420 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 30
28669348 TGTGTCAAGC
28669358 GCCGTGGACCATACGGGTTAGCCCAATTAG
1 GCCGTGGACCATACGGGTTAGCCCAATTAG
* *
28669388 GCCGTGTGAGCCATA-GAGGTTGGCCCAGTTAG
1 GCCGTG-GA-CCATACG-GGTTAGCCCAATTAG
28669420 G
1 G
28669421 TCATGTGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.21
31 3 0.11
32 19 0.68
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.21
Consensus pattern (30 bp):
GCCGTGGACCATACGGGTTAGCCCAATTAG
Found at i:28674782 original size:21 final size:21
Alignment explanation
Indices: 28674758--28674800 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28674748 TTCTGTTTAG
*
28674758 TCTTTCGAGCTTCTT-TTCAGC
1 TCTTACGAGCTT-TTGTTCAGC
*
28674779 TCTTACGATCTTTTGTTCAGC
1 TCTTACGAGCTTTTGTTCAGC
28674800 T
1 T
28674801 TTCAAGCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.49
Consensus pattern (21 bp):
TCTTACGAGCTTTTGTTCAGC
Found at i:28679070 original size:70 final size:67
Alignment explanation
Indices: 28678938--28679070 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
28678928 TAAACAAATA
* ** * *
28678938 TAATGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAATGACGTAGCTTTGCCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAAAGACATAGCTTTGCCTTTTAA
28679003 TT
66 TT
* *
28679005 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAAAGACATAGTTTTGTCTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAAAGACATAGCTTTGCCTTT
28679070 T
63 T
28679071 CTTATTCAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 19 0.34
68 3 0.05
69 2 0.04
70 32 0.57
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAAAGACATAGCTTTGCCTTTTAA
TT
Found at i:28679968 original size:20 final size:20
Alignment explanation
Indices: 28679943--28679992 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28679933 TTTTAGGGAT
*
28679943 GCCTATGTGGCATCTTGTCA
1 GCCTATGTGGCATCCTGTCA
* *
28679963 GCCTATATGACATCCTGTCA
1 GCCTATGTGGCATCCTGTCA
*
28679983 GCCTTTGTGG
1 GCCTATGTGG
28679993 TGTACTCTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (20 bp):
GCCTATGTGGCATCCTGTCA
Found at i:28683123 original size:16 final size:17
Alignment explanation
Indices: 28683088--28683121 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28683078 TGTAATTATA
28683088 TATATTTTAAAATTTTT
1 TATATTTTAAAATTTTT
28683105 TATA-TTTAATAATTTTT
1 TATATTTTAA-AATTTTT
28683122 ATTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTTTAAAATTTTT
Found at i:28686094 original size:17 final size:17
Alignment explanation
Indices: 28686072--28686111 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
28686062 AATCAACCTT
28686072 CACCTCCGGCACCAATC
1 CACCTCCGGCACCAATC
*
28686089 CACCT-C--CACCGATC
1 CACCTCCGGCACCAATC
28686103 CACCTCCGG
1 CACCTCCGG
28686112 TCCTTCACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
14 12 0.63
15 1 0.05
16 1 0.05
17 5 0.26
ACGTcount: A:0.20, C:0.55, G:0.12, T:0.12
Consensus pattern (17 bp):
CACCTCCGGCACCAATC
Found at i:28688497 original size:61 final size:61
Alignment explanation
Indices: 28688431--28688757 Score: 280
Period size: 61 Copynumber: 5.4 Consensus size: 61
28688421 TTTAAATTAT
* * *
28688431 ATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
1 ATTTTATAGTATCATATATTATAATTTTAGTAAATTTATATAAGAATATTTAATATTAAGA
* * ** * * * *
28688492 ATTTTATTA-AATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCAA-ATT-A-T
1 ATTTTA-TAGTATCATATATTATAATTTTAGTAAATTTATATAAGAA-TATTT-AATATTAAGA
* *
28688551 ATTTTATAGTATCATATATTATAATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATAATTTTAGTAAATTTATATAAGAATATTTAATATTAAGA
* * ** * * * *
28688612 ATTTTATTA-AATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCAA-ATT-A-T
1 ATTTTA-TAGTATCATATATTATAATTTTAGTAAATTTATATAAGAA-TATTT-AATATTAAGA
* * *
28688671 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATAATTTTAGTAAATTTATATAAGAATATTTAATATTAAGA
* *
28688732 ATTTTATTA-AATCATATATTTTAATT
1 ATTTTA-TAGTATCATATATTATAATT
28688758 AAAATATATT
Statistics
Matches: 205, Mismatches: 44, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
58 6 0.03
59 71 0.35
60 28 0.14
61 91 0.44
62 9 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATAATTTTAGTAAATTTATATAAGAATATTTAATATTAAGA
Found at i:28688554 original size:120 final size:120
Alignment explanation
Indices: 28688397--28688780 Score: 705
Period size: 120 Copynumber: 3.2 Consensus size: 120
28688387 TATATTTAGA
* * *
28688397 AAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 AAAA-TATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGT
* *
28688462 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
28688518 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
1 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
*
28688583 AATTTATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
66 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
28688638 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
1 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
28688703 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
66 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
28688758 AAAATATATTTAATAATAATTAT
1 AAAATATATTTAATAATAATTAT
28688781 GTTAAAATAT
Statistics
Matches: 256, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
120 252 0.98
121 4 0.02
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (120 bp):
AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
Found at i:28689020 original size:16 final size:16
Alignment explanation
Indices: 28688999--28689031 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28688989 TTGATTTGCT
28688999 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
28689015 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
28689031 A
1 A
28689032 ATTCAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:28689427 original size:13 final size:14
Alignment explanation
Indices: 28689401--28689432 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28689391 TCAAATTTAG
28689401 TAAA-ATAACATTT
1 TAAATATAACATTT
28689414 TAAATATAAC-TTT
1 TAAATATAACATTT
28689427 TAAATA
1 TAAATA
28689433 GTAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATATAACATTT
Done.