Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004288.1 Hibiscus syriacus cultivar Beakdansim tig00009404_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 195039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:737 original size:33 final size:33
Alignment explanation
Indices: 700--898 Score: 81
Period size: 33 Copynumber: 5.8 Consensus size: 33
690 TCTTTATATA
700 AAAATAAAATATAAATATTATTATTATTATTTT
1 AAAATAAAATATAAATATTATTATTATTATTTT
** * * *
733 AAAATATTAGATTAAT-TTATTTAATATTA-TTT
1 AAAATAAAATATAAATATTA-TTATTATTATTTT
* **
765 -AAGTAAATATTATTAAAATATTA-TATCTAAAATTTT
1 AAAATAAA-A-TA-T-AAATATTATTAT-TATTATTTT
* * *
801 ATAAATAAAATATTAAGATTATTATGT-TT-TATT
1 A-AAATAAAATATAAATATTATTAT-TATTATTTT
* *
834 AAAATAAAACTATTAGACATTA-TATTAATTATTTAAT
1 AAAATAAAA-TA-TAAATATTATTATT-ATTATTT--T
*
871 AAAATAAGAATA-ATATATTATTAATTAT
1 AAAATAA-AATATAAATATTATT-ATTAT
899 ATCAATTACT
Statistics
Matches: 119, Mismatches: 26, Indels: 39
0.65 0.14 0.21
Matches are distributed among these distances:
31 4 0.03
32 16 0.13
33 30 0.25
34 17 0.14
35 19 0.16
36 11 0.09
37 14 0.12
38 8 0.07
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (33 bp):
AAAATAAAATATAAATATTATTATTATTATTTT
Found at i:825 original size:23 final size:24
Alignment explanation
Indices: 768--825 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
758 ATTATTTAAG
**
768 TAAATATTATTA-AAATATTATATC
1 TAAA-ATTATTATAAATAAAATATC
792 TAAAATT-TTATAAATAAAATAT-
1 TAAAATTATTATAAATAAAATATC
*
814 TAAGATTATTAT
1 TAAAATTATTAT
826 GTTTTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.31
23 16 0.55
24 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAAATTATTATAAATAAAATATC
Found at i:1105 original size:17 final size:16
Alignment explanation
Indices: 1083--1160 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
1073 TTATATAAAC
1083 ATAATAATAATAGTAAT
1 ATAATAATAATA-TAAT
*
1100 ATAATAATAATATAGT
1 ATAATAATAATATAAT
*
1116 ATAA-AAT-AT-TAAA
1 ATAATAATAATATAAT
*
1129 ATTATCAATAAATATAAT
1 ATAAT-AAT-AATATAAT
*
1147 TTAATAATTAATAT
1 ATAATAA-TAATAT
1161 TTTTACTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 5 0.10
14 2 0.04
15 6 0.12
16 7 0.15
17 21 0.44
18 7 0.15
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAATAATAATATAAT
Found at i:4028 original size:18 final size:18
Alignment explanation
Indices: 4005--4039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3995 TTCCATCCGG
*
4005 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
4023 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4040 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:5362 original size:18 final size:18
Alignment explanation
Indices: 5341--5375 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5331 CAGTCAACGG
5341 GTCAACGGGTCGGGTCGA
1 GTCAACGGGTCGGGTCGA
5359 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
5376 GGTCGTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGA
Found at i:9178 original size:18 final size:18
Alignment explanation
Indices: 9155--9189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9145 TTCCATCCGG
*
9155 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
9173 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
9190 GTCATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:10515 original size:18 final size:18
Alignment explanation
Indices: 10492--10531 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
10482 ACGGGTCAAC
10492 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
10510 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
10528 GGTC
1 GGTC
10532 GTGACCGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:13643 original size:18 final size:18
Alignment explanation
Indices: 13620--13654 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13610 GGTCACGACC
13620 CGACCCGACCCGTTGACT
1 CGACCCGACCCGTTGACT
13638 CGACCCGACCCGTTGAC
1 CGACCCGACCCGTTGAC
13655 CATTGACCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACT
Found at i:14983 original size:18 final size:18
Alignment explanation
Indices: 14957--14991 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14947 TCGAAAGGAC
*
14957 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
14975 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
14992 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:19997 original size:18 final size:18
Alignment explanation
Indices: 19971--20005 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19961 TCGAAAGGAC
*
19971 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
19989 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
20006 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:21223 original size:31 final size:32
Alignment explanation
Indices: 21170--21233 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
21160 GGTCAACGAC
21170 AGTCAACGGGTCAACGGTCAACGGGTCGGGTCG
1 AGTCAACGGGTC-ACGGTCAACGGGTCGGGTCG
*
21203 AGTCAACGGGTC-GGGTCAACGGGTCGGGTCG
1 AGTCAACGGGTCACGGTCAACGGGTCGGGTCG
21234 GGTCGTGACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 18 0.60
33 12 0.40
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (32 bp):
AGTCAACGGGTCACGGTCAACGGGTCGGGTCG
Found at i:21229 original size:13 final size:13
Alignment explanation
Indices: 21196--21232 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
21186 GTCAACGGGT
*
21196 CGGGTCGAGTCAA
1 CGGGTCGGGTCAA
21209 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
21222 CGGGTCGGGTC
1 CGGGTCGGGTC
21233 GGGTCGTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:21230 original size:18 final size:18
Alignment explanation
Indices: 21185--21237 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
21175 ACGGGTCAAC
21185 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
21203 AGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
21216 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
21234 GGTC
1 GGTC
21238 GTGACCGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 12 0.43
18 16 0.57
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:26364 original size:13 final size:13
Alignment explanation
Indices: 26346--26370 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26336 CGGTCAACGG
26346 GTCAACGGGTCGA
1 GTCAACGGGTCGA
26359 GTCAACGGGTCG
1 GTCAACGGGTCG
26371 GGTCGGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:26378 original size:31 final size:32
Alignment explanation
Indices: 26343--26419 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 32
26333 CGACGGTCAA
*
26343 CGGGTCAACGGGTCGA-GTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGAGGTAAACGGGTCGGGT
*
26374 CGGGTCAACGGATC-AGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGAGGTAAACGGGTCGGGT
26405 CGGGTCAACGGGTCG
1 CGGGTCAACGGGTCG
26420 GGTCGGGTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (32 bp):
CGGGTCAACGGGTCGAGGTAAACGGGTCGGGT
Found at i:26425 original size:18 final size:18
Alignment explanation
Indices: 26337--26427 Score: 84
Period size: 18 Copynumber: 5.2 Consensus size: 18
26327 GGTCAACGAC
26337 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
*
26358 AGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
* *
26376 GGTCAA-----CGGATCA
1 GGTCAACGGGTCGGGTCG
*
26389 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
26407 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
26425 GGT
1 GGT
26428 TGTGACCGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
13 10 0.18
18 37 0.65
21 10 0.18
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:31822 original size:3 final size:3
Alignment explanation
Indices: 31814--31870 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
31804 GTTGTCATAT
31814 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
31862 ATA ACA ATA
1 ATA ATA ATA
31871 GGCTAAATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38922 original size:20 final size:21
Alignment explanation
Indices: 38885--38924 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
38875 AAATTAAGTT
38885 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
38906 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
38925 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:39301 original size:64 final size:65
Alignment explanation
Indices: 39141--39302 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
39131 GAATTAATTG
* * * **** *
39141 AAACATCGAATGTATTCCATGCACCGATGCATTCTCCATGCATCGACGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGACGCACTCAGAATATTTTCA
* * * **
39206 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGTATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGACGCACTCAGAATATTTTCA
39270 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTCATGCATCGATGCACA
39303 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 32 0.39
65 51 0.61
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGACGCACTCAGAATATTTTCA
Found at i:45121 original size:20 final size:21
Alignment explanation
Indices: 45092--45147 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
45082 TTTGTGCTTC
*
45092 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
45112 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
45134 ATGCATCGATGCAT
1 ATGCATCGATGCAT
45148 AAGATCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:46721 original size:21 final size:21
Alignment explanation
Indices: 46679--46722 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
46669 ACCCCGGGAG
*
46679 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
46700 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
46721 CT
1 CT
46723 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:47496 original size:20 final size:21
Alignment explanation
Indices: 47459--47498 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
47449 AAATTAAGTT
47459 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
47480 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
47499 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:47784 original size:65 final size:63
Alignment explanation
Indices: 47668--47874 Score: 220
Period size: 65 Copynumber: 3.2 Consensus size: 63
47658 ATTTGAGGTG
* * * * *
47668 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
47732 C
63 C
* *
47733 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * * **
47798 ATACATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
47862 ATGCATCGATGCA
1 ATGCACCGATGCA
47875 CACTTGGTGC
Statistics
Matches: 122, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 36 0.30
65 83 0.68
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:49061 original size:23 final size:21
Alignment explanation
Indices: 49007--49063 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
48997 AGTCGAGGGC
*
49007 TCTACGAGGTCCTTCGGGACA
1 TCTATGAGGTCCTTCGGGACA
* *
49028 TATATGTGGTCCTTCGGGACAA
1 TCTATGAGGTCCTTCGGGAC-A
49050 TTCTATGAGGTCCT
1 -TCTATGAGGTCCT
49064 CTAGGATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 17 0.59
22 1 0.03
23 11 0.38
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (21 bp):
TCTATGAGGTCCTTCGGGACA
Found at i:52213 original size:30 final size:30
Alignment explanation
Indices: 52179--52239 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
52169 TTCGATATAA
*
52179 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
52209 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
52239 C
1 C
52240 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:57158 original size:23 final size:21
Alignment explanation
Indices: 57105--57167 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
57095 TTTTGGTGCA
*
57105 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
57126 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
57147 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
57168 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:57175 original size:21 final size:21
Alignment explanation
Indices: 57107--57188 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
57097 TTGGTGCAGA
* *
57107 GGGAATCGATTCCCCCC-CTG
1 GGGAACCGATTCCCCCCACAG
*
57127 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
57151 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
57172 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
57189 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 32 0.64
23 16 0.32
24 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:59630 original size:30 final size:30
Alignment explanation
Indices: 59596--59659 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
59586 TTCGATATAA
* *
59596 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTC
59626 CAAATTAAGTTAAAGTAATTTTAAGATTTC
1 CAAATTAAGTTAAAGTAATTTTAAGATTTC
59656 CAAA
1 CAAA
59660 CGATTTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTC
Found at i:70981 original size:27 final size:27
Alignment explanation
Indices: 70946--71006 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
70936 TCCCTTGACG
*
70946 GGTGCATCGATGCACTATCTATGCATC
1 GGTGCATCGATGCACTATCAATGCATC
*
70973 GGTGCATCGATGCACTATCAATGCATT
1 GGTGCATCGATGCACTATCAATGCATC
71000 GGTGCAT
1 GGTGCAT
71007 AAATCTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (27 bp):
GGTGCATCGATGCACTATCAATGCATC
Found at i:75424 original size:27 final size:27
Alignment explanation
Indices: 75389--75449 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
75379 TCCTTTGACG
*
75389 GGTGCATCGATGCACTATTTATGCATC
1 GGTGCATCGATGCACTATCTATGCATC
*
75416 GGTGCATCGATGCACTATCTATGCATT
1 GGTGCATCGATGCACTATCTATGCATC
75443 GGTGCAT
1 GGTGCAT
75450 AAATCTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (27 bp):
GGTGCATCGATGCACTATCTATGCATC
Found at i:80619 original size:9 final size:9
Alignment explanation
Indices: 80605--80704 Score: 56
Period size: 9 Copynumber: 10.4 Consensus size: 9
80595 GGCTGCTGGA
80605 AACCGGTTT
1 AACCGGTTT
80614 AACCGGTTTT
1 AACCGG-TTT
*
80624 CAACCAGTTCT
1 -AACCGGTT-T
*
80635 GACCGGTTT
1 AACCGGTTT
*
80644 GACCGGTTT
1 AACCGGTTT
* *
80653 CAACCAGTTCG
1 -AACCGGTT-T
80664 AACCGGTTT
1 AACCGGTTT
* *
80673 GACCGGTCTG
1 AACCGGT-TT
*
80683 AATCGGTTT
1 AACCGGTTT
* *
80692 GACCGGTCT
1 AACCGGTTT
80701 AACC
1 AACC
80705 CGACCCGACC
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
9 32 0.47
10 30 0.44
11 6 0.09
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:80668 original size:29 final size:30
Alignment explanation
Indices: 80605--80679 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
80595 GGCTGCTGGA
*
80605 AACCGGTTTAACCGGTTTTCAACCAGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCAGTTCTG
80636 -ACCGGTTTGACCGGTTTCAACCAGTTC-G
1 AACCGGTTTGACCGGTTTCAACCAGTTCTG
80664 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
80680 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCAGTTCTG
Found at i:80728 original size:22 final size:22
Alignment explanation
Indices: 80702--80743 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
80692 GACCGGTCTA
80702 ACCCGACCCGACCGTTGACCCG
1 ACCCGACCCGACCGTTGACCCG
80724 ACCCGACCCGACCGTTGACC
1 ACCCGACCCGACCGTTGACC
80744 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.21, T:0.10
Consensus pattern (22 bp):
ACCCGACCCGACCGTTGACCCG
Found at i:87917 original size:9 final size:9
Alignment explanation
Indices: 87903--87959 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 9
87893 GGCTGCTGGA
87903 AACCGGTTT
1 AACCGGTTT
87912 AACCGGTTTT
1 AACCGG-TTT
87922 CAACCGGTTCT
1 -AACCGGTT-T
*
87933 GACCGGTTT
1 AACCGGTTT
*
87942 GACCGGTTT
1 AACCGGTTT
87951 CAACCGGTT
1 -AACCGGTT
87960 CGAACCGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 16 0.38
10 19 0.45
11 7 0.17
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.32
Consensus pattern (9 bp):
AACCGGTTT
Found at i:87939 original size:10 final size:10
Alignment explanation
Indices: 87924--87983 Score: 58
Period size: 9 Copynumber: 6.3 Consensus size: 10
87914 CCGGTTTTCA
87924 ACCGGTTCTG
1 ACCGGTTCTG
87934 ACCGGTT-TG
1 ACCGGTTCTG
*
87943 ACCGGTT-TCA
1 ACCGGTTCT-G
87953 ACCGGTTC-G
1 ACCGGTTCTG
87962 AACCGG-TCTG
1 -ACCGGTTCTG
87972 ACCGG-TCTG
1 ACCGGTTCTG
87981 ACC
1 ACC
87984 CGACCCGACC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
9 24 0.55
10 20 0.45
ACGTcount: A:0.15, C:0.32, G:0.28, T:0.25
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:87966 original size:29 final size:30
Alignment explanation
Indices: 87903--87977 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
87893 GGCTGCTGGA
*
87903 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
87934 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
87962 AACCGGTCTGACCGGT
1 AACCGGTTTGACCGGT
87978 CTGACCCGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 27 0.66
30 13 0.32
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:87990 original size:5 final size:5
Alignment explanation
Indices: 87980--88032 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
87970 TGACCGGTCT
* *
87980 GACCC GACCC GACCGTT GACCC GACCC GACCTTT GACCC GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACC--C GACCC GACCC GACCC
88029 GACC
1 GACC
88033 GTTGACTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.21, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:88001 original size:17 final size:17
Alignment explanation
Indices: 87979--88027 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
87969 CTGACCGGTC
87979 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
87996 TGACCCGACCCGACCTT
1 TGACCCGACCCGACCGT
88013 TGACCCGACCCGACC
1 TGACCCGACCCGACC
88028 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:88006 original size:22 final size:22
Alignment explanation
Indices: 87997--88038 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
87987 CCCGACCGTT
*
87997 GACCCGACCCGACCTTTGACCC
1 GACCCGACCCGACCGTTGACCC
88019 GACCCGACCCGACCGTTGAC
1 GACCCGACCCGACCGTTGAC
88039 TGTTGACCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.21, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:88045 original size:7 final size:7
Alignment explanation
Indices: 88029--88059 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
88019 GACCCGACCC
88029 GACCGTT
1 GACCGTT
*
88036 GACTGTT
1 GACCGTT
88043 GACCGTT
1 GACCGTT
88050 GACCGTT
1 GACCGTT
88057 GAC
1 GAC
88060 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:88657 original size:12 final size:12
Alignment explanation
Indices: 88640--88664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88630 GTGGTACACG
88640 AATTCATTGGTT
1 AATTCATTGGTT
88652 AATTCATTGGTT
1 AATTCATTGGTT
88664 A
1 A
88665 TTGTTTTATT
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:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (12 bp):
AATTCATTGGTT
Found at i:90833 original size:18 final size:18
Alignment explanation
Indices: 90810--90849 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
90800 AATTGAATAT
90810 AATATTATATATAAACAA
1 AATATTATATATAAACAA
*
90828 AATATTATATATAAACAT
1 AATATTATATATAAACAA
90846 AATA
1 AATA
90850 ATAATACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATTATATATAAACAA
Found at i:91002 original size:34 final size:34
Alignment explanation
Indices: 90931--91004 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
90921 TGAAATGTAA
* * *
90931 ATATAATCTTAATATATTATATATATATATATAT
1 ATATAATCTTAATAAATTATATAAATACATATAT
* *
90965 ATATAATCTTATATAAATTATA-AAATACATTTTT
1 ATATAATCTTA-ATAAATTATATAAATACATATAT
90999 ATATAA
1 ATATAA
91005 ATATTTTCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 25 0.74
35 9 0.26
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (34 bp):
ATATAATCTTAATAAATTATATAAATACATATAT
Found at i:95716 original size:14 final size:14
Alignment explanation
Indices: 95699--95764 Score: 96
Period size: 14 Copynumber: 4.7 Consensus size: 14
95689 GTAACTCGAA
95699 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
*
95713 CTGAGTCAACTCAT
1 CTGAGTCAACTCGT
*
95727 TTGAGTCAACTCGT
1 CTGAGTCAACTCGT
*
95741 CTGTGTCAACTCGT
1 CTGAGTCAACTCGT
*
95755 CCGAGTCAAC
1 CTGAGTCAAC
95765 CTGTTGACTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:95787 original size:13 final size:13
Alignment explanation
Indices: 95769--95793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95759 GTCAACCTGT
95769 TGACTTTGACCGC
1 TGACTTTGACCGC
95782 TGACTTTGACCG
1 TGACTTTGACCG
95794 AAAAGTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (13 bp):
TGACTTTGACCGC
Found at i:96311 original size:38 final size:38
Alignment explanation
Indices: 96260--96337 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
96250 TTAAGCAAAT
*
96260 AACCTCAGAATCTCTAAATTCTATTTATCCTCGTTAAA
1 AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
96298 AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
1 AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
96336 AA
1 AA
96338 ATTTAATATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (38 bp):
AACCTCAGAATCTCTAAATTCTATTTATCCTCATTAAA
Found at i:107634 original size:16 final size:15
Alignment explanation
Indices: 107602--107649 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
107592 ACGAGAGATT
107602 AGAGAAGTAGAGAGA
1 AGAGAAGTAGAGAGA
*
107617 AGAGAACGTAG-GAGG
1 AGAGAA-GTAGAGAGA
107632 A-AGAAGTAGAGA-A
1 AGAGAAGTAGAGAGA
107645 AGAGA
1 AGAGA
107650 TGAAGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 10 0.36
16 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.40, T:0.06
Consensus pattern (15 bp):
AGAGAAGTAGAGAGA
Found at i:119736 original size:48 final size:46
Alignment explanation
Indices: 119639--119739 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 46
119629 CACAGTATCA
*
119639 TAAAATAATTATTAAATTTATCAAATCATTATAAAACATTCATTCAT
1 TAAAATAATTATTAAATTTATCAAATCATTATAAAAAATT-ATTCAT
* * *
119686 TAAAGATAATTATTAAATTTTATCAATTTATTATAAAATAATT-TTTAT
1 TAAA-ATAATTATTAAA-TTTATCAAATCATTATAAAA-AATTATTCAT
119734 TAAAAT
1 TAAAAT
119740 TTATGGTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
47 6 0.13
48 20 0.43
49 18 0.38
50 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.45
Consensus pattern (46 bp):
TAAAATAATTATTAAATTTATCAAATCATTATAAAAAATTATTCAT
Found at i:119841 original size:31 final size:31
Alignment explanation
Indices: 119770--119841 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
119760 TAATATCACT
** * *
119770 ATTATTTTACCATAATTTAATAAATTTAATG
1 ATTATTTTATAATAATTTAACAAATTTAATA
**
119801 ATTATTTTATAATAATTTAACGTATTTAATA
1 ATTATTTTATAATAATTTAACAAATTTAATA
119832 ATTATTTTAT
1 ATTATTTTAT
119842 TTTTTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (31 bp):
ATTATTTTATAATAATTTAACAAATTTAATA
Found at i:120065 original size:3 final size:3
Alignment explanation
Indices: 120057--120106 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
120047 AATTATTTAC
120057 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
120105 TT
1 TT
120107 GTTACCGGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:122146 original size:34 final size:34
Alignment explanation
Indices: 122102--122173 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
122092 GCCCACATCG
* * *
122102 TTTTTGTTTTAAATTTCGAATAATATTATTTTTA
1 TTTTTATTTTAAATTTCGAATAATATAATTTGTA
122136 TTTTTATTTTAAATTTCGAATAATATAATTTGTA
1 TTTTTATTTTAAATTTCGAATAATATAATTTGTA
122170 TTTT
1 TTTT
122174 AAAAACATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (34 bp):
TTTTTATTTTAAATTTCGAATAATATAATTTGTA
Found at i:122718 original size:21 final size:21
Alignment explanation
Indices: 122692--122746 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
122682 TCCATATGGT
122692 ATGTAACCCTGCGAGCTCGGA
1 ATGTAACCCTGCGAGCTCGGA
* *
122713 ATGTAACCCTACGGGCTCGGA
1 ATGTAACCCTGCGAGCTCGGA
*
122734 ATGTAACCTTGCG
1 ATGTAACCCTGCG
122747 GAGATGGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGTAACCCTGCGAGCTCGGA
Found at i:122777 original size:21 final size:21
Alignment explanation
Indices: 122751--122792 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
122741 CTTGCGGAGA
*
122751 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
122772 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
122793 GGGTATGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.40, T:0.26
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:123094 original size:3 final size:3
Alignment explanation
Indices: 123079--123127 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
123069 AGTTAAAAAA
* *
123079 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
123126 TA
1 TA
123128 AGTGTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:124490 original size:14 final size:16
Alignment explanation
Indices: 124466--124498 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
124456 GTTTATTTTG
124466 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
124481 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
124496 TTT
1 TTT
124499 AGTCACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:136746 original size:17 final size:16
Alignment explanation
Indices: 136722--136788 Score: 100
Period size: 16 Copynumber: 4.1 Consensus size: 16
136712 AAAAAGGAAC
136722 AAAT-AAAAAGATAAAA
1 AAATGAAAAAGA-AAAA
136738 AAATGAAAAAGAAAAA
1 AAATGAAAAAGAAAAA
*
136754 AAATGAAAATGAAAAA
1 AAATGAAAAAGAAAAA
136770 AAATGAAAAATGAAAAA
1 AAATGAAAAA-GAAAAA
136787 AA
1 AA
136789 GAAATGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
16 32 0.68
17 15 0.32
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAATGAAAAAGAAAAA
Found at i:136801 original size:8 final size:8
Alignment explanation
Indices: 136711--136806 Score: 55
Period size: 8 Copynumber: 12.5 Consensus size: 8
136701 TGCTTGATGA
*
136711 AAAAAAGG
1 AAAAAATG
*
136719 AACAAAT-
1 AAAAAATG
*
136726 AAAAAGATA
1 AAAAA-ATG
136735 AAAAAATG
1 AAAAAATG
*
136743 AAAAAGA-A
1 AAAAA-ATG
136751 AAAAAATG
1 AAAAAATG
136759 --AAAATG
1 AAAAAATG
136765 AAAAAAAATG
1 --AAAAAATG
136775 -AAAAATG
1 AAAAAATG
136782 -AAAAA--
1 AAAAAATG
*
136787 AAGAAATG
1 AAAAAATG
136795 AAAAAATG
1 AAAAAATG
136803 AAAA
1 AAAA
136807 GAGAAAAGGA
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
6 10 0.14
7 17 0.25
8 30 0.43
9 6 0.09
10 6 0.09
ACGTcount: A:0.77, C:0.01, G:0.12, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:136811 original size:20 final size:18
Alignment explanation
Indices: 136722--136812 Score: 88
Period size: 16 Copynumber: 5.2 Consensus size: 18
136712 AAAAAGGAAC
136722 AAAT-AAAAA-GATAAAA-
1 AAATGAAAAATGA-AAAAG
136738 AAATGAAAAA-GAAAAA-
1 AAATGAAAAATGAAAAAG
136754 AAATG-AAAATGAAAAA-
1 AAATGAAAAATGAAAAAG
136770 AAATGAAAAATGAAAAAAAG
1 AAATGAAAAATG--AAAAAG
136790 AAATGAAAAAATGAAAAGAG
1 AAATG-AAAAATGAAAA-AG
136810 AAA
1 AAA
136813 AGGAGGGTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.06
16 24 0.36
17 13 0.19
19 9 0.13
20 10 0.15
21 7 0.10
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (18 bp):
AAATGAAAAATGAAAAAG
Found at i:138254 original size:105 final size:105
Alignment explanation
Indices: 138030--138284 Score: 323
Period size: 105 Copynumber: 2.4 Consensus size: 105
138020 CTCGCTTGAG
* *
138030 GGATCGACATTTCCAATGAATAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * *
138095 TGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
* * * * *
138137 GAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* * **
138202 AGAAAAACATGTT-CTTTCTAAGTCCACCGCAAAAGGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAGGAGGT
*
138242 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATC
138285 CACGAGAAAA
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
104 5 0.04
105 110 0.87
106 1 0.01
107 10 0.08
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (105 bp):
GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
Found at i:138472 original size:3 final size:3
Alignment explanation
Indices: 138457--138496 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
138447 AGTTAAAAAA
* *
138457 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
138497 AGTGTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:139845 original size:14 final size:16
Alignment explanation
Indices: 139821--139853 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
139811 GTTTATTTTG
139821 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
139836 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
139851 TTT
1 TTT
139854 AGTCACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:145046 original size:12 final size:12
Alignment explanation
Indices: 145029--145080 Score: 86
Period size: 12 Copynumber: 4.3 Consensus size: 12
145019 AACTCGAGAA
145029 TCAATTTTGAGC
1 TCAATTTTGAGC
145041 TCAATTTTGAGC
1 TCAATTTTGAGC
*
145053 TCGATTTTGAGC
1 TCAATTTTGAGC
*
145065 TCGATTTTGAGC
1 TCAATTTTGAGC
145077 TCAA
1 TCAA
145081 CATGTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (12 bp):
TCAATTTTGAGC
Found at i:150805 original size:35 final size:36
Alignment explanation
Indices: 150754--150824 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
150744 AACATCTACC
* * *
150754 AAAATTTTACCAAACTTTG-AAAAACATTTTTCAAA
1 AAAAATTTACAAAACTTTGAAAAAACATTTTCCAAA
150789 AAAAATTTACAAAACTTTGAAAAAACATTTTCCAAA
1 AAAAATTTACAAAACTTTGAAAAAACATTTTCCAAA
150825 GTTGGTTGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (36 bp):
AAAAATTTACAAAACTTTGAAAAAACATTTTCCAAA
Found at i:151422 original size:21 final size:21
Alignment explanation
Indices: 151396--151438 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
151386 CACATAATCG
* *
151396 GGTTTAGGGTTTAGGGTTTAT
1 GGTTTAGAGTTTAGAGTTTAT
*
151417 GGTTTAGATTTTAGAGTTTAT
1 GGTTTAGAGTTTAGAGTTTAT
151438 G
1 G
151439 ATTCATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.49
Consensus pattern (21 bp):
GGTTTAGAGTTTAGAGTTTAT
Found at i:151601 original size:11 final size:11
Alignment explanation
Indices: 151546--151608 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
151536 GTATTATAAA
151546 ATTTTTAATAT
1 ATTTTTAATAT
*
151557 ATATTTAA-A-
1 ATTTTTAATAT
151566 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
151577 ATCAATAATGT
1 ATTTTTAATAT
151588 ATTTTTAATAT
1 ATTTTTAATAT
151599 ATTTTTAATA
1 ATTTTTAATA
151609 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.10
10 8 0.21
11 27 0.69
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:151731 original size:17 final size:16
Alignment explanation
Indices: 151709--151743 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
151699 GGCTCGTTAA
151709 GAACTCGAGTCGAGCTC
1 GAACTCGAGTCGAG-TC
151726 GAACTCGAGTCGAGTC
1 GAACTCGAGTCGAGTC
151742 GA
1 GA
151744 GTCCATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.17
Consensus pattern (16 bp):
GAACTCGAGTCGAGTC
Found at i:158464 original size:26 final size:27
Alignment explanation
Indices: 158412--158475 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
158402 TAATATACTG
158412 ATTTATATGCATTTATCATTTACTTTTTTT
1 ATTTATATGCATTTATCA--TA-TTTTTTT
*
158442 ATTTATATGCTTTTATC--ATTTTTTT
1 ATTTATATGCATTTATCATATTTTTTT
158467 ATTTTATAT
1 A-TTTATAT
158476 TGTAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.25
26 8 0.25
30 16 0.50
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (27 bp):
ATTTATATGCATTTATCATATTTTTTT
Found at i:162097 original size:45 final size:45
Alignment explanation
Indices: 162003--162178 Score: 282
Period size: 45 Copynumber: 3.9 Consensus size: 45
161993 GTAACCATGC
* * *
162003 AAATAAGCTTACGATCTTATGGAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATTGGTA
162047 AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATTGGTA
* **
162092 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTAATA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATTGGTA
*
162137 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTG
1 AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATTG
162179 ATAAGAAATT
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 23 0.19
45 101 0.81
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGCAAGTATATTGGTA
Found at i:162120 original size:25 final size:25
Alignment explanation
Indices: 162047--162120 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
162037 TATATTGGTA
162047 AAATAAGCTTACGAGCTTATGGGAT
1 AAATAAGCTTACGAGCTTATGGGAT
* *
162072 AAAT-GGC--A--AG-TATATTGG-T
1 AAATAAGCTTACGAGCT-TATGGGAT
162091 AAAATAAGCTTACGAGCTTATGGGAT
1 -AAATAAGCTTACGAGCTTATGGGAT
162117 AAAT
1 AAAT
162121 GGTAAGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 2 0.06
22 1 0.03
23 1 0.03
24 2 0.06
25 15 0.42
26 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.28
Consensus pattern (25 bp):
AAATAAGCTTACGAGCTTATGGGAT
Found at i:164264 original size:92 final size:92
Alignment explanation
Indices: 164096--164381 Score: 346
Period size: 92 Copynumber: 3.1 Consensus size: 92
164086 AAATTATGAA
* * * * ** *
164096 GGGTCCACATATTCCGTCACAAAATTTAGAGTTTTGTTTATTTA--TGCTCATTACCTCCAATTT
1 GGGTCCACATGTTTCGTCACAAAATTTAGAGTTTT-TTTAATTACCCGCTCATTTTCTTCAATTT
* *
164159 ACCTCCATTGAAACATAAAATTTGTGGC
65 CCCTCCATTGAAACATAAAATTTGTGAC
*
164187 GGGTACACATGTTTCGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATTTTCTTCAATTTC
1 GGGTCCACATGTTTCGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATTTTCTTCAATTTC
*
164252 CCTCCATTGAAACATGAAATTTGTGAC
66 CCTCCATTGAAACATAAAATTTGTGAC
* * *
164279 GAGTCCACATG-TTCCTCACAAAATTTAGAGTTTTTTTTAATTACCCGCTTA-TTTCTTCCAATT
1 GGGTCCACATGTTTCGTCACAAAATTTAGAG-TTTTTTTAATTACCCGCTCATTTTCTT-CAATT
* * * *
164342 TCTCTACATTGAAACATAACATTTGTGAT
64 TCCCTCCATTGAAACATAAAATTTGTGAC
*
164371 GGGTTCACATG
1 GGGTCCACATG
164382 CACAAAATTT
Statistics
Matches: 169, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
90 7 0.04
91 56 0.33
92 106 0.63
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (92 bp):
GGGTCCACATGTTTCGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATTTTCTTCAATTTC
CCTCCATTGAAACATAAAATTTGTGAC
Found at i:164417 original size:85 final size:86
Alignment explanation
Indices: 164111--164426 Score: 264
Period size: 92 Copynumber: 3.5 Consensus size: 86
164101 CACATATTCC
* * * * * * *
164111 GTCACAAAATTTAGAGTTTTGTTTATTTA--TGCTCATTACCTCCAATTTACCTCCATTGAAACA
1 GTCACAAAATTTAGAGTTTT-TTTAATTACCCGCTTATT-TCTTCAATTTCCCTACATTGAAACA
* * * *
164174 TAAAATTTGTGGCGGGTACACATGTTT
64 TGAAATTTGTGACGAGTCCACA----T
* *
164201 CGTCACAAAATTTAGAGTTTTTTTAATTACCCGCTCATTTTCTTCAATTTCCCTCCATTGAAACA
1 -GTCACAAAATTTAGAGTTTTTTTAATTACCCGCTTA-TTTCTTCAATTTCCCTACATTGAAACA
164266 TGAAATTTGTGACGAGTCCACAT
64 TGAAATTTGTGACGAGTCCACAT
*
164289 GTTCCTCACAAAATTTAGAGTTTTTTTTAATTACCCGCTTATTTCTTCCAATTTCTCTACATTGA
1 G----TCACAAAATTTAGAG-TTTTTTTAATTACCCGCTTATTTCTT-CAATTTCCCTACATTGA
* * *
164354 AACAT-AACATTTGTGATGGGTTCACAT
60 AACATGAA-ATTTGTGACGAGTCCACAT
* * * *
164381 G-CACAAAATTTAGA-ATTTTTTACTTACTCACTTATTTCGTTCAATT
1 GTCACAAAATTTAGAGTTTTTTTAATTACCCGCTTATTTC-TTCAATT
164427 CCTTCAATTT
Statistics
Matches: 195, Mismatches: 19, Indels: 28
0.81 0.08 0.12
Matches are distributed among these distances:
85 25 0.13
86 2 0.01
87 14 0.07
88 1 0.01
90 7 0.04
91 43 0.22
92 101 0.52
93 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (86 bp):
GTCACAAAATTTAGAGTTTTTTTAATTACCCGCTTATTTCTTCAATTTCCCTACATTGAAACATG
AAATTTGTGACGAGTCCACAT
Found at i:165821 original size:33 final size:33
Alignment explanation
Indices: 165779--165847 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
165769 TATTTAATTA
165779 AATAAAAATTTAGATTCATAATATTTTGGAGGG
1 AATAAAAATTTAGATTCATAATATTTTGGAGGG
* *
165812 AATACAAATTTGGATTCATAATATTTTGGAGGG
1 AATAAAAATTTAGATTCATAATATTTTGGAGGG
165845 AAT
1 AAT
165848 GAAATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (33 bp):
AATAAAAATTTAGATTCATAATATTTTGGAGGG
Found at i:173375 original size:26 final size:26
Alignment explanation
Indices: 173339--173392 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
173329 GCTAAGTGGA
**
173339 TATGGTGGGCATGACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
173365 TATGGTGGGCACAACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
173391 TA
1 TA
173393 GAACTTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (26 bp):
TATGGTGGGCACAACCTTATGTGTAT
Found at i:179609 original size:22 final size:22
Alignment explanation
Indices: 179569--179611 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
179559 ACTGATCGTT
* **
179569 ATATATGATGTTTTTCATGAAC
1 ATATATGATATTTAACATGAAC
179591 ATATATGATATTTAACATGAA
1 ATATATGATATTTAACATGAA
179612 TGATATTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
ATATATGATATTTAACATGAAC
Found at i:179859 original size:26 final size:26
Alignment explanation
Indices: 179823--179876 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
179813 ACTAAGTGCA
*
179823 TATGGTGGGCACTACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
*
179849 TATGGTGGGCACGATCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
179875 TA
1 TA
179877 GCACTTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:181876 original size:31 final size:30
Alignment explanation
Indices: 181838--181896 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
181828 TTTTTTTTTC
*
181838 TTTTTCATAT-TTTTATTGTTTTGTTTTCCAT
1 TTTTTCATATCTTTT-TTCTTTT-TTTTCCAT
181869 TTTTTCATATCTTTTTTCTTTTTTTTCC
1 TTTTTCATATCTTTTTTCTTTTTTTTCC
181897 CGAACAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.23
31 16 0.62
32 4 0.15
ACGTcount: A:0.10, C:0.14, G:0.03, T:0.73
Consensus pattern (30 bp):
TTTTTCATATCTTTTTTCTTTTTTTTCCAT
Found at i:190722 original size:21 final size:22
Alignment explanation
Indices: 190696--190738 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
190686 GTGAACAGTG
*
190696 AGGGTATCGGTA-CACTGTAGC
1 AGGGTATCCGTACCACTGTAGC
*
190717 AGGGTATCCGTACCCCTGTAGC
1 AGGGTATCCGTACCACTGTAGC
190739 GTTCTGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (22 bp):
AGGGTATCCGTACCACTGTAGC
Found at i:191217 original size:45 final size:44
Alignment explanation
Indices: 191166--191361 Score: 306
Period size: 45 Copynumber: 4.4 Consensus size: 44
191156 TTATCCTTTG
191166 AGCTCGTAAGCTTATTTTATCAATATACTTACCATTTATTCCATA
1 AGCTCGTAAGCTTATTTTA-CAATATACTTACCATTTATTCCATA
191211 AGCTCGTAAGCTTATTTTAGCAATATACTTACC-TCTTATTCCATA
1 AGCTCGTAAGCTTATTTTA-CAATATACTTACCAT-TTATTCCATA
*
191256 AGCTCATAAGCTTATTTTACCAATATACTTACCATTTATTCCATA
1 AGCTCGTAAGCTTATTTTA-CAATATACTTACCATTTATTCCATA
*
191301 AGCTCGTAAGCTTATTTTACAAATATACTTGCCA-TTATTCCATA
1 AGCTCGTAAGCTTATTTTAC-AATATACTTACCATTTATTCCATA
*
191345 AGCTTGTAAGCTTATTT
1 AGCTCGTAAGCTTATTT
191362 GCATGCATAC
Statistics
Matches: 142, Mismatches: 6, Indels: 7
0.92 0.04 0.05
Matches are distributed among these distances:
44 28 0.20
45 113 0.80
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (44 bp):
AGCTCGTAAGCTTATTTTACAATATACTTACCATTTATTCCATA
Found at i:194385 original size:2 final size:2
Alignment explanation
Indices: 194380--194445 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
194370 AACAAGTGAA
194380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
194422 AT AT AT AT -T AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
194446 TATCATATCT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 60 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:194513 original size:17 final size:17
Alignment explanation
Indices: 194477--194545 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
194467 TCTCTTTCCC
194477 TTTCTCTTTTTCTTTCT
1 TTTCTCTTTTTCTTTCT
*
194494 TTTCT-TTTTTCTATTTT
1 TTTCTCTTTTTCT-TTCT
** *
194511 TTTCTC-CGTT-TTTGT
1 TTTCTCTTTTTCTTTCT
194526 TTTCT-TTTATTCTTTCT
1 TTTCTCTTT-TTCTTTCT
194543 TTT
1 TTT
194546 TTTCCATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
15 8 0.20
16 10 0.25
17 22 0.55
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTCTCTTTTTCTTTCT
Found at i:194514 original size:22 final size:24
Alignment explanation
Indices: 194460--194516 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
194450 ATATCTCATC
194460 ATTTTTTTCTCTTTCCCTTTCTCT
1 ATTTTTTTCTCTTTCCCTTTCTCT
* *
194484 -TTTTCTTTCT-TTT-CTTTTTTCT
1 ATTTT-TTTCTCTTTCCCTTTCTCT
194506 ATTTTTTTCTC
1 ATTTTTTTCTC
194517 CGTTTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 12 0.43
23 11 0.39
24 5 0.18
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.74
Consensus pattern (24 bp):
ATTTTTTTCTCTTTCCCTTTCTCT
Found at i:194556 original size:33 final size:32
Alignment explanation
Indices: 194493--194556 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
194483 TTTTTCTTTC
*
194493 TTTTCTTTTTTCTATTTTTTTCTCCGTTTTTG
1 TTTTCTTTTTTCTATTTTTTTCTCCATTTTTG
*
194525 TTTTCTTTTATTCT-TTCTTTTTTTCCATTTTT
1 TTTTCTTTT-TTCTATT-TTTTTCTCCATTTTT
194557 TCTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.77
Consensus pattern (32 bp):
TTTTCTTTTTTCTATTTTTTTCTCCATTTTTG
Done.