Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 104 of 168
Found at i:30738131 original size:43 final size:43
Alignment explanation
Indices: 30737962--30738132 Score: 133
Period size: 43 Copynumber: 4.0 Consensus size: 43
30737952 ACATAGGATT
* *
30737962 TCGATATGT-ATTTTCGTGTAAGACCACATCTGGGACGTTGGCA
1 TCGATATGTGA-TTACGTGTGAGACCACATCTGGGACGTTGGCA
** *
30738005 TCGACT-TGTG-TATACGTG-GAAGACCATGTCTGGGACATTGGCA
1 TCGA-TATGTGAT-TACGTGTG-AGACCACATCTGGGACGTTGGCA
* * *
30738048 TCG-TATTTGATT-TGTGTAAGACC-CTATCTGGGACAG-TGGCA
1 TCGATATGTGATTACGTGTGAGACCAC-ATCTGGGAC-GTTGGCA
* * *
30738089 TCGATATGTGATTACATGTGAGACCACGTCTAGGACGTTGGCA
1 TCGATATGTGATTACGTGTGAGACCACATCTGGGACGTTGGCA
30738132 T
1 T
30738133 TGTACGAGCC
Statistics
Matches: 98, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
41 25 0.26
42 14 0.14
43 57 0.58
44 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTGAGACCACATCTGGGACGTTGGCA
Found at i:30738322 original size:16 final size:17
Alignment explanation
Indices: 30738293--30738324 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
30738283 TGAATTGATG
30738293 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
30738310 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
30738325 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:30743993 original size:44 final size:44
Alignment explanation
Indices: 30743895--30744130 Score: 188
Period size: 44 Copynumber: 5.5 Consensus size: 44
30743885 TAAATCACAG
** * * * *
30743895 ATCTTATCTCTTTGAAGTTGCAGTAGAGTAGA-TCATG--GCGA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCTACAA
*
30743936 ATCTTATCTCCCTGAAGTTGCAGTAGA-TCAGATTAAAGCCA-ATA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGT-AGATTAAAGCTACA-A
* * * *
30743980 ATCTTATCTCCC------TGCAGTGGAGTGGATTGAAGTTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCTACAA
* * * *
30744018 GTCTTATCTCCCTGAAGTTGCAGTAGAGTAGACTAAAGATAGCGA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCTA-CAA
* * * *
30744063 ATCTTATCTCCCTGAATTTGTAGTGGAGTAGATTGAAGCTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCTACAA
*
30744107 ATCCTATCTCCCTGAAGTTGCAGT
1 ATCTTATCTCCCTGAAGTTGCAGT
30744131 GGAGCGGATT
Statistics
Matches: 152, Mismatches: 29, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
38 28 0.18
39 2 0.01
40 1 0.01
41 28 0.18
42 3 0.02
44 54 0.36
45 36 0.24
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTAAAGCTACAA
Found at i:30744154 original size:44 final size:45
Alignment explanation
Indices: 30744022--30744235 Score: 127
Period size: 44 Copynumber: 4.7 Consensus size: 45
30744012 TTACAAGTCT
* * * *
30744022 TATCTCCCTGAAGTTGCAGTAGAGTAGACT-AAA-GATAGCGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATA--GAATCC
* * * * * * *
30744067 TATCTCCCTGAATTTGTAGTGGAGTAGATTGAAGCTACA-AATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATAGAATCC
*
30744111 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGAT-GAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATAGAATCC
* * * * * *
30744155 TATAC-CTCTAAAGTTGCAGTAGG-TCGGATTAAATCTACCATAGCAAGCC
1 TAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTAAA---ACGATAG-AATCC
*
30744204 TTATCTCTCTGAAGTTGCAGTGGAGCA-ATTAA
1 -TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA
30744236 CCCTATCTCC
Statistics
Matches: 132, Mismatches: 24, Indels: 22
0.74 0.13 0.12
Matches are distributed among these distances:
44 64 0.48
45 29 0.22
46 2 0.02
47 6 0.05
48 1 0.01
49 12 0.09
50 18 0.14
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATAGAATCC
Found at i:30755774 original size:36 final size:36
Alignment explanation
Indices: 30755732--30755803 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
30755722 ACATTTATTA
*
30755732 GTATAAAAATCTTTGTTATTTCTTTTCATATTTAGG
1 GTATAAAAATCTTTGTAATTTCTTTTCATATTTAGG
30755768 GTATAAAAATCTTTGTAATTTCTTTTCATATTTAGG
1 GTATAAAAATCTTTGTAATTTCTTTTCATATTTAGG
30755804 AGTTTTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.51
Consensus pattern (36 bp):
GTATAAAAATCTTTGTAATTTCTTTTCATATTTAGG
Found at i:30760872 original size:2 final size:2
Alignment explanation
Indices: 30760865--30760893 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30760855 CATTAAGAAA
30760865 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
30760894 AAAACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30762866 original size:16 final size:17
Alignment explanation
Indices: 30762835--30762867 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30762825 AAACATTAAA
30762835 ATATTTAAATTTATTAT
1 ATATTTAAATTTATTAT
*
30762852 ATATTTACA-TTATTAT
1 ATATTTAAATTTATTAT
30762868 TTATACTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTAAATTTATTAT
Found at i:30763212 original size:22 final size:21
Alignment explanation
Indices: 30763167--30763213 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
30763157 CAAAATTTTG
* * *
30763167 AACCCTAAATCTAAAATCTCA
1 AACCCTAAATCAAAAAACTAA
30763188 AACCCTAAACTCAAAAAACTAA
1 AACCCTAAA-TCAAAAAACTAA
30763210 AACC
1 AACC
30763214 ACAAAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (21 bp):
AACCCTAAATCAAAAAACTAA
Found at i:30763278 original size:20 final size:20
Alignment explanation
Indices: 30763253--30763316 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
30763243 CATAACTTCG
30763253 AAACCCTGAACCTAAATCTT
1 AAACCCTGAACCTAAATCTT
* *
30763273 AAACCCTGAA-CTCAAAGCTC
1 AAACCCTGAACCT-AAATCTT
**
30763293 AAGTCCTGAACCTTAAATCTT
1 AAACCCTGAACC-TAAATCTT
30763314 AAA
1 AAA
30763317 TCCAAACCCT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.06
20 23 0.68
21 8 0.24
22 1 0.03
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (20 bp):
AAACCCTGAACCTAAATCTT
Found at i:30764200 original size:3 final size:3
Alignment explanation
Indices: 30764192--30764226 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30764182 ATTTTTAAGT
30764192 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30764227 CAAGTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30765737 original size:36 final size:35
Alignment explanation
Indices: 30765618--30765734 Score: 144
Period size: 35 Copynumber: 3.3 Consensus size: 35
30765608 TACTTTTTGT
* *
30765618 TTGGTGTGTTTCGAAGGGACTAGCTCTTTTGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
**
30765653 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
* * * * *
30765688 ATGGTGTGTTTTGGAGGGATTAGCTCGTGTGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
30765723 TCTGGTGTGTTT
1 T-TGGTGTGTTT
30765735 TGGTTGGACT
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 59 0.86
36 10 0.14
ACGTcount: A:0.15, C:0.12, G:0.34, T:0.39
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
Found at i:30766265 original size:32 final size:32
Alignment explanation
Indices: 30766229--30766294 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
30766219 GATGTTTCAA
*
30766229 TGCAACTAGAAATGGTATGTATTAATGATATG
1 TGCAACTAGAAATGGTACGTATTAATGATATG
30766261 TGCAACTAGAAATGGTACGTATTAATGATATG
1 TGCAACTAGAAATGGTACGTATTAATGATATG
30766293 TG
1 TG
30766295 TATTTTAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (32 bp):
TGCAACTAGAAATGGTACGTATTAATGATATG
Found at i:30767305 original size:22 final size:23
Alignment explanation
Indices: 30767280--30767323 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
30767270 GTAGTTGCTG
30767280 ACTCGTTTAAACGAT-TGGGATT
1 ACTCGTTTAAACGATGTGGGATT
*
30767302 ACTCGTTTAAACGGTGTGGGAT
1 ACTCGTTTAAACGATGTGGGAT
30767324 AACTTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (23 bp):
ACTCGTTTAAACGATGTGGGATT
Found at i:30774201 original size:24 final size:25
Alignment explanation
Indices: 30774152--30774233 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 25
30774142 TTTAGTTTTT
*
30774152 TTTAATATTT-ATATTTTTTGAA-A
1 TTTAATATTTAATATTTTTTAAATA
30774175 TTTAATATTTAATA-TTTTTAAATA
1 TTTAATATTTAATATTTTTTAAATA
** *
30774199 TTTTTTATTAAATATTCTTTTAATATA
1 TTTAATATTTAATATT-TTTTAA-ATA
30774226 TTT-ATATT
1 TTTAATATT
30774234 ATAGTATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
23 17 0.35
24 15 0.31
25 1 0.02
26 10 0.20
27 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (25 bp):
TTTAATATTTAATATTTTTTAAATA
Found at i:30774209 original size:14 final size:15
Alignment explanation
Indices: 30774192--30774220 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30774182 TTTAATATTT
30774192 TTAAATATT-TTTTA
1 TTAAATATTCTTTTA
30774206 TTAAATATTCTTTTA
1 TTAAATATTCTTTTA
30774221 ATATATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAATATTCTTTTA
Found at i:30774233 original size:26 final size:25
Alignment explanation
Indices: 30774174--30774234 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
30774164 ATTTTTTGAA
*
30774174 ATTTAATATTTAATATTTTTAAATAT
1 ATTT-ATATTAAATATTTTTAAATAT
* *
30774200 -TTTTTATTAAATATTCTTTTAATAT
1 ATTTATATTAAATATT-TTTAAATAT
30774225 ATTTATATTA
1 ATTTATATTA
30774235 TAGTATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 10 0.34
25 11 0.38
26 8 0.28
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTATATTAAATATTTTTAAATAT
Found at i:30783587 original size:48 final size:48
Alignment explanation
Indices: 30783529--30783625 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
30783519 GTTTGGTGAG
30783529 GCATCGGTTCAAGAGGAAAATGTACTAAAAACTATTTTACGAGAGTAT
1 GCATCGGTTCAAGAGGAAAATGTACTAAAAACTATTTTACGAGAGTAT
* * * *
30783577 GCATCTGTTCAAGGGGAAAGTGTGCTAAAAACTATTTTACGAGAGTAT
1 GCATCGGTTCAAGAGGAAAATGTACTAAAAACTATTTTACGAGAGTAT
30783625 G
1 G
30783626 AGCAATGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (48 bp):
GCATCGGTTCAAGAGGAAAATGTACTAAAAACTATTTTACGAGAGTAT
Found at i:30785969 original size:19 final size:19
Alignment explanation
Indices: 30785945--30785982 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30785935 AATTCAAATT
*
30785945 TATATTAATATTAAATAAA
1 TATATTAACATTAAATAAA
30785964 TATATTAACATTAAATAAA
1 TATATTAACATTAAATAAA
30785983 ATAAAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TATATTAACATTAAATAAA
Found at i:30786139 original size:6 final size:6
Alignment explanation
Indices: 30786130--30786156 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30786120 GATTTTATAC
30786130 TAATAT TAATAT TAATAT TAATAT TAA
1 TAATAT TAATAT TAATAT TAATAT TAA
30786157 ATAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATAT
Found at i:30786163 original size:179 final size:177
Alignment explanation
Indices: 30785841--30786173 Score: 465
Period size: 178 Copynumber: 1.9 Consensus size: 177
30785831 AAATTAACCT
* * * * *
30785841 TCAAATATTAAAAATAGTTTCAATTTAATCCTAATTCTATAAAATTCAAAAAAATGTATAAAATT
1 TCAAATATTAAAAATAATTTCAATTTAATCCTAATTCTAAAAAATTCAAAAAAATATACAAAAAT
* *
30785906 ACATAAATATTTTGAAAAATATAATAATAAATTCAAATTTATATTAATATTAAATAAATATATTA
66 ACATAAATATTTTAAAAAATATAATAATAAATTCAAATTTATACTAATATTAAATAAATATATTA
30785971 ACATTAAATAAAATAAAAATTCCCCCTTCTACCCTATCCCACTCCCCC
131 ACATTAAATAAAATAAAAA-TCCCCCTTCTACCCTATCCCACTCCCCC
* * *
30786019 TCAAATTTTACAAATAATTTCAATTTAATCCTAATTCTAAAAAATTC-AAAATATATACAAAAAT
1 TCAAATATTAAAAATAATTTCAATTTAATCCTAATTCTAAAAAATTCAAAAAAATATACAAAAAT
* * * *
30786083 ACTTAAATATTTTCAAAAAAGTATAATAATAAATTTAGATTTTATACTAATATT-AAT-ATTAAT
66 ACATAAATATTTT-AAAAAA-TATAATAATAAATTCA-AATTTATACTAATATTAAATAAAT-AT
*
30786146 ATTAATATTAAATAAAATAAAAATCCCC
127 ATTAACATTAAATAAAATAAAAATCCCC
30786174 TCCCACCCTA
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
177 25 0.18
178 55 0.40
179 42 0.31
180 14 0.10
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.36
Consensus pattern (177 bp):
TCAAATATTAAAAATAATTTCAATTTAATCCTAATTCTAAAAAATTCAAAAAAATATACAAAAAT
ACATAAATATTTTAAAAAATATAATAATAAATTCAAATTTATACTAATATTAAATAAATATATTA
ACATTAAATAAAATAAAAATCCCCCTTCTACCCTATCCCACTCCCCC
Found at i:30786291 original size:31 final size:29
Alignment explanation
Indices: 30786253--30786314 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
30786243 AGAAGGGATT
*
30786253 TTTATTTAATATTAATATATTTATATTTATA
1 TTTATTTAACATT-A-ATATTTATATTTATA
30786284 TTTATTTAACATTAATATTTATATTTATA
1 TTTATTTAACATTAATATTTATATTTATA
30786313 TT
1 TT
30786315 AAATTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 17 0.57
30 1 0.03
31 12 0.40
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTATTTAACATTAATATTTATATTTATA
Found at i:30786322 original size:18 final size:18
Alignment explanation
Indices: 30786301--30786339 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30786291 AACATTAATA
30786301 TTTATATTTA-TATTAAAT
1 TTTAT-TTTATTATTAAAT
*
30786319 TTTATTTTATTATTATAT
1 TTTATTTTATTATTAAAT
30786337 TTT
1 TTT
30786340 TTAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTATTATTAAAT
Found at i:30786327 original size:23 final size:25
Alignment explanation
Indices: 30786250--30786337 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 25
30786240 TGGAGAAGGG
* *
30786250 ATTTTTATTTAATATTAATATATTTAT
1 ATTTATATTT-ATATTAACAT-TTTAT
*
30786277 ATTTATATTTAT-TTAACA-TTAAT
1 ATTTATATTTATATTAACATTTTAT
30786300 ATTTATATTTATATTAA-ATTTTAT
1 ATTTATATTTATATTAACATTTTAT
30786324 -TTTAT-TATTATATT
1 ATTTATAT-TTATATT
30786338 TTTTAAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.02
23 29 0.54
24 8 0.15
25 5 0.09
26 2 0.04
27 9 0.17
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTATATTTATATTAACATTTTAT
Found at i:30786343 original size:27 final size:30
Alignment explanation
Indices: 30786302--30786370 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
30786292 ACATTAATAT
30786302 TTATATTTATATTAAAT-TTTAT-T-TTATTA
1 TTATATTT-T-TTAAATATTTATGTATTATTA
*
30786331 TTATATTTTTTAAATATTTATGTATTTTTA
1 TTATATTTTTTAAATATTTATGTATTATTA
30786361 -TATATTTTTT
1 TTATATTTTTT
30786371 TGAATTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 6 0.17
28 6 0.17
29 19 0.53
30 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (30 bp):
TTATATTTTTTAAATATTTATGTATTATTA
Found at i:30790770 original size:21 final size:21
Alignment explanation
Indices: 30790731--30790771 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30790721 TTATACTACA
* *
30790731 AAAAATAAATATGCGTATATG
1 AAAAATAAATATACATATATG
*
30790752 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
30790772 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:30790815 original size:29 final size:28
Alignment explanation
Indices: 30790778--30790832 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
30790768 ATATTTTTTT
*
30790778 AAAAATAATTAAATATAAAA-AAAGAATA
1 AAAAATAATT-AATAAAAAATAAAGAATA
30790806 AAAAACTAATTAATAAAAAATAAAGAA
1 AAAAA-TAATTAATAAAAAATAAAGAA
30790833 AATGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (28 bp):
AAAAATAATTAATAAAAAATAAAGAATA
Found at i:30791412 original size:26 final size:26
Alignment explanation
Indices: 30791359--30791412 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
30791349 ATCTTCTAAG
* *
30791359 ATTGCATATGATATCTAAGATTATAT
1 ATTGCATATCATATCTAAGATTACAT
*
30791385 ATTGCATATCATATCTAAGATTGCAT
1 ATTGCATATCATATCTAAGATTACAT
30791411 AT
1 AT
30791413 CCCTGAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (26 bp):
ATTGCATATCATATCTAAGATTACAT
Found at i:30792551 original size:132 final size:132
Alignment explanation
Indices: 30791740--30792502 Score: 1261
Period size: 132 Copynumber: 5.8 Consensus size: 132
30791730 TAGGACTTAC
* *
30791740 AATCTTCAA-CATATTCCACTGTTGACCAGGG-AGATATG-ATTACTGGTTTCAATGTACTCCAC
1 AATCTTCAATC-TATTCCACTGTTGTCCAGGGAAG-TA-GAATTACTGGCTTCAATGTACTCCAC
*
30791802 TG-TAACCACAGGGAGGTAAAATCCGCAATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
63 -GATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
30791866 ACCTGA
127 ACCTGA
30791872 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACGAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACGAT
30791937 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
30792002 GA
131 GA
* *
30792004 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTAGATTCAATGTACTCCACGAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACGAT
*
30792069 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAATACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
30792134 GA
131 GA
*
30792136 AATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACGAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACGAT
* * *
30792201 AACCACAGGGAGGTAAAATCCGCCATCTTCGATTTGCTCCACTACTACTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
30792266 GA
131 GA
* * *
30792268 AATCTTCAATCTATTCCACTGTTGTTCAGGGAAATAGAATTACTGGTTTCAATGTACTCCACTG-
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCAC-GA
* * *
30792332 TAACCAC-GGAGAGGTAAAATCCGCCATCTTCGATCCGCTCCACTACTGCTTAAGGAGATAAGAT
65 TAACCACAGG-GAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAC
30792396 CTGA
129 CTGA
*
30792400 AATCTTCAATCGATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTG-
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCAC-GA
30792464 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
65 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
30792503 TCGCTGTCAA
Statistics
Matches: 598, Mismatches: 26, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
131 4 0.01
132 588 0.98
133 6 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACGAT
AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
GA
Found at i:30798664 original size:24 final size:22
Alignment explanation
Indices: 30798606--30798664 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
30798596 ATATGTATAC
*
30798606 TAAAATAAAT-ATATACATATAGA
1 TAAAA-AAATAAT-TACATATAAA
30798629 TAAAAAAATAATTACATATAAA
1 TAAAAAAATAATTACATATAAA
30798651 TAAATAAAAATAAT
1 T-AA-AAAAATAAT
30798665 AATTATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.44
23 9 0.28
24 9 0.28
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAAAAAATAATTACATATAAA
Found at i:30798721 original size:21 final size:21
Alignment explanation
Indices: 30798682--30798722 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30798672 TTATACTACA
* *
30798682 AAAAATAAATATGCGTATATG
1 AAAAATAAATATACATATATG
*
30798703 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
30798723 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:30798766 original size:29 final size:28
Alignment explanation
Indices: 30798729--30798783 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
30798719 ATATTTTTTT
*
30798729 AAAAATAATTAAATATAAAA-AAAGAATA
1 AAAAATAATT-AATAAAAAATAAAGAATA
30798757 AAAAACTAATTAATAAAAAATAAAGAA
1 AAAAA-TAATTAATAAAAAATAAAGAA
30798784 AATGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (28 bp):
AAAAATAATTAATAAAAAATAAAGAATA
Found at i:30799363 original size:26 final size:26
Alignment explanation
Indices: 30799310--30799363 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
30799300 ATCTTCTAAG
* *
30799310 ATTGCATATGATATCTAAGATTATAT
1 ATTGCATATCATATCTAAGATTACAT
*
30799336 ATTGCATATCATATCTAAGATTGCAT
1 ATTGCATATCATATCTAAGATTACAT
30799362 AT
1 AT
30799364 CCCTGAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (26 bp):
ATTGCATATCATATCTAAGATTACAT
Found at i:30810584 original size:2 final size:2
Alignment explanation
Indices: 30810577--30810610 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30810567 GTTTATAAAG
30810577 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30810611 GTTGGCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:30812611 original size:3 final size:3
Alignment explanation
Indices: 30812603--30812635 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
30812593 AAATATCCAA
30812603 AAG AAG AAG CAA- AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG
30812636 CAAGCAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30812617 original size:12 final size:12
Alignment explanation
Indices: 30812600--30812638 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
30812590 GAAAAATATC
30812600 CAAAAGAAGAAG
1 CAAAAGAAGAAG
30812612 CAAAAGAAGAAG
1 CAAAAGAAGAAG
30812624 -AAGAAGAAGAAG
1 CAA-AAGAAGAAG
30812636 CAA
1 CAA
30812639 GCAACTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.67, C:0.08, G:0.26, T:0.00
Consensus pattern (12 bp):
CAAAAGAAGAAG
Found at i:30814345 original size:13 final size:13
Alignment explanation
Indices: 30814327--30814351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30814317 TTTTTTATAG
30814327 AAATATAATAATA
1 AAATATAATAATA
30814340 AAATATAATAAT
1 AAATATAATAAT
30814352 TATTTATCAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATAATA
Found at i:30814488 original size:15 final size:16
Alignment explanation
Indices: 30814463--30814493 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
30814453 CTATTAGTAG
30814463 TTTTTTAAATATTTTA
1 TTTTTTAAATATTTTA
30814479 TTTTTT-AATATTTTA
1 TTTTTTAAATATTTTA
30814494 CTATACTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTAAATATTTTA
Found at i:30814738 original size:61 final size:61
Alignment explanation
Indices: 30814643--30814766 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
30814633 CCATAAATAC
30814643 TTTAGGAAATGGGCATTTTCTGGTACTATGCCCATTTAAATTCGTTTATATTTGAAATTAG
1 TTTAGGAAATGGGCATTTTCTGGTACTATGCCCATTTAAATTCGTTTATATTTGAAATTAG
30814704 TTTAGGAAATGGGCATTTTCTGGTACTATGCCCATTTAAATTCGTTTATATTTGAAATTAG
1 TTTAGGAAATGGGCATTTTCTGGTACTATGCCCATTTAAATTCGTTTATATTTGAAATTAG
30814765 TT
1 TT
30814767 AATTTAAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (61 bp):
TTTAGGAAATGGGCATTTTCTGGTACTATGCCCATTTAAATTCGTTTATATTTGAAATTAG
Found at i:30814969 original size:5 final size:5
Alignment explanation
Indices: 30814959--30814995 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
30814949 TTGCATATTC
*
30814959 ATAAT ATAAT ATAAT ATAAT ATAAT GTAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
30814996 GTTACAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:30815500 original size:15 final size:14
Alignment explanation
Indices: 30815483--30815532 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
30815473 TCAAAATTCA
30815483 AAAATATAAAAATT
1 AAAATATAAAAATT
30815497 AAAAT-TAATCAAATT
1 AAAATATAA--AAATT
30815512 AAAATATAAAAATT
1 AAAATATAAAAATT
30815526 -AAATATA
1 AAAATATA
30815533 CAACTCACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 10 0.30
14 10 0.30
15 10 0.30
16 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:30815523 original size:23 final size:23
Alignment explanation
Indices: 30815484--30815527 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
30815474 CAAAATTCAA
*
30815484 AAATATAAAAATTAAAATTAATC
1 AAATATAAAAATAAAAATTAATC
30815507 AAAT-TAAAATATAAAAATTAA
1 AAATATAAAA-ATAAAAATTAA
30815528 ATATACAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATATAAAAATAAAAATTAATC
Found at i:30818116 original size:13 final size:11
Alignment explanation
Indices: 30818088--30818130 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
30818078 AGTTAAATAT
30818088 TATTTTATTAA
1 TATTTTATTAA
30818099 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
30818112 TA-TTTATTAT
1 TATTTTATTAA
30818122 TATTTTATT
1 TATTTTATT
30818131 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:30818117 original size:23 final size:23
Alignment explanation
Indices: 30818091--30818134 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
30818081 TAAATATTAT
30818091 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
30818114 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
30818135 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:30821760 original size:11 final size:11
Alignment explanation
Indices: 30821744--30821789 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
30821734 CATTTTTCTA
30821744 AATAAAATAAT
1 AATAAAATAAT
30821755 AAT-AAATATAT
1 AATAAAATA-AT
*
30821766 AAGTAAAATATT
1 AA-TAAAATAAT
30821778 AATAAAATAAT
1 AATAAAATAAT
30821789 A
1 A
30821790 TTTAACTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 5 0.17
11 16 0.53
12 4 0.13
13 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:30822169 original size:3 final size:3
Alignment explanation
Indices: 30822163--30822206 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
30822153 CTTAATCATC
30822163 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
30822207 CATTTTAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:30823773 original size:44 final size:44
Alignment explanation
Indices: 30823716--30823806 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
30823706 ATTGAAATAA
*
30823716 AATAGAAATTGTGATAATTTTACAT-TTT-AAAATAATTATACTTT
1 AATAGAAATTGTGATAA--TTACATATTTAAAAATAATTATAATTT
*
30823760 AATAGAAGTTGTGATAATTACATATTTAAAAATAATTATAATTT
1 AATAGAAATTGTGATAATTACATATTTAAAAATAATTATAATTT
30823804 AAT
1 AAT
30823807 TTAAATTTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 6 0.14
43 3 0.07
44 34 0.79
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (44 bp):
AATAGAAATTGTGATAATTACATATTTAAAAATAATTATAATTT
Found at i:30825019 original size:40 final size:40
Alignment explanation
Indices: 30824964--30825044 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
30824954 TATTGTTCAC
30824964 ATTCATAAAACTATTGCTAGTTTGCATACTTGAAAATTCT
1 ATTCATAAAACTATTGCTAGTTTGCATACTTGAAAATTCT
30825004 ATTCATAAAACTATTGCTAGTTTGCATACTTGAAAATTCT
1 ATTCATAAAACTATTGCTAGTTTGCATACTTGAAAATTCT
30825044 A
1 A
30825045 ACATTATTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (40 bp):
ATTCATAAAACTATTGCTAGTTTGCATACTTGAAAATTCT
Found at i:30829941 original size:105 final size:104
Alignment explanation
Indices: 30829759--30829973 Score: 394
Period size: 105 Copynumber: 2.1 Consensus size: 104
30829749 GATGTTTATA
*
30829759 CTTTTCTAGGGTTGCTTTTGGTATGAAATTTTCTTTATCAAAATAAATGTTATGGAAAAGAAGTA
1 CTTTTCTAGGGTTGCTTTTGGTATGAAATTTTCTTTATCAAAATAAATGTTATGGAAAAGAAGAA
*
30829824 AGAAAACAAAGCTCATTTTCTCCCGTACGTCTCTTGTCTT
66 AGAAAACAAAGCTCATTTTCTCCCATACGTCTC-TGTCTT
*
30829864 CTTTTCTAGGGTTGCTTTTGGTATGAAATTTTCTTTCTCAAAATAAATGTTATGGAAAAGAAGAA
1 CTTTTCTAGGGTTGCTTTTGGTATGAAATTTTCTTTATCAAAATAAATGTTATGGAAAAGAAGAA
30829929 AGAAAACAAAGCTCATTTTCTCCCATACGTCTCTGTCTT
66 AGAAAACAAAGCTCATTTTCTCCCATACGTCTCTGTCTT
30829968 CTTTTC
1 CTTTTC
30829974 ATGATTGATT
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 12 0.11
105 95 0.89
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (104 bp):
CTTTTCTAGGGTTGCTTTTGGTATGAAATTTTCTTTATCAAAATAAATGTTATGGAAAAGAAGAA
AGAAAACAAAGCTCATTTTCTCCCATACGTCTCTGTCTT
Found at i:30830237 original size:2 final size:2
Alignment explanation
Indices: 30830230--30830255 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30830220 AAAGCTTAGA
30830230 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
30830256 TAAATTACCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30841150 original size:21 final size:21
Alignment explanation
Indices: 30841126--30841165 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30841116 CAACTATTCC
*
30841126 TATTTTTATATATTTTTTTTT
1 TATTTTTATATAATTTTTTTT
*
30841147 TATTTTTTTATAATTTTTT
1 TATTTTTATATAATTTTTT
30841166 AAAGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (21 bp):
TATTTTTATATAATTTTTTTT
Found at i:30847139 original size:64 final size:65
Alignment explanation
Indices: 30846938--30847184 Score: 273
Period size: 64 Copynumber: 3.8 Consensus size: 65
30846928 TTGTTACAAG
* * *
30846938 ACTTAGATAGCACACTTGTTTAAAGTGGTTTTACCTCTTTAAGATAATACGCTTCTTTAAAGCGA
1 ACTTAGATAGCACACTTCTTTAAAGTGGTTTTACCTCTTTAAGGTAATACGCTTCTTTAAAGAGA
* * * * *
30847003 ACTTAGATAGATAACATACATCTTTAAAGTGCTTTTACCTATTTCAA-GTAATACACTTCTTTAA
1 ACTTAGATAG----CACACTTCTTTAAAGTGGTTTTACCTCTTT-AAGGTAATACGCTTCTTTAA
*
30847067 AGAAA
61 AGAGA
* * * * *
30847072 ACTTTGATAGCACACTTCTTTATAGTGGATTTACCTCTTTAAGGT-ATATGCTTCTTTAAAGTGA
1 ACTTAGATAGCACACTTCTTTAAAGTGGTTTTACCTCTTTAAGGTAATACGCTTCTTTAAAGAGA
* * * *
30847136 ACTTAAATAGCTCACTTTTTTAAAGTGGCTTTACCTCTTTAAGGTAATA
1 ACTTAGATAGCACACTTCTTTAAAGTGGTTTTACCTCTTTAAGGTAATA
30847185 ATAAAAGGTG
Statistics
Matches: 149, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
64 56 0.38
65 39 0.26
69 52 0.35
70 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (65 bp):
ACTTAGATAGCACACTTCTTTAAAGTGGTTTTACCTCTTTAAGGTAATACGCTTCTTTAAAGAGA
Found at i:30867341 original size:30 final size:30
Alignment explanation
Indices: 30867300--30867362 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
30867290 TTTTTTTTGA
*
30867300 AAGATCCGAAACATGATCTTCAACGGTAGC
1 AAGATCCGAAACATGATCTTCAACGGTAAC
*
30867330 AAGATCGGAAACATGATCTTCAACGGTAAC
1 AAGATCCGAAACATGATCTTCAACGGTAAC
30867360 AAG
1 AAG
30867363 CTTGGCGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (30 bp):
AAGATCCGAAACATGATCTTCAACGGTAAC
Found at i:30867430 original size:81 final size:81
Alignment explanation
Indices: 30867295--30867494 Score: 328
Period size: 81 Copynumber: 2.5 Consensus size: 81
30867285 TTTTTTTTTT
* * * *
30867295 TTTGAAAGATCCGAAACATGATCTTCAACGGTAGCAAGATCGGAAACATGATCTTCAACGGTAAC
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
30867360 AAGCTTGGCGGTGAAG
66 AAGCTTGGCGGTGAAG
* * *
30867376 TTTGAAATATACGAAGCAGGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAGCGGTAAC
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
*
30867441 AAGCTTGGCGGTGATG
66 AAGCTTGGCGGTGAAG
30867457 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAG
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAG
30867495 CTTGGCGGTG
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 109 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.23
Consensus pattern (81 bp):
TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
AAGCTTGGCGGTGAAG
Found at i:30868545 original size:38 final size:39
Alignment explanation
Indices: 30868494--30868577 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 39
30868484 GTTGCAAATT
*
30868494 TTTTAATTGACATGTGAAAAA-TAGTCTTA-TACTTTATA
1 TTTTAATTGACATGTGAAAAATTAGTCTTATTAATTT-TA
* * *
30868532 TTTTAATTTACATGTTAAAAATTATTCTTATTAATTTTA
1 TTTTAATTGACATGTGAAAAATTAGTCTTATTAATTTTA
30868571 TTTTAAT
1 TTTTAAT
30868578 ATACTAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 19 0.47
39 16 0.40
40 5 0.12
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (39 bp):
TTTTAATTGACATGTGAAAAATTAGTCTTATTAATTTTA
Found at i:30874603 original size:5 final size:6
Alignment explanation
Indices: 30874587--30874611 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30874577 AGGTTTTTGG
30874587 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
30874612 AAGGCTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:30876512 original size:19 final size:19
Alignment explanation
Indices: 30876488--30876539 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
30876478 CACCTCTTTT
*
30876488 TGCATT-CATTTTATTCATA
1 TGCATTACATTTCA-TCATA
30876507 TGCATTACATTTCATCATA
1 TGCATTACATTTCATCATA
*
30876526 TGCATTATATTTCA
1 TGCATTACATTTCA
30876540 CAAAAGACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (19 bp):
TGCATTACATTTCATCATA
Found at i:30883179 original size:51 final size:50
Alignment explanation
Indices: 30883106--30883779 Score: 305
Period size: 51 Copynumber: 14.3 Consensus size: 50
30883096 AATGGAATAA
*
30883106 ATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
1 ATTAAAGCTACAAG-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* *
30883157 ATTAAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAATAG
1 ATTAAAGCTACAAG-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* * * * * *
30883208 ATTGAA--TA-TAG--CGAATCTTATTTCCCTGAAGTTGCAATGGAACAA
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
*
30883253 ATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGT-GAAGTAG
1 ATTAAAGCTACAAG-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAA-CAG
* * * * * * *
30883304 ATTGAAG--A-TAG--CGAATCTTATTTCCCTGAAGTTGTAGTGGAATAA
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
** * * * *
30883349 ATTAAAGCTACAAACCACAAATCCTATAC-CCCTGAAGTTGCAATGGGACGG
1 ATTAAAGCTAC-AAGTACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAACAG
* * * * * * * * *
30883400 ATTGAAG-T-CATTA-TGGCGAATATTATCTCCTTGAAGTTGTAGAGGAGCAT
1 ATTAAAGCTACA--AGT-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* **
30883450 ATTAAAGC--C----ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAG
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* ** *
30883494 ATTGAAGCT---AG--CAAATCTTATCTCTATGAAGTTGCAGTAGAACAG
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* * * * ** *
30883539 ATTGAAG---C---TACAAATCTTATCTCTCTGATGTTGTAGTATAGCAG
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* * * *
30883583 ATTGAAGC--C----ACAAATTTTATCTCCTTGAAGTTGCAGTGGAGCAG
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* * * * * * *
30883627 ATGAAAG--A-TA-T-CAAATTTTATTTCACT-AGAGTTGTAGTGGAATAG
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGA-AGTTGCAGTGGAACAG
* * ** *
30883672 ATTAAAGCTACGAGTTATAAATCTTATCTCATTGAAGTTGCAGTGGAGCAG
1 ATTAAAGCTACAAG-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* *
30883723 ATTGAAGCTAC---T---AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
* *
30883767 ATTGAAGCAACAA
1 ATTAAAGCTACAA
30883780 TTTCTATATC
Statistics
Matches: 485, Mismatches: 97, Indels: 87
0.72 0.14 0.13
Matches are distributed among these distances:
44 145 0.30
45 134 0.28
46 3 0.01
47 5 0.01
48 8 0.02
49 6 0.01
50 34 0.07
51 149 0.31
52 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTAAAGCTACAAGTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
Found at i:30883291 original size:96 final size:96
Alignment explanation
Indices: 30883125--30883551 Score: 449
Period size: 96 Copynumber: 4.5 Consensus size: 96
30883115 ACAAGTTAAA
*
30883125 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCCCT
* *
30883190 AAAGTTGCAGTGGAATAGATTGAATATAGCG
66 GAAGTTGCAGTGGAATAGATTGAAGATAGCG
* *
30883221 AATCTTATTTCCCTGAAGTTGCAATGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCCCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCCCT
30883286 GAAGTTGCAGT-GAAGTAGATTGAAGATAGCG
66 GAAGTTGCAGTGGAA-TAGATTGAAGATAGCG
* * * *** *
30883317 AATCTTATTTCCCTGAAGTTGTAGTGGAATAAATTAAAGCTACAAACCACAAATCCTATAC-CCC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACAAATCTTAT-CTCCC
* * **
30883381 TGAAGTTGCAATGGGACGGATTGAAGTCATTATGGCG
65 TGAAGTTGCAGTGGAATAGATTGAAG--A-TA--GCG
* * * * * * *
30883418 AATATTATCTCCTTGAAGTTGTAGAGGAGCATATTAAAGC--C-----ACAAATCTTATCTCCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCCCT
* * *
30883476 GAAGTTGCAGTGGAGTAGATTGAAGCTAGCA
66 GAAGTTGCAGTGGAATAGATTGAAGATAGCG
** * * *
30883507 AATCTTATCTCTATGAAGTTGCAGTAGAACAGATTGAAGCTACAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAA
30883552 ATCTTATCTC
Statistics
Matches: 277, Mismatches: 41, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
89 33 0.12
91 3 0.01
93 1 0.00
94 33 0.12
95 3 0.01
96 161 0.58
97 3 0.01
98 1 0.00
99 3 0.01
101 36 0.13
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (96 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCCCT
GAAGTTGCAGTGGAATAGATTGAAGATAGCG
Found at i:30883306 original size:147 final size:146
Alignment explanation
Indices: 30883027--30883297 Score: 416
Period size: 147 Copynumber: 1.8 Consensus size: 146
30883017 GATTAAAGCC
* ** * * * *
30883027 ACAAATCTTATCTCTCTGGAGTTACATTGGAGCAGATTGAATATACGAATTTTATTTCCTTGAAC
1 ACAAATCTTATCTCCCTAAAGTTACAGTGGAACAGATTGAATATACGAATCTTATTTCCCTGAAC
* *
30883092 TTGTAATGGAATAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
66 TTGCAATGGAACAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
30883157 ATTAAAGCTACAAGTT
131 ATTAAAGCTACAAGTT
* *
30883173 ACAAATCTTATCTCCCTAAAGTTGCAGTGGAATAGATTGAATATAGCGAATCTTATTTCCCTGAA
1 ACAAATCTTATCTCCCTAAAGTTACAGTGGAACAGATTGAATATA-CGAATCTTATTTCCCTGAA
* *
30883238 GTTGCAATGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTG
65 CTTGCAATGGAACAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTG
30883298 AAGTAGATTG
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
146 38 0.34
147 73 0.66
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (146 bp):
ACAAATCTTATCTCCCTAAAGTTACAGTGGAACAGATTGAATATACGAATCTTATTTCCCTGAAC
TTGCAATGGAACAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGGAACAG
ATTAAAGCTACAAGTT
Found at i:30883382 original size:147 final size:144
Alignment explanation
Indices: 30883087--30883394 Score: 327
Period size: 147 Copynumber: 2.1 Consensus size: 144
30883077 TTTATTTCCT
* * *
30883087 TGAACTTGTAATGGAATAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGG
1 TGAAGTTGCAATGGAACAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGG
* * *
30883152 AACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAATAGATTGAATAT
66 AACAGATTAAAGC-ACAAG-T-CAAATCTTATCTCCCTAAAGTTGCAGTGGAATAAATTAAATAA
* * * **
30883217 AGCGAATCTTATTTCCC
128 AACAAATCCTATACCCC
*
30883234 TGAAGTTGCAATGGAACAAATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGT-G
1 TGAAGTTGCAATGGAACAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * * * *
30883298 AAGTAGATTGAAG-A-TAG-CGAATCTTATTTCCCTGAAGTTGTAGTGGAATAAATTAAAGCTAC
66 AA-CAGATTAAAGCACAAGTCAAATCTTATCTCCCTAAAGTTGCAGTGGAATAAATTAAA--T--
30883360 AAACCACAAATCCTATACCCC
126 AAA--ACAAATCCTATACCCC
30883381 TGAAGTTGCAATGG
1 TGAAGTTGCAATGG
30883395 GACGGATTGA
Statistics
Matches: 135, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
141 34 0.25
143 1 0.01
144 2 0.01
145 3 0.02
146 3 0.02
147 92 0.68
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (144 bp):
TGAAGTTGCAATGGAACAAATTAAAGCTACAAGTTAAAAATCTTATCTCCCTGAAGTTGCAGTGG
AACAGATTAAAGCACAAGTCAAATCTTATCTCCCTAAAGTTGCAGTGGAATAAATTAAATAAAAC
AAATCCTATACCCC
Found at i:30883584 original size:44 final size:44
Alignment explanation
Indices: 30883422--30883779 Score: 244
Period size: 44 Copynumber: 7.9 Consensus size: 44
30883412 ATGGCGAATA
* * *
30883422 TTATCTC-CTTGAAGTTGTAG-AGGAGCATATTAAAGCCACAAATC
1 TTATCTCTC-TGAAGTTGCAGTA-GAGCAGATTGAAGCCACAAATC
* * *
30883466 TTATCTC-CTTGAAGTTGCAGTGGAGTAGATTGAAGCTAGCAAATC
1 TTATCTCTC-TGAAGTTGCAGTAGAGCAGATTGAAGCCA-CAAATC
* * *
30883511 TTATCTCTATGAAGTTGCAGTAGAACAGATTGAAGCTACAAATC
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATC
* * * *
30883555 TTATCTCTCTGATGTTGTAGTATAGCAGATTGAAGCCACAAATT
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATC
* ** *
30883599 TTATCTC-CTTGAAGTTGCAGTGGAGCAGA-TGAAAGATATCAAATT
1 TTATCTCTC-TGAAGTTGCAGTAGAGCAGATTG-AAGCCA-CAAATC
* * * * ** * *
30883644 TTATTTCACT-AGAGTTGTAGTGGAATAGATTAAAGCTACGAGTTATAAATC
1 TTATCTCTCTGA-AGTTGCAGTAGAGCAGATTGAAGC--C-----ACAAATC
* * *
30883695 TTATCTCAT-TGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATC
1 TTATCTC-TCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATC
* * *
30883739 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAACAA
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAA
30883780 TTTCTATATC
Statistics
Matches: 251, Mismatches: 44, Indels: 38
0.75 0.13 0.11
Matches are distributed among these distances:
43 3 0.01
44 144 0.57
45 69 0.27
46 2 0.01
51 31 0.12
52 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (44 bp):
TTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATC
Found at i:30883610 original size:133 final size:134
Alignment explanation
Indices: 30883422--30883774 Score: 376
Period size: 133 Copynumber: 2.6 Consensus size: 134
30883412 ATGGCGAATA
* * * *
30883422 TTATCTCCTTGAAGTTGTAG-AGGAGCATATTAAAGCCACAAATCTTATCTCCTTGAAGTTGCAG
1 TTATCTCATTGAAGTTGCAGTA-GAGCAGATTGAAGCCACAAATCTTATCTCCTTGAAGTTGCAG
* *
30883486 TGGAGTAGATTGAAGCTAGCAAATCTTATCT--CTATGAAGTTGCAGTAGAACAGATTGAAGCTA
65 TGGAGCAGATTGAAGCTAGCAAATCTTATCTCACTA-G-AGTTGCAGTAGAACAGATTAAAGCTA
30883549 C-AAATC
128 CTAAATC
* * * *
30883555 TTATCTC-TCTGATGTTGTAGTATAGCAGATTGAAGCCACAAATTTTATCTCCTTGAAGTTGCAG
1 TTATCTCAT-TGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATCTTATCTCCTTGAAGTTGCAG
* * * * * * *
30883619 TGGAGCAGA-TGAAAGATATCAAATTTTATTTCACTAGAGTTGTAGTGGAATAGATTAAAGCTAC
65 TGGAGCAGATTG-AAGCTAGCAAATCTTATCTCACTAGAGTTGCAGTAGAACAGATTAAAGCTAC
30883683 GAGTTATAAATC
129 ------TAAATC
* * * *
30883695 TTATCTCATTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATCTTATCTCCCTGAAGTTGCAGT
1 TTATCTCATTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATCTTATCTCCTTGAAGTTGCAGT
30883760 GGAGCAGATTGAAGC
66 GGAGCAGATTGAAGC
30883775 AACAATTTCT
Statistics
Matches: 183, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
132 3 0.02
133 101 0.55
134 2 0.01
135 3 0.02
140 71 0.39
141 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (134 bp):
TTATCTCATTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATCTTATCTCCTTGAAGTTGCAGT
GGAGCAGATTGAAGCTAGCAAATCTTATCTCACTAGAGTTGCAGTAGAACAGATTAAAGCTACTA
AATC
Found at i:30885150 original size:50 final size:51
Alignment explanation
Indices: 30885096--30885280 Score: 241
Period size: 51 Copynumber: 3.6 Consensus size: 51
30885086 TGAAAGTGAT
*
30885096 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-ATA
* * * *
30885146 GGTCACATGTGTCGTACTATGTGCAGGCTACTATGTGTACCGGATAGTTTC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATA
* * * *
30885197 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-ATA
*
30885249 -GTCACACGTGTAGTACTATGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
30885281 TGTGAACCAA
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
50 41 0.35
51 73 0.63
52 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATA
Found at i:30885214 original size:101 final size:101
Alignment explanation
Indices: 30885098--30885284 Score: 306
Period size: 101 Copynumber: 1.8 Consensus size: 101
30885088 AAAGTGATGG
* *
30885098 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-G-ATAGGTCACATGTGTCGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGAATA-GTCACACGTGTAGT
30885161 ACTATGTGCAGGCTACTATGTGTACCGGATAGTTTCGA
64 ACTATGTGCAGGCTACTATGTGTACCGGATAGTTTCGA
*
30885199 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATAGTCACACGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGG-AATAGTCACACGTGTAGTA
30885264 CTATGTGCAGGCTACTATGTG
65 CTATGTGCAGGCTACTATGTG
30885285 AACCAAACAT
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
100 2 0.03
101 41 0.51
102 34 0.43
103 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGAATAGTCACACGTGTAGTAC
TATGTGCAGGCTACTATGTGTACCGGATAGTTTCGA
Found at i:30885790 original size:10 final size:11
Alignment explanation
Indices: 30885768--30885794 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
30885758 CTGACTTTGG
30885768 AAAATTGTAAA
1 AAAATTGTAAA
30885779 AAAATTGTAAA
1 AAAATTGTAAA
30885790 AAAAT
1 AAAAT
30885795 AATTATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (11 bp):
AAAATTGTAAA
Found at i:30888819 original size:17 final size:17
Alignment explanation
Indices: 30888784--30888838 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
30888774 ATTGTCATTG
30888784 TTAT-TTTTTTATTTTATT
1 TTATATTTTTTA--TTATT
*
30888802 TT-TATGTTTTTGTTATT
1 TTATAT-TTTTTATTATT
30888819 TTACTATTTTTTATTATT
1 TTA-TATTTTTTATTATT
30888837 TT
1 TT
30888839 CGGCATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 8 0.26
18 15 0.48
19 8 0.26
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (17 bp):
TTATATTTTTTATTATT
Found at i:30890437 original size:21 final size:23
Alignment explanation
Indices: 30890411--30890460 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
30890401 ATTTCATGGC
*
30890411 TTTTTTAG-AAATTTGGG-TTTT
1 TTTTTTAGAAAATTTGGGATATT
*
30890432 TTTTTTGGAAAATTTGGGATATT
1 TTTTTTAGAAAATTTGGGATATT
30890455 TTTTTT
1 TTTTTT
30890461 GTAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
22 9 0.36
23 9 0.36
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.62
Consensus pattern (23 bp):
TTTTTTAGAAAATTTGGGATATT
Found at i:30890444 original size:22 final size:22
Alignment explanation
Indices: 30890411--30890461 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
30890401 ATTTCATGGC
* *
30890411 TTTTTTAGAAATTTGGG-TTTT
1 TTTTTTGGAAATTTGGGATATT
30890432 TTTTTTGGAAAATTTGGGATATT
1 TTTTTTGG-AAATTTGGGATATT
30890455 TTTTTTG
1 TTTTTTG
30890462 TAATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 9 0.35
23 10 0.38
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.61
Consensus pattern (22 bp):
TTTTTTGGAAATTTGGGATATT
Found at i:30890466 original size:21 final size:20
Alignment explanation
Indices: 30890411--30890467 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
30890401 ATTTCATGGC
* *
30890411 TTTTTTAGAAATTTGGGTTT
1 TTTTTTTGAAATTTGGGTAT
30890431 TTTTTTTGGAAAATTTGGGATAT
1 TTTTTTT-G-AAATTTGGG-TAT
*
30890454 TTTTTTTGTAATTT
1 TTTTTTTGAAATTT
30890468 TTATAGGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
22 10 0.32
23 9 0.29
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (20 bp):
TTTTTTTGAAATTTGGGTAT
Found at i:30907405 original size:31 final size:29
Alignment explanation
Indices: 30907362--30907420 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
30907352 AGAATAGTTT
30907362 ATTAAATAAAAATAAAATAATATTTTTTGAA
1 ATTAAATAAAAATAAAA-AAT-TTTTTTGAA
*
30907393 ATTAAA-ACAAAATAATAAATTTTTTTGA
1 ATTAAATA-AAAATAAAAAATTTTTTTGA
30907421 CAATGCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
30 4 0.15
31 14 0.54
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
ATTAAATAAAAATAAAAAATTTTTTTGAA
Found at i:30907415 original size:27 final size:26
Alignment explanation
Indices: 30907365--30907416 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
30907355 ATAGTTTATT
* *
30907365 AAATAAAAATAAAATAATATTTTTTG
1 AAATAAAAACAAAATAATAATTTTTG
*
30907391 AAATTAAAACAAAATAATAAATTTTT
1 AAATAAAAACAAAATAAT-AATTTTT
30907417 TTGACAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATAAAAACAAAATAATAATTTTTG
Found at i:30919803 original size:15 final size:15
Alignment explanation
Indices: 30919779--30919815 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
30919769 AACTCGACTC
30919779 GACTCGAAATTTTTT
1 GACTCGAAATTTTTT
*
30919794 GACTCTAAATTTTTT
1 GACTCGAAATTTTTT
30919809 GACTCGA
1 GACTCGA
30919816 TTCGAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (15 bp):
GACTCGAAATTTTTT
Found at i:30924325 original size:7 final size:7
Alignment explanation
Indices: 30924313--30924339 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30924303 AAAAAAACTT
30924313 ATAAATA
1 ATAAATA
30924320 ATAAATA
1 ATAAATA
30924327 ATAAATA
1 ATAAATA
30924334 ATAAAT
1 ATAAAT
30924340 TTTAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAAATA
Found at i:30924775 original size:179 final size:178
Alignment explanation
Indices: 30924484--30924839 Score: 459
Period size: 179 Copynumber: 2.0 Consensus size: 178
30924474 AAAAATCCCT
* * *
30924484 TTAACAATTAACTTTAACTATTGATCGTTAAAGTTAACGACCCCTAGTTTTTTCAATTAAAGTCA
1 TTAACAATTAACTTTAACTATTAATCATTAAAGTTAACGACCCCTAGTTTTTTAAATTAAAGTCA
** ** * *
30924549 TTGCGTGTCGTAACACAACATGACATGTGGCGAAAATGATAAAAAAAAAATCAATAAAAGTTATA
66 TCACGTGTCACAACACAACATGACATGTAGCGAAAATAATAAAAAAAAAATCAATAAAAGTTATA
* * *
30924614 GAAAAATTAT-AAAATGCTTCTTTGGTATGGTAATTTTTAT-AATTTTTTC
131 GAAAAATTATGAAAAT--TT-TTTGATACGATAATTTTTATAAATTTTTTC
* *
30924663 TTAACAATTAACTTTAATTGTTAATCATTAAAGTTAAACGACCCCTAGTTTGTTTAAATTAAAGT
1 TTAACAATTAACTTTAACTATTAATCATTAAAGTT-AACGACCCCTAGTTT-TTTAAATTAAAGT
* * *** *
30924728 CATCATGTGTCACAACATAGTGTGACATGTAGC-AAAA-AATGAAAAAAAAATCAATAAAAGTTA
64 CATCACGTGTCACAACACAACATGACATGTAGCGAAAATAATAAAAAAAAAATCAATAAAAGTTA
30924791 TAGAAAAATTATGAAAATTTTTTGATACGATAATTTTTATAAATTTTTT
129 TAGAAAAATTATGAAAATTTTTTGATACGATAATTTTTATAAATTTTTT
30924840 TACGAAATTT
Statistics
Matches: 153, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
177 17 0.11
178 10 0.07
179 67 0.44
180 24 0.16
181 35 0.23
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (178 bp):
TTAACAATTAACTTTAACTATTAATCATTAAAGTTAACGACCCCTAGTTTTTTAAATTAAAGTCA
TCACGTGTCACAACACAACATGACATGTAGCGAAAATAATAAAAAAAAAATCAATAAAAGTTATA
GAAAAATTATGAAAATTTTTTGATACGATAATTTTTATAAATTTTTTC
Found at i:30924918 original size:28 final size:29
Alignment explanation
Indices: 30924887--30924952 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
30924877 CTTACGACGT
* *
30924887 TATAAAATTTAATATTTTTTTAT-ATTTC
1 TATAAAATTTAATAATCTTTTATGATTTC
* * *
30924915 TAT-ATATTTTATAATCTTTTATGATTTT
1 TATAAAATTTAATAATCTTTTATGATTTC
30924943 TATAAAATTT
1 TATAAAATTT
30924953 TACCATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 15 0.50
28 10 0.33
29 5 0.17
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (29 bp):
TATAAAATTTAATAATCTTTTATGATTTC
Found at i:30924953 original size:19 final size:18
Alignment explanation
Indices: 30924886--30924965 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
30924876 TCTTACGACG
*
30924886 TTATAAAATTTAATATTT
1 TTATAAAATTTTATATTT
* *
30924904 TT-TTATATTTCTATATATT
1 TTATAAAATTT-TATAT-TT
**
30924923 TTATAATCTTTTATGATTT
1 TTATAAAATTTTAT-ATTT
*
30924942 TTATAAAATTTTACCATTT
1 TTATAAAATTTTA-TATTT
30924961 TTATA
1 TTATA
30924966 TTTTTTTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 6 0.12
18 6 0.12
19 29 0.59
20 8 0.16
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (18 bp):
TTATAAAATTTTATATTT
Found at i:30925048 original size:18 final size:17
Alignment explanation
Indices: 30925027--30925061 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30925017 TTTAATAATA
*
30925027 TTTATAGATTTTAATTTT
1 TTTATAAATTTT-ATTTT
30925045 TTTATAAATTTTATTTT
1 TTTATAAATTTTATTTT
30925062 CTAATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTATAAATTTTATTTT
Found at i:30925221 original size:90 final size:92
Alignment explanation
Indices: 30925080--30925300 Score: 280
Period size: 90 Copynumber: 2.5 Consensus size: 92
30925070 TAATAAAATC
* *
30925080 AGGGGCTTAATTACTTTTTTTTTTGAAAAAGTTTGAGAGTCTTTTTGATGCATTTTAAAAATTCA
1 AGGGGCTTAATTACTTCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAATTCA
* *
30925145 AGTACCCAATTGAGT-AAAAAAAAAGT
66 AATACCCAAATGAGTGAAAAAAAAAGT
* * * *
30925171 AGGGGCTTAATTGCTTCTTTTTTT-AAAAGGTTTGAGAGTCTTTTTAATGCATTTTGAAAGTTCA
1 AGGGGCTTAATTACTTCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAATTCA
*
30925235 AATACCTAAATGAGTGAAAAAAAAAG-
66 AATACCCAAATGAGTGAAAAAAAAAGT
* *
30925261 -GGAG-TTAATTA---CTTTTTTTGAAAAAGTTTGAG-GGCTTTTT
1 AGGGGCTTAATTACTTCTTTTTTTGAAAAAGTTTGAGAGTCTTTTT
30925301 GCACCCTTAA
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
85 15 0.13
86 11 0.10
88 6 0.05
89 3 0.03
90 48 0.42
91 32 0.28
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (92 bp):
AGGGGCTTAATTACTTCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAATTCA
AATACCCAAATGAGTGAAAAAAAAAGT
Found at i:30931291 original size:33 final size:33
Alignment explanation
Indices: 30931254--30931319 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
30931244 TAAAATATTT
30931254 AAAATATTTTAATATAATTTTATATAAAAATAA
1 AAAATATTTTAATATAATTTTATATAAAAATAA
*
30931287 AAAATATTTTAATATACTTTTATATAAAAATAA
1 AAAATATTTTAATATAATTTTATATAAAAATAA
30931320 TTATATTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
AAAATATTTTAATATAATTTTATATAAAAATAA
Found at i:30931385 original size:26 final size:25
Alignment explanation
Indices: 30931356--30931454 Score: 89
Period size: 26 Copynumber: 3.9 Consensus size: 25
30931346 ATATTATTTT
30931356 TATTAAATTATATTTAATAATAATTA
1 TATTAAA-TATATTTAATAATAATTA
*
30931382 TATTAAAATATATTTAA-AATATTTTTA
1 TATT-AAATATATTTAATAATA--ATTA
**
30931409 TTATTAAATATAATTTAATAATAATCC
1 -TATTAAATAT-ATTTAATAATAATTA
30931436 TATT-AA-A-ATTTAATAATAA
1 TATTAAATATATTTAATAATAA
30931455 CAAACATCGA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
22 12 0.19
24 1 0.02
25 6 0.10
26 17 0.27
27 13 0.21
28 10 0.16
29 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTAAATATATTTAATAATAATTA
Found at i:30931621 original size:16 final size:16
Alignment explanation
Indices: 30931600--30931634 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
30931590 CTAATTATTG
30931600 ATTACAACTCTATTCT
1 ATTACAACTCTATTCT
*
30931616 ATTACAACTCTATTTT
1 ATTACAACTCTATTCT
30931632 ATT
1 ATT
30931635 CCAATAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:30934066 original size:30 final size:30
Alignment explanation
Indices: 30934006--30934066 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
30933996 TTTATCATCT
* * **
30934006 AAAACTCGTGCTTTTTGAACTATTACCAAA
1 AAAACTCGTGCTTCTTGAACCAAAACCAAA
*
30934036 AAAACTCGTGCTTCTTGAACCAAAAGCAAA
1 AAAACTCGTGCTTCTTGAACCAAAACCAAA
30934066 A
1 A
30934067 GCTGTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (30 bp):
AAAACTCGTGCTTCTTGAACCAAAACCAAA
Found at i:30939287 original size:2 final size:2
Alignment explanation
Indices: 30939238--30939276 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
30939228 CAATCAAAGA
30939238 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
30939277 GTTTGTCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:30941743 original size:3 final size:3
Alignment explanation
Indices: 30941735--30941789 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
30941725 TAATAAAGCG
30941735 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
30941783 TTA TTA T
1 TTA TTA T
30941790 GTAATGCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30944249 original size:83 final size:83
Alignment explanation
Indices: 30944110--30944275 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
30944100 TTCACCACTT
30944110 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
1 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
30944175 AAGAGTTAGCTGTACCAG
66 AAGAGTTAGCTGTACCAG
* *
30944193 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGTTTCCTGCAAATATAAAGCAGGTCATCTTAC
1 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
30944258 AAGAGTTAGCTGTACCAG
66 AAGAGTTAGCTGTACCAG
30944276 CAAAGTCAGT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (83 bp):
AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
AAGAGTTAGCTGTACCAG
Found at i:30960387 original size:10 final size:10
Alignment explanation
Indices: 30960372--30960400 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
30960362 GGTTATATGT
30960372 TTTGGGAGTG
1 TTTGGGAGTG
30960382 TTTGGGAGTG
1 TTTGGGAGTG
30960392 TTTGGGAGT
1 TTTGGGAGT
30960401 TCCCAAGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.48, T:0.41
Consensus pattern (10 bp):
TTTGGGAGTG
Found at i:30964509 original size:27 final size:27
Alignment explanation
Indices: 30964471--30964802 Score: 420
Period size: 27 Copynumber: 12.3 Consensus size: 27
30964461 TGCGATTCGT
*
30964471 GGTAAAATGACTGAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
* *
30964498 GGTAAAATGACTAAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
*
30964525 GGTAAAA-TAATCGAAATACCCTCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
* ** * * *
30964552 GGTAATACGATTGAAATTCCCTTGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
30964579 GGTAAAATTA-TCGAAATACCCTCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
* *
30964606 GGTAAAATGACTAAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
*
30964633 GGTAAAATTACTAAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
* * *
30964660 GGTAAAATAACTAAAATACTCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
30964687 GGTAAAATTACTGAAATACCC-CTGAAG
1 GGTAAAATTACTGAAATACCCTC-GAAG
*
30964714 AGTAAAATTA-TCGAAATACCCTCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
*
30964741 GGTAAAATTACGGAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
* *
30964768 GGTAAAATTACCGAAATACCCCCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
30964795 GGTAAAAT
1 GGTAAAAT
30964803 GGCTGTTATA
Statistics
Matches: 270, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.02
27 261 0.97
28 4 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (27 bp):
GGTAAAATTACTGAAATACCCTCGAAG
Found at i:30971804 original size:15 final size:15
Alignment explanation
Indices: 30971784--30971812 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30971774 TAGCCATGGG
30971784 ATGTCACGACACACT
1 ATGTCACGACACACT
30971799 ATGTCACGACACAC
1 ATGTCACGACACAC
30971813 CCCTAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (15 bp):
ATGTCACGACACACT
Found at i:30976340 original size:6 final size:6
Alignment explanation
Indices: 30976329--30976373 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
30976319 ATCTTTATTA
* * * *
30976329 GTATCT GTATCT GTATTT GTATTT GTATTT GTATCT ATATCT GTA
1 GTATCT GTATCT GTATCT GTATCT GTATCT GTATCT GTATCT GTA
30976374 ACTCATCTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.56
Consensus pattern (6 bp):
GTATCT
Found at i:30976340 original size:18 final size:18
Alignment explanation
Indices: 30976319--30976373 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
30976309 CAGTATATGC
30976319 ATCTTTATTAGTATCTGT
1 ATCTTTATTAGTATCTGT
* * *
30976337 ATCTGTATTTGTATTTGT
1 ATCTTTATTAGTATCTGT
30976355 AT-TTGTATCTA-TATCTGT
1 ATCTT-TAT-TAGTATCTGT
30976373 A
1 A
30976374 ACTCATCTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (18 bp):
ATCTTTATTAGTATCTGT
Found at i:30977690 original size:21 final size:22
Alignment explanation
Indices: 30977660--30977706 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
30977650 TTGAATGTAT
* *
30977660 AAAAGCAAAATGAGTACAAAGA
1 AAAAGCAAAAGGAGTAAAAAGA
*
30977682 AAAAG-AAAAGGTGTAAAAAGA
1 AAAAGCAAAAGGAGTAAAAAGA
30977703 AAAA
1 AAAA
30977707 AAACAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGCAAAAGGAGTAAAAAGA
Found at i:30978223 original size:11 final size:12
Alignment explanation
Indices: 30978193--30978221 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
30978183 AATTAATTAG
30978193 GTTTTTAATTTA
1 GTTTTTAATTTA
30978205 GTTTTTAATTTA
1 GTTTTTAATTTA
30978217 GTTTT
1 GTTTT
30978222 AAATAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (12 bp):
GTTTTTAATTTA
Found at i:30986893 original size:18 final size:18
Alignment explanation
Indices: 30986870--30986905 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30986860 ATATCATGAT
* *
30986870 AATGCCGTCGATGCTAAG
1 AATGCCATCGACGCTAAG
30986888 AATGCCATCGACGCTAAG
1 AATGCCATCGACGCTAAG
30986906 GATAAAAAGA
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:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (18 bp):
AATGCCATCGACGCTAAG
Found at i:30989612 original size:13 final size:13
Alignment explanation
Indices: 30989594--30989618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30989584 CAAATTTTAT
30989594 AACAATATATTAA
1 AACAATATATTAA
30989607 AACAATATATTA
1 AACAATATATTA
30989619 CATTAATAAT
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AACAATATATTAA
Found at i:30989655 original size:52 final size:52
Alignment explanation
Indices: 30989589--30989721 Score: 221
Period size: 52 Copynumber: 2.6 Consensus size: 52
30989579 AGTTACAAAT
* * * *
30989589 TTTATAACAATATATTAAAACAATATATTACATTAATAATTAAGGTGTAGTA
1 TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGCAGTA
30989641 TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGCAGTA
1 TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGCAGTA
*
30989693 TTTATAACAGTATATTAAAATAGTATATT
1 TTTATAACAGTATATTAAAACAGTATATT
30989722 TATAACAGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (52 bp):
TTTATAACAGTATATTAAAACAGTATATTACATTAAAAATTAAGGTGCAGTA
Found at i:30989664 original size:13 final size:13
Alignment explanation
Indices: 30989637--30989670 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
30989627 ATTAAGGTGT
*
30989637 AGTAT-TTATAAC
1 AGTATATTAAAAC
30989649 AGTATATTAAAAC
1 AGTATATTAAAAC
30989662 AGTATATTA
1 AGTATATTA
30989671 CATTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:30989709 original size:27 final size:27
Alignment explanation
Indices: 30989627--30989737 Score: 79
Period size: 27 Copynumber: 4.2 Consensus size: 27
30989617 TACATTAATA
*
30989627 ATTAAGGTGTAGTATTTATAACAGTAT
1 ATTAAGGTGCAGTATTTATAACAGTAT
** * * *
30989654 ATTAA--AACAGTA--TATTACATTAAAA
1 ATTAAGGTGCAGTATTTATAACAGT--AT
30989679 ATTAAGGTGCAGTATTTATAACAGTAT
1 ATTAAGGTGCAGTATTTATAACAGTAT
** *
30989706 ATTAAAATAGTA-TATTTATAACAGTAT
1 ATTAAGGT-GCAGTATTTATAACAGTAT
30989733 ATTAA
1 ATTAA
30989738 AACATTATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 14
0.69 0.15 0.15
Matches are distributed among these distances:
23 7 0.11
25 10 0.16
27 37 0.59
28 2 0.03
29 7 0.11
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (27 bp):
ATTAAGGTGCAGTATTTATAACAGTAT
Found at i:30989719 original size:13 final size:13
Alignment explanation
Indices: 30989688--30989883 Score: 223
Period size: 13 Copynumber: 14.8 Consensus size: 13
30989678 AATTAAGGTG
*
30989688 CAGTAT-TTATAA
1 CAGTATATTAAAA
30989700 CAGTATATTAAAA
1 CAGTATATTAAAA
* *
30989713 TAGTATATTTATAA
1 CAGTATA-TTAAAA
30989727 CAGTATATTAAAA
1 CAGTATATTAAAA
*
30989740 CATTATATTAAAA
1 CAGTATATTAAAA
* *
30989753 CAATATATTTATAA
1 CAGTATA-TTAAAA
*
30989767 CAGTATACTAAAA
1 CAGTATATTAAAA
30989780 CAGTATATTAAAA
1 CAGTATATTAAAA
* *
30989793 TAGTATATTTATAA
1 CAGTATA-TTAAAA
30989807 CAGTATATTAAAA
1 CAGTATATTAAAA
* *
30989820 TAGTATATTTATAA
1 CAGTATA-TTAAAA
30989834 CAGTATATTAAAA
1 CAGTATATTAAAA
* *
30989847 CCGTATATTTATAA
1 CAGTATA-TTAAAA
30989861 CAGTATATTAAAA
1 CAGTATATTAAAA
30989874 CAGTATATTA
1 CAGTATATTA
30989884 CAAATTTTAT
Statistics
Matches: 154, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
12 6 0.04
13 93 0.60
14 55 0.36
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (13 bp):
CAGTATATTAAAA
Found at i:30989738 original size:27 final size:27
Alignment explanation
Indices: 30989691--30989882 Score: 271
Period size: 27 Copynumber: 7.1 Consensus size: 27
30989681 TAAGGTGCAG
*
30989691 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAACAGTA
*
30989718 TATTTATAACAGTATATTAAAACATTA
1 TATTTATAACAGTATATTAAAACAGTA
* * *
30989745 TA-TTAAAACAATATATTTATAACAGTA
1 TATTTATAACAGTATA-TTAAAACAGTA
* * *
30989772 TA-CTAAAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAACAGTA
*
30989798 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAACAGTA
*
30989825 TATTTATAACAGTATATTAAAACCGTA
1 TATTTATAACAGTATATTAAAACAGTA
30989852 TATTTATAACAGTATATTAAAACAGTA
1 TATTTATAACAGTATATTAAAACAGTA
30989879 TATT
1 TATT
30989883 ACAAATTTTA
Statistics
Matches: 148, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
26 22 0.15
27 126 0.85
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (27 bp):
TATTTATAACAGTATATTAAAACAGTA
Found at i:30989748 original size:40 final size:40
Alignment explanation
Indices: 30989688--30989883 Score: 177
Period size: 40 Copynumber: 4.9 Consensus size: 40
30989678 AATTAAGGTG
* * * *
30989688 CAGTAT-TTATAACAGTATA-TTAAAATAGTATATTTATAA
1 CAGTATATTAAAACAGTATATTTATAACAGTATA-TTAAAA
* * * *
30989727 CAGTATATTAAAACATTATA-TTAAAACAATATATTTATAA
1 CAGTATATTAAAACAGTATATTTATAACAGTATA-TTAAAA
* * * *
30989767 CAGTATACTAAAACAGTATA-TTAAAATAGTATATTTATAA
1 CAGTATATTAAAACAGTATATTTATAACAGTATA-TTAAAA
*
30989807 CAGTATATTAAAATAGTATATTTATAACAGTATATTAAAA
1 CAGTATATTAAAACAGTATATTTATAACAGTATATTAAAA
* * *
30989847 CCGTATATTTATAACAGTATA-TTAAAACAGTATATTA
1 CAGTATA-TTAAAACAGTATATTTATAACAGTATATTA
30989884 CAAATTTTAT
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 6 0.04
40 109 0.80
41 22 0.16
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (40 bp):
CAGTATATTAAAACAGTATATTTATAACAGTATATTAAAA
Found at i:30989764 original size:67 final size:67
Alignment explanation
Indices: 30989691--30989905 Score: 298
Period size: 67 Copynumber: 3.3 Consensus size: 67
30989681 TAAGGTGCAG
* *
30989691 TATTTATAACAGTATATTAAAATAGTATATTTATAACAGTATATTAAAACATTATATTAAAACAA
1 TATTTATAACAGTATATTAAAACAGTATATTTATAACAGTATATTAAAACAGTATATTAAAACAA
30989756 TA
66 TA
* * * * *
30989758 TATTTATAACAGTATACTAAAACAGTATA-TTAAAATAGTATATTTATAACAGTATATTAAAATA
1 TATTTATAACAGTATATTAAAACAGTATATTTATAACAGTATA-TTAAAACAGTATATTAAAACA
*
30989822 GTA
65 ATA
*
30989825 TATTTATAACAGTATATTAAAACCGTATATTTATAACAGTATATTAAAACAGTATATT---ACAA
1 TATTTATAACAGTATATTAAAACAGTATATTTATAACAGTATATTAAAACAGTATATTAAAACAA
30989887 -A
66 TA
30989888 T-TTTATAACAGTATATTA
1 TATTTATAACAGTATATTA
30989906 CATTAAAAAT
Statistics
Matches: 131, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
62 17 0.13
63 2 0.02
64 2 0.02
66 11 0.08
67 88 0.67
68 11 0.08
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (67 bp):
TATTTATAACAGTATATTAAAACAGTATATTTATAACAGTATATTAAAACAGTATATTAAAACAA
TA
Found at i:30990489 original size:11 final size:11
Alignment explanation
Indices: 30990475--30990505 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
30990465 TCAATCATAC
30990475 TAGAAAGAGAA
1 TAGAAAGAGAA
30990486 TAGAAAGAGAA
1 TAGAAAGAGAA
30990497 TAGAAAGAG
1 TAGAAAGAG
30990506 CCTTCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (11 bp):
TAGAAAGAGAA
Found at i:31000234 original size:32 final size:32
Alignment explanation
Indices: 31000192--31000320 Score: 206
Period size: 32 Copynumber: 4.1 Consensus size: 32
31000182 CATAGCCATG
* *
31000192 TGTCAGACACGGATGAGACACACGCCCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
* *
31000224 TGTCGCACACGGTTGAGACACACGCCCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
*
31000256 TGTCACACACGGCTGAGACACACG-TCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
31000287 TGTCACACACGGCTGAGACACACGCCCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
31000319 TG
1 TG
31000321 AGGCTGTGTG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 30 0.34
32 59 0.66
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (32 bp):
TGTCACACACGGCTGAGACACACGCCCGTGTC
Found at i:31000304 original size:63 final size:64
Alignment explanation
Indices: 31000192--31000320 Score: 206
Period size: 63 Copynumber: 2.0 Consensus size: 64
31000182 CATAGCCATG
* * *
31000192 TGTCAGACACGGATGAGACACACGCCCGTGTCTGTCGCACACGGTTGAGACACACGCCCGTGTC
1 TGTCACACACGGATGAGACACACGCCCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
* *
31000256 TGTCACACACGGCTGAGACACACG-TCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
1 TGTCACACACGGATGAGACACACGCCCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
31000319 TG
1 TG
31000321 AGGCTGTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
63 38 0.63
64 22 0.37
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (64 bp):
TGTCACACACGGATGAGACACACGCCCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
Found at i:31002192 original size:29 final size:29
Alignment explanation
Indices: 31002159--31002321 Score: 136
Period size: 29 Copynumber: 5.6 Consensus size: 29
31002149 CATGGTTGTT
*
31002159 ACCATCCCTTTTCATAGTTGATGGTCATC
1 ACCATCCCTTTTCATAATTGATGGTCATC
* * *
31002188 ACCATCCCTTTTCATAATCGATAG-C-TGA
1 ACCATCCCTTTTCATAATTGATGGTCAT-C
* * * * *
31002216 AGCTATCCCTTTTCATAATCGGTAGTCGA-A
1 A-CCATCCCTTTTCATAATTGATGGTC-ATC
* * *
31002246 ACTATCCCTTTTCAT-ATTCAATGGTCGTC
1 ACCATCCCTTTTCATAATT-GATGGTCATC
* *
31002275 ACCATCCTTTTTCATAGTTGATGGTCATC
1 ACCATCCCTTTTCATAATTGATGGTCATC
31002304 ACCATCCCTTTTCATAAT
1 ACCATCCCTTTTCATAAT
31002322 CGATAGCCGA
Statistics
Matches: 107, Mismatches: 19, Indels: 16
0.75 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 4 0.04
29 97 0.91
30 5 0.05
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCATAATTGATGGTCATC
Found at i:31002280 original size:87 final size:87
Alignment explanation
Indices: 31002162--31002347 Score: 225
Period size: 87 Copynumber: 2.1 Consensus size: 87
31002152 GGTTGTTACC
* *
31002162 ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAATCGATAG-C-TGAAGCTATCCC
1 ATCCCTTTTCATAGTTAATGGTCATCACCATCCCTTTTCATAATCGATAGTCAT-AA-CCATCCC
* *
31002225 TTTTCATAATCGGTAGTCGAAACT
64 TTTTCATAATCGATAGCCGAAACT
* * * * * *
31002249 ATCCCTTTTCATA-TTCAATGGTCGTCACCATCCTTTTTCATAGTTGATGGTCATCACCATCCCT
1 ATCCCTTTTCATAGTT-AATGGTCATCACCATCCCTTTTCATAATCGATAGTCATAACCATCCCT
*
31002313 TTTCATAATCGATAGCCGAAGCT
65 TTTCATAATCGATAGCCGAAACT
31002336 ATCCCTTTTCAT
1 ATCCCTTTTCAT
31002348 TGGTTGATGA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.02
87 80 0.94
88 2 0.02
89 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (87 bp):
ATCCCTTTTCATAGTTAATGGTCATCACCATCCCTTTTCATAATCGATAGTCATAACCATCCCTT
TTCATAATCGATAGCCGAAACT
Found at i:31005725 original size:11 final size:11
Alignment explanation
Indices: 31005709--31005741 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
31005699 AATCAGTCCC
31005709 TTGACCCACTA
1 TTGACCCACTA
*
31005720 TTGACCCACTG
1 TTGACCCACTA
31005731 TTGACCCACTA
1 TTGACCCACTA
31005742 AGGGAATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.27
Consensus pattern (11 bp):
TTGACCCACTA
Found at i:31013850 original size:40 final size:41
Alignment explanation
Indices: 31013806--31013885 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
31013796 TAACAGTTTG
* *
31013806 GGCCTTAGCCCATCTCAGTA-CAGTATCAAAT-ATGCAGTAA
1 GGCCTTAGCCCATCACAGTATCAGTAGC-AATCATGCAGTAA
31013846 GGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
1 GGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
31013886 TTCAGTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 22 0.61
41 14 0.39
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (41 bp):
GGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTAA
Found at i:31016900 original size:14 final size:14
Alignment explanation
Indices: 31016881--31016907 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31016871 ATTAGCATTA
31016881 CATTTCATTACATG
1 CATTTCATTACATG
31016895 CATTTCATTACAT
1 CATTTCATTACAT
31016908 AAAAAGTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (14 bp):
CATTTCATTACATG
Found at i:31018414 original size:32 final size:32
Alignment explanation
Indices: 31018375--31018442 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
31018365 GCCTTGCCTG
31018375 GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
1 GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
* *
31018407 GAAGAGGAAGGAATTGGAAAAGAAGCACTAAA
1 GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
31018439 GAAG
1 GAAG
31018443 GAAAACACGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.53, C:0.07, G:0.34, T:0.06
Consensus pattern (32 bp):
GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
Found at i:31019508 original size:16 final size:16
Alignment explanation
Indices: 31019482--31019522 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
31019472 AGATATAACC
31019482 ATTTATTTTTA-TTTTT
1 ATTT-TTTTTATTTTTT
31019498 ATTCTTTTTTATTTTTT
1 ATT-TTTTTTATTTTTT
31019515 ATTTTTTT
1 ATTTTTTT
31019523 CTTTCTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (16 bp):
ATTTTTTTTATTTTTT
Found at i:31027049 original size:45 final size:47
Alignment explanation
Indices: 31026886--31027057 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 47
31026876 TATTTCTGTG
* * * *** * *
31026886 TTCTCGAGTCCACAACGTATGTAGGAGCTCAAAACCTAAT-CCTATA
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
* *
31026932 TTCTCGAGTCCGCAACGTATGCAAGAGCTCGGAACCTAATATTG-TA
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
* * *
31026978 TTCTCAAGTCTGCAACATATGCAAGAGCTTGGAACCT-AT-TCGATA
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
* * *
31027023 TTCTCGAGTCCGCAATGTACGTAAGAGCTTGGAAC
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAAC
31027058 TTGGGCAAAG
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
44 2 0.02
45 33 0.31
46 70 0.67
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (47 bp):
TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
Found at i:31035610 original size:27 final size:27
Alignment explanation
Indices: 31035579--31035856 Score: 303
Period size: 27 Copynumber: 10.3 Consensus size: 27
31035569 AGAGGTCAAT
31035579 AAATGACTGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
31035606 AAATGACCGAAATACGCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
***
31035633 AAATGA-TCGAAATACCCTTGTAGGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
* *
31035660 AAATGACTGGAATACCGCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
31035687 AAATGACCGAAATACCGCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * *
31035714 AAATAACTGAAATACCCCCACAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * * *
31035741 AAATGA-TCATATTACTCCCATAAGGTA
1 AAATGACTGA-AATACCCCCATAGGGTA
* * *
31035768 AAATGACCGTATTACCCCCA-ATGGGTA
1 AAATGACTGAAATACCCCCATA-GGGTA
* *
31035795 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
*
31035822 AAATGACCGAAATA-CCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
31035848 AAATGACTG
1 AAATGACTG
31035857 TTATACCCTT
Statistics
Matches: 211, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
26 22 0.10
27 187 0.89
28 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCATAGGGTA
Found at i:31036095 original size:26 final size:26
Alignment explanation
Indices: 31036019--31036099 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
31036009 TGGAGGAAGT
* * *
31036019 ATACTGTTATTGGCAGCTTTGCTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
* * * * *
31036045 ATATTTTTACTGGAAACCTTACTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
*
31036071 ATACTATTACTGGTAGCTTTGCTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
31036097 ATA
1 ATA
31036100 TTGGTGTGTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGAAGCTTTGCTGCG
Found at i:31037927 original size:42 final size:42
Alignment explanation
Indices: 31037780--31037937 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 42
31037770 TAACAATGTC
* *
31037780 ATATCCCAAATATGGTC-TACATGTAATCTCATATCGATGCCA
1 ATATCCCAAACATGGTCTTACACG-AATCTCATATCGATGCCA
* ** * *
31037822 ATAGCCCAGCCATGGTCTTACACGAAATCACATATCGATGCCG
1 ATATCCCAAACATGGTCTTACACG-AATCTCATATCGATGCCA
* * *
31037865 ATGTCCCAAACATGGTCTTACACGAAGTTTCATATCGATGTC-
1 ATATCCCAAACATGGTCTTACACGAA-TCTCATATCGATGCCA
* *
31037907 ATATCCCAGATATGGTCTTACACGTAATCTC
1 ATATCCCAAACATGGTCTTACACG-AATCTC
31037938 GGTAAACCTA
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 39 0.41
43 55 0.59
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
ATATCCCAAACATGGTCTTACACGAATCTCATATCGATGCCA
Found at i:31042578 original size:3 final size:3
Alignment explanation
Indices: 31042572--31042613 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
31042562 AAACTACTAT
31042572 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31042614 AATTACTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31043831 original size:17 final size:17
Alignment explanation
Indices: 31043809--31043848 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
31043799 ACAAATTATT
31043809 TTTGGGCTT-GTTGGGTA
1 TTTGGGCTTGGTT-GGTA
31043826 TTTGGGCTTGGTTGGTA
1 TTTGGGCTTGGTTGGTA
31043843 TTTGGG
1 TTTGGG
31043849 TTAGGCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.47
Consensus pattern (17 bp):
TTTGGGCTTGGTTGGTA
Found at i:31044042 original size:29 final size:30
Alignment explanation
Indices: 31043993--31044052 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
31043983 AGTATAAGGT
31043993 TTAAATTTTTAAAAATAAAAG-TATAAAAA
1 TTAAATTTTTAAAAATAAAAGATATAAAAA
**
31044022 TTAAA-TTTTAAATTTATAAAGAATATAAAAA
1 TTAAATTTTTAAAAATA-AAAG-ATATAAAAA
31044053 CTTATCACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 9 0.35
29 9 0.35
31 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
TTAAATTTTTAAAAATAAAAGATATAAAAA
Found at i:31046387 original size:7 final size:7
Alignment explanation
Indices: 31046345--31046385 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
31046335 TTGGTAATTG
31046345 GTTGATA
1 GTTGATA
31046352 GTTGATA
1 GTTGATA
31046359 GTTGATA
1 GTTGATA
31046366 GTTGATA
1 GTTGATA
*
31046373 GTTGATT
1 GTTGATA
31046380 GTTGAT
1 GTTGAT
31046386 TGCAGTGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (7 bp):
GTTGATA
Found at i:31048461 original size:5 final size:5
Alignment explanation
Indices: 31048451--31048480 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
31048441 ACGATTTCGG
*
31048451 TTTCT TTTCT TTTCT TTTCT TTTCT CTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
31048481 GCGTTCAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Done.