Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005606.1 Hibiscus syriacus cultivar Beakdansim tig00013040_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: 3509357
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1991725 original size:18 final size:18
Alignment explanation
Indices: 1991702--1991737 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1991692 AAGCCGGTTG
*
1991702 TGATTGGGATTTTGATTT
1 TGATTGAGATTTTGATTT
1991720 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
1991738 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:1992720 original size:18 final size:18
Alignment explanation
Indices: 1992697--1992733 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1992687 TGAAATTTAT
1992697 ATTGAAATTAAAACTCAA
1 ATTGAAATTAAAACTCAA
* *
1992715 ATTGAAATTTAAATTCAA
1 ATTGAAATTAAAACTCAA
1992733 A
1 A
1992734 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTAAAACTCAA
Found at i:1993147 original size:25 final size:25
Alignment explanation
Indices: 1993119--1993168 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1993109 CATTATTTTC
*
1993119 CAAATAATATACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
1993144 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
1993169 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:1993321 original size:20 final size:20
Alignment explanation
Indices: 1993272--1993321 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1993262 CGGTTTGCGA
1993272 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
1993292 TTTTGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
1993312 TTTCGCGTTG
1 TTTCGCGTTG
1993322 ATCGCAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:1996043 original size:14 final size:15
Alignment explanation
Indices: 1996007--1996044 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1995997 AAAATCATTG
1996007 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1996022 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1996037 AAAAATTA
1 AAAAATTA
1996045 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1996224 original size:19 final size:18
Alignment explanation
Indices: 1996181--1996227 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1996171 CAAAACATTT
1996181 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
1996199 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
1996218 GTGTTGCGAA
1 GTGTTGCGAA
1996228 TTTGAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:1996245 original size:21 final size:21
Alignment explanation
Indices: 1996221--1996314 Score: 102
Period size: 20 Copynumber: 4.6 Consensus size: 21
1996211 TAAATTCGTG
1996221 TTGCGAATTTGAAATTTCGCA
1 TTGCGAATTTGAAATTTCGCA
*
1996242 TTGCGAATTTGAAATTCCGCA
1 TTGCGAATTTGAAATTTCGCA
* * **
1996263 TTGCGAATTTG-ACTTTTGTG
1 TTGCGAATTTGAAATTTCGCA
* * *
1996283 TTGCGAATTTG-ACTATCGCG
1 TTGCGAATTTGAAATTTCGCA
1996303 TTGCGAATTTGA
1 TTGCGAATTTGA
1996315 CTTATGTGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 32 0.51
21 31 0.49
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.39
Consensus pattern (21 bp):
TTGCGAATTTGAAATTTCGCA
Found at i:1996288 original size:20 final size:20
Alignment explanation
Indices: 1996263--1996328 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
1996253 AAATTCCGCA
1996263 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
* * *
1996283 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTG
*
1996303 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTTTGTG
1996323 TTGCGA
1 TTGCGA
1996329 TTTACAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTTGTG
Found at i:1996344 original size:40 final size:40
Alignment explanation
Indices: 1996242--1996335 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
1996232 AAATTTCGCA
* *
1996242 TTGCGAATTTGA-AATTCCGCATTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACAA-T-CGCGTTGCGAATTTGACTTATGTG
*
1996283 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACAATCGCGTTGCGAATTTGACTTATGTG
1996323 TTGCG-ATTT-ACAA
1 TTGCGAATTTGACAA
1996336 ATTTGCGTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.06
39 4 0.08
40 27 0.56
41 13 0.27
42 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (40 bp):
TTGCGAATTTGACAATCGCGTTGCGAATTTGACTTATGTG
Found at i:1996363 original size:20 final size:20
Alignment explanation
Indices: 1996326--1996363 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1996316 TTATGTGTTG
*
1996326 CGATTTACAAATTTGCGTTA
1 CGATTTACAAATTCGCGTTA
*
1996346 CGATTTACAGATTCGCGT
1 CGATTTACAAATTCGCGT
1996364 GGAGAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTA
Found at i:1996850 original size:2 final size:2
Alignment explanation
Indices: 1996843--1996870 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1996833 AATTTGTATG
1996843 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
1996871 CAATATCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2000736 original size:20 final size:21
Alignment explanation
Indices: 2000700--2000750 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
2000690 TCAAATGGTC
*
2000700 CAATTTC-ACATTCTAAC-AT
1 CAATTTCAACACTCTAACAAT
2000719 CAATTTCAACACTCTAACAAT
1 CAATTTCAACACTCTAACAAT
2000740 -AATTTCCAACA
1 CAATTT-CAACA
2000751 TAGTACAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 7 0.25
20 14 0.50
21 7 0.25
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.31
Consensus pattern (21 bp):
CAATTTCAACACTCTAACAAT
Found at i:2011297 original size:29 final size:30
Alignment explanation
Indices: 2011214--2011303 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 30
2011204 AGCCAAATTG
*
2011214 TAACTTTTTAAAATTTT-CATTTTGGTC-CT
1 TAAC-TTTTCAAATTTTACATTTTGGTCACT
*
2011243 TGAACTTTTCCAAATTTTA-TTCTTTGGTCACT
1 T-AACTTTT-CAAATTTTACAT-TTTGGTCACT
2011275 TAACTTTT-AAATTTTACATTTTGGTCACT
1 TAACTTTTCAAATTTTACATTTTGGTCACT
2011304 ATCTAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
29 23 0.44
30 12 0.23
31 14 0.27
32 3 0.06
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (30 bp):
TAACTTTTCAAATTTTACATTTTGGTCACT
Found at i:2014425 original size:162 final size:156
Alignment explanation
Indices: 2014117--2014451 Score: 422
Period size: 162 Copynumber: 2.0 Consensus size: 156
2014107 TATTTATTTA
2014117 CTATATTTATCTATTTTGGTGTTTATTTATTATTTATGGATATTATACCATTTTTTCATATATTT
1 CTATATTTATCTATTTTGGTGTTTATTTATTATTTATGGATATTATACCATTTTTTCATATATTT
2014182 ATATCACTATTCTTATATATACGTATAGATATTACTATAGTATATTTTTCTTTTCATCTCATTTT
66 ATATCACTATTCTTATATATACGTATAGATATTACTATAGTATATTTTTCTTTTCATCTCA--TT
2014247 ATTTATTTCCTTTTATTATTCATATTAATACT
129 ATTTA--T--TTTTATTATTCATATTAATACT
*
2014279 CTATATTTATCTATTTTGGTGTTT-TATTATTATTTATGTTATATTATACCATTTTTTTCATATA
1 CTATATTTATCTATTTTGGTGTTTAT-TTATTATTTATG-GATATTATACCA-TTTTTTC--ATA
2014343 TATTTTATATCACTA-TCTTATATATACGTATAGATATATTACTATTAGTATTATTTTTCTTTTC
61 TA-TTTATATCACTATTCTTATATATACGTATAG--ATATTACTA-TAGTA-TATTTTTCTTTTC
2014407 ATTCTCATTTTATTTTATTTCCTTTTATTATTTCATATTAATACT
121 A-TCTCA--TTA-TTTA--T--TTTTATTA-TTCATATTAATACT
2014452 TGTTTAAACG
Statistics
Matches: 159, Mismatches: 1, Indels: 15
0.91 0.01 0.09
Matches are distributed among these distances:
161 1 0.01
162 36 0.23
163 11 0.07
164 7 0.04
166 23 0.14
167 12 0.08
168 9 0.06
169 5 0.03
170 14 0.09
171 10 0.06
172 17 0.11
173 14 0.09
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.58
Consensus pattern (156 bp):
CTATATTTATCTATTTTGGTGTTTATTTATTATTTATGGATATTATACCATTTTTTCATATATTT
ATATCACTATTCTTATATATACGTATAGATATTACTATAGTATATTTTTCTTTTCATCTCATTAT
TTATTTTTATTATTCATATTAATACT
Found at i:2014902 original size:4 final size:4
Alignment explanation
Indices: 2014877--2014953 Score: 55
Period size: 4 Copynumber: 17.8 Consensus size: 4
2014867 GTTTCCTTAT
* * ** *
2014877 TTTA TTTG TTTC TTTGA TTTA TTTA TTTA TTTA TTCC TTTCA TTTTA CTTA
1 TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTT-A -TTTA TTTA
2014928 TTAGTA TTTTA TTTA TTTA TTTA TTT
1 TT--TA -TTTA TTTA TTTA TTTA TTT
2014954 CCTCTAACAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
4 45 0.78
5 6 0.10
6 5 0.09
7 2 0.03
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:2014914 original size:41 final size:45
Alignment explanation
Indices: 2014853--2014953 Score: 106
Period size: 45 Copynumber: 2.4 Consensus size: 45
2014843 TTTTATCATC
* * * *
2014853 ATTT-TTTA-TTATTTGTTTCC-TT-ATTTTATTTGTT-TCTTTG
1 ATTTATTTATTTATTTGATTCCTTTCATTTTACTTATTATATTTG
*
2014893 ATTTATTTATTTATTT-ATTCCTTTCATTTTACTTATTAGTATTTT
1 ATTTATTTATTTATTTGATTCCTTTCATTTTACTTATTA-TATTTG
2014938 ATTTATTTATTTATTT
1 ATTTATTTATTTATTT
2014954 CCTCTAACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 4 0.08
41 8 0.16
42 8 0.16
43 10 0.20
45 20 0.40
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (45 bp):
ATTTATTTATTTATTTGATTCCTTTCATTTTACTTATTATATTTG
Found at i:2015873 original size:6 final size:6
Alignment explanation
Indices: 2015862--2015905 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
2015852 TTTCTTGCCA
*
2015862 TTTATT TTTATT TTTATT ATTATT ATTT-TT ATTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT -TTTATT -TTTATT TTTATT T
2015906 AACTGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:2015881 original size:15 final size:16
Alignment explanation
Indices: 2015861--2015905 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
2015851 TTTTCTTGCC
2015861 ATTTATTTTTATTTTT
1 ATTTATTTTTATTTTT
*
2015877 A-TTATTATTATTTTT
1 ATTTATTTTTATTTTT
2015892 ATTTATTTTTATTT
1 ATTTATTTTTATTT
2015906 AACTGTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTATTTTTATTTTT
Found at i:2019276 original size:38 final size:35
Alignment explanation
Indices: 2019215--2019287 Score: 119
Period size: 38 Copynumber: 2.0 Consensus size: 35
2019205 ATCTGGTACT
2019215 TCCACCCAACTCAAAGAACCAAGGAGGGAAAGGGA
1 TCCACCCAACTCAAAGAACCAAGGAGGGAAAGGGA
2019250 TCCACCCAAACTCAAAGAGAACCAAGGAGGGAAAGGGA
1 TCCACCC-AACTC-AA-AGAACCAAGGAGGGAAAGGGA
2019288 AAGGGAGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 7 0.20
36 5 0.14
37 2 0.06
38 21 0.60
ACGTcount: A:0.44, C:0.25, G:0.26, T:0.05
Consensus pattern (35 bp):
TCCACCCAACTCAAAGAACCAAGGAGGGAAAGGGA
Found at i:2019386 original size:34 final size:35
Alignment explanation
Indices: 2019343--2019414 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 35
2019333 TCAACAACCT
2019343 CGACACACATGCAGTTTCACC-TACCCAATGGATC
1 CGACACACATGCAGTTTCACCTTACCCAATGGATC
2019377 CGACACACATGCAGTTTCACCTTACCCAATGGATC
1 CGACACACATGCAGTTTCACCTTACCCAATGGATC
2019412 CGA
1 CGA
2019415 TGAAGCCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 21 0.57
35 16 0.43
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (35 bp):
CGACACACATGCAGTTTCACCTTACCCAATGGATC
Found at i:2026251 original size:105 final size:105
Alignment explanation
Indices: 2026069--2026743 Score: 1066
Period size: 105 Copynumber: 6.4 Consensus size: 105
2026059 TTGTCAACGA
* * *
2026069 CAATTTCGGTGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
2026134 TTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCC
66 TTCACGAAGAAGGGACCGCTGGTTGTCAACAACAACTTCC
*
2026174 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTTAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
2026239 TTCACGAAGAAGGGACCGCTGGTTGTCAACAACAACTTCC
66 TTCACGAAGAAGGGACCGCTGGTTGTCAACAACAACTTCC
2026279 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
** *
2026344 TTCACGACTAAGGGACCGCTGGTTGTCAATAACAAC-TCC
66 TTCACGAAGAAGGGACCGCTGGTTGTCAACAACAACTTCC
* *
2026383 TCAATTTCAGAGCCAATTTTAACTTCACAGTGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 -CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
2026448 CTTCACGATGAAGGGACCGCTGGTTGTCAACAACTACTTCC
65 CTTCACGAAGAAGGGACCGCTGGTTGTCAACAACAACTTCC
* * *
2026489 CAATTTCAGAGCCAATTTCAACTTCACTGCGAAGGATATTGGACTCTAGACAACGTAAGTTCAAC
1 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
2026554 TTCAC-AACGAAGGGACCGATGGTTGTCAACAACAACTTCC
66 TTCACGAA-GAAGGGACCGCTGGTTGTCAACAACAACTTCC
* * *
2026594 CAATTTCAGAGCCCATTTTTAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAA
1 CAATTTCAGAG-CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
2026659 CTTCACGATGAAGGGACCGCTGAGTTGTCAACAACAATTTCC
65 CTTCACGAAGAAGGGACCGCTG-GTTGTCAACAACAACTTCC
* * * *
2026701 CAATTCCAGAGCCAATTTTCAACTTCACGGCGAAAGATTTTGG
1 CAATTTCAGAGCCAA-TTTCAACTTCACAGCGAAGGATATTGG
2026744 CCTCGGAACA
Statistics
Matches: 527, Mismatches: 36, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
104 4 0.01
105 398 0.76
106 73 0.14
107 52 0.10
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (105 bp):
CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
TTCACGAAGAAGGGACCGCTGGTTGTCAACAACAACTTCC
Found at i:2028925 original size:17 final size:17
Alignment explanation
Indices: 2028905--2028944 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2028895 CATTTTTTTA
2028905 TTATTTGTTTCTTT-ATT
1 TTATTTGTTTCTTTGA-T
2028922 TTATTTGTTTCTTTGAT
1 TTATTTGTTTCTTTGAT
2028939 TTATTT
1 TTATTT
2028945 ATTCCTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (17 bp):
TTATTTGTTTCTTTGAT
Found at i:2028941 original size:22 final size:23
Alignment explanation
Indices: 2028916--2028966 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2028906 TATTTGTTTC
**
2028916 TTTATTTTATTTGTTTC-TTTGA
1 TTTATTTTATTCCTTTCATTTGA
2028938 TTTA-TTTATTCCTTTCATTTGA
1 TTTATTTTATTCCTTTCATTTGA
*
2028960 CTTATTT
1 TTTATTT
2028967 AGTATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 12 0.50
23 2 0.08
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTATTTTATTCCTTTCATTTGA
Found at i:2028946 original size:4 final size:4
Alignment explanation
Indices: 2028896--2028990 Score: 50
Period size: 4 Copynumber: 23.0 Consensus size: 4
2028886 TTTTATCATC
* * * * *
2028896 ATTT TTTT A-TT ATTT GTTT CTTT ATTTT ATTT GTTT CTTT GATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT -ATTT ATTT
* * * *
2028945 ATTC CTTT CATTT GACTT ATTT A-GT ATTTT ATTT ATTT ATTT ATTT
1 ATTT ATTT -ATTT -ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT
2028991 CCTCTAACAT
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
3 5 0.07
4 48 0.71
5 15 0.22
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:2030116 original size:30 final size:29
Alignment explanation
Indices: 2030081--2030168 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 29
2030071 AGCCAAATTG
2030081 TAACTTTTTAAAATTTCCATTTTGGTC-CT
1 TAACTTTTTAAAATTT-CATTTTGGTCACT
** *
2030110 TGAACTTTTCCAAATTTTATACTTTGGTCACT
1 T-AACTTTTTAAAATTTCAT--TTTGGTCACT
2030142 TAAC-TTTTAAAATTTACATTTTGGTCA
1 TAACTTTTTAAAATTT-CATTTTGGTCA
2030169 TTATCTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
29 11 0.23
30 22 0.46
31 12 0.25
32 3 0.06
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (29 bp):
TAACTTTTTAAAATTTCATTTTGGTCACT
Found at i:2037159 original size:59 final size:59
Alignment explanation
Indices: 2037060--2037184 Score: 178
Period size: 59 Copynumber: 2.1 Consensus size: 59
2037050 CAGCAGGCTA
** * *
2037060 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
2037119 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
2037178 CATATTC
1 CATATTC
2037185 AGGATAGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:2037287 original size:20 final size:20
Alignment explanation
Indices: 2037250--2037288 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2037240 TATATTGGGC
* *
2037250 TATTGTCTATTGTTTATGGA
1 TATTGTCTATGGTATATGGA
*
2037270 TATTTTCTATGGTATATGG
1 TATTGTCTATGGTATATGG
2037289 TTATGGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGA
Found at i:2037356 original size:47 final size:47
Alignment explanation
Indices: 2037305--2037400 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
2037295 AATAATGGCG
*
2037305 AGTATATTGATAAAATAAGCTTATGAGCTTATGGAATTTAAATGGTA
1 AGTATATTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTA
* * * *
2037352 AGTATTTTGGTAATATAAGCTTACGAGTTTATGGAATTTAAATGGTA
1 AGTATATTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTA
2037399 AG
1 AG
2037401 GGATTTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (47 bp):
AGTATATTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTA
Found at i:2044526 original size:59 final size:59
Alignment explanation
Indices: 2044427--2044563 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
2044417 CAGCAGGCTG
** * * *
2044427 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
* ** *
2044486 CATATTCGGGACTTTACTTAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
2044545 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
2044564 CGGTGCTTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
Found at i:2044654 original size:20 final size:20
Alignment explanation
Indices: 2044617--2044655 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2044607 TATATTGGGC
* *
2044617 TATTGTCTATTGTTTATGGA
1 TATTGTCTATGGTATATGGA
*
2044637 TATTTTCTATGGTATATGG
1 TATTGTCTATGGTATATGG
2044656 TTATGGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGA
Found at i:2044733 original size:47 final size:45
Alignment explanation
Indices: 2044656--2044765 Score: 143
Period size: 47 Copynumber: 2.4 Consensus size: 45
2044646 TGGTATATGG
* *
2044656 TTATGGAAT-AATGGTGAGTTTATTGATAAAATAAGCTTATGAGC
1 TTATGGAATAAATGGTAAGTTTATTGATAAAATAAGCTTACGAGC
*
2044700 TTATGGAATTTAAATGGTAAGTATT-TTGGTAAAATAAGCTTACGAGC
1 TTATGGAA--TAAATGGTAAGT-TTATTGATAAAATAAGCTTACGAGC
*
2044747 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
2044766 GGATTTTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
44 8 0.14
45 11 0.19
46 1 0.02
47 36 0.62
48 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTTTATTGATAAAATAAGCTTACGAGC
Found at i:2047361 original size:137 final size:135
Alignment explanation
Indices: 2047073--2047379 Score: 334
Period size: 137 Copynumber: 2.3 Consensus size: 135
2047063 ATGATCTAGA
* * * * *
2047073 TTCTAGTCAAAACTTTCAGGC-CAAGTTTGACTTCATGACGAAGGATATTTATATAAAAAGCAAG
1 TTCTAGTCAAAACTTTCAGGCTAAATTTTGACTTCAGGAAGAAGGATATTGATATAAAAAGCAAG
* * * * * * * * *
2047137 TTCAAAATTGACTCAACTCGCATTGAGGAGTTGTCTACAGTCTAGCTAAACTCAGCAGCGAGGAG
66 TTCAAAATTGACTCAACTCGAATTGAAGAGTCGTATACAATCTAGCTAAAATCAGAAGCAAGGAA
*
2047202 CTAGT
131 ATAGT
* *
2047207 TTCTAGTCAAGACTTTCAGGCTAAATTTTGACTTCAGGAAGAAGGATATTCGAGT-TCAAAAGCA
1 TTCTAGTCAAAACTTTCAGGCTAAATTTTGACTTCAGGAAGAAGGATATT-GA-TATAAAAAGCA
* * * *
2047271 AGTTCAAAATTGACTTAACTCAGAATTGAAGAGTCGTATGCAATCTAGTTAAAAT-A-AATGTTA
64 AGTTCAAAATTGACTCAACTC-GAATTGAAGAGTCGTATACAATCTAGCTAAAATCAGAA-G-CA
2047334 AGGAAATAGT
126 AGGAAATAGT
* *
2047344 TTCTAGTCAAAATTTTCAAGCTAAATTTTGACTTCA
1 TTCTAGTCAAAACTTTCAGGCTAAATTTTGACTTCA
2047380 TGATAAATGA
Statistics
Matches: 143, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
134 20 0.14
135 25 0.17
136 31 0.22
137 67 0.47
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (135 bp):
TTCTAGTCAAAACTTTCAGGCTAAATTTTGACTTCAGGAAGAAGGATATTGATATAAAAAGCAAG
TTCAAAATTGACTCAACTCGAATTGAAGAGTCGTATACAATCTAGCTAAAATCAGAAGCAAGGAA
ATAGT
Found at i:2050987 original size:16 final size:17
Alignment explanation
Indices: 2050953--2050997 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
2050943 ACCGATTTGG
*
2050953 TATTGACCCGA-CCTGA
1 TATTGACCCGATCCTAA
2050969 TATTGACCCGATCC-AA
1 TATTGACCCGATCCTAA
*
2050985 TATTGAACCGATC
1 TATTGACCCGATC
2050998 TGAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 24 0.92
17 2 0.08
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (17 bp):
TATTGACCCGATCCTAA
Found at i:2051435 original size:19 final size:19
Alignment explanation
Indices: 2051411--2051476 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2051401 TATGCATTGG
* *
2051411 GCTATGAATTTGAAACTAA
1 GCTATGAATATGAAAATAA
* *
2051430 GCTATGAATATGAAATTAT
1 GCTATGAATATGAAAATAA
* *
2051449 GCAATGAATATGAAAATAC
1 GCTATGAATATGAAAATAA
*
2051468 GTTATGAAT
1 GCTATGAAT
2051477 TTGGAAATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.32
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:2051484 original size:19 final size:19
Alignment explanation
Indices: 2051413--2051495 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 19
2051403 TGCATTGGGC
* * * *
2051413 TATGAATTTGAAACTAAGC
1 TATGAATATGAAAATACGT
* * *
2051432 TATGAATATGAAATTATGC
1 TATGAATATGAAAATACGT
*
2051451 AATGAATATGAAAATACGT
1 TATGAATATGAAAATACGT
* * *
2051470 TATGAATTTGGAAATATGT
1 TATGAATATGAAAATACGT
*
2051489 TCTGAAT
1 TATGAAT
2051496 CGAGAATGAA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (19 bp):
TATGAATATGAAAATACGT
Found at i:2051577 original size:13 final size:13
Alignment explanation
Indices: 2051530--2051585 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 13
2051520 GGTATTCATT
*
2051530 ATGAAAATGAGAG
1 ATGAAAATGAAAG
* *
2051543 -TTAAAATGAATG
1 ATGAAAATGAAAG
*
2051555 -TGAAATTGAAAG
1 ATGAAAATGAAAG
2051567 ATGAAAATGAAAG
1 ATGAAAATGAAAG
2051580 ATGAAA
1 ATGAAA
2051586 GTTTTTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
12 18 0.51
13 17 0.49
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.21
Consensus pattern (13 bp):
ATGAAAATGAAAG
Found at i:2051848 original size:2 final size:2
Alignment explanation
Indices: 2051784--2051829 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2051774 ATTTTTAAGT
2051784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2051826 TA TA
1 TA TA
2051830 CACGCACACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2058009 original size:19 final size:18
Alignment explanation
Indices: 2057956--2058013 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
2057946 TGCATTGGTC
**
2057956 TATGAATTTGAAATTAAAC
1 TATGAATTTGAAA-TAAGT
*
2057975 TATGAATATGAGAATAAGT
1 TATGAATTTGA-AATAAGT
2057994 TATGAATTTTGAAATAAGT
1 TATGAA-TTTGAAATAAGT
2058013 T
1 T
2058014 TTAAATTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.38
Consensus pattern (18 bp):
TATGAATTTGAAATAAGT
Found at i:2061707 original size:130 final size:130
Alignment explanation
Indices: 2061474--2061731 Score: 516
Period size: 130 Copynumber: 2.0 Consensus size: 130
2061464 AAGCCTTGGA
2061474 TCAGTTTATGACTTGTTGCAAACTAGGCAAGTTCAAAGCCAACATCATATGTTTTAACTTTGGCC
1 TCAGTTTATGACTTGTTGCAAACTAGGCAAGTTCAAAGCCAACATCATATGTTTTAACTTTGGCC
2061539 TCAAACCTTCAATAAACAAATCACGTTGAGCCTTGTTATTGGGAACTACCTCAGTAGAAAACTAC
66 TCAAACCTTCAATAAACAAATCACGTTGAGCCTTGTTATTGGGAACTACCTCAGTAGAAAACTAC
2061604 TCAGTTTATGACTTGTTGCAAACTAGGCAAGTTCAAAGCCAACATCATATGTTTTAACTTTGGCC
1 TCAGTTTATGACTTGTTGCAAACTAGGCAAGTTCAAAGCCAACATCATATGTTTTAACTTTGGCC
2061669 TCAAACCTTCAATAAACAAATCACGTTGAGCCTTGTTATTGGGAACTACCTCAGTAGAAAACT
66 TCAAACCTTCAATAAACAAATCACGTTGAGCCTTGTTATTGGGAACTACCTCAGTAGAAAACT
2061732 TCAGCTTGTT
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (130 bp):
TCAGTTTATGACTTGTTGCAAACTAGGCAAGTTCAAAGCCAACATCATATGTTTTAACTTTGGCC
TCAAACCTTCAATAAACAAATCACGTTGAGCCTTGTTATTGGGAACTACCTCAGTAGAAAACTAC
Found at i:2063308 original size:49 final size:49
Alignment explanation
Indices: 2063126--2063396 Score: 307
Period size: 49 Copynumber: 5.6 Consensus size: 49
2063116 GAATACCATG
* * * * *
2063126 AGTGGCACC-GTTATGCCAAAATACACTGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATACATTTAACTTTCATT
* * * * *
2063174 AGTGGCACCTTTAATGCTG-AATGAACCGTTGTGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATACATTTAACTTTCATT
* * * *
2063222 AGTGGCA-CTTTTATGCCGAAATGCATCGTTGTGCATTTAACATTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATACATTTAACTTTCATT
* * *
2063270 AGTGGCACCTTTTATGCCTAAATGCACCATTACACATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATACATTTAACTTTCATT
* * *
2063319 ACTGGAACCTTTTATGTCGAAATGCACCGTTATGA-ATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTAT-ACATTTAACTTTCATT
* *
2063368 AGTGACACCTTTTATGCCGAAATACACCG
1 AGTGGCACCTTTTATGCCGAAATGCACCG
2063397 CACCCTCGAT
Statistics
Matches: 188, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
47 9 0.05
48 74 0.39
49 104 0.55
50 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGCACCGTTATACATTTAACTTTCATT
Found at i:2071717 original size:15 final size:15
Alignment explanation
Indices: 2071699--2071729 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2071689 GTGGTGGAGG
2071699 TCTCACATCGACTGC
1 TCTCACATCGACTGC
*
2071714 TCTCACATTGACTGC
1 TCTCACATCGACTGC
2071729 T
1 T
2071730 GATGGTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.32
Consensus pattern (15 bp):
TCTCACATCGACTGC
Found at i:2074520 original size:16 final size:16
Alignment explanation
Indices: 2074499--2074532 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2074489 TTCTCTCTTC
*
2074499 TTCCTTGCCCCCCTTT
1 TTCCTTGCCCCCATTT
2074515 TTCCTTGCCCCCATTT
1 TTCCTTGCCCCCATTT
2074531 TT
1 TT
2074533 TGCGACTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.44, G:0.06, T:0.47
Consensus pattern (16 bp):
TTCCTTGCCCCCATTT
Found at i:2074531 original size:15 final size:16
Alignment explanation
Indices: 2074499--2074531 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2074489 TTCTCTCTTC
*
2074499 TTCCTTGCCCCCCTTT
1 TTCCTTGCCCCCCATT
2074515 TTCCTTG-CCCCCATT
1 TTCCTTGCCCCCCATT
2074530 TT
1 TT
2074532 TTGCGACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.03, C:0.45, G:0.06, T:0.45
Consensus pattern (16 bp):
TTCCTTGCCCCCCATT
Found at i:2076057 original size:140 final size:142
Alignment explanation
Indices: 2075875--2076157 Score: 552
Period size: 140 Copynumber: 2.0 Consensus size: 142
2075865 ATCCTTTAAC
2075875 TTTCCTTAAACCTCTATATCACTTAAGGTTTTAAACCAACCATTAAACTAGAGGAAAAACCAACT
1 TTTCCTTAAACCTCTATATCACTTAAGGTTTTAAACCAACCATTAAACTAGAGGAAAAACCAACT
2075940 T-GAGGAAACTCACCTTTGGCTATGGAGAGAAT-GGCACACGGGGAGGAGGATAAGAGAAGATAA
66 TGGAGGAAACTCACCTTTGGCTATGGAGAGAATGGGCACACGGGGAGGAGGATAAGAGAAGATAA
2076003 CTTGGCTTTTTT
131 CTTGGCTTTTTT
2076015 TTTCCTTAAACCTCTATATCACTTAAGGTTTTAAACCAACCATTAAACTAGAGGAAAAACCAACT
1 TTTCCTTAAACCTCTATATCACTTAAGGTTTTAAACCAACCATTAAACTAGAGGAAAAACCAACT
2076080 TGGAGGAAACTCACCTTTGGCTATGGAGAGAATGGGCACACGGGGAGGAGGATAAGAGAAGATAA
66 TGGAGGAAACTCACCTTTGGCTATGGAGAGAATGGGCACACGGGGAGGAGGATAAGAGAAGATAA
2076145 CTTGGCTTTTTT
131 CTTGGCTTTTTT
2076157 T
1 T
2076158 AACTTTTCCC
Statistics
Matches: 141, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
140 66 0.47
141 31 0.22
142 44 0.31
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (142 bp):
TTTCCTTAAACCTCTATATCACTTAAGGTTTTAAACCAACCATTAAACTAGAGGAAAAACCAACT
TGGAGGAAACTCACCTTTGGCTATGGAGAGAATGGGCACACGGGGAGGAGGATAAGAGAAGATAA
CTTGGCTTTTTT
Found at i:2077312 original size:19 final size:20
Alignment explanation
Indices: 2077288--2077357 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 20
2077278 GCAAAAATGT
*
2077288 TATCGATACCATAATA-GGG
1 TATCGATACCATAGTAGGGG
*
2077307 TATCGATACCATAGTATGGTAG
1 TATCGATACCATAGTA-GG-GG
*
2077329 TATCGATACCATGGTAGGGG
1 TATCGATACCATAGTAGGGG
2077349 TATCGATAC
1 TATCGATAC
2077358 TGAGGAGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 15 0.34
20 10 0.23
21 3 0.07
22 16 0.36
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
TATCGATACCATAGTAGGGG
Found at i:2077837 original size:54 final size:55
Alignment explanation
Indices: 2077697--2077849 Score: 164
Period size: 55 Copynumber: 2.8 Consensus size: 55
2077687 TAAGAGCACA
* * ** ***
2077697 AAAACCTAAGAAATTCGTACTAAGGGTATGAATTTTGGTATGGGCACTTTGTGTGC
1 AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTACATGTGC
* * * *
2077753 AAAAATAAGAAGTTTATACTAAGTGTATGAATTTCCGTATGGGTACTACATGTGC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTACATGTGC
* * *
2077808 -GAACTAAGAAATTCATACTAAGTGTATGAAGTTCTGTATGGG
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
2077850 AAATATGAGA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
54 36 0.45
55 40 0.50
56 4 0.05
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTACATGTGC
Found at i:2078171 original size:68 final size:68
Alignment explanation
Indices: 2078057--2078443 Score: 582
Period size: 68 Copynumber: 5.7 Consensus size: 68
2078047 AGTTTCAGAA
*
2078057 CTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
2078122 GGC
66 GGC
* * *
2078125 CTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCACTTAGATGAAAGGCTAAGTGCCTTTAA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
2078190 GG-
66 GGC
* * * *
2078192 CTAACTATGCATTTAACAGAATGGTGTCAATTAAGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
2078257 GGC
66 GGC
* * * * *
2078260 CTAACTTTGCATTTAATAGAAATGG-GTCAATTATGCCAGTTAGATGAAAGACTAACTGCCTTTG
1 CTAACTGTGCATTTGACAGAAA-GGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
2078324 AGGC
65 AGGC
* * * *
2078328 CTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGACATTTAGATGAAAGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
2078393 GGC
66 GGC
2078396 CTAACTGTGCATTTGGA-AGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 CTAACTGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2078444 GGTTAAATAC
Statistics
Matches: 288, Mismatches: 27, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
67 62 0.22
68 223 0.77
69 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:2078303 original size:135 final size:135
Alignment explanation
Indices: 2078057--2078443 Score: 573
Period size: 135 Copynumber: 2.9 Consensus size: 135
2078047 AGTTTCAGAA
*
2078057 CTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
* * *
2078122 GGCCTAA-TTGTGCATTTGACAGAAAGGTGTCAATTATGCCACTTAGATGAAAGGCTAAGTGCCT
66 GGCCTAACTT-TGCATTTGA-AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAACTGCCT
2078186 TTAAGG-
129 TTAAGGC
* * * *
2078192 CTAACTATGCATTTAACAGAATGGTGTCAATTAAGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
*
2078257 GGCCTAACTTTGCATTTAATAGAAATGG-GTCAATTATGCCAGTTAGATGAAAGACTAACTGCCT
66 GGCCTAACTTTGCATTTGA-AGAAA-GGTGTCAATTATGCCAGTTAGATGAAAGACTAACTGCCT
*
2078321 TTGAGGC
129 TTAAGGC
* * * *
2078328 CTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGACATTTAGATGAAAGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
*
2078393 GGCCTAACTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
66 GGCCTAACTTTGCATTT-GAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2078444 GGTTAAATAC
Statistics
Matches: 226, Mismatches: 21, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
135 120 0.53
136 105 0.46
137 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (135 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGCCTAACTTTGCATTTGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAACTGCCTTT
AAGGC
Found at i:2078588 original size:81 final size:80
Alignment explanation
Indices: 2078393--2078836 Score: 495
Period size: 81 Copynumber: 5.6 Consensus size: 80
2078383 GTGCCTTTGA
* * * *
2078393 GGCCTAACTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA-GGTTAAATACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACATCGT
*
2078457 GAGTAAAACATGAAT
66 GAGTAAAAAATGAAT
* * * *
2078472 GGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCATTTAGATGAACGGTTAAATATCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACATCGT
2078537 AGAGTAAAAAATGAAT
66 -GAGTAAAAAATGAAT
* * * * *
2078553 GGCCTAGCTGTGCATTTTGCAGAAAGGTGTTAATTATGTCAGTGAGATGAACAGTT-AA-ATCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACATCG-
*
2078616 TGAGTAAAAGATGAAT
65 TGAGTAAAAAATGAAT
* * * * * *
2078632 AGCCTAGCTGTGCA-TTGGCAGAAAGATGTTAATTATGTCAGTTAGATGAATGGTTAAACAACGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACATCG-
*
2078696 TGAGTAAAAGATGAAT
65 TGAGTAAAAAATGAAT
* * * * *
2078712 GACCTAGCTGGGAATTTGGCAGAAAGGTGTCAATTATGCCAGGTAGATGAACAGTTAAACA-CTG
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACATC-G
2078776 TGAGTAAAAGAAT-AAT
65 TGAGTAAAA-AATGAAT
* * * * * * *
2078792 GGACTAGCTGTGCATTTGACAAAAAAGTGGCAAATATGCAAGTTA
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTA
2078837 TAGAAGGCTA
Statistics
Matches: 314, Mismatches: 43, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
78 36 0.11
79 81 0.26
80 92 0.29
81 105 0.33
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (80 bp):
GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACATCGT
GAGTAAAAAATGAAT
Found at i:2078720 original size:159 final size:159
Alignment explanation
Indices: 2078395--2078807 Score: 503
Period size: 159 Copynumber: 2.6 Consensus size: 159
2078385 GCCTTTGAGG
* * * *
2078395 CCTAACTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA-GGTTAAATACCG-TG
1 CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTGAGATGAACAGTTAAAT--CGTTG
* * * *
2078458 AGTAAAACATGAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCATTTAGATGAA
64 AGTAAAAGATGAATGGCCTAGCTGTGCA-TTGGAAGAAAGATGTCAATTATGCCAGTTAGATGAA
* * *
2078523 CGGTTAAATATCGTAGAGTAAAAAATGAATGG
128 CGGTTAAACAACGTAGAGTAAAAAATGAATGA
* * *
2078555 CCTAGCTGTGCATTTTGCAGAAAGGTGTTAATTATGTCAGTGAGATGAACAGTTAAATCGTTGAG
1 CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTGAGATGAACAGTTAAATCGTTGAG
* * * * *
2078620 TAAAAGATGAATAGCCTAGCTGTGCATTGGCAGAAAGATGTTAATTATGTCAGTTAGATGAATGG
66 TAAAAGATGAATGGCCTAGCTGTGCATTGGAAGAAAGATGTCAATTATGCCAGTTAGATGAACGG
* *
2078685 TTAAACAACGTTGAGTAAAAGATGAATGA
131 TTAAACAACGTAGAGTAAAAAATGAATGA
* * *
2078714 CCTAGCTGGGAATTTGGCAGAAAGGTGTCAATTATGCCAG-GTAGATGAACAGTTAAA-CACTGT
1 CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTG-AGATGAACAGTTAAATC-GT-T
*
2078777 GAGTAAAAGAAT-AATGGACTAGCTGTGCATT
63 GAGTAAAAG-ATGAATGGCCTAGCTGTGCATT
2078808 TGACAAAAAA
Statistics
Matches: 218, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
158 2 0.01
159 110 0.50
160 97 0.44
161 9 0.04
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (159 bp):
CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTGAGATGAACAGTTAAATCGTTGAG
TAAAAGATGAATGGCCTAGCTGTGCATTGGAAGAAAGATGTCAATTATGCCAGTTAGATGAACGG
TTAAACAACGTAGAGTAAAAAATGAATGA
Found at i:2080933 original size:20 final size:21
Alignment explanation
Indices: 2080896--2080934 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2080886 ATACTATGGG
2080896 TAGTATCGATACCACAGGGGT
1 TAGTATCGATACCACAGGGGT
2080917 TAGTATCGATACC-CAGGG
1 TAGTATCGATACCACAGGG
2080935 TGAAAGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (21 bp):
TAGTATCGATACCACAGGGGT
Found at i:2080942 original size:21 final size:21
Alignment explanation
Indices: 2080897--2080949 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2080887 TACTATGGGT
**
2080897 AGTATCGATACCACAGGGGTT
1 AGTATCGATACCACAGGGGAA
2080918 AGTATCGATACC-CAGGGTGAA
1 AGTATCGATACCACAGGG-GAA
*
2080939 AGTATCAATAC
1 AGTATCGATAC
2080950 TCGTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (21 bp):
AGTATCGATACCACAGGGGAA
Found at i:2081323 original size:22 final size:22
Alignment explanation
Indices: 2081289--2081353 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
2081279 CAATCCCTGC
* *
2081289 AGTGCTAAGGCACTTTAGTATT
1 AGTGCAAATGCACTTTAGTATT
2081311 AGTGCAAATGCACTTTAGTATT
1 AGTGCAAATGCACTTTAGTATT
*
2081333 AGTGCAAATGCACTTTCGTAT
1 AGTGCAAATGCACTTTAGTAT
2081354 CAGTACTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (22 bp):
AGTGCAAATGCACTTTAGTATT
Found at i:2082134 original size:17 final size:17
Alignment explanation
Indices: 2082109--2082151 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
2082099 TGAAAGCATT
*
2082109 TATAGATTTGAAAAAAA
1 TATATATTTGAAAAAAA
2082126 TATATATTTTTGAAAAAAA
1 TATATA--TTTGAAAAAAA
2082145 TATATAT
1 TATATAT
2082152 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
19 17 0.74
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
TATATATTTGAAAAAAA
Found at i:2082137 original size:19 final size:19
Alignment explanation
Indices: 2082115--2082151 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2082105 CATTTATAGA
2082115 TTTGAAAAAAATATATATT
1 TTTGAAAAAAATATATATT
2082134 TTTGAAAAAAATATATAT
1 TTTGAAAAAAATATATAT
2082152 AATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTGAAAAAAATATATATT
Found at i:2082192 original size:18 final size:19
Alignment explanation
Indices: 2082148--2082193 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2082138 AAAAAAATAT
*
2082148 ATATAATATATTTTTTGAAA
1 ATAT-ATATAGTTTTTGAAA
*
2082168 A-ACATATAGTTTTT-AAA
1 ATATATATAGTTTTTGAAA
2082185 ATATATATA
1 ATATATATA
2082194 ATATATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 1 0.05
20 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATATATAGTTTTTGAAA
Found at i:2082197 original size:23 final size:22
Alignment explanation
Indices: 2082171--2082231 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
2082161 TTTGAAAAAC
* *
2082171 ATATAGTTTTTAAAATATATATA
1 ATATAGTTTTTAAAAAAAAT-TA
2082194 ATATA-TAATTTTAAAAAAAATTA
1 ATATAGT--TTTTAAAAAAAATTA
*
2082217 ATATAGTTTTGAAAA
1 ATATAGTTTTTAAAA
2082232 CATGTGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 8 0.25
23 12 0.38
24 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
ATATAGTTTTTAAAAAAAATTA
Found at i:2082198 original size:46 final size:44
Alignment explanation
Indices: 2082115--2082231 Score: 107
Period size: 46 Copynumber: 2.6 Consensus size: 44
2082105 CATTTATAGA
2082115 TTTGAAAAAAATATATATTTTTGAAAAAAATATATATAATATATTT
1 TTTGAAAAAAATATATATTTTTGAAAAAAATATATAT-ATA-ATTT
* * *
2082161 TTTGAAAAACATATA-GTTTTT-AAAATATATATAATATATAA--T
1 TTTGAAAAAAATATATATTTTTGAAAA-AAATAT-ATATATAATTT
* *
2082203 TTTAAAAAAAATTAATATAGTTTTGAAAA
1 TTTGAAAAAAA-T-ATATATTTTTGAAAA
2082232 CATGTGTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
42 10 0.17
43 1 0.02
44 8 0.14
45 17 0.29
46 22 0.38
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (44 bp):
TTTGAAAAAAATATATATTTTTGAAAAAAATATATATATAATTT
Found at i:2082231 original size:63 final size:67
Alignment explanation
Indices: 2082124--2082293 Score: 176
Period size: 63 Copynumber: 2.6 Consensus size: 67
2082114 ATTTGAAAAA
* *
2082124 AATATATATTTTTGAAAAAAATATATATAATATATTTTTTGAAAAACATATAGTTTTT-AAAATA
1 AATATATAATTTT-AAAAAAATATATATAATATATGTTTTG-AAAACATAT-GTTTTTAAAAATA
2082188 TATAT
63 TATAT
*
2082193 AATATATAATTTT-AAAAAA-A-AT-TAATATA-GTTTTGAAAACATGTGTTTTTAAAAAATATA
1 AATATATAATTTTAAAAAAATATATATAATATATGTTTTGAAAACATATGTTTTT-AAAAATATA
2082253 TAT
65 TAT
** * *
2082256 AATATATGGTTATGAAGAAAATATATAT-AT-TATGTTTT
1 AATATATAATT-TTAAAAAAATATATATAATATATGTTTT
2082294 ATTTTCATTT
Statistics
Matches: 86, Mismatches: 7, Indels: 18
0.77 0.06 0.16
Matches are distributed among these distances:
61 6 0.07
62 8 0.09
63 25 0.29
64 8 0.09
65 7 0.08
66 4 0.05
67 15 0.17
68 1 0.01
69 12 0.14
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (67 bp):
AATATATAATTTTAAAAAAATATATATAATATATGTTTTGAAAACATATGTTTTTAAAAATATAT
AT
Found at i:2082327 original size:16 final size:16
Alignment explanation
Indices: 2082306--2082351 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 16
2082296 TTTCATTTTC
2082306 TTCATTTATTTACTTT
1 TTCATTTATTTACTTT
2082322 TTCA-TTA-TTA-TTT
1 TTCATTTATTTACTTT
*
2082335 CT-ATTTATTTACTTT
1 TTCATTTATTTACTTT
2082350 TT
1 TT
2082352 TTCATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
12 1 0.04
13 7 0.28
14 6 0.24
15 7 0.28
16 4 0.16
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCATTTATTTACTTT
Found at i:2086470 original size:21 final size:22
Alignment explanation
Indices: 2086446--2086487 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
2086436 GGTGGTCTTG
2086446 ATGGAAGATGGT-TGATGGTAT
1 ATGGAAGATGGTATGATGGTAT
2086467 ATGGAAGATGGTAATGATGGT
1 ATGGAAGATGGT-ATGATGGT
2086488 GTATCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (22 bp):
ATGGAAGATGGTATGATGGTAT
Found at i:2088391 original size:59 final size:58
Alignment explanation
Indices: 2088304--2088595 Score: 370
Period size: 59 Copynumber: 4.9 Consensus size: 58
2088294 CATATTTAGA
* *
2088304 ATTGCACTAAAGGATACCTAGTGGATATGGTGGTCATGACCTTATGTGTCATATTCGGG
1 ATTGCACTAAA-GATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATTCGGG
*
2088363 ATTGCACTAAATGATACCTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTTCGGG
1 ATTGCACTAAA-GATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATA-TTCGGG
* * * * **
2088423 ACTGCACTGAAAGATACCAAGTGCATATGGTGGGCATGACCTTTTGTGTAATATTTTAGG
1 ATTGCACT-AAAGATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATA-TTCGGG
* * *
2088483 -TTGCACTAAAGAATGCCAAGTGTATATGGTGGGCATGACCTTATGTGTCATATTCGGG
1 ATTGCACTAAAG-ATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATTCGGG
* ** *
2088541 ATTGCATTAAAAGATACCTAGTAAATATGGTGGGCACGACCTTATGTGTCATATT
1 ATTGCACT-AAAGATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATT
2088596 TTGTTTAGCA
Statistics
Matches: 204, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
58 8 0.04
59 134 0.66
60 59 0.29
61 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (58 bp):
ATTGCACTAAAGATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATTCGGG
Found at i:2088517 original size:119 final size:118
Alignment explanation
Indices: 2088306--2088597 Score: 374
Period size: 119 Copynumber: 2.5 Consensus size: 118
2088296 TATTTAGAAT
* * **
2088306 TGCACTAAAGGATACCTAGTGGATATGGTGGTCATGACCTTATGTGTCATA-TTCGGGATTGCAC
1 TGCACTAAA-GATACCTAGTGAATATGGTGGGCATGACCTTATGTGTCATATTTTAGGATTGCAC
*
2088370 TAAATGATACCTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTTCGGGAC
65 TAAATGATACCAAGTGCATATGGTGGGCACGACCTTATGTGTCATA-TTCGGGAC
* * * *
2088425 TGCACTGAAAGATACCAAGTGCATATGGTGGGCATGACCTTTTGTGTAATATTTTAGG-TTGCAC
1 TGCACT-AAAGATACCTAGTGAATATGGTGGGCATGACCTTATGTGTCATATTTTAGGATTGCAC
* * * *
2088489 TAAA-GAATGCCAAGTGTATATGGTGGGCATGACCTTATGTGTCATATTCGGGAT
65 TAAATG-ATACCAAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCGGGAC
* * *
2088543 TGCATTAAAAGATACCTAGTAAATATGGTGGGCACGACCTTATGTGTCATATTTT
1 TGCACT-AAAGATACCTAGTGAATATGGTGGGCATGACCTTATGTGTCATATTTT
2088598 GTTTAGCACT
Statistics
Matches: 150, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
118 55 0.37
119 88 0.59
120 7 0.05
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (118 bp):
TGCACTAAAGATACCTAGTGAATATGGTGGGCATGACCTTATGTGTCATATTTTAGGATTGCACT
AAATGATACCAAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCGGGAC
Found at i:2095451 original size:54 final size:54
Alignment explanation
Indices: 2095358--2095753 Score: 431
Period size: 54 Copynumber: 7.3 Consensus size: 54
2095348 CAGTTGAGAC
* * * * * * *
2095358 GCACACATAGTGCCGATACGGACGTTCATAAATATATTATGAATTCCTTGGGTTT
1 GCACACTTAGTACCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGG-TT
* * * *
2095413 G-ACACTTAGTACCTAAATGGTCGTTCATAAGCACATTATGAATTTCGTGGGTT
1 GCACACTTAGTACCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTT
* * *
2095466 GCACACTTAGTGA-CTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTT
1 GCACACTTAGT-ACCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTT
* ** * *
2095520 GCACACTTAGTGCCTATACGGTTTTTCATAAACATATTATGAATTTCGTGGGTT
1 GCACACTTAGTACCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTT
* * * **
2095574 GCACACTTAGTGCCAAAACTTTCGTTCATAAACACATTATGAATTCCGTGGGTT
1 GCACACTTAGTACCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTT
* * * *
2095628 GAACACTTAGTACCTATACGATCGTTCATAAACACATTACGAATTCCATGGGTT
1 GCACACTTAGTACCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTT
* **
2095682 GTACACTTAGTACCTATACGGAT-GTTCATAAAC-CTATTATGAATTCTTTGGGTT
1 GCACACTTAGTACCTATACGG-TCGTTCATAAACAC-ATTATGAATTCCGTGGGTT
* *
2095736 ACACACTTAGTGCCTATA
1 GCACACTTAGTACCTATA
2095754 GTACACATAG
Statistics
Matches: 288, Mismatches: 48, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
53 4 0.01
54 281 0.98
55 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (54 bp):
GCACACTTAGTACCTATACGGTCGTTCATAAACACATTATGAATTCCGTGGGTT
Found at i:2095636 original size:162 final size:162
Alignment explanation
Indices: 2095358--2095749 Score: 504
Period size: 162 Copynumber: 2.4 Consensus size: 162
2095348 CAGTTGAGAC
* * * * *
2095358 GCACACATAGTGCCGATACGGACGTTCATAAATATATTATGAATTCCTTGGGTTTG-ACACTTAG
1 GCACACTTAGTGCCTATACGGATGTTCATAAACATATTATGAATTTCTTGGG-TTGCACACTTAG
* * * * *
2095422 TACCTAAATGGTCGTTCATAAGCACATTATGAATTTCGTGGGTTGCACACTTAGTGA-CTATACG
65 TGCCAAAATGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGAACACTTAGT-ACCTATACG
* * * * *
2095486 GTCGTTCATCAACATATGATGAATTCCGTGGGTT
129 ATCGTTCATAAACACATGACGAATTCCATGGGTT
* * *
2095520 GCACACTTAGTGCCTATACGGTTTTTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGT
1 GCACACTTAGTGCCTATACGGATGTTCATAAACATATTATGAATTTCTTGGGTTGCACACTTAGT
*
2095585 GCCAAAACT-TTCGTTCATAAACACATTATGAATTCCGTGGGTTGAACACTTAGTACCTATACGA
66 GCCAAAA-TGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGAACACTTAGTACCTATACGA
*
2095649 TCGTTCATAAACACATTACGAATTCCATGGGTT
130 TCGTTCATAAACACATGACGAATTCCATGGGTT
* * * *
2095682 GTACACTTAGTACCTATACGGATGTTCATAAACCTATTATGAA-TTCTTTGGGTTACACACTTAG
1 GCACACTTAGTGCCTATACGGATGTTCATAAACATATTATGAATTTC-TTGGGTTGCACACTTAG
2095746 TGCC
65 TGCC
2095750 TATAGTACAC
Statistics
Matches: 199, Mismatches: 27, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
161 7 0.04
162 191 0.96
163 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (162 bp):
GCACACTTAGTGCCTATACGGATGTTCATAAACATATTATGAATTTCTTGGGTTGCACACTTAGT
GCCAAAATGGTCGTTCATAAACACATTATGAATTCCGTGGGTTGAACACTTAGTACCTATACGAT
CGTTCATAAACACATGACGAATTCCATGGGTT
Found at i:2096290 original size:21 final size:21
Alignment explanation
Indices: 2096266--2096319 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2096256 TCAATACCCA
*
2096266 TATCAATATCGGTACTAATTG
1 TATCAATATCGATACTAATTG
*
2096287 TATCAATACCGATACTAATTG
1 TATCAATATCGATACTAATTG
*
2096308 CATCAATATCGA
1 TATCAATATCGA
2096320 CATTGTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
TATCAATATCGATACTAATTG
Found at i:2101354 original size:54 final size:54
Alignment explanation
Indices: 2101228--2101465 Score: 282
Period size: 54 Copynumber: 4.4 Consensus size: 54
2101218 ATTTCATTGA
* * ** * * *
2101228 GTTGCACACGTAGTGCCTATACGGTCATTCAT-AAAATATATTATGAATTTTGTGG
1 GTTGCACACTTAGTACCTATACGGTTGTTCATCAACA-A-ATGATGAATTTCGTGG
* * * *
2101283 TTTGCACA-TATAATACCTTTACGGTTGTTCATCAACATATGATGAATTTCGTGG
1 GTTGCACACT-TAGTACCTATACGGTTGTTCATCAACAAATGATGAATTTCGTGG
*
2101337 GTTGCACACTTAGTACCTATACGGTTGTTCATCAACAAATGATGAATTTTGTGG
1 GTTGCACACTTAGTACCTATACGGTTGTTCATCAACAAATGATGAATTTCGTGG
* * * *
2101391 GTTGCATACTTAGTGCCTATACGATTGTTCATCAACAAATGATGAATTTCGTAG
1 GTTGCACACTTAGTACCTATACGGTTGTTCATCAACAAATGATGAATTTCGTGG
*
2101445 GTTGCACACTTAGTGCCTATA
1 GTTGCACACTTAGTACCTATA
2101466 GTGCACATAG
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
54 130 0.82
55 25 0.16
56 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (54 bp):
GTTGCACACTTAGTACCTATACGGTTGTTCATCAACAAATGATGAATTTCGTGG
Found at i:2101420 original size:108 final size:109
Alignment explanation
Indices: 2101228--2101465 Score: 311
Period size: 108 Copynumber: 2.2 Consensus size: 109
2101218 ATTTCATTGA
* * *
2101228 GTTGCACACGTAGTGCCTATACGGTCATTCATAAAATATATTATGAATTTTGTGGTTTGCACATA
1 GTTGCACACTTAGTGCCTATACGGTCATTCATAAAATATATGATGAATTTTGTGGGTTGCACATA
* * * *
2101293 TAATACCTTTACGGTTGTTCATCAACATATGATGAATTTCGTGG
66 TAATACCTATACGATTGTTCATCAACAAATGATGAATTTCGTAG
* ** * *
2101337 GTTGCACACTTAGTACCTATACGGTTGTTCATCAACA-A-ATGATGAATTTTGTGGGTTGCATAC
1 GTTGCACACTTAGTGCCTATACGGTCATTCAT-AAAATATATGATGAATTTTGTGGGTTGCACA-
* *
2101400 T-TAGTGCCTATACGATTGTTCATCAACAAATGATGAATTTCGTAG
64 TATAATACCTATACGATTGTTCATCAACAAATGATGAATTTCGTAG
2101445 GTTGCACACTTAGTGCCTATA
1 GTTGCACACTTAGTGCCTATA
2101466 GTGCACATAG
Statistics
Matches: 112, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
108 79 0.71
109 30 0.27
110 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (109 bp):
GTTGCACACTTAGTGCCTATACGGTCATTCATAAAATATATGATGAATTTTGTGGGTTGCACATA
TAATACCTATACGATTGTTCATCAACAAATGATGAATTTCGTAG
Found at i:2101917 original size:17 final size:16
Alignment explanation
Indices: 2101891--2101922 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2101881 ATTTTGTAAT
2101891 CCATAGTATCGATACC
1 CCATAGTATCGATACC
2101907 CCATCAGTATCGATAC
1 CCAT-AGTATCGATAC
2101923 TAATTACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (16 bp):
CCATAGTATCGATACC
Found at i:2105924 original size:112 final size:112
Alignment explanation
Indices: 2105764--2105992 Score: 307
Period size: 112 Copynumber: 2.0 Consensus size: 112
2105754 GTTATATATG
* * * * ** * *
2105764 CATTTCGATATACTTTGTAGATAAAAGTTATCTATCGATTTTTCTTAATGCATAACGGTGCATTT
1 CATTTCGACATACTTCGTAGATAAAAGTTATCGATCAATTTTGATTAATGCATAACAGTGCAGTT
*
2105829 TCTGCATAAAA-TGAGCCACCCATGGTATTCATAATGAGGTGAATTAC
66 TCGGCATAAAAGT-AGCCACCCATGGTATTCATAATGAGGTGAATTAC
** * *
2105876 CATTTCGACATACTTCGTTTATGAAAGTTATCGATCAATTTTGATTAATGCATAACATTGCAGTT
1 CATTTCGACATACTTCGTAGATAAAAGTTATCGATCAATTTTGATTAATGCATAACAGTGCAGTT
* *
2105941 TCGGCATAATAGTTGCCACCCATGGTATTCATAATGAGGTGAATTAC
66 TCGGCATAAAAGTAGCCACCCATGGTATTCATAATGAGGTGAATTAC
2105988 CATTT
1 CATTT
2105993 GGTTACTTCG
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
112 100 0.99
113 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (112 bp):
CATTTCGACATACTTCGTAGATAAAAGTTATCGATCAATTTTGATTAATGCATAACAGTGCAGTT
TCGGCATAAAAGTAGCCACCCATGGTATTCATAATGAGGTGAATTAC
Found at i:2112893 original size:111 final size:112
Alignment explanation
Indices: 2112761--2112990 Score: 372
Period size: 111 Copynumber: 2.1 Consensus size: 112
2112751 GTTATAGGTG
* *
2112761 CATTTAGACATACTTCATGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAACGGTGCATTT
1 CATTTCGACATACTTCATGTATGAAAGTTATCCATCAATTTTGCTTAATGCATAACGGTGCATTT
* * *
2112826 TCGGCATAAAAGGTG-CATCCATGGTATTCATAATGAGGTGAATTAC
66 TCGGCATAAAAAGTGCCACCCATGGTATTCATAATAAGGTGAATTAC
** **
2112872 CATTTCGACATACTTTGTGTATGAAAGTTATCCATTGATTTTGCTTAATGCATAACGGTGCATTT
1 CATTTCGACATACTTCATGTATGAAAGTTATCCATCAATTTTGCTTAATGCATAACGGTGCATTT
2112937 TCGGCATAAAAAGTGCCACCCATGGTATTCATAATAAGGTGAATTAC
66 TCGGCATAAAAAGTGCCACCCATGGTATTCATAATAAGGTGAATTAC
2112984 CATTTCG
1 CATTTCG
2112991 GCATTTCGGT
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
111 73 0.67
112 36 0.33
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (112 bp):
CATTTCGACATACTTCATGTATGAAAGTTATCCATCAATTTTGCTTAATGCATAACGGTGCATTT
TCGGCATAAAAAGTGCCACCCATGGTATTCATAATAAGGTGAATTAC
Found at i:2113904 original size:123 final size:123
Alignment explanation
Indices: 2113717--2113962 Score: 492
Period size: 123 Copynumber: 2.0 Consensus size: 123
2113707 AACACAAATC
2113717 TGGTCGAAATCTCTTGTAACCATTCGGCCATGCTCCTTCAAGCCTTATAAATAGGCTACTTCTTT
1 TGGTCGAAATCTCTTGTAACCATTCGGCCATGCTCCTTCAAGCCTTATAAATAGGCTACTTCTTT
2113782 TCATTTGTGAACACACAACTTTGATTATTAAGTCAAGTGAAATTACTATGCTTTCTCA
66 TCATTTGTGAACACACAACTTTGATTATTAAGTCAAGTGAAATTACTATGCTTTCTCA
2113840 TGGTCGAAATCTCTTGTAACCATTCGGCCATGCTCCTTCAAGCCTTATAAATAGGCTACTTCTTT
1 TGGTCGAAATCTCTTGTAACCATTCGGCCATGCTCCTTCAAGCCTTATAAATAGGCTACTTCTTT
2113905 TCATTTGTGAACACACAACTTTGATTATTAAGTCAAGTGAAATTACTATGCTTTCTCA
66 TCATTTGTGAACACACAACTTTGATTATTAAGTCAAGTGAAATTACTATGCTTTCTCA
2113963 AGTCCTTGTG
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (123 bp):
TGGTCGAAATCTCTTGTAACCATTCGGCCATGCTCCTTCAAGCCTTATAAATAGGCTACTTCTTT
TCATTTGTGAACACACAACTTTGATTATTAAGTCAAGTGAAATTACTATGCTTTCTCA
Found at i:2120733 original size:18 final size:18
Alignment explanation
Indices: 2120710--2120744 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2120700 GGAAAGGTGC
2120710 AGTTTGTCTATGATGTGT
1 AGTTTGTCTATGATGTGT
2120728 AGTTTGTCTATGATGTG
1 AGTTTGTCTATGATGTG
2120745 CAGGAATAGC
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:0.06, G:0.29, T:0.49
Consensus pattern (18 bp):
AGTTTGTCTATGATGTGT
Found at i:2121397 original size:23 final size:23
Alignment explanation
Indices: 2121367--2121415 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2121357 TGGTGGTTGG
*
2121367 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
2121390 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
2121413 TTT
1 TTT
2121416 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:2131775 original size:17 final size:17
Alignment explanation
Indices: 2131753--2131795 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2131743 TATATGTGTG
2131753 GTTTTGAAGCA-GACATA
1 GTTTTGAAGCATG-CATA
*
2131770 GTTTTGAAAGCATGTATA
1 GTTTTG-AAGCATGCATA
2131788 GTTTTGAA
1 GTTTTGAA
2131796 AAAAACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 14 0.61
19 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (17 bp):
GTTTTGAAGCATGCATA
Found at i:2131852 original size:40 final size:40
Alignment explanation
Indices: 2131797--2131903 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
2131787 AGTTTTGAAA
* * * * *
2131797 AAAACATATATAATATATTTTTTGAATACATATA-GTTTTT
1 AAAATATATATAATATA-TTTTTAAAAACAAATAGGTATTT
* *
2131837 AAAATATATAAAATATAGTTTTAAAAACAAATAGGTATTT
1 AAAATATATATAATATATTTTTAAAAACAAATAGGTATTT
*
2131877 AATATATATATAATATAGTTTTTAAAA
1 AAAATATATATAATATA-TTTTTAAAA
2131904 TATATAATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 12 0.22
40 35 0.64
41 8 0.15
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (40 bp):
AAAATATATATAATATATTTTTAAAAACAAATAGGTATTT
Found at i:2131856 original size:23 final size:23
Alignment explanation
Indices: 2131826--2131920 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 23
2131816 TTTTGAATAC
2131826 ATATAGTTTTTAAAATATATAAA
1 ATATAGTTTTTAAAATATATAAA
*
2131849 ATATAG-TTTT-AAA-A-A-CAA
1 ATATAGTTTTTAAAATATATAAA
* * * *
2131867 ATA-GGTATTTAATATATATATA
1 ATATAGTTTTTAAAATATATAAA
*
2131889 ATATAGTTTTTAAAATATATAAT
1 ATATAGTTTTTAAAATATATAAA
2131912 ATATAGTTT
1 ATATAGTTT
2131921 CGAAAAAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
17 1 0.02
18 8 0.15
19 3 0.05
20 2 0.04
21 4 0.07
22 8 0.15
23 29 0.53
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44
Consensus pattern (23 bp):
ATATAGTTTTTAAAATATATAAA
Found at i:2131893 original size:63 final size:62
Alignment explanation
Indices: 2131826--2131956 Score: 190
Period size: 63 Copynumber: 2.1 Consensus size: 62
2131816 TTTTGAATAC
* * *
2131826 ATATAGTTTTTAAAATATATAAAATATAGTTTTAAAAACAAATAGGTATTTAATATATATATA
1 ATATAGTTTTTAAAATATATAAAATATAGTTTCAAAAA-AAATAGGTATTTAAAACATATATA
* * * *
2131889 ATATAGTTTTTAAAATATATAATATATAGTTTCGAAAAAAATAGTTTTTTAAAACATATATA
1 ATATAGTTTTTAAAATATATAAAATATAGTTTCAAAAAAAATAGGTATTTAAAACATATATA
2131951 ATATAG
1 ATATAG
2131957 AGTTTGAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
62 26 0.43
63 35 0.57
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (62 bp):
ATATAGTTTTTAAAATATATAAAATATAGTTTCAAAAAAAATAGGTATTTAAAACATATATA
Found at i:2131926 original size:23 final size:25
Alignment explanation
Indices: 2131877--2131926 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
2131867 ATAGGTATTT
**
2131877 AATATATATATAATATAGTTTTTAA
1 AATATATATATAATATAGTTTCGAA
2131902 AATATATA-AT-ATATAGTTTCGAA
1 AATATATATATAATATAGTTTCGAA
2131925 AA
1 AA
2131927 AAATAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
24 2 0.09
25 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
AATATATATATAATATAGTTTCGAA
Found at i:2131942 original size:39 final size:38
Alignment explanation
Indices: 2131891--2131996 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 38
2131881 TATATATAAT
2131891 ATAG-TTTTTAAA-ATATATAATATATAGTTTCGAAAAAA
1 ATAGTTTTTTAAACATATATAATATATAGTTT-G-AAAAA
* *
2131929 ATAGTTTTTTAAAACATATATAATATAGAGTTTGAAAAC
1 ATAGTTTTTT-AAACATATATAATATATAGTTTGAAAAA
* *
2131968 TTATGTTTTTTAATATATATATAA-ATATA
1 ATA-GTTTTTTAA-ACATATATAATATATA
2131997 ATATATTGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
38 4 0.07
39 17 0.29
40 20 0.34
41 17 0.29
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (38 bp):
ATAGTTTTTTAAACATATATAATATATAGTTTGAAAAA
Found at i:2131978 original size:41 final size:40
Alignment explanation
Indices: 2131891--2131966 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
2131881 TATATATAAT
*
2131891 ATAG-TTTTT-AAAATATATAATATATAGTTTCGAAAAAA
1 ATAGTTTTTTAAAAATATATAATATAGAGTTTCGAAAAAA
2131929 ATAGTTTTTTAAAACATATATAATATAGAGTTT-GAAAA
1 ATAGTTTTTTAAAA-ATATATAATATAGAGTTTCGAAAA
2131967 CTTATGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 4 0.12
39 5 0.15
40 8 0.24
41 17 0.50
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (40 bp):
ATAGTTTTTTAAAAATATATAATATAGAGTTTCGAAAAAA
Found at i:2131996 original size:41 final size:39
Alignment explanation
Indices: 2131891--2131988 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 39
2131881 TATATATAAT
*
2131891 ATAG-TTTTTAAAATATATAATATATAGTTTCGAAAAAA
1 ATAGTTTTTTAAAATATATAATATAGAGTTTCGAAAAAA
*
2131929 ATAGTTTTTTAAAACATATATAATATAGAGTTT-G-AAAAC
1 ATAGTTTTTT-AAA-ATATATAATATAGAGTTTCGAAAAAA
* *
2131968 TTATGTTTTTTAATATATATA
1 ATA-GTTTTTTAAAATATATA
2131989 TAAATATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
38 11 0.21
39 13 0.25
40 11 0.21
41 17 0.33
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (39 bp):
ATAGTTTTTTAAAATATATAATATAGAGTTTCGAAAAAA
Found at i:2132066 original size:17 final size:15
Alignment explanation
Indices: 2132033--2132071 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
2132023 TATATATATA
*
2132033 TATTATTTTTTATTT
1 TATTATTTTTTACTT
2132048 TATTCATTTATTTACTT
1 TATT-ATTT-TTTACTT
2132065 TATTATT
1 TATTATT
2132072 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTATTTTTTACTT
Found at i:2137442 original size:47 final size:47
Alignment explanation
Indices: 2137389--2137495 Score: 178
Period size: 47 Copynumber: 2.3 Consensus size: 47
2137379 GGCTATTCTC
*
2137389 TACGAGCTTGTGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
* * *
2137436 TACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
2137483 TACGAGCTTATGG
1 TACGAGCTTATGG
2137496 GATAAATGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (47 bp):
TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
Found at i:2153752 original size:17 final size:17
Alignment explanation
Indices: 2153730--2153765 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2153720 GAGGATTTAG
*
2153730 AAATAATGAAAGTAAAT
1 AAATAATAAAAGTAAAT
*
2153747 AAATAATAAAAGTCAAT
1 AAATAATAAAAGTAAAT
2153764 AA
1 AA
2153766 CGAATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (17 bp):
AAATAATAAAAGTAAAT
Found at i:2158432 original size:423 final size:423
Alignment explanation
Indices: 2157646--2158497 Score: 1521
Period size: 423 Copynumber: 2.0 Consensus size: 423
2157636 AAACATAAAA
*
2157646 AAATTCATAAATGTGAATCGAATTAAGAGGCATTTTATTTCTTCGACTTAGACTACCTGCACGTT
1 AAATTCATAAATGTGAATCGAATTAAGAGGCATTTTATTTCTTCGACTTAGACTACATGCACGTT
*
2157711 GGCATCTTTCATAGGTTTTTAAAAATAATTACAGTCATGAAAGATGTTAGGCCAAAAGAAACGAC
66 GGCATCTTTCATAGGTTTTTAAAAATAATTACAGTCATGAAAGACGTTAGGCCAAAAGAAACGAC
2157776 ACTCTAAAATTCAATGGGCAGTCTACTTCGGTCTAAGTAACCACCGCAAGAGTAAGAATGACAGA
131 ACTCTAAAATTCAATGGGCAGTCTACTTCGGTCTAAGTAACCACCGCAAGAGTAAGAATGACAGA
* *
2157841 AATTTAAGATAAAATTTACGTCATCTTTGGCAATTCATCGTCGAATTACCTGATCTGAGCATGCT
196 AATTTAAGATAAAATTTACCTCACCTTTGGCAATTCATCGTCGAATTACCTGATCTGAGCATGCT
* *
2157906 TCCAAAGCTAAGGATCATCCTATATATTAAATCAGGATTTTCACTTTATCTTTTTAATTTTAACT
261 TCCAAAGCTAAGGATCATCCTATATATTAAATCAGGATTTTCACTTTATCTTGTTAACTTTAACT
* *
2157971 CTTGGCAAATCTAATAGTAATTTACATGTGGCCAAATAATTTAACATATCCGCGAACCATGATGT
326 CTTGGCAAATCTAATAGTAATTTACATGTGGCCAAATAATTTAACATATACGCGAAACATGATGT
*
2158036 AACCTTTTGTTCCACTATTAGATTTTATGC-GAG
391 AACCTTTTGTTCCACTATTAGACTTTATGCAG-G
2158069 AAATTCATAAATGTGAATCGAATTAAGAGGCATTTTATTTCTTCGACTTAGACTACATGCACGTT
1 AAATTCATAAATGTGAATCGAATTAAGAGGCATTTTATTTCTTCGACTTAGACTACATGCACGTT
2158134 GGCATCTTTCATAGGTTTTTAAAAATAATTACAGTCATGAAAGACGTTAGGCCAAAAGAAACGAC
66 GGCATCTTTCATAGGTTTTTAAAAATAATTACAGTCATGAAAGACGTTAGGCCAAAAGAAACGAC
*
2158199 ACTCTAAAATTCAATGGGCAGTCTGA-TTCGGTTTGAAGTAACCACCGCAAGAGTAAGAATGACA
131 ACTCTAAAATTCAATGGGCAGTCT-ACTTCGGTCT-AAGTAACCACCGCAAGAGTAAGAATGACA
* *
2158263 GAAATTTAAGATAGAATTTACCTCACCTTTGGCAATTCATCGTCTAATTACCTGATCTGAGCATG
194 GAAATTTAAGATAAAATTTACCTCACCTTTGGCAATTCATCGTCGAATTACCTGATCTGAGCATG
*
2158328 CTTCCAAAGCTAAGGATCATCCTATATATTAAATCAGGATTTTCACTTTATCTTGTTAACTTTAG
259 CTTCCAAAGCTAAGGATCATCCTATATATTAAATCAGGATTTTCACTTTATCTTGTTAACTTTAA
*
2158393 CT-TTGGCAAATCTAATAGTAATTTACATGTGGCCAAATAATTTACCATATACGCGAAACATGAT
324 CTCTTGGCAAATCTAATAGTAATTTACATGTGGCCAAATAATTTAACATATACGCGAAACATGAT
*
2158457 GTAACCTTTTGTTCCACTATTAGACTTTCTGCAGG
389 GTAACCTTTTGTTCCACTATTAGACTTTATGCAGG
2158492 AAATTC
1 AAATTC
2158498 TTTTAAAATC
Statistics
Matches: 411, Mismatches: 15, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
423 255 0.62
424 156 0.38
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (423 bp):
AAATTCATAAATGTGAATCGAATTAAGAGGCATTTTATTTCTTCGACTTAGACTACATGCACGTT
GGCATCTTTCATAGGTTTTTAAAAATAATTACAGTCATGAAAGACGTTAGGCCAAAAGAAACGAC
ACTCTAAAATTCAATGGGCAGTCTACTTCGGTCTAAGTAACCACCGCAAGAGTAAGAATGACAGA
AATTTAAGATAAAATTTACCTCACCTTTGGCAATTCATCGTCGAATTACCTGATCTGAGCATGCT
TCCAAAGCTAAGGATCATCCTATATATTAAATCAGGATTTTCACTTTATCTTGTTAACTTTAACT
CTTGGCAAATCTAATAGTAATTTACATGTGGCCAAATAATTTAACATATACGCGAAACATGATGT
AACCTTTTGTTCCACTATTAGACTTTATGCAGG
Found at i:2161407 original size:137 final size:137
Alignment explanation
Indices: 2161141--2161555 Score: 546
Period size: 137 Copynumber: 3.0 Consensus size: 137
2161131 GTCATAGGTG
* * * *
2161141 CATTTTGATATACA-TTGTATATGATGGTTATCGATCGATTTTGTTTAATGCATATGTTGCATTT
1 CATTTTGACATACATTTGTGTATGAAGGTTATCGATCGATTTTGTCTAATGCATATGTTGCATTT
* * ** *
2161205 TCGTATCAGTACTATGTGCACTTTTGGCACTAGATGTGCAACCATGGTGCTAATAATGAGATTAT
66 TCGTATCAGTACTATGTGTACTTTCGGCACTAGATGTGCAACCATGGTATTCATAATGAGATTAT
2161270 GAATTAC
131 GAATTAC
* * * *
2161277 CATTTTAACATACATTTGTGTATGAAGGTTATCGATAGATATTGTCTAATGCATATGTTACATTT
1 CATTTTGACATACATTTGTGTATGAAGGTTATCGATCGATTTTGTCTAATGCATATGTTGCATTT
* * *
2161342 TCATATCAGTATTATGTGTACTTTCGGCACTAGATGTGCAACCATGGTATTCATAATGAGTTTAT
66 TCGTATCAGTACTATGTGTACTTTCGGCACTAGATGTGCAACCATGGTATTCATAATGAGATTAT
*
2161407 GAATTAG
131 GAATTAC
* *
2161414 CATTTCGACATACATTTGTGTATGAAGGTTATCGATCGATTTTGTCTAATGCATATATTGCATTT
1 CATTTTGACATACATTTGTGTATGAAGGTTATCGATCGATTTTGTCTAATGCATATGTTGCATTT
* * * * * * * * *
2161479 TTGTATCAGTACTATATGTACCTTCCGCACTATG-TGTGCATCCATGGAATTCATAATAAGCTTG
66 TCGTATCAGTACTATGTGTACTTTCGGCACTA-GATGTGCAACCATGGTATTCATAATGAGATTA
*
2161543 TGAATTTC
130 TGAATTAC
2161551 CATTT
1 CATTT
2161556 CGTCACTTAG
Statistics
Matches: 241, Mismatches: 36, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
136 12 0.05
137 228 0.95
138 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (137 bp):
CATTTTGACATACATTTGTGTATGAAGGTTATCGATCGATTTTGTCTAATGCATATGTTGCATTT
TCGTATCAGTACTATGTGTACTTTCGGCACTAGATGTGCAACCATGGTATTCATAATGAGATTAT
GAATTAC
Found at i:2165219 original size:12 final size:12
Alignment explanation
Indices: 2165202--2165234 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2165192 CAAAAAGAAG
2165202 AAAAGAAAATCA
1 AAAAGAAAATCA
2165214 AAAAGAAAATCA
1 AAAAGAAAATCA
2165226 AAAAGAAAA
1 AAAAGAAAA
2165235 ACCTACAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (12 bp):
AAAAGAAAATCA
Found at i:2168146 original size:20 final size:20
Alignment explanation
Indices: 2168114--2168163 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2168104 TTCGGTGCCA
*
2168114 AAATACATACAAAGACACCC
1 AAATACATTCAAAGACACCC
*
2168134 AAATGCATTCAAAGACACCC
1 AAATACATTCAAAGACACCC
2168154 AAATACATTC
1 AAATACATTC
2168164 CAAATGCCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (20 bp):
AAATACATTCAAAGACACCC
Found at i:2172619 original size:24 final size:24
Alignment explanation
Indices: 2172592--2172637 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2172582 TATTTTAATA
2172592 AAAATATTAATTATTAA-AATATTT
1 AAAATA-TAATTATTAACAATATTT
*
2172616 AAAATATACTTATTAACAATAT
1 AAAATATAATTATTAACAATAT
2172638 GATATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATATAATTATTAACAATATTT
Found at i:2172717 original size:13 final size:13
Alignment explanation
Indices: 2172694--2172736 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2172684 ATAATATATA
2172694 ATTTATCAAAAAAT
1 ATTT-TCAAAAAAT
*
2172708 ATTTTCAAAAACT
1 ATTTTCAAAAAAT
*
2172721 ATTTTATAAAAAAT
1 ATTTT-CAAAAAAT
2172735 AT
1 AT
2172737 ACTTCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTTCAAAAAAT
Found at i:2178383 original size:35 final size:35
Alignment explanation
Indices: 2178324--2178435 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 35
2178314 AAAACATTCC
* *
2178324 TCAATTTCATTATAAATCCC-AAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCTAAATTTCAAAATAAT
*
2178359 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
* *
2178394 TCAATTACATTCTAAACCCTAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAACCCTAAATTTC-AAAATAAT
2178429 TCAATTT
1 TCAATTT
2178436 AAGGAGAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.07
35 63 0.93
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
Found at i:2179502 original size:35 final size:34
Alignment explanation
Indices: 2179453--2179565 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
2179443 TAAAAAGACA
* *
2179453 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
2179488 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
2179523 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
2179558 GAAATTGA
1 GAAATTGA
2179566 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:2180483 original size:2 final size:2
Alignment explanation
Indices: 2180478--2180510 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2180468 TCTAATAAAT
2180478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2180511 GATAATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2181193 original size:7 final size:7
Alignment explanation
Indices: 2181181--2181247 Score: 134
Period size: 7 Copynumber: 9.6 Consensus size: 7
2181171 TAAATTCTTC
2181181 TTTCCTT
1 TTTCCTT
2181188 TTTCCTT
1 TTTCCTT
2181195 TTTCCTT
1 TTTCCTT
2181202 TTTCCTT
1 TTTCCTT
2181209 TTTCCTT
1 TTTCCTT
2181216 TTTCCTT
1 TTTCCTT
2181223 TTTCCTT
1 TTTCCTT
2181230 TTTCCTT
1 TTTCCTT
2181237 TTTCCTT
1 TTTCCTT
2181244 TTTC
1 TTTC
2181248 ACAATATTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCCTT
Found at i:2183495 original size:21 final size:21
Alignment explanation
Indices: 2183471--2183530 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
2183461 GACATGTGAA
* **
2183471 ATCTATGTCCTGAAGGATGTC
1 ATCTATGTCCCGAAGGACATC
2183492 ATCTATGTCCCGAAGGACATC
1 ATCTATGTCCCGAAGGACATC
2183513 ATCTATGTCCCGAAGGAC
1 ATCTATGTCCCGAAGGAC
2183531 CTATCCATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (21 bp):
ATCTATGTCCCGAAGGACATC
Found at i:2183675 original size:22 final size:22
Alignment explanation
Indices: 2183650--2183698 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2183640 TCATGTATTT
2183650 ATATCAT-TTCTCTTATGATCAC
1 ATATCATCTTCTCTTATGA-CAC
* *
2183672 ATAT-TTCTTCTCTTCTGACAC
1 ATATCATCTTCTCTTATGACAC
2183693 ATATCA
1 ATATCA
2183699 CATATATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATCATCTTCTCTTATGACAC
Found at i:2186511 original size:205 final size:205
Alignment explanation
Indices: 2186159--2186574 Score: 823
Period size: 205 Copynumber: 2.0 Consensus size: 205
2186149 CATGATTACC
2186159 TAGATTGAATCTCTTTTGTTCGGAGTCAAAGGCAACCCCGTCACAAAATCCATCGTTACATTCTC
1 TAGATTGAATCTCTTTTGTTCGGAGTCAAAGGCAACCCCGTCACAAAATCCATCGTTACATTCTC
2186224 TCATTTCCACTAAGGAATAGACATTGGTTGTAATAGTCCTGACGAAACTTGTTGCTCAGCTTTGA
66 TCATTTCCACTAAGGAATAGACATTGGTTGTAATAGTCCTGACGAAACTTGTTGCTCAGCTTTGA
2186289 CTTTCTGGCAAGTCAAACACTTGAATACAAATTTCGTAATATTCTTTTTCATTCTTGGTCACCAG
131 CTTTCTGGCAAGTCAAACACTTGAATACAAATTTCGTAATATTCTTTTTCATTCTTGGTCACCAG
2186354 TATCAACTCT
196 TATCAACTCT
2186364 TAGATTGAATCTCTTTTGTTCGGAGTCAAAGGCAACCCCGTCACAAAATCCATCGTTACATTCTC
1 TAGATTGAATCTCTTTTGTTCGGAGTCAAAGGCAACCCCGTCACAAAATCCATCGTTACATTCTC
2186429 TCATTTCCACTAAGGAATAGACATTGGTTGTAATAGTCCTGACGAAACTTGTTGCTCAGCTTTGA
66 TCATTTCCACTAAGGAATAGACATTGGTTGTAATAGTCCTGACGAAACTTGTTGCTCAGCTTTGA
2186494 CTTTCTGGCAAGTCAAACACTTGAATACAAATTTCGTAATATTCTTTTTCATTCTTGGTCACCAG
131 CTTTCTGGCAAGTCAAACACTTGAATACAAATTTCGTAATATTCTTTTTCATTCTTGGTCACCAG
2186559 TATCAACTCT
196 TATCAACTCT
2186569 TGAGAT
1 T-AGAT
2186575 CCATATACAT
Statistics
Matches: 210, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
205 206 0.98
206 4 0.02
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (205 bp):
TAGATTGAATCTCTTTTGTTCGGAGTCAAAGGCAACCCCGTCACAAAATCCATCGTTACATTCTC
TCATTTCCACTAAGGAATAGACATTGGTTGTAATAGTCCTGACGAAACTTGTTGCTCAGCTTTGA
CTTTCTGGCAAGTCAAACACTTGAATACAAATTTCGTAATATTCTTTTTCATTCTTGGTCACCAG
TATCAACTCT
Found at i:2190549 original size:24 final size:22
Alignment explanation
Indices: 2190521--2190574 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 22
2190511 ATATCATGAT
2190521 ATCACATATTTCATTTCTCTTATG
1 ATCACATATTTC--TTCTCTTATG
*
2190545 ATCACATATTTCTTCTCTTCTG
1 ATCACATATTTCTTCTCTTATG
2190567 -TCACATAT
1 ATCACATAT
2190575 CATATATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 8 0.28
22 9 0.31
24 12 0.41
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (22 bp):
ATCACATATTTCTTCTCTTATG
Found at i:2192481 original size:16 final size:16
Alignment explanation
Indices: 2192460--2192518 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
2192450 CTAACATGGA
2192460 CTAAATTTAAAGAAAT
1 CTAAATTTAAAGAAAT
*
2192476 CTAAATTTAAGGACTAACT
1 CTAAATTTAAAGA--AA-T
* *
2192495 CTAAATGATAAAGTAAT
1 CTAAAT-TTAAAGAAAT
2192512 CTAAATT
1 CTAAATT
2192519 AGAACTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 12 0.35
17 7 0.21
18 4 0.12
19 7 0.21
20 4 0.12
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.32
Consensus pattern (16 bp):
CTAAATTTAAAGAAAT
Found at i:2192769 original size:28 final size:29
Alignment explanation
Indices: 2192713--2192772 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2192703 AAGAAAATAG
2192713 AATGTAAAGTGCAAAAATCAAAGGACTGA
1 AATGTAAAGTGCAAAAATCAAAGGACTGA
* *
2192742 AATGTAAA-TGCTAAAATTTAAAGG-CTGA
1 AATGTAAAGTGC-AAAAATCAAAGGACTGA
2192770 AAT
1 AAT
2192773 TAGACTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.23
Consensus pattern (29 bp):
AATGTAAAGTGCAAAAATCAAAGGACTGA
Found at i:2192852 original size:31 final size:31
Alignment explanation
Indices: 2192810--2192884 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
2192800 ATGTAATTAG
* *
2192810 AGTTAGGGGTTAATTAATTAGCAAAGTTAAC
1 AGTTAGTGGTTAATAAATTAGCAAAGTTAAC
* **
2192841 GGTTAGTGGTTAATAAATTAGTGAAGTTAAC
1 AGTTAGTGGTTAATAAATTAGCAAAGTTAAC
2192872 AGTTAGTGGTTAA
1 AGTTAGTGGTTAA
2192885 ATTAGAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (31 bp):
AGTTAGTGGTTAATAAATTAGCAAAGTTAAC
Found at i:2195803 original size:41 final size:40
Alignment explanation
Indices: 2195758--2195859 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 40
2195748 GAGGTCTTAT
* *
2195758 AGATGGCCCGAATGACTTATCATCTTGCTCGACAGACTGAC
1 AGATGGCCCGAA-GACTTATCATCATGCTCGAAAGACTGAC
* * *
2195799 AGATGACCCGGAAGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCC-GAAGACTT-ATCATCATGCTCGAAAGACTGAC
*
2195841 TGATGGCCCGAAGGACTTA
1 AGATGGCCCGAA-GACTTA
2195860 CCAATTTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (40 bp):
AGATGGCCCGAAGACTTATCATCATGCTCGAAAGACTGAC
Found at i:2198477 original size:23 final size:23
Alignment explanation
Indices: 2198459--2198519 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2198449 CTCGTATAAA
2198459 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
2198482 TGCATCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2198505 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
2198520 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2199232 original size:63 final size:63
Alignment explanation
Indices: 2199165--2199324 Score: 191
Period size: 63 Copynumber: 2.5 Consensus size: 63
2199155 ATCCCTTGAC
* *
2199165 GGGTGCATCGATGCACTATCTATGCATCGATACA-TAAATCCCATTCGATGTTTGTA-TTTAAGG
1 GGGTGCATCGATGCACTA-CTGTGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAAG
* ** *
2199228 GGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTAC-TGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
** *
2199292 GATTGCATCGATGCACCA-TGTGCATCGATACAC
1 GGGTGCATCGATGCACTACTGTGCATCGATACAC
2199325 CTTGAACAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
62 16 0.19
63 47 0.55
64 22 0.26
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (63 bp):
GGGTGCATCGATGCACTACTGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
Found at i:2202771 original size:18 final size:18
Alignment explanation
Indices: 2202748--2202792 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2202738 GAAGTACGTC
2202748 TGAATTCAATTTCAAGCA
1 TGAATTCAATTTCAAGCA
2202766 TGAATTCAATTTCAAGCA
1 TGAATTCAATTTCAAGCA
2202784 TGAATTCAA
1 TGAATTCAA
2202793 CTTCTTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (18 bp):
TGAATTCAATTTCAAGCA
Found at i:2206625 original size:26 final size:26
Alignment explanation
Indices: 2206581--2206636 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
2206571 TATCCACTAT
** *
2206581 TACCCACTAACCATCTAATACATCAC
1 TACCCACTAACCAAATAATACACCAC
* *
2206607 TACCCGCTAACCAAATAATCCACCAC
1 TACCCACTAACCAAATAATACACCAC
2206633 TACC
1 TACC
2206637 TACCTAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.41, G:0.02, T:0.20
Consensus pattern (26 bp):
TACCCACTAACCAAATAATACACCAC
Found at i:2207484 original size:11 final size:10
Alignment explanation
Indices: 2207467--2207533 Score: 57
Period size: 11 Copynumber: 6.5 Consensus size: 10
2207457 AAATGTACCC
2207467 TTTTTATTAT
1 TTTTTATTAT
2207477 TATTTTATTAT
1 T-TTTTATTAT
*
2207488 TATTTTTTTAT
1 T-TTTTATTAT
2207499 CTTTTTAATT-T
1 -TTTTT-ATTAT
* *
2207510 ATTTTGTTA-
1 TTTTTATTAT
2207519 TTTTTATTAT
1 TTTTTATTAT
2207529 TTTTT
1 TTTTT
2207534 CTCAATTTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
9 9 0.20
10 10 0.22
11 24 0.52
12 3 0.07
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:2207523 original size:9 final size:9
Alignment explanation
Indices: 2207467--2207532 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
2207457 AAATGTACCC
2207467 TTTTTATTA
1 TTTTTATTA
*
2207476 TTATT-TTA
1 TTTTTATTA
*
2207484 TTATTATT-
1 TTTTTATTA
2207492 TTTTTATCT-
1 TTTTTAT-TA
*
2207501 TTTTAATT-
1 TTTTTATTA
*
2207509 TATTTTGTTA
1 T-TTTTATTA
2207519 TTTTTATTA
1 TTTTTATTA
2207528 TTTTT
1 TTTTT
2207533 TCTCAATTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 16 0.34
9 30 0.64
10 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTTATTA
Found at i:2207530 original size:21 final size:22
Alignment explanation
Indices: 2207479--2207530 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2207469 TTTATTATTA
*
2207479 TTTTATTA-TTATTTTTTTATC
1 TTTTATTATTTATTTTGTTATC
*
2207500 TTTT-TAATTTATTTTGTTAT-
1 TTTTATTATTTATTTTGTTATC
2207520 TTTTATTATTT
1 TTTTATTATTT
2207531 TTTCTCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATTATTTATTTTGTTATC
Found at i:2210673 original size:21 final size:20
Alignment explanation
Indices: 2210644--2210716 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
2210634 AGATCTAATC
*
2210644 AGAACAAAGAGAGAGAAAAA
1 AGAAAAAAGAGAGAGAAAAA
*
2210664 AGAAAAAAAGAGAGAAAAATAA
1 AG-AAAAAAGAGAGAGAAA-AA
2210686 AGAAAAAAGCA-A-AGAAAAA
1 AGAAAAAAG-AGAGAGAAAAA
*
2210705 ATAAAAAAGAGA
1 AGAAAAAAGAGA
2210717 AACAAAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
18 1 0.02
19 11 0.24
20 6 0.13
21 22 0.49
22 5 0.11
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (20 bp):
AGAAAAAAGAGAGAGAAAAA
Found at i:2210677 original size:19 final size:18
Alignment explanation
Indices: 2210653--2210716 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
2210643 CAGAACAAAG
2210653 AGAGAGAAAAAAGAAAAAA
1 AGAGAGAAAAAA-AAAAAA
2210672 AGAGAGAAAAATAAAGAAAAA
1 AGAGAG-AAAA-AAA-AAAAA
* *
2210693 AGCAAAGAAAAAATAAAAA
1 AG-AGAGAAAAAAAAAAAA
2210712 AGAGA
1 AGAGA
2210717 AACAAAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.05
19 13 0.34
20 7 0.18
21 13 0.34
22 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.03
Consensus pattern (18 bp):
AGAGAGAAAAAAAAAAAA
Found at i:2210693 original size:12 final size:11
Alignment explanation
Indices: 2210662--2210747 Score: 54
Period size: 11 Copynumber: 7.9 Consensus size: 11
2210652 GAGAGAGAAA
2210662 AAAGAAAAAA-
1 AAAGAAAAAAT
*
2210672 AGAGAGAAAAAT
1 AAAGA-AAAAAT
*
2210684 AAAGAAAAAAGC
1 AAAGAAAAAA-T
2210696 AAAGAAAAAAT
1 AAAGAAAAAAT
* *
2210707 -AA-AAAAGAG
1 AAAGAAAAAAT
*
2210716 AAACAAAAACA-
1 AAAGAAAAA-AT
*
2210727 AAGGAAAAAAT
1 AAAGAAAAAAT
*
2210738 GAAGAAAAAA
1 AAAGAAAAAA
2210748 AAGACAAGAC
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
9 5 0.09
10 9 0.16
11 29 0.50
12 15 0.26
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAAT
Found at i:2210723 original size:19 final size:17
Alignment explanation
Indices: 2210655--2210736 Score: 62
Period size: 19 Copynumber: 4.6 Consensus size: 17
2210645 GAACAAAGAG
2210655 AGAGAAAAAAGAAAAAAA
1 AGAGAAAAAA-AAAAAAA
2210673 GAGAGAAAAATAAAGAAAAA
1 -AGAGAAAAA-AAA-AAAAA
2210693 AGCA-AAGAAAAAATAAAAA
1 AG-AGAA-AAAAAA-AAAAA
* *
2210712 AGAG-AAACAAAAACAA
1 AGAGAAAAAAAAAAAAA
2210728 AG-GAAAAAA
1 AGAGAAAAAA
2210737 TGAAGAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
15 1 0.02
16 10 0.19
17 5 0.09
18 2 0.04
19 25 0.47
20 10 0.19
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (17 bp):
AGAGAAAAAAAAAAAAA
Found at i:2210724 original size:42 final size:42
Alignment explanation
Indices: 2210657--2210736 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
2210647 ACAAAGAGAG
* * *
2210657 AGAAAAAAGAAAAAAAGAGAGAAAAATAAA-GAAAAAAGCAA
1 AGAAAAAAGAAAAAAAGAAACAAAAACAAAGGAAAAAAGCAA
*
2210698 AGAAAAAATAAAAAAGAGAAACAAAAACAAAGGAAAAAA
1 AGAAAAAAGAAAAAA-AGAAACAAAAACAAAGGAAAAAA
2210737 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 14 0.42
42 12 0.36
43 7 0.21
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.03
Consensus pattern (42 bp):
AGAAAAAAGAAAAAAAGAAACAAAAACAAAGGAAAAAAGCAA
Found at i:2210743 original size:42 final size:40
Alignment explanation
Indices: 2210657--2210747 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 40
2210647 ACAAAGAGAG
* * *
2210657 AGAAAAAAGAAAAAAAGAGAGAAAAATAAAGAAAAAAGCAA
1 AGAAAAAAGAAAAAAAGAAACAAAAACAAAGAAAAAAG-AA
*
2210698 AGAAAAAATAAAAAAGAGAAACAAAAACAAAGGAAAAAATG-A
1 AGAAAAAAGAAAAAA-AGAAACAAAAACAAA-GAAAAAA-GAA
2210740 AGAAAAAA
1 AGAAAAAA
2210748 AAGACAAGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
41 14 0.33
42 21 0.49
43 7 0.16
44 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (40 bp):
AGAAAAAAGAAAAAAAGAAACAAAAACAAAGAAAAAAGAA
Found at i:2211829 original size:32 final size:32
Alignment explanation
Indices: 2211768--2211851 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
2211758 CAATGGGGCA
* *
2211768 ATCTTTGAAGATTCAACATCAAATGTTGGGAC
1 ATCTTTGGAGATTCAACATCAAATATTGGGAC
* * * *
2211800 ATTTTTGGAGATTCAATATCGAATATTGGGGC
1 ATCTTTGGAGATTCAACATCAAATATTGGGAC
* *
2211832 ATCTTTGGGGATTGAACATC
1 ATCTTTGGAGATTCAACATC
2211852 CTGATGCAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (32 bp):
ATCTTTGGAGATTCAACATCAAATATTGGGAC
Found at i:2212954 original size:26 final size:26
Alignment explanation
Indices: 2212925--2212988 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
2212915 CCCACTAACC
*
2212925 ACCATTACCCACTAACCACCTAATCT
1 ACCACTACCCACTAACCACCTAATCT
*
2212951 ACCACTACCCACTAACCACCTAATCC
1 ACCACTACCCACTAACCACCTAATCT
*
2212977 ACTACTACCCAC
1 ACCACTACCCAC
2212989 CTAATTACCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (26 bp):
ACCACTACCCACTAACCACCTAATCT
Found at i:2214061 original size:6 final size:6
Alignment explanation
Indices: 2214047--2214087 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
2214037 TGAATTGGGT
2214047 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
2214088 CGTAATTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:2217126 original size:20 final size:20
Alignment explanation
Indices: 2217088--2217126 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2217078 AAATAAATAA
* *
2217088 ATATTATTATTTAATTAAAT
1 ATATTATTATATAACTAAAT
*
2217108 ATATTTTTATATAACTAAA
1 ATATTATTATATAACTAAA
2217127 ATAATAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTATTATATAACTAAAT
Done.