Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_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: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1721194 original size:13 final size:13
Alignment explanation
Indices: 1721106--1721182 Score: 82
Period size: 13 Copynumber: 5.3 Consensus size: 13
1721096 AGTAGTCAAC
1721106 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
1721122 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1721135 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
1721153 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1721166 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1721179 GGTC
1 GGTC
1721183 GGGTAAACGG
Statistics
Matches: 56, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
13 30 0.54
14 1 0.02
15 1 0.02
16 12 0.21
17 1 0.02
18 11 0.20
ACGTcount: A:0.18, C:0.23, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1724986 original size:18 final size:18
Alignment explanation
Indices: 1724963--1724997 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1724953 TTCCATCCGG
*
1724963 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1724981 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1724998 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1726116 original size:8 final size:8
Alignment explanation
Indices: 1726097--1726174 Score: 71
Period size: 8 Copynumber: 10.4 Consensus size: 8
1726087 GTCAACAGTA
1726097 GTCAAC-G
1 GTCAACGG
1726104 GTCAACGG
1 GTCAACGG
1726112 GTCAACGG
1 GTCAACGG
1726120 GTCAACGG
1 GTCAACGG
1726128 GT---CGG
1 GTCAACGG
*
1726133 GTCAACGA
1 GTCAACGG
*
1726141 GTCGAGTCGG
1 GTC-A-ACGG
1726151 GTCAACGG
1 GTCAACGG
1726159 GT---CGG
1 GTCAACGG
1726164 GTCAACGG
1 GTCAACGG
1726172 GTC
1 GTC
1726175 GGGTCGGGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
5 10 0.17
7 6 0.10
8 35 0.60
9 2 0.03
10 5 0.09
ACGTcount: A:0.21, C:0.24, G:0.40, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:1726155 original size:31 final size:31
Alignment explanation
Indices: 1726117--1726197 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
1726107 AACGGGTCAA
1726117 CGGGTCAACGGGTCGGGTCAACGAGTCGAGT
1 CGGGTCAACGGGTCGGGTCAACGAGTCGAGT
* *
1726148 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGAGTCGAGT
* *
1726179 CGGGTAAACGGGTTGGGTC
1 CGGGTCAACGGGTCGGGTC
1726198 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGAGTCGAGT
Found at i:1726177 original size:18 final size:18
Alignment explanation
Indices: 1726109--1726201 Score: 88
Period size: 18 Copynumber: 5.3 Consensus size: 18
1726099 CAACGGTCAA
1726109 CGGGTCAACGGGTCAACGGGT
1 CGGGTCAACGGGT---CGGGT
* *
1726130 CGGGTCAACGAGTCGAGT
1 CGGGTCAACGGGTCGGGT
1726148 CGGGTCAA-----CGGGT
1 CGGGTCAACGGGTCGGGT
1726161 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
* *
1726179 CGGGTAAACGGGTTGGGT
1 CGGGTCAACGGGTCGGGT
1726197 CGGGT
1 CGGGT
1726202 TGTGACCGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
13 12 0.19
18 38 0.61
21 12 0.19
ACGTcount: A:0.16, C:0.20, G:0.46, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:1726191 original size:13 final size:13
Alignment explanation
Indices: 1726103--1726179 Score: 82
Period size: 13 Copynumber: 5.3 Consensus size: 13
1726093 AGTAGTCAAC
1726103 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
1726119 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1726132 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
1726150 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1726163 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1726176 GGTC
1 GGTC
1726180 GGGTAAACGG
Statistics
Matches: 56, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
13 30 0.54
14 1 0.02
15 1 0.02
16 12 0.21
17 1 0.02
18 11 0.20
ACGTcount: A:0.18, C:0.23, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1728890 original size:10 final size:10
Alignment explanation
Indices: 1728851--1728891 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1728841 AGTAACCAAC
1728851 AACTATAACA
1 AACTATAACA
1728861 AACTAATAACA
1 AACT-ATAACA
*
1728872 AACCATAACA
1 AACTATAACA
*
1728882 AACTCTAACA
1 AACTATAACA
1728892 TAGTTTATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.17
Consensus pattern (10 bp):
AACTATAACA
Found at i:1730219 original size:2 final size:2
Alignment explanation
Indices: 1730206--1730289 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
1730196 TTAAAATGGA
*
1730206 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1730248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1730290 GAAGTAAGAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1733160 original size:21 final size:21
Alignment explanation
Indices: 1733114--1733158 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1733104 ATATTATGTC
1733114 ATTTATTTTCTTTTTTCTTAA
1 ATTTATTTTCTTTTTTCTTAA
*
1733135 ATTTATTGTT-TTTTTT-TTCA
1 ATTTATT-TTCTTTTTTCTTAA
1733155 ATTT
1 ATTT
1733159 TAAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 13 0.59
22 2 0.09
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (21 bp):
ATTTATTTTCTTTTTTCTTAA
Found at i:1733484 original size:20 final size:21
Alignment explanation
Indices: 1733459--1733507 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1733449 AATCTTTTAT
**
1733459 TTTTTTATATTG-AGGTTGTG
1 TTTTTTATATTGTACATTGTG
* *
1733479 TTTTTTTTGTTGTACATTGTG
1 TTTTTTATATTGTACATTGTG
1733500 TTTTTTAT
1 TTTTTTAT
1733508 TTAATGAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.12, C:0.02, G:0.18, T:0.67
Consensus pattern (21 bp):
TTTTTTATATTGTACATTGTG
Found at i:1735606 original size:30 final size:30
Alignment explanation
Indices: 1735572--1735633 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1735562 TTATTTATCC
1735572 AACAATTTAAAAAGAACATCTAAAATTTAA
1 AACAATTTAAAAAGAACATCTAAAATTTAA
*
1735602 AACAATTTAAAAAGAACGTCTAAAATTTAA
1 AACAATTTAAAAAGAACATCTAAAATTTAA
1735632 AA
1 AA
1735634 GTTTATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.26
Consensus pattern (30 bp):
AACAATTTAAAAAGAACATCTAAAATTTAA
Found at i:1739180 original size:26 final size:26
Alignment explanation
Indices: 1739151--1739201 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1739141 CGGTTTCAAA
1739151 CAATGAGCCATATGGACAGGGACAAG
1 CAATGAGCCATATGGACAGGGACAAG
1739177 CAATGAGCCATATGGACAGGGACAA
1 CAATGAGCCATATGGACAGGGACAA
1739202 ATGCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.29, T:0.12
Consensus pattern (26 bp):
CAATGAGCCATATGGACAGGGACAAG
Found at i:1739859 original size:32 final size:32
Alignment explanation
Indices: 1739822--1739894 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
1739812 TTCGAATCTC
* *
1739822 GTCAATATCAGACCGGTTGATTTTTGGGTC-G
1 GTCAATATCAGACCGATTGATTTTCGGGTCAG
*
1739853 GATCAATATCAGATCGATTGATTTTCGGGTCAG
1 G-TCAATATCAGACCGATTGATTTTCGGGTCAG
1739886 GTCAATATC
1 GTCAATATC
1739895 GGATTGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.92
33 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (32 bp):
GTCAATATCAGACCGATTGATTTTCGGGTCAG
Found at i:1740261 original size:55 final size:56
Alignment explanation
Indices: 1740190--1740302 Score: 192
Period size: 55 Copynumber: 2.0 Consensus size: 56
1740180 ACCTATTTGG
*
1740190 TGAAGAATTAAATTTTGAATTATAAATATTATTCTCAATTAAAGTTTTTAATTAGA
1 TGAAGAATTAAATTTTGAATTATAAATATTATTCTCAACTAAAGTTTTTAATTAGA
* *
1740246 TGAA-AATTAAATTTTGAATTATAAATTTTATTCTCAACTAAATTTTTTAATTAGA
1 TGAAGAATTAAATTTTGAATTATAAATATTATTCTCAACTAAAGTTTTTAATTAGA
1740301 TG
1 TG
1740303 TTAGATGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 50 0.93
56 4 0.07
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (56 bp):
TGAAGAATTAAATTTTGAATTATAAATATTATTCTCAACTAAAGTTTTTAATTAGA
Found at i:1742176 original size:15 final size:15
Alignment explanation
Indices: 1742156--1742192 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1742146 ATATTTAGCT
*
1742156 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
1742171 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1742186 GGGCGGG
1 GGGCGGG
1742193 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1747858 original size:29 final size:31
Alignment explanation
Indices: 1747814--1747872 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
1747804 TTTTTTCATA
1747814 AAAAAATAATATGCATATTTAATAATTTTTC
1 AAAAAATAATATGCATATTTAATAATTTTTC
1747845 AAAAAA-AA-ATGCATATTTAATAATTTTT
1 AAAAAATAATATGCATATTTAATAATTTTT
1747873 GTACAATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 20 0.71
30 2 0.07
31 6 0.21
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (31 bp):
AAAAAATAATATGCATATTTAATAATTTTTC
Found at i:1748207 original size:18 final size:19
Alignment explanation
Indices: 1748168--1748208 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1748158 CACTCAATGT
1748168 AAAACACTATTTTCATTAA
1 AAAACACTATTTTCATTAA
1748187 AAAACACTATTTTCATTAA
1 AAAACACTATTTTCATTAA
1748206 AAA
1 AAA
1748209 GATGTAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAACACTATTTTCATTAA
Found at i:1750524 original size:19 final size:19
Alignment explanation
Indices: 1750497--1750533 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1750487 ATGAAGTGGT
1750497 TCATATTATTAATTTTGGG
1 TCATATTATTAATTTTGGG
*
1750516 TCATCTTATTAATTTTGG
1 TCATATTATTAATTTTGG
1750534 TTACTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (19 bp):
TCATATTATTAATTTTGGG
Found at i:1757671 original size:146 final size:143
Alignment explanation
Indices: 1757355--1757762 Score: 581
Period size: 146 Copynumber: 2.8 Consensus size: 143
1757345 ATTTTTTATT
* *
1757355 TTAAATAAATCATAAAA-AGTAATTAATTAATAAGAATTTTCTATTTTTGGGTATGTAAAGAATC
1 TTAAATAAATCATAAAATAGTAATTAATTAATATGATTTTTCTATTTTTGGGTATGTAAAGAATC
** *
1757419 A-TGAGCTGCTAATTCTTTCAAAAAACTAATAAGGACTGAAATTTTCATCAGATGAGCTGTTAAT
66 AGTGAGCTGCTAATTCTTTCAATCAACTAATAAGGATTGAAATTTTCATCAGATGAGCTGTTAAT
1757483 AGTTATTTTGATA
131 AGTTATTTTGATA
* * *
1757496 TAAAATAAATCATGAAAATAGTAATTAATTAATATGATTTTTCTATTTTCGGGCATGTAAAGAAT
1 TTAAATAAATCAT-AAAATAGTAATTAATTAATATGATTTTTCTATTTTTGGGTATGTAAAGAAT
* * *
1757561 CAGGTGGGCTGCTAATTCTTTCAGTCAACTAATAAGGATTGAAATTTTCATCAGATGGAGTTGTT
65 CA-GTGAGCTGCTAATTCTTTCAATCAACTAATAAGGATTGAAATTTTCATCAGAT-GAGCTGTT
*
1757626 AATTGTTATTTTGATA
128 AATAGTTATTTTGATA
* *
1757642 TTAAATAAATCATAAAAATAATAATTAATTAATATGATTTTTCTATTTTTGGGTATTTAAAGAAT
1 TTAAATAAATCAT-AAAATAGTAATTAATTAATATGATTTTTCTATTTTTGGGTATGTAAAGAAT
* * * *
1757707 CAGACGAGCTGCTGATTCTTACAATCAACTAATAAGGATCG-AATTTTCATCA-ATGA
65 CAG-TGAGCTGCTAATTCTTTCAATCAACTAATAAGGATTGAAATTTTCATCAGATGA
1757763 ATATGTATTG
Statistics
Matches: 237, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
141 12 0.05
142 4 0.02
143 46 0.19
144 2 0.01
145 59 0.25
146 114 0.48
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (143 bp):
TTAAATAAATCATAAAATAGTAATTAATTAATATGATTTTTCTATTTTTGGGTATGTAAAGAATC
AGTGAGCTGCTAATTCTTTCAATCAACTAATAAGGATTGAAATTTTCATCAGATGAGCTGTTAAT
AGTTATTTTGATA
Found at i:1759272 original size:2 final size:2
Alignment explanation
Indices: 1759265--1759295 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1759255 TCTATGCGGT
1759265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1759296 CATGCGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1765520 original size:2 final size:2
Alignment explanation
Indices: 1765513--1765604 Score: 64
Period size: 2 Copynumber: 52.0 Consensus size: 2
1765503 CCGCCCCGAT
* *
1765513 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1765552 TA TA TA T- TA -A T- TA TA TA TA TA -A TA T- TT TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1765588 TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1765605 AAATATTTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 24
0.73 0.04 0.24
Matches are distributed among these distances:
1 12 0.16
2 62 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1765572 original size:34 final size:35
Alignment explanation
Indices: 1765512--1765613 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 35
1765502 CCCGCCCCGA
*
1765512 TTATATATATATATA-T-A-TATATATATAATATT
1 TTATATATTTATATATTAATTATATATATAATATT
1765544 TTATAT-TTTATATATTAATTATATATATAATATT
1 TTATATATTTATATATTAATTATATATATAATATT
*
1765578 TTATATATTT-TATATTAATTATATATAAAATATT
1 TTATATATTTATATATTAATTATATATATAATATT
1765612 TT
1 TT
1765614 CGGGTTTGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
31 7 0.11
32 7 0.11
33 1 0.02
34 46 0.72
35 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATATATTTATATATTAATTATATATATAATATT
Found at i:1766479 original size:10 final size:10
Alignment explanation
Indices: 1766464--1766529 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
1766454 AATAAGTATG
1766464 ATAATTTAAT
1 ATAATTTAAT
1766474 ATAATTTAAT
1 ATAATTTAAT
* *
1766484 AAAATATAAT
1 ATAATTTAAT
* *
1766494 GATTATTTTAT
1 -ATAATTTAAT
*
1766505 ACTAATTTGAT
1 A-TAATTTAAT
*
1766516 AAAATTTAAT
1 ATAATTTAAT
1766526 -TAAT
1 ATAAT
1766530 ATTTTGTAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
9 3 0.07
10 26 0.60
11 14 0.33
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:1766511 original size:32 final size:31
Alignment explanation
Indices: 1766461--1766543 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
1766451 CATAATAAGT
* *
1766461 ATGATAATTTAATATAATTTAATAAAATATA
1 ATGATTATTTTATATAATTTAATAAAATATA
* *
1766492 ATGATTATTTTATACTAATTTGATAAAATTTA
1 ATGATTATTTTATA-TAATTTAATAAAATATA
* * *
1766524 ATTAATATTTTGTAATAATT
1 ATGATTATTTTAT-ATAATT
1766544 CGATAGAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 12 0.28
32 30 0.70
33 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (31 bp):
ATGATTATTTTATATAATTTAATAAAATATA
Found at i:1766554 original size:32 final size:32
Alignment explanation
Indices: 1766482--1766575 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
1766472 ATATAATTTA
* * * * *
1766482 ATAAAATATAATGATTATTTTATACTAATTTG
1 ATAAAATTTAATTAATATTTTATAATAATTCG
*
1766514 ATAAAATTTAATTAATATTTTGTAATAATTCG
1 ATAAAATTTAATTAATATTTTATAATAATTCG
* **
1766546 ATAGAATTTAA-TAATTATAATATAATAATT
1 ATAAAATTTAATTAA-TATTTTATAATAATT
1766576 TTTAAATTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 3 0.06
32 48 0.94
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (32 bp):
ATAAAATTTAATTAATATTTTATAATAATTCG
Found at i:1766583 original size:22 final size:22
Alignment explanation
Indices: 1766558--1766606 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1766548 AGAATTTAAT
1766558 AATTATAA-TATAATAATTTTTA
1 AATT-TAAGTATAATAATTTTTA
* *
1766580 AATTTAAGTATCATATTTTTTA
1 AATTTAAGTATAATAATTTTTA
1766602 AATTT
1 AATTT
1766607 TTAATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTAAGTATAATAATTTTTA
Found at i:1772263 original size:25 final size:25
Alignment explanation
Indices: 1772235--1772285 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1772225 TTAAATTAAT
1772235 TGAATCGAGTTATTTAGTTTTTGAA
1 TGAATCGAGTTATTTAGTTTTTGAA
1772260 TGAATCGAGTTATTTAGTTTTTGAA
1 TGAATCGAGTTATTTAGTTTTTGAA
1772285 T
1 T
1772286 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (25 bp):
TGAATCGAGTTATTTAGTTTTTGAA
Found at i:1772672 original size:17 final size:17
Alignment explanation
Indices: 1772650--1772686 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1772640 ACTCTAAAAA
*
1772650 AACTGGACCGGCCAGCG
1 AACTGGACCGACCAGCG
*
1772667 AACTGGACCGATCAGCG
1 AACTGGACCGACCAGCG
1772684 AAC
1 AAC
1772687 CGAACGTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.32, G:0.30, T:0.08
Consensus pattern (17 bp):
AACTGGACCGACCAGCG
Found at i:1772897 original size:14 final size:14
Alignment explanation
Indices: 1772878--1772904 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1772868 CGGTTCCTTG
1772878 CGGTTCATTAGAAC
1 CGGTTCATTAGAAC
1772892 CGGTTCATTAGAA
1 CGGTTCATTAGAA
1772905 ATGATCGATT
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:0.19, G:0.22, T:0.30
Consensus pattern (14 bp):
CGGTTCATTAGAAC
Found at i:1777614 original size:81 final size:81
Alignment explanation
Indices: 1777474--1777653 Score: 215
Period size: 81 Copynumber: 2.2 Consensus size: 81
1777464 GCGAAACTGG
* * **
1777474 GTTTGTA-AAAAA-GCCGCTAAAGTACTACTCTGTTACGGTGTTTTTGAAAGACGCCACTATAAA
1 GTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTACGGCGTTTTTGAAAAAAACCACTATAAA
*
1777537 TTAATC-CTATTACGCC
66 TGAA-CACTATTACGCC
* * * *
1777553 GTTTGTATAAAAACGTCGCTAAAGTACTACTCT-TTGCGGCGTTTGTTGAAAAAAACTACTATAG
1 GTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTACGGCGTTT-TTGAAAAAAACCACTATAA
* *
1777617 ATGAACACTATTGCGGC
65 ATGAACACTATTACGCC
1777634 GTTTGTATAAAAACGCCGCT
1 GTTTGTATAAAAACGCCGCT
1777654 TAATTTACTA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
79 7 0.08
80 15 0.18
81 63 0.74
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (81 bp):
GTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTACGGCGTTTTTGAAAAAAACCACTATAAA
TGAACACTATTACGCC
Found at i:1779909 original size:39 final size:39
Alignment explanation
Indices: 1779855--1779929 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
1779845 TTGCTGTTAT
1779855 TGAATATATTACTCGGATTAGTCATGTTTTCCAAAAGTA
1 TGAATATATTACTCGGATTAGTCATGTTTTCCAAAAGTA
*
1779894 TGAATATATTACTCGGATTAGTCGTGTTTTCCAAAA
1 TGAATATATTACTCGGATTAGTCATGTTTTCCAAAA
1779930 ATACTCGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (39 bp):
TGAATATATTACTCGGATTAGTCATGTTTTCCAAAAGTA
Found at i:1780574 original size:3 final size:3
Alignment explanation
Indices: 1780566--1780612 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
1780556 GGTTCTTCCT
*
1780566 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1780613 GATTGTTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1780629 original size:21 final size:20
Alignment explanation
Indices: 1780609--1780647 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1780599 TTATTATTAT
1780609 TATTGA-TTGTTTAGATTTTA
1 TATTGATTTGTTT-GATTTTA
*
1780629 TATTTATTTGTTTGATTTT
1 TATTGATTTGTTTGATTTT
1780648 CCTTTGTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (20 bp):
TATTGATTTGTTTGATTTTA
Found at i:1781082 original size:16 final size:17
Alignment explanation
Indices: 1781061--1781112 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
1781051 TTTTTAATTT
1781061 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
1781077 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
1781092 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
1781109 AATT
1 AATT
1781113 TATTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:1797662 original size:16 final size:16
Alignment explanation
Indices: 1797641--1797673 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1797631 AAGCACTAGA
1797641 GCCAAGTATACTCGCT
1 GCCAAGTATACTCGCT
1797657 GCCAAGTATACTCGCT
1 GCCAAGTATACTCGCT
1797673 G
1 G
1797674 TTCAAGGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (16 bp):
GCCAAGTATACTCGCT
Found at i:1805745 original size:21 final size:21
Alignment explanation
Indices: 1805721--1805764 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1805711 TTGTTTTTAT
* *
1805721 ATTATGAAA-TAATTAAAATAA
1 ATTAT-AAATTAAATAAAAAAA
1805742 ATTATAAATTAAATAAAAAAA
1 ATTATAAATTAAATAAAAAAA
1805763 AT
1 AT
1805765 AGTATCGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATTATAAATTAAATAAAAAAA
Found at i:1814945 original size:118 final size:116
Alignment explanation
Indices: 1814772--1814982 Score: 316
Period size: 118 Copynumber: 1.8 Consensus size: 116
1814762 CCTAAAAGTA
* * *
1814772 CACTAGTATATATATTGATGTGATTGCATTTTGTGTGCACATTACGATTCTGATATGATAGCACT
1 CACTAGTATATATATTGATATGATTGCACTTTGTGTGCACATTACAATTCTGATATGATAGCACT
* *
1814837 GTGTATGA-TTATATGTTCTGATTCTGATATACTGTAGTGTACCAGTGGGTG
66 GTGTAT-ATTTATATATTCTGATTATGATATACTGTAGTGTACCAGTGGGTG
*
1814888 CACTAGTATATATATTTTGATATGATTGCACTTTGTGTGCACATTACAATTTTGATATGATAGCA
1 CACTAGTATATATA--TTGATATGATTGCACTTTGTGTGCACATTACAATTCTGATATGATAGCA
* *
1814953 TTGTGTGTATTTATATATTCTGATTATGAT
64 CTGTGTATATTTATATATTCTGATTATGAT
1814983 GATATCACTG
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 14 0.17
117 1 0.01
118 69 0.82
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (116 bp):
CACTAGTATATATATTGATATGATTGCACTTTGTGTGCACATTACAATTCTGATATGATAGCACT
GTGTATATTTATATATTCTGATTATGATATACTGTAGTGTACCAGTGGGTG
Found at i:1815675 original size:2 final size:2
Alignment explanation
Indices: 1815668--1815709 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1815658 TTAGGCAATG
1815668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1815710 GATCAACTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1817168 original size:28 final size:27
Alignment explanation
Indices: 1817123--1817197 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
1817113 CTATAATCAG
* * *
1817123 ATTAATTTGTAACATTTAATGAT-GAA
1 ATTATTTTATAACTTTTAATGATCGAA
* * *
1817149 ATGTCATTTTATAATTTTTAGTGATCGGA
1 AT-T-ATTTTATAACTTTTAATGATCGAA
1817178 ATTATTTTATAACTTTTAAT
1 ATTATTTTATAACTTTTAAT
1817198 AATCAAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
26 2 0.05
27 16 0.42
28 16 0.42
29 4 0.11
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (27 bp):
ATTATTTTATAACTTTTAATGATCGAA
Found at i:1817265 original size:29 final size:29
Alignment explanation
Indices: 1817177--1817266 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
1817167 TAGTGATCGG
* *
1817177 AATTA-TTTTATAACTTTTAATAATCAAAAA
1 AATTATTTTTA-AATTTTTAATAAT-TAAAA
* ***
1817207 TAATT-TTTTT-AATTTTTGAT-ATTTGGA
1 -AATTATTTTTAAATTTTTAATAATTAAAA
1817234 AATTATTTTTAAATTTTTAATAATTAAAA
1 AATTATTTTTAAATTTTTAATAATTAAAA
1817263 AATT
1 AATT
1817267 CAATCGAGAC
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
26 4 0.09
27 6 0.13
28 11 0.24
29 16 0.36
31 8 0.18
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (29 bp):
AATTATTTTTAAATTTTTAATAATTAAAA
Found at i:1820903 original size:3 final size:3
Alignment explanation
Indices: 1820895--1820922 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1820885 TCAACTGTTT
1820895 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1820923 CACATGTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1828924 original size:19 final size:18
Alignment explanation
Indices: 1828887--1828927 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
1828877 CATCAACAAA
1828887 AATTAATTTTTTTTAAAT
1 AATTAATTTTTTTTAAAT
1828905 AATTATATTATTTTTT-AAT
1 AATTA-ATT-TTTTTTAAAT
1828924 AATT
1 AATT
1828928 TTCAACCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTAATTTTTTTTAAAT
Found at i:1836846 original size:16 final size:17
Alignment explanation
Indices: 1836805--1836846 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1836795 ATGGACTATT
1836805 TTAATAAAAATTAAAACA
1 TTAA-AAAAATTAAAACA
*
1836823 TT-AAAAAA-TAAAATA
1 TTAAAAAAATTAAAACA
1836838 TTAAAAAAA
1 TTAAAAAAA
1836847 GAATAAGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 1 0.05
18 2 0.09
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
TTAAAAAAATTAAAACA
Found at i:1836851 original size:14 final size:15
Alignment explanation
Indices: 1836809--1836845 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1836799 ACTATTTTAA
* *
1836809 TAAAAATTAAAACAT
1 TAAAAAATAAAATAT
1836824 TAAAAAATAAAATAT
1 TAAAAAATAAAATAT
1836839 TAAAAAA
1 TAAAAAA
1836846 AGAATAAGAG
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:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAATAAAATAT
Found at i:1838746 original size:18 final size:19
Alignment explanation
Indices: 1838705--1838748 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1838695 CCTGTGCATC
1838705 TTTATGAAATATATTAATTA
1 TTTAT-AAATATATTAATTA
1838725 TTTATAAATTATATT-A-TA
1 TTTATAAA-TATATTAATTA
1838743 TTTATA
1 TTTATA
1838749 TTTATAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 4 0.17
20 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTATAAATATATTAATTA
Found at i:1839725 original size:15 final size:15
Alignment explanation
Indices: 1839684--1839732 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
1839674 ACGACTATAA
1839684 AATAATATATATTTTT
1 AATAATATATA-TTTT
1839700 AA-AAT-TATATTTT
1 AATAATATATATTTT
1839713 AATAATATATATTTT
1 AATAATATATATTTT
1839728 AATAA
1 AATAA
1839733 AGTAAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.19
14 7 0.23
15 16 0.52
16 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATAATATATATTTT
Found at i:1843081 original size:2 final size:2
Alignment explanation
Indices: 1843070--1843107 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1843060 TTTTCAATTT
1843070 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1843108 TATGAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1843324 original size:20 final size:20
Alignment explanation
Indices: 1843299--1843336 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1843289 AATCCTATTC
* *
1843299 CTGGTAATGTTATATTCCCA
1 CTGGTAATCTTACATTCCCA
1843319 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1843337 GAGAGCCAAA
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:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1857016 original size:16 final size:16
Alignment explanation
Indices: 1856995--1857045 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1856985 GCATTTAAGT
1856995 CTTTTTAGGTACATAA
1 CTTTTTAGGTACATAA
*
1857011 CTTTTT---TA-ATAGT
1 CTTTTTAGGTACATA-A
1857024 CTTTTTAGGTACATAA
1 CTTTTTAGGTACATAA
1857040 CTTTTT
1 CTTTTT
1857046 TAATGGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
16 14 0.50
17 3 0.11
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (16 bp):
CTTTTTAGGTACATAA
Found at i:1857018 original size:17 final size:17
Alignment explanation
Indices: 1856996--1857047 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
1856986 CATTTAAGTC
1856996 TTTTTAGGTACATAACT
1 TTTTTAGGTACATAACT
* *
1857013 TTTTTA-ATA-GT--C-
1 TTTTTAGGTACATAACT
1857025 TTTTTAGGTACATAACT
1 TTTTTAGGTACATAACT
1857042 TTTTTA
1 TTTTTA
1857048 ATGGTTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 6 0.23
13 3 0.12
14 1 0.04
15 1 0.04
16 3 0.12
17 12 0.46
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (17 bp):
TTTTTAGGTACATAACT
Found at i:1857028 original size:29 final size:29
Alignment explanation
Indices: 1856992--1857075 Score: 118
Period size: 29 Copynumber: 2.9 Consensus size: 29
1856982 GGTGCATTTA
1856992 AGTCTTTTTAGGTACATAACTTTTTTAAT
1 AGTCTTTTTAGGTACATAACTTTTTTAAT
1857021 AGTCTTTTTAGGTACATAACTTTTTTAAT
1 AGTCTTTTTAGGTACATAACTTTTTTAAT
* *
1857050 GGT-TCATTTAGGTATC-TAACTTTTTT
1 AGTCT-TTTTAGGTA-CATAACTTTTTT
1857076 TGTTGCAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.02
29 49 0.96
30 1 0.02
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (29 bp):
AGTCTTTTTAGGTACATAACTTTTTTAAT
Found at i:1857128 original size:31 final size:31
Alignment explanation
Indices: 1857091--1857164 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1857081 CAATTAGCTC
* *
1857091 TATCCAACTTTTATTTTTTGGTGCATTTAAG
1 TATCCAACTTTTATTTTTTGGTGCAATTAAA
* *
1857122 TATCCAAATTTCATTTTTTGGTGCAATTAAA
1 TATCCAACTTTTATTTTTTGGTGCAATTAAA
1857153 TA-CTCAACTTTT
1 TATC-CAACTTTT
1857165 TCTAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (31 bp):
TATCCAACTTTTATTTTTTGGTGCAATTAAA
Found at i:1867169 original size:25 final size:25
Alignment explanation
Indices: 1867116--1867169 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1867106 AAAATGGTTC
*
1867116 GGTTCGGTTTGGTTTGGCTTTAAAT
1 GGTTCGGTTTGGTTCGGCTTTAAAT
1867141 GGTTCGGTTTTCGGTTCGG-TTTAAA-
1 GGTTCGG-TTT-GGTTCGGCTTTAAAT
1867166 GGTT
1 GGTT
1867170 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 11 0.42
26 9 0.35
27 6 0.23
ACGTcount: A:0.11, C:0.09, G:0.33, T:0.46
Consensus pattern (25 bp):
GGTTCGGTTTGGTTCGGCTTTAAAT
Found at i:1868330 original size:2 final size:2
Alignment explanation
Indices: 1868325--1868392 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1868315 CCATATGTTC
1868325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1868367 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
1868393 CCATAAATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1868706 original size:194 final size:194
Alignment explanation
Indices: 1868435--1868830 Score: 774
Period size: 194 Copynumber: 2.0 Consensus size: 194
1868425 ATATTCTTTT
1868435 CTTAAAAATAATGGGGTGCAAAATTTTTTATTTTTTTTCATTTTTCTTTGATATATTATACTAAA
1 CTTAAAAATAATGGGGTGCAAAATTTTTTATTTTTTTTCATTTTTCTTTGATATATTATACTAAA
1868500 TTTCAATTTTTTTCCTAAATAATGGGGATGCACTTGACTCCTAGGGGGCCTGGTACATCCGCTCA
66 TTTCAATTTTTTTCCTAAATAATGGGGATGCACTTGACTCCTAGGGGGCCTGGTACATCCGCTCA
1868565 TGATACATATATACATACATACCATCAAATCAAAACGGATAAATAATTTGGCTCATAAATAAAA
131 TGATACATATATACATACATACCATCAAATCAAAACGGATAAATAATTTGGCTCATAAATAAAA
1868629 CTTAAAAATAATGGGGTGCAAAATTTTTTATTTTTTTTCATTTTTCTTTGATATATTATACTAAA
1 CTTAAAAATAATGGGGTGCAAAATTTTTTATTTTTTTTCATTTTTCTTTGATATATTATACTAAA
*
1868694 TTTCAATTTTTTTCCTAAATAATGGGGATGCACTTGACTCCTAGGGGGCCTGGTGCATCCGCTCA
66 TTTCAATTTTTTTCCTAAATAATGGGGATGCACTTGACTCCTAGGGGGCCTGGTACATCCGCTCA
1868759 TGATACATATATACATACATACCATCAAATCAAAACGGATAAATAATTTGGCTCATAAATAAAA
131 TGATACATATATACATACATACCATCAAATCAAAACGGATAAATAATTTGGCTCATAAATAAAA
*
1868823 CATAAAAA
1 CTTAAAAA
1868831 GAAATCCAAA
Statistics
Matches: 200, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 200 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (194 bp):
CTTAAAAATAATGGGGTGCAAAATTTTTTATTTTTTTTCATTTTTCTTTGATATATTATACTAAA
TTTCAATTTTTTTCCTAAATAATGGGGATGCACTTGACTCCTAGGGGGCCTGGTACATCCGCTCA
TGATACATATATACATACATACCATCAAATCAAAACGGATAAATAATTTGGCTCATAAATAAAA
Found at i:1869842 original size:3 final size:3
Alignment explanation
Indices: 1869834--1869868 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1869824 AATTAATCAG
*
1869834 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1869869 GATGATGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1878244 original size:13 final size:15
Alignment explanation
Indices: 1878209--1878243 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1878199 GGAAGAAGTT
1878209 TATATATGAAGAATA
1 TATATATGAAGAATA
1878224 TATATATGAAGAATA
1 TATATATGAAGAATA
1878239 TATAT
1 TATAT
1878244 GTACATATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (15 bp):
TATATATGAAGAATA
Found at i:1879132 original size:20 final size:20
Alignment explanation
Indices: 1879107--1879179 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
1879097 AATTGGGAAA
1879107 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1879127 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1879147 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
*
1879167 ATCGCAATACGAT
1 ATCGCAATGCGAT
1879180 TTACGTATTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1879221 original size:142 final size:142
Alignment explanation
Indices: 1879049--1879325 Score: 348
Period size: 142 Copynumber: 2.0 Consensus size: 142
1879039 TCTACAGTGT
* * * **
1879049 CGTTGCGATTTTCCCAATTCGCAATTCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAA
1 CGTTGCGATTTTCACAATTCACAATGCGAATAAGTAAATCGCAACGCG-ATTAAGAAAATCGCAA
* * *
1879114 TGCG-A-TACTGACTATCGCAATGCG-ATAC-TGACTATCGCAATGCG-ATACTTACTATCGCAA
65 TGCGAATTACGGA-AATCGCAATGCGAATACGT-A-AATCGCAATGCGAAT-CTTACTATCGCAA
1879174 TACGATTTACGTATTCG
126 TACGATTTACGTATTCG
* * * *
1879191 CGTTGCGATTTTCATAATTCACAATGCGAATACGTAAATCGCAATGCGATTAAGTAAATCGCAAT
1 CGTTGCGATTTTCACAATTCACAATGCGAATAAGTAAATCGCAACGCGATTAAGAAAATCGCAAT
* *
1879256 GCGAATTAGGGAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACTATCGCAATGCGA
66 GCGAATTACGGAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACTATCGCAATACGA
1879321 TTTAC
131 TTTAC
1879326 ATAGCGCCAT
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
141 17 0.15
142 87 0.75
143 11 0.09
144 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (142 bp):
CGTTGCGATTTTCACAATTCACAATGCGAATAAGTAAATCGCAACGCGATTAAGAAAATCGCAAT
GCGAATTACGGAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACTATCGCAATACGA
TTTACGTATTCG
Found at i:1879237 original size:20 final size:20
Alignment explanation
Indices: 1879212--1879320 Score: 139
Period size: 20 Copynumber: 5.4 Consensus size: 20
1879202 TCATAATTCA
1879212 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* *
1879232 CAATGCGATTAAGTAAATCG
1 CAATGCGAATACGTAAATCG
* *
1879252 CAATGCGAATTAGGGAAATCG
1 CAATGCGAA-TACGTAAATCG
1879273 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* *
1879293 CAATGCGAAT-CTTACTATCG
1 CAATGCGAATACGTA-AATCG
1879313 CAATGCGA
1 CAATGCGA
1879321 TTTACATAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:1879240 original size:41 final size:40
Alignment explanation
Indices: 1879105--1879328 Score: 131
Period size: 40 Copynumber: 5.5 Consensus size: 40
1879095 CGAATTGGGA
*
1879105 AAATCGCAATGCGA-TAC-TGACTATCGCAATGCG-ATAC-T
1 AAATCGCAATGCGATTACAT-A-AATCGCAATGCGAATACGT
* * * * *
1879143 GACTATCGCAATGCGA-TACTTACTATCGCAATACGATTTACGT
1 -A-AATCGCAATGCGATTACATA-AATCGCAATGCGA-ATACGT
* ** * * *
1879186 -ATTCGCGTTGCGATTTTCATAATTCACAATGCGAATACGT
1 AAATCGCAATGCGA-TTACATAAATCGCAATGCGAATACGT
* *
1879226 AAATCGCAATGCGATTA-AGTAAATCGCAATGCGAATTAGGG
1 AAATCGCAATGCGATTACA-TAAATCGCAATGCGAA-TACGT
* * *
1879267 AAATCGCAATGCGAATACGTAAATCGCAATGCGAAT-CTT
1 AAATCGCAATGCGATTACATAAATCGCAATGCGAATACGT
*
1879306 ACTATCGCAATGCGATTTACATA
1 A-AATCGCAATGCGA-TTACATA
1879329 GCGCCATTCG
Statistics
Matches: 142, Mismatches: 30, Indels: 24
0.72 0.15 0.12
Matches are distributed among these distances:
39 3 0.02
40 71 0.50
41 60 0.42
42 7 0.05
43 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (40 bp):
AAATCGCAATGCGATTACATAAATCGCAATGCGAATACGT
Found at i:1879869 original size:20 final size:20
Alignment explanation
Indices: 1879844--1879891 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1879834 GAGAATGAAA
1879844 ATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAAATAACT
1879864 ATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAAATAACT
1879884 ATCGCAAC
1 ATCGCAAC
1879892 AAGAGAATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.27, G:0.19, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGGAAATAACT
Found at i:1880026 original size:20 final size:19
Alignment explanation
Indices: 1879918--1880049 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
1879908 GAAACCAAAA
* *
1879918 TCGCATTGCGATGTTCATT
1 TCGCGTTGCGATTTTCATT
1879937 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1879956 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1879975 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1879989 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1880008 TCCGCGTTGCGATTATCATT
1 T-CGCGTTGCGATTTTCATT
*
1880028 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1880048 TC
1 TC
1880050 AACCAAATGA
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 3 0.03
19 50 0.52
20 31 0.32
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1882218 original size:42 final size:42
Alignment explanation
Indices: 1882142--1882230 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1882132 GACTCGCCTG
* * *
1882142 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1882184 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
1882226 TCATC
1 TCATC
1882231 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1883636 original size:14 final size:14
Alignment explanation
Indices: 1883617--1883652 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1883607 ATTGTTTAAT
1883617 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1883631 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1883645 TGATTTGT
1 TGATTTGT
1883653 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1883796 original size:14 final size:14
Alignment explanation
Indices: 1883777--1883833 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1883767 GCGAAATGAA
1883777 AATCGCAACGATAG
1 AATCGCAACGATAG
*
1883791 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--AT-AG
*
1883810 AATCGCAACGAGAG
1 AATCGCAACGATAG
1883824 AATCGCAACG
1 AATCGCAACG
1883834 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGATAG
Found at i:1883804 original size:33 final size:33
Alignment explanation
Indices: 1883759--1883848 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1883749 AAAAAGTACT
* *
1883759 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1883792 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
1883825 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
1883849 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1883818 original size:19 final size:19
Alignment explanation
Indices: 1883759--1883819 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1883749 AAAAAGTACT
*
1883759 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1883778 ATCGCAA--CG--AT-AGA
1 ATCGCAACGCGAAATGAAA
1883792 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1883811 ATCGCAACG
1 ATCGCAACG
1883820 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 9 0.26
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 18 0.51
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1883866 original size:19 final size:19
Alignment explanation
Indices: 1883844--1883974 Score: 96
Period size: 19 Copynumber: 7.7 Consensus size: 19
1883834 CGAAATTAAA
*
1883844 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1883863 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
1883879 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1883896 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
1883910 TAC-CATATGCGATTTTCAT
1 TTCGCAT-TGCGATTTTCAT
1883929 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1883945 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1883962 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1883975 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 9, Indels: 34
0.67 0.07 0.26
Matches are distributed among these distances:
13 3 0.03
14 20 0.23
16 14 0.16
17 14 0.16
19 32 0.37
20 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1883890 original size:33 final size:33
Alignment explanation
Indices: 1883848--1883974 Score: 195
Period size: 33 Copynumber: 3.8 Consensus size: 33
1883838 ATTAAATTCG
1883848 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
1883881 CGTTGCGATTTTCATTTCGCATTGCGAAAT-AC-
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCACT
* *
1883913 CATATGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGT-TGCGATTTTCATTTCGCATTGCGATTCACT
1883947 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1883975 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
32 4 0.05
33 77 0.91
34 4 0.05
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1884293 original size:13 final size:13
Alignment explanation
Indices: 1884275--1884300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1884265 TGATTACATA
1884275 CTTGTATAGTTGG
1 CTTGTATAGTTGG
1884288 CTTGTATAGTTGG
1 CTTGTATAGTTGG
1884301 TGGATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (13 bp):
CTTGTATAGTTGG
Found at i:1890186 original size:14 final size:15
Alignment explanation
Indices: 1890167--1890199 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1890157 AAAAGTGAAA
1890167 AAAAGAATCAC-TAG
1 AAAAGAATCACTTAG
*
1890181 AAAAGAATCTCTTAG
1 AAAAGAATCACTTAG
1890196 AAAA
1 AAAA
1890200 AAAAAAGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (15 bp):
AAAAGAATCACTTAG
Found at i:1892305 original size:35 final size:36
Alignment explanation
Indices: 1892234--1892307 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1892224 AGCTAATATC
1892234 CTTTTCAGATATCAAACTCCAAATCCCTTCGTCCGA
1 CTTTTCAGATATCAAACTCCAAATCCCTTCGTCCGA
1892270 CTTTTCAGATATCAAACTCCAAAT-CCTTCGTCCGA
1 CTTTTCAGATATCAAACTCCAAATCCCTTCGTCCGA
1892305 CTT
1 CTT
1892308 AATAATTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 14 0.37
36 24 0.63
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.32
Consensus pattern (36 bp):
CTTTTCAGATATCAAACTCCAAATCCCTTCGTCCGA
Found at i:1893043 original size:222 final size:222
Alignment explanation
Indices: 1892628--1893080 Score: 779
Period size: 222 Copynumber: 2.0 Consensus size: 222
1892618 CGATTCAGAG
*
1892628 ACTCCATCTTCGGAGTTAATAGCGGAAACGGGATCACCCTCAACAACATCCCTTGAATTTTGTTC
1 ACTCCATCTTCGGAGTTAATAGCGGAAACGGGATCACCCCCAACAACATCCCTTGAATTTTGTTC
1892693 ATCAACAGGCTCCCCATGACACAATTCAACTGGCTCCTCCTCCTGATCCCCAGTTCCGATGCTAT
66 ATCAACAGGCTCCCCATGACACAATTCAACTGGCTCCTCCTCCTGATCCCCAGTTCCGATGCTAT
1892758 ATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCACCCTCTTCACCAATGCAATTGTCG
131 ATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCACCCTCTTCACCAATGCAATTGTCG
1892823 TTTTTCTCGCTATTCGACTCCTCTGGA
196 TTTTTCTCGCTATTCGACTCCTCTGGA
*
1892850 ACTCCATCTTCTGAGTTAATAGCGGAAAACGGGATCACCCCCAACAACATCCCTTGAA-TTTGTT
1 ACTCCATCTTCGGAGTTAATAGCGG-AAACGGGATCACCCCCAACAACATCCCTTGAATTTTGTT
* * * *
1892914 CATCAATAGGGCTCTCCCCGTGACACAATTCAATTGGCTCCTCCTCGTGATCCCCAGTTCCGATG
65 CATCAACA-GG--CTCCCCATGACACAATTCAACTGGCTCCTCCTCCTGATCCCCAGTTCCGATG
*
1892979 CTATATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCT-C-CTC-CTTCACCAATGCAATT
127 CTATATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCACCCTCTTCACCAATGCAATT
1893041 GTCGTTTTTCTCGCTATTCGACTCCTCTGGA
192 GTCGTTTTTCTCGCTATTCGACTCCTCTGGA
1893072 ACTCCATCT
1 ACTCCATCT
1893081 ATGACGTCGT
Statistics
Matches: 220, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
222 93 0.42
223 35 0.16
224 1 0.00
225 91 0.41
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (222 bp):
ACTCCATCTTCGGAGTTAATAGCGGAAACGGGATCACCCCCAACAACATCCCTTGAATTTTGTTC
ATCAACAGGCTCCCCATGACACAATTCAACTGGCTCCTCCTCCTGATCCCCAGTTCCGATGCTAT
ATTCATCTTCAACTAAATAGGATTCGGATTTCACTTCTCCACCCTCTTCACCAATGCAATTGTCG
TTTTTCTCGCTATTCGACTCCTCTGGA
Found at i:1896488 original size:18 final size:19
Alignment explanation
Indices: 1896460--1896495 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1896450 TCAATGTTTC
1896460 TAAAAATTCATTTTTCCAA
1 TAAAAATTCATTTTTCCAA
1896479 TAAAAA-TCATTTTTCCA
1 TAAAAATTCATTTTTCCA
1896496 TACAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAATTCATTTTTCCAA
Found at i:1897680 original size:31 final size:31
Alignment explanation
Indices: 1897642--1897704 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1897632 TAGAAGGAAA
1897642 GTGAGCCTTCTAGCTTTAGCTACTTAATGGG
1 GTGAGCCTTCTAGCTTTAGCTACTTAATGGG
1897673 GTGAGCCTTCTAGCTTTAGCTACTTAATGGG
1 GTGAGCCTTCTAGCTTTAGCTACTTAATGGG
1897704 G
1 G
1897705 GTGGTTAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (31 bp):
GTGAGCCTTCTAGCTTTAGCTACTTAATGGG
Found at i:1897989 original size:2 final size:2
Alignment explanation
Indices: 1897977--1898008 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1897967 AGATTCGAAC
1897977 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
1898009 AATGTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1898436 original size:55 final size:56
Alignment explanation
Indices: 1898375--1898554 Score: 202
Period size: 56 Copynumber: 3.2 Consensus size: 56
1898365 TTTATTTTTT
* * * * *
1898375 TAGATATATTTGATTTTAGGG-TCTCTA-TTTTATGTTTCTTAATAGCAACAACTAA
1 TAGATATACTCGA-TTTAGGGACCTCTATTTTTATGCTTATTAATAGCAACAACTAA
* * *
1898430 TAGATATACTCGATTTCGGGACCTCTATTTTTATGCTTATTAATGGCAACAACTGA
1 TAGATATACTCGATTTAGGGACCTCTATTTTTATGCTTATTAATAGCAACAACTAA
* * ** * * *
1898486 TAGATATACTCGATTTCGGGACCCCTATTTTTATATTTATTAATATCAACAATTGA
1 TAGATATACTCGATTTAGGGACCTCTATTTTTATGCTTATTAATAGCAACAACTAA
1898542 TAGATATACTCGA
1 TAGATATACTCGA
1898555 CACTCCTATA
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
54 6 0.06
55 16 0.15
56 87 0.80
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (56 bp):
TAGATATACTCGATTTAGGGACCTCTATTTTTATGCTTATTAATAGCAACAACTAA
Found at i:1898489 original size:56 final size:56
Alignment explanation
Indices: 1898397--1898554 Score: 237
Period size: 56 Copynumber: 2.8 Consensus size: 56
1898387 ATTTTAGGGT
* *
1898397 CTCTA-TTTTATGTTTCTTAATAGCAACAACTAATAGATATACTCGATTTCGGGAC
1 CTCTATTTTTATGTTTATTAATAGCAACAACTGATAGATATACTCGATTTCGGGAC
* *
1898452 CTCTATTTTTATGCTTATTAATGGCAACAACTGATAGATATACTCGATTTCGGGAC
1 CTCTATTTTTATGTTTATTAATAGCAACAACTGATAGATATACTCGATTTCGGGAC
* * * *
1898508 CCCTATTTTTATATTTATTAATATCAACAATTGATAGATATACTCGA
1 CTCTATTTTTATGTTTATTAATAGCAACAACTGATAGATATACTCGA
1898555 CACTCCTATA
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 5 0.05
56 87 0.95
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (56 bp):
CTCTATTTTTATGTTTATTAATAGCAACAACTGATAGATATACTCGATTTCGGGAC
Found at i:1899169 original size:12 final size:13
Alignment explanation
Indices: 1899143--1899175 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1899133 ATTCGTATAT
*
1899143 AATAAAAAATTTA
1 AATAAAAAATCTA
1899156 AATAAAAAA-CTA
1 AATAAAAAATCTA
1899168 AATAAAAA
1 AATAAAAA
1899176 TCAGATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAAAAATCTA
Found at i:1902055 original size:38 final size:38
Alignment explanation
Indices: 1902004--1902079 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1901994 GTTTCACCTA
1902004 AGCTTACACGCGATGCAGGAAAACAATTTGACGATCGC
1 AGCTTACACGCGATGCAGGAAAACAATTTGACGATCGC
1902042 AGCTTACACGCGATGCAGGAAAACAATTTGACGATCGC
1 AGCTTACACGCGATGCAGGAAAACAATTTGACGATCGC
1902080 TCCTGTATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (38 bp):
AGCTTACACGCGATGCAGGAAAACAATTTGACGATCGC
Found at i:1904877 original size:22 final size:22
Alignment explanation
Indices: 1904836--1904878 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1904826 AAATTTTCGT
*
1904836 ATAATTTAATATTTTTTTATTA
1 ATAATTTAATATTTTATTATTA
1904858 ATAATTTAAT-TTTTAATTATT
1 ATAATTTAATATTTT-ATTATT
1904879 TTAAAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATAATTTAATATTTTATTATTA
Found at i:1905106 original size:3 final size:3
Alignment explanation
Indices: 1905098--1905134 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1905088 TTCGCATGAC
1905098 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1905135 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1905120 original size:17 final size:17
Alignment explanation
Indices: 1905098--1905130 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1905088 TTCGCATGAC
1905098 AATAATAATAATAATAT
1 AATAATAATAATAATAT
1905115 AATAATAATAATAATA
1 AATAATAATAATAATA
1905131 ATAAAGCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:1917325 original size:21 final size:21
Alignment explanation
Indices: 1917311--1917351 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1917301 ATTTAATATT
1917311 AATTTAT-AAATATTTGAATGA
1 AATTTATAAAATATTT-AATGA
1917332 AATTTATACAAATATTTAAT
1 AATTTATA-AAATATTTAAT
1917352 CGTTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
AATTTATAAAATATTTAATGA
Found at i:1922296 original size:13 final size:13
Alignment explanation
Indices: 1922278--1922303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1922268 CAGCAGCAGA
1922278 AAATCACTTTTCG
1 AAATCACTTTTCG
1922291 AAATCACTTTTCG
1 AAATCACTTTTCG
1922304 CCATTGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATCACTTTTCG
Found at i:1924942 original size:42 final size:42
Alignment explanation
Indices: 1924895--1924979 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1924885 CTATCTTGTC
1924895 ATGTTTTTATTATTTCTGTTATTACGGTTAGTTTTACCAATT
1 ATGTTTTTATTATTTCTGTTATTACGGTTAGTTTTACCAATT
1924937 ATGTTTTTATTATTTCTGTTATTACGGTTAGTTTTACCAATT
1 ATGTTTTTATTATTTCTGTTATTACGGTTAGTTTTACCAATT
1924979 A
1 A
1924980 CTAATAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.56
Consensus pattern (42 bp):
ATGTTTTTATTATTTCTGTTATTACGGTTAGTTTTACCAATT
Found at i:1926768 original size:19 final size:19
Alignment explanation
Indices: 1926744--1926799 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
1926734 AAAACTGAAA
1926744 TCGGTTTTTTTGGTTCGGT
1 TCGGTTTTTTTGGTTCGGT
**
1926763 TCGGTTTTTTT--AACGGT
1 TCGGTTTTTTTGGTTCGGT
* *
1926780 TCGGGTTTTTCGGTTCGGT
1 TCGGTTTTTTTGGTTCGGT
1926799 T
1 T
1926800 TTTCGGTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 13 0.45
19 16 0.55
ACGTcount: A:0.04, C:0.12, G:0.30, T:0.54
Consensus pattern (19 bp):
TCGGTTTTTTTGGTTCGGT
Found at i:1926779 original size:17 final size:15
Alignment explanation
Indices: 1926757--1926802 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
1926747 GTTTTTTTGG
1926757 TTCGGTTCGGTTTTT
1 TTCGGTTCGGTTTTT
*
1926772 TTAACGGTTCGG-GTTT
1 TT--CGGTTCGGTTTTT
1926788 TTCGGTTCGGTTTTT
1 TTCGGTTCGGTTTTT
1926803 CGGTTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 5 0.19
17 8 0.31
ACGTcount: A:0.04, C:0.13, G:0.28, T:0.54
Consensus pattern (15 bp):
TTCGGTTCGGTTTTT
Found at i:1931939 original size:23 final size:20
Alignment explanation
Indices: 1931900--1931943 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
1931890 TTCATATTAT
1931900 ATTTATATTTATTTTATGTA
1 ATTTATATTTATTTTATGTA
1931920 ATTTATCATATTATTGTTATGTA
1 ATTTAT-AT-TTATT-TTATGTA
1931943 A
1 A
1931944 ACGTTGAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 5 0.24
23 8 0.38
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTTATATTTATTTTATGTA
Found at i:1932566 original size:2 final size:2
Alignment explanation
Indices: 1932559--1932593 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1932549 AAAATTTCAC
1932559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1932594 ATGTGAACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1933514 original size:21 final size:22
Alignment explanation
Indices: 1933490--1933534 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1933480 GCTTACGAAC
*
1933490 AAATTTAAAAAAT-AATTTATT
1 AAATTTAAAAAATAAAATTATT
**
1933511 AAATTTTTAAAATAAAATTATT
1 AAATTTAAAAAATAAAATTATT
1933533 AA
1 AA
1933535 TAATATTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTTAAAAAATAAAATTATT
Found at i:1943139 original size:12 final size:12
Alignment explanation
Indices: 1943124--1943161 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1943114 GTTATTTAAA
*
1943124 CGGGTTTTGGGC
1 CGGGTATTGGGC
*
1943136 CGGGTATTGGGT
1 CGGGTATTGGGC
1943148 CGGGTATTGGGC
1 CGGGTATTGGGC
1943160 CG
1 CG
1943162 AGAATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.05, C:0.16, G:0.50, T:0.29
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:1943172 original size:2 final size:2
Alignment explanation
Indices: 1943165--1943268 Score: 74
Period size: 2 Copynumber: 54.5 Consensus size: 2
1943155 TGGGCCGAGA
* * *
1943165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA AT -T AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
1943206 AT AA AT AT AT AT TT TT TT AT TT AA AT -T AA AT TT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1943245 AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1943269 AATAATTATT
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
1 5 0.06
2 74 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1944344 original size:20 final size:20
Alignment explanation
Indices: 1944250--1944618 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1944240 GATTTTCCAT
* ** *
1944250 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1944270 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1944290 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1944310 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1944330 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1944350 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1944370 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1944390 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1944410 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1944430 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1944450 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1944470 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1944490 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1944510 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1944530 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1944550 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1944570 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1944590 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1944610 AATCACAAC
1 AATCGCAAC
1944619 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1945331 original size:24 final size:24
Alignment explanation
Indices: 1945292--1945338 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1945282 AAATTTGGTC
1945292 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1945316 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1945339 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1947862 original size:19 final size:19
Alignment explanation
Indices: 1947840--1948164 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
1947830 CGGAAAATAC
*
1947840 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1947859 AATC-CAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1947872 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1947892 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1947906 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1947925 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1947944 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1947958 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1947977 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1947996 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1948010 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1948029 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
* *
1948048 AATCGAAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1948067 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1948086 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1948105 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1948119 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1948138 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1948157 AATCGCAA
1 AATCGCAA
1948165 CGAGATAATC
Statistics
Matches: 267, Mismatches: 12, Indels: 54
0.80 0.04 0.16
Matches are distributed among these distances:
13 9 0.03
14 41 0.15
15 3 0.01
16 14 0.05
17 11 0.04
18 7 0.03
19 169 0.63
20 13 0.05
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1947891 original size:33 final size:34
Alignment explanation
Indices: 1947840--1948164 Score: 290
Period size: 33 Copynumber: 9.2 Consensus size: 34
1947830 CGGAAAATAC
*
1947840 AATCGCAACGCGAAATGAAAATC-CAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
* *
1947872 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACAATGAA
1947906 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
* * * *
1947944 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGCAACAATGAA
* *
1947977 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
*
1948010 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
* *
1948048 AATCGAAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
*
1948086 AATCGCAATGCGAAATGAAAATCGCAACGAA--AG
1 AATCGCAATGCGAAATGAAAATCGCAAC-AATGAA
1948119 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
1948157 AATCGCAA
1 AATCGCAA
1948165 CGAGATAATC
Statistics
Matches: 244, Mismatches: 26, Indels: 40
0.79 0.08 0.13
Matches are distributed among these distances:
31 1 0.00
32 16 0.07
33 105 0.43
34 18 0.07
35 6 0.02
36 3 0.01
37 2 0.01
38 86 0.35
39 6 0.02
40 1 0.00
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGAA
Found at i:1948090 original size:161 final size:157
Alignment explanation
Indices: 1947867--1948186 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
1947857 AAAATCCAAC
* *
1947867 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGAAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
1947932 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1947997 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
1948024 ATGAAAATCGCAATGC-GAAATTAAAATCGAAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCG-AA-ACG--A-GAAAATCGCAATGCGAAATGAAAA
1948088 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
1948153 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
1948185 AT
1 AT
1948187 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 12 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGAAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1948202 original size:52 final size:52
Alignment explanation
Indices: 1947867--1948186 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
1947857 AAAATCCAAC
1947867 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1947920 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1947972 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * *
1948024 ATGAAAATCGCAATGCGAAATTAAAATCGAAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCG-CA-ACG--A-GAGAATCGCAATGCGAA
*
1948081 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1948133 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1948185 AT
1 AT
1948187 TATAAACGCA
Statistics
Matches: 253, Mismatches: 9, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 183 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 44 0.17
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1948302 original size:19 final size:19
Alignment explanation
Indices: 1948193--1948294 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1948183 AAATTATAAA
1948193 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1948212 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1948232 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1948248 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1948265 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1948284 CGCATTGCGAT
1 CGCATTGCGAT
1948295 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1948420 original size:14 final size:14
Alignment explanation
Indices: 1948401--1948437 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1948391 CATCAATTAC
1948401 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1948415 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1948429 ACAAATCAA
1 ACAAATCAA
1948438 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1948449 original size:12 final size:12
Alignment explanation
Indices: 1948432--1948504 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
1948422 ATCTTTTACA
1948432 AATCAATTAAAC
1 AATCAATTAAAC
*
1948444 AATCAA--AAATTG
1 AATCAATTAAA--C
**
1948456 AATCAACTTTTAC
1 AATCAA-TTAAAC
1948469 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
1948482 AATCAA-AAAAC
1 AATCAATTAAAC
1948493 AATCAATTAAAC
1 AATCAATTAAAC
1948505 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:1948466 original size:38 final size:38
Alignment explanation
Indices: 1948418--1948490 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1948408 AACTTTTACA
*
1948418 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
1948456 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1948491 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:1950348 original size:19 final size:19
Alignment explanation
Indices: 1950308--1950442 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1950298 TAGTTTACTT
* *
1950308 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1950328 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1950347 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1950366 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
1950380 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1950399 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1950413 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1950432 TCGCAATGCGA
1 TCGCAACGCGA
1950443 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1950383 original size:14 final size:14
Alignment explanation
Indices: 1950364--1950420 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1950354 GCGAAATGAA
*
1950364 AATCGCAACGACAG
1 AATCGCAACGAAAG
1950378 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
1950395 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1950411 AATCGCAACG
1 AATCGCAACG
1950421 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1950387 original size:33 final size:33
Alignment explanation
Indices: 1950345--1950437 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
1950335 GCGAAACCAA
*
1950345 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1950378 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1950411 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1950438 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1950434 original size:52 final size:54
Alignment explanation
Indices: 1950308--1950442 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
1950298 TAGTTTACTT
*
1950308 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
1950366 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
1950413 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
1950443 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:1950460 original size:19 final size:19
Alignment explanation
Indices: 1950438--1950566 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1950428 AAAATCGCAA
1950438 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1950457 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1950471 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1950490 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1950504 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1950523 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1950542 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1950562 TGCGA
1 TGCGA
1950567 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1950480 original size:33 final size:33
Alignment explanation
Indices: 1950438--1950529 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1950428 AAAATCGCAA
1950438 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1950471 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1950504 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1950530 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1950729 original size:93 final size:93
Alignment explanation
Indices: 1950609--1950988 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
1950599 TTGAATGGAT
1950609 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1950674 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1950702 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1950767 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1950795 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1950859 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1950887 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1950952 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1950980 AAATTTACT
1 AAATTTACT
1950989 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1950922 original size:185 final size:186
Alignment explanation
Indices: 1950609--1950988 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
1950599 TTGAATGGAT
1950609 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1950674 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1950739 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1950795 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1950859 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1950924 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1950980 AAATTTACT
1 AAATTTACT
1950989 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1952714 original size:14 final size:14
Alignment explanation
Indices: 1952695--1952784 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1952685 TTGAAATGAA
1952695 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1952709 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1952726 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1952742 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1952761 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1952775 AATCGCAACG
1 AATCGCAACG
1952785 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1952732 original size:33 final size:33
Alignment explanation
Indices: 1952687--1952801 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1952677 TCTTTTGGTT
1952687 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1952720 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1952753 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1952786 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1952802 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1952733 original size:19 final size:18
Alignment explanation
Indices: 1952694--1952806 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1952684 GTTGAAATGA
1952694 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1952709 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1952726 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1952742 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1952759 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1952775 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1952792 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1952807 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1952837 original size:14 final size:14
Alignment explanation
Indices: 1952818--1952872 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1952808 TTTGGTTTCG
1952818 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1952832 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1952851 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1952865 CGTTGCGA
1 CGTTGCGA
1952873 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1952883 original size:20 final size:20
Alignment explanation
Indices: 1952858--1952913 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1952848 TCGCGTTGCG
1952858 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
***
1952878 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
1952898 ATTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGAC
1952914 TCTTCTGCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:1953034 original size:33 final size:33
Alignment explanation
Indices: 1952992--1953062 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1952982 AATACTAACT
*
1952992 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1953025 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1953058 TGAAA
1 TGAAA
1953063 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1953295 original size:22 final size:22
Alignment explanation
Indices: 1953243--1953297 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1953233 TGGTTGTGAG
**
1953243 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1953265 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1953287 GGATTTCTTCG
1 GGATTTCTTCG
1953298 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1953468 original size:20 final size:20
Alignment explanation
Indices: 1953443--1953636 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1953433 CTTTAAATAT
1953443 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1953463 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1953485 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1953504 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1953524 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1953544 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1953564 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1953584 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1953604 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1953624 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1953637 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Done.