Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 30
Found at i:1328869 original size:15 final size:14
Alignment explanation
Indices: 1328851--1328885 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1328841 TTACTTTTTA
1328851 ATTTTTTTAAAATAT
1 ATTTTTTT-AAATAT
1328866 ATTTTTTTAAATAT
1 ATTTTTTTAAATAT
*
1328880 GTTTTT
1 ATTTTT
1328886 AGGGAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
ATTTTTTTAAATAT
Found at i:1337902 original size:22 final size:22
Alignment explanation
Indices: 1337867--1337939 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
1337857 CTGAGTACCA
*
1337867 TATGAGATTTGTCCCGAATGACC
1 TATGA-ATATGTCCCGAATGACC
*
1337890 TATGAATATGTCCCGAAGGACC
1 TATGAATATGTCCCGAATGACC
* *
1337912 TATGAGTATGTCCCGAATGACA
1 TATGAATATGTCCCGAATGACC
1337934 TATGAA
1 TATGAA
1337940 ACCCTCGACT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 39 0.89
23 5 0.11
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (22 bp):
TATGAATATGTCCCGAATGACC
Found at i:1338549 original size:19 final size:19
Alignment explanation
Indices: 1338525--1338577 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1338515 CCTTAACATG
*
1338525 TGTATCGATACACTACCTA
1 TGTATCGATACACAACCTA
1338544 TGTATCGATACACAACCTA
1 TGTATCGATACACAACCTA
1338563 TGTATCGATACACAA
1 TGTATCGATACACAA
1338578 ATTACATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAACCTA
Found at i:1356836 original size:20 final size:20
Alignment explanation
Indices: 1356810--1356944 Score: 173
Period size: 20 Copynumber: 6.7 Consensus size: 20
1356800 AGTTTCCAGA
*
1356810 TTCGCAATGCGATACTGACT
1 TTCGCAACGCGATACTGACT
* * *
1356830 ATCGCAACGCGATAGT-ACAAA
1 TTCGCAACGCGATACTGAC--T
*
1356851 ATCGCAACGCGATACTGACT
1 TTCGCAACGCGATACTGACT
*
1356871 TTCGCAACGTGATACTGACT
1 TTCGCAACGCGATACTGACT
*
1356891 TTCGCAACGCGATACTTACT
1 TTCGCAACGCGATACTGACT
1356911 TTCGCAACGCGATACTGACT
1 TTCGCAACGCGATACTGACT
*
1356931 TTCGCAACGAGATA
1 TTCGCAACGCGATA
1356945 ATACATAATC
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCGATACTGACT
Found at i:1357159 original size:22 final size:22
Alignment explanation
Indices: 1357131--1357174 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1357121 CACTCTCTCA
1357131 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1357153 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1357175 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1357486 original size:20 final size:20
Alignment explanation
Indices: 1357437--1357495 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1357427 TTTATTCTCT
* **
1357437 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1357457 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
1357477 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1357496 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1357686 original size:25 final size:24
Alignment explanation
Indices: 1357632--1357686 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1357622 TGTTTATTAT
* *
1357632 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1357656 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1357682 TGTTT
1 TGTTT
1357687 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1359003 original size:20 final size:20
Alignment explanation
Indices: 1358953--1359019 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1358943 TAGTTTACTT
*
1358953 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
1358973 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
1358993 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
1359012 TCGCAACG
1 TCGCAACG
1359020 ATAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1359014 original size:19 final size:19
Alignment explanation
Indices: 1358992--1359088 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
1358982 GAAAATGGCT
1358992 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1359011 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
1359025 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1359044 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1359058 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1359077 ATCGCAATGCGA
1 ATCGCAATGCGA
1359089 TTTGTGTTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.31
15 3 0.05
16 4 0.06
17 4 0.06
18 3 0.05
19 31 0.48
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1359027 original size:14 final size:14
Alignment explanation
Indices: 1359008--1359066 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1358998 ATGCGAAATG
1359008 AAAATCGCAACGAT
1 AAAATCGCAACGAT
1359022 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
*
1359040 GAAAATCGCAACGAC
1 -AAAATCGCAACGAT
1359055 AAAATCGCAACG
1 AAAATCGCAACG
1359067 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 22 0.56
15 1 0.03
16 2 0.05
17 2 0.05
18 2 0.05
19 10 0.26
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:1359034 original size:33 final size:33
Alignment explanation
Indices: 1358992--1359083 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
1358982 GAAAATGGCT
*
1358992 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1359025 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1359058 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1359084 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1359100 original size:19 final size:19
Alignment explanation
Indices: 1359095--1359160 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
1359085 GCGATTTGTG
*
1359095 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1359114 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
1359130 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1359147 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1359161 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 4 0.10
17 4 0.10
18 3 0.08
19 19 0.49
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1359179 original size:20 final size:20
Alignment explanation
Indices: 1359145--1359219 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
1359135 TTGCGATTTT
* *
1359145 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGA
1359164 CATTTCCGCGTTGCGATAGA
1 CATTTCCGCGTTGCGATAGA
1359184 CATTTCCGCGTTGCGATA-A
1 CATTTCCGCGTTGCGATAGA
*
1359203 TCATTTTCGCGTTGCGA
1 -CATTTCCGCGTTGCGA
1359220 AAGTAAGTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.12
20 45 0.88
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGA
Found at i:1359230 original size:20 final size:20
Alignment explanation
Indices: 1359207--1359245 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1359197 CGATAATCAT
*
1359207 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCATTGCGAAAGTAAG
*
1359227 TTTCGTATTGCGAAAGTAA
1 TTTCGCATTGCGAAAGTAA
1359246 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTCGCATTGCGAAAGTAAG
Found at i:1359647 original size:21 final size:20
Alignment explanation
Indices: 1359587--1359647 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
1359577 GACTCACCTG
*
1359587 TCATCCCTTAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* **
1359607 CCAATCGTTCAAGAAG-CCCCT
1 TC-ATCCCTCAAG-AGTCCCCT
1359628 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
1359648 CCCACCGTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.25, C:0.41, G:0.11, T:0.23
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:1359674 original size:41 final size:42
Alignment explanation
Indices: 1359584--1359674 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
1359574 CCCGACTCAC
* * *
1359584 CTGTCATCCCTTAAGAGTCCCCTCCAATCGTTCAAGAAGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAAGCCA
* * *
1359626 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAAGCCA
1359667 CTGTCATC
1 CTGTCATC
1359675 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 22 0.52
42 20 0.48
ACGTcount: A:0.23, C:0.41, G:0.14, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAAGCCA
Found at i:1361115 original size:14 final size:14
Alignment explanation
Indices: 1361081--1361119 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1361071 TTGATTGTTT
1361081 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1361095 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1361109 TGTTGATTTGT
1 AATTGATTTGT
1361120 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1361287 original size:19 final size:19
Alignment explanation
Indices: 1361259--1361342 Score: 150
Period size: 19 Copynumber: 4.4 Consensus size: 19
1361249 GCAACGAGAG
*
1361259 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1361278 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1361297 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1361316 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1361335 AATCGCAA
1 AATCGCAA
1361343 CTAGAAAATC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 62 1.00
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1361410 original size:20 final size:20
Alignment explanation
Indices: 1361387--1361455 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1361377 GCGATTTTAT
1361387 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1361407 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
* *
1361427 CGTTGCGATAGTCATTTTCC
1 CGTTGCGATAGCCATTTTCG
*
1361447 CGTCGCGAT
1 CGTTGCGAT
1361456 TTCCCCGTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.14, C:0.26, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:1362155 original size:20 final size:20
Alignment explanation
Indices: 1362001--1362154 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
1361991 GATTCTGTAT
* *
1362001 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
1362021 AATCTCGTTGCGAAAGTCA-
1 TATCGCGTTGCGAAAGTCAG
1362040 TAATCGCGTTGCGAAAGTCAG
1 T-ATCGCGTTGCGAAAGTCAG
* *
1362061 AATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1362081 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
1362101 TATCGTGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1362122 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1362142 TATCGCATTGCGA
1 TATCGCGTTGCGA
1362155 TTTTCCGAAT
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.03
20 95 0.84
21 13 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1362169 original size:41 final size:41
Alignment explanation
Indices: 1361981--1362176 Score: 134
Period size: 40 Copynumber: 4.8 Consensus size: 41
1361971 AACTTTGAAA
* * * *
1361981 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTCAGT
* * ** * * *
1362022 ATCTCGTTGCGA--AAGTCATAATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTAAT-ATCGCGTTGCGATAGTCAGT
* *** * *
1362062 ATCGCGTTGC-A-AAAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-AATATCGCGTTGCGATAGTCAGT
** *
1362102 ATCGTGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTCAGT
1362143 ATCGCATTGCGATTTTCCG-AAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT--GTAATATCGCGTTGCGAT
1362177 TTACTTATTC
Statistics
Matches: 127, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
39 4 0.03
40 59 0.46
41 59 0.46
42 4 0.03
43 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTCAGT
Found at i:1362237 original size:21 final size:22
Alignment explanation
Indices: 1362185--1362237 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1362175 ATTTACTTAT
1362185 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1362206 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1362227 TCGCATTGCGA
1 TCGCATTGCGA
1362238 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1367686 original size:22 final size:23
Alignment explanation
Indices: 1367643--1367696 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
1367633 TACAATAATC
*
1367643 AATG-GTATGTATTCTATAATAT
1 AATGTGTATGTATTATATAATAT
* *
1367665 TATGTGTAT-TATTATATTATAT
1 AATGTGTATGTATTATATAATAT
1367687 AATGT-TATGT
1 AATGTGTATGT
1367697 TATATACTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.73
23 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (23 bp):
AATGTGTATGTATTATATAATAT
Found at i:1368514 original size:39 final size:39
Alignment explanation
Indices: 1368470--1368620 Score: 239
Period size: 39 Copynumber: 3.9 Consensus size: 39
1368460 CTTCGGTTTG
* *
1368470 TGCTCCTGTAACGCCTACTCTCATCGATGTCCCGGCTTC
1 TGCTCCTGTAACGCCTACTGTCATCAATGTCCCGGCTTC
*
1368509 TGCTCCTGTAACGCCCACTGTCATCAATGTCCCGGCTTC
1 TGCTCCTGTAACGCCTACTGTCATCAATGTCCCGGCTTC
*
1368548 TGCTCCTGTAACGCCTACTGTCATCGATGTCCCGGCTTC
1 TGCTCCTGTAACGCCTACTGTCATCAATGTCCCGGCTTC
* * *
1368587 TGCTCCTGCAACGTCTACTGTCATCAATATCCCG
1 TGCTCCTGTAACGCCTACTGTCATCAATGTCCCG
1368621 TTTATCCGTG
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 103 1.00
ACGTcount: A:0.15, C:0.37, G:0.18, T:0.30
Consensus pattern (39 bp):
TGCTCCTGTAACGCCTACTGTCATCAATGTCCCGGCTTC
Found at i:1369568 original size:17 final size:18
Alignment explanation
Indices: 1369539--1369579 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
1369529 AAGACAAAAA
*
1369539 AAAAGGAAAAAAACATAT
1 AAAAGGAAAAAAACAGAT
1369557 AAAAGG-AAAAAACAGAT
1 AAAAGGAAAAAAACAGAT
1369574 AAAAGG
1 AAAAGG
1369580 TTACATTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGGAAAAAAACAGAT
Found at i:1371052 original size:16 final size:17
Alignment explanation
Indices: 1371017--1371054 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1371007 ATGATGCTTA
1371017 GGAAAAAAAACTTGATG
1 GGAAAAAAAACTTGATG
1371034 GGAACAAAAAA-TTGA-G
1 GGAA-AAAAAACTTGATG
1371050 GGAAA
1 GGAAA
1371055 TAGAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 5 0.25
17 8 0.40
18 6 0.30
ACGTcount: A:0.55, C:0.05, G:0.26, T:0.13
Consensus pattern (17 bp):
GGAAAAAAAACTTGATG
Found at i:1377454 original size:21 final size:19
Alignment explanation
Indices: 1377430--1377468 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1377420 TCAATTGTAT
1377430 ATCATCAGAAAACAATATTTA
1 ATCAT-AGAAAACAA-ATTTA
*
1377451 ATCATTGAAAACAAATTT
1 ATCATAGAAAACAAATTT
1377469 GAATTTTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (19 bp):
ATCATAGAAAACAAATTTA
Found at i:1378448 original size:19 final size:21
Alignment explanation
Indices: 1378420--1378468 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1378410 GTAAGAATGA
* *
1378420 TATCGGTACC-TATGGGG-AG
1 TATCGATACCATAAGGGGTAG
1378439 TATCGATACCATAAGGGGTAG
1 TATCGATACCATAAGGGGTAG
1378460 TATCGATAC
1 TATCGATAC
1378469 TATTACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 6 0.23
21 11 0.42
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (21 bp):
TATCGATACCATAAGGGGTAG
Found at i:1390396 original size:19 final size:19
Alignment explanation
Indices: 1390354--1390393 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
1390344 AAAAGAGAGT
1390354 GAATTTCGTGCTTAAAATG
1 GAATTTCGTGCTTAAAATG
1390373 GAATTT-GTGCTTAAAATG
1 GAATTTCGTGCTTAAAATG
1390391 GAA
1 GAA
1390394 ATTCTGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (19 bp):
GAATTTCGTGCTTAAAATG
Found at i:1394850 original size:29 final size:30
Alignment explanation
Indices: 1394810--1394872 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1394800 CTATAATGTA
*
1394810 AAAATTTAAAAGTTTAGGG-CT-AAAGTAT
1 AAAATTTAAAAGTTTAGGGACTAAAAATAT
*
1394838 AAAATTATGAAAGTTTAGGGACTAAAAATAT
1 AAAATT-TAAAAGTTTAGGGACTAAAAATAT
1394869 AAAA
1 AAAA
1394873 AATCAAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 12 0.40
30 2 0.07
31 10 0.33
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (30 bp):
AAAATTTAAAAGTTTAGGGACTAAAAATAT
Found at i:1395316 original size:17 final size:18
Alignment explanation
Indices: 1395287--1395327 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1395277 TCATTAAGGG
*
1395287 CAATTTAGAATTTTGGAT
1 CAATTTAGAATTTTGAAT
*
1395305 CAATTT-GAATTTTTAAT
1 CAATTTAGAATTTTGAAT
1395322 CAATTT
1 CAATTT
1395328 TTTTAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (18 bp):
CAATTTAGAATTTTGAAT
Found at i:1397173 original size:16 final size:17
Alignment explanation
Indices: 1397152--1397184 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1397142 ATATAATATG
*
1397152 ATTTATTTTA-TATGTT
1 ATTTATCTTATTATGTT
1397168 ATTTATCTTATTATGTT
1 ATTTATCTTATTATGTT
1397185 GCCTCACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTATCTTATTATGTT
Found at i:1405517 original size:20 final size:20
Alignment explanation
Indices: 1405488--1405527 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1405478 AATAAGGTTC
*
1405488 AAATGTTCATTGTAGTTGGT
1 AAATGCTCATTGTAGTTGGT
1405508 AAATGCTCATTGTAGTTGGT
1 AAATGCTCATTGTAGTTGGT
1405528 GTGCCCTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (20 bp):
AAATGCTCATTGTAGTTGGT
Found at i:1407501 original size:20 final size:20
Alignment explanation
Indices: 1407476--1407515 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1407466 CAGAAGAATA
1407476 CTTTATAACCCTTTTTCATT
1 CTTTATAACCCTTTTTCATT
1407496 CTTTATAACCCTTTTTCATT
1 CTTTATAACCCTTTTTCATT
1407516 TGGGGTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.00, T:0.55
Consensus pattern (20 bp):
CTTTATAACCCTTTTTCATT
Found at i:1414467 original size:18 final size:19
Alignment explanation
Indices: 1414444--1414483 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1414434 AGTATAGTAC
1414444 AATATAATTATTT-TTAAA
1 AATATAATTATTTCTTAAA
*
1414462 AATATAATTTTTTCTTAAA
1 AATATAATTATTTCTTAAA
1414481 AAT
1 AAT
1414484 GTTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATAATTATTTCTTAAA
Found at i:1426650 original size:18 final size:18
Alignment explanation
Indices: 1426629--1426663 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1426619 GACTTTGACC
*
1426629 TGACCGTTGACCTGCCCT
1 TGACCGTTGACATGCCCT
1426647 TGACCGTTGACATGCCC
1 TGACCGTTGACATGCCC
1426664 GTTAACTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.37, G:0.23, T:0.26
Consensus pattern (18 bp):
TGACCGTTGACATGCCCT
Found at i:1428469 original size:29 final size:30
Alignment explanation
Indices: 1428424--1428483 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1428414 TGGCAGAGTT
1428424 AAAAATTATTTTGGGGTGTCAAATCTAGAG
1 AAAAATTATTTTGGGGTGTCAAATCTAGAG
* *
1428454 AAAATTTATTTT-GGGTGTCAGATCTAGAG
1 AAAAATTATTTTGGGGTGTCAAATCTAGAG
1428483 A
1 A
1428484 TTGTATGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAAATTATTTTGGGGTGTCAAATCTAGAG
Found at i:1435531 original size:25 final size:26
Alignment explanation
Indices: 1435494--1435598 Score: 69
Period size: 25 Copynumber: 4.1 Consensus size: 26
1435484 CATCTTAGTG
* * *
1435494 TATAAATACTTAAATTCATAATATTT
1 TATATATACTTAAATTAAAAATATTT
*
1435520 TATATATA-TTAACTTAAAAATATTT
1 TATATATACTTAAATTAAAAATATTT
*
1435545 T-TATATTAACTT--ATTAAATATATTT
1 TATATA-T-ACTTAAATTAAAAATATTT
* *
1435570 TAT-TAGTAACAT-AATTTAAAATATTT
1 TATATA-T-ACTTAAATTAAAAATATTT
1435596 TAT
1 TAT
1435599 TTTTATTTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
24 4 0.06
25 35 0.55
26 23 0.36
27 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.50
Consensus pattern (26 bp):
TATATATACTTAAATTAAAAATATTT
Found at i:1435552 original size:22 final size:24
Alignment explanation
Indices: 1435524--1435572 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
1435514 ATATTTTATA
1435524 TATATTAACTTA-AAAATAT-TTT
1 TATATTAACTTATAAAATATATTT
*
1435546 TATATTAACTTATTAAATATATTT
1 TATATTAACTTATAAAATATATTT
1435570 TAT
1 TAT
1435573 TAGTAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.50
23 6 0.25
24 6 0.25
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTAACTTATAAAATATATTT
Found at i:1435621 original size:2 final size:2
Alignment explanation
Indices: 1435614--1435649 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1435604 TTTTCATTAA
1435614 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
1435650 TTTATGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1435820 original size:31 final size:31
Alignment explanation
Indices: 1435785--1435852 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1435775 CAATTACCAC
1435785 ATCTTAATTAAATAAAAACAAAAGTGATCAT
1 ATCTTAATTAAATAAAAACAAAAGTGATCAT
*
1435816 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACAAAAGTGATCAT
1435847 ATCTTA
1 ATCTTA
1435853 TGTTTAGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGATCAT
Found at i:1436045 original size:31 final size:32
Alignment explanation
Indices: 1435971--1436061 Score: 139
Period size: 31 Copynumber: 2.8 Consensus size: 32
1435961 TTAAAAATTT
*
1435971 AGGTACTAAAATGAAACAAAAAAGTTAACAATG
1 AGGTACTAAAATGAAAC-AAAAAGTAAACAATG
* *
1436004 AGATACTAAAATGAAACAAAAAGTAAACACTG
1 AGGTACTAAAATGAAACAAAAAGTAAACAATG
1436036 -GGTACTAAAATGAAACAAAAAGTAAA
1 AGGTACTAAAATGAAACAAAAAGTAAA
1436062 TGTTATGTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 25 0.46
32 13 0.24
33 16 0.30
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.16
Consensus pattern (32 bp):
AGGTACTAAAATGAAACAAAAAGTAAACAATG
Found at i:1448844 original size:12 final size:12
Alignment explanation
Indices: 1448822--1448849 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1448812 TTTTTTTTCG
1448822 TTTTATTTTTAA
1 TTTTATTTTTAA
1448834 TTTTATTTTTAA
1 TTTTATTTTTAA
1448846 TTTT
1 TTTT
1448850 TTTACTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:1450353 original size:17 final size:17
Alignment explanation
Indices: 1450331--1450402 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
1450321 AATTCAGTGT
*
1450331 TAGTTTAATAAATTAAC
1 TAGTTTAATAAATGAAC
* * *
1450348 TAGTTTGATGAATGGAC
1 TAGTTTAATAAATGAAC
*
1450365 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
1450382 TAATTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
1450400 TAG
1 TAG
1450403 ATGCATGAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
17 29 0.67
18 14 0.33
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1452654 original size:21 final size:22
Alignment explanation
Indices: 1452612--1452654 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1452602 AATTATAAAT
* * *
1452612 TTTAAATAATAATTAGTCAAAA
1 TTTAAATAAAAATTAATAAAAA
1452634 TTTAAA-AAAAATTAATAAAAA
1 TTTAAATAAAAATTAATAAAAA
1452655 AGTTAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTAAATAAAAATTAATAAAAA
Found at i:1453096 original size:21 final size:21
Alignment explanation
Indices: 1453070--1453209 Score: 151
Period size: 21 Copynumber: 6.8 Consensus size: 21
1453060 CGTGAACTTC
1453070 GACTATCGCAATGCGAATTTG
1 GACTATCGCAATGCGAATTTG
*
1453091 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCGAATTTG
*
1453112 GACTATCGCAATGCGAATATG
1 GACTATCGCAATGCGAATTTG
* * * * *
1453133 TA-AATCACAATGCG-ATAGTC
1 GACTATCGCAATGCGAAT-TTG
*
1453153 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCGAATTTG
*
1453174 GACTATCGCAATGCGAATATG
1 GACTATCGCAATGCGAATTTG
* *
1453195 TA-AATCGCAATGCGA
1 GACTATCGCAATGCGA
1453210 TAGTCGAAGT
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.02
20 24 0.24
21 71 0.72
22 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (21 bp):
GACTATCGCAATGCGAATTTG
Found at i:1453202 original size:41 final size:41
Alignment explanation
Indices: 1453071--1453209 Score: 144
Period size: 41 Copynumber: 3.4 Consensus size: 41
1453061 GTGAACTTCG
*
1453071 ACTATCGCAATGCGAATTTGGACTATCGCAATGCGAACT-TGG
1 ACTATCGCAATGCGAA-TTGGACTATCGCAATGCGAA-TATGT
* * *
1453113 ACTATCGCAATGCGAATATGTA-AATCACAATGCG-ATA-GT
1 ACTATCGCAATGCGAAT-TGGACTATCGCAATGCGAATATGT
1453152 CGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGT
1 --ACTATCGCAATGCGAA-TTGGACTATCGCAATGCGAATATGT
*
1453196 A-AATCGCAATGCGA
1 ACTATCGCAATGCGA
1453210 TAGTCGAAGT
Statistics
Matches: 81, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 42 0.52
42 31 0.38
43 3 0.04
44 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
ACTATCGCAATGCGAATTGGACTATCGCAATGCGAATATGT
Found at i:1453230 original size:62 final size:62
Alignment explanation
Indices: 1453091--1453216 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
1453081 TGCGAATTTG
1453091 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCACAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCACAATGCGATAGTC
*
1453153 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCACAATGCGATAGTC
1453215 GA
1 GA
1453217 AGTTCGCATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (62 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCACAATGCGATAGTC
Found at i:1453245 original size:62 final size:63
Alignment explanation
Indices: 1453113--1453301 Score: 174
Period size: 62 Copynumber: 3.0 Consensus size: 63
1453103 GCGAACTTGG
* * * * ***
1453113 ACTATCGCAATGCGAATATGTAAATCACAATGCGATAGTCG-ACTATCGCAATGCGA-ACTTGG
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT-TCGCATTGCGATAGTCCA
1453175 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCA
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCA
* * ** * *
1453238 AGT-TCGCATTAG-G-ATAATCCAAGTTCGCATTGCGATAGTTC-AAGTTCGCATTGCGATAGTC
1 ACTATCGCAAT-GCGAAT-ATGTAA-ATCGCAATGCGATAG-TCGAAGTTCGCATTGCGATAGTC
1453299 CA
62 CA
1453301 A
1 A
1453302 ATTCACGTTG
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
61 2 0.02
62 61 0.56
63 43 0.40
64 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (63 bp):
ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCA
Found at i:1453323 original size:21 final size:21
Alignment explanation
Indices: 1453199--1453322 Score: 169
Period size: 21 Copynumber: 5.9 Consensus size: 21
1453189 AATATGTAAA
* *
1453199 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
1453220 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
1453241 TCGCATTAG-GATAATCCAAGT
1 TCGCATT-GCGATAGTCCAAGT
*
1453262 TCGCATTGCGATAGTTCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
1453283 TCGCATTGCGATAGTCCAAAT
1 TCGCATTGCGATAGTCCAAGT
* *
1453304 TCACGTTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
1453323 AATCGCAACG
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
20 1 0.01
21 90 0.98
22 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:1453423 original size:6 final size:6
Alignment explanation
Indices: 1453412--1453456 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1453402 GACACGTATT
* * *
1453412 ACCACG ACCACG ATCACG ACCACG ACCACG ATCACG ACCAAG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1453457 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.36, C:0.44, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:1453435 original size:18 final size:18
Alignment explanation
Indices: 1453412--1453456 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1453402 GACACGTATT
1453412 ACCACGACCACGATCACG
1 ACCACGACCACGATCACG
1453430 ACCACGACCACGATCACG
1 ACCACGACCACGATCACG
*
1453448 ACCAAGACC
1 ACCACGACC
1453457 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.44, G:0.16, T:0.04
Consensus pattern (18 bp):
ACCACGACCACGATCACG
Found at i:1453620 original size:21 final size:21
Alignment explanation
Indices: 1453571--1453629 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
1453561 CCAAGCCTTC
1453571 GACTATCGCAA--CGAACTTG
1 GACTATCGCAATGCGAACTTG
*
1453590 GAATAAATCGCAATGCGAACTTG
1 GACT--ATCGCAATGCGAACTTG
1453613 GACTATCGCAATGCGAA
1 GACTATCGCAATGCGAA
1453630 TATGTAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.09
21 20 0.59
23 11 0.32
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (21 bp):
GACTATCGCAATGCGAACTTG
Found at i:1453642 original size:20 final size:20
Alignment explanation
Indices: 1453593--1453648 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1453583 GAACTTGGAA
1453593 TAAATCGCAATGCGAACTTG
1 TAAATCGCAATGCGAACTTG
* *
1453613 GACTATCGCAATGCGAA-TATG
1 TA-AATCGCAATGCGAACT-TG
1453634 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
1453649 TAGTCGAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGAACTTG
Found at i:1454462 original size:4 final size:4
Alignment explanation
Indices: 1454453--1454554 Score: 78
Period size: 4 Copynumber: 24.0 Consensus size: 4
1454443 GGAGGTAATT
* * * *
1454453 TTTA TTTA TTTA CTCTA TAGTA TTTA TTTA TTTA TTTCGA ATAA TTTA
1 TTTA TTTA TTTA -TTTA T-TTA TTTA TTTA TTTA TTT--A TTTA TTTA
* * **
1454501 TTTA TTTA TGTA TTCA TTTA TTTCA AATA CTTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA -TTTA TTTA TTTA TTTA TTTA
1454551 TTTA
1 TTTA
1454555 AAAGGGTATG
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
4 65 0.84
5 10 0.13
6 2 0.03
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (4 bp):
TTTA
Found at i:1454499 original size:18 final size:17
Alignment explanation
Indices: 1454478--1454554 Score: 61
Period size: 18 Copynumber: 4.5 Consensus size: 17
1454468 TATAGTATTT
1454478 ATTTATTTATTTCGAATA
1 ATTTATTTATTTC-AATA
*
1454496 ATTTATTTATTT--ATGT
1 ATTTATTTATTTCAAT-A
*
1454512 ATTCATTTATTTCAAATA
1 ATTTATTTATTTC-AATA
* * *
1454530 CTTTATTTATTT-ATTT
1 ATTTATTTATTTCAATA
1454546 ATTTATTTA
1 ATTTATTTA
1454555 AAAGGGTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
15 2 0.04
16 21 0.45
18 22 0.47
19 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTATTTATTTCAATA
Found at i:1454535 original size:34 final size:34
Alignment explanation
Indices: 1454477--1454554 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
1454467 CTATAGTATT
*
1454477 TATTTATTTATTTCGAATAATTTATTTATTTATG
1 TATTTATTTATTTCAAATAATTTATTTATTTATG
* * *
1454511 TATTCATTTATTTCAAATACTTTATTTATTTATT
1 TATTTATTTATTTCAAATAATTTATTTATTTATG
1454545 TATTTATTTA
1 TATTTATTTA
1454555 AAAGGGTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (34 bp):
TATTTATTTATTTCAAATAATTTATTTATTTATG
Found at i:1456300 original size:13 final size:14
Alignment explanation
Indices: 1456277--1456313 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
1456267 AATCATGTGC
1456277 ACATGATATTTTAA
1 ACATGATATTTTAA
1456291 ACAT-ATATTTTAA
1 ACATGATATTTTAA
1456304 ACATGTATAT
1 ACATG-ATAT
1456314 GGCACACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.62
14 4 0.19
15 4 0.19
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (14 bp):
ACATGATATTTTAA
Found at i:1458843 original size:27 final size:27
Alignment explanation
Indices: 1458813--1458865 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1458803 TCACCTATTC
1458813 GACTCAGTCAGCATTTCAACATATGAT
1 GACTCAGTCAGCATTTCAACATATGAT
* * * *
1458840 GACTTATTCATCATTTCAGCATATGA
1 GACTCAGTCAGCATTTCAACATATGA
1458866 CACCTCCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (27 bp):
GACTCAGTCAGCATTTCAACATATGAT
Found at i:1459183 original size:358 final size:358
Alignment explanation
Indices: 1458521--1459242 Score: 1381
Period size: 358 Copynumber: 2.0 Consensus size: 358
1458511 GTGGATGATG
*
1458521 AGGTCTCGTAGGTAGGTCATTTATGAACGCATATTCGACTACAATGTTTCAAATTATTACATGTT
1 AGGTTTCGTAGGTAGGTCATTTATGAACGCATATTCGACTACAATGTTTCAAATTATTACATGTT
*
1458586 GTAGTACGAACAAATGGGAATCCACATATACTGATCAAGGGGGAGTAAGCACAAAAAATTTATAG
66 GTAGTACGAACAAATGGGAATCCACATATACTGATCAAGGAGGAGTAAGCACAAAAAATTTATAG
*
1458651 GCCTCCCCCAAACCATCCGTCGATGCAATGTCCCCCGACGCAAGGATGTGCTAGAGGATAATCAA
131 GCCTCCCCCAAACCATCCGTCGATGCAATGTCCCCCGACGCAAGGATGTGCTAGAGGAGAATCAA
1458716 GTCGAAATAGGCAAAAGCACACTCAAGCCTCATCGGAAATGACACAAACACTTGCAGAACATCAG
196 GTCGAAATAGGCAAAAGCACACTCAAGCCTCATCGGAAATGACACAAACACTTGCAGAACATCAG
1458781 ATACCACTGACGGCACCTACATTCACCTATTCGACTCAGTCAGCATTTCAACATATGATGACTTA
261 ATACCACTGACGGCACCTACATTCACCTATTCGACTCAGTCAGCATTTCAACATATGATGACTTA
1458846 TTCATCATTTCAGCATATGACACCTCCGACGAA
326 TTCATCATTTCAGCATATGACACCTCCGACGAA
*
1458879 AGGTTTCGTAGGTAGGTCATTTATGAACGCATATTCGACTACAGTGTTTCAAATTATTACATGTT
1 AGGTTTCGTAGGTAGGTCATTTATGAACGCATATTCGACTACAATGTTTCAAATTATTACATGTT
1458944 GTAGTACGAACAAATGGGAATCCACATATACTGATCAAGGAGGAGTAAGCACAAAAAATTTATAG
66 GTAGTACGAACAAATGGGAATCCACATATACTGATCAAGGAGGAGTAAGCACAAAAAATTTATAG
*
1459009 GCCTCCCCCAAACCGTCCGTCGATGCAATGTCCCCCGACGCAAGGATGTGCTAGAGGAGAATCAA
131 GCCTCCCCCAAACCATCCGTCGATGCAATGTCCCCCGACGCAAGGATGTGCTAGAGGAGAATCAA
*
1459074 GTTGAAATAGGCAAAAGCACACTCAAGCCTCATCGGAAATGACACAAACACTTGCAGAACATCAG
196 GTCGAAATAGGCAAAAGCACACTCAAGCCTCATCGGAAATGACACAAACACTTGCAGAACATCAG
1459139 ATACCACTGACGGCACCTACATTCACCTATTCGACTCAGTCAGCATTTCAACATATGATGACTTA
261 ATACCACTGACGGCACCTACATTCACCTATTCGACTCAGTCAGCATTTCAACATATGATGACTTA
*
1459204 TTCATCATTTCAGCATATGACACCTCTGACGAA
326 TTCATCATTTCAGCATATGACACCTCCGACGAA
1459237 AGGTTT
1 AGGTTT
1459243 TTTCGTCGAC
Statistics
Matches: 357, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
358 357 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (358 bp):
AGGTTTCGTAGGTAGGTCATTTATGAACGCATATTCGACTACAATGTTTCAAATTATTACATGTT
GTAGTACGAACAAATGGGAATCCACATATACTGATCAAGGAGGAGTAAGCACAAAAAATTTATAG
GCCTCCCCCAAACCATCCGTCGATGCAATGTCCCCCGACGCAAGGATGTGCTAGAGGAGAATCAA
GTCGAAATAGGCAAAAGCACACTCAAGCCTCATCGGAAATGACACAAACACTTGCAGAACATCAG
ATACCACTGACGGCACCTACATTCACCTATTCGACTCAGTCAGCATTTCAACATATGATGACTTA
TTCATCATTTCAGCATATGACACCTCCGACGAA
Found at i:1459201 original size:27 final size:27
Alignment explanation
Indices: 1459171--1459223 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1459161 TCACCTATTC
1459171 GACTCAGTCAGCATTTCAACATATGAT
1 GACTCAGTCAGCATTTCAACATATGAT
* * * *
1459198 GACTTATTCATCATTTCAGCATATGA
1 GACTCAGTCAGCATTTCAACATATGA
1459224 CACCTCTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (27 bp):
GACTCAGTCAGCATTTCAACATATGAT
Found at i:1459657 original size:28 final size:27
Alignment explanation
Indices: 1459625--1459686 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 27
1459615 TAAATTTGTA
*
1459625 ATTTTTAGTTAATCGAACTCAATTTTCT
1 ATTTTTAGTTAATCAAACTCAATTTT-T
* *
1459653 TTTTTTAGTTAATCAAACTCTATTTTT
1 ATTTTTAGTTAATCAAACTCAATTTTT
1459680 ATTTTTA
1 ATTTTTA
1459687 ATAATATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.56
Consensus pattern (27 bp):
ATTTTTAGTTAATCAAACTCAATTTTT
Found at i:1461353 original size:23 final size:22
Alignment explanation
Indices: 1461327--1461374 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1461317 GTGTTGCACG
1461327 TTTTCATATGCCTTTATGACATT
1 TTTTCATATG-CTTTATGACATT
* *
1461350 TTTTCTTATGCTTTTTGACATT
1 TTTTCATATGCTTTATGACATT
1461372 TTT
1 TTT
1461375 CAGTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.60
Consensus pattern (22 bp):
TTTTCATATGCTTTATGACATT
Found at i:1461824 original size:2 final size:2
Alignment explanation
Indices: 1461817--1461850 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1461807 TAGTTGCTTC
1461817 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
1461851 GTTATGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1462412 original size:17 final size:17
Alignment explanation
Indices: 1462390--1462422 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1462380 GTTTTAGTCC
*
1462390 TTCAATTTTATATTTTA
1 TTCAATTTGATATTTTA
1462407 TTCAATTTGATATTTT
1 TTCAATTTGATATTTT
1462423 GACTAATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTCAATTTGATATTTTA
Found at i:1463372 original size:18 final size:19
Alignment explanation
Indices: 1463330--1463384 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 19
1463320 TTTGATTCAC
1463330 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
*
1463350 GGAATATAAGATTACCA-G
1 GGAATGTAAGATTACCAGG
1463368 GGAATGTAAGATTACCA
1 GGAATGTAAGATTACCA
1463385 AGAATATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 17 0.52
20 16 0.48
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:1473255 original size:42 final size:40
Alignment explanation
Indices: 1473172--1473281 Score: 123
Period size: 42 Copynumber: 2.7 Consensus size: 40
1473162 TGTTTGTAAA
* *
1473172 AAAACACCACTAAAGAACTGACTTTTGTGGGGTTTGTAAC
1 AAAACACCACTAAAGAACTGACTTTTGTGGGATTTATAAC
*
1473212 AAAACATCACTAAAGAACGTGACTTTT-TGCGGCATTTATAAC
1 AAAACACCACTAAAGAAC-TGACTTTTGTG-GG-ATTTATAAC
* * *
1473254 AAAACGCCGCTAAAGAACTTAACTTTTG
1 AAAACACCACTAAAGAAC-TGACTTTTG
1473282 CGCTTTTGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 19 0.33
41 10 0.17
42 29 0.50
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (40 bp):
AAAACACCACTAAAGAACTGACTTTTGTGGGATTTATAAC
Found at i:1473317 original size:40 final size:41
Alignment explanation
Indices: 1473172--1473330 Score: 124
Period size: 40 Copynumber: 3.9 Consensus size: 41
1473162 TGTTTGTAAA
* * * * ** *
1473172 AAAACACCACTAAAGAA-CTGACTTTTGTGGGGTTTGTAAC
1 AAAACGCCGCTAAAGAACCTAACTTTTGCGGCATTTATAAC
** * * *
1473212 AAAACATCACTAAAGAACGTGACTTTTTGCGGCATTTATAAC
1 AAAACGCCGCTAAAGAACCTAAC-TTTTGCGGCATTTATAAC
* * * *
1473254 AAAACGCCGCTAAAGAACTTAACTTTTGC-GCTTTTGTAAT
1 AAAACGCCGCTAAAGAACCTAACTTTTGCGGCATTTATAAC
* *
1473294 AAAACGCCGCTAATGAACCTAACTTTTTGCGTCATTT
1 AAAACGCCGCTAAAGAACCTAAC-TTTTGCGGCATTT
1473331 GTTGATTTAA
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
40 45 0.46
41 16 0.16
42 36 0.37
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (41 bp):
AAAACGCCGCTAAAGAACCTAACTTTTGCGGCATTTATAAC
Found at i:1473322 original size:41 final size:41
Alignment explanation
Indices: 1473221--1473330 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 41
1473211 CAAAACATCA
* *
1473221 CTAAAGAACGTGACTTTTTGCGGCATTTATAACAAAACGCCG
1 CTAAAGAACCTAACTTTTTGC-GCATTTATAACAAAACGCCG
* * * *
1473263 CTAAAGAACTTAAC-TTTTGCGCTTTTGTAATAAAACGCCG
1 CTAAAGAACCTAACTTTTTGCGCATTTATAACAAAACGCCG
*
1473303 CTAATGAACCTAACTTTTTGCGTCATTT
1 CTAAAGAACCTAACTTTTTGCG-CATTT
1473331 GTTGATTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 29 0.50
41 13 0.22
42 16 0.28
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (41 bp):
CTAAAGAACCTAACTTTTTGCGCATTTATAACAAAACGCCG
Found at i:1474024 original size:34 final size:34
Alignment explanation
Indices: 1473967--1474034 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1473957 TCCATTTCGA
*
1473967 GATTACATCAATCCGGACGAAATTACTTCCAAGG
1 GATTACATCAATCCGGACAAAATTACTTCCAAGG
* * * *
1474001 GATTACATCAATTCGGGCAAAATTTCTTCTAAGG
1 GATTACATCAATCCGGACAAAATTACTTCCAAGG
1474035 TAGTGGCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (34 bp):
GATTACATCAATCCGGACAAAATTACTTCCAAGG
Found at i:1475363 original size:30 final size:30
Alignment explanation
Indices: 1475329--1475390 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1475319 TAAAATATAA
* *
1475329 AATTTA-TCAGTTTTTCGGATAATTTCATTT
1 AATTTATTCACTTTTT-GAATAATTTCATTT
*
1475359 AATTTATTGACTTTTTGAATAATTTCATTT
1 AATTTATTCACTTTTTGAATAATTTCATTT
1475389 AA
1 AA
1475391 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (30 bp):
AATTTATTCACTTTTTGAATAATTTCATTT
Found at i:1475588 original size:59 final size:59
Alignment explanation
Indices: 1475480--1475591 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
1475470 ATACGAGATC
1475480 ATCTTACGTAAATAGTTTTAGATACTTTGCAATAATTTGAAATATTTTTCAATTAGGCA
1 ATCTTACGTAAATAGTTTTAGATACTTTGCAATAATTTGAAATATTTTTCAATTAGGCA
* * *
1475539 ATCTTACGTGAATAGTTTT-GTATACCTTTTCAATAATTTGAGATA-TTTTCAAT
1 ATCTTACGTAAATAGTTTTAG-ATA-CTTTGCAATAATTTGAAATATTTTTCAAT
1475592 AATTTGAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
58 1 0.02
59 29 0.60
60 18 0.38
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (59 bp):
ATCTTACGTAAATAGTTTTAGATACTTTGCAATAATTTGAAATATTTTTCAATTAGGCA
Found at i:1475589 original size:19 final size:19
Alignment explanation
Indices: 1475565--1475606 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1475555 TTTGTATACC
1475565 TTTTCAATAATTTGAGATA
1 TTTTCAATAATTTGAGATA
1475584 TTTTCAATAATTTGAGATA
1 TTTTCAATAATTTGAGATA
1475603 TTTT
1 TTTT
1475607 TCGATTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (19 bp):
TTTTCAATAATTTGAGATA
Found at i:1476742 original size:25 final size:24
Alignment explanation
Indices: 1476709--1476768 Score: 102
Period size: 25 Copynumber: 2.5 Consensus size: 24
1476699 TATTTGTAGT
1476709 AGAAAAATAATATTTATTATAATG
1 AGAAAAATAATATTTATTATAATG
1476733 ATGAAAAATAATATTTATTATAATG
1 A-GAAAAATAATATTTATTATAATG
*
1476758 ACAAAAATAAT
1 AGAAAAATAAT
1476769 GGCACCATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 10 0.29
25 24 0.71
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (24 bp):
AGAAAAATAATATTTATTATAATG
Found at i:1480128 original size:63 final size:64
Alignment explanation
Indices: 1479977--1480129 Score: 163
Period size: 63 Copynumber: 2.4 Consensus size: 64
1479967 AAGGTGTATT
* ** *
1479977 GATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAACATCGAATGCAATTAGTGCATC
1 GATGCACAAGTAGTGCATCGATGCATCTCCATTAAAAT-AAAACATCGAATGCAATTAGTGCACC
* * * *
1480041 GATGCATAAGGCA-TGCATCAATGCATC-CCATTAATAAT-AAACATCGAATGCATTTTA-TGCA
1 GATGCACAA-GTAGTGCATCGATGCATCTCCATTAA-AATAAAACATCGAATGCA-ATTAGTGCA
1480102 CC
63 CC
1480104 GATGCACAAGTAGTGCATCGATGCAT
1 GATGCACAAGTAGTGCATCGATGCAT
1480130 ACCTTCATTA
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
62 2 0.03
63 39 0.53
64 26 0.36
65 6 0.08
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
GATGCACAAGTAGTGCATCGATGCATCTCCATTAAAATAAAACATCGAATGCAATTAGTGCACC
Found at i:1480548 original size:29 final size:29
Alignment explanation
Indices: 1480506--1480615 Score: 170
Period size: 29 Copynumber: 3.8 Consensus size: 29
1480496 TATGTGATAT
1480506 GAGAACATGACATGAGATACATGATCACAA
1 GAGAA-ATGACATGAGATACATGATCACAA
* *
1480536 GAGAAATGACATGAGCTACACGATCACAA
1 GAGAAATGACATGAGATACATGATCACAA
1480565 GAGAAATGACATGA-ACTACATGATCACAA
1 GAGAAATGACATGAGA-TACATGATCACAA
1480594 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGATACATGA
1480616 ACATATAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
28 7 0.09
29 62 0.84
30 5 0.07
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (29 bp):
GAGAAATGACATGAGATACATGATCACAA
Found at i:1483696 original size:96 final size:99
Alignment explanation
Indices: 1483585--1484169 Score: 320
Period size: 101 Copynumber: 5.6 Consensus size: 99
1483575 TTTAAACAAA
* *
1483585 AATATGTTAATTCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAACAAAAA-A-AA-T
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTATATTTACAATAAAAACAAAAATATAATT
* *
1483647 TAAA-TAAACTTACCAAACCACTCAAATACGATTT
65 TAAACTAAACTTACCAAACCACTCAAATACAACTT
*
1483681 AATATGTAAAATCAAAATAAATAGT-TCAATAATTTATA-TTACTCAATAAAAAATAAAAATATA
1 AATATGTAAAATCAAAATAAATAGTCT-AATAATTTATATTTA--CAAT-AAAAACAAAAATATA
* *
1483744 ATTTAAACTACACTTACCAAACTACTCAAATACAACTT
62 ATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
* *
1483782 AATATGTAAAATCAAGATAAATAGTCTAATAA-TTATAATTTA-AATTAAAAGCAAAATTTATAC
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTAT-ATTTACAA-TAAAAACAAAA---ATA-
* * * * * * *
1483845 TAAAAATTACA-TGAAAATTTA-AATTTAACTTAC-CAAAGCACTCGAATACAATTT
60 T--AATTTAAACT--AAACTTACCA---AAC-CACTCAAA-TA--C-AA-C----TT
* *
1483899 AATCTGTAAAATCAAAATAAATAGTCTAATTAATTTATTTTTACAATAAAAACACAAAATAAAAC
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTATATTTACAATAAAAACA-AAAAT-----
* *** * *
1483964 AATAAATTTAAAAGTAAACTTACCAAGGTACTCAAATACGATTT
59 -AT-AATTT-AAACTAAACTTACCAAACCACTCAAATACAACTT
* * * *
1484008 AATCTGTAAAATAAAAATAATTAGTCTAATAATTTATA-TTACTCAATAAAAA-AACAAGGTAAT
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTATATTTA--CAATAAAAACAA-AA-AT-AT
* ** *
1484071 AATTTAAACTACACTTA-CAAAGTTTTAATCAAATACAACTT
61 AATTTAAACTAAACTTACCAAA---CCACTCAAATACAACTT
* *
1484112 AAAATGTAAAATTAAAATAAATAGTCTAATAA-TTATAATTTA-AATTAAAAACAAAAAT
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTAT-ATTTACAA-TAAAAACAAAAAT
1484170 TACACTAAAA
Statistics
Matches: 385, Mismatches: 46, Indels: 110
0.71 0.09 0.20
Matches are distributed among these distances:
94 3 0.01
95 10 0.03
96 29 0.08
97 10 0.03
98 1 0.00
99 12 0.03
100 10 0.03
101 59 0.15
102 20 0.05
103 18 0.05
104 48 0.12
105 10 0.03
106 5 0.01
107 4 0.01
108 18 0.05
109 43 0.11
111 1 0.00
112 2 0.01
114 1 0.00
115 1 0.00
116 2 0.01
117 33 0.09
118 19 0.05
119 9 0.02
120 11 0.03
121 4 0.01
122 2 0.01
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (99 bp):
AATATGTAAAATCAAAATAAATAGTCTAATAATTTATATTTACAATAAAAACAAAAATATAATTT
AAACTAAACTTACCAAACCACTCAAATACAACTT
Found at i:1484002 original size:109 final size:105
Alignment explanation
Indices: 1483585--1484279 Score: 413
Period size: 117 Copynumber: 6.5 Consensus size: 105
1483575 TTTAAACAAA
* * *
1483585 AATATGTTAATTCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAC-------AAAAA
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTATTTTTACAATAAAAACAAAAATAAAAAA
*
1483643 -AAA-TTAAA-TAAACTTACCAAACCACTCAAATACGATTT
65 TAAATTTAAACTAAACTTACCAAACCACTCAAATACAATTT
* * *
1483681 AATATGTAAAATCAAAATAAATAGT-TCAATAATTTA-TATTAC--TCAATA-AAAAAT-AAAAA
1 AATATGTAAAATCAAAATAAATAGTCT-AATAATTTATTTTTACAATAAAAACAAAAATAAAAAA
* * *
1483740 TATAATTTAAACTACACTTACCAAACTACTCAAATACAACTT
65 TA-AATTTAAACTAAACTTACCAAACCACTCAAATACAATTT
* * *
1483782 AATATGTAAAATCAAGATAAATAGTCTAATAA-TTATAATTTA-AATTAAAAGCAAAATTTATAC
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTAT-TTTTACAA-TAAAAAC-AAA---A-A-
* * * *
1483845 TAAAAATTACATGAAAATTTAAATTTAACTTACCAAAGCACTCGAATACAATTT
58 T-AAAA--A-AT--AAATTTAAACTAAACTTACCAAACCACTCAAATACAATTT
*
1483899 AATCTGTAAAATCAAAATAAATAGTCTAATTAATTTATTTTTACAATAAAAACACAAAATAAAAC
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTATTTTTACAATAAAAACA-AAAATAAAA-
* *** *
1483964 AATAAATTTAAAAGTAAACTTACCAAGGTACTCAAATACGATTT
63 AATAAATTT-AAACTAAACTTACCAAACCACTCAAATACAATTT
* * * * * ***
1484008 AATCTGTAAAATAAAAATAATTAGTCTAATAATTTA-TATTACTCAAT-AAAA-AAACA-AGGTA
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTATTTTTA--CAATAAAAACAAAAATAAAAA
* ** * *
1484069 AT-AATTTAAACTACACTTA-CAAAGTTTTAATCAAATACAACTT
64 ATAAATTTAAACTAAACTTACCAAA---CCACTCAAATACAATTT
* * *
1484112 AAAATGTAAAATTAAAATAAATAGTCTAATAA-TTATAATTTA-AATTAAAAACAAAAATTACAC
1 AATATGTAAAATCAAAATAAATAGTCTAATAATTTAT-TTTTACAA-TAAAAAC--AAA--A-A-
*
1484175 TAAAAATTACATAAAAATTTAAATTAAACTTACCAAACCACT-AGAATACAATTT
58 T-AAAA--A-AT--AAATTTAAACTAAACTTACCAAACCACTCA-AATACAATTT
* * *
1484229 AATATAT-AAATCAAAATAAATAATCTAATTAATTTATATTT-CAAATAAAAA
1 AATATGTAAAATCAAAATAAATAGTCTAA-TAATTTATTTTTAC-AATAAAAA
1484280 TTAAAAATGT
Statistics
Matches: 465, Mismatches: 68, Indels: 111
0.72 0.11 0.17
Matches are distributed among these distances:
92 4 0.01
94 4 0.01
95 8 0.02
96 25 0.05
97 5 0.01
98 1 0.00
99 2 0.00
100 8 0.02
101 58 0.12
102 16 0.03
103 9 0.02
104 51 0.11
105 4 0.01
106 6 0.01
107 8 0.02
108 17 0.04
109 60 0.13
110 4 0.01
111 2 0.00
112 4 0.01
113 5 0.01
114 1 0.00
115 3 0.01
116 24 0.05
117 89 0.19
118 22 0.05
119 21 0.05
120 4 0.01
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (105 bp):
AATATGTAAAATCAAAATAAATAGTCTAATAATTTATTTTTACAATAAAAACAAAAATAAAAAAT
AAATTTAAACTAAACTTACCAAACCACTCAAATACAATTT
Found at i:1484189 original size:11 final size:12
Alignment explanation
Indices: 1484164--1484193 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1484154 AATTAAAAAC
1484164 AAAAATTACACT
1 AAAAATTACACT
1484176 AAAAATTACA-T
1 AAAAATTACACT
1484187 AAAAATT
1 AAAAATT
1484194 TAAATTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAATTACACT
Found at i:1484303 original size:330 final size:327
Alignment explanation
Indices: 1483633--1484303 Score: 944
Period size: 330 Copynumber: 2.0 Consensus size: 327
1483623 ATTTACAATA
* * *
1483633 AAAACAAAAAAAATT-AAATAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATCAAA
1 AAAACAATAAAATTTAAAATAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATAAAA
1483697 ATAAATAGTTCAATAATTTATATTACTCAATAAAAAATAAAAATATAATTTAAACTACACTTACC
66 ATAAATAGTTCAATAATTTATATTACTCAATAAAAAATAAAAATATAATTTAAACTACACTTACC
* * *
1483762 AAACTACTCAAATACAACTTAATATGTAAAATCAAGATAAATAGTCTAATAATTATAATTTAAAT
131 AAACTAATCAAATACAACTTAAAATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAAT
* * * * * * *
1483827 TAAAAGCAAAATTTATACTAAAAATTACATGAAAATTTAAATTTAACTTACCAAAGCACTCGAAT
196 TAAAAACAAAAATTACACTAAAAATTACATAAAAATTTAAATTAAACTTACCAAACCACTAGAAT
* * * *
1483892 ACAATTTAATCTGTAAAATCAAAATAAATAGTCTAATTAATTTATTTTTACAATAAAAACACAAA
261 ACAATTTAATATATAAAATCAAAATAAATAATCTAATTAATTTATTTTCACAATAAAAACACAAA
1483957 AT
326 AT
*** *
1483959 AAAACAAT-AAATTTAAAAGTAAACTTACCAAGGTACTCAAATACGATTTAATCTGTAAAATAAA
1 AAAACAATAAAATTTAAAA-TAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATAAA
* **
1484023 AATAATTAG-TCTAATAATTTATATTACTCAATAAAAAA-ACAAGGTAATAATTTAAACTACACT
65 AATAAATAGTTC-AATAATTTATATTACTCAATAAAAAATA-AAAAT-ATAATTTAAACTACACT
* *
1484086 TA-CAAAGTTTTAATCAAATACAACTTAAAATGTAAAATTAAAATAAATAGTCTAATAATTATAA
127 TACCAAA---CTAATCAAATACAACTTAAAATGTAAAATCAAAATAAATAGTCTAATAATTATAA
1484150 TTTAAATTAAAAACAAAAATTACACTAAAAATTACATAAAAATTTAAATTAAACTTACCAAACCA
189 TTTAAATTAAAAACAAAAATTACACTAAAAATTACATAAAAATTTAAATTAAACTTACCAAACCA
1484215 CTAGAATACAATTTAATATAT-AAATCAAAATAAATAATCTAATTAATTTATATTTCA-AATAAA
254 CTAGAATACAATTTAATATATAAAATCAAAATAAATAATCTAATTAATTTAT-TTTCACAATAAA
*
1484278 AATTA-AAAAT
318 AA-CACAAAAT
**
1484288 GTAACAATAAAATTTA
1 AAAACAATAAAATTTA
1484304 CACTAAATTT
Statistics
Matches: 305, Mismatches: 29, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
325 5 0.02
326 13 0.04
327 81 0.27
328 19 0.06
329 48 0.16
330 139 0.46
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.31
Consensus pattern (327 bp):
AAAACAATAAAATTTAAAATAAACTTACCAAACCACTCAAATACGATTTAATATGTAAAATAAAA
ATAAATAGTTCAATAATTTATATTACTCAATAAAAAATAAAAATATAATTTAAACTACACTTACC
AAACTAATCAAATACAACTTAAAATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAAT
TAAAAACAAAAATTACACTAAAAATTACATAAAAATTTAAATTAAACTTACCAAACCACTAGAAT
ACAATTTAATATATAAAATCAAAATAAATAATCTAATTAATTTATTTTCACAATAAAAACACAAA
AT
Found at i:1484756 original size:36 final size:38
Alignment explanation
Indices: 1484662--1484757 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
1484652 CGAAGTTTTT
1484662 TTTTTTTCTGAAGATGCCAAGTAGTCTCAGAGTCTTCA
1 TTTTTTTCTGAAGATGCCAAGTAGTCTCAGAGTCTTCA
* * *
1484700 TTTTTTTCCGAAGACGCCAAGTAAT-TCTAGAGTCTT-A
1 TTTTTTTCTGAAGATGCCAAGTAGTCTC-AGAGTCTTCA
*
1484737 -TTTTTTCTGAAGATACCAAGT
1 TTTTTTTCTGAAGATGCCAAGT
1484758 GATCTTGGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
36 18 0.35
37 3 0.06
38 30 0.59
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.40
Consensus pattern (38 bp):
TTTTTTTCTGAAGATGCCAAGTAGTCTCAGAGTCTTCA
Found at i:1495802 original size:7 final size:7
Alignment explanation
Indices: 1495792--1495820 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1495782 ATGAAATAAC
1495792 AAATTAA
1 AAATTAA
1495799 AAATTAA
1 AAATTAA
1495806 AAATTAA
1 AAATTAA
1495813 AAATTAA
1 AAATTAA
1495820 A
1 A
1495821 GTAAAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:1499190 original size:21 final size:21
Alignment explanation
Indices: 1499166--1499216 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1499156 TTTTCTTCCC
*
1499166 AAATCAGAATGAAAATCCCTA
1 AAATCAAAATGAAAATCCCTA
1499187 AAATCAAAATGAAAATCCCTA
1 AAATCAAAATGAAAATCCCTA
1499208 AAATCAAAA
1 AAATCAAAA
1499217 CCCCCAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.59, C:0.18, G:0.06, T:0.18
Consensus pattern (21 bp):
AAATCAAAATGAAAATCCCTA
Found at i:1500191 original size:23 final size:23
Alignment explanation
Indices: 1500165--1500213 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1500155 ATAAAGAACC
*
1500165 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
1500188 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
1500211 AAA
1 AAA
1500214 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:1503675 original size:60 final size:59
Alignment explanation
Indices: 1503540--1503686 Score: 154
Period size: 60 Copynumber: 2.4 Consensus size: 59
1503530 AATATAATGA
* *
1503540 ATAGTCAGGTGACCATTTTGTAACTTTTAATAGTAAAGGGATTCAACAAAGTAACACTCT
1 ATAGTCAGG-GACCATTTTGTAACTTTTAATAGTAAAGAGATTCAACAAAGTAACACCCT
* * ** * **
1503600 ATAGTCAAAGAACCATTTTGTAACTTTTAATAGTCGAGAGACTT-AATAAAGTAGTACCCT
1 ATAGTC-AGGGACCATTTTGTAACTTTTAATAGTAAAGAGA-TTCAACAAAGTAACACCCT
1503660 ATAGTCGAGGGACCATTTTTGT-ACTTT
1 ATAGTC-AGGGACCA-TTTTGTAACTTT
1503687 ATCCTAATAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
60 62 0.86
61 10 0.14
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (59 bp):
ATAGTCAGGGACCATTTTGTAACTTTTAATAGTAAAGAGATTCAACAAAGTAACACCCT
Found at i:1505243 original size:20 final size:21
Alignment explanation
Indices: 1505192--1505245 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1505182 CCCACCTTTA
1505192 AAATTCGTCCATTTGAAATTT
1 AAATTCGTCCATTTGAAATTT
* * * *
1505213 TAGTTCATCCATTT-TAATTT
1 AAATTCGTCCATTTGAAATTT
1505233 AAATTCGTCCATT
1 AAATTCGTCCATT
1505246 AACATAAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.46
Consensus pattern (21 bp):
AAATTCGTCCATTTGAAATTT
Found at i:1505300 original size:31 final size:31
Alignment explanation
Indices: 1505265--1505327 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1505255 TTCTACGTCT
1505265 TATATGGGTTTGGGTTTTCATAATTATAATG
1 TATATGGGTTTGGGTTTTCATAATTATAATG
1505296 TATATGGGTTTGGGTTTTCATAATTATAATG
1 TATATGGGTTTGGGTTTTCATAATTATAATG
1505327 T
1 T
1505328 GTAGAAATTA
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:0.25, C:0.03, G:0.22, T:0.49
Consensus pattern (31 bp):
TATATGGGTTTGGGTTTTCATAATTATAATG
Found at i:1506632 original size:4 final size:4
Alignment explanation
Indices: 1506625--1506652 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1506615 GGTTACTCGC
1506625 GCAT GCAT GCAT GCAT GCAT GCAT GCAT
1 GCAT GCAT GCAT GCAT GCAT GCAT GCAT
1506653 AAACGGTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (4 bp):
GCAT
Found at i:1509262 original size:21 final size:22
Alignment explanation
Indices: 1509221--1509276 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
1509211 GAGCACCGAG
1509221 AATGTC-AGAGATGTAAACATTC
1 AATGTCAAGAGATG-AAACATTC
1509243 AATGTCAAGAGATG-AACATTC
1 AATGTCAAGAGATGAAACATTC
1509264 AATGTCAAGAGAT
1 AATGTCAAGAGAT
1509277 TGAGAGTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 20 0.61
22 6 0.18
23 7 0.21
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (22 bp):
AATGTCAAGAGATGAAACATTC
Found at i:1519161 original size:13 final size:13
Alignment explanation
Indices: 1519143--1519170 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1519133 TTCTTACTGC
1519143 TCAGACGAGTTCT
1 TCAGACGAGTTCT
1519156 TCAGACGAGTTCT
1 TCAGACGAGTTCT
1519169 TC
1 TC
1519171 TTTTGGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (13 bp):
TCAGACGAGTTCT
Found at i:1521744 original size:23 final size:22
Alignment explanation
Indices: 1521718--1521763 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1521708 CCCCCTTTCA
1521718 ATTTTCTTT-CTTTTTTCATTTTT
1 ATTTT-TTTACTTTTTT-ATTTTT
1521741 ATTTTTTTCACTTTTTTATTTTT
1 ATTTTTTT-ACTTTTTTATTTTT
1521764 TTCCTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.14
23 11 0.52
24 7 0.33
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (22 bp):
ATTTTTTTACTTTTTTATTTTT
Found at i:1521748 original size:17 final size:17
Alignment explanation
Indices: 1521713--1521765 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1521703 TTGAACCCCC
* *
1521713 TTTCAATTTTCTTTCTTT
1 TTTCATTTTTATTT-TTT
1521731 TTTCATTTTTATTTTTT
1 TTTCATTTTTATTTTTT
** *
1521748 TCACTTTTTTATTTTTT
1 TTTCATTTTTATTTTTT
1521765 T
1 T
1521766 CCTTTTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCATTTTTATTTTTT
Found at i:1521766 original size:17 final size:17
Alignment explanation
Indices: 1521728--1521772 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1521718 ATTTTCTTTC
1521728 TTTTTTCA--TTTTTAT
1 TTTTTTCACTTTTTTAT
1521743 TTTTTTCACTTTTTTAT
1 TTTTTTCACTTTTTTAT
1521760 TTTTTTC-CTTTTT
1 TTTTTTCACTTTTT
1521773 CAAGTGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 14 0.50
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTCACTTTTTTAT
Found at i:1530881 original size:9 final size:8
Alignment explanation
Indices: 1530846--1530936 Score: 60
Period size: 8 Copynumber: 11.2 Consensus size: 8
1530836 CTCATTTCAA
1530846 TTTTCTTTT
1 TTTTC-TTT
1530855 TTTTCTTT
1 TTTTCTTT
*
1530863 TTGGTCTTT
1 TT-TTCTTT
*
1530872 TTTTC-AT
1 TTTTCTTT
**
1530879 TTTTCCCT
1 TTTTCTTT
**
1530887 TTTTCCCT
1 TTTTCTTT
1530895 TTTTCTATT
1 TTTTCT-TT
*
1530904 TTTTCTAT
1 TTTTCTTT
**
1530912 TTTTC-AG
1 TTTTCTTT
1530919 TTTTCTTT
1 TTTTCTTT
1530927 TTTTCTTT
1 TTTTCTTT
1530935 TT
1 TT
1530937 CGAGTGTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
7 12 0.18
8 37 0.54
9 19 0.28
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.76
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1536062 original size:119 final size:118
Alignment explanation
Indices: 1535851--1536082 Score: 288
Period size: 119 Copynumber: 2.0 Consensus size: 118
1535841 CTTCTAAGCT
* * * *
1535851 ACAAGTTCTTCTTATTATGAACTTTTTGCTCGCTTCGGACGATTTCTTCTCGTTATGAACCTTTC
1 ACAAGTTCTTCTCATTATGAACTTTTTGCTCGCTTCGGACGAGTTCTTCTCATTATGAACCCTTC
* *** ** * *
1535916 CCTTTGAAATGTTTATCCGTCTTCTTCTGTGATGAATTTGAGTAAAAAGTCGA
66 CATTTGAAATGACAATCCACCTCCTTCTGTGATGAATTTGAGCAAAAAGTCGA
*
1535969 ACAAGTTCTTCTCATTATGAACTTTTT-CTTC-CTCCTCGGATGAGTTCTTCTCATTATGAACCC
1 ACAAGTTCTTCTCATTATGAACTTTTTGC-TCGCT--TCGGACGAGTTCTTCTCATTATGAACCC
* *
1536032 TTCTATTTGAAATGACAATCCACCTCCTTCTGTGATGGATTTGAGCAAAAA
63 TTCCATTTGAAATGACAATCCACCTCCTTCTGTGATGAATTTGAGCAAAAA
1536083 TGGTAATGTT
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
117 3 0.03
118 28 0.29
119 65 0.68
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (118 bp):
ACAAGTTCTTCTCATTATGAACTTTTTGCTCGCTTCGGACGAGTTCTTCTCATTATGAACCCTTC
CATTTGAAATGACAATCCACCTCCTTCTGTGATGAATTTGAGCAAAAAGTCGA
Found at i:1536369 original size:44 final size:44
Alignment explanation
Indices: 1536295--1536384 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
1536285 CGAGAGTGAC
* *
1536295 AATGTTGATGTTGATCAACATCTTTCTGTGATAGAATCGAGCAA
1 AATGGTGATGTTGATCAACATCTTTATGTGATAGAATCGAGCAA
* * * *
1536339 AATGGTGATGTTGATCCAACTTC-TTATGTGATGGATTCGAGTAA
1 AATGGTGATGTTGAT-CAACATCTTTATGTGATAGAATCGAGCAA
1536383 AA
1 AA
1536385 GATTGAACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 33 0.85
45 6 0.15
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (44 bp):
AATGGTGATGTTGATCAACATCTTTATGTGATAGAATCGAGCAA
Found at i:1536454 original size:214 final size:212
Alignment explanation
Indices: 1535960--1536702 Score: 862
Period size: 214 Copynumber: 3.5 Consensus size: 212
1535950 AATTTGAGTA
* * * *
1535960 AAAAGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCCTCGGATGAGTTCTTCTCATTA
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCACGGACGAGTTCTTCTCATTA
* * * * *
1536025 TGAACCCTTCTATTTGAAATGACAATCCACCTCCTTCTGTGATGGATTTGAGC-A-A---A-AAT
66 TGAACCCTTCCATTGGAAATGACAGTCCACCTCCTTCTGTGATGGAATCGAGCGAGAGTGACAAT
* * * * * * * * ** * * *
1536084 GGTAATGTTGATCCACCTCCTTCTATGATGGAATCGAACCAAATATTGAT-TATGA-CTTATCTC
131 GTTGATGTTGAT-CAACTCTTTCTGTGATAGAATCGAGCAAAATGGTGATGT-TGATC-CAACTT
** *
1536147 CTCCTGTGATAGAATCGAGC
193 CTTATGTGATAGATTCGAGC
* * * *
1536167 AAAAG-GGAAACAAGATCTTCTCATTATGAACTTTATTGTTCCT-CATCGGACGAGTTCTTCTCA
1 AAAAGTTG-AACAAGTTCTTCTCATTATGAAC-TTCTTCTTCCTCCA-CGGACGAGTTCTTCTCA
* * * *
1536230 TTATGAACCCTTCTATTAGAAATGACAGTCAACCTCATTCTGTGATGGAATCGAGCGAGAGTGAC
63 TTATGAACCCTTCCATTGGAAATGACAGTCCACCTCCTTCTGTGATGGAATCGAGCGAGAGTGAC
1536295 AATGTTGATGTTGATCAACATCTTTCTGTGATAGAATCGAGCAAAATGGTGATGTTGATCCAACT
128 AATGTTGATGTTGATCAAC-TCTTTCTGTGATAGAATCGAGCAAAATGGTGATGTTGATCCAACT
* *
1536360 TCTTATGTGATGGATTCGAGT
192 TCTTATGTGATAGATTCGAGC
*
1536381 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCACGGACGTGTTCTTCTCATT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCACGGACGAGTTCTTCTCATT
* * * *
1536446 ATGAACCCTTCCACTGGAAATGAC-GATCCACCTCCTTCTATTATGGAATCGAGTGAGAGTGACA
65 ATGAACCCTTCCATTGGAAATGACAG-TCCACCTCCTTCTGTGATGGAATCGAGCGAGAGTGACA
* * *
1536510 ACGTTGATGTTGATCTAGCTCTTTCTGTGATAGAATTGAGCAAAATGGTGATGTTGATCCAACTT
129 ATGTTGATGTTGATC-AACTCTTTCTGTGATAGAATCGAGCAAAATGGTGATGTTGATCCAACTT
1536575 CTTATGTGATAGATTCGAGC
193 CTTATGTGATAGATTCGAGC
* *
1536595 AAAACGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCTCAGACGAGTTCTTCTCATT
1 AAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCACGGACGAGTTCTTCTCATT
* * *
1536660 ATGAACTCTTCCATTGGAAACGA-TGATCCACCTCCTTCTGTGA
65 ATGAACCCTTCCATTGGAAATGACAG-TCCACCTCCTTCTGTGA
1536703 GGGATTTAAA
Statistics
Matches: 461, Mismatches: 56, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
206 1 0.00
207 28 0.06
208 75 0.16
209 1 0.00
210 1 0.00
213 5 0.01
214 320 0.69
215 29 0.06
216 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (212 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCACGGACGAGTTCTTCTCATTA
TGAACCCTTCCATTGGAAATGACAGTCCACCTCCTTCTGTGATGGAATCGAGCGAGAGTGACAAT
GTTGATGTTGATCAACTCTTTCTGTGATAGAATCGAGCAAAATGGTGATGTTGATCCAACTTCTT
ATGTGATAGATTCGAGC
Found at i:1539227 original size:9 final size:9
Alignment explanation
Indices: 1539215--1539275 Score: 63
Period size: 10 Copynumber: 6.7 Consensus size: 9
1539205 TTTTTATTTA
1539215 TTTTTTCAT
1 TTTTTTCAT
1539224 TTTTTT-AT
1 TTTTTTCAT
*
1539232 TTTTTTTATT
1 TTTTTTCA-T
*
1539242 TTTTTTTAT
1 TTTTTTCAT
1539251 TTTTGTTCA-
1 TTTT-TTCAT
1539260 TTTTTTCTAT
1 TTTTTTC-AT
1539270 TTTTTT
1 TTTTTT
1539276 TCTATTTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
8 11 0.24
9 17 0.37
10 18 0.39
ACGTcount: A:0.10, C:0.05, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:1539228 original size:19 final size:18
Alignment explanation
Indices: 1539204--1539284 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 18
1539194 TCCTTTCAAT
1539204 TTTTTTATTTATTTTTTCA
1 TTTTTT-TTTATTTTTTCA
1539223 TTTTTTTATT-TTTTTT-A
1 TTTTTTT-TTATTTTTTCA
1539240 TTTTTTTTTATTTTTGTTCA
1 TTTTTTTTTA-TTTT-TTCA
1539260 TTTTTTCTATT-TTTTTTCTA
1 TTTTTT-T-TTATTTTTTC-A
1539280 TTTTT
1 TTTTT
1539285 CTATTTTATT
Statistics
Matches: 54, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.04
17 8 0.15
18 11 0.20
19 13 0.24
20 17 0.31
21 1 0.02
22 2 0.04
ACGTcount: A:0.11, C:0.05, G:0.01, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTATTTTTTCA
Found at i:1539247 original size:29 final size:28
Alignment explanation
Indices: 1539203--1539291 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 28
1539193 CTCCTTTCAA
*
1539203 TTTTTTTATTTATTTTTTCATTTTTTTAT
1 TTTTTTTATTT-TTTTTTTATTTTTTTAT
1539232 TTTTTTTA-TTTTTTTTTATTTTTGTTCAT
1 TTTTTTTATTTTTTTTTTATTTTT-TT-AT
* * *
1539261 TTTTTCTATTTTTTTTCTATTTTTCTAT
1 TTTTTTTATTTTTTTTTTATTTTTTTAT
1539289 TTT
1 TTT
1539292 ATTTGTTTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.23
28 9 0.17
29 18 0.34
30 14 0.26
ACGTcount: A:0.11, C:0.06, G:0.01, T:0.82
Consensus pattern (28 bp):
TTTTTTTATTTTTTTTTTATTTTTTTAT
Found at i:1539283 original size:9 final size:9
Alignment explanation
Indices: 1539213--1539291 Score: 67
Period size: 8 Copynumber: 8.7 Consensus size: 9
1539203 TTTTTTTATT
1539213 TATTTTTTC
1 TATTTTTTC
1539222 -ATTTTTT-
1 TATTTTTTC
*
1539229 TATTTTTTT
1 TATTTTTTC
*
1539238 TATTTTTTTT
1 TA-TTTTTTC
1539248 TATTTTTGT-
1 TATTTTT-TC
1539257 TCATTTTTTC
1 T-ATTTTTTC
1539267 TATTTTTTTTC
1 TA--TTTTTTC
1539278 TA-TTTTTC
1 TATTTTTTC
1539286 TATTTT
1 TATTTT
1539292 ATTTGTTTGA
Statistics
Matches: 61, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
8 22 0.36
9 13 0.21
10 17 0.28
11 9 0.15
ACGTcount: A:0.11, C:0.06, G:0.01, T:0.81
Consensus pattern (9 bp):
TATTTTTTC
Found at i:1539285 original size:19 final size:19
Alignment explanation
Indices: 1539197--1539291 Score: 104
Period size: 19 Copynumber: 4.9 Consensus size: 19
1539187 TGAACCCTCC
*
1539197 TTTCAATTTTTTTATTTATT
1 TTTCTATTTTTTTATTT-TT
1539217 TTT-TCATTTTTTTATTTTT
1 TTTCT-ATTTTTTTATTTTT
* *
1539236 TTTATTTTTTTTTATTTTT
1 TTTCTATTTTTTTATTTTT
*
1539255 GTTC-ATTTTTTCTATTTTT
1 TTTCTATTTTTT-TATTTTT
*
1539274 TTTCTATTTTTCTATTTT
1 TTTCTATTTTTTTATTTT
1539292 ATTTGTTTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 6 0.09
19 36 0.56
20 22 0.34
ACGTcount: A:0.13, C:0.06, G:0.01, T:0.80
Consensus pattern (19 bp):
TTTCTATTTTTTTATTTTT
Found at i:1541277 original size:21 final size:21
Alignment explanation
Indices: 1541253--1541331 Score: 158
Period size: 21 Copynumber: 3.8 Consensus size: 21
1541243 AATTCTTCTA
1541253 TTAATCCTTGTACTCTATGAT
1 TTAATCCTTGTACTCTATGAT
1541274 TTAATCCTTGTACTCTATGAT
1 TTAATCCTTGTACTCTATGAT
1541295 TTAATCCTTGTACTCTATGAT
1 TTAATCCTTGTACTCTATGAT
1541316 TTAATCCTTGTACTCT
1 TTAATCCTTGTACTCT
1541332 TCTTTGGAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (21 bp):
TTAATCCTTGTACTCTATGAT
Found at i:1546810 original size:15 final size:15
Alignment explanation
Indices: 1546786--1546842 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1546776 TGAACCCTCA
*
1546786 TTTCAATTTTTTTTT
1 TTTCATTTTTTTTTT
1546801 TTTCATTTTTGTCTTTT
1 TTTCATTTTT-T-TTTT
***
1546818 TTTCATTTTTCCCTT
1 TTTCATTTTTTTTTT
1546833 TTTCATTTTT
1 TTTCATTTTT
1546843 CCTATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 1 0.03
17 14 0.39
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTCATTTTTTTTTT
Found at i:1546833 original size:17 final size:16
Alignment explanation
Indices: 1546797--1546867 Score: 90
Period size: 17 Copynumber: 4.3 Consensus size: 16
1546787 TTCAATTTTT
*
1546797 TTTTTTTCATTTTTGTC
1 TTTTTTTCATTTTT-CC
1546814 TTTTTTTCATTTTTCC
1 TTTTTTTCATTTTTCC
*
1546830 -CTTTTTCATTTTTCC
1 TTTTTTTCATTTTTCC
1546845 TATTTTTTCTATTTTTCC
1 T-TTTTTTC-ATTTTTCC
1546863 TTTTT
1 TTTTT
1546868 CCTTTTTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.29
16 1 0.02
17 24 0.50
18 9 0.19
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTTTTTCATTTTTCC
Found at i:1546835 original size:32 final size:32
Alignment explanation
Indices: 1546799--1546875 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
1546789 CAATTTTTTT
*
1546799 TTTTTCATTTTTGTCT-TTTTTTC-ATTTTTCCC
1 TTTTTCATTTTT-CCTATTTTTTCTATTTTT-CC
1546831 TTTTTCATTTTTCCTATTTTTTCTATTTTTCC
1 TTTTTCATTTTTCCTATTTTTTCTATTTTTCC
*
1546863 TTTTTCCTTTTTC
1 TTTTTCATTTTTC
1546876 AAGTGTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 2 0.05
32 33 0.80
33 6 0.15
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.73
Consensus pattern (32 bp):
TTTTTCATTTTTCCTATTTTTTCTATTTTTCC
Found at i:1546843 original size:15 final size:15
Alignment explanation
Indices: 1546816--1546875 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
1546806 TTTTTGTCTT
1546816 TTTTTCATTTTTCCC
1 TTTTTCATTTTTCCC
*
1546831 TTTTTCATTTTTCCTAT
1 TTTTTCATTTTTCC--C
1546848 TTTTTCTATTTTT-CC
1 TTTTTC-ATTTTTCCC
*
1546863 TTTTTCCTTTTTC
1 TTTTTCATTTTTC
1546876 AAGTGTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.13
15 20 0.53
17 7 0.18
18 6 0.16
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTCATTTTTCCC
Found at i:1546851 original size:25 final size:24
Alignment explanation
Indices: 1546823--1546874 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1546813 CTTTTTTTCA
*
1546823 TTTTTCCCTTTTTCATTTTTCCTAT
1 TTTTTCCATTTTTCATTTTTCCT-T
* *
1546848 TTTTTCTATTTTTCCTTTTTCCTT
1 TTTTTCCATTTTTCATTTTTCCTT
1546872 TTT
1 TTT
1546875 CAAGTGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTCCATTTTTCATTTTTCCTT
Found at i:1557301 original size:119 final size:117
Alignment explanation
Indices: 1557079--1557310 Score: 290
Period size: 119 Copynumber: 2.0 Consensus size: 117
1557069 CTTCTGAGCT
* * *
1557079 ACAAGTTCTTCTTATTATGAACTTTTCGCTCACTTCGGACGATTTATTCTCGTTATGAACCCTTC
1 ACAAGTTCTTCTTATTATGAACTTTTCCCTCACTTCGGACGAGTTATTCTCATTATGAACCCTTC
* * ** *
1557144 TTTTGAAATGTTGATCCACCTTCTTCTGTGATGAATTTGAGTAAAAATTTGA
66 ATTGGAAATGACGATCCACCTTCTTCTGTGATGAATTTGAGCAAAAATTTGA
* *
1557196 ACAAGTTCTTCTTATTATGAACTTCTTCTTCCTC-C-TCGGATGAGTTCTTCTCATTATGAACCC
1 ACAAGTTCTTCTTATTATGAACTT-TTC--CCTCACTTCGGACGAGTTATTCTCATTATGAACCC
* *
1557259 TTCCATTGGAAATGACGATCCACC-TCATTTTGTGATGGATTTGAGCAAAAAT
63 TT-CATTGGAAATGACGATCCACCTTC-TTCTGTGATGAATTTGAGCAAAAAT
1557311 GGCAATGTTG
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
117 24 0.24
118 31 0.32
119 40 0.41
120 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (117 bp):
ACAAGTTCTTCTTATTATGAACTTTTCCCTCACTTCGGACGAGTTATTCTCATTATGAACCCTTC
ATTGGAAATGACGATCCACCTTCTTCTGTGATGAATTTGAGCAAAAATTTGA
Found at i:1557639 original size:20 final size:20
Alignment explanation
Indices: 1557614--1557677 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1557604 TGCAAAAGGT
1557614 TGAACAAGTTCTTCTCATTA
1 TGAACAAGTTCTTCTCATTA
** *
1557634 TGAACATCTTCTTC-C-TTC
1 TGAACAAGTTCTTCTCATTA
* *
1557652 TCGGACGAGTTCTTCTCATTA
1 T-GAACAAGTTCTTCTCATTA
1557673 TGAAC
1 TGAAC
1557678 TCTTCTATTG
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 3 0.09
19 10 0.31
20 16 0.50
21 3 0.09
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.39
Consensus pattern (20 bp):
TGAACAAGTTCTTCTCATTA
Found at i:1557671 original size:214 final size:208
Alignment explanation
Indices: 1557155--1557718 Score: 670
Period size: 207 Copynumber: 2.7 Consensus size: 208
1557145 TTTGAAATGT
* * * * ** *
1557155 TGATCCACCTTCTTCTGTGATGAATTTGAGTAAAAATTTGAACAAGTTCTTCTTATTATGAACTT
1 TGATCCAACTTCTTCTGTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* *
1557220 CTTCTTCCTCCTCGGATGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGACGATCCACCTC
66 CTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACCTC
* * * * *
1557285 ATTTTGTGATGGATTTGAGCAAAAATGGCAATGTTGATCCACCTCCTTCTATGGTGGAATCGAAC
131 CTTTTGTGATGGAATTGAGCAAAAATGGCAATGCTGATCCACCTCCTTCTATGATAGAATCGAAC
* * *
1557350 CAAATGTTGATGT
196 AAAATGGTGATGC
* * *
1557363 TGA--CATATCTCCTTCTGTGATAGAATCGAGCAAAAGG--GAAACAAGTTCTTCTCATTATGAA
1 TGATCCA-A-CTTCTTCTGTGATGGATTCGAGCAAAAGGTTG-AACAAGTTCTTCTCATTATGAA
* *
1557424 CTTCTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATTAT-AGTCAA
63 CTTCTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATGA-TCCA
** * * *
1557488 CCTCCTTTTGTGATGGAATTGAGCGAGAGTGACAATGTTAATGCTGATCTACCTCTTTCTGTGAT
127 CCTCCTTTTGTGATGGAATTGAGC-A-A---A-AATGGCAATGCTGATCCACCTCCTTCTATGAT
* *
1557553 ATAATCGAGCAAAATGGTGATGC
186 AGAATCGAACAAAATGGTGATGC
* * *
1557576 TGATCCAACTTCTTATGTGATGGATTCGTGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACAT
1 TGATCCAACTTCTTCTGTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* * * *
1557641 CTTCTTCCTTCTCGGACGAGTTCTTCTCATTATGAACTCTTCTATTGGAAAAGATGATCCACCTC
66 CTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACCTC
*
1557706 CTTCTGTGATGGA
131 CTTTTGTGATGGA
1557719 TTTAAATCTA
Statistics
Matches: 299, Mismatches: 42, Indels: 24
0.82 0.12 0.07
Matches are distributed among these distances:
206 4 0.01
207 101 0.34
208 25 0.08
209 1 0.00
212 1 0.00
213 69 0.23
214 94 0.31
215 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (208 bp):
TGATCCAACTTCTTCTGTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
CTTCTTCCTCCTCGGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACCTC
CTTTTGTGATGGAATTGAGCAAAAATGGCAATGCTGATCCACCTCCTTCTATGATAGAATCGAAC
AAAATGGTGATGC
Found at i:1558096 original size:102 final size:102
Alignment explanation
Indices: 1557949--1558166 Score: 328
Period size: 102 Copynumber: 2.1 Consensus size: 102
1557939 GTTATATCAG
**
1557949 GTGAGATAAATTTTTGTTTCGAGTGAAACAATTACAGGTTTTGTGTTTCAAGGGAAACTGTCTCA
1 GTGAGATAAATTTTTGTTTCGAGTGAAACAATTACAAATTTTGTGTTTCAAGGGAAACTGTCTCA
* * *
1558014 AGCGAGACGAAATTGATTTTAAGGAAAACAATTTTAA
66 AGCGAGACGAAATTGATTTTAAGAAAAACAATCTCAA
* * *
1558051 GTGAGATGAATTTTTGTTTCGAGTGAAACAATTCCAAATTTTGTGTTTCGAGGGAAACTGTCTCA
1 GTGAGATAAATTTTTGTTTCGAGTGAAACAATTACAAATTTTGTGTTTCAAGGGAAACTGTCTCA
* **
1558116 AGCGAGATGAGGTTGATTTTAAGAAAAACAATCTCAA
66 AGCGAGACGAAATTGATTTTAAGAAAAACAATCTCAA
*
1558153 GTGATATAAATTTT
1 GTGAGATAAATTTT
1558167 GTCGTATCAG
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (102 bp):
GTGAGATAAATTTTTGTTTCGAGTGAAACAATTACAAATTTTGTGTTTCAAGGGAAACTGTCTCA
AGCGAGACGAAATTGATTTTAAGAAAAACAATCTCAA
Found at i:1560263 original size:7 final size:7
Alignment explanation
Indices: 1560248--1560532 Score: 281
Period size: 7 Copynumber: 39.4 Consensus size: 7
1560238 CTCATTTCAA
1560248 TTTTCTT
1 TTTTCTT
1560255 TCTTT-TT
1 T-TTTCTT
1560262 TCTTTCTT
1 T-TTTCTT
*
1560270 TTTTCAT
1 TTTTCTT
*
1560277 TTTTATT
1 TTTTCTT
1560284 TTTTCACTT
1 TTTT--CTT
1560293 TTTTCATTT
1 TTTTC--TT
1560302 TTTTCACTT
1 TTTT--CTT
1560311 TTTTCTATT
1 TTTTC--TT
1560320 TTTTCTAT
1 TTTTCT-T
1560328 TTTT-TCT
1 TTTTCT-T
*
1560335 TCTT-TT
1 TTTTCTT
1560341 TTTTCTT
1 TTTTCTT
1560348 TTTTCTT
1 TTTTCTT
1560355 TTTTCTT
1 TTTTCTT
1560362 TTTTCTT
1 TTTTCTT
1560369 TTTTCTT
1 TTTTCTT
*
1560376 TTTTCAT
1 TTTTCTT
*
1560383 TTTTCAT
1 TTTTCTT
1560390 TTTTCTT
1 TTTTCTT
1560397 TTTTCTT
1 TTTTCTT
1560404 TTTTCTT
1 TTTTCTT
1560411 TTTTCTT
1 TTTTCTT
1560418 TTTTCTT
1 TTTTCTT
1560425 TTTTC-T
1 TTTTCTT
1560431 TTTTCTTT
1 TTTTC-TT
1560439 TTTTCTT
1 TTTTCTT
1560446 TTTTCTT
1 TTTTCTT
*
1560453 TTTCCTT
1 TTTTCTT
*
1560460 TTTCCTT
1 TTTTCTT
*
1560467 TTTCCTT
1 TTTTCTT
*
1560474 TTTCCTT
1 TTTTCTT
*
1560481 TTTCCTT
1 TTTTCTT
*
1560488 TTTCCTT
1 TTTTCTT
*
1560495 TTTCCTT
1 TTTTCTT
*
1560502 TTTCCTT
1 TTTTCTT
*
1560509 TTTCCTT
1 TTTTCTT
*
1560516 TTTCCTT
1 TTTTCTT
*
1560523 TTTCCTT
1 TTTTCTT
1560530 TTT
1 TTT
1560533 CGAGTGTAAT
Statistics
Matches: 254, Mismatches: 10, Indels: 28
0.87 0.03 0.10
Matches are distributed among these distances:
6 10 0.04
7 201 0.79
8 17 0.07
9 25 0.10
11 1 0.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:1560469 original size:1 final size:1
Alignment explanation
Indices: 1560327--1560455 Score: 78
Period size: 1 Copynumber: 129.0 Consensus size: 1
1560317 ATTTTTTCTA
* * * * * * * ** **
1560327 TTTTTTCTTCTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCATTTTTCATTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
1560392 TTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTCTTTTTTTCTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1560456 CCTTTTTCCT
Statistics
Matches: 90, Mismatches: 38, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 90 1.00
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:1560854 original size:20 final size:21
Alignment explanation
Indices: 1560814--1560855 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1560804 ACAAATGAGA
1560814 ATGTTGTGGCAAAATGAAATGG
1 ATGTTGTGG-AAAATGAAATGG
*
1560836 ATGTTGTGG-AAATGGAATGG
1 ATGTTGTGGAAAATGAAATGG
1560856 TGGTGCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGAAAATGAAATGG
Found at i:1565389 original size:9 final size:9
Alignment explanation
Indices: 1565377--1565404 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1565367 ATTATTTCCA
1565377 TAAAATTTT
1 TAAAATTTT
1565386 TAAAATTTT
1 TAAAATTTT
1565395 TAAAATTTT
1 TAAAATTTT
1565404 T
1 T
1565405 CTCTCATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAAAATTTT
Found at i:1565765 original size:16 final size:16
Alignment explanation
Indices: 1565744--1565774 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1565734 AAAACTAATA
1565744 AAAGAATTCGACCATT
1 AAAGAATTCGACCATT
1565760 AAAGAATTCGACCAT
1 AAAGAATTCGACCAT
1565775 AAAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (16 bp):
AAAGAATTCGACCATT
Found at i:1567993 original size:13 final size:13
Alignment explanation
Indices: 1567977--1568003 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1567967 TCGGGATTTA
1567977 TGATTATCTCTTC
1 TGATTATCTCTTC
1567990 TGATTATCTCTTC
1 TGATTATCTCTTC
1568003 T
1 T
1568004 TCAATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (13 bp):
TGATTATCTCTTC
Found at i:1570179 original size:29 final size:29
Alignment explanation
Indices: 1570141--1570224 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
1570131 CCTATAGTTG
*
1570141 AGGATTATTTTGTAACATTCAATAGTTAT
1 AGGATTATTTTATAACATTCAATAGTTAT
* *
1570170 AGGATCATTTTATAACATTCAATATTTAT
1 AGGATTATTTTATAACATTCAATAGTTAT
* * *
1570199 ATGATTATTTTATAACTTTTAATAGT
1 AGGATTATTTTATAACATTCAATAGT
1570225 CATGGACTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (29 bp):
AGGATTATTTTATAACATTCAATAGTTAT
Found at i:1573653 original size:25 final size:25
Alignment explanation
Indices: 1573624--1573709 Score: 122
Period size: 25 Copynumber: 3.5 Consensus size: 25
1573614 ATCTTAGAAA
1573624 AATATAATT-TATTTAAATATTTTTT
1 AATATAATTAT-TTTAAATATTTTTT
*
1573649 AATATTATTATTTTAAATATTTTTT
1 AATATAATTATTTTAAATATTTTTT
*
1573674 AATATTATTATTTTAAATATTTTTT
1 AATATAATTATTTTAAATATTTTTT
*
1573699 AA-ATAAGTATT
1 AATATAATTATT
1573710 ATTTCTATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
24 7 0.12
25 49 0.86
26 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
AATATAATTATTTTAAATATTTTTT
Done.