Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 42
Found at i:4360712 original size:20 final size:20
Alignment explanation
Indices: 4360678--4360735 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
4360668 GCGATTCTCT
**
4360678 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATTCTCATTTCCA
*
4360698 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCA
*
4360718 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
4360736 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCA
Found at i:4362773 original size:42 final size:42
Alignment explanation
Indices: 4362713--4362835 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
4362703 GCCCGACTCG
* * *
4362713 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
4362755 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
4362797 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
4362836 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:4362793 original size:21 final size:21
Alignment explanation
Indices: 4362769--4362835 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4362759 TCATTCCTCG
4362769 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
4362790 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
4362811 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
4362832 AGAG
1 AGAG
4362836 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:4364214 original size:14 final size:14
Alignment explanation
Indices: 4364195--4364230 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4364185 TTTGTTTAAT
4364195 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4364209 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4364223 TGATTTGT
1 TGATTTGT
4364231 TTAACTGATG
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:4364361 original size:19 final size:19
Alignment explanation
Indices: 4364337--4364403 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
4364327 AAAAAGTACT
4364337 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
4364356 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
4364370 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4364389 ATCGCAACGCGAAAT
1 ATCGCAATGCGAAAT
4364404 TAAATTCGCG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.24
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4364430 original size:19 final size:19
Alignment explanation
Indices: 4364408--4364558 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
4364398 CGAAATTAAA
4364408 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4364427 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4364442 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
4364460 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
4364474 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4364493 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4364508 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
4364526 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
4364545 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4364559 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4364454 original size:33 final size:32
Alignment explanation
Indices: 4364412--4364538 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
4364402 ATTAAATTCG
4364412 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
4364445 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
4364478 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
4364511 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4364539 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:4364495 original size:66 final size:66
Alignment explanation
Indices: 4364405--4364537 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
4364395 ACGCGAAATT
*
4364405 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4364470 G
66 G
*
4364471 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4364536 G
66 G
4364537 A
1 A
4364538 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:4366830 original size:12 final size:12
Alignment explanation
Indices: 4366813--4366837 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4366803 TCTTCGGGGA
4366813 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4366825 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4366837 C
1 C
4366838 AAGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4368128 original size:20 final size:20
Alignment explanation
Indices: 4368103--4368180 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
4368093 ATTCATTTGA
4368103 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4368123 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4368143 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
4368163 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
4368181 CGCAATGCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:4368223 original size:14 final size:15
Alignment explanation
Indices: 4368203--4368275 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
4368193 TGAAAATCGC
4368203 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
4368218 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
4368235 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
4368253 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
4368269 -TTGCGAT
1 ATTGCGAT
4368276 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:4368240 original size:19 final size:19
Alignment explanation
Indices: 4368199--4368265 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
4368189 GAAATGAAAA
4368199 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
4368215 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4368232 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
4368250 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
4368266 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:4368401 original size:14 final size:14
Alignment explanation
Indices: 4368382--4368418 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4368372 CATCAATTAA
4368382 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
4368396 ACAAATCATCTTTT
1 ACAAATCAACATTT
4368410 ACAAATCAA
1 ACAAATCAA
4368419 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:4370347 original size:14 final size:14
Alignment explanation
Indices: 4370328--4370385 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4370318 TTTCATTTCG
4370328 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4370342 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4370358 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4370374 CGTTGCGATTTT
1 CGTTGCGATTTT
4370386 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4370392 original size:33 final size:33
Alignment explanation
Indices: 4370312--4370401 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 33
4370302 GCGGAAATAA
*
4370312 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
4370345 TGCGA-TTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
4370377 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
4370402 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
Found at i:4370420 original size:20 final size:19
Alignment explanation
Indices: 4370386--4370440 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
4370376 TTGCGATTTT
*
4370386 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4370405 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
4370425 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
4370441 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4370948 original size:18 final size:18
Alignment explanation
Indices: 4370922--4370966 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4370912 GTCGATCAGA
*
4370922 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4370940 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4370958 TGATGGCTC
1 TGATGGCTC
4370967 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:4372312 original size:20 final size:20
Alignment explanation
Indices: 4372287--4372324 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4372277 AATAGTTTCT
4372287 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
4372307 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
4372325 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:4372615 original size:22 final size:22
Alignment explanation
Indices: 4372588--4372631 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4372578 GATGGAGATA
4372588 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
4372610 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
4372632 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:4372844 original size:20 final size:20
Alignment explanation
Indices: 4372819--4372912 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
4372809 GATTATGTAT
4372819 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
4372839 TATCGCGTTGCGAAAGT-ACG
1 TATCGCGTTGCGAAAGTCA-G
* *** * *
4372859 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
4372880 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
4372900 TATCGCATTGCGA
1 TATCGCGTTGCGA
4372913 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.02
20 46 0.77
21 12 0.20
22 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:4372884 original size:41 final size:41
Alignment explanation
Indices: 4372839--4372916 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
4372829 CGAAAGTCAG
* * *
4372839 TATCGCGTTGCGAAAGT-ACGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTCA-GTATCGCATTGCGATTTTTTAT
*
4372880 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
4372917 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTTTAT
Found at i:4372913 original size:20 final size:19
Alignment explanation
Indices: 4372799--4372913 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
4372789 TGCTTTGAAA
*
4372799 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* *
4372820 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* *
4372840 ATCGCGTTGCGAAAGTACGT
1 ATCGCATTGCGATAGTA-GT
* * ** *
4372860 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA--TAGTAGT
4372881 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
4372901 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4372914 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.07
20 47 0.62
21 22 0.29
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:4372931 original size:21 final size:21
Alignment explanation
Indices: 4372902--4372994 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
4372892 ATAGTCAGTA
4372902 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
4372923 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
4372943 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
** * **
4372964 TCGGGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
4372984 TCGCATTGCGA
1 TCGCATTGCGA
4372995 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:4372932 original size:41 final size:41
Alignment explanation
Indices: 4372902--4372994 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
4372892 ATAGTCAGTA
* *
4372902 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
4372943 TCGCATTGCGATTTTCCCAATTCGGGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
4372984 TCGCATTGCGA
1 TCGCATTGCGA
4372995 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:4378288 original size:21 final size:21
Alignment explanation
Indices: 4378264--4378307 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4378254 TTTATATTAA
4378264 TTGTTCATTCTATTAGTAGTG
1 TTGTTCATTCTATTAGTAGTG
4378285 TTGTTCATTCTATTAGTAGTG
1 TTGTTCATTCTATTAGTAGTG
4378306 TT
1 TT
4378308 TATCCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (21 bp):
TTGTTCATTCTATTAGTAGTG
Found at i:4384278 original size:13 final size:13
Alignment explanation
Indices: 4384262--4384297 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4384252 CATCTCTGTC
*
4384262 TTTCTTTCTTTAT
1 TTTCTTTCATTAT
4384275 TTTCTTTCATTAT
1 TTTCTTTCATTAT
4384288 TTTCATTTCA
1 TTTC-TTTCA
4384298 CAATGCTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTTTCATTAT
Found at i:4388421 original size:20 final size:19
Alignment explanation
Indices: 4388388--4388453 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
4388378 CTGTGGGTAC
* *
4388388 CGATACTAAGCCTTCAGTAT
1 CGATACTGACCCTT-AGTAT
4388408 CGATACTGACCCTTAGGTAT
1 CGATACTGACCCTTA-GTAT
* * *
4388428 TGATATTGACCCATGAGTAT
1 CGATACTGACCC-TTAGTAT
4388448 CGATAC
1 CGATAC
4388454 CATTTTTAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.92
21 2 0.05
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (19 bp):
CGATACTGACCCTTAGTAT
Found at i:4388559 original size:30 final size:30
Alignment explanation
Indices: 4388509--4388579 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
4388499 CCTATGGAGA
*
4388509 GTATCGGTACCGGTATCGATACCACCTTAG
1 GTATCGGTACCGGCATCGATACCACCTTAG
* *
4388539 GTATTGGTGCCGGCATCGATACCACCTTAG
1 GTATCGGTACCGGCATCGATACCACCTTAG
4388569 GTATCGGTACC
1 GTATCGGTACC
4388580 AAAATTGTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (30 bp):
GTATCGGTACCGGCATCGATACCACCTTAG
Found at i:4389532 original size:31 final size:31
Alignment explanation
Indices: 4389465--4389524 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
4389455 CAATTTAAGG
*
4389465 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4389496 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4389525 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:4389616 original size:19 final size:19
Alignment explanation
Indices: 4389589--4389655 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4389579 AATGTTTTTA
* *
4389589 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
4389608 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* **
4389627 TGAACAGTAAATCACTGCT
1 TGAACAGTAAATTACTATT
4389646 TGAACAGTAA
1 TGAACAGTAA
4389656 CCCGAGGCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:4389786 original size:21 final size:21
Alignment explanation
Indices: 4389760--4389801 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4389750 ATTTGAATAT
*
4389760 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
4389781 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
4389802 CCCATTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:4389862 original size:21 final size:21
Alignment explanation
Indices: 4389829--4389868 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
4389819 TTTTTGCAGA
*
4389829 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
4389851 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
4389869 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:4390122 original size:34 final size:32
Alignment explanation
Indices: 4390083--4390152 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
4390073 TTTTGTAAAG
*
4390083 GGGAAAGGTTATAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
4390117 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
4390149 GGGA
1 GGGA
4390153 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:4393856 original size:17 final size:16
Alignment explanation
Indices: 4393824--4393858 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4393814 GTTAAACTCT
*
4393824 TATTTTTATTACTAAA
1 TATTTTTATTAATAAA
4393840 TATTTTTATTAGATAAA
1 TATTTTTATTA-ATAAA
4393857 TA
1 TA
4393859 AAGTCTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TATTTTTATTAATAAA
Found at i:4401009 original size:30 final size:30
Alignment explanation
Indices: 4400975--4401032 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4400965 ATGTTCGTTT
*
4400975 TTTTAGTTTAGTGTCTAACATTTTTTTTTG
1 TTTTAGTTTAGTGCCTAACATTTTTTTTTG
* *
4401005 TTTTAGTTTGGTGCCTAACGTTTTTTTT
1 TTTTAGTTTAGTGCCTAACATTTTTTTT
4401033 CGTCACTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.62
Consensus pattern (30 bp):
TTTTAGTTTAGTGCCTAACATTTTTTTTTG
Found at i:4401479 original size:26 final size:26
Alignment explanation
Indices: 4401443--4401494 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4401433 TCATGGCAGC
4401443 AAGGCACTTCGATTAG-GCTGGGCGGT
1 AAGGCACTTCGATT-GTGCTGGGCGGT
4401469 AAGGCACTTCGATTGTGCTGGGCGGT
1 AAGGCACTTCGATTGTGCTGGGCGGT
4401495 GACAGGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.17, C:0.19, G:0.38, T:0.25
Consensus pattern (26 bp):
AAGGCACTTCGATTGTGCTGGGCGGT
Found at i:4403711 original size:68 final size:68
Alignment explanation
Indices: 4403586--4403717 Score: 156
Period size: 68 Copynumber: 1.9 Consensus size: 68
4403576 GCGACTCTCT
* * * * * * * *
4403586 GTCTAAATTAGAATGGGTGAACCATAAATAACCATCACAACTCATTTGATCTCGTCAATAATAAT
1 GTCTAAATCAGAATGGATGAACCAGAAATAACCAACACAACCCATTTAATATCGTCAACAATAAT
4403651 CGC
66 CGC
* * * *
4403654 GTCTAAATCAGAATGGATGAACCGGCAATAACTAACACAACCCATTTAATATTGTCAACAATAA
1 GTCTAAATCAGAATGGATGAACCAGAAATAACCAACACAACCCATTTAATATCGTCAACAATAA
4403718 ACACATTTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 52 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (68 bp):
GTCTAAATCAGAATGGATGAACCAGAAATAACCAACACAACCCATTTAATATCGTCAACAATAAT
CGC
Found at i:4404536 original size:19 final size:19
Alignment explanation
Indices: 4404509--4404554 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4404499 TGATTTCATG
4404509 TTGACCGGTCCAAACCGGT
1 TTGACCGGTCCAAACCGGT
* **
4404528 TTGATCGGTCTGAACCGGT
1 TTGACCGGTCCAAACCGGT
4404547 TTGACCGG
1 TTGACCGG
4404555 GTTGACCGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.26
Consensus pattern (19 bp):
TTGACCGGTCCAAACCGGT
Found at i:4404553 original size:9 final size:9
Alignment explanation
Indices: 4404522--4404570 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
4404512 ACCGGTCCAA
4404522 ACCGGTTTG
1 ACCGGTTTG
* *
4404531 ATCGGTCTG
1 ACCGGTTTG
4404540 AACCGGTTTG
1 -ACCGGTTTG
*
4404550 ACCGGGTTG
1 ACCGGTTTG
*
4404559 ACCGGTCTG
1 ACCGGTTTG
4404568 ACC
1 ACC
4404571 AGACCCGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
9 25 0.78
10 7 0.22
ACGTcount: A:0.14, C:0.27, G:0.33, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:4404639 original size:29 final size:29
Alignment explanation
Indices: 4404601--4404791 Score: 187
Period size: 29 Copynumber: 6.7 Consensus size: 29
4404591 CCCGACCCAA
*
4404601 TGACATTCTGGGAATTTTTGTGAAAAATG
1 TGACATTCTGGGAATTTTTGTGAAAAAAG
* * *
4404630 TGACATTCTGGGATTTTTTATGAAAAATG
1 TGACATTCTGGGAATTTTTGTGAAAAAAG
* *
4404659 TAACATTCTGGGAATTTTTGTGAAAAAAA
1 TGACATTCTGGGAATTTTTGTGAAAAAAG
* *
4404688 TGACATTCTGGGGA-TTTTGTGGAAAAAGG
1 TGACATTCTGGGAATTTTTGT-GAAAAAAG
* * *
4404717 TGATATTATGGGGATTTTTGT--AAAAA-
1 TGACATTCTGGGAATTTTTGTGAAAAAAG
*
4404743 TGACAATT-TGGGAATTATTT-TAAAAAAAG
1 TGAC-ATTCTGGGAATT-TTTGTGAAAAAAG
* *
4404772 TGACATTTTAGGAATTTTTG
1 TGACATTCTGGGAATTTTTG
4404792 AATGTGGACT
Statistics
Matches: 136, Mismatches: 17, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
26 11 0.08
27 10 0.07
28 17 0.12
29 92 0.68
30 6 0.04
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (29 bp):
TGACATTCTGGGAATTTTTGTGAAAAAAG
Found at i:4404763 original size:87 final size:87
Alignment explanation
Indices: 4404599--4404791 Score: 222
Period size: 87 Copynumber: 2.3 Consensus size: 87
4404589 GACCCGACCC
* *
4404599 AATGACATTCTGGGAATTTTTGTGAAAAATGTGACATTCTGGGATTTTTTATGAAAAATGTAACA
1 AATGACATTCTGGGAATTTTTGTGAAAAAGGTGACATTATGGGATTTTTTATGAAAAATGTAACA
4404664 TTCTGGGAATTTTTGTGAAAAA
66 TTCTGGGAATTTTTGTGAAAAA
* * *
4404686 AATGACATTCTGGGGA-TTTTGTGGAAAAAGGTGATATTATGGGGA-TTTTTGT-AAAAATG--A
1 AATGACATTCTGGGAATTTTTGT-GAAAAAGGTGACATTAT-GGGATTTTTTATGAAAAATGTAA
4404746 CAATT-TGGGAATTATTT-T-AAAAA
64 C-ATTCTGGGAATT-TTTGTGAAAAA
* *
4404769 AAGTGACATTTTAGGAATTTTTG
1 AA-TGACATTCTGGGAATTTTTG
4404792 AATGTGGACT
Statistics
Matches: 92, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
83 7 0.08
84 22 0.24
85 11 0.12
86 13 0.14
87 35 0.38
88 4 0.04
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (87 bp):
AATGACATTCTGGGAATTTTTGTGAAAAAGGTGACATTATGGGATTTTTTATGAAAAATGTAACA
TTCTGGGAATTTTTGTGAAAAA
Found at i:4405856 original size:26 final size:26
Alignment explanation
Indices: 4405803--4405856 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
4405793 AGGGTAACTC
*
4405803 TTTTATGAGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* *
4405829 TTTTATGAGATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
4405855 TT
1 TT
4405857 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:4411943 original size:2 final size:2
Alignment explanation
Indices: 4411877--4411932 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
4411867 GAGAATGAGC
4411877 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
4411919 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
4411933 TTTGTATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4414409 original size:18 final size:18
Alignment explanation
Indices: 4414386--4414420 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4414376 TTATTTTGTA
4414386 ATATTAATAAATCAATAG
1 ATATTAATAAATCAATAG
4414404 ATATTAATAAATCAATA
1 ATATTAATAAATCAATA
4414421 TTTTTTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATTAATAAATCAATAG
Found at i:4414523 original size:18 final size:18
Alignment explanation
Indices: 4414500--4414541 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4414490 CTATGTTTAA
4414500 TATTAAAAAATATTGATT
1 TATTAAAAAATATTGATT
* **
4414518 TATTAATATCTATTGATT
1 TATTAAAAAATATTGATT
4414536 TATTAA
1 TATTAA
4414542 TTTAAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (18 bp):
TATTAAAAAATATTGATT
Found at i:4418719 original size:7 final size:7
Alignment explanation
Indices: 4418673--4418730 Score: 57
Period size: 7 Copynumber: 8.1 Consensus size: 7
4418663 TTTAAATTAT
*
4418673 TTAATCA
1 TTAATAA
*
4418680 TTATTAA
1 TTAATAA
4418687 GTTAATAA
1 -TTAATAA
4418695 TT--TAA
1 TTAATAA
4418700 TTGAATAAA
1 TT-AAT-AA
4418709 TTAATAA
1 TTAATAA
4418716 TTAATAA
1 TTAATAA
4418723 TTAATAA
1 TTAATAA
4418730 T
1 T
4418731 CTAGCCTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
5 5 0.12
7 24 0.56
8 10 0.23
9 4 0.09
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (7 bp):
TTAATAA
Found at i:4426746 original size:2 final size:2
Alignment explanation
Indices: 4426739--4427114 Score: 358
Period size: 2 Copynumber: 210.0 Consensus size: 2
4426729 TAATGACTAT
4426739 TA TA TA TA TA TA TA TA TA -A T- TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
4426778 TA TA -A T- TA T- TA TA TA TA TA -A TT TA -A T- TGA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
4426815 -A T- TA T- TA TA TGA TA T- TA TA TA TA TA -A T- TA TA TA -A T-
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4426850 TA TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
4426890 -A T- TT TA TA TA TA -A T- TA TT TA TA TA TA TA TA -A T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4426925 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA -A T- TA T- TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4426963 TA TA TA TA -A TA -A T- TA T- TA TA TA TA TA TA -A T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4426998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4427039 -A TA -A TA TA TA TA TA TA TA TA -A T- TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4427077 TA TA TA TA TA TA TA TA TA TA T- TA -A T- TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4427115 ATAATTGATA
Statistics
Matches: 317, Mismatches: 9, Indels: 96
0.75 0.02 0.23
Matches are distributed among these distances:
1 46 0.15
2 268 0.85
3 3 0.01
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4428805 original size:111 final size:111
Alignment explanation
Indices: 4428367--4428945 Score: 867
Period size: 110 Copynumber: 5.2 Consensus size: 111
4428357 TAACGCTTAT
* * * * * * ** *
4428367 AAAGTATCGATAC-TTTATAAAAATGTATCGATATTTTACACTATAACATATAAAAATATGACAA
1 AAAGTATAGATCCTTTTATAAAAA-GGATAGATACTTTACAATATAACAGGTAAAAATATGATAA
4428431 AACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
65 AACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
*
4428478 AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGT-AAAATATGATAAA
1 AAAGTATAGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGATAAA
*
4428542 ACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* *
4428588 AAAATATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGT-AAAATATGATAAA
1 AAAGTATAGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGATAAA
*
4428652 ACCAGTTTCATTATGACAAAATCGGTAAAATTTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
*
4428698 AAAGTATAGATCCTTTTATAAAAAAGATAGATACTTTACAATATAACAGGTAAAAATATGATAAA
1 AAAGTATAGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGATAAA
* * * *
4428763 ACTAATTTCATTATGACAAAAACGGTAAAATTTACTTAATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* * * *
4428809 AAAGTATATATCATTTTATAAAAAGGATAGATACTTTACAATATAATAGGTAAAAATATGACAAA
1 AAAGTATAGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGATAAA
* * *
4428874 ATCAGTTTCATTATGACAAAAACGGTAAAATTTATCTAATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* *
4428920 AAAGTATAAATACTTTTTATAAAAAG
1 AAAGTATAGAT-CCTTTTATAAAAAG
4428946 AATCGATATT
Statistics
Matches: 434, Mismatches: 31, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
110 213 0.49
111 198 0.46
112 23 0.05
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (111 bp):
AAAGTATAGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGATAAA
ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
Found at i:4428808 original size:221 final size:221
Alignment explanation
Indices: 4428371--4428944 Score: 873
Period size: 221 Copynumber: 2.6 Consensus size: 221
4428361 GCTTATAAAG
* * * * * **
4428371 TATCGATAC-TTTATAAAAATGTATCGATATTTTACACTATAACATATAAAAATATGACAAAACC
1 TATCGATCCTTTTATAAAAA-GGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACC
*
4428435 AGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTATAAA
65 AGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAA
* * *
4428500 AAGGATAGATACTTTACAATATAACAGGTAAAATATGATAAAACCAGTTTCATTATGACAAAACC
130 AAAGATAGATACTTTACAATATAACAGGTAAAATATGATAAAACCAATTTCATTATGACAAAAAC
*
4428565 GGTAAAATTTACCTGATATGTTGAAAA
195 GGTAAAATTTACCTAATATGTTGAAAA
*
4428592 TATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGT-AAAATATGATAAAACCA
1 TATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACCA
*
4428656 GTTTCATTATGACAAAATCGGTAAAATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAA
66 GTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAA
*
4428721 AAGATAGATACTTTACAATATAACAGGTAAAAATATGATAAAACTAATTTCATTATGACAAAAAC
131 AAGATAGATACTTTACAATATAACAGGT-AAAATATGATAAAACCAATTTCATTATGACAAAAAC
* *
4428786 GGTAAAATTTACTTAATATGTTGAAAG
195 GGTAAAATTTACCTAATATGTTGAAAA
** * * *
4428813 TATATATCATTTTATAAAAAGGATAGATACTTTACAATATAATAGGTAAAAATATGACAAAATCA
1 TATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACCA
* * * *
4428878 GTTTCATTATGACAAAAACGGTAAAATTTATCTAATATGTTGAAAGTATAAATACTTTTTATAAA
66 GTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATAGAT-CCTTTTATAAA
4428943 AA
130 AA
4428945 GAATCGATAT
Statistics
Matches: 321, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
220 106 0.33
221 129 0.40
222 74 0.23
223 12 0.04
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (221 bp):
TATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAAACCA
GTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATAGATCCTTTTATAAAA
AAGATAGATACTTTACAATATAACAGGTAAAATATGATAAAACCAATTTCATTATGACAAAAACG
GTAAAATTTACCTAATATGTTGAAAA
Found at i:4429598 original size:111 final size:111
Alignment explanation
Indices: 4429404--4429852 Score: 607
Period size: 111 Copynumber: 4.0 Consensus size: 111
4429394 GTATCGATAT
*
4429404 TTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAACGGTAAAATTTA
1 TTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGGTAAAATTTA
** *
4429469 CCTAATATGTTGAAAGTATCTATCCTTTTATAAAAAGGATTAATAC
66 CCTAATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATCAATAC
*
4429515 TTTACAATATAACAAT-TAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGATAAAATTT
1 TTTACAATATAAC-ATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGGTAAAATTT
* * ** * **
4429579 ACCTGATATGTTGAAAGTATCGATATTTTTATATAAAGGATCGGTAC
65 ACCTAATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATCAATAC
* * *
4429626 TTTACAATATAACATGTATAAATATGACAAAATCAGTTTCATTATGACAAAACCA-TTAAAATTT
1 TTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAA-AAGGTAAAATTT
* * *
4429690 ATCTAATATGTTGAAAATATAGATCCTTTTATAAAAAGGATAAATAC
65 ACCTAATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATCAATAC
* **
4429737 TTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTA
1 TTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGGTAAAATTTA
* * * *
4429802 CTTGATATGTTGAAAGTATATA-CACTTTTTATAAAAAAGGATCGATAC
66 CCTAATATGTTGAAAGTATAGATC-C-TTTTAT-AAAAAGGATCAATAC
4429850 TTT
1 TTT
4429853 TTTGAAAGTT
Statistics
Matches: 297, Mismatches: 34, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
110 4 0.01
111 268 0.90
112 9 0.03
113 16 0.05
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (111 bp):
TTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGGTAAAATTTA
CCTAATATGTTGAAAGTATAGATCCTTTTATAAAAAGGATCAATAC
Found at i:4429774 original size:222 final size:223
Alignment explanation
Indices: 4429388--4429852 Score: 716
Period size: 222 Copynumber: 2.1 Consensus size: 223
4429378 TAATAGCGCC
* *
4429388 TATAAAGTATCGATATTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACA
1 TATAAAGGATCGATACTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACA
* * ** *
4429453 AAAACGGTAAAATTTACCTAATATGTTGAAAGTATCTATCCTTTTATAAAAAGGATTAATACTTT
66 AAAACAGTAAAATTTACCTAATATGTTGAAAATATAGATCCTTTTATAAAAAGGATAAATACTTT
*
4429518 ACAATATAACAATTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGATAAAATTTACCT
131 ACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGATAAAATTTACCT
* *
4429583 GATATGTTGAAAGTATCGATA-TTTTTA
196 GATATGTTGAAAGTATAGACACTTTTTA
* *
4429610 TATAAAGGATCGGTACTTTACAATATAACATGTATAAATATGACAAAATCAGTTTCATTATGACA
1 TATAAAGGATCGATACTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACA
* * *
4429675 AAACCATTAAAATTTATCTAATATGTTGAAAATATAGATCCTTTTATAAAAAGGATAAATACTTT
66 AAAACAGTAAAATTTACCTAATATGTTGAAAATATAGATCCTTTTATAAAAAGGATAAATACTTT
* ** * *
4429740 ACAATATAACAGGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCGGTAAAATTTACTT
131 ACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGATAAAATTTACCT
*
4429805 GATATGTTGAAAGTATATACACTTTTTA
196 GATATGTTGAAAGTATAGACACTTTTTA
*
4429833 TAAAAAAGGATCGATACTTT
1 T-ATAAAGGATCGATACTTT
4429853 TTTGAAAGTT
Statistics
Matches: 218, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
222 195 0.89
223 7 0.03
224 16 0.07
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (223 bp):
TATAAAGGATCGATACTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACA
AAAACAGTAAAATTTACCTAATATGTTGAAAATATAGATCCTTTTATAAAAAGGATAAATACTTT
ACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAAAGATAAAATTTACCT
GATATGTTGAAAGTATAGACACTTTTTA
Found at i:4432326 original size:36 final size:36
Alignment explanation
Indices: 4432286--4432373 Score: 142
Period size: 36 Copynumber: 2.4 Consensus size: 36
4432276 TTCCTCTTCC
4432286 GTCAACCCCGAATGCTTCTGCTCCAG-CCCCTTCTCT
1 GTCAACCCCGAATGCTTCTGCTCC-GTCCCCTTCTCT
* *
4432322 GTCAATCCCGAATGCTTCTGCTCCGTCTCCTTCTCT
1 GTCAACCCCGAATGCTTCTGCTCCGTCCCCTTCTCT
4432358 GTCAACCCCGAATGCT
1 GTCAACCCCGAATGCT
4432374 CCTCGGCGCC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
35 1 0.02
36 47 0.98
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.30
Consensus pattern (36 bp):
GTCAACCCCGAATGCTTCTGCTCCGTCCCCTTCTCT
Found at i:4434286 original size:35 final size:35
Alignment explanation
Indices: 4434247--4434352 Score: 169
Period size: 35 Copynumber: 3.0 Consensus size: 35
4434237 AAATAAATTA
4434247 TTTATCATTAAATACTATATATAACAGTAATTAGG
1 TTTATCATTAAATACTATATATAACAGTAATTAGG
* *
4434282 TTTATCATTAAATATTATATTTGAA-AGTAATTAGG
1 TTTATCATTAAATACTATATAT-AACAGTAATTAGG
*
4434317 TTTATCGTTAAATACTATATATAACAGTAATTAGG
1 TTTATCATTAAATACTATATATAACAGTAATTAGG
4434352 T
1 T
4434353 GTGATATAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
34 2 0.03
35 60 0.94
36 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTATCATTAAATACTATATATAACAGTAATTAGG
Found at i:4434946 original size:14 final size:14
Alignment explanation
Indices: 4434927--4434982 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
4434917 CGTTCGTGAA
4434927 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
4434941 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
4434954 --TT-GTTTATGTT
1 CGTTCGATTATGTT
4434965 CGTTCGATTATGTT
1 CGTTCGATTATGTT
4434979 CGTT
1 CGTT
4434983 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:4434961 original size:24 final size:24
Alignment explanation
Indices: 4434934--4435003 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
4434924 GAACGTTCGA
*
4434934 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
4434958 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
4434982 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
4435004 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:4435743 original size:10 final size:10
Alignment explanation
Indices: 4435728--4435802 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
4435718 GGGTCTCCAA
4435728 CGTTTATGTT
1 CGTTTATGTT
4435738 CGTTTATGTT
1 CGTTTATGTT
4435748 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
4435759 ATGTTCGTGTT
1 -CGTTTATGTT
4435770 CGTTTATGTT
1 CGTTTATGTT
4435780 CG----TGTT
1 CGTTTATGTT
4435786 CGTTTATGTT
1 CGTTTATGTT
4435796 CGTTTAT
1 CGTTTAT
4435803 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:4435759 original size:16 final size:16
Alignment explanation
Indices: 4435734--4435798 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
4435724 CCAACGTTTA
4435734 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
4435750 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
4435766 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4435782 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4435798 T
1 T
4435799 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4435889 original size:16 final size:16
Alignment explanation
Indices: 4435868--4435900 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4435858 AAAAAAAATT
4435868 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4435884 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4435900 T
1 T
4435901 CTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4444561 original size:3 final size:3
Alignment explanation
Indices: 4444516--4444542 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4444506 AGCCTTTATT
4444516 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
4444543 TCTACACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4445979 original size:20 final size:23
Alignment explanation
Indices: 4445956--4446005 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 23
4445946 AGATATATTG
4445956 TATTTAATATT-TCAAAAT-T-T
1 TATTTAATATTATCAAAATATAT
* *
4445976 TATTTTATATTATTAAAATATAT
1 TATTTAATATTATCAAAATATAT
4445999 TATTTAA
1 TATTTAA
4446006 CTACTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 6 0.25
22 1 0.04
23 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTAATATTATCAAAATATAT
Found at i:4448699 original size:8 final size:8
Alignment explanation
Indices: 4448686--4448728 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
4448676 TAAGGGTTTT
4448686 GATTTAGA
1 GATTTAGA
4448694 GATTTAGA
1 GATTTAGA
4448702 GATTTAGA
1 GATTTAGA
*
4448710 TA-TTA-A
1 GATTTAGA
*
4448716 GATTTAGG
1 GATTTAGA
4448724 GATTT
1 GATTT
4448729 CATTACTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 2 0.07
7 6 0.20
8 22 0.73
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (8 bp):
GATTTAGA
Found at i:4448718 original size:14 final size:16
Alignment explanation
Indices: 4448686--4448728 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
4448676 TAAGGGTTTT
4448686 GATTTAGAGATTTAGA
1 GATTTAGAGATTTAGA
*
4448702 GATTTAGATA-TTA-A
1 GATTTAGAGATTTAGA
*
4448716 GATTTAGGGATTT
1 GATTTAGAGATTT
4448729 CATTACTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.39
15 5 0.22
16 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (16 bp):
GATTTAGAGATTTAGA
Found at i:4449836 original size:30 final size:29
Alignment explanation
Indices: 4449800--4449985 Score: 159
Period size: 30 Copynumber: 6.3 Consensus size: 29
4449790 GACTAAGATG
* * *
4449800 GTAAAAATCTAAAATCCTAAGGACTTAAGT
1 GTAAAAAACT-AAATTCTAGGGACTTAAGT
* *
4449830 GTAAAAAAACTAAAGTATAGGGA-TCTAAGT
1 GT-AAAAAACTAAATTCTAGGGACT-TAAGT
4449860 GTAAAAAACTAAATTCTAGGGAC-TACAGT
1 GTAAAAAACTAAATTCTAGGGACTTA-AGT
4449889 GTAAAAAAACTAAATTCTAGGGA-TTAGAGT
1 GT-AAAAAACTAAATTCTAGGGACTTA-AGT
* * *
4449919 GTAAAAAACCTAAAGTATAGGAAC-TAAGGT
1 GTAAAAAA-CTAAATTCTAGGGACTTAA-GT
*
4449949 GTAAAAAATCTAAAGTCTAGGGAC-TAAG-
1 GTAAAAAA-CTAAATTCTAGGGACTTAAGT
*
4449977 ATAAAAAAC
1 GTAAAAAAC
4449986 AAAACAATTC
Statistics
Matches: 132, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.01
28 9 0.07
29 32 0.24
30 83 0.63
31 7 0.05
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (29 bp):
GTAAAAAACTAAATTCTAGGGACTTAAGT
Found at i:4449896 original size:60 final size:58
Alignment explanation
Indices: 4449800--4449985 Score: 207
Period size: 59 Copynumber: 3.2 Consensus size: 58
4449790 GACTAAGATG
* * * *
4449800 GTAAAAATCTAAAATCCTAAGGACTTAAGTGTAAAAAAACTAAAGTATAGGGATCTAAGT
1 GTAAAAAACT-AAATTCTAGGGAC-TAAGTGTAAAAAAACTAAAGTCTAGGGATCTAAGT
*
4449860 GTAAAAAACTAAATTCTAGGGACTACAGTGTAAAAAAACTAAATTCTAGGGAT-TAGAGT
1 GTAAAAAACTAAATTCTAGGGACTA-AGTGTAAAAAAACTAAAGTCTAGGGATCTA-AGT
* * * *
4449919 GTAAAAAACCTAAAGTATAGGAACTAAGGTGTAAAAAATCTAAAGTCTAGGGA-CTAAG-
1 GTAAAAAA-CTAAATTCTAGGGACTAA-GTGTAAAAAAACTAAAGTCTAGGGATCTAAGT
*
4449977 ATAAAAAAC
1 GTAAAAAAC
4449986 AAAACAATTC
Statistics
Matches: 110, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
57 1 0.01
58 11 0.10
59 50 0.45
60 48 0.44
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (58 bp):
GTAAAAAACTAAATTCTAGGGACTAAGTGTAAAAAAACTAAAGTCTAGGGATCTAAGT
Found at i:4451164 original size:3 final size:3
Alignment explanation
Indices: 4451154--4451201 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
4451144 TGTATTTTTT
* *
4451154 TAA T-A TAA TAA TAA TAA T-A TAA T-A TAA TAA CAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4451199 TAA
1 TAA
4451202 AAAAATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:4451178 original size:19 final size:19
Alignment explanation
Indices: 4451154--4451191 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4451144 TGTATTTTTT
*
4451154 TAATATAATAATAATAATA
1 TAATATAATAACAATAATA
4451173 TAATATAATAACAATAATA
1 TAATATAATAACAATAATA
4451192 ACAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATATAATAACAATAATA
Found at i:4454584 original size:17 final size:17
Alignment explanation
Indices: 4454559--4454591 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4454549 TTTAGTGACT
4454559 AAAAATATA-ATTTTAA
1 AAAAATATATATTTTAA
4454575 AAAAATTATATATTTTA
1 AAAAA-TATATATTTTA
4454592 GCTCGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAATATATATTTTAA
Found at i:4457379 original size:18 final size:18
Alignment explanation
Indices: 4457349--4457461 Score: 79
Period size: 18 Copynumber: 6.4 Consensus size: 18
4457339 CATTTCACTG
*
4457349 TTATAAGAT-ATTTACAA
1 TTATCAGATGATTTACAA
* ****
4457366 TTATCATATGATTTTTGG
1 TTATCAGATGATTTACAA
4457384 TTATCAGAT-ATTTACAA
1 TTATCAGATGATTTACAA
* * * * *
4457401 TTATTAAATAATTTTCAG
1 TTATCAGATGATTTACAA
*
4457419 TTATCAGATGA-TTAAAA
1 TTATCAGATGATTTACAA
* *
4457436 TTATCAGATGTTTTACAG
1 TTATCAGATGATTTACAA
4457454 TTATCAGA
1 TTATCAGA
4457462 CGTAGAATAA
Statistics
Matches: 69, Mismatches: 24, Indels: 5
0.70 0.24 0.05
Matches are distributed among these distances:
17 31 0.45
18 38 0.55
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (18 bp):
TTATCAGATGATTTACAA
Found at i:4457415 original size:35 final size:35
Alignment explanation
Indices: 4457348--4457461 Score: 115
Period size: 35 Copynumber: 3.3 Consensus size: 35
4457338 ACATTTCACT
* * * **
4457348 GTTATAAGATATTTACAATTATCATATGATTTTTG
1 GTTATCAGATATTTACAATTATCAAATAATTTTCA
*
4457383 GTTATCAGATATTTACAATTATTAAATAATTTTCA
1 GTTATCAGATATTTACAATTATCAAATAATTTTCA
* * *
4457418 GTTATCAGATGA-TTAAAATTATCAGAT-GTTTTACA
1 GTTATCAGAT-ATTTACAATTATCAAATAATTTT-CA
4457453 GTTATCAGA
1 GTTATCAGA
4457462 CGTAGAATAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
34 4 0.06
35 62 0.93
36 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (35 bp):
GTTATCAGATATTTACAATTATCAAATAATTTTCA
Found at i:4461133 original size:45 final size:45
Alignment explanation
Indices: 4461069--4461184 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 45
4461059 CGGATACGGG
** * * *
4461069 TACATGTATGTTTGGATATTGTAATGCTTGGGTATAGTTGTTGGA
1 TACATGTATGTTTGGATATTACAATGCTCGAGTATAGTGGTTGGA
* * *
4461114 TACATGTATTTTTGGATATTACGATGCTCGAGTGTAGTGGTTGGA
1 TACATGTATGTTTGGATATTACAATGCTCGAGTATAGTGGTTGGA
* * *
4461159 TACATGTATGTTCGTATACTACAATG
1 TACATGTATGTTTGGATATTACAATG
4461185 TGTATAGTTG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (45 bp):
TACATGTATGTTTGGATATTACAATGCTCGAGTATAGTGGTTGGA
Found at i:4461212 original size:16 final size:17
Alignment explanation
Indices: 4461182--4461213 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4461172 GTATACTACA
4461182 ATGTGTATAGTTGTTGG
1 ATGTGTATAGTTGTTGG
4461199 ATGTGTAT-GTTGTTG
1 ATGTGTATAGTTGTTG
4461214 TTGTTGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (17 bp):
ATGTGTATAGTTGTTGG
Found at i:4477569 original size:2 final size:2
Alignment explanation
Indices: 4477562--4477614 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
4477552 CGGAGTTATG
4477562 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
4477604 AT AT ACT AT AT
1 AT AT A-T AT AT
4477615 GAAAATGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4478012 original size:23 final size:24
Alignment explanation
Indices: 4477982--4478034 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
4477972 TCCTTCGGGA
4477982 CATAGTGGTCC-TCGGGGAC-ATTT
1 CATAGTGGTCCTTC-GGGACAATTT
4478005 CATAGTGGTCCTTCGGGACAGATTT
1 CATAGTGGTCCTTCGGGACA-ATTT
4478030 CATAG
1 CATAG
4478035 CCCATAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 16 0.59
24 2 0.07
25 9 0.33
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (24 bp):
CATAGTGGTCCTTCGGGACAATTT
Found at i:4481204 original size:25 final size:25
Alignment explanation
Indices: 4481176--4481300 Score: 214
Period size: 25 Copynumber: 5.0 Consensus size: 25
4481166 AGTTAGGGGA
*
4481176 TTAGGGTTTGAAACCCTAGTCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
4481201 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
4481226 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
4481251 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
4481276 TTAGGGTTTAAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
4481301 GGGTTGTTGG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 96 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:4481403 original size:3 final size:3
Alignment explanation
Indices: 4481395--4481450 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
4481385 GCAAAAATTG
* **
4481395 TAA TAA TAA TAA TAA TAA -AA -AA TAA -GA TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4481440 TAA TAA -AA TAA
1 TAA TAA TAA TAA
4481451 CGGAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 7 0.16
3 37 0.84
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:4481713 original size:48 final size:44
Alignment explanation
Indices: 4481659--4481809 Score: 139
Period size: 41 Copynumber: 3.4 Consensus size: 44
4481649 GTGACATGGC
*
4481659 TCCTACGTGATGAGGAGATCTGGTCATCTTTAGGGATGATAACTCGGT
1 TCCTACGTGATGAGGAGATCTGGTCATC--TA-GG-TGATAACACGGT
* * * *
4481707 TCCTACGTAATGAGGACGA-CTGGTTATC-AGGT--TGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTCATCTAGGTGATAACACGGT
* * *
4481748 TCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGGTCATCT--AGGTGATAACACGGT
4481794 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
4481810 CGGCTGGTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
40 2 0.02
41 26 0.32
43 1 0.01
44 6 0.07
45 1 0.01
46 21 0.26
48 23 0.28
49 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (44 bp):
TCCTACGTGATGAGGAGATCTGGTCATCTAGGTGATAACACGGT
Found at i:4481829 original size:89 final size:89
Alignment explanation
Indices: 4481650--4481944 Score: 355
Period size: 89 Copynumber: 3.2 Consensus size: 89
4481640 CGTCTAAGGG
* * * * *
4481650 TGACATGGCTCCTACGTGATGAGGAGATCTGGTCATCTTTAGGGATGATAACTCGGTTCCTACGT
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGCCATC-TAAAGG-TGATAACTCGGTTCCTACGT
* *
4481715 AATGAGGACGACTGGTTATC-A-GGT
64 GATGAGGACGGCTGGTTATCTATGGT
* *
4481739 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACTCGGTTCCTACGTGA
4481804 TGAGGACGGCTGGTTATCTATGGT
66 TGAGGACGGCTGGTTATCTATGGT
* * *
4481828 TGACACGGCTCATACATGATGAAGA-ACTCTGGCCACCTTTAGGAAGGGTGATAACTCGGTTCCT
1 TGACACGGCTCCTACGTGATGAAGAGA-TCTGGCCA--TCTA--AA-GGTGATAACTCGGTTCCT
*
4481892 ACGTGATAAGGACGGCTGGTTATCCTAAT-GT
60 ACGTGATGAGGACGGCTGGTTAT-CT-ATGGT
4481923 TGACACGGCTCCTACGTGATGA
1 TGACACGGCTCCTACGTGATGA
4481945 GGAAGTCTGG
Statistics
Matches: 180, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
87 37 0.21
88 6 0.03
89 67 0.37
91 3 0.02
93 2 0.01
94 39 0.22
95 24 0.13
96 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (89 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACTCGGTTCCTACGTGA
TGAGGACGGCTGGTTATCTATGGT
Found at i:4481848 original size:43 final size:42
Alignment explanation
Indices: 4481710--4481849 Score: 122
Period size: 46 Copynumber: 3.2 Consensus size: 42
4481700 ACTCGGTTCC
* *
4481710 TACGTAATGAGGACGACTGGTTATC-AGGTTGACACGGCTCT
1 TACGTGATGAGGACGACTGGTTATCTAGGTTGACACGGCTCA
* ** * * *
4481751 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACGA-CTGGTTATCT--AGGT--TGACACGGCTCA
*
4481797 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCA
1 TACGTGATGAGGACGACTGGTTATCTA-GGTTGACACGGCTCA
*
4481840 TACATGATGA
1 TACGTGATGA
4481850 AGAACTCTGG
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
40 2 0.03
41 18 0.24
43 18 0.24
44 5 0.07
45 3 0.04
46 29 0.38
47 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (42 bp):
TACGTGATGAGGACGACTGGTTATCTAGGTTGACACGGCTCA
Found at i:4482924 original size:7 final size:8
Alignment explanation
Indices: 4482895--4482931 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
4482885 TCCTTTATTT
4482895 ATTTTTTC
1 ATTTTTTC
*
4482903 TTCTTTTTC
1 AT-TTTTTC
4482912 ATTTTTTC
1 ATTTTTTC
4482920 ATTTTTTC
1 ATTTTTTC
4482928 ATTT
1 ATTT
4482932 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Found at i:4496529 original size:25 final size:25
Alignment explanation
Indices: 4496501--4496625 Score: 223
Period size: 25 Copynumber: 5.0 Consensus size: 25
4496491 AGTTAGGGGA
*
4496501 TTAGGGTTTGAAACCCTAGTCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
4496526 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
4496551 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
4496576 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
4496601 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
4496626 GGGTTGTTGG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 97 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:4496728 original size:3 final size:3
Alignment explanation
Indices: 4496720--4496780 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
4496710 GCAAAAATTG
* **
4496720 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4496764 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
4496781 CGGAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:4499413 original size:2 final size:2
Alignment explanation
Indices: 4499406--4499450 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
4499396 TTTAAAATTA
4499406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
4499447 AT AT
1 AT AT
4499451 GATTTTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4499508 original size:2 final size:2
Alignment explanation
Indices: 4499503--4499531 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4499493 GGGTTATACT
4499503 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 T
4499532 TACTTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4507558 original size:2 final size:2
Alignment explanation
Indices: 4507553--4507591 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4507543 TTTTTTTTAA
*
4507553 AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4507592 ATGGATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4509199 original size:4 final size:4
Alignment explanation
Indices: 4509190--4509313 Score: 99
Period size: 4 Copynumber: 31.5 Consensus size: 4
4509180 CAATAGCTTT
* * * * * *
4509190 TACA TACA TACA TACA TACA T--A TATA TATA TATA TATA TATA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
4509236 TACA TATA TACA TATA TACA TACA TACA TATA TATA TATA TACA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
4509284 TATA TATA TACA TACA TATA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
4509314 TATATATATA
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.02
4 105 0.98
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (4 bp):
TACA
Found at i:4509203 original size:8 final size:8
Alignment explanation
Indices: 4509190--4509325 Score: 159
Period size: 8 Copynumber: 17.2 Consensus size: 8
4509180 CAATAGCTTT
*
4509190 TACATACA
1 TACATATA
*
4509198 TACATACA
1 TACATATA
4509206 TACATATA
1 TACATATA
4509214 T--ATATA
1 TACATATA
*
4509220 TATATATA
1 TACATATA
*
4509228 TATATATA
1 TACATATA
4509236 TACATATA
1 TACATATA
4509244 TACATATA
1 TACATATA
*
4509252 TACATACA
1 TACATATA
4509260 TACATATA
1 TACATATA
*
4509268 TATATATA
1 TACATATA
4509276 TACATATA
1 TACATATA
*
4509284 TATATATA
1 TACATATA
*
4509292 TACATACA
1 TACATATA
* *
4509300 TATATACA
1 TACATATA
4509308 TACATATA
1 TACATATA
*
4509316 TATATATA
1 TACATATA
4509324 TA
1 TA
4509326 TAAATACATA
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
6 6 0.05
8 107 0.95
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:4509318 original size:4 final size:4
Alignment explanation
Indices: 4509209--4509327 Score: 148
Period size: 4 Copynumber: 29.8 Consensus size: 4
4509199 ACATACATAC
* * *
4509209 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ACAT ATAT ACAT ATAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
4509257 ACAT ACAT ATAT ATAT ATAT ACAT ATAT ATAT ATAT ACAT ACAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
4509305 ACAT ACAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATA
4509328 AATACATATG
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 103 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:4510124 original size:15 final size:15
Alignment explanation
Indices: 4510099--4510136 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4510089 AAAGAAGTTT
*
4510099 AACATATTTATAT-C
1 AACACATTTATATCC
4510113 AGACACATTTATATCC
1 A-ACACATTTATATCC
4510129 AACACATT
1 AACACATT
4510137 AACTCGATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (15 bp):
AACACATTTATATCC
Found at i:4512167 original size:2 final size:2
Alignment explanation
Indices: 4512109--4512150 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4512099 TGAATGTTGG
4512109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
4512150 A
1 A
4512151 CACACACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4513426 original size:21 final size:22
Alignment explanation
Indices: 4513400--4513443 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
4513390 ATGTAATTTA
4513400 ATTATT-TTATTTATAT-TTTCT
1 ATTATTATTA-TTATATGTTTCT
4513421 ATTATTATTATTATATGTTTCT
1 ATTATTATTATTATATGTTTCT
4513443 A
1 A
4513444 CTTACTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTATTATTATATGTTTCT
Found at i:4524228 original size:25 final size:25
Alignment explanation
Indices: 4524194--4524262 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
4524184 GGGTAGAGGG
4524194 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
4524219 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
4524244 TCTACGCGGTCCTTCGGGA
1 TCTACGCGGTCCTTCGGGA
4524263 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:4524421 original size:23 final size:23
Alignment explanation
Indices: 4524377--4524421 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4524367 ATTACTATAT
*
4524377 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
4524400 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
4524422 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:4525795 original size:25 final size:24
Alignment explanation
Indices: 4525767--4525823 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
4525757 TAATTTTATA
* **
4525767 TGTTCGTTTATATTCATTTGTTTG
1 TGTTCGTTTACATTCATTCATTTG
* *
4525791 TTGTTAGTTTACCTTCATTCATTTG
1 -TGTTCGTTTACATTCATTCATTTG
4525816 TGTTCGTT
1 TGTTCGTT
4525824 GATAATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (24 bp):
TGTTCGTTTACATTCATTCATTTG
Found at i:4528120 original size:9 final size:9
Alignment explanation
Indices: 4528098--4528135 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
4528088 TTTTTGTTTC
4528098 ATTACTA-T
1 ATTACTATT
4528106 -TTACTATT
1 ATTACTATT
4528114 ATTACTATT
1 ATTACTATT
*
4528123 ATTATTATT
1 ATTACTATT
4528132 ATTA
1 ATTA
4528136 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
7 6 0.22
8 1 0.04
9 20 0.74
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTACTATT
Found at i:4535309 original size:18 final size:18
Alignment explanation
Indices: 4535266--4535376 Score: 114
Period size: 18 Copynumber: 5.9 Consensus size: 18
4535256 AGGGATTATC
* *
4535266 AGTGGTCATTCGGGACAAAC
1 AGTGGTCCTTCGGGAC--AT
4535286 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
** * *
4535304 AGTGGTTATTCGGAACAACC
1 AGTGGTCCTTCGGGAC-A-T
4535324 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
4535342 AGTTGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
4535360 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
4535377 AATATTTAGT
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
18 46 0.61
19 2 0.03
20 28 0.37
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:4535327 original size:38 final size:38
Alignment explanation
Indices: 4535266--4535376 Score: 136
Period size: 38 Copynumber: 3.0 Consensus size: 38
4535256 AGGGATTATC
*
4535266 AGTGGTCATTCGGGACAAACAGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGAACAAACAGTGGTCCTTCGGGACAT
* *
4535304 AGTGGTTATTCGGAACAACCAGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGAACAAACAGTGGTCCTTCGGGACAT
* * * * *
4535342 AGTTGTCCTTCGGGAC--ATAGTGGTCTTTCGGGACA
1 AGTGGTCATTCGGAACAAACAGTGGTCCTTCGGGACA
4535377 AATATTTAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 16 0.25
38 47 0.75
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.27
Consensus pattern (38 bp):
AGTGGTCATTCGGAACAAACAGTGGTCCTTCGGGACAT
Found at i:4552231 original size:12 final size:12
Alignment explanation
Indices: 4552214--4552241 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4552204 AAACAAAAAT
4552214 AAATATGTTCAC
1 AAATATGTTCAC
4552226 AAATATGTTCAC
1 AAATATGTTCAC
4552238 AAAT
1 AAAT
4552242 CAAACATATA
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:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (12 bp):
AAATATGTTCAC
Found at i:4553662 original size:483 final size:484
Alignment explanation
Indices: 4552754--4553720 Score: 1596
Period size: 483 Copynumber: 2.0 Consensus size: 484
4552744 ATTCCAAAAT
*
4552754 AGATTTAGAAAAGATATGCTCTATTTTAGGAAAATACCTTATATTTGGGTTAAAATATTCGTAAG
1 AGATTTAGAAAAGATATGCTCTATTTTAGGAAAATACCTCATATTTGGGTTAAAATATTCGTAAG
*
4552819 CCTACAAAGTAACTGACCGGTTTAGACATTAACGTTACCCATACTGTGCACGTCTGCACATGTAC
66 CCTACAAAGTAACTGACCGGTTCAGACATTAACGTTACCCATACTGTGCACGTCTGCACATGTAC
* * *
4552884 AAACCAACAATTGGTTCCACATTTTGCTCAACAACGTTTGGATCAGTTTCTCATTCAAAGCTCCA
131 AAACCAACAATTAGTTCCACATTTTGCTCAACAACGTTTGAATCAATTTCTCATTCAAAGCTCCA
*
4552949 AAAGTATCAAAAAAAATTCCCAACAACCCCCCACATGAATGAAATTGAACATTTTATGAAAACCA
196 AAAGTATC-AAAAAAATTCCCAACAACCCCCCACATGAATGAAATTGAACATTTTATCAAAACCA
*
4553014 TTTTGACTCGATGTGATGATAGACTTTATGATCGATAATTACACAGGATAGGTAGGTGTCCTCCT
260 TTTTGACTCGATGTGATGATAGACTTTACGATCGATAATTACACAGGATAGGTAGGTGTCCTCCT
*
4553079 TTGAACATTTCCTTGTGACAACATATTTACTTTACTAGCTGACCAATAGACGTGATGTCCTTGAA
325 TTGAACATTTCCTTGTGACAACATATTTACTTTACTAGCTGACCAATAGACGTGATGTCATTGAA
* * *
4553144 TTGTTATATCGTTTGTGTAAAGGATAATATATTTCACACATCTACCCCTTTGACAAGAATTTTAG
390 CTGTTATATCGTTCGTGTAAAGGATAATATATTTCACACAACTACCCCTTTGACAAGAATTTTAG
4553209 TTCTCATAGGTATGTCCTTAAAGCCATGGC
455 TTCTCATAGGTATGTCCTTAAAGCCATGGC
* * * *
4553239 AGATTTAGAACAGATATGCTCTATTTTAGGAAAATATCTCATGTTTGGGTTAAAATATTTGTAAG
1 AGATTTAGAAAAGATATGCTCTATTTTAGGAAAATACCTCATATTTGGGTTAAAATATTCGTAAG
* * * *
4553304 CCTACAAGGTAACTGACCGGTTCGGACATTAACGTTACCCATATTGTGCACGTCTGCACATGTAT
66 CCTACAAAGTAACTGACCGGTTCAGACATTAACGTTACCCATACTGTGCACGTCTGCACATGTAC
4553369 AAACCAACAATTAGTTCCACATTTTGCTCAACAACGTTTGAATCAATTTCTCATTCAAAGCTCCA
131 AAACCAACAATTAGTTCCACATTTTGCTCAACAACGTTTGAATCAATTTCTCATTCAAAGCTCCA
*** * * *
4553434 AAAGTATC-AAATTTTTTCCAACAATCCCCCACATGAATGAAATTGATCATTTTATCAAAACCAT
196 AAAGTATCAAAAAAATTCCCAACAACCCCCCACATGAATGAAATTGAACATTTTATCAAAACCAT
* * *
4553498 TTTGACTCGATGTGGTGATAGACTTTACGATCGATAATTGCATAGGATAGGTAGGTGTCCTCCTT
261 TTTGACTCGATGTGATGATAGACTTTACGATCGATAATTACACAGGATAGGTAGGTGTCCTCCTT
* **
4553563 TGAGCA-TTCCATTGTGACAGTATATTTACTTTACTAGCTGACCAATAGACGTGATGTCATTGAA
326 TGAACATTTCC-TTGTGACAACATATTTACTTTACTAGCTGACCAATAGACGTGATGTCATTGAA
4553627 CTGTTATATCGTTCGTGTAAAGGATAATATATTTCACACAACTACCCCTTTGACAAGAATTTTAG
390 CTGTTATATCGTTCGTGTAAAGGATAATATATTTCACACAACTACCCCTTTGACAAGAATTTTAG
* **
4553692 TTCTCATGGGTATGTTTTTAAAGCCATGG
455 TTCTCATAGGTATGTCCTTAAAGCCATGG
4553721 ACATTGTCTG
Statistics
Matches: 447, Mismatches: 34, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
482 4 0.01
483 253 0.57
485 190 0.43
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (484 bp):
AGATTTAGAAAAGATATGCTCTATTTTAGGAAAATACCTCATATTTGGGTTAAAATATTCGTAAG
CCTACAAAGTAACTGACCGGTTCAGACATTAACGTTACCCATACTGTGCACGTCTGCACATGTAC
AAACCAACAATTAGTTCCACATTTTGCTCAACAACGTTTGAATCAATTTCTCATTCAAAGCTCCA
AAAGTATCAAAAAAATTCCCAACAACCCCCCACATGAATGAAATTGAACATTTTATCAAAACCAT
TTTGACTCGATGTGATGATAGACTTTACGATCGATAATTACACAGGATAGGTAGGTGTCCTCCTT
TGAACATTTCCTTGTGACAACATATTTACTTTACTAGCTGACCAATAGACGTGATGTCATTGAAC
TGTTATATCGTTCGTGTAAAGGATAATATATTTCACACAACTACCCCTTTGACAAGAATTTTAGT
TCTCATAGGTATGTCCTTAAAGCCATGGC
Found at i:4555532 original size:39 final size:39
Alignment explanation
Indices: 4555489--4555578 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
4555479 ATTTCGTTTT
* *
4555489 AGAAAATAAAT-ACAATAATTTATTTTCTTTTATAATACA
1 AGAAACTAAATCA-AATAATTTATTTTCTTTTATAAAACA
*
4555528 AGAAACTAAATCAAATGATTTATTTTCTTTTATAAAACA
1 AGAAACTAAATCAAATAATTTATTTTCTTTTATAAAACA
*
4555567 GGAAACTAAATC
1 AGAAACTAAATC
4555579 CAACGATATG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (39 bp):
AGAAACTAAATCAAATAATTTATTTTCTTTTATAAAACA
Found at i:4555616 original size:39 final size:38
Alignment explanation
Indices: 4555534--4555813 Score: 208
Period size: 39 Copynumber: 7.3 Consensus size: 38
4555524 TACAAGAAAC
* * * * * * *
4555534 TAAATCAAATGATTTATTTTCTTTTATAAAACAGGAAAC
1 TAAATCCAACGATTTA-TTTCATTTACAAAATAGAAAAA
* *
4555573 TAAATCCAACGATATGTTTCGATTTACAAAATAGAAAAA
1 TAAATCCAACGATTTATTTC-ATTTACAAAATAGAAAAA
** * * *
4555612 TAAATGTAACGATTTATTTCCTTTTACAAAACA-AGAAGA
1 TAAATCCAACGATTTATTT-CATTTACAAAATAGA-AAAA
* * *
4555651 TAAAT-TACCGATTTATTTTCATTTACAAAATAGAAAAT
1 TAAATCCAACGATTTA-TTTCATTTACAAAATAGAAAAA
* *
4555689 TAAATCCAACGGTTTATTTCATTTTA-AAAATAGGAAAA
1 TAAATCCAACGATTTATTTCA-TTTACAAAATAGAAAAA
** * * * *
4555727 TAAATTTAATGATTTATTTCCTTCTACAAAATAGGAAAG
1 TAAATCCAACGATTTATTTCATT-TACAAAATAGAAAAA
* * *
4555766 TAAATCCAACGATTTATTTCCTTTAAAAAAAAG-AAAA
1 TAAATCCAACGATTTATTTCATTTACAAAATAGAAAAA
*
4555803 TAAATTCAACG
1 TAAATCCAACG
4555814 TTTTTTTTAC
Statistics
Matches: 193, Mismatches: 39, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
37 15 0.08
38 73 0.38
39 104 0.54
40 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (38 bp):
TAAATCCAACGATTTATTTCATTTACAAAATAGAAAAA
Found at i:4555705 original size:77 final size:75
Alignment explanation
Indices: 4555534--4555813 Score: 274
Period size: 77 Copynumber: 3.6 Consensus size: 75
4555524 TACAAGAAAC
* * * * * * * * *
4555534 TAAATCAAATGATTTATTTTCTTTTATAAAACAGGAAACTAAATCCAACGATATGTTTCGATTTA
1 TAAATCCAACGATTTATTTCCTTTTA-AAAAAAAGAAAATAAAT-TAACGATTTATTTC-ATTTA
4555599 CAAAATAGAAAAA
63 CAAAATAGAAAAA
** * * *
4555612 TAAATGTAACGATTTATTTCCTTTTACAAAACAAGAAGATAAATTACCGATTTATTTTCATTTAC
1 TAAATCCAACGATTTATTTCCTTTTA-AAAAAAAGAAAATAAATTAACGATTTA-TTTCATTTAC
*
4555677 AAAATAGAAAAT
64 AAAATAGAAAAA
* * * * * *
4555689 TAAATCCAACGGTTTATTTCATTTTAAAAATAGGAAAATAAATTTAATGATTTATTTCCTTCTAC
1 TAAATCCAACGATTTATTTCCTTTTAAAAAAAAGAAAATAAA-TTAACGATTTATTTCATT-TAC
* *
4555754 AAAATAGGAAAG
64 AAAATAGAAAAA
4555766 TAAATCCAACGATTTATTTCC-TTTAAAAAAAAGAAAATAAATTCAACG
1 TAAATCCAACGATTTATTTCCTTTTAAAAAAAAGAAAATAAATT-AACG
4555814 TTTTTTTTAC
Statistics
Matches: 168, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
75 2 0.01
76 40 0.24
77 86 0.51
78 40 0.24
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (75 bp):
TAAATCCAACGATTTATTTCCTTTTAAAAAAAAGAAAATAAATTAACGATTTATTTCATTTACAA
AATAGAAAAA
Found at i:4556353 original size:45 final size:45
Alignment explanation
Indices: 4556210--4556392 Score: 155
Period size: 45 Copynumber: 4.1 Consensus size: 45
4556200 GAATTAATCC
* *
4556210 TTTAATTTT-ACCAACCCAATAATCACAA-GAAATTAATCATTTGATT
1 TTTAATTTTCA-CAACCCAATAATGA-AAGGAAACTAATCATTTGA-T
* * * *
4556256 TTTAATTTTCGCAATCCAATAATAGAAAGG-AACTAATCGTTTAAT
1 TTTAATTTTCACAACCCAATAAT-GAAAGGAAACTAATCATTTGAT
* * *
4556301 TTCAATTTTCATAACCCAATAATGAAAGGAAACTAATAATTTGAT
1 TTTAATTTTCACAACCCAATAATGAAAGGAAACTAATCATTTGAT
* *
4556346 TTTAA-TTTC-CGAA-CCAAGTAATCAAAAGG-AACTAATCCTTTGAT
1 TTTAATTTTCAC-AACCCAA-TAAT-GAAAGGAAACTAATCATTTGAT
4556390 TTT
1 TTT
4556393 TTGACAACAC
Statistics
Matches: 112, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
43 4 0.04
44 32 0.29
45 41 0.37
46 33 0.29
47 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (45 bp):
TTTAATTTTCACAACCCAATAATGAAAGGAAACTAATCATTTGAT
Found at i:4556388 original size:44 final size:44
Alignment explanation
Indices: 4556191--4556434 Score: 150
Period size: 45 Copynumber: 5.7 Consensus size: 44
4556181 AACAAACAAA
* * *
4556191 AATCAAAAGGAATTAATCCTTTAATTTT-A---CC-AACCCAAT
1 AATCAAAAGGAACTAATCATTTGATTTTAATTTCCGAACCCAAT
* * * * *
4556230 AATCACAAGAAATTAATCATTTGATTTTTAATTTTCGCAATCCAAT
1 AATCAAAAGGAACTAATCATTTGA-TTTTAATTTCCG-AACCCAAT
* * * **
4556276 AAT-AGAAAGGAACTAATCGTTTAATTTCAATTTTCATAACCCAAT
1 AATCA-AAAGGAACTAATCATTTGATTTTAA-TTTCCGAACCCAAT
* *
4556321 AAT-GAAAGGAAACTAATAATTTGATTTTAATTTCCGAA-CCAAGT
1 AATCAAAAGG-AACTAATCATTTGATTTTAATTTCCGAACCCAA-T
* ** *
4556365 AATCAAAAGGAACTAATCCTTTGATTTT--TTGAC-AACACAAT
1 AATCAAAAGGAACTAATCATTTGATTTTAATTTCCGAACCCAAT
** * *
4556406 ACCCAAAAGAAAATAATCATTTGATTTTA
1 AATCAAAAGGAACTAATCATTTGATTTTA
4556435 CTGGAAACTC
Statistics
Matches: 157, Mismatches: 34, Indels: 25
0.73 0.16 0.12
Matches are distributed among these distances:
39 20 0.13
40 4 0.03
41 27 0.17
42 6 0.04
43 4 0.03
44 32 0.20
45 37 0.24
46 27 0.17
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (44 bp):
AATCAAAAGGAACTAATCATTTGATTTTAATTTCCGAACCCAAT
Found at i:4556431 original size:85 final size:84
Alignment explanation
Indices: 4556191--4556434 Score: 226
Period size: 85 Copynumber: 2.8 Consensus size: 84
4556181 AACAAACAAA
* * * *
4556191 AATCAAAAGGAATTAATCCTTTA-ATTTTACCAACCCAATAATCACAAGAAATTAATCATTTGAT
1 AATCAAAAGGAACTAATCCTTTATTTTTTA-CAACCCAATAATCAAAAGAAAATAATCATTTGA-
*
4556255 TTTTAATTTTCGCAATCCAAT
64 TTTTAATTTCCGCAATCCAAT
* * * * * *
4556276 AAT-AGAAAGGAACTAATCGTTTAATTTCAATTTTCATAACCCAATAATGAAAGGAAACTAATAA
1 AATCA-AAAGGAACTAATCCTTT-A-TT---TTTT-ACAACCCAATAATCAAAAGAAAATAATCA
4556340 TTTGATTTTAATTTCCG-AA-CCAAGT
59 TTTGATTTTAATTTCCGCAATCCAA-T
* **
4556365 AATCAAAAGGAACTAATCCTTTGATTTTTTGACAACACAATACCCAAAAGAAAATAATCATTTGA
1 AATCAAAAGGAACTAATCCTTT-ATTTTTT-ACAACCCAATAATCAAAAGAAAATAATCATTTGA
4556430 TTTTA
64 TTTTA
4556435 CTGGAAACTC
Statistics
Matches: 128, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
84 1 0.01
85 53 0.41
86 1 0.01
88 6 0.05
89 23 0.18
90 12 0.09
91 31 0.24
92 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (84 bp):
AATCAAAAGGAACTAATCCTTTATTTTTTACAACCCAATAATCAAAAGAAAATAATCATTTGATT
TTAATTTCCGCAATCCAAT
Found at i:4560954 original size:24 final size:25
Alignment explanation
Indices: 4560906--4560954 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
4560896 CTTCCATGTT
4560906 CTAAATTAAGAAATTATTTTTATTAA
1 CTAAATTAAG-AATTATTTTTATTAA
*
4560932 CTAAATTAAG-ATTTTTTTTATTA
1 CTAAATTAAGAATTATTTTTATTA
4560955 TTGGTCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
26 10 0.45
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (25 bp):
CTAAATTAAGAATTATTTTTATTAA
Found at i:4565166 original size:30 final size:30
Alignment explanation
Indices: 4565132--4565191 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4565122 AAATGGGAAA
4565132 TAATATTAAAAGTAAATAAAGAAATAAAAC
1 TAATATTAAAAGTAAATAAAGAAATAAAAC
4565162 TAATATTAAAAGTAAATAAAGAAATAAAAC
1 TAATATTAAAAGTAAATAAAGAAATAAAAC
4565192 AAAGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (30 bp):
TAATATTAAAAGTAAATAAAGAAATAAAAC
Found at i:4565333 original size:17 final size:17
Alignment explanation
Indices: 4565311--4565345 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4565301 GAGCACTAGT
4565311 ATAGACCAATATGCCCC
1 ATAGACCAATATGCCCC
*
4565328 ATAGACTAATATGCCCC
1 ATAGACCAATATGCCCC
4565345 A
1 A
4565346 CACATATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (17 bp):
ATAGACCAATATGCCCC
Found at i:4566928 original size:11 final size:11
Alignment explanation
Indices: 4566893--4566935 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
4566883 ATTTTTATAC
4566893 TTAA-CTCAAT
1 TTAAGCTCAAT
* *
4566903 TGAAGCTAAAAT
1 TTAAGCT-CAAT
4566915 TTAAGCTCAAT
1 TTAAGCTCAAT
4566926 TTAAGCTCAA
1 TTAAGCTCAA
4566936 ACTCGAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.11
11 15 0.56
12 9 0.33
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (11 bp):
TTAAGCTCAAT
Found at i:4577092 original size:2 final size:2
Alignment explanation
Indices: 4577085--4577111 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4577075 GATCTAAAGA
4577085 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 A
4577112 AGCAAAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4584970 original size:16 final size:16
Alignment explanation
Indices: 4584922--4584970 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 16
4584912 TTTTAAAGAT
4584922 TTTTAAATTACTAAAA
1 TTTTAAATTACTAAAA
*
4584938 --TTAAA-TATTTGAAAA
1 TTTTAAATTA-CT-AAAA
4584953 TTTTAAATTACTAAAA
1 TTTTAAATTACTAAAA
4584969 TT
1 TT
4584971 AAAACATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 2 0.08
14 6 0.23
15 4 0.15
16 6 0.23
17 6 0.23
18 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTTAAATTACTAAAA
Found at i:4585098 original size:12 final size:13
Alignment explanation
Indices: 4585081--4585109 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4585071 CTTTACTATC
4585081 TAAATT-AAGAAT
1 TAAATTAAAGAAT
4585093 TAAATTAAAGAAT
1 TAAATTAAAGAAT
4585106 TAAA
1 TAAA
4585110 AAAATTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
TAAATTAAAGAAT
Found at i:4585121 original size:16 final size:17
Alignment explanation
Indices: 4585094--4585125 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4585084 ATTAAGAATT
4585094 AAATTAAAGAATTAAAA
1 AAATTAAAGAATTAAAA
4585111 AAATT-AAGAATTAAA
1 AAATTAAAGAATTAAA
4585126 TTCTAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
AAATTAAAGAATTAAAA
Found at i:4587970 original size:31 final size:31
Alignment explanation
Indices: 4587784--4587954 Score: 306
Period size: 31 Copynumber: 5.5 Consensus size: 31
4587774 AGGGTCGAGG
*
4587784 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4587815 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4587846 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4587877 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4587908 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4587939 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
4587955 TGGAATCTAT
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 135 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4590012 original size:31 final size:31
Alignment explanation
Indices: 4589974--4590039 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
4589964 AGTTACGTCG
* *
4589974 GGGACCATATTGAAAACGGACTAAATGTTGA
1 GGGACCATATTGAAAACGGAATAAATATTGA
* *
4590005 GGGACCATATTGCAAACGGAATAAATATTGG
1 GGGACCATATTGAAAACGGAATAAATATTGA
4590036 GGGA
1 GGGA
4590040 TTGTATTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (31 bp):
GGGACCATATTGAAAACGGAATAAATATTGA
Found at i:4591472 original size:31 final size:31
Alignment explanation
Indices: 4591432--4591498 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
4591422 TAATACTTAT
* *
4591432 AATAAAATCCC-CTAACATTTAGTCCGTTTGC
1 AATATAATCCCTC-AACATTTAGTCCGATTGC
* *
4591463 AATATAATCCTTCAATATTTAGTCCGATTGC
1 AATATAATCCCTCAACATTTAGTCCGATTGC
4591494 AATAT
1 AATAT
4591499 GGTCCCTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (31 bp):
AATATAATCCCTCAACATTTAGTCCGATTGC
Found at i:4601249 original size:2 final size:2
Alignment explanation
Indices: 4601242--4601276 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4601232 CTTCTTAATT
4601242 TA 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 T
4601277 TTGAAGATGG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4605328 original size:160 final size:160
Alignment explanation
Indices: 4605064--4605383 Score: 622
Period size: 160 Copynumber: 2.0 Consensus size: 160
4605054 TTGGAGTTCT
4605064 AAAGCTTTCAGAAAACCCAATACCCTCCTAGGTTTAGATTATCCTTAATCCTATAAACTCATAAG
1 AAAGCTTTCAGAAAACCCAATACCCTCCTAGGTTTAGATTATCCTTAATCCTATAAACTCATAAG
4605129 CAAAATACAAGCCAGCACCATACTAAAGTAGAAAAGCTTAAATATTGGAAATAATGAGACAAAAT
66 CAAAATACAAGCCAGCACCATACTAAAGTAGAAAAGCTTAAATATTGGAAATAATGAGACAAAAT
4605194 ATACAAGTTATGAGAATATCATCGACAACA
131 ATACAAGTTATGAGAATATCATCGACAACA
* *
4605224 AAAGCTTTCCGAAAACCCAATGCCCTCCTAGGTTTAGATTATCCTTAATCCTATAAACTCATAAG
1 AAAGCTTTCAGAAAACCCAATACCCTCCTAGGTTTAGATTATCCTTAATCCTATAAACTCATAAG
4605289 CAAAATACAAGCCAGCACCATACTAAAGTAGAAAAGCTTAAATATTGGAAATAATGAGACAAAAT
66 CAAAATACAAGCCAGCACCATACTAAAGTAGAAAAGCTTAAATATTGGAAATAATGAGACAAAAT
4605354 ATACAAGTTATGAGAATATCATCGACAACA
131 ATACAAGTTATGAGAATATCATCGACAACA
4605384 CGAAAACCAT
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 158 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (160 bp):
AAAGCTTTCAGAAAACCCAATACCCTCCTAGGTTTAGATTATCCTTAATCCTATAAACTCATAAG
CAAAATACAAGCCAGCACCATACTAAAGTAGAAAAGCTTAAATATTGGAAATAATGAGACAAAAT
ATACAAGTTATGAGAATATCATCGACAACA
Found at i:4622643 original size:42 final size:41
Alignment explanation
Indices: 4622578--4622744 Score: 253
Period size: 42 Copynumber: 4.0 Consensus size: 41
4622568 GAAGTATTAT
*
4622578 CAGGTCCCTTATGTTGTGTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTT-TGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
4622621 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
4622663 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
* *
4622705 CAGGTCCCTTTGTTGTGTGCAAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
4622745 TCCTAGGCTC
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
41 4 0.03
42 103 0.88
43 10 0.09
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:4629086 original size:29 final size:30
Alignment explanation
Indices: 4628909--4629087 Score: 212
Period size: 29 Copynumber: 6.2 Consensus size: 30
4628899 GATCGAGTGA
* **
4628909 TATTTTGTGAA-TTAATTCGAAATGGGTGC
1 TATTTTGGGAATTTAATTCGAAAAAGGTGC
*
4628938 TATTTTGGGAA-TTAATTCGAAATAGGTGC
1 TATTTTGGGAATTTAATTCGAAAAAGGTGC
*
4628967 TATTTTGGGAATTTAATTCGAAAAA-GTGT
1 TATTTTGGGAATTTAATTCGAAAAAGGTGC
*
4628996 TATTTTGGAAATTTAATTCGAAAAA-GTGC
1 TATTTTGGGAATTTAATTCGAAAAAGGTGC
4629025 TATTTTGGGAATTTAATTCG--AAAGTGTGC
1 TATTTTGGGAATTTAATTCGAAAAAG-GTGC
* *
4629054 TATTTTGGTAA-TTAATT-GAAAAAGGGTGA
1 TATTTTGGGAATTTAATTCGAAAAA-GGTGC
4629083 TATTT
1 TATTT
4629088 CTGTAAAATG
Statistics
Matches: 135, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
27 4 0.03
28 6 0.04
29 112 0.83
30 13 0.10
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (30 bp):
TATTTTGGGAATTTAATTCGAAAAAGGTGC
Found at i:4630076 original size:42 final size:42
Alignment explanation
Indices: 4630013--4630219 Score: 226
Period size: 42 Copynumber: 4.9 Consensus size: 42
4630003 AGAAGTATTA
4630013 TCAGGTCCCTTTTGCTGTGTGCAAAGG-TAAGCCTTACAGTTTC
1 TCAGGTCCC-TTTGCTGTGTGC-AAGGATAAGCCTTACAGTTTC
*
4630056 TCAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAATTTAC
1 TCAGGTCCCTTTGCTGTGTGC-AAGGATAAGCCTTACAGTTT-C
* *
4630099 -CAAGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTC
1 TCAGGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTC
* **
4630140 CCAGGTCCCTTTGCTGTGTGCAAGGATAAATCTTACAGTTT-
1 TCAGGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTC
* * *
4630181 TCATAGG-CTCCTATGCTTTGTGCACAGGTTAAGCCTTAC
1 TC--AGGTC-CCTTTGCTGTGTGCA-AGGATAAGCCTTAC
4630220 TGGTATATAG
Statistics
Matches: 142, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
41 6 0.04
42 99 0.70
43 26 0.18
44 11 0.08
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (42 bp):
TCAGGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTC
Done.