Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008871.1 Hibiscus syriacus cultivar Beakdansim tig00112106_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: 94199
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3305 original size:19 final size:19
Alignment explanation
Indices: 3281--3317 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3271 ATGACCAACA
* *
3281 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
3300 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
3318 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:3356 original size:20 final size:20
Alignment explanation
Indices: 3302--3356 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
3292 CGATCTCTAA
*
3302 ATCGCAACGCGATCTCCAGT
1 ATCGCAACGCGATTTCCAGT
** *
3322 ATCGCAAATCAATTTCCAG-
1 ATCGCAACGCGATTTCCAGT
3341 ATTCGCAACGCGATTT
1 A-TCGCAACGCGATTT
3357 TGACTATCGT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTTCCAGT
Found at i:4277 original size:14 final size:14
Alignment explanation
Indices: 4248--4284 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4238 AGAAAAAGAA
4248 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
4263 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
4277 GAAGAAAA
1 GAAGAAAA
4285 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:6334 original size:12 final size:12
Alignment explanation
Indices: 6319--6349 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6309 CAAGAAAAAG
6319 GCAATCAAAATC
1 GCAATCAAAATC
6331 GCAATCAAAATC
1 GCAATCAAAATC
*
6343 CCAATCA
1 GCAATCA
6350 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.29, G:0.06, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:6659 original size:140 final size:140
Alignment explanation
Indices: 6407--6689 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 140
6397 GCAAACATTG
*
6407 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTATGCATGTATTAGAAACTTGAGT
1 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGAAACTTGAGT
* *
6472 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGATTATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACA
*
6537 CGAATTTGAC
131 AGAATTTGAC
* *
6547 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGAAACTTGAGT
*
6612 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACA
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACA
6677 AGAATTTGAC
131 AGAATTTGAC
6687 TAT
1 TAT
6690 CGCAACGTGA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTACGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGAAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACA
AGAATTTGAC
Found at i:6685 original size:20 final size:20
Alignment explanation
Indices: 6660--6760 Score: 148
Period size: 20 Copynumber: 5.0 Consensus size: 20
6650 TTACACATTC
* *
6660 ATTTGAATATCGCAACAAGA
1 ATTTGACTATCGCAACGAGA
*
6680 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGAGA
*
6700 ATTTGATTATCGCAACGAGA
1 ATTTGACTATCGCAACGAGA
*
6720 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGAGA
*
6740 ATTTGACTATCGCAACAAGA
1 ATTTGACTATCGCAACGAGA
6760 A
1 A
6761 AATCGCAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGAGA
Found at i:6715 original size:40 final size:40
Alignment explanation
Indices: 6660--6760 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 40
6650 TTACACATTC
*
6660 ATTTGAATATCGCAACAAGAATTTGACTATCGCAACGTGA
1 ATTTGAATATCGCAACAAGAATTTGACTATCGCAACGGGA
* *
6700 ATTTGATTATCGCAACGAGAATTTGACTATCGCAACGGGA
1 ATTTGAATATCGCAACAAGAATTTGACTATCGCAACGGGA
*
6740 ATTTGACTATCGCAACAAGAA
1 ATTTGAATATCGCAACAAGAA
6761 AATCGCAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (40 bp):
ATTTGAATATCGCAACAAGAATTTGACTATCGCAACGGGA
Found at i:6824 original size:20 final size:20
Alignment explanation
Indices: 6795--6892 Score: 151
Period size: 20 Copynumber: 4.9 Consensus size: 20
6785 GCAACGCGAA
*
6795 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
6815 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
6835 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
6855 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
6875 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
6893 AAGTGTACAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:8487 original size:21 final size:21
Alignment explanation
Indices: 8461--8538 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
8451 GATGACATGT
8461 GCCTCTTGAACGATGGGAGGG
1 GCCTCTTGAACGATGGGAGGG
* ** **
8482 GACTCTTGAGGGATGATAGGG
1 GCCTCTTGAACGATGGGAGGG
*
8503 GCCTCTTGAACGATAGGAGGG
1 GCCTCTTGAACGATGGGAGGG
8524 GCCTCTTGAACGATG
1 GCCTCTTGAACGATG
8539 ATAGGTGAGT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (21 bp):
GCCTCTTGAACGATGGGAGGG
Found at i:8540 original size:42 final size:42
Alignment explanation
Indices: 8441--8543 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 42
8431 GTGGGAGAGA
* * * * *
8441 CCTCTTCAACGATGACATGTGCCTCTTGAACGATGGGAGGGG
1 CCTCTTGAACGATGATAGGGGCCTCTTGAACGATAGGAGGGG
* **
8483 ACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGAGGGG
1 CCTCTTGAACGATGATAGGGGCCTCTTGAACGATAGGAGGGG
8525 CCTCTTGAACGATGATAGG
1 CCTCTTGAACGATGATAGG
8544 TGAGTCGGGC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGATAGGGGCCTCTTGAACGATAGGAGGGG
Found at i:9126 original size:19 final size:20
Alignment explanation
Indices: 9102--9140 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
9092 GCAACAAGAT
*
9102 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
9121 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
9141 TTCGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:9237 original size:20 final size:20
Alignment explanation
Indices: 9212--9260 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
9202 GCGATTATCC
9212 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
9232 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
9252 CGTTGCGAT
1 CGTTGCGAT
9261 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:9270 original size:20 final size:20
Alignment explanation
Indices: 9212--9279 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
9202 GCGATTATCC
*
9212 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* *
9232 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
9252 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATAGTAAGTTTCG
*
9272 TGTTGCGA
1 CGTTGCGA
9280 CTATTCTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.03
20 39 0.98
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:11184 original size:20 final size:20
Alignment explanation
Indices: 11161--11236 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
11151 TATGAAACTT
11161 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
11181 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
11201 AAAATTGCAACACAAAAATG
1 AAAATCGCAACACGAAAATG
** *
11221 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
11237 TTTGACTATC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.53, C:0.21, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:11284 original size:33 final size:34
Alignment explanation
Indices: 11244--11315 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
11234 GAATTTGACT
*
11244 ATCGCAACGAG-ATAATCGCAACT-CGAAA-TGAAA
1 ATCGCAACGAGAAAAATCGCAA-TGCGAAACT-AAA
11277 ATCGCAACGAGAAAAATCGCAATGCGAAACTAAA
1 ATCGCAACGAGAAAAATCGCAATGCGAAACTAAA
11311 ATCGC
1 ATCGC
11316 GTTGCGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
33 12 0.34
34 22 0.63
35 1 0.03
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAAAAATCGCAATGCGAAACTAAA
Found at i:11730 original size:22 final size:22
Alignment explanation
Indices: 11705--11755 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
11695 GATGGAGATA
11705 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGTCGAAGATGGG
*
11727 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGAAGATGGG
*
11749 GTCGGAT
1 GACGGAT
11756 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGAAGATGGG
Found at i:11953 original size:20 final size:20
Alignment explanation
Indices: 11930--12056 Score: 105
Period size: 20 Copynumber: 6.2 Consensus size: 20
11920 TTATCGCAAC
*
11930 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAAAATCGCGTT
*
11950 GCGATAGTCAAAATCGCTTT
1 GCGATAGTCAAAATCGCGTT
** *
11970 GCGATTATGT-ATTATCACGTT
1 GCGA-TA-GTCAAAATCGCGTT
11991 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAAAATCGCGTT
** **
12011 GCGATTATGT-ATTATCGTATT
1 GCGA-TA-GTCAAAATCGCGTT
* *
12032 GCGATAGTCAGAATCGTGTT
1 GCGATAGTCAAAATCGCGTT
12052 GCGAT
1 GCGAT
12057 TTATATATTC
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.05
20 51 0.60
21 26 0.31
22 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCGTT
Found at i:11995 original size:61 final size:61
Alignment explanation
Indices: 11898--12015 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
11888 TGGCGCTTTG
* * *
11898 AAAATCGCATTGCGATTTTGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGATAGTC
1 AAAATCGCATTGCGATTATGTATTATCACAACGCGATAGTCAAAATCGCGTTGCGATAGTC
* ***
11959 AAAATCGCTTTGCGATTATGTATTATCACGTTGCGATAGTCAAAATCGCGTTGCGAT
1 AAAATCGCATTGCGATTATGTATTATCACAACGCGATAGTCAAAATCGCGTTGCGAT
12016 TATGTATTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (61 bp):
AAAATCGCATTGCGATTATGTATTATCACAACGCGATAGTCAAAATCGCGTTGCGATAGTC
Found at i:12088 original size:41 final size:41
Alignment explanation
Indices: 11942--12076 Score: 166
Period size: 41 Copynumber: 3.3 Consensus size: 41
11932 GATAGTCAGA
* * *
11942 ATCGCGTTGCGATAGTCAAAATCGCTTTGCGATTATGTATT
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTATATATT
* * *
11983 ATCACGTTGCGATAGTCAAAATCGCGTTGCGATTATGTATT
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTATATATT
* * *
12024 ATCGTATTGCGATAGTCAGAATCGTGTTGCGATT-TATA-T
1 ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTATATATT
12063 ATTCGCATTGCGAT
1 A-TCGCATTGCGAT
12077 TTTCTAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 2 0.02
40 14 0.17
41 68 0.81
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAAAATCGCGTTGCGATTATATATT
Found at i:12096 original size:102 final size:102
Alignment explanation
Indices: 11898--12116 Score: 244
Period size: 102 Copynumber: 2.1 Consensus size: 102
11888 TGGCGCTTTG
* *
11898 AAAATCGCATTGCGATTTTGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAAAA
1 AAAATCGCGTTGCGATTATGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAAAA
* * ** **
11963 TCGCTTTGCGATTATGTATTATCACGTTGCGATAGTC
66 TCGCATTGCGATTATCTAAAATCACAATGCGATAGTC
* ** * *
12000 AAAATCGCGTTGCGATTATGTATTATCGTATTGCGATAGTCAGAATCGTGTTGCGATTTA-T-AT
1 AAAATCGCGTTGCGATTATGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGA--TAGTCAA
* * *
12063 ATTCGCATTGCGATTTTCTAAAATCGCAATGCGATAGTC
64 AATCGCATTGCGATTATCTAAAATCACAATGCGATAGTC
**
12102 AAAATTACGTTGCGA
1 AAAATCGCGTTGCGA
12117 ATCTGGAAAC
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
102 94 0.97
103 1 0.01
104 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (102 bp):
AAAATCGCGTTGCGATTATGTATTATCGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAAAA
TCGCATTGCGATTATCTAAAATCACAATGCGATAGTC
Found at i:12154 original size:20 final size:19
Alignment explanation
Indices: 12131--12195 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
12121 GGAAACTGAT
*
12131 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCG
* *
12151 TTGCGATTTAGAGATCGCT
1 TTGCGATCTAGAGATCGCG
* * *
12170 TTGCGATTTAGATATCGCA
1 TTGCGATCTAGAGATCGCG
12189 TTGCGAT
1 TTGCGAT
12196 TTTGTTGATC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 33 0.82
20 7 0.17
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.34
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCG
Found at i:12166 original size:19 final size:19
Alignment explanation
Indices: 12142--12197 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
12132 TGCGATACTG
*
12142 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
12161 GAGATCGCTTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
12180 GATATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
12198 TGTTGATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:17819 original size:42 final size:41
Alignment explanation
Indices: 17773--17974 Score: 265
Period size: 42 Copynumber: 5.0 Consensus size: 41
17763 GCTCCACACA
* *
17773 CACCTCCTCTACCTCCACCACCTCCATTGAAGTCTGGTGCCC
1 CACCTCCTC-ACCTCCACCACCCCCATTGATGTCTGGTGCCC
* * *
17815 CACCT-C-CACCACCACCGCCCCCATTGAAGTCTGGTGCCC
1 CACCTCCTCACCTCCACCACCCCCATTGATGTCTGGTGCCC
*
17854 CA----C-CACCTCCACCGCCCCCATTGATGTCTGGTGCCC
1 CACCTCCTCACCTCCACCACCCCCATTGATGTCTGGTGCCC
*
17890 CACCTCCTCCACCTCCACCACCCCTATTGATGTCTGGTGCCC
1 CACCTCCT-CACCTCCACCACCCCCATTGATGTCTGGTGCCC
17932 CACCTCCTCCACCTCCACCACCCCCATTGATGTCTGGTGCCC
1 CACCTCCT-CACCTCCACCACCCCCATTGATGTCTGGTGCCC
17974 C
1 C
17975 TCCAAAATTT
Statistics
Matches: 146, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
36 34 0.23
39 31 0.21
40 2 0.01
41 1 0.01
42 78 0.53
ACGTcount: A:0.15, C:0.50, G:0.13, T:0.21
Consensus pattern (41 bp):
CACCTCCTCACCTCCACCACCCCCATTGATGTCTGGTGCCC
Found at i:17860 original size:36 final size:36
Alignment explanation
Indices: 17783--17944 Score: 171
Period size: 36 Copynumber: 4.2 Consensus size: 36
17773 CACCTCCTCT
* *
17783 ACCTCCACCACCTCCATTGAAGTCTGGTGCCCCACCTCC
1 ACCTCCACCGCCCCCATTGAAGTCTGGTGCCCCA---CC
*
17822 ACCACCACCGCCCCCATTGAAGTCTGGTGCCCCACC
1 ACCTCCACCGCCCCCATTGAAGTCTGGTGCCCCACC
*
17858 ACCTCCACCGCCCCCATTGATGTCTGGTGCCCCACCTCCTCC
1 ACCTCCACCGCCCCCATTGAAGTCTGGTGCCCCA------CC
* * *
17900 ACCTCCACCACCCCTATTGATGTCTGGTGCCCCACC
1 ACCTCCACCGCCCCCATTGAAGTCTGGTGCCCCACC
*
17936 TCCTCCACC
1 ACCTCCACC
17945 TCCACCACCC
Statistics
Matches: 109, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
36 44 0.40
39 31 0.28
42 34 0.31
ACGTcount: A:0.16, C:0.51, G:0.14, T:0.20
Consensus pattern (36 bp):
ACCTCCACCGCCCCCATTGAAGTCTGGTGCCCCACC
Found at i:17902 original size:84 final size:79
Alignment explanation
Indices: 17783--17974 Score: 248
Period size: 78 Copynumber: 2.4 Consensus size: 79
17773 CACCTCCTCT
* * * *
17783 ACCTCCACCACCTCCATTGAAGTCTGGTGCCCCA---CCTCCACCACCACCGCCCCCATTGAAGT
1 ACCTCCACCACCCCCATTGATGTCTGGTGCCCCACCTCCTCCACCTCCACCACCCCCATTGAAGT
17845 CTGGTGCCCCA-CC
66 CTGGTGCCCCACCC
* * *
17858 ACCTCCACCGCCCCCATTGATGTCTGGTGCCCCACCTCCTCCACCTCCACCACCCCTATTGATGT
1 ACCTCCACCACCCCCATTGATGTCTGGTGCCCCACCTCCTCCACCTCCACCACCCCCATTGAAGT
17923 CTGGTGCCCCACCTCCTCC
66 CTGGTGCCCCA----C-CC
17942 ACCTCCACCACCCCCATTGATGTCTGGTGCCCC
1 ACCTCCACCACCCCCATTGATGTCTGGTGCCCC
17975 TCCAAAATTT
Statistics
Matches: 100, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
75 31 0.31
78 35 0.35
84 34 0.34
ACGTcount: A:0.16, C:0.50, G:0.14, T:0.20
Consensus pattern (79 bp):
ACCTCCACCACCCCCATTGATGTCTGGTGCCCCACCTCCTCCACCTCCACCACCCCCATTGAAGT
CTGGTGCCCCACCC
Found at i:18130 original size:66 final size:66
Alignment explanation
Indices: 18060--18248 Score: 200
Period size: 66 Copynumber: 2.9 Consensus size: 66
18050 AGCCCCGCCC
* * * *
18060 CCACCACCTCCACCT-TCGCGAGGGGCACCATCCCCACCCCCACCTCCCATGCGTGGAGCGCCAG
1 CCACCACCACCACCTAT-GCGAGGAGCACCAGCACCACCCCCACCTCCCATGCGTGGAGCGCCAG
18124 CA
65 CA
* * * * * *
18126 CCACCTCCACCTCCTATGCGTGGAGCTCCAGCACCACCTCCACCTCCTATGCGTGGAGCGCCAGC
1 CCACCACCACCACCTATGCGAGGAGCACCAGCACCACCCCCACCTCCCATGCGTGGAGCGCCAGC
18191 A
66 A
* * * * * * * *
18192 CCGCCTCCACCTCCTATGCGTGGAGCGCCAGCACCGCCTCCACCTCCTATGCGTGGA
1 CCACCACCACCACCTATGCGAGGAGCACCAGCACCACCCCCACCTCCCATGCGTGGA
18249 CCTCCTGCAC
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 108 0.99
67 1 0.01
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.15
Consensus pattern (66 bp):
CCACCACCACCACCTATGCGAGGAGCACCAGCACCACCCCCACCTCCCATGCGTGGAGCGCCAGC
A
Found at i:18272 original size:33 final size:33
Alignment explanation
Indices: 18093--18248 Score: 267
Period size: 33 Copynumber: 4.7 Consensus size: 33
18083 GGCACCATCC
* *
18093 CCACCCCCACCTCCCATGCGTGGAGCGCCAGCA
1 CCACCTCCACCTCCTATGCGTGGAGCGCCAGCA
*
18126 CCACCTCCACCTCCTATGCGTGGAGCTCCAGCA
1 CCACCTCCACCTCCTATGCGTGGAGCGCCAGCA
18159 CCACCTCCACCTCCTATGCGTGGAGCGCCAGCA
1 CCACCTCCACCTCCTATGCGTGGAGCGCCAGCA
*
18192 CCGCCTCCACCTCCTATGCGTGGAGCGCCAGCA
1 CCACCTCCACCTCCTATGCGTGGAGCGCCAGCA
*
18225 CCGCCTCCACCTCCTATGCGTGGA
1 CCACCTCCACCTCCTATGCGTGGA
18249 CCTCCTGCAC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 118 1.00
ACGTcount: A:0.17, C:0.47, G:0.21, T:0.15
Consensus pattern (33 bp):
CCACCTCCACCTCCTATGCGTGGAGCGCCAGCA
Found at i:18281 original size:66 final size:66
Alignment explanation
Indices: 18084--18305 Score: 266
Period size: 66 Copynumber: 3.4 Consensus size: 66
18074 TTCGCGAGGG
* * * *
18084 GCACCATCCCCACCCCCACCTCCCATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTGG
1 GCACCAGCACCACCTCCACCTCCTATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTGG
18149 A
66 A
* *
18150 GCTCCAGCACCACCTCCACCTCCTATGCGTGGAGCGCCAGCACCGCCTCCACCTCCTATGCGTGG
1 GCACCAGCACCACCTCCACCTCCTATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTGG
18215 A
66 A
* * * * * * * * *
18216 GCGCCAGCACCGCCTCCACCTCCTATGCGTGGACCTCCTGCACCTCCCCCGCCTCCTCT-CGGTG
1 GCACCAGCACCACCTCCACCTCCTATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGC-GTG
18280 GA
65 GA
* * *
18282 GCACCACCACCACCACCTCCTCCT
1 GCACCAGCACCACCTCCACCTCCT
18306 GGAGGTCGAG
Statistics
Matches: 135, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
65 1 0.01
66 134 0.99
ACGTcount: A:0.16, C:0.50, G:0.18, T:0.16
Consensus pattern (66 bp):
GCACCAGCACCACCTCCACCTCCTATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTGG
A
Found at i:18304 original size:99 final size:99
Alignment explanation
Indices: 18084--18305 Score: 286
Period size: 99 Copynumber: 2.2 Consensus size: 99
18074 TTCGCGAGGG
* *
18084 GCACCATCC-CCACCCCCACCTCCCATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTG
1 GCACCA-CCACCACCACCACCTCCTATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTG
* *
18148 GAGCTCCAGCACCACCTCCACCTCCTATGCGTGGA
65 GACCTCCAGCACCACCCCCACCTCCTATGCGTGGA
* * * * *
18183 GCGCCAGCACCGCCTCCACCTCCTATGCGTGGAGCGCCAGCACCGCCTCCACCTCCTATGCGTGG
1 GCACCACCACCACCACCACCTCCTATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTGG
* * * *
18248 ACCTCCTGCACCTCCCCCGCCTCCTCT-CGGTGGA
66 ACCTCCAGCACCACCCCCACCTCCTATGC-GTGGA
*
18282 GCACCACCACCACCACCTCCTCCT
1 GCACCACCACCACCACCACCTCCT
18306 GGAGGTCGAG
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
98 2 0.02
99 102 0.98
ACGTcount: A:0.16, C:0.50, G:0.18, T:0.16
Consensus pattern (99 bp):
GCACCACCACCACCACCACCTCCTATGCGTGGAGCGCCAGCACCACCTCCACCTCCTATGCGTGG
ACCTCCAGCACCACCCCCACCTCCTATGCGTGGA
Found at i:36915 original size:20 final size:20
Alignment explanation
Indices: 36870--36915 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
36860 GACCAACAAA
* *
36870 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
36890 -TCGCAACGCGATCTCCAGT
1 ATCGCAACGCGATCTCCAAT
36909 ATCGCAA
1 ATCGCAA
36916 ATTCGCGCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:36949 original size:20 final size:20
Alignment explanation
Indices: 36926--37002 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
36916 ATTCGCGCTG
36926 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
36946 CATTTCGCATTGCGATAGTCTA
1 CATTTCGCGTTGCGAT--TTTC
*
36968 CA-GT-GTCGTTGCGATTTTC
1 CATTTCG-CGTTGCGATTTTC
36987 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
37003 AGTTGAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
19 4 0.09
20 26 0.59
21 10 0.23
22 4 0.09
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:37019 original size:41 final size:41
Alignment explanation
Indices: 36930--37023 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
36920 GCGCTGCATT
* *
36930 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAA
*
36971 T-GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAA
1 TCG-CGTTGCGATTTTCCATTTCGCATTGCGATAGTCT-AAAA
37012 TCGCGTTGCGAT
1 TCGCGTTGCGAT
37024 AGTGTACAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
40 2 0.04
41 44 0.94
42 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAA
Found at i:37057 original size:41 final size:41
Alignment explanation
Indices: 37012--37132 Score: 215
Period size: 41 Copynumber: 3.0 Consensus size: 41
37002 TAGTTGAAAA
*
37012 TCGCGTTGCGATAGTGTACAGTGTTATTGCGATTTTCCATT
1 TCGCGTTACGATAGTGTACAGTGTTATTGCGATTTTCCATT
37053 TCGCGTTACGATAGTGTACAGTGTTATTGCGATTTTCCATT
1 TCGCGTTACGATAGTGTACAGTGTTATTGCGATTTTCCATT
* *
37094 TCGCGTTACGATAGTGTACAATGTTGTTGCGATTTTCCA
1 TCGCGTTACGATAGTGTACAGTGTTATTGCGATTTTCCA
37133 AATTCGATGC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (41 bp):
TCGCGTTACGATAGTGTACAGTGTTATTGCGATTTTCCATT
Found at i:37085 original size:62 final size:62
Alignment explanation
Indices: 36950--37067 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
36940 ATTTTCCATT
* *
36950 TCGCATTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCATTGCGATAGTCTACAGTGTCATTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAA
* * *
37012 TCGCGTTGCGATAGTGTACAGTGTTATTGCGATTTTCCATTTCGCGTTACGATAGT
1 TCGCATTGCGATAGTCTACAGTGTCATTGCGATTTTCCATTTCGCGTTACGATAGT
37068 GTACAGTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (62 bp):
TCGCATTGCGATAGTCTACAGTGTCATTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAA
Found at i:37767 original size:6 final size:6
Alignment explanation
Indices: 37753--37782 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
37743 TCTCGTCTCG
*
37753 GGTCGT GGTCAT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
37783 AGTAATACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.47, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:38350 original size:16 final size:16
Alignment explanation
Indices: 38329--38364 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
38319 AGACTTATTG
38329 AAAATAAAAATAA-AAT
1 AAAATAAAAA-AATAAT
38345 AAAATAAAAAAATAAT
1 AAAATAAAAAAATAAT
38361 AAAA
1 AAAA
38365 AATATCGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAAATAAT
Found at i:38357 original size:18 final size:18
Alignment explanation
Indices: 38334--38368 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38324 TATTGAAAAT
38334 AAAAATAA-AATAAAATAA
1 AAAAATAATAA-AAAATAA
38352 AAAAATAATAAAAAATA
1 AAAAATAATAAAAAATA
38369 TCGAAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATAATAAAAAATAA
Found at i:38362 original size:87 final size:88
Alignment explanation
Indices: 38230--38395 Score: 221
Period size: 87 Copynumber: 1.9 Consensus size: 88
38220 GTCATACAGA
* * * * *
38230 CAGACTTATTGAAAATTTAAAATAAGAAAAAATAAAAGAACAATAAAGAATATTGACAG-TCGAC
1 CAGACTTATTGAAAATTAAAAATAAGAAAAAATAAAAAAACAATAAAAAATATCGA-AGATCAAC
*
38294 AATTAACATTAAAATAGGTGCCGC
65 AATCAACATTAAAATAGGTGCCGC
*
38318 CAGACTTATTGAAAA-TAAAAATAA-AATAAAATAAAAAAATAATAAAAAATATCGAAGATCAAC
1 CAGACTTATTGAAAATTAAAAATAAGAA-AAAATAAAAAAACAATAAAAAATATCGAAGATCAAC
*
38381 AATCAATATTAAAAT
65 AATCAACATTAAAAT
38396 TAATATCGCC
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 4 0.06
87 49 0.72
88 15 0.22
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (88 bp):
CAGACTTATTGAAAATTAAAAATAAGAAAAAATAAAAAAACAATAAAAAATATCGAAGATCAACA
ATCAACATTAAAATAGGTGCCGC
Found at i:40601 original size:18 final size:18
Alignment explanation
Indices: 40569--40603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40559 TGTGTGTCTA
* *
40569 TCCCTATCTCGGTCACGT
1 TCCCTATCGCAGTCACGT
40587 TCCCTATCGCAGTCACG
1 TCCCTATCGCAGTCACG
40604 GTCACGATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.40, G:0.17, T:0.29
Consensus pattern (18 bp):
TCCCTATCGCAGTCACGT
Found at i:48612 original size:23 final size:24
Alignment explanation
Indices: 48567--48643 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
48557 GCCGTTCCGA
*
48567 TCCTCCTGTGATGGCCCCCGCGGT
1 TCCTCCTGCGATGGCCCCCGCGGT
*
48591 TCCTCCTGCGAT-GACCCCGCGGT
1 TCCTCCTGCGATGGCCCCCGCGGT
* *
48614 TCTTCCTGCGATGGCCCCCACGGT
1 TCCTCCTGCGATGGCCCCCGCGGT
48638 TCCTCC
1 TCCTCC
48644 GGTTGCTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.06, C:0.44, G:0.25, T:0.25
Consensus pattern (24 bp):
TCCTCCTGCGATGGCCCCCGCGGT
Found at i:58539 original size:22 final size:22
Alignment explanation
Indices: 58511--58555 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
58501 GAAAGGTTTG
58511 AGCTTTACGACGTGCTACCAAT
1 AGCTTTACGACGTGCTACCAAT
58533 AGCTTTACGACGTGCTACCAAT
1 AGCTTTACGACGTGCTACCAAT
58555 A
1 A
58556 CTTACTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (22 bp):
AGCTTTACGACGTGCTACCAAT
Found at i:66081 original size:14 final size:14
Alignment explanation
Indices: 66062--66099 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
66052 AAGTAAACGG
*
66062 GTTGACTCGGACGA
1 GTTGACTCAGACGA
*
66076 GTTGACTTAGACGA
1 GTTGACTCAGACGA
66090 GTTGACTCAG
1 GTTGACTCAG
66100 GCAGGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:69330 original size:25 final size:25
Alignment explanation
Indices: 69302--69365 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
69292 TAATAATGTC
*
69302 AAAATAATTAAAATCATTACATTTA
1 AAAATAATTAAAATCATTAAATTTA
* ** *
69327 AAAATAATCATTATTATTAAATTTA
1 AAAATAATTAAAATCATTAAATTTA
69352 AAAATAATTAAAAT
1 AAAATAATTAAAAT
69366 TTTAATGATA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAATAATTAAAATCATTAAATTTA
Found at i:70447 original size:3 final size:3
Alignment explanation
Indices: 70432--70494 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
70422 GGTTAAAAAA
*
70432 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
70479 TAT TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TA
70495 AGTGTGTTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 3 0.05
3 53 0.95
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:71826 original size:2 final size:2
Alignment explanation
Indices: 71819--71886 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
71809 TTGTTAAACG
71819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71861 TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
71887 GTCTTGGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:71918 original size:48 final size:48
Alignment explanation
Indices: 71864--71968 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
71854 ATATATATAT
* *
71864 ATATATATATTATATATAT-ATATGTCTTGGAAACTGATTTTTTTGTTC
1 ATATATATATTATATATATAACATGTCTTGGAAACTGA-TTCTTTGTTC
* * *
71912 ATATATATA-TATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATTATATATATAACATGTCTTGGAAACTGATTCTTTGTTC
*
71959 ATATACATAT
1 ATATATATAT
71969 ATTTGTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 23 0.47
48 26 0.53
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (48 bp):
ATATATATATTATATATATAACATGTCTTGGAAACTGATTCTTTGTTC
Found at i:71986 original size:47 final size:48
Alignment explanation
Indices: 71885--71978 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 48
71875 ATATATATAT
* *
71885 ATGTCTTGGAAACTGATTTTTTTGTTCATATATATATATTTGTTTAAC
1 ATGTCTTGGAAACTGATTTCTTTGTTCATATACATATATTTGTTTAAC
71933 ATGTCTTGGAAACTGA-TTCTTTGTTCATATACATATATTTGTTTAA
1 ATGTCTTGGAAACTGATTTCTTTGTTCATATACATATATTTGTTTAA
71979 TGTGTCTTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 28 0.64
48 16 0.36
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.50
Consensus pattern (48 bp):
ATGTCTTGGAAACTGATTTCTTTGTTCATATACATATATTTGTTTAAC
Found at i:72098 original size:2 final size:2
Alignment explanation
Indices: 72093--72154 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
72083 TTTTTTGTTC
72093 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
72135 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
72155 TTATTTAATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72278 original size:2 final size:2
Alignment explanation
Indices: 72271--72302 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
72261 GCTTAGCTGG
72271 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
72303 TTTAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72430 original size:24 final size:24
Alignment explanation
Indices: 72403--72448 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
72393 ATATTCTTTA
72403 TATCATTTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
72427 TATCATTTATTTAATAAGTATA
1 TATCATTTATTTAATAAGTATA
72449 ATGTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
TATCATTTATTTAATAAGTATAGT
Found at i:84208 original size:7 final size:7
Alignment explanation
Indices: 84177--84265 Score: 64
Period size: 7 Copynumber: 12.6 Consensus size: 7
84167 TGAAGAAAAA
*
84177 AAAAAGG
1 AAAAATG
84184 AACAAAT-
1 AA-AAATG
84191 AAAAGATG
1 AAAA-ATG
84199 AAAAATG
1 AAAAATG
84206 AAAAA-G
1 AAAAATG
84212 AAAAA--
1 AAAAATG
84217 AAAAATG
1 AAAAATG
84224 AAAAAAAATG
1 ---AAAAATG
84234 AAAAATG
1 AAAAATG
84241 AAAAA--
1 AAAAATG
84246 AAGAAATG
1 AA-AAATG
84254 AAAAAATG
1 -AAAAATG
84262 AAAA
1 AAAA
84266 GAGAAAAAGG
Statistics
Matches: 69, Mismatches: 1, Indels: 24
0.73 0.01 0.26
Matches are distributed among these distances:
5 7 0.10
6 11 0.16
7 30 0.43
8 12 0.17
9 2 0.03
10 7 0.10
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:84254 original size:30 final size:28
Alignment explanation
Indices: 84199--84273 Score: 109
Period size: 28 Copynumber: 2.6 Consensus size: 28
84189 ATAAAAGATG
84199 AAAAATGAAAAAGAAAAAAAAAATGAAA
1 AAAAATGAAAAAGAAAAAAAAAATGAAA
84227 AAAAATGAAAAATGAAAAAAAGAAATG--A
1 AAAAATGAAAAA-GAAAAAAA-AAATGAAA
84255 AAAAATGAAAAGAGAAAAA
1 AAAAATGAAAA-AGAAAAA
84274 GGAGGGTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
28 30 0.68
29 9 0.20
30 5 0.11
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (28 bp):
AAAAATGAAAAAGAAAAAAAAAATGAAA
Found at i:84257 original size:42 final size:39
Alignment explanation
Indices: 84169--84273 Score: 97
Period size: 42 Copynumber: 2.5 Consensus size: 39
84159 ACTATGCTTG
* *
84169 AAGAAAAAAAAAAGGAACAAATAAAAGATGAAAAATGAAA
1 AAGAAAAAAAAAAGAAAAAAATAAAAGATGAAAAA-GAAA
84209 AAGAAAAAAAAAATGAAAAAAAATGAAAA-ATGAAAAA-AAGA
1 AAGAAAAAAAAAA-G-AAAAAAAT-AAAAGATGAAAAAGAA-A
*
84250 AATGAAAAAATGAAAAGAGAAAAA
1 AA-GAAAAAA--AAAAGAAAAAAA
84274 GGAGGGTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
40 15 0.27
41 4 0.07
42 27 0.49
43 5 0.09
44 4 0.07
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (39 bp):
AAGAAAAAAAAAAGAAAAAAATAAAAGATGAAAAAGAAA
Found at i:84265 original size:20 final size:19
Alignment explanation
Indices: 84199--84271 Score: 89
Period size: 18 Copynumber: 3.8 Consensus size: 19
84189 ATAAAAGATG
*
84199 AAAAATGAAAAAGAAA-AA
1 AAAAATGAAAAAGAAATGA
84217 AAAAATGAAAAA-AAATG-
1 AAAAATGAAAAAGAAATGA
84234 AAAAATGAAAAAAAGAAATGA
1 AAAAATG--AAAAAGAAATGA
84255 AAAAATGAAAAGAGAAA
1 AAAAATGAAAA-AGAAA
84272 AAGGAGGGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
17 10 0.21
18 12 0.25
19 9 0.19
20 10 0.21
21 7 0.15
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAATGAAAAAGAAATGA
Found at i:84272 original size:35 final size:35
Alignment explanation
Indices: 84171--84273 Score: 108
Period size: 35 Copynumber: 3.0 Consensus size: 35
84161 TATGCTTGAA
*
84171 GAAAAAAA-AAAGGAACAAAT-AAAAGATGAAAAAT
1 GAAAAAAAGAAA-GAAAAAATGAAAAGATGAAAAAT
* *
84205 G--AAAAAGAAAAAAAAAATGAAAAAAAATGAAAAAT
1 GAAAAAAAGAAAGAAAAAATG--AAAAGATGAAAAAT
84240 GAAAAAAAGAAATGAAAAAATGAAAAGA-GAAAAA
1 GAAAAAAAGAAA-GAAAAAATGAAAAGATGAAAAA
84274 GGAGGGTTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
32 11 0.19
33 3 0.05
34 1 0.02
35 20 0.35
36 5 0.09
37 9 0.16
38 8 0.14
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.08
Consensus pattern (35 bp):
GAAAAAAAGAAAGAAAAAATGAAAAGATGAAAAAT
Found at i:85447 original size:92 final size:92
Alignment explanation
Indices: 85280--85449 Score: 277
Period size: 92 Copynumber: 1.8 Consensus size: 92
85270 AAGGATCAGT
* * *
85280 ATTTCCAATTGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGA
1 ATTTCCAATGGAGAGCTCATAATAAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGA
85345 GAAGAACTTGTTCAACTTCGCATCAAC
66 GAAGAACTTGTTCAACTTCGCATCAAC
* * *
85372 ATTTTCAATGGAGAGCTCATAATGAGAAGAACTCGTCCGAAAGAGGGAGAAGAAGTTCATAATGA
1 ATTTCCAATGGAGAGCTCATAATAAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGA
*
85437 GAAGAGCTTGTTC
66 GAAGAACTTGTTC
85450 GACCTATCAC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 71 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (92 bp):
ATTTCCAATGGAGAGCTCATAATAAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACTTCGCATCAAC
Found at i:85723 original size:91 final size:92
Alignment explanation
Indices: 85607--85773 Score: 266
Period size: 91 Copynumber: 1.8 Consensus size: 92
85597 AAAGAGATGG
*
85607 ATCAACATTTCCAATGGAGAGTTCATAAT-AAGAAGAACTCATCCAAT-GAGATAGAAGAAGTTC
1 ATCAACATTTCCAATGGAGAGTTCATAATGAA-AAGAACTCATCCAATAGAGAGAGAAGAAGTTC
85670 ATAATGAGAAGAACTTGTTCAACTTCGC
65 ATAATGAGAAGAACTTGTTCAACTTCGC
* * * *
85698 ATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCAATAGAGAGAGAAGAAGTTCA
85763 TAATGAGAAGA
66 TAATGAGAAGA
85774 GCTTTTTTGA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 41 0.59
92 28 0.41
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (92 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCAATAGAGAGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTCGC
Found at i:85962 original size:332 final size:332
Alignment explanation
Indices: 85291--85978 Score: 1067
Period size: 332 Copynumber: 2.1 Consensus size: 332
85281 TTTCCAATTG
*
85291 AGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATAAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
85356 TCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCGTCCGAAAGAGGGAG
66 TCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCATCCGAAAGAGGGAG
* *
85421 AAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATTAGTG
131 AAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTG
* * * * * *
85486 ACACCTCGCTTGAGGGATTGATATTTTCAGAAGAGTTCATAATGAGAATAACTCGTCCTAAAGGA
196 ACACCTCGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGA
* * *
85551 GAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCATCACAGAAAGAGATGGATCAACATT
261 GAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCACAGAAAGAGATGAACCAACATT
*
85616 TCCAATGG
326 TCC-ATGA
*
85624 AGAGTTCATAATAAGAAGAACTCATCC-A-ATGAGATAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGAGTTCATAATAAGAAGAACTCATCCGACA-GAGAGAGAAGAAGTTCATAATGAGAAGAACTTG
* * *
85687 TTCAACTTCGCATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTCATCCGATAGAGGGA
65 TTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCATCCGAAAGAGGGA
* * *
85752 GAAGAAGTTCATAATGAGAAGAGCTTTTTTGACCTATCACTTGATTCACGACATTTCGAATCAGT
130 GAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGT
*
85817 GATACCTCGCTTGAGGGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAA
195 GACACCTCGCTTGAGGGATCGACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCATAAA
* ** *
85882 GGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGTGAACCAAC
258 GGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCACAGAAAGAGATGAACCAAC
85947 ATTTCC-TGA
323 ATTTCCATGA
*
85956 AGAGTTCATAATGAGAAGAACTC
1 AGAGTTCATAATAAGAAGAACTC
85979 GTCCTAAAGG
Statistics
Matches: 324, Mismatches: 28, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
331 1 0.00
332 201 0.62
333 28 0.09
334 94 0.29
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (332 bp):
AGAGTTCATAATAAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCATCCGAAAGAGGGAG
AAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTG
ACACCTCGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGA
GAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCACAGAAAGAGATGAACCAACATT
TCCATGA
Found at i:86161 original size:3 final size:3
Alignment explanation
Indices: 86146--86188 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
86136 GGTTAAAAAA
* *
86146 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
86189 AGTGTGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:87525 original size:93 final size:89
Alignment explanation
Indices: 87419--87926 Score: 250
Period size: 91 Copynumber: 5.4 Consensus size: 89
87409 TTCTTTGTTC
* *
87419 ATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATAT
1 ATATACATATATATTTATTTAATGTGTCTT-GGAAGAAT-ACCATT-TTTATTTGTTTAACATAT
87484 AGCTTAGTTGGATATTTGTTAAACGTAT
63 AGCTTAGTTGGATATTTGTTAAACGT-T
* * * *
87512 ATATATATATATATTTATTTAATGTGTCTTGGAA-ACT--GA-TTTT-TTTGTTCATATATATAT
1 ATATACATATATATTTATTTAATGTGTCTTGGAAGAATACCATTTTTATTTGTT--TA-ACATAT
** * ** * **
87572 ATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTT
63 AGCTTAG-TT-GGATAT-TTGTTAA---A--C---GTT
*
87610 CATATACATATATATTTGTTTAATGTGTCTTAGGAAGAATAGCCATTATTTATTTGTTTAACATA
1 -ATATACATATATATTTATTTAATGTGTCTT-GGAAGAATA-CCATT-TTTATTTGTTTAACATA
87675 TAGCTTAGTTGGATATTTGTTAAACG-T
62 TAGCTTAGTTGGATATTTGTTAAACGTT
* * * * * *
87702 ATATATATATATATTTATTTAATGTGTCTTGGAA-ACT--GATTTTTTTGTTCATATATATATAT
1 ATATACATATATATTTATTTAATGTGTCTTGGAAGAATACCATTTTTAT-TT-GT-T-TA-ACAT
** * ** * * *
87764 ATATATTTGTTTAACATGTCTTGGAAACTGATTCT
61 ATAGCTTAGTTGGATATTTGTT--AAAC-G--T-T
* * * *
87799 TTGTTCATATACATATATATTTGTTTAATGTGTCTTAGGAAGAATAGCCATTATTTATTTGTTTA
1 ATATACATAT--ATAT-T-TAT--TTAATGTGTCTT-GGAAGAATA-CCATT-TTTATTTGTTTA
87864 ACATATAGCTTAGTTGGATATTTGTTAAACG-T
57 ACATATAGCTTAGTTGGATATTTGTTAAACGTT
87896 ATAT--ATATAT-TTTATTTAATGTGTCTTGGAA
1 ATATACATATATATTTATTTAATGTGTCTTGGAA
87927 ACTGATTTTT
Statistics
Matches: 305, Mismatches: 63, Indels: 100
0.65 0.13 0.21
Matches are distributed among these distances:
85 10 0.03
86 8 0.03
87 8 0.03
88 23 0.08
89 6 0.02
90 26 0.09
91 36 0.12
92 10 0.03
93 31 0.10
94 1 0.00
95 4 0.01
96 2 0.01
97 10 0.03
98 2 0.01
99 34 0.11
100 5 0.02
101 10 0.03
102 7 0.02
103 14 0.05
104 31 0.10
105 7 0.02
106 4 0.01
107 7 0.02
108 5 0.02
109 4 0.01
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.48
Consensus pattern (89 bp):
ATATACATATATATTTATTTAATGTGTCTTGGAAGAATACCATTTTTATTTGTTTAACATATAGC
TTAGTTGGATATTTGTTAAACGTT
Found at i:87571 original size:50 final size:49
Alignment explanation
Indices: 87512--87839 Score: 232
Period size: 49 Copynumber: 6.7 Consensus size: 49
87502 TTAAACGTAT
* *
87512 ATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGA-TTCTTTGTTC
**
87562 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTCTTTGTTC
* * * *
87611 ATATACATATATATTTGTTTAATGTGTCTTAGGAAGAATAGCCATTATTTATT-
1 ATATATATATATATTTGTTTAATGTGTCTT-GGAA-ACT-G--ATTCTTTGTTC
* * * * * ** ****
87664 -TGTTTA-ACATA-TAGCTT-A---G--TTGGATATTTG-TTAAACG-T-
1 ATATATATATATATTTGTTTAATGTGTCTTGGA-AACTGATTCTTTGTTC
* *
87702 ATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGA-TTCTTTGTTC
**
87752 ATATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ----ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTCTTTGTTC
*
87805 ATATACATATATATTTGTTTAATGTGTCTTAGGAA
1 ATATATATATATATTTGTTTAATGTGTCTT-GGAA
87840 GAATAGCCAT
Statistics
Matches: 213, Mismatches: 41, Indels: 48
0.71 0.14 0.16
Matches are distributed among these distances:
38 1 0.00
39 7 0.03
40 4 0.02
41 3 0.01
42 2 0.01
43 4 0.02
44 3 0.01
45 1 0.00
46 4 0.02
47 5 0.02
48 3 0.01
49 65 0.31
50 48 0.23
51 6 0.03
52 4 0.02
53 9 0.04
54 44 0.21
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTCTTTGTTC
Found at i:87639 original size:49 final size:50
Alignment explanation
Indices: 87512--87645 Score: 207
Period size: 50 Copynumber: 2.7 Consensus size: 50
87502 TTAAACGTAT
* *
87512 ATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTCTTTGTTC
**
87562 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGA-TTCTTTGTTC
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTCTTTGTTC
*
87611 ATATACATATATATTTGTTTAATGTGTCTTAGGAA
1 ATATATATATATATTTGTTTAATGTGTCTT-GGAA
87646 GAATAGCCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
49 36 0.47
50 40 0.53
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (50 bp):
ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTCTTTGTTC
Found at i:87769 original size:54 final size:53
Alignment explanation
Indices: 87701--87818 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 53
87691 TTGTTAAACG
** *
87701 TATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATA
1 TATATATATATATATTTATTTAACATGTCTTGGAAACTGA-TTCTTTGTTCATA
*
87755 TATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTCATA
1 TATATATATATATATTTATTTAACATGTCTTGGAAACTGATTCTTTGTTCATA
*
87808 TACATATATAT
1 TATATATATAT
87819 TTGTTTAATG
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
53 22 0.37
54 37 0.63
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (53 bp):
TATATATATATATATTTATTTAACATGTCTTGGAAACTGATTCTTTGTTCATA
Found at i:87831 original size:194 final size:194
Alignment explanation
Indices: 87397--88090 Score: 1019
Period size: 194 Copynumber: 3.5 Consensus size: 194
87387 GTACATTTAC
* *
87397 CTTGGAAATTGATTCTTTGTTCATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACC
1 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAGCC
*
87462 ATTGTTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACGTATATATATATATATATT
66 ATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACG--TATATATATATATATT
87527 TATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC----ATATATATATATATTTGTTTAACATG
129 TATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATATATATATATATTTGTTTAACATG
87588 T
194 T
*
87589 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAATGTGTCTTAGGAAGAATAGCC
1 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAGCC
87654 ATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACGTATATATATATATATTTA
66 ATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACGTATATATATATATATTTA
87719 TTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATATATATATATATTTGTTTAACATGT
131 TTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATATATATATATATTTGTTTAACATGT
*
87783 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAATGTGTCTTAGGAAGAATAGCC
1 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAGCC
87848 ATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACG--TATATATATAT-TTTA
66 ATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACGTATATATATATATATTTA
* *
87910 TTTAATGTGTCTTGGAAACTGATTTTTGTCATATAT-ATATATATATATATATATATATATTTAT
131 TTTAATGTGTCTTGGAAACTGATTTTT-T--TGT-TCATATATATATATATATAT-T-TGTTTA-
*
87974 TTATTTAATGTGT
189 --A---CA--TGT
* * *
87987 CTTGGAAACTGATTTTTTTTTGTTCATATATATATATATTTGTTTAACATGTCTTAGGAAGAATA
1 CTTGGAAACTGA---TTCTTTGTTCATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATA
* * * *
88052 GGCA-TATTTTTTTGTTTAACGTATAGCTTAGCTGGATAT
63 GCCATTATTTATTTGTTTAACATATAGCTTAGTTGGATAT
88091 ATATATATAT
Statistics
Matches: 466, Mismatches: 15, Indels: 28
0.92 0.03 0.06
Matches are distributed among these distances:
190 51 0.11
191 31 0.07
192 120 0.26
194 159 0.34
195 2 0.00
196 5 0.01
199 1 0.00
202 1 0.00
204 15 0.03
206 32 0.07
207 49 0.11
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (194 bp):
CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAGCC
ATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACGTATATATATATATATTTA
TTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATATATATATATATTTGTTTAACATGT
Found at i:87947 original size:2 final size:2
Alignment explanation
Indices: 87940--87969 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
87930 GATTTTTGTC
87940 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
87970 TTATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88234 original size:23 final size:24
Alignment explanation
Indices: 88208--88252 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
88198 ATATTCTTTA
88208 TATCA-TTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
88231 TATCATTTATTTAATAAGTATA
1 TATCATTTATTTAATAAGTATA
88253 ATGTTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (24 bp):
TATCATTTATTTAATAAGTATAGT
Found at i:91358 original size:25 final size:25
Alignment explanation
Indices: 91323--91370 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
91313 ATATTTTATT
*
91323 TTCATCCTAAAATTTTATAAATTCG
1 TTCATCCTAAAATTTTAAAAATTCG
*
91348 TTCATCTTAAAATTTTAAAAATT
1 TTCATCCTAAAATTTTAAAAATT
91371 TATTAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (25 bp):
TTCATCCTAAAATTTTAAAAATTCG
Found at i:91882 original size:2 final size:2
Alignment explanation
Indices: 91875--91901 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
91865 TTCTAACACT
91875 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 T
91902 TTGAATTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92825 original size:29 final size:28
Alignment explanation
Indices: 92756--92830 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
92746 AATTCTCCCC
92756 TAAAAATTATAAAAATAT-GATTAGAATA
1 TAAAAA-TATAAAAATATAGATTAGAATA
* * * * *
92784 TACATATTTAAAAATATATATTAGAAGTT
1 TAAAAATATAAAAATATAGATTAGAA-TA
*
92813 TAAAAATATAAAATTATA
1 TAAAAATATAAAAATATA
92831 AAATAAGATG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
27 10 0.28
28 11 0.31
29 15 0.42
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (28 bp):
TAAAAATATAAAAATATAGATTAGAATA
Done.