Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 37 of 51
Found at i:9334427 original size:14 final size:14
Alignment explanation
Indices: 9334408--9334528 Score: 98
Period size: 14 Copynumber: 7.6 Consensus size: 14
9334398 GTTGAAATGA
9334408 AATCGCAACGAGAG
1 AATCGCAACGAGAG
9334422 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
9334439 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
9334455 AATCGCAACGCGAATGAA
1 AATCGCAA--CG-A-GAG
9334473 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
9334487 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
9334506 AATCGCAACGAGAG
1 AATCGCAACGAGAG
9334520 AATCGCAAC
1 AATCGCAAC
9334529 TCGAAATGAA
Statistics
Matches: 89, Mismatches: 4, Indels: 28
0.74 0.03 0.23
Matches are distributed among these distances:
14 37 0.42
15 2 0.02
16 12 0.13
17 9 0.10
18 11 0.12
19 18 0.20
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:9334445 original size:33 final size:33
Alignment explanation
Indices: 9334401--9334546 Score: 251
Period size: 33 Copynumber: 4.5 Consensus size: 33
9334391 TCTTTTGGTT
9334401 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
9334433 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
9334466 G-AATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
9334498 GAAATGAAAATCGCAACGAGAGAATCGCAACTC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
9334531 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
9334547 TGCGATTTTG
Statistics
Matches: 107, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
32 35 0.33
33 72 0.67
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:9334484 original size:65 final size:66
Alignment explanation
Indices: 9334401--9334546 Score: 251
Period size: 65 Copynumber: 2.2 Consensus size: 66
9334391 TCTTTTGGTT
* *
9334401 GAAATG-AAATCGCAACGAGAGAATCGCAACGCGAGATGACAATCGCAACGAGAGAATCGCAACG
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACG
9334465 C
66 C
*
9334466 G-AATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACG
9334530 C
66 C
9334531 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
9334547 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
64 4 0.05
65 58 0.76
66 14 0.18
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (66 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACG
C
Found at i:9334544 original size:19 final size:17
Alignment explanation
Indices: 9334403--9334546 Score: 89
Period size: 14 Copynumber: 8.8 Consensus size: 17
9334393 TTTTGGTTGA
9334403 AATG-AAATCGCAA-CG
1 AATGAAAATCGCAACCG
*
9334418 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAAC-CG
*
9334434 AGATGACAATCGCAA-CG
1 A-ATGAAAATCGCAACCG
*
9334451 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAAC-CG
9334467 AATGAAAATCGCAA-CG
1 AATGAAAATCGCAACCG
*
9334483 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAAC-CG
9334499 AAATGAAAATCGCAA-CG
1 -AATGAAAATCGCAACCG
*
9334516 -A-GAGAATCGCAACTCG
1 AATGAAAATCGCAAC-CG
9334532 AAATGAAAATCGCAA
1 -AATGAAAATCGCAA
9334547 TGCGATTTTG
Statistics
Matches: 101, Mismatches: 8, Indels: 36
0.70 0.06 0.25
Matches are distributed among these distances:
13 1 0.01
14 39 0.39
15 3 0.03
16 10 0.10
17 5 0.05
18 13 0.13
19 30 0.30
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (17 bp):
AATGAAAATCGCAACCG
Found at i:9334585 original size:31 final size:33
Alignment explanation
Indices: 9334547--9334615 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 33
9334537 AAAATCGCAA
**
9334547 TGCGATTTTGGTTTCGCGTTGCGA-T-TCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
9334578 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
9334611 TGCGA
1 TGCGA
9334616 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 22 0.65
32 1 0.03
33 11 0.32
ACGTcount: A:0.09, C:0.22, G:0.26, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:9334778 original size:33 final size:33
Alignment explanation
Indices: 9334736--9334806 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
9334726 AATACTAACT
9334736 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
***
9334769 TGAAAATCGCAACGAGAGAATCTTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
9334802 TGAAA
1 TGAAA
9334807 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:9335037 original size:22 final size:21
Alignment explanation
Indices: 9334986--9335039 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
9334976 TGGTTGTGAG
**
9334986 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
**
9335007 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
9335029 GGATTTCTTCG
1 GGATTTCTTCG
9335040 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:9335248 original size:20 final size:20
Alignment explanation
Indices: 9335184--9335375 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
9335174 CTTTAAATAT
9335184 CGCGTTGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9335203 CGCGTTGCGATTTATGTATTA
1 CGCGTTGCGATTTACGGA-TA
*
9335224 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9335243 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
9335263 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
9335283 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
9335304 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9335324 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
9335344 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
9335364 CGCGTTGCGATT
1 CGCGTTGCGATT
9335376 ATTGAAAATC
Statistics
Matches: 145, Mismatches: 22, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
19 12 0.08
20 113 0.78
21 20 0.14
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:9335348 original size:61 final size:61
Alignment explanation
Indices: 9335186--9335357 Score: 240
Period size: 61 Copynumber: 2.9 Consensus size: 61
9335176 TTAAATATCG
** *
9335186 CGTTGCGA-TTACGGATACGCGTTGCGATTTATGTATTATCGTTGCGA-TTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTTACGGATACA
* * *** *
9335245 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTTACGGATACA
*
9335306 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTT
9335358 CATATTCGCG
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 8 0.08
60 31 0.33
61 56 0.59
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (61 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTTACGGATACA
Found at i:9335352 original size:81 final size:81
Alignment explanation
Indices: 9335183--9335375 Score: 223
Period size: 81 Copynumber: 2.4 Consensus size: 81
9335173 GCTTTAAATA
** * * *
9335183 TCGCGTTGCGA-TTACGGATACGCGTTGCGA-TTTATGTATTATCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
9335246 GTTGCGATATACGGAT
66 GTTGCGATATACGGAT
* * *
9335262 ACGCATTGCGATTTACCCATACGCGTTGCGATTTTACGGA-TACACGTTGCGATTTACGGATACG
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTA-ACGTTGCGATTTACGGATACG
* *
9335326 CGTTGCGATTTATGTG-T
65 CGTTGCGATATACG-GAT
* * *
9335343 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACACATACGCGTTGCGATT
9335376 ATTGAAAATC
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
79 9 0.09
80 19 0.20
81 66 0.69
82 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (81 bp):
TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
GTTGCGATATACGGAT
Found at i:9336107 original size:22 final size:24
Alignment explanation
Indices: 9336066--9336118 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
9336056 TATATATATC
9336066 ATTTTTAGTAATTTAATTTTTATT
1 ATTTTTAGTAATTTAATTTTTATT
* *
9336090 ATTTTTA-T-ATTTACTTTTTTTT
1 ATTTTTAGTAATTTAATTTTTATT
9336112 ACTTTTT
1 A-TTTTT
9336119 TATGTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 13 0.50
23 6 0.23
24 7 0.27
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTAGTAATTTAATTTTTATT
Found at i:9341725 original size:12 final size:13
Alignment explanation
Indices: 9341705--9341733 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
9341695 ATACCCAACA
9341705 TTATATTTTATTT
1 TTATATTTTATTT
9341718 TTAT-TTTTATTT
1 TTATATTTTATTT
9341730 TTAT
1 TTAT
9341734 CACACCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATATTTTATTT
Found at i:9342127 original size:9 final size:9
Alignment explanation
Indices: 9342115--9342160 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
9342105 ATATATTCAT
9342115 TATATATAA
1 TATATATAA
*
9342124 TATATTTAA
1 TATATATAA
*
9342133 TAT-T-TAG
1 TATATATAA
9342140 TATATATAA
1 TATATATAA
*
9342149 TATATTTAA
1 TATATATAA
9342158 TAT
1 TAT
9342161 TTACTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 24 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
TATATATAA
Found at i:9342143 original size:25 final size:25
Alignment explanation
Indices: 9342115--9342163 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
9342105 ATATATTCAT
9342115 TATATATAATATATTTAATATTTAG
1 TATATATAATATATTTAATATTTAG
9342140 TATATATAATATATTTAATATTTA
1 TATATATAATATATTTAATATTTA
9342164 CTAATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATATATAATATATTTAATATTTAG
Found at i:9345111 original size:59 final size:60
Alignment explanation
Indices: 9345046--9345161 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
9345036 AAACCATAAC
* * * * *
9345046 TCTTATTTTAAATTGATTCTTAAACTTTTTAATATTCCAATTTCAT-CCCAAACTATGAA
1 TCTTATTTTAAATTAATCCTTAAACTATTGAAAATTCCAATTTCATCCCCAAACTATGAA
* *
9345105 TCTTATTTTAAATTAATCCTTAAACTATTGAAAATTTCAATTTTATCCCCAAACTAT
1 TCTTATTTTAAATTAATCCTTAAACTATTGAAAATTCCAATTTCATCCCCAAACTAT
9345162 AACATTCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 39 0.80
60 10 0.20
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (60 bp):
TCTTATTTTAAATTAATCCTTAAACTATTGAAAATTCCAATTTCATCCCCAAACTATGAA
Found at i:9345216 original size:60 final size:59
Alignment explanation
Indices: 9345079--9345217 Score: 140
Period size: 60 Copynumber: 2.3 Consensus size: 59
9345069 ACTTTTTAAT
* * **
9345079 ATTCCAATTTCATCCCAAACTATGAATCTTATTTTAAATTAATCCTTAAACTATTGAAA
1 ATTCCAATTTAATCCCAAACTATGAATCTTATTCTAAATTAATCCCCAAACTATTGAAA
* * * *
9345138 ATTTCAATTTTATCCCCAAACTAT-AA-CATTCATTCTAAATTAGTCCCCAAAC-ATTTTAAA
1 ATTCCAATTTAAT-CCCAAACTATGAATC-TT-ATTCTAAATTAATCCCCAAACTA-TTGAAA
9345198 CATTCCAATTTAATCCCAAA
1 -ATTCCAATTTAATCCCAAA
9345218 TTTATCCAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
58 1 0.02
59 16 0.24
60 38 0.58
61 11 0.17
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (59 bp):
ATTCCAATTTAATCCCAAACTATGAATCTTATTCTAAATTAATCCCCAAACTATTGAAA
Found at i:9346294 original size:21 final size:20
Alignment explanation
Indices: 9346260--9346301 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
9346250 TTGACAGAAC
9346260 CCGTTGACTTTGACTTTGAT
1 CCGTTGACTTTGACTTTGAT
*
9346280 CCGTTTACTGTTGACTTTGAT
1 CCGTTGACT-TTGACTTTGAT
9346301 C
1 C
9346302 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.45
Consensus pattern (20 bp):
CCGTTGACTTTGACTTTGAT
Found at i:9352081 original size:24 final size:23
Alignment explanation
Indices: 9352049--9352095 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
9352039 ATAAAATTTT
* *
9352049 CACCGAAGTGCCACGTAGAATATG
1 CACCAAAGTGCCACATAG-ATATG
9352073 CACCAAAGTGCCACATAGATATG
1 CACCAAAGTGCCACATAGATATG
9352096 TCCGAAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (23 bp):
CACCAAAGTGCCACATAGATATG
Found at i:9352324 original size:30 final size:30
Alignment explanation
Indices: 9352271--9352344 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
9352261 TTTTATCCAT
* * *
9352271 ATAGAACACTTTCGCATAGAGCATTTTCAC
1 ATAGAACACATTCACATAAAGCATTTTCAC
* *
9352301 GTATAACACATTCACATAAAGCATTTTCAC
1 ATAGAACACATTCACATAAAGCATTTTCAC
9352331 ATAGAACACATTCA
1 ATAGAACACATTCA
9352345 TATGTTAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (30 bp):
ATAGAACACATTCACATAAAGCATTTTCAC
Found at i:9352344 original size:15 final size:15
Alignment explanation
Indices: 9352271--9352344 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
9352261 TTTTATCCAT
*
9352271 ATAGAACACTTTCGC
1 ATAGAACACTTTCAC
* *
9352286 ATAGAGCATTTTCAC
1 ATAGAACACTTTCAC
* * *
9352301 GTATAACACATTCAC
1 ATAGAACACTTTCAC
*
9352316 ATA-AAGCATTTTCAC
1 ATAGAA-CACTTTCAC
*
9352331 ATAGAACACATTCA
1 ATAGAACACTTTCA
9352345 TATGTTAATA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
14 2 0.05
15 40 0.91
16 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (15 bp):
ATAGAACACTTTCAC
Found at i:9358615 original size:55 final size:55
Alignment explanation
Indices: 9358477--9358878 Score: 522
Period size: 55 Copynumber: 7.3 Consensus size: 55
9358467 TTTATTAGAA
** * *** *
9358477 TGCACA-AGTAGTGCCTACACGGTAATTCATCAACTCATGATGAATTTTATGG-GT
1 TGCACACA-TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
9358531 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATACCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
** * * *
9358586 TTTACACATAGTGCCTGTATGGTTATTCATCAACTAATGATGAATTTCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
9358641 TGCACACATAGTG-CTGTACGGTTATTCATCAACTTATGATGAATTTCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * **
9358695 TGCATACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTATGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * *
9358750 TGAACACATAGTGCCTGTATGATTATTCATCAGCTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
9358805 TGTACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
9358860 TTCACACATAGTTCCTGTA
1 TGCACACATAGTGCCTGTA
9358879 GTACACGTAG
Statistics
Matches: 304, Mismatches: 41, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
54 93 0.31
55 211 0.69
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:9358628 original size:109 final size:109
Alignment explanation
Indices: 9358485--9358871 Score: 551
Period size: 109 Copynumber: 3.5 Consensus size: 109
9358475 AATGCACAAG
** * * *
9358485 TAGTGCCTACACGGTAATTCATCAACTCATGATGAATTTTATGG-GTTGCACACATAGTGCATGT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGATTTGCACACATAGTGC-TGT
* *
9358549 ACGGTTATTCATCAACTCATGATGAATACCGTGGATTTTTACACA
65 ACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACA
* * *
9358594 TAGTGCCTGTATGGTTATTCATCAACTAATGATGAATTTCGTGGATTTGCACACATAGTGCTGTA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGATTTGCACACATAGTGCTGTA
* * * *
9358659 CGGTTATTCATCAACTTATGATGAATTTCGTGGATTTGCATACA
66 CGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACA
* * *
9358703 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTATGTGGATTTGAACACATAGTGCCTGT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGATTTGCACACATAGTG-CTGT
* * *
9358768 ATGATTATTCATCAGCTCATGATGAATTCCGTGGATTTGTACACA
65 ACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACA
* *
9358813 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTTCACACATAGT
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGATTTGCACACATAGT
9358872 TCCTGTAGTA
Statistics
Matches: 245, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
109 133 0.54
110 112 0.46
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (109 bp):
TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGATTTGCACACATAGTGCTGTA
CGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGTACACA
Found at i:9358778 original size:164 final size:165
Alignment explanation
Indices: 9358477--9358871 Score: 575
Period size: 164 Copynumber: 2.4 Consensus size: 165
9358467 TTTATTAGAA
** * ** *
9358477 TGCACA-AGTAGTGCCTACACGGTAATTCATCAACTCATGATGAATTTTATGG-GTTGCACACAT
1 TGCACACA-TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACAT
**
9358540 AGTGCATGTACGGTTATTCATCAACTCATGATGAATACCGTGGATTTTTACACATAGTGCCTGTA
65 AGTGCATGTACGGTTATTCATCAACTCATGATGAATACCGTGGATTTGAACACATAGTGCCTGTA
* *
9358605 TGGTTATTCATCAACTAATGATGAATTTCGTGGATT
130 TGATTATTCATCAACTAATGATGAATTCCGTGGATT
* *
9358641 TGCACACATAGTG-CTGTACGGTTATTCATCAACTTATGATGAATTTCGTGGATTTGCATACATA
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATA
*
9358705 GTGCATGTACGGTTATTCATCAACTCATGATGAATTA-TGTGGATTTGAACACATAGTGCCTGTA
66 GTGCATGTACGGTTATTCATCAACTCATGATGAA-TACCGTGGATTTGAACACATAGTGCCTGTA
* *
9358769 TGATTATTCATCAGCTCATGATGAATTCCGTGGATT
130 TGATTATTCATCAACTAATGATGAATTCCGTGGATT
* *
9358805 TGTACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCTGTGGATTTTCACACAT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGATTTGCACACAT
9358869 AGT
65 AGT
9358872 TCCTGTAGTA
Statistics
Matches: 207, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
163 32 0.15
164 126 0.61
165 49 0.24
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (165 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATA
GTGCATGTACGGTTATTCATCAACTCATGATGAATACCGTGGATTTGAACACATAGTGCCTGTAT
GATTATTCATCAACTAATGATGAATTCCGTGGATT
Found at i:9359263 original size:19 final size:19
Alignment explanation
Indices: 9359235--9359297 Score: 117
Period size: 19 Copynumber: 3.3 Consensus size: 19
9359225 ACTATATTAT
9359235 GGTACCGATGCTCCATTTC
1 GGTACCGATGCTCCATTTC
*
9359254 GGTACAGATGCTCCATTTC
1 GGTACCGATGCTCCATTTC
9359273 GGTACCGATGCTCCATTTC
1 GGTACCGATGCTCCATTTC
9359292 GGTACC
1 GGTACC
9359298 ATACCATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.30
Consensus pattern (19 bp):
GGTACCGATGCTCCATTTC
Found at i:9359306 original size:16 final size:18
Alignment explanation
Indices: 9359235--9359306 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
9359225 ACTATATTAT
*
9359235 GGTACCGATGCTCCATTTC
1 GGTACCGAT-CACCATTTC
* *
9359254 GGTACAGATGCTCCATTTC
1 GGTACCGAT-CACCATTTC
*
9359273 GGTACCGATGCTCCATTTC
1 GGTACCGAT-CACCATTTC
9359292 GGTACC-AT-ACCATTT
1 GGTACCGATCACCATTT
9359307 TTGCATTCTG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.12
18 2 0.04
19 42 0.84
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.32
Consensus pattern (18 bp):
GGTACCGATCACCATTTC
Found at i:9365203 original size:55 final size:55
Alignment explanation
Indices: 9365062--9365518 Score: 512
Period size: 55 Copynumber: 8.3 Consensus size: 55
9365052 TTTATTAGAA
* * * * *
9365062 TGCACA-AGTAGTTCCTATACGGTAATTCATCAACTCATGATAAATTCCGTGG-GT
1 TGCACACA-TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
9365116 TGCACACATAATTCCTGTACGATTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
9365171 TGCACACATAGTGCATGTACGGTTATTAATCAACTCATGATGAATAT--GAT-GATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAAT-TCCG-TGGATT
* * **
9365225 TCCACACATAGTGCCTGTACGGTTATTCATAAACTCATGATGAATTTTGTGGA-T
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
9365279 TGTCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGACT
1 TG-CACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * **
9365335 TGCACAGATAGTGCCTGTACGGTTATACATCAACTCATGATGAATTCTGTATATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * ** **
9365390 TGCACATATAGTGCATGTACAATTATTCATCAACTCATGATGAATTCTATGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
9365445 TGCACACATAGTTCCTATATGGTTATTCATCAACTCATGATTAATTCCATGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
9365500 TTCACACATAATGCTTGTA
1 TGCACACATAGTGCCTGTA
9365519 TAACACTTAG
Statistics
Matches: 345, Mismatches: 49, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.00
54 94 0.27
55 246 0.71
56 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:9367290 original size:45 final size:45
Alignment explanation
Indices: 9367236--9367667 Score: 336
Period size: 45 Copynumber: 9.7 Consensus size: 45
9367226 TATAACATAT
* * *
9367236 TTTTCTGTTGATAATGCACCAATATGCATTTCAACTATAATATAC
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
9367281 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * *
9367326 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATAC
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
*** * * *
9367371 TTTTCA-GTTGATAATTTTCCCATATACATTTCAACTCTAGCATAC
1 TTTT-ATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* ** ** * *
9367416 TTTTCTGTTGATAATGTGCCCATATATATTTCAACTCTAGCATAC
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * ** * * *
9367461 TTTTTCTTTTGATAATGTGCCCACATACATTTCAACTCTA-T-T--
1 -TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * * * * * *
9367503 TCTGATGATAATAATGC-CCCATATGCATTTTAACTCTAGCATAC
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * * * * **
9367547 TTTTCTATTGATAATGTACCCATATACATTTCAACTAAAGTATGT
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * * * * * *
9367592 TTTTTTGTTGGTAATGTACCCATATACATTTCTACTATAGCATCC
1 TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * * **
9367637 TTTCATGCTAATAATAAACCCATATGCATTT
1 TTTTATGTTGATAATGCACCCATATGCATTT
9367668 GTATTTTCAT
Statistics
Matches: 319, Mismatches: 60, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
40 18 0.06
41 10 0.03
42 1 0.00
44 11 0.03
45 243 0.76
46 36 0.11
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.41
Consensus pattern (45 bp):
TTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
Found at i:9367356 original size:90 final size:90
Alignment explanation
Indices: 9367236--9367667 Score: 408
Period size: 90 Copynumber: 4.8 Consensus size: 90
9367226 TATAACATAT
* * * ** *
9367236 TTTTCTGTTGATAATGCACCAATATGCATTTCAACTATAATATACTTTTATGTTGATAATGCACC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTATGTTGATAATGTACC
*
9367301 CATATGCATTTCAACTATAGTATAC
66 CATATACATTTCAACTATAGTATAC
* * *
9367326 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATACTTTTCA-GTTGATAATTTTC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTT-ATGTTGATAATGTAC
* *
9367390 CCATATACATTTCAACTCTAGCATAC
65 CCATATACATTTCAACTATAGTATAC
* * * * * *
9367416 TTTTCTGTTGATAATGTGCCCATATATATTTCAACTCTAGCATACTTTTTCTTTTGATAATGTGC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC-TTTTATGTTGATAATGTAC
* *
9367481 CCACATACATTTCAACTCTA-T-T--
65 CCATATACATTTCAACTATAGTATAC
* ** * * * * * * * *
9367503 TCTGATGATAATAATG-CCCCATATGCATTTTAACTCTAGCATACTTTTCTATTGATAATGTACC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTATGTTGATAATGTACC
* **
9367567 CATATACATTTCAACTAAAGTATGT
66 CATATACATTTCAACTATAGTATAC
* * * * * * * **
9367592 TTTTTTGTTGGTAATGTACCCATATACATTTCTACTATAGCATCCTTTCATGCTAATAATAAACC
1 TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTATGTTGATAATGTACC
*
9367657 CATATGCATTT
66 CATATACATTT
9367668 GTATTTTCAT
Statistics
Matches: 280, Mismatches: 54, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
85 34 0.12
86 25 0.09
87 12 0.04
89 11 0.04
90 164 0.59
91 34 0.12
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.41
Consensus pattern (90 bp):
TTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTATGTTGATAATGTACC
CATATACATTTCAACTATAGTATAC
Found at i:9367574 original size:85 final size:84
Alignment explanation
Indices: 9367417--9367582 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 84
9367407 CTAGCATACT
* * * * *
9367417 TTTCTGTTGATAATGTGCCCATATATATTTCAACTCTAGCATACTTTTTCTTTTGATAATGTGCC
1 TTTCTGATGATAATATGCCCATATACATTTCAACTCTAGCATACTTTTTCTATTGATAATGTACC
9367482 CACATACATTTCAACTCTA
66 CACATACATTTCAACTCTA
* *
9367501 TTTCTGATGATAATAATGCCCCATATGCATTTTAACTCTAGCATAC-TTTTCTATTGATAATGTA
1 TTTCTGATGATAAT-ATG-CCCATATACATTTCAACTCTAGCATACTTTTTCTATTGATAATGTA
*
9367565 CCCATATACATTTCAACT
64 CCCACATACATTTCAACT
9367583 AAAGTATGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
84 13 0.18
85 35 0.49
86 24 0.33
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (84 bp):
TTTCTGATGATAATATGCCCATATACATTTCAACTCTAGCATACTTTTTCTATTGATAATGTACC
CACATACATTTCAACTCTA
Found at i:9368215 original size:22 final size:22
Alignment explanation
Indices: 9368184--9368238 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
9368174 CAGTACCCTG
9368184 GGTATCGATACTGTTCTTCCCA
1 GGTATCGATACTGTTCTTCCCA
*
9368206 GGTATAGATACTGTTCTTCCCA
1 GGTATCGATACTGTTCTTCCCA
9368228 GGTATCGATAC
1 GGTATCGATAC
9368239 CTTTTGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (22 bp):
GGTATCGATACTGTTCTTCCCA
Found at i:9370010 original size:23 final size:23
Alignment explanation
Indices: 9369976--9370054 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
9369966 AAAATTTGCA
*
9369976 CCGAAGTG-CCACATAGATATGTC
1 CCGAAG-GACCACGTAGATATGTC
* *
9369999 CCGAAGGACCACGTAGAATTTATC
1 CCGAAGGACCACGTAG-ATATGTC
* *
9370023 CCAAAGGACCACGCAGA-ATTGTC
1 CCGAAGGACCACGTAGATA-TGTC
9370046 CCGAAGGAC
1 CCGAAGGAC
9370055 TGCGTAGAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.02
23 25 0.56
24 19 0.42
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (23 bp):
CCGAAGGACCACGTAGATATGTC
Found at i:9370063 original size:23 final size:24
Alignment explanation
Indices: 9369995--9370063 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
9369985 CACATAGATA
9369995 TGTCCCGAAGGACCACGTAGAATT
1 TGTCCCGAAGGACCACGTAGAATT
* * *
9370019 TATCCCAAAGGACCACGCAGAA-T
1 TGTCCCGAAGGACCACGTAGAATT
**
9370042 TGTCCCGAAGGACTGCGTAGAA
1 TGTCCCGAAGGACCACGTAGAA
9370064 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (24 bp):
TGTCCCGAAGGACCACGTAGAATT
Found at i:9375188 original size:55 final size:55
Alignment explanation
Indices: 9375055--9375497 Score: 478
Period size: 54 Copynumber: 8.2 Consensus size: 55
9375045 AATGCATAAG
* * * * *
9375055 TAGTGCCTATACGGTAATTCATCAACTCATGATGAATTCCGTGG-GTTGCACACA
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
* * *
9375109 TAGTCCCTGTAC-GATTAATCATCAACTCATGATGAATTTCATGGATTTGCACACA
1 TAGTGCCTGTACAG-TTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
* * * * * *
9375164 TAGTGCATGTACATTTATTAATCAATTCATGATGAATTAT-GTGGGTTTTCACACA
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATT-TCGTGGATTTGCACACA
* * *
9375219 TAGTGCCTGTACGGTTATTAATCAACTTATGATGAA-TTCGTGGATTTGCACACA
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
* * ** * **
9375273 TAGTGTCTGTACGGTTATTCATCAA-TTGTGATAAATTTCGTGGATTTGCATTCA
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
9375327 TAGTGCCTGTAC-GTTATTCATCAACTCATGATGAA-TTCTGTGGATTTGCACACA
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTC-GTGGATTTGCACACA
* * *
9375381 TAGTACATGTACGGTTATTCATCAACT--T-ATGAA-TTCTGTGGATTTGCACACA
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTC-GTGGATTTGCACACA
* * * * *
9375433 TAGTGCCTGTATAGTTATTCATCAACTCATGATTAATTTCGTGGATTTTCGCTCA
1 TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
9375488 T-GTGCCTGTA
1 TAGTGCCTGTA
9375498 AAACACTTAG
Statistics
Matches: 331, Mismatches: 45, Indels: 26
0.82 0.11 0.06
Matches are distributed among these distances:
52 47 0.14
53 26 0.08
54 140 0.42
55 114 0.34
56 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (55 bp):
TAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
Found at i:9377476 original size:45 final size:44
Alignment explanation
Indices: 9377422--9377556 Score: 193
Period size: 45 Copynumber: 3.0 Consensus size: 44
9377412 TATAACATAT
*
9377422 TTTTCTGTTGATAATGCACCAATATGCATTTCAACTGTAGTATAC
1 TTTTCTGTTGATAATGCACC-ATATGCATTTCAACTATAGTATAC
9377467 TTTTCTGTTGATAATGCACCCATATGCATTT-ACACTATAGTATAC
1 TTTTCTGTTGATAATGCA-CCATATGCATTTCA-ACTATAGTATAC
*
9377512 TTTTCTGTTGATAATGTAACCATATAG-ATTTCAACTATAGTATAC
1 TTTTCTGTTGATAATG-CACCATAT-GCATTTCAACTATAGTATAC
9377557 ACAATATCAT
Statistics
Matches: 83, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
44 1 0.01
45 77 0.93
46 5 0.06
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (44 bp):
TTTTCTGTTGATAATGCACCATATGCATTTCAACTATAGTATAC
Found at i:9379868 original size:23 final size:24
Alignment explanation
Indices: 9379811--9379879 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 24
9379801 GCCACATATA
*
9379811 TGTCCCGAAGGACCGCATAGAAGT
1 TGTCCCGAAGGACCGCGTAGAAGT
* * *
9379835 TATCCCAAAGGACCACGTAGAA-T
1 TGTCCCGAAGGACCGCGTAGAAGT
9379858 TGTCCCGAAGGACCGCGTAGAA
1 TGTCCCGAAGGACCGCGTAGAA
9379880 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (24 bp):
TGTCCCGAAGGACCGCGTAGAAGT
Found at i:9382272 original size:3 final size:3
Alignment explanation
Indices: 9382264--9382295 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
9382254 ATATGTAAAT
*
9382264 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9382296 TTATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9382764 original size:131 final size:131
Alignment explanation
Indices: 9382591--9382829 Score: 331
Period size: 131 Copynumber: 1.8 Consensus size: 131
9382581 TTTAGGGAAT
* ** * ** *
9382591 GATGATAACACGGTTCTTACGTGATGAGGACGGCTAGTTATCTAGGGTTGACACTGCTCCTACGT
1 GATGATAACACGGTTCCTACACGATGAGGACGACTAGTTATCTAAAGTTGACACGGCTCCTACGT
* *
9382656 GATGAGGAGGTCTGGTCGGTG-GATGACACGGTTACTACATGATAAAGATGGTTGACCATCTTTA
66 AATGAGGAAGTCTGGTCGG-GAGATGACACGGTTACTACATGATAAAGATGGTTGACCATCTTTA
9382720 AA
130 AA
9382722 GATGATAACACGGTTCCTACACGATGAGGATC-AC-AGGTTATCTAAAGTTGACACGGCTCCTAC
1 GATGATAACACGGTTCCTACACGATGAGGA-CGACTA-GTTATCTAAAGTTGACACGGCTCCTAC
* *
9382785 GTAATGAGGAAGTCTGGTCGGGAGATGACACGGTTCCTACGTGAT
64 GTAATGAGGAAGTCTGGTCGGGAGATGACACGGTTACTACATGAT
9382830 GAGGACGGCA
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
130 2 0.02
131 91 0.97
132 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (131 bp):
GATGATAACACGGTTCCTACACGATGAGGACGACTAGTTATCTAAAGTTGACACGGCTCCTACGT
AATGAGGAAGTCTGGTCGGGAGATGACACGGTTACTACATGATAAAGATGGTTGACCATCTTTAA
A
Found at i:9382990 original size:64 final size:62
Alignment explanation
Indices: 9382854--9382999 Score: 159
Period size: 65 Copynumber: 2.3 Consensus size: 62
9382844 ATCTTTAGGT
* * *
9382854 ATTTGTTTCAAGGGAAATAGACTCAAAGATGATTGTTTCAAGAGAATGTCTCAAGAAAGACAA
1 ATTTGTTTCAAGAGAAAAAGACTCAAAGATGA-CGTTTCAAGAGAATGTCTCAAGAAAGACAA
* * * * *
9382917 ATTTTTGTTTTAAGAGAAAAAGACTCAAAGATCG-CGTTTCAAGAGAAACTGTCTCTATAGAGAT
1 A--TTTGTTTCAAGAGAAAAAGACTCAAAGAT-GACGTTTCAAGAG-AA-TGTCTCAAGAAAGAC
9382981 AA
61 AA
9382983 ATTTGTTTCAAGAGAAA
1 ATTTGTTTCAAGAGAAA
9383000 CAATCTCAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
63 1 0.01
64 25 0.36
65 28 0.41
66 15 0.22
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (62 bp):
ATTTGTTTCAAGAGAAAAAGACTCAAAGATGACGTTTCAAGAGAATGTCTCAAGAAAGACAA
Found at i:9385153 original size:25 final size:25
Alignment explanation
Indices: 9385125--9385176 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
9385115 TGTATACCCT
*
9385125 ATTCGACTCCCGATCATAATGCCCC
1 ATTCGACTCCCGATCAGAATGCCCC
9385150 ATTCGACTCCCGATCAGAATGCCCC
1 ATTCGACTCCCGATCAGAATGCCCC
9385175 AT
1 AT
9385177 CATACATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.23
Consensus pattern (25 bp):
ATTCGACTCCCGATCAGAATGCCCC
Found at i:9390881 original size:3 final size:3
Alignment explanation
Indices: 9390873--9390925 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
9390863 TAATATGTAA
*
9390873 AAT AAT AAT AAT AAT AAT AAT -AT AAAT AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
9390918 AAT AAT AA
1 AAT AAT AA
9390926 AGCGAGAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:9392137 original size:178 final size:178
Alignment explanation
Indices: 9391838--9392199 Score: 688
Period size: 178 Copynumber: 2.0 Consensus size: 178
9391828 TGTTTTGCAC
9391838 TATTGGGACACACTGAGCTCCCTAGCTAACTCCCCTATCTTTCCATTTTCAGATATTTTGAATAG
1 TATTGGGACACACTGAGCTCCCTAGCTAACTCCCCTATCTTTCCATTTTCAGATATTTTGAATAG
*
9391903 GCTGCCAGATCGACACTTGCAGGATCGACACATTCCTTACAGAATATTTTGTTGTAATGTTTTAA
66 GCTCCCAGATCGACACTTGCAGGATCGACACATTCCTTACAGAATATTTTGTTGTAATGTTTTAA
9391968 TCTTCCAAGCTGCCTTCTTGTGGGTAACATGTGCCTATTATTTTGAGA
131 TCTTCCAAGCTGCCTTCTTGTGGGTAACATGTGCCTATTATTTTGAGA
*
9392016 TATTGGGACACACTGAGCTCCCTAGCTCACTCCCCTATCTTTCCATTTTCAGATATTTTGAATAG
1 TATTGGGACACACTGAGCTCCCTAGCTAACTCCCCTATCTTTCCATTTTCAGATATTTTGAATAG
* *
9392081 GCTCCCAGATCGGCACTTGCAGGATCGACACATTTCTTACAGAATATTTTGTTGTAATGTTTTAA
66 GCTCCCAGATCGACACTTGCAGGATCGACACATTCCTTACAGAATATTTTGTTGTAATGTTTTAA
9392146 TCTTCCAAGCTGCCTTCTTGTGGGTAACATGTGCCTATTATTTTGAGA
131 TCTTCCAAGCTGCCTTCTTGTGGGTAACATGTGCCTATTATTTTGAGA
9392194 TATTGG
1 TATTGG
9392200 CTTTATGGAC
Statistics
Matches: 180, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 180 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (178 bp):
TATTGGGACACACTGAGCTCCCTAGCTAACTCCCCTATCTTTCCATTTTCAGATATTTTGAATAG
GCTCCCAGATCGACACTTGCAGGATCGACACATTCCTTACAGAATATTTTGTTGTAATGTTTTAA
TCTTCCAAGCTGCCTTCTTGTGGGTAACATGTGCCTATTATTTTGAGA
Found at i:9392505 original size:29 final size:31
Alignment explanation
Indices: 9392424--9392508 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 31
9392414 AGAAATGTTC
* *
9392424 AAAAGTTTAAGGACTAATTTAGAATCATAGT
1 AAAAGTTTAGGGACTAATTTAAAATCATAGT
* * * *
9392455 CATAGTTTAGGGA-TAAAATTAAAAT-AT-TT
1 AAAAGTTTAGGGACT-AATTTAAAATCATAGT
9392484 AAAAGTTTAGGGACTAATTTAAAAT
1 AAAAGTTTAGGGACTAATTTAAAAT
9392509 GAGTCATACT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
29 21 0.49
30 4 0.09
31 18 0.42
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (31 bp):
AAAAGTTTAGGGACTAATTTAAAATCATAGT
Found at i:9393931 original size:22 final size:24
Alignment explanation
Indices: 9393879--9393936 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
9393869 AAAATTTAGA
*
9393879 TTTTTTAAATTTATATAAAATAAT
1 TTTTTTAAAATTATATAAAATAAT
*
9393903 TTATTTTAAAATT-TA-AAAATAGT
1 TT-TTTTAAAATTATATAAAATAAT
*
9393926 TTTTTTGAAAT
1 TTTTTTAAAAT
9393937 ATTGCATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 8 0.27
23 9 0.30
24 4 0.13
25 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
TTTTTTAAAATTATATAAAATAAT
Found at i:9394581 original size:26 final size:26
Alignment explanation
Indices: 9394552--9394624 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
9394542 TATATTAAAT
*
9394552 TTAAAAATAGTTTTTATATTAA-TTTA
1 TTAAAAATA-TTTTTATATTAACTTAA
*
9394578 TTAAATATA-TTTTATTATTAACTTAA
1 TTAAAAATATTTTTA-TATTAACTTAA
9394604 TTCAAAAATATTTTTAT-TTAA
1 TT-AAAAATATTTTTATATTAA
9394625 AAGTATGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 5 0.12
25 6 0.15
26 17 0.43
27 7 0.17
28 5 0.12
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (26 bp):
TTAAAAATATTTTTATATTAACTTAA
Found at i:9394583 original size:24 final size:22
Alignment explanation
Indices: 9394537--9394603 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 22
9394527 TCATAACATT
9394537 TTTTATATATTAAATTTAAAAATA
1 TTTT-TATATT-AATTTAAAAATA
*
9394561 GTTTTTATATTAATTTATTAAATA
1 -TTTTTATATTAATTTA-AAAATA
*
9394585 TATTTTATTATTAACTTAA
1 T-TTTTA-TATTAATTTAA
9394604 TTCAAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 7 0.19
24 16 0.44
25 13 0.36
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (22 bp):
TTTTTATATTAATTTAAAAATA
Found at i:9394614 original size:27 final size:25
Alignment explanation
Indices: 9394536--9394624 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 25
9394526 TTCATAACAT
9394536 TTTTTATA-T-ATTAAATTTAAAAATA
1 TTTTTATATTAATT-AA-TTAAAAATA
* *
9394561 GTTTTTATATTAATTTATTAAATATA
1 -TTTTTATATTAATTAATTAAAAATA
9394587 -TTTTATTATTAACTTAATTCAAAAATA
1 TTTTTA-TATTAA-TTAATT-AAAAATA
9394614 TTTTTAT-TTAA
1 TTTTTATATTAA
9394625 AAGTATGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.09
25 6 0.11
26 25 0.47
27 9 0.17
28 8 0.15
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (25 bp):
TTTTTATATTAATTAATTAAAAATA
Found at i:9394621 original size:25 final size:26
Alignment explanation
Indices: 9394516--9394618 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 26
9394506 TTATAAATAC
* *
9394516 TTAACTTAAATTC-ATAACATTTTTTA
1 TTAA-TTAAATTCAAAAATATTTTTTA
*
9394542 -TATATTAAATTTAAAAATAGTTTTTATA
1 TTA-ATTAAATTCAAAAATA-TTTTT-TA
* *
9394570 TTAATT-TATT-AAATATATTTTATTA
1 TTAATTAAATTCAAAAATATTTT-TTA
9394595 TTAACTT-AATTCAAAAATATTTTT
1 TTAA-TTAAATTCAAAAATATTTTT
9394619 ATTTAAAAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
25 19 0.31
26 18 0.29
27 18 0.29
28 5 0.08
29 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (26 bp):
TTAATTAAATTCAAAAATATTTTTTA
Found at i:9395605 original size:12 final size:12
Alignment explanation
Indices: 9395588--9395612 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9395578 TTACATTTTC
9395588 TTTTCATTTTAG
1 TTTTCATTTTAG
9395600 TTTTCATTTTAG
1 TTTTCATTTTAG
9395612 T
1 T
9395613 CTTTAATATA
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTCATTTTAG
Found at i:9395842 original size:32 final size:32
Alignment explanation
Indices: 9395791--9395860 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
9395781 TTTATATTCA
*
9395791 AAATAATGATGTAAAACATACCA-AGTGTACAT
1 AAATAATGATATAAAACATACCATA-TGTACAT
* * * *
9395823 AAATAATGATATGACACATATCATATGTGCAT
1 AAATAATGATATAAAACATACCATATGTACAT
9395855 AAATAA
1 AAATAA
9395861 AATAAATTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.27
Consensus pattern (32 bp):
AAATAATGATATAAAACATACCATATGTACAT
Found at i:9398293 original size:32 final size:32
Alignment explanation
Indices: 9398193--9398293 Score: 85
Period size: 32 Copynumber: 3.2 Consensus size: 32
9398183 TCCTTGTGTG
* * * * * *
9398193 GGCTCTAAGGCCACAAGGTAATTCCTTGAGTA
1 GGCTCTTAGGCCCCAAGATACTCCCTTAAGTA
* * * **
9398225 GACTCTTAGGCCCTAAGGTACTCCCTTTGGTA
1 GGCTCTTAGGCCCCAAGATACTCCCTTAAGTA
* *
9398257 GGCTCTTAGGCCCCAAGATAGTCCCTTAAGTT
1 GGCTCTTAGGCCCCAAGATACTCCCTTAAGTA
9398289 GGCTC
1 GGCTC
9398294 CAATGCCCAA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (32 bp):
GGCTCTTAGGCCCCAAGATACTCCCTTAAGTA
Found at i:9399921 original size:19 final size:19
Alignment explanation
Indices: 9399899--9399939 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9399889 AATATGATCT
9399899 ATTTA-TTGAAATTTAATTA
1 ATTTACTTGAAA-TTAATTA
*
9399918 ATTTACTTTAAATTAATTA
1 ATTTACTTGAAATTAATTA
9399937 ATT
1 ATT
9399940 AGAGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTACTTGAAATTAATTA
Found at i:9401340 original size:63 final size:63
Alignment explanation
Indices: 9401221--9401340 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
9401211 ATTTATGATG
* * *
9401221 ATCATGCAGAATGCAAAGATGAAAATGCATATGCAAAAGTGATGGTCCTTTAAAATGTTATGC
1 ATCATGCAGAATGCAAAGATGAAAATGCAGATGCAAAAGTGATGATCCTCTAAAATGTTATGC
* * * * *
9401284 ATCATGCAGAATGCGAAGATGCAAATGCAGATGTAAAATTGATGATCCTCTGAAATG
1 ATCATGCAGAATGCAAAGATGAAAATGCAGATGCAAAAGTGATGATCCTCTAAAATG
9401341 CAATGCAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (63 bp):
ATCATGCAGAATGCAAAGATGAAAATGCAGATGCAAAAGTGATGATCCTCTAAAATGTTATGC
Found at i:9402818 original size:2 final size:2
Alignment explanation
Indices: 9402811--9402897 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
9402801 GTAACAAAAC
9402811 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
*
9402853 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9402894 AT AT
1 AT AT
9402898 GTACATATGT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9405066 original size:32 final size:32
Alignment explanation
Indices: 9404998--9405083 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
9404988 AGGCATTTCC
* * *
9404998 TTGGGTGGGCTCTAAGGCCCCAAGCTACTTCT
1 TTGGGTAGGCTCTAAGGCCCCAAGCTACTCCA
* ** *
9405030 TTGGGTAGGCTCTTAGGCCTTAAGGTACTCCA
1 TTGGGTAGGCTCTAAGGCCCCAAGCTACTCCA
* *
9405062 TTGGGTAGGATCTCAGGCCCCA
1 TTGGGTAGGCTCTAAGGCCCCA
9405084 GGATATTCCC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (32 bp):
TTGGGTAGGCTCTAAGGCCCCAAGCTACTCCA
Found at i:9407126 original size:15 final size:17
Alignment explanation
Indices: 9407097--9407128 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9407087 TCTAGAGTTA
9407097 ATATATGTATATTTAAT
1 ATATATGTATATTTAAT
9407114 ATATATG-AT-TTTAAT
1 ATATATGTATATTTAAT
9407129 TATCCCGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATATATGTATATTTAAT
Found at i:9407821 original size:21 final size:19
Alignment explanation
Indices: 9407779--9407825 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
9407769 ATTTTAGAAA
9407779 ATTAAGATAAGAACATAAG
1 ATTAAGATAAGAACATAAG
9407798 ATTAAGATTAAG-ACAATGAAG
1 ATTAAGA-TAAGAAC-AT-AAG
9407819 ATTAAGA
1 ATTAAGA
9407826 CAACAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 10 0.40
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (19 bp):
ATTAAGATAAGAACATAAG
Found at i:9407834 original size:15 final size:15
Alignment explanation
Indices: 9407801--9407835 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9407791 ACATAAGATT
**
9407801 AAGATTAAGACAATG
1 AAGATTAAGACAACA
9407816 AAGATTAAGACAACA
1 AAGATTAAGACAACA
9407831 AAGAT
1 AAGAT
9407836 ACACGAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (15 bp):
AAGATTAAGACAACA
Found at i:9419399 original size:42 final size:41
Alignment explanation
Indices: 9419336--9419429 Score: 143
Period size: 42 Copynumber: 2.3 Consensus size: 41
9419326 TTCTCCAAAA
* *
9419336 TCCCGTGTTTGTTTGATGTAATTCGTTTTCCGGAAAATATTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGG-AAATATTT
*
9419378 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAATATTT
*
9419419 TCCAGTGTTTG
1 TCCCGTGTTTG
9419430 GTTAGAGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 17 0.35
42 31 0.65
ACGTcount: A:0.16, C:0.17, G:0.20, T:0.47
Consensus pattern (41 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAATATTT
Found at i:9419673 original size:16 final size:16
Alignment explanation
Indices: 9419652--9419736 Score: 64
Period size: 16 Copynumber: 5.0 Consensus size: 16
9419642 ATATTTAAAA
9419652 TATATT-TATTAATATT
1 TATATTATATTAATA-T
*
9419668 TATATTATATTTATAT
1 TATATTATATTAATAT
9419684 TATATTATATTTTTAATAT
1 TATATTATA---TTAATAT
* * *
9419703 TATAATAAAATAATAAAT
1 TATATTATATTAAT--AT
*
9419721 TATATTATAATAATAT
1 TATATTATATTAATAT
9419737 AAGATATTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
16 22 0.39
17 7 0.12
18 14 0.25
19 13 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:9419677 original size:11 final size:11
Alignment explanation
Indices: 9419642--9419706 Score: 66
Period size: 11 Copynumber: 6.3 Consensus size: 11
9419632 AATTATTAAA
* *
9419642 ATATTTAAAAT
1 ATATTTATATT
*
9419653 ATATTTAT-TA
1 ATATTTATATT
9419663 ATATTTATATT
1 ATATTTATATT
9419674 ATATTTATATT
1 ATATTTATATT
9419685 ATA-TTATATT
1 ATATTTATATT
*
9419695 -T-TTAATATT
1 ATATTTATATT
9419704 ATA
1 ATA
9419707 ATAAAATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
9 7 0.16
10 16 0.36
11 22 0.49
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATTTATATT
Found at i:9419691 original size:21 final size:22
Alignment explanation
Indices: 9419642--9419706 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
9419632 AATTATTAAA
* * *
9419642 ATATTTAAAATATATTTAT-TA
1 ATATTTATATTATATTTATATT
9419663 ATATTTATATTATATTTATATT
1 ATATTTATATTATATTTATATT
*
9419685 ATA-TTATATT-T-TTAATATT
1 ATATTTATATTATATTTATATT
9419704 ATA
1 ATA
9419707 ATAAAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.26
20 1 0.03
21 24 0.62
22 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTATATTATATTTATATT
Found at i:9419724 original size:18 final size:18
Alignment explanation
Indices: 9419701--9419735 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9419691 TATTTTTAAT
9419701 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
9419719 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
9419736 TAAGATATTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:9419726 original size:23 final size:23
Alignment explanation
Indices: 9419699--9419749 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
9419689 TATATTTTTA
*
9419699 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAAGAAATT
* *
9419722 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAAGAAATT
9419745 ATATT
1 ATATT
9419750 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAAGAAATT
Found at i:9419991 original size:27 final size:28
Alignment explanation
Indices: 9419961--9420016 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
9419951 ATTATAAAAA
9419961 TAATA-TTTAATAATAAATAA-ATT-ATTT
1 TAATATTTTAA-AAT-AATAATATTAATTT
9419988 TAATATTTTAAAATAATAATATTAATTT
1 TAATATTTTAAAATAATAATATTAATTT
9420016 T
1 T
9420017 TATGATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.19
27 11 0.42
28 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATATTTTAAAATAATAATATTAATTT
Found at i:9420012 original size:22 final size:22
Alignment explanation
Indices: 9419975--9420033 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
9419965 ATTTAATAAT
* *
9419975 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAAT-TTTTA
9419998 AAAT-AATAATATTAATTTTTA
1 AAATAAATAATATTAATTTTTA
**
9420019 TGATAAATAATATTA
1 AAATAAATAATATTA
9420034 TTTATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATAAATAATATTAATTTTTA
Found at i:9420178 original size:14 final size:14
Alignment explanation
Indices: 9420159--9420186 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9420149 AAAATGTAAT
9420159 TCATTTTACGGAAA
1 TCATTTTACGGAAA
9420173 TCATTTTACGGAAA
1 TCATTTTACGGAAA
9420187 ACGTTTTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TCATTTTACGGAAA
Found at i:9420193 original size:14 final size:14
Alignment explanation
Indices: 9420160--9420193 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9420150 AAATGTAATT
*
9420160 CATTTTACGGAAAT
1 CATTTTACGGAAAA
9420174 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
9420188 CGTTTT
1 CATTTT
9420194 CCAGAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:9420227 original size:20 final size:20
Alignment explanation
Indices: 9420190--9420228 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9420180 ACGGAAAACG
**
9420190 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
9420210 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
9420229 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:9420254 original size:30 final size:29
Alignment explanation
Indices: 9420202--9420278 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 29
9420192 TTCCAGAAAT
9420202 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
9420231 GTAATTCATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
*
9420261 GTAATTCATTTTCTAGAA
1 GTAATTCATTTTCCAGAA
9420279 AACCAATTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 18 0.40
30 27 0.60
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:9420276 original size:15 final size:15
Alignment explanation
Indices: 9420202--9420273 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
9420192 TTCCAGAAAT
9420202 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
9420217 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
9420231 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
9420246 GTAATTCAAATTCTA
1 GTAATTCATTTTCCA
9420261 GTAATTCATTTTC
1 GTAATTCATTTTC
9420274 TAGAAAACCA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
14 12 0.26
15 35 0.74
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:9420641 original size:38 final size:39
Alignment explanation
Indices: 9420577--9420669 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 39
9420567 GTCAAATATA
*
9420577 TGCACCGTAGTGCTTACACATAAGGTCGTGCCCACCATT
1 TGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCATT
9420616 TGCACCGAAGTGC-TACACATAAGGTCGTGCCCACCATT
1 TGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCATT
* **
9420654 TACAATGAAGTGCTTA
1 TGCACCGAAGTGCTTA
9420670 ATTAATATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 35 0.71
39 14 0.29
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
TGCACCGAAGTGCTTACACATAAGGTCGTGCCCACCATT
Found at i:9421896 original size:44 final size:44
Alignment explanation
Indices: 9421846--9421929 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
9421836 CAAATGTTAT
9421846 AATCTTACTAACATAGGCATTCTTTGGAAAATAAATTCCTAATA
1 AATCTTACTAACATAGGCATTCTTTGGAAAATAAATTCCTAATA
9421890 AATCTTACTAACATAGGCATTCTTTGGAAAATAAATTCCT
1 AATCTTACTAACATAGGCATTCTTTGGAAAATAAATTCCT
9421930 GATGCTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (44 bp):
AATCTTACTAACATAGGCATTCTTTGGAAAATAAATTCCTAATA
Found at i:9423735 original size:18 final size:18
Alignment explanation
Indices: 9423712--9423782 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 18
9423702 AGGCTATTTT
9423712 GGTATCGATACTCATGGG
1 GGTATCGATACTCATGGG
*
9423730 GGTATCGATAC-CAAGGG
1 GGTATCGATACTCATGGG
*
9423747 TAGAGTATCGATACTCTATATAGG
1 --G-GTATCGATACTC---ATGGG
9423771 GGTATCGATACT
1 GGTATCGATACT
9423783 GAGGTAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
17 5 0.12
18 11 0.26
19 1 0.02
20 10 0.23
21 12 0.28
22 1 0.02
24 3 0.07
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (18 bp):
GGTATCGATACTCATGGG
Found at i:9428832 original size:12 final size:12
Alignment explanation
Indices: 9428796--9428833 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
9428786 TTTTAAATTT
9428796 TAAATATAAAAA
1 TAAATATAAAAA
* *
9428808 AAAATTTAAAAA
1 TAAATATAAAAA
9428820 TAAATATAAAAA
1 TAAATATAAAAA
9428832 TA
1 TA
9428834 CATTATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAATATAAAAA
Found at i:9438602 original size:54 final size:54
Alignment explanation
Indices: 9438575--9438810 Score: 411
Period size: 54 Copynumber: 4.4 Consensus size: 54
9438565 TTACATGGGG
* *
9438575 TGCACACATAGTGCCAATACATAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGT
*
9438629 TGCACACAT-GTTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGT
1 TGCACACATAG-TGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGT
**
9438683 TGCACACATAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGT
9438737 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGT
9438791 TGCACACATAGTGCCAATAC
1 TGCACACATAGTGCCAATAC
9438811 GGTAAATGAA
Statistics
Matches: 174, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
53 1 0.01
54 172 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGT
Found at i:9438711 original size:108 final size:108
Alignment explanation
Indices: 9438522--9438810 Score: 418
Period size: 108 Copynumber: 2.7 Consensus size: 108
9438512 AGTGGTTTTC
* ** * * * * * * * *
9438522 GCACACATAGAGCTGATACGGTAATTCACAAACTCACTATGAATTACATGGGGTGCACACATAGT
1 GCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGT
*
9438587 GCCAATACATAAATTCATAAACTAATTATGAATTTCTTAGGTT
66 GCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGTT
9438630 GCACACAT-GTTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
1 GCACACATAG-TGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
** *
9438694 TGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAGGTT
65 TGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGTT
*
9438738 GCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGT
1 GCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGT
9438803 GCCAATAC
66 GCCAATAC
9438811 GGTAAATGAA
Statistics
Matches: 162, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 160 0.99
109 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (108 bp):
GCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGT
GCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGTT
Found at i:9444584 original size:25 final size:26
Alignment explanation
Indices: 9444542--9444591 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
9444532 TTATTCATTA
**
9444542 ATTTCATTTATGTCATCCTTTCATGT
1 ATTTCATTTATGGAATCCTTTCATGT
9444568 ATTTCA-TTATGGAATCCTTTCATG
1 ATTTCATTTATGGAATCCTTTCATG
9444592 CCTTAATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (26 bp):
ATTTCATTTATGGAATCCTTTCATGT
Found at i:9444634 original size:46 final size:46
Alignment explanation
Indices: 9444568--9444672 Score: 158
Period size: 46 Copynumber: 2.3 Consensus size: 46
9444558 CCTTTCATGT
*
9444568 ATTTCA-TTATGGAATCCTTTCATGCCTTAATGCATCATTTCATAC
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCACCATTTCATAC
* * * *
9444613 ATTTCATTTATGGCATCCTTTCATGCCTTAGTGCACCCTTTCATGC
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCACCATTTCATAC
9444659 ATTTCATTTATGGA
1 ATTTCATTTATGGA
9444673 TTTGTTTTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.11
46 47 0.89
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (46 bp):
ATTTCATTTATGGAATCCTTTCATGCCTTAATGCACCATTTCATAC
Found at i:9450900 original size:46 final size:45
Alignment explanation
Indices: 9450840--9450943 Score: 154
Period size: 46 Copynumber: 2.3 Consensus size: 45
9450830 TTATTCATTA
* * *
9450840 ATTTCATTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATACAT-ATTTCATGC
* *
9450886 ATTTCATTTGTGGCATCCTTTCATGCCTTAGTACATATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATACATATTTCATGC
9450931 ATTTCATTTATGG
1 ATTTCATTTATGG
9450944 ATTTGTTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 20 0.38
46 32 0.62
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.46
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATACATATTTCATGC
Found at i:9452622 original size:45 final size:45
Alignment explanation
Indices: 9452573--9452704 Score: 203
Period size: 45 Copynumber: 2.9 Consensus size: 45
9452563 CAACTATGGT
* *
9452573 ATCCTTTCATGCCAATAATGCACCCATATGCGTTATTATTTTGGC
1 ATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGGC
* * *
9452618 ATCCTTTCATGCCGATAATGCA-CTAGTATGCTTTGTTATTTTGGC
1 ATCCTTTCATGCCGATAATGCACCCA-TATGCATTATTATTTTGGC
9452663 ATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTT
1 ATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTT
9452705 TTTTCATTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
44 2 0.03
45 74 0.95
46 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (45 bp):
ATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTGGC
Found at i:9459288 original size:45 final size:45
Alignment explanation
Indices: 9459239--9459330 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
9459229 ATTTCAACTA
* *
9459239 TGGCATCCTTTTATGCCAATAATGCACACATATGCATTATTATTT
1 TGGCATCCTTTCATGCCAATAATGCACACATATGCAATATTATTT
** *
9459284 TGGCATCCTTTCATGCTGATAATGCACCCATATGCAATATTATTT
1 TGGCATCCTTTCATGCCAATAATGCACACATATGCAATATTATTT
9459329 TG
1 TG
9459331 TTCATTCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (45 bp):
TGGCATCCTTTCATGCCAATAATGCACACATATGCAATATTATTT
Found at i:9459779 original size:22 final size:22
Alignment explanation
Indices: 9459737--9459790 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
9459727 TGGCTCCTCA
9459737 GTATCGATAC--CCATACCATG
1 GTATCGATACTACCATACCATG
*
9459757 GTATCGATACTACCATACTATG
1 GTATCGATACTACCATACCATG
*
9459779 GTACCGATACTA
1 GTATCGATACTA
9459791 TGCTATGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.33
22 20 0.67
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (22 bp):
GTATCGATACTACCATACCATG
Found at i:9462389 original size:35 final size:35
Alignment explanation
Indices: 9462349--9462416 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
9462339 AGTGGTTTTC
* * * *
9462349 GCACACGTATTGCCGATACGATAATTCACAAACGT
1 GCACACATAGTGCCAATACGAAAATTCACAAACGT
*
9462384 GCACACATAGTGCCAATACGAAAATTCATAAAC
1 GCACACATAGTGCCAATACGAAAATTCACAAAC
9462417 TAATTATGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (35 bp):
GCACACATAGTGCCAATACGAAAATTCACAAACGT
Found at i:9462467 original size:54 final size:54
Alignment explanation
Indices: 9462383--9462670 Score: 404
Period size: 54 Copynumber: 5.4 Consensus size: 54
9462373 TTCACAAACG
*
9462383 TGCACACATAGTGCCAATACGAAAATTCATAAACTAATTATGAATTTATTAGGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTATTAGGT
* *
9462437 TGCACACATAATGCCAATATTGAAAA-TCATAAACTTATTATGAATTTCA-TAGGT
1 TGCACACATAGTGCCAATA-CGAAAATTCATAAACTTATTATGAATTT-ATTAGGT
* * * * *
9462491 TGCACACATACTACCAATACGAAAATTCATACACTTATTATAAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTATTAGGT
* *
9462545 TGCACACATAGTGTCAATAC-AGAAATTCATAAA-TTATTATGAATTTATTGGGT
1 TGCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTATTAGGT
* *
9462598 TGCACACATAGTGCCAATTCGAAAATTCATAAACTTATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTATTAGGT
*
9462652 TGCACACATAGTTCCAATA
1 TGCACACATAGTGCCAATA
9462671 GGGTAAATGC
Statistics
Matches: 205, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
53 52 0.25
54 147 0.72
55 6 0.03
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTATTAGGT
Found at i:9462634 original size:107 final size:108
Alignment explanation
Indices: 9462383--9462670 Score: 427
Period size: 107 Copynumber: 2.7 Consensus size: 108
9462373 TTCACAAACG
* * *
9462383 TGCACACATAGTGCCAATACGAAAATTCATAAACTAATTATGAATTTATTAGGTTGCACACATAA
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
**
9462448 TGCCAATATTGAAAATCATAAACTTATTATGAATTTCATAGGT
66 TGCCAATACAGAAAATCATAAACTTATTATGAATTTCATAGGT
* * * *
9462491 TGCACACATACTACCAATACGAAAATTCATACACTTATTATAAATTTCTTAGGTTGCACACATAG
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
* * *
9462556 TGTCAATACAGAAATTCATAAA-TTATTATGAATTT-ATTGGGT
66 TGCCAATACAGAAAATCATAAACTTATTATGAATTTCA-TAGGT
*
9462598 TGCACACATAGTGCCAATTCGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
*
9462663 TTCCAATA
66 TGCCAATA
9462671 GGGTAAATGC
Statistics
Matches: 160, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
106 1 0.01
107 83 0.52
108 76 0.47
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (108 bp):
TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
TGCCAATACAGAAAATCATAAACTTATTATGAATTTCATAGGT
Found at i:9463019 original size:14 final size:14
Alignment explanation
Indices: 9463000--9463029 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9462990 AATACCCCTC
9463000 CTATGGTATCGATA
1 CTATGGTATCGATA
9463014 CTATGGTATCGATA
1 CTATGGTATCGATA
9463028 CT
1 CT
9463030 CCTTTTCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (14 bp):
CTATGGTATCGATA
Found at i:9468419 original size:131 final size:129
Alignment explanation
Indices: 9468163--9468478 Score: 320
Period size: 131 Copynumber: 2.4 Consensus size: 129
9468153 TTGAAAAATT
* * * *
9468163 ATGGAGCAAATCTACCTCGATTCAATATTCCTTGAAGAGTAGTGCAA-TAATCAAAAGTCTTAGG
1 ATGGAGCAAATCTACCTCGATTCAATCTTCCTTGAAGAGCAGTG-AAGGAATCAAAAGTCTCAGG
* * * *
9468227 TCTAATCTTCCCTAAAGAGTAGCAGAGCAAATCTCATTTCCAGATTTGATCCTTCTTGAAGAGCA
65 TCTAATCTCCCCTAAAGAGTAACAGAGCAAATCCCATTTCCAAATTTGATCCTTCTTGAAGAGCA
* *
9468292 ATGGAGCAAATATACCTCAATTCAATCTTCCTTGAAGAGCAGTGAAGCGAATCAAAAGT-TACCA
1 ATGGAGCAAATCTACCTCGATTCAATCTTCCTTGAAGAGCAGTGAAG-GAATCAAAAGTCT--CA
* * * *
9468356 GTTTTGATCTCCCCTAAAGTGTAAC-GAGACAAATCCCATTTCCAAATTTGATATCC-T-TTGAA
63 GGTCTAATCTCCCCTAAAGAGTAACAGAG-CAAATCCCATTTCCAAATTTG--ATCCTTCTTGAA
**
9468418 GAGTG
125 GAGCA
* * * * *
9468423 GTGGATCAAATCTACCTTGATTTAA-CTATCCTTAAAGAGCAGTGAAGTGAATCAAA
1 ATGGAGCAAATCTACCTCGATTCAATCT-TCCTTGAAGAGCAGTGAAG-GAATCAAA
9468479 TTTTCATATA
Statistics
Matches: 155, Mismatches: 24, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
128 2 0.01
129 41 0.26
130 15 0.10
131 92 0.59
132 1 0.01
133 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (129 bp):
ATGGAGCAAATCTACCTCGATTCAATCTTCCTTGAAGAGCAGTGAAGGAATCAAAAGTCTCAGGT
CTAATCTCCCCTAAAGAGTAACAGAGCAAATCCCATTTCCAAATTTGATCCTTCTTGAAGAGCA
Found at i:9468853 original size:9 final size:9
Alignment explanation
Indices: 9468812--9468837 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9468802 TCATTTTTAT
9468812 TTATTATTG
1 TTATTATTG
9468821 TTATTATTG
1 TTATTATTG
9468830 TTATTATT
1 TTATTATT
9468838 AATATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (9 bp):
TTATTATTG
Found at i:9473952 original size:49 final size:49
Alignment explanation
Indices: 9473871--9473967 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
9473861 AATCCGCGTA
*
9473871 TCAAGGCAATGTTGCAGCAACAAATAATTCATCAAAGTTTGATATTGTG
1 TCAAGGCAATGTTGCAGCAACAAATAACTCATCAAAGTTTGATATTGTG
** *
9473920 TCAAGGCAATGTTGTGGCAACAGATAACTCATCAAAGTTTGATATTGT
1 TCAAGGCAATGTTGCAGCAACAAATAACTCATCAAAGTTTGATATTGT
9473968 TATAGCAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (49 bp):
TCAAGGCAATGTTGCAGCAACAAATAACTCATCAAAGTTTGATATTGTG
Found at i:9476751 original size:23 final size:22
Alignment explanation
Indices: 9476701--9476753 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
9476691 CCCCATATCA
*
9476701 GATTATAATATCAAACTTTAGT
1 GATTATATTATCAAACTTTAGT
9476723 GATTATATTATCAAACTTTTAGT
1 GATTATATTATCAAAC-TTTAGT
*
9476746 GGTTATAT
1 GATTATAT
9476754 GTATTAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (22 bp):
GATTATATTATCAAACTTTAGT
Found at i:9477551 original size:24 final size:24
Alignment explanation
Indices: 9477519--9477566 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
9477509 ATACTTAGTC
*
9477519 GGGATAGTAAAGGCAGTATGACAT
1 GGGATAGTAAAGACAGTATGACAT
9477543 GGGATAGTAAAGACAGTATGACAT
1 GGGATAGTAAAGACAGTATGACAT
9477567 TACACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.31, T:0.21
Consensus pattern (24 bp):
GGGATAGTAAAGACAGTATGACAT
Found at i:9489319 original size:29 final size:29
Alignment explanation
Indices: 9489229--9489372 Score: 114
Period size: 29 Copynumber: 5.0 Consensus size: 29
9489219 CTGAAGCAAA
* * * *
9489229 TAGAAACAGGACGGGGATATACTCCCATG
1 TAGAATCAGGAAGGAGATATAATCCCATG
* * * *
9489258 CAGAATTAGGACA-AAGATAT-ATCCCATA
1 TAGAATCAGGA-AGGAGATATAATCCCATG
*
9489286 TAGAATCAGGAAGGAGATACAATCCCATG
1 TAGAATCAGGAAGGAGATATAATCCCATG
* * * *
9489315 TAGAATCAAGACGGTGATATAATCTCATG
1 TAGAATCAGGAAGGAGATATAATCCCATG
* *
9489344 CAGAATCAGG-AGTGAGATATAATCTCATG
1 TAGAATCAGGAAG-GAGATATAATCCCATG
9489373 CAAAATCAAG
Statistics
Matches: 89, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.01
28 21 0.24
29 67 0.75
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (29 bp):
TAGAATCAGGAAGGAGATATAATCCCATG
Found at i:9492257 original size:11 final size:11
Alignment explanation
Indices: 9492243--9492269 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9492233 TACTTTAGTT
9492243 TTTTCTTTTTC
1 TTTTCTTTTTC
9492254 TTTTCTTTTTC
1 TTTTCTTTTTC
9492265 TTTTC
1 TTTTC
9492270 CTCTCAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:9501160 original size:75 final size:75
Alignment explanation
Indices: 9501037--9501178 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 75
9501027 GTGTTGTGTC
* * * **
9501037 AGATTAGTTTGTTACAAATCCTTTTTAGAAACTCATATCGTCAAATTATCTCATTCTTTATAAAC
1 AGATTAGTTTGTTAAAAATCCTCTCTAGAAACTCATATAATCAAATTATCTCATTCTTTATAAAC
9501102 TTGTCGTATT
66 TTGTCGTATT
*
9501112 AGATTAGTTTGTTAAAAATGCTCTCTAGAAACTCATATAATCAAATTATCTCATTCTTTATAAAC
1 AGATTAGTTTGTTAAAAATCCTCTCTAGAAACTCATATAATCAAATTATCTCATTCTTTATAAAC
9501177 TT
66 TT
9501179 ACAAACTGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (75 bp):
AGATTAGTTTGTTAAAAATCCTCTCTAGAAACTCATATAATCAAATTATCTCATTCTTTATAAAC
TTGTCGTATT
Found at i:9509939 original size:28 final size:29
Alignment explanation
Indices: 9509880--9509952 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
9509870 AATAGCATCT
9509880 TTTTTAAAAAAATTACCAAAATATCACAA
1 TTTTTAAAAAAATTACCAAAATATCACAA
* * * *
9509909 TTTTCAAAATAATTACTAAAATATCA-TA
1 TTTTTAAAAAAATTACCAAAATATCACAA
9509937 TTTTTAAAAAAATTAC
1 TTTTTAAAAAAATTAC
9509953 GAAATTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 15 0.39
29 23 0.61
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (29 bp):
TTTTTAAAAAAATTACCAAAATATCACAA
Found at i:9510012 original size:29 final size:29
Alignment explanation
Indices: 9509980--9510047 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
9509970 AAATTATGAA
*
9509980 AATAGCACCCTTTTCAAAATAATTACTAG
1 AATAGCACCCTTTTCAAAATAATTACCAG
*
9510009 AATAGCACCCTTTTCCAAATAATTACCAG
1 AATAGCACCCTTTTCAAAATAATTACCAG
*
9510038 AATAGTACCC
1 AATAGCACCC
9510048 GGTCAACGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (29 bp):
AATAGCACCCTTTTCAAAATAATTACCAG
Found at i:9517108 original size:29 final size:29
Alignment explanation
Indices: 9517076--9517131 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
9517066 AAATAACATC
9517076 ATTTTCAAAA-ACATTACCAAAATATCACA
1 ATTTTCAAAATA-ATTACCAAAATATCACA
* *
9517105 ATTTTCAAAATAATTACTACAATATCA
1 ATTTTCAAAATAATTACCAAAATATCA
9517132 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (29 bp):
ATTTTCAAAATAATTACCAAAATATCACA
Found at i:9524043 original size:19 final size:20
Alignment explanation
Indices: 9524019--9524061 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
9524009 TATGGAAAGG
9524019 TAAACAAATAAAA-GTTGTC
1 TAAACAAATAAAATGTTGTC
9524038 TAAACAAATAAAATGTTGTC
1 TAAACAAATAAAATGTTGTC
9524058 TAAA
1 TAAA
9524062 AGTTGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (20 bp):
TAAACAAATAAAATGTTGTC
Found at i:9530871 original size:2 final size:2
Alignment explanation
Indices: 9530858--9530894 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
9530848 GAGACATTAT
*
9530858 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9530895 CATCGTACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:9531526 original size:44 final size:44
Alignment explanation
Indices: 9531469--9531641 Score: 229
Period size: 44 Copynumber: 3.9 Consensus size: 44
9531459 CATGATTGGC
* * *
9531469 ACCTTTCTACCAATAATGTACCGTTATGCATTTTCATTTATGGT
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
* * *
9531513 ACCTTTTTGCCAATAATGCATCGTTATGTATTTTCATTTATGGA
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
* *
9531557 ACCTTTCTGCCAATAATGAACCGTTATGCATTTTCATTTATGGC
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
** * * *
9531601 ATATTTCTGCCAACAATGCACCGTTGTGCATTTGCATTTAT
1 ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
9531642 TTTAGAGCAA
Statistics
Matches: 112, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 112 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (44 bp):
ACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGA
Found at i:9534381 original size:78 final size:78
Alignment explanation
Indices: 9534287--9534444 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
9534277 GCTTATCTCA
9534287 TCTTATTTGTATAGTTAACATGGGTAGTAACATGTACTTGGATTAATTCTAGCTCATACACATCT
1 TCTTATTTGTATAGTTAACATGGGTAGTAACATGTACTTGGATTAATTCTAGCTCATACACATCT
9534352 AACTTGAATGTTT
66 AACTTGAATGTTT
9534365 TCTTATTTGTATAGTTAACATGGGTAGTAACATGTACTTGGATTAATTCTAGCTCATACACATCT
1 TCTTATTTGTATAGTTAACATGGGTAGTAACATGTACTTGGATTAATTCTAGCTCATACACATCT
9534430 AACTTGAATGTTT
66 AACTTGAATGTTT
9534443 TC
1 TC
9534445 ATCACTTACA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (78 bp):
TCTTATTTGTATAGTTAACATGGGTAGTAACATGTACTTGGATTAATTCTAGCTCATACACATCT
AACTTGAATGTTT
Found at i:9535649 original size:70 final size:69
Alignment explanation
Indices: 9535537--9535678 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 69
9535527 CATTGAATGA
9535537 AATGATGAATAAAAAACAAAAGCTGGAGGTATGTATGTGGCAAAAGCTACATGTTTTGTTAATTA
1 AATGATGAATAAAAAACAAAAGCTGGAGGTATGTATGTGGCAAAAGCTACATGTTTTGTTAATTA
9535602 TGTT
66 TGTT
9535606 AATGATGAATAAAAAACAAAAGCCTGGAGGTATGTATGTGGCAAAAGCTACATGTTTTGTTAATT
1 AATGATGAATAAAAAACAAAAG-CTGGAGGTATGTATGTGGCAAAAGCTACATGTTTTGTTAATT
9535671 ATGTT
65 ATGTT
9535676 AAT
1 AAT
9535679 TGTGGTTATA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 22 0.31
70 50 0.69
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (69 bp):
AATGATGAATAAAAAACAAAAGCTGGAGGTATGTATGTGGCAAAAGCTACATGTTTTGTTAATTA
TGTT
Found at i:9537023 original size:31 final size:31
Alignment explanation
Indices: 9536985--9537046 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
9536975 CTATAGGAAG
*
9536985 TACATTGATTGATGATGAAAAATAAGAACTC
1 TACATTGATTGATGATGAAAAAGAAGAACTC
*
9537016 TACATTGATTGATGTTGAAAAAGAAGAACTC
1 TACATTGATTGATGATGAAAAAGAAGAACTC
9537047 ATATTATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.29
Consensus pattern (31 bp):
TACATTGATTGATGATGAAAAAGAAGAACTC
Found at i:9540560 original size:13 final size:13
Alignment explanation
Indices: 9540542--9540571 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9540532 TGGGTTCAAA
9540542 ACCCCTCAACAAC
1 ACCCCTCAACAAC
*
9540555 ACCCCTCAGCAAC
1 ACCCCTCAACAAC
9540568 ACCC
1 ACCC
9540572 ATTTCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.57, G:0.03, T:0.07
Consensus pattern (13 bp):
ACCCCTCAACAAC
Found at i:9542435 original size:90 final size:89
Alignment explanation
Indices: 9542314--9542490 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
9542304 TAATATCGAA
* * * *
9542314 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATTAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAAAATGAT
9542379 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
9542404 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAAAATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAAAATGATT
*
9542469 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
9542491 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 32 0.39
90 50 0.61
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAAAATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:9555410 original size:127 final size:127
Alignment explanation
Indices: 9555178--9555445 Score: 324
Period size: 127 Copynumber: 2.1 Consensus size: 127
9555168 GCGATCACGG
* * * *
9555178 ACCGTTATTTAAATCTCTAATTAGGTTAATTTGATAAAGTTTGCGATGATCATGTGTATTACAAT
1 ACCGTTATTTAAATCCCTAATTAAGTTAATTTGATAAAGTTTGCGATGATCACGGGTATTACAAT
** ** *
9555243 CATATAATAATGGTATCGAACGCACCGCTACTGCTATATAGC-AGTCTCTATGGCGGTTGTGA
66 CATATAATAATGGTATCGAACGCACCGCTACCACTATATAGCGAG-AGCTATGGCGGTTGCGA
* * * *
9555305 ACCGTTATTTAAATCCCTAATTAAGTTAATTTGAT-AAGTTTTCGGTGATTACGGGTATTACAGT
1 ACCGTTATTTAAATCCCTAATTAAGTTAATTTGATAAAGTTTGCGATGATCACGGGTATTACAAT
* * * * * *
9555369 CATATAATAATGGTATTGGACAGCAGCGCTACCATTGTATAGCGAGAGCTATTGCGGTTGCGA
66 CATATAATAATGGTATCGAAC-GCACCGCTACCACTATATAGCGAGAGCTATGGCGGTTGCGA
*
9555432 ACCATTATTTAAAT
1 ACCGTTATTTAAAT
9555446 ATCTCATTTA
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
126 42 0.35
127 75 0.63
128 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (127 bp):
ACCGTTATTTAAATCCCTAATTAAGTTAATTTGATAAAGTTTGCGATGATCACGGGTATTACAAT
CATATAATAATGGTATCGAACGCACCGCTACCACTATATAGCGAGAGCTATGGCGGTTGCGA
Found at i:9558774 original size:12 final size:12
Alignment explanation
Indices: 9558759--9558783 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9558749 AAAAGTGCGG
9558759 TAAAAATATTTT
1 TAAAAATATTTT
9558771 TAAAAATATTTT
1 TAAAAATATTTT
9558783 T
1 T
9558784 GAAAGTGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:9559855 original size:19 final size:19
Alignment explanation
Indices: 9559833--9559869 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9559823 ATCTTAACTA
9559833 AATTAAAAAATCAATTTAG
1 AATTAAAAAATCAATTTAG
* *
9559852 AATTATATAATCAATTTA
1 AATTAAAAAATCAATTTA
9559870 AGTTATATTG
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:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTAAAAAATCAATTTAG
Found at i:9565599 original size:24 final size:24
Alignment explanation
Indices: 9565571--9565624 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
9565561 TCTGACGATG
9565571 ACCTACTCAAACAGACACCTACGA
1 ACCTACTCAAACAGACACCTACGA
* *
9565595 ACCTACTCAAACCGACACCTTCGA
1 ACCTACTCAAACAGACACCTACGA
9565619 ACCTAC
1 ACCTAC
9565625 GTACGGAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (24 bp):
ACCTACTCAAACAGACACCTACGA
Found at i:9565991 original size:20 final size:19
Alignment explanation
Indices: 9565960--9565997 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9565950 CTCAATTTTA
9565960 ACTAAGTAGTACCGATACT
1 ACTAAGTAGTACCGATACT
*
9565979 ACTAAGATAGTACTGATAC
1 ACTAAG-TAGTACCGATAC
9565998 CATGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (19 bp):
ACTAAGTAGTACCGATACT
Found at i:9570205 original size:20 final size:19
Alignment explanation
Indices: 9570177--9570247 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 19
9570167 TGTGCACTTG
*
9570177 GTATTGATACTACTCACATA
1 GTATCGATACTACTCAC-TA
* ** *
9570197 GTATCGATACTGTTCTTGCTTG
1 GTATCGATAC--TACTCAC-TA
9570219 GTATCGATACTACTCATCTA
1 GTATCGATACTACTCA-CTA
9570239 GTATCGATA
1 GTATCGATA
9570248 TTGTTTTTGT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 22 0.58
21 1 0.03
22 15 0.39
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (19 bp):
GTATCGATACTACTCACTA
Found at i:9570232 original size:42 final size:42
Alignment explanation
Indices: 9570173--9570291 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
9570163 ATTTTGTGCA
*
9570173 CTTGGTATTGATACTACTCA-CATAGTATCGATACTGTTCTTG
1 CTTGGTATCGATACTACTCATC-TAGTATCGATACTGTTCTTG
* *
9570215 CTTGGTATCGATACTACTCATCTAGTATCGATATTGTTTTTG
1 CTTGGTATCGATACTACTCATCTAGTATCGATACTGTTCTTG
* * * **
9570257 TTTAGTATCGATAATGTTCAT-TCAGTATCGATACT
1 CTTGGTATCGATACTACTCATCT-AGTATCGATACT
9570292 ACACGATAGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (42 bp):
CTTGGTATCGATACTACTCATCTAGTATCGATACTGTTCTTG
Found at i:9570311 original size:21 final size:20
Alignment explanation
Indices: 9570280--9570333 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
9570270 ATGTTCATTC
*
9570280 AGTATCGATACTACACGATAGG
1 AGTATCAATACTACAC--TAGG
*
9570302 -GTATCAATACTCCACTAGG
1 AGTATCAATACTACACTAGG
*
9570321 AGTACCAATACTA
1 AGTATCAATACTA
9570334 TTTGACGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 4 0.15
20 10 0.37
21 13 0.48
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (20 bp):
AGTATCAATACTACACTAGG
Found at i:9572366 original size:15 final size:15
Alignment explanation
Indices: 9572346--9572375 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9572336 GGGGGAGTAA
*
9572346 TTTTTCAAAGTAAAT
1 TTTTTCAAAATAAAT
9572361 TTTTTCAAAATAAAT
1 TTTTTCAAAATAAAT
9572376 CTTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTTTCAAAATAAAT
Found at i:9575736 original size:13 final size:13
Alignment explanation
Indices: 9575718--9575756 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
9575708 TTCATAAATC
9575718 TATGACGCGCATT
1 TATGACGCGCATT
***
9575731 TATGACAAACATT
1 TATGACGCGCATT
9575744 TATGACGCGCATT
1 TATGACGCGCATT
9575757 GCGTGTCATT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:9575875 original size:85 final size:85
Alignment explanation
Indices: 9575728--9575893 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 85
9575718 TATGACGCGC
* ** * *
9575728 ATTTATGACAAACATTTATGACGCGCATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACAAACATTTATGACGCACATTGCGTGTCATTGAAGAACACGTCATAAATAAAGATGA
*
9575793 CACACATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
** ** * *
9575813 ATTTATGACACGCATTTATGACTTACATTGTGTGTCATTGAAGAACATGTCATTAAA-AAAGATG
1 ATTTATGACAAACATTTATGACGCACATTGCGTGTCATTGAAGAACACGTCA-TAAATAAAGATG
9575877 ACACACATTCGTGTGTC
65 ACACACATTCGTGTGTC
9575894 GTGATTGTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 64 0.94
86 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACAAACATTTATGACGCACATTGCGTGTCATTGAAGAACACGTCATAAATAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:9575975 original size:2 final size:2
Alignment explanation
Indices: 9575968--9576000 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
9575958 ATGCATCATA
9575968 AT AT AT AT AT AT AT AT AT AT CAT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
9576001 AGCAATCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9595576 original size:15 final size:16
Alignment explanation
Indices: 9595558--9595617 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
9595548 CCCATTTTTA
9595558 TCATTTTCA-TTTATT
1 TCATTTTCATTTTATT
*
9595573 TCATTTGCTATTTTTATT
1 TCATTTTC-A-TTTTATT
*
9595591 TTATTTT-ATTTTATT
1 TCATTTTCATTTTATT
9595606 TCA-TTTCATTTT
1 TCATTTTCATTTT
9595618 CTATTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 3 0.08
15 21 0.57
16 2 0.05
18 11 0.30
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.70
Consensus pattern (16 bp):
TCATTTTCATTTTATT
Found at i:9595592 original size:5 final size:5
Alignment explanation
Indices: 9595584--9595644 Score: 61
Period size: 5 Copynumber: 11.8 Consensus size: 5
9595574 CATTTGCTAT
* *
9595584 TTTTA TTTTA TTTTA TTTTA TTTCA TTTCA TTTTCTA TTTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTT-TA -TTTTA TTTTA
*
9595632 -TTTA ATTTA TTTT
1 TTTTA TTTTA TTTT
9595645 TAGGTTCGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.08
5 36 0.72
6 5 0.10
7 5 0.10
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:9595604 original size:33 final size:33
Alignment explanation
Indices: 9595567--9595643 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
9595557 ATCATTTTCA
9595567 TTTATTTCATTTGCTATTTT-TA-TTTTATTTTAT
1 TTTATTTCATTT-C-ATTTTCTATTTTTATTTTAT
9595600 TTTATTTCATTTCATTTTCTATTTTTATTTTAT
1 TTTATTTCATTTCATTTTCTATTTTTATTTTAT
*
9595633 TTAATTT-ATTT
1 TTTATTTCATTT
9595644 TTAGGTTCGC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 5 0.12
32 7 0.17
33 29 0.71
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.73
Consensus pattern (33 bp):
TTTATTTCATTTCATTTTCTATTTTTATTTTAT
Done.