Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 29
Found at i:4796212 original size:82 final size:82
Alignment explanation
Indices: 4796125--4796384 Score: 238
Period size: 82 Copynumber: 3.2 Consensus size: 82
4796115 GATTCTGACT
* * * *
4796125 ATCGCATTGTGATTTCCCAAATTCGCGTTGCGATTTTCCTAATTCGCAATGCGA-ATACGAAAAT
1 ATCGCATTGCGATTTCCCAAATTCGCATTGCGATTTTCCTAATTCACAATGCGATATACG-AAAC
4796189 CGCAATGCGATTTACGTA
65 CGCAATGCGATTTACGTA
* ** * * * *
4796207 ATCGCATTGCGATTTTCTTAATTCGCATTGCGATTTTTCTAATTCACATTGCGATTTACGTAACC
1 ATCGCATTGCGATTTCCCAAATTCGCATTGCGATTTTCCTAATTCACAATGCGATATACGAAACC
*
4796272 GCATTGCGATTTACGTA
66 GCAATGCGATTTACGTA
* * ** * * * * * * * **
4796289 ACCGCATTGCGATTTACGTAA-CCGCATTGCGATTTACGTAA-TCGCATTGCGATTTTACTAATT
1 ATCGCATTGCGATTTCCCAAATTCGCATTGCGATTTTCCTAATTCACAATGCGA-TATACGAAAC
* *
4796352 CGCACTTCGATTTACGTA
65 CGCAATGCGATTTACGTA
4796370 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
4796385 TACTAATTCG
Statistics
Matches: 149, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
80 10 0.07
81 52 0.35
82 83 0.56
83 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (82 bp):
ATCGCATTGCGATTTCCCAAATTCGCATTGCGATTTTCCTAATTCACAATGCGATATACGAAACC
GCAATGCGATTTACGTA
Found at i:4796233 original size:41 final size:40
Alignment explanation
Indices: 4796188--4796425 Score: 288
Period size: 41 Copynumber: 5.8 Consensus size: 40
4796178 AATACGAAAA
*
4796188 TCGCAATGCGATTTACGTAATCGCATTGCGATTTTCTTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTC-TAAT
* * *
4796229 TCGCATTGCGATTTTTC-TAATTCACATTGCGATTTACGTAA-
1 TCGCATTGCGA-TTTACGTAA-TCGCATTGCGATTTTC-TAAT
* * *
4796270 CCGCATTGCGATTTACGTAACCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTC-TAAT
*
4796310 CCGCATTGCGATTTACGTAATCGCATTGCGATTTTACTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTT-CTAAT
4796351 TCGCACTT-CGATTTACGTAATCGCATTGCGATTTTACTAAT
1 TCGCA-TTGCGATTTACGTAATCGCATTGCGATTTT-CTAAT
4796392 TCGCACTT-CGATTTACGTAATCGCATTGCGATTT
1 TCGCA-TTGCGATTTACGTAATCGCATTGCGATTT
4796426 AGTAAATCGC
Statistics
Matches: 179, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
40 58 0.32
41 98 0.55
42 23 0.13
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCTAAT
Found at i:4796328 original size:122 final size:121
Alignment explanation
Indices: 4796189--4796430 Score: 334
Period size: 122 Copynumber: 2.0 Consensus size: 121
4796179 ATACGAAAAT
*
4796189 CGCAATGCGATTTACGTAATCGCATTGCGATTTT-CTTAATTCGCA-TTGCGATTTTTC-TAATT
1 CGCAATGCGATTTACGTAATCGCATTGCGATTTTAC-TAATTCGCACTT-CGA-TTTACGTAA-T
4796251 CACATTGCGA-TTTACGTAA-CCGCA-TTGCGATTTACGTAACCGCATTGCGATTTACGTAAC
62 CACATTGCGATTTTAC-TAATCCGCACTT-CGATTTACGTAACCGCATTGCGATTTA-GTAAC
* *
4796311 CGCATTGCGATTTACGTAATCGCATTGCGATTTTACTAATTCGCACTTCGATTTACGTAATCGCA
1 CGCAATGCGATTTACGTAATCGCATTGCGATTTTACTAATTCGCACTTCGATTTACGTAATCACA
* *
4796376 TTGCGATTTTACTAATTCGCACTTCGATTTACGTAATCGCATTGCGATTTAGTAA
66 TTGCGATTTTACTAATCCGCACTTCGATTTACGTAACCGCATTGCGATTTAGTAA
4796431 ATCGCAACGA
Statistics
Matches: 109, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
121 21 0.19
122 83 0.76
123 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (121 bp):
CGCAATGCGATTTACGTAATCGCATTGCGATTTTACTAATTCGCACTTCGATTTACGTAATCACA
TTGCGATTTTACTAATCCGCACTTCGATTTACGTAACCGCATTGCGATTTAGTAAC
Found at i:4799899 original size:19 final size:20
Alignment explanation
Indices: 4799857--4799911 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
4799847 CAATCATCTT
*
4799857 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
*
4799877 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
4799896 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
4799912 AGAGAATTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:4799931 original size:33 final size:33
Alignment explanation
Indices: 4799884--4800008 Score: 205
Period size: 33 Copynumber: 3.8 Consensus size: 33
4799874 GGAAATGACT
4799884 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
4799917 ATTGCAATGTGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4799950 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4799983 ATCGCAAAGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
4800009 ATTTAGTTTC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 84 1.00
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4799944 original size:19 final size:19
Alignment explanation
Indices: 4799864--4800008 Score: 86
Period size: 19 Copynumber: 8.4 Consensus size: 19
4799854 CTTAATGTCT
* **
4799864 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
4799884 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4799903 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
4799917 ATTGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4799936 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
4799950 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
4799969 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
4799983 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4800002 ATCGCAA
1 ATCGCAA
4800009 ATTTAGTTTC
Statistics
Matches: 96, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
14 29 0.30
15 3 0.03
16 4 0.04
17 5 0.05
18 3 0.03
19 43 0.45
20 9 0.09
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4800052 original size:33 final size:33
Alignment explanation
Indices: 4800015--4800094 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
4800005 GCAAATTTAG
* *
4800015 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
*
4800048 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
*
4800081 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
4800095 AGTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCAATTTTCA
Found at i:4800093 original size:19 final size:18
Alignment explanation
Indices: 4800036--4800094 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
4800026 GATTTTGTCG
*
4800036 TTGCAATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
4800054 GTTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
4800069 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
4800087 ATTGCGAT
1 -TTGCGAT
4800095 AGTCATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.19
16 7 0.22
17 7 0.22
19 12 0.38
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:4800211 original size:14 final size:14
Alignment explanation
Indices: 4800192--4800228 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4800182 CATCAATTAA
4800192 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4800206 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4800220 ACAAATCAA
1 ACAAATCAA
4800229 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4801664 original size:42 final size:42
Alignment explanation
Indices: 4801618--4801697 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
4801608 CGATGACAAT
* * *
4801618 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
4801660 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
4801698 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:4802248 original size:33 final size:34
Alignment explanation
Indices: 4802206--4802281 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 34
4802196 TGATTTTTGG
4802206 TTTCGCGTTGCG-ATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGTATTCTCTCGTTGCGATTTTCA
4802239 TTTCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCG----T-ATTCTCTCGTTGCGATTTTCA
4802278 TTTC
1 TTTC
4802282 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
33 12 0.32
39 25 0.68
ACGTcount: A:0.09, C:0.24, G:0.18, T:0.49
Consensus pattern (34 bp):
TTTCGCGTTGCGTATTCTCTCGTTGCGATTTTCA
Found at i:4802249 original size:19 final size:19
Alignment explanation
Indices: 4802225--4802281 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
4802215 GCGATTCTCT
4802225 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4802244 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
4802264 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
4802282 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4802269 original size:20 final size:20
Alignment explanation
Indices: 4802218--4802279 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
4802208 TCGCGTTGCG
4802218 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
4802238 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
4802257 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
4802277 ATT
1 ATT
4802280 TCAACCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:4802482 original size:94 final size:94
Alignment explanation
Indices: 4802370--4802745 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
4802360 ATGGATTGCA
* *
4802370 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
4802434 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
4802463 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
4802528 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
4802557 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
4802622 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
4802651 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
4802711 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
4802741 TTACT
1 TTACT
4802746 AAGCAATCTA
Statistics
Matches: 274, Mismatches: 6, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
90 33 0.12
91 1 0.00
92 3 0.01
93 27 0.10
94 210 0.77
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4804459 original size:20 final size:20
Alignment explanation
Indices: 4804434--4804496 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
4804424 TTTTGGTTGA
4804434 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
4804454 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
4804473 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
4804494 AAT
1 AAT
4804497 CACAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:4804511 original size:33 final size:33
Alignment explanation
Indices: 4804432--4804586 Score: 193
Period size: 33 Copynumber: 4.5 Consensus size: 33
4804422 TCTTTTGGTT
*
4804432 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCACAACGC
**
4804471 GGAAATGACTATCGCAACGAGAGAATCACAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCACAACGC
4804505 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
* * *
4804538 GAAATGAAAATCTCAACGAGAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
4804571 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
4804587 TGCGATTTTG
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
33 76 0.72
34 10 0.09
36 1 0.01
37 1 0.01
38 3 0.03
40 15 0.14
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAACGC
Found at i:4810781 original size:18 final size:19
Alignment explanation
Indices: 4810760--4810798 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
4810750 AAATTTTAAA
4810760 TTCAAAAT-T-ATTTTGTTT
1 TTCAAAATATGATTTT-TTT
4810778 TTCAAAATATGATTTTTTT
1 TTCAAAATATGATTTTTTT
4810797 TT
1 TT
4810799 ATCAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTCAAAATATGATTTTTTT
Found at i:4813483 original size:31 final size:31
Alignment explanation
Indices: 4813421--4813502 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
4813411 CTTTAATTGG
* *
4813421 ATTTAGGGATCAAATTGATATTTCACCTAAA
1 ATTTAGAGATCAAATTAATATTTCACCTAAA
* * **
4813452 ATTTAGAGATTAAATTAATATTTTATTTAAA
1 ATTTAGAGATCAAATTAATATTTCACCTAAA
*
4813483 A-TTAAAG-TCAAATTAATATT
1 ATTTAGAGATCAAATTAATATT
4813503 ATATCTAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 12 0.28
30 5 0.12
31 26 0.60
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (31 bp):
ATTTAGAGATCAAATTAATATTTCACCTAAA
Found at i:4813514 original size:29 final size:31
Alignment explanation
Indices: 4813429--4813529 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
4813419 GGATTTAGGG
* * *
4813429 ATCAAATTGATATT-TCACCTAAAATT-TAGA
1 ATCAAATTAATATTAT-ATCTAAAATTCAAGA
* * *
4813459 GATTAAATTAATATTTTATTTAAAATT-AA-A
1 -ATCAAATTAATATTATATCTAAAATTCAAGA
* *
4813489 GTCAAATTAATATTATATCTAGAATTCAAGA
1 ATCAAATTAATATTATATCTAAAATTCAAGA
4813520 ATCAAATTAA
1 ATCAAATTAA
4813530 AATTTAACCA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 21 0.38
30 3 0.05
31 31 0.55
32 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.39
Consensus pattern (31 bp):
ATCAAATTAATATTATATCTAAAATTCAAGA
Found at i:4815152 original size:29 final size:29
Alignment explanation
Indices: 4815109--4815191 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
4815099 CTCACCTAAC
*
4815109 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
4815139 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
4815168 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4815192 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:4819885 original size:29 final size:29
Alignment explanation
Indices: 4819842--4819924 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
4819832 CTCACCTAAC
*
4819842 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
4819872 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
4819901 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4819925 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:4826600 original size:12 final size:12
Alignment explanation
Indices: 4826583--4826617 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4826573 AATATTGATG
4826583 TTTTAAAATAAT
1 TTTTAAAATAAT
*
4826595 TTTTAAAAAAAT
1 TTTTAAAATAAT
*
4826607 ATTTAAAATAA
1 TTTTAAAATAA
4826618 ATGATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTTTAAAATAAT
Found at i:4826995 original size:16 final size:16
Alignment explanation
Indices: 4826974--4827005 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4826964 TACATAGTTT
4826974 TGCTTATGTCCATGAA
1 TGCTTATGTCCATGAA
4826990 TGCTTATGTCCATGAA
1 TGCTTATGTCCATGAA
4827006 GGGAATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
TGCTTATGTCCATGAA
Found at i:4838916 original size:23 final size:23
Alignment explanation
Indices: 4838890--4838950 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
4838880 ATTCTCCTAT
4838890 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
* **
4838913 GGGGGAATCAGTT-CCCTTTTAA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
4838935 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
4838951 TCTGCCCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:4838949 original size:22 final size:21
Alignment explanation
Indices: 4838869--4838951 Score: 55
Period size: 22 Copynumber: 3.9 Consensus size: 21
4838859 CCAGAACCCC
*
4838869 AGGGGGTATCGATTCTCC--TA
1 AGGGGGAATCGATTC-CCTTTA
* * *
4838889 TGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATT-CCCTT-TA
4838912 AGGGGGAATC-AGTTCCCTTTTA
1 AGGGGGAATCGA-TTCCC-TTTA
*
4838934 AGGGGGTATCGATTCCCT
1 AGGGGGAATCGATTCCCT
4838952 CTGCCCTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
20 13 0.27
21 2 0.04
22 18 0.38
23 15 0.31
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCTTTA
Found at i:4846426 original size:26 final size:27
Alignment explanation
Indices: 4846387--4846442 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
4846377 TGCTTTACTC
4846387 AAATTCGACATTCAAGTTTTTAA-GAA
1 AAATTCGACATTCAAGTTTTTAAGGAA
*
4846413 AAATTCGACGTTCAAGTTTTTAAGGAA
1 AAATTCGACATTCAAGTTTTTAAGGAA
4846440 AAA
1 AAA
4846443 AGATATACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (27 bp):
AAATTCGACATTCAAGTTTTTAAGGAA
Found at i:4850332 original size:2 final size:2
Alignment explanation
Indices: 4850325--4850399 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
4850315 TAAACGTTAC
4850325 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
4850367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4850400 GTAGTTGAAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4860843 original size:14 final size:12
Alignment explanation
Indices: 4860827--4860901 Score: 75
Period size: 11 Copynumber: 6.1 Consensus size: 12
4860817 ACCTGAAAAT
4860827 AAAATAAAACTAA
1 AAAATAAAA-TAA
4860840 TAAAATAAAAT-A
1 -AAAATAAAATAA
4860852 AAAAT-AAATAA
1 AAAATAAAATAA
4860863 AAAATAAAAATAA
1 AAAAT-AAAATAA
4860876 ATAAAT-AAATAA
1 A-AAATAAAATAA
*
4860888 AATATAAATATAA
1 AAAATAAA-ATAA
4860901 A
1 A
4860902 TATAAATTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
10 4 0.07
11 14 0.26
12 10 0.19
13 13 0.24
14 13 0.24
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:4860857 original size:6 final size:6
Alignment explanation
Indices: 4860822--4860907 Score: 63
Period size: 6 Copynumber: 14.3 Consensus size: 6
4860812 ACATGACCTG
* *
4860822 AAAAT- AAAATA AAACTA ATAAA-A TAAAATA AAAATA AATA-A AAAATA
1 AAAATA AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA
* * *
4860869 AAAATA AATAA-A TAAATA AAATATA AATATA AATATA AA
1 AAAATA AA-AATA AAAATA AAA-ATA AAAATA AAAATA AA
4860908 TTTATCGGGC
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
5 11 0.17
6 44 0.67
7 11 0.17
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:4860862 original size:4 final size:4
Alignment explanation
Indices: 4860853--4860897 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
4860843 AATAAAATAA
*
4860853 AAAT AAAT AAA- AAAT -AA- AAAT AAAT AAAT AAAT AAA- ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4860897 A
1 A
4860898 TAAATATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
3 9 0.26
4 26 0.74
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:4860870 original size:36 final size:37
Alignment explanation
Indices: 4860827--4860907 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 37
4860817 ACCTGAAAAT
*
4860827 AAAATAAAACT-AATAAAATAAAATAAAA-ATAAATA-A
1 AAAATAAAAATAAAT-AAAT-AAATAAAATATAAATATA
4860863 AAAATAAAAATAAATAAATAAATAAAATATAAATATA
1 AAAATAAAAATAAATAAATAAATAAAATATAAATATA
*
4860900 AATATAAA
1 AAAATAAA
4860908 TTTATCGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
35 8 0.20
36 21 0.52
37 11 0.28
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (37 bp):
AAAATAAAAATAAATAAATAAATAAAATATAAATATA
Found at i:4860881 original size:25 final size:25
Alignment explanation
Indices: 4860823--4860903 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
4860813 CATGACCTGA
4860823 AAATAAAATAAAACTAATAAAAT-AAAAT
1 AAAT-AAAT-AAA-TAA-AAAATAAAAAT
4860851 -AA-AAATAAATAAAAAATAAAAAT
1 AAATAAATAAATAAAAAATAAAAAT
* *
4860874 AAATAAATAAATAAAATATAAATAT
1 AAATAAATAAATAAAAAATAAAAAT
4860899 AAATA
1 AAATA
4860904 TAAATTTATC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
22 5 0.10
23 8 0.17
24 5 0.10
25 28 0.58
27 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (25 bp):
AAATAAATAAATAAAAAATAAAAAT
Found at i:4860908 original size:6 final size:6
Alignment explanation
Indices: 4860839--4860908 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
4860829 AATAAAACTA
* * *
4860839 ATAAA- ATAAA- ATAAAA ATAAAT A-AAAA ATAAAA ATAAAT AAATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT --ATAAAT
4860886 A-AAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT
4860909 TTATCGGGCC
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
5 19 0.33
6 32 0.56
8 6 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAT
Found at i:4866858 original size:81 final size:81
Alignment explanation
Indices: 4866702--4866862 Score: 259
Period size: 81 Copynumber: 2.0 Consensus size: 81
4866692 CACAACTAAT
* * * * *
4866702 CCATTATTCTTTTATTCAACAGTGTTTAACTGTTCATCTAACTGGTATAATTGGCACCTTTCTAC
1 CCATTATTATTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTAC
4866767 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
**
4866783 CCATTATTATTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTAC
1 CCATTATTATTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTAC
4866848 CAATTGCACAGTTAG
66 CAATTGCACAGTTAG
4866863 ACCTCAAATG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (81 bp):
CCATTATTATTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTAC
CAATTGCACAGTTAGG
Found at i:4866929 original size:68 final size:67
Alignment explanation
Indices: 4866809--4867061 Score: 310
Period size: 68 Copynumber: 3.7 Consensus size: 67
4866799 CAATGGTATT
* * * * ** * * *
4866809 TAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCA-ATTGCACAGTTAGACCTCAAATG
1 TAACCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATA-AGCACAGTTAGGCCTCAAAGG
4866873 CAC
65 CAC
* * *
4866876 ATAATCTTTCATCTAACTGGCATAAATGACACATTTATGTCATAAGCATAGTTAGGCCTCAAAGG
1 -TAACCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATAAGCACAGTTAGGCCTCAAAGG
4866941 CAC
65 CAC
* * *
4866944 TTAACCTTTCATCTAACTGACATAAATGACACATTTCTATCATAAGAACAGTTAGGCCTCAAAGG
1 -TAACCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATAAGCACAGTTAGGCCTCAAAGG
4867009 CAC
65 CAC
* *
4867012 TCAGCCTTTCATCTAACTGGCATAAATAACACATTTCTGTCATAAGCACA
1 T-AACCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATAAGCACA
4867062 ACTAAGCCTA
Statistics
Matches: 159, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
67 1 0.01
68 157 0.99
69 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (67 bp):
TAACCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATAAGCACAGTTAGGCCTCAAAGGC
AC
Found at i:4867044 original size:136 final size:136
Alignment explanation
Indices: 4866808--4867059 Score: 346
Period size: 136 Copynumber: 1.9 Consensus size: 136
4866798 TCAATGGTAT
* * * * * * *
4866808 TTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGACCTCAAATG
1 TTAACCGTTCATCTAACTGACATAAATGACACATTTCTACCAATAGAACAGTTAGACCTCAAAGG
* *
4866873 CACATAATCTTTCATCTAACTGGCATAAATGACACATTTATGTCATAAGCATAGTTAGGCCTCAA
66 CACATAACCTTTCATCTAACTGGCATAAATAACACATTTATGTCATAAGCATAGTTAGGCCTCAA
4866938 AGGCAC
131 AGGCAC
* * *
4866944 TTAACCTTTCATCTAACTGACATAAATGACACATTTCTATC-ATAAGAACAGTTAGGCCTCAAAG
1 TTAACCGTTCATCTAACTGACATAAATGACACATTTCTACCAAT-AGAACAGTTAGACCTCAAAG
* *
4867008 GCAC-TCAGCCTTTCATCTAACTGGCATAAATAACACATTTCTGTCATAAGCA
65 GCACAT-AACCTTTCATCTAACTGGCATAAATAACACATTTATGTCATAAGCA
4867060 CAACTAAGCC
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
135 3 0.03
136 97 0.97
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (136 bp):
TTAACCGTTCATCTAACTGACATAAATGACACATTTCTACCAATAGAACAGTTAGACCTCAAAGG
CACATAACCTTTCATCTAACTGGCATAAATAACACATTTATGTCATAAGCATAGTTAGGCCTCAA
AGGCAC
Found at i:4867406 original size:56 final size:53
Alignment explanation
Indices: 4867283--4867430 Score: 188
Period size: 56 Copynumber: 2.7 Consensus size: 53
4867273 CATATAGTTT
* * *
4867283 CCCATACGAACATTCATACACTTGGTAAGAATTTCTTAGTTCGCACACATAGTG
1 CCCATACGAA-ATTCATACACTTAGTATGAATTTCTTAGTTCGCACACAAAGTG
* *
4867337 CCCATACGAAAATTCATACACTTAGTATGAATTTCCTTATTTTTGCACACAAAGTG
1 CCCATACG-AAATTCATACACTTAGTATGAATTT-CTTA-GTTCGCACACAAAGTG
* *
4867393 CCCATACAGAAATTCATACACTAAGTATGAATATCTTA
1 CCCATAC-GAAATTCATACACTTAGTATGAATTTCTTA
4867431 CAATTTTTGC
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
54 29 0.35
55 10 0.12
56 43 0.52
57 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.31
Consensus pattern (53 bp):
CCCATACGAAATTCATACACTTAGTATGAATTTCTTAGTTCGCACACAAAGTG
Found at i:4868008 original size:20 final size:19
Alignment explanation
Indices: 4867965--4868037 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
4867955 ATGTTGCATG
*
4867965 GTATCGATAC-CCTTATCA
1 GTATCGATACTACTTATCA
* *
4867983 TGGTATCGATACTACCTTTTCC
1 --GTATCGATACTA-CTTATCA
4868005 GTATCGATACTGA-TTATCA
1 GTATCGATACT-ACTTATCA
4868024 GTATCGATACTACT
1 GTATCGATACTACT
4868038 CAGTTAATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 1 0.02
19 16 0.36
20 21 0.48
21 1 0.02
22 5 0.11
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (19 bp):
GTATCGATACTACTTATCA
Found at i:4871740 original size:19 final size:19
Alignment explanation
Indices: 4871716--4871752 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4871706 ATGACCAACA
*
4871716 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
4871735 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
4871753 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4872657 original size:24 final size:24
Alignment explanation
Indices: 4872625--4872678 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4872615 GTATTCGAAA
4872625 TTTGATCTTGGCCAATACCCGGAC
1 TTTGATCTTGGCCAATACCCGGAC
* * *
4872649 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGCCAATACCCGGAC
4872673 TTTGAT
1 TTTGAT
4872679 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGCCAATACCCGGAC
Found at i:4874958 original size:18 final size:18
Alignment explanation
Indices: 4874935--4874969 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4874925 AGCAAAAGGC
*
4874935 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
4874953 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
4874970 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:4875165 original size:20 final size:20
Alignment explanation
Indices: 4875140--4875276 Score: 195
Period size: 20 Copynumber: 6.8 Consensus size: 20
4875130 TTACACATTC
*
4875140 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
4875160 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
4875180 ATTTGACTATCACAACGTGA
1 ATTTGACTATCGCAACGCGA
*
4875200 ATTTCACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
4875220 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
4875240 ATTTGATTATCGCAATAG-GA
1 ATTTGACTATCGCAA-CGCGA
4875260 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
4875277 AGAAAATCGC
Statistics
Matches: 104, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.01
20 102 0.98
21 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:4875377 original size:20 final size:20
Alignment explanation
Indices: 4875348--4875425 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
4875338 GCAACGCGAA
4875348 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
4875368 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
4875388 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
4875408 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
4875426 AAGTGTACCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:4875589 original size:67 final size:68
Alignment explanation
Indices: 4875477--4875655 Score: 190
Period size: 71 Copynumber: 2.6 Consensus size: 68
4875467 GATTGAAATC
*
4875477 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGC--ACAAATAAGAA-TTA-TTTACACAT
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAAAATAAGAATTTATTTTACACAT
4875538 CAATTA
63 CAATTA
* * *
4875544 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAATAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAA-AA-AATAAGAA-T-TTATTTTACACA
4875608 TCAATTA
62 TCAATTA
* * *
4875615 AACAAACCAACTTTTA-AGAATCAATTAAACAATCAAAAAAA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAA
4875656 GTGTACCCCA
Statistics
Matches: 97, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
63 16 0.16
65 1 0.01
66 1 0.01
67 25 0.26
69 2 0.02
70 6 0.06
71 46 0.47
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (68 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAAAATAAGAATTTATTTTACACATCAA
TTA
Found at i:4877007 original size:21 final size:21
Alignment explanation
Indices: 4876941--4877058 Score: 83
Period size: 21 Copynumber: 5.6 Consensus size: 21
4876931 GTGAATCGGG
* * * *
4876941 CTCTTGAATGGTGGGAAGGAC
1 CTCTTGAACGATGGGAGGGGC
* ** * *
4876962 CTCTTCAACGATGACAGTGAC
1 CTCTTGAACGATGGGAGGGGC
*
4876983 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGC
** **
4877004 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
4877025 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGGGAGGGGC
*
4877046 CTCTTGAATGATG
1 CTCTTGAACGATG
4877059 ACAGGTGAGT
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:4877008 original size:42 final size:42
Alignment explanation
Indices: 4876957--4877063 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
4876947 AATGGTGGGA
* * *
4876957 AGGACCTCTTCAACGATGACAGTGACCTCTTGAACGATGGGAG
1 AGGA-CTCTTGAACGATGACAGGGACCTCTTGAACGATAGGAG
* ** * *
4877000 GGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGAG
1 AGGACTCTTGAACGATGACAGGGACCTCTTGAACGATAGGAG
* *
4877042 AGGCCTCTTGAATGATGACAGG
1 AGGACTCTTGAACGATGACAGG
4877064 TGAGTCGGGC
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
42 48 0.94
43 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (42 bp):
AGGACTCTTGAACGATGACAGGGACCTCTTGAACGATAGGAG
Found at i:4877564 original size:20 final size:20
Alignment explanation
Indices: 4877539--4877582 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4877529 AATAGTTTCT
4877539 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
4877559 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
4877579 GAAA
1 GAAA
4877583 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:4877592 original size:20 final size:20
Alignment explanation
Indices: 4877569--4877635 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
4877559 GAAACTTAAA
4877569 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
4877589 ATCGCAACGCGGAAATGACA
1 ATCGCAACGCGAAAATGACT
**
4877609 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
4877629 ATCGCAA
1 ATCGCAA
4877636 TGGGATAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4877666 original size:19 final size:19
Alignment explanation
Indices: 4877642--4877695 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
4877632 GCAATGGGAT
* * *
4877642 AATCGCAATGTGAAATAAA
1 AATCGCAACGCGAAACAAA
*
4877661 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
*
4877680 AATCGCAACGCAAAAC
1 AATCGCAACGCGAAAC
4877696 TAAATTCGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:4879806 original size:20 final size:20
Alignment explanation
Indices: 4879718--4879829 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 20
4879708 TAAACTTAAA
* * **
4879718 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAATATGACT
* *
4879738 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATATGACT
* * *
4879758 ATCGTAACGCAAATTTGACT
1 ATCGCAACGCGAATATGACT
*
4879778 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
* **
4879798 ATCGCAACGTGAA-ATGAAA
1 ATCGCAACGCGAATATGACT
4879817 ATCGCAACGCGAA
1 ATCGCAACGCGAA
4879830 ACTAAAATCG
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 15 0.19
20 63 0.81
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:4879822 original size:19 final size:19
Alignment explanation
Indices: 4879798--4879840 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4879788 GAATTTGACT
*
4879798 ATCGCAACGTGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
4879817 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
4879836 ATCGC
1 ATCGC
4879841 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:4880248 original size:22 final size:22
Alignment explanation
Indices: 4880221--4880271 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4880211 GATGGAGATA
4880221 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
4880243 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
4880265 GACGGAT
1 GACGGAT
4880272 GTCACTGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:4880466 original size:20 final size:20
Alignment explanation
Indices: 4880438--4880549 Score: 136
Period size: 20 Copynumber: 5.6 Consensus size: 20
4880428 ATTTTGTATT
4880438 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
4880458 ATCGTGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
4880478 ATCGTGTTGAGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
4880498 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * *
4880518 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
4880538 ATCGCGTTGCGA
1 ATCGCGTTGCGA
4880550 ATCTGGAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 76 0.97
21 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:4880559 original size:20 final size:21
Alignment explanation
Indices: 4880536--4880589 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
4880526 GCGATAGTCA
4880536 AAATCGCGTTGCGAAT-CTGG
1 AAATCGCGTTGCGAATACTGG
* **
4880556 AAATTGATTTGCG-ATACTGG
1 AAATCGCGTTGCGAATACTGG
*
4880576 AGATCGCGTTGCGA
1 AAATCGCGTTGCGA
4880590 TTTAGAGATC
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
AAATCGCGTTGCGAATACTGG
Found at i:4885026 original size:16 final size:15
Alignment explanation
Indices: 4885005--4885035 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4884995 AGAGACACTC
4885005 GAGTTCTTATAAGGTT
1 GAGTTCTTAT-AGGTT
4885021 GAGTTCTTATAGGTT
1 GAGTTCTTATAGGTT
4885036 TTAAATTCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (15 bp):
GAGTTCTTATAGGTT
Found at i:4886915 original size:22 final size:22
Alignment explanation
Indices: 4886881--4886922 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4886871 CCATCTAATA
* *
4886881 ACTAAAGTGCCTTAGCACTGGT
1 ACTAAACTACCTTAGCACTGGT
4886903 ACTAAACTACCTTAGCACTG
1 ACTAAACTACCTTAGCACTG
4886923 ATACAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (22 bp):
ACTAAACTACCTTAGCACTGGT
Found at i:4887979 original size:20 final size:19
Alignment explanation
Indices: 4887954--4888001 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
4887944 TTTCGATATT
*
4887954 GATACCAAGCCTTTGGTATG
1 GATACCAA-CCTTTGGTATA
*
4887974 GATACCCAATCTTTGGTATA
1 GATA-CCAACCTTTGGTATA
4887994 GATACCAA
1 GATACCAA
4888002 TTCATCCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (19 bp):
GATACCAACCTTTGGTATA
Found at i:4888039 original size:21 final size:21
Alignment explanation
Indices: 4887987--4888039 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4887977 ACCCAATCTT
**
4887987 TGGTATAGATACCAATTCATC
1 TGGTATAGATACCAACCCATC
* * *
4888008 CGATATGGATACCAACCCATC
1 TGGTATAGATACCAACCCATC
4888029 TGGTATAGATA
1 TGGTATAGATA
4888040 TCAGTCCTCT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (21 bp):
TGGTATAGATACCAACCCATC
Found at i:4891481 original size:19 final size:19
Alignment explanation
Indices: 4891442--4891503 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
4891432 CAAGTTAACC
* * *
4891442 TGACCTGACCCGTTAATTT
1 TGACCCGACCCGTTGACTT
*
4891461 TGACCCGACTCGTTGACTT
1 TGACCCGACCCGTTGACTT
* *
4891480 TGATCCGGCCCGTTGACTT
1 TGACCCGACCCGTTGACTT
4891499 TGACC
1 TGACC
4891504 TTTGAACGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.32
Consensus pattern (19 bp):
TGACCCGACCCGTTGACTT
Found at i:4900830 original size:21 final size:22
Alignment explanation
Indices: 4900798--4900847 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
4900788 CACGACTCGG
4900798 TTTTAT-TAACTTCCAT-TACTT
1 TTTTATGTAACTT-CATCTACTT
*
4900819 TTTTATGT-ACTTTATCCTACTT
1 TTTTATGTAACTTCAT-CTACTT
4900841 TTTTATG
1 TTTTATG
4900848 AGTTAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 10 0.40
22 13 0.52
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTTATGTAACTTCATCTACTT
Found at i:4902482 original size:2 final size:2
Alignment explanation
Indices: 4902475--4902500 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4902465 TCATACACAA
4902475 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
4902501 TAAAATGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4903740 original size:24 final size:23
Alignment explanation
Indices: 4903712--4903798 Score: 120
Period size: 24 Copynumber: 3.7 Consensus size: 23
4903702 ATTCAATTCA
4903712 AGTATCAGATCAGAATCCATGTC
1 AGTATCAGATCAGAATCCATGTC
*
4903735 ATGTATTAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCATGTC
*
4903759 AGTATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCATGTC
* *
4903782 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
4903799 TCAAATCAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
23 22 0.39
24 35 0.61
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATGTC
Found at i:4913877 original size:10 final size:9
Alignment explanation
Indices: 4913842--4913969 Score: 103
Period size: 10 Copynumber: 13.3 Consensus size: 9
4913832 GCTGCTGGAA
*
4913842 ACCGGTTTA
1 ACCGGTTTG
*
4913851 ACCGGTTTTCA
1 ACCGG-TTT-G
4913862 ACCGGTTCTG
1 ACCGGTT-TG
4913872 ACCGGTTTG
1 ACCGGTTTG
*
4913881 ACCGGTTTCA
1 ACCGGTTT-G
*
4913891 ACCGGTTCG
1 ACCGGTTTG
4913900 AACCGGTTTG
1 -ACCGGTTTG
*
4913910 ACCGGTTTCA
1 ACCGGTTT-G
*
4913920 ACCGGTTCG
1 ACCGGTTTG
4913929 AACCGGTTTG
1 -ACCGGTTTG
*
4913939 ACCGGTCTG
1 ACCGGTTTG
*
4913948 AATCGGTTTG
1 -ACCGGTTTG
*
4913958 ACCGGTCTG
1 ACCGGTTTG
4913967 ACC
1 ACC
4913970 CGACCCGACC
Statistics
Matches: 97, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
9 41 0.42
10 49 0.51
11 7 0.07
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:4913886 original size:19 final size:19
Alignment explanation
Indices: 4913862--4913969 Score: 100
Period size: 19 Copynumber: 5.7 Consensus size: 19
4913852 CCGGTTTTCA
4913862 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGGTTTG
* *
4913881 ACCGGTT-TCAACCGGTTCG
1 ACCGGTTCT-GACCGGTTTG
*
4913900 AACCGGTT-TGACCGGTTTCA
1 -ACCGGTTCTGACCGGTTT-G
4913920 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
*
4913939 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
4913958 ACCGG-TCTGACC
1 ACCGGTTCTGACC
4913970 CGACCCGACC
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
18 5 0.07
19 54 0.72
20 16 0.21
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:4913955 original size:29 final size:29
Alignment explanation
Indices: 4913841--4913944 Score: 174
Period size: 29 Copynumber: 3.6 Consensus size: 29
4913831 GGCTGCTGGA
*
4913841 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTC-G
4913872 -ACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTTTCAACCGGTTCG
4913900 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTTTCAACCGGTTCG
4913929 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
4913945 CTGAATCGGT
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
28 1 0.01
29 57 0.80
30 13 0.18
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:4913976 original size:5 final size:5
Alignment explanation
Indices: 4913966--4914044 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
4913956 TGACCGGTCT
* *
4913966 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
4914015 GACCC GACCGTT GA-CC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
4914045 GTTGACCGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
4 2 0.03
5 48 0.79
6 1 0.02
7 10 0.16
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:4913992 original size:22 final size:22
Alignment explanation
Indices: 4913966--4914051 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
4913956 TGACCGGTCT
4913966 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
4913988 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
4914010 GACCCGACCCGACCGTTGA-CC
1 GACCCGACCCGACCGTTGACCC
4914031 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
4914052 GTTGACCGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 21 0.33
22 42 0.67
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:4914041 original size:26 final size:27
Alignment explanation
Indices: 4914005--4914059 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
4913995 CCCGACCGTT
4914005 GACCCGACCCGACC-CGACCGTTGACC
1 GACCCGACCCGACCGCGACCGTTGACC
*
4914031 GACCCGACCCGACCGTTGACCGTTGACC
1 GACCCGACCCGACCG-CGACCGTTGACC
4914059 G
1 G
4914060 TTGACCATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 14 0.54
28 12 0.46
ACGTcount: A:0.18, C:0.45, G:0.25, T:0.11
Consensus pattern (27 bp):
GACCCGACCCGACCGCGACCGTTGACC
Found at i:4914053 original size:7 final size:7
Alignment explanation
Indices: 4914041--4914071 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4914031 GACCCGACCC
4914041 GACCGTT
1 GACCGTT
4914048 GACCGTT
1 GACCGTT
4914055 GACCGTT
1 GACCGTT
*
4914062 GACCATT
1 GACCGTT
4914069 GAC
1 GAC
4914072 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:4921501 original size:10 final size:9
Alignment explanation
Indices: 4921466--4921564 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
4921456 GCTGCTGGAA
*
4921466 ACCGGTTTA
1 ACCGGTTTG
*
4921475 ACCGGTTTTCA
1 ACCGG-TTT-G
4921486 ACCGGTTCTG
1 ACCGGTT-TG
4921496 ACCGGTTTG
1 ACCGGTTTG
*
4921505 ACCGGTTTCA
1 ACCGGTTT-G
*
4921515 ACCGGTTCG
1 ACCGGTTTG
4921524 AACCGGTTTG
1 -ACCGGTTTG
**
4921534 ACCGGTCTAA
1 ACCGGT-TTG
*
4921544 ATCGGTTTG
1 ACCGGTTTG
*
4921553 ACCGGTCTG
1 ACCGGTTTG
4921562 ACC
1 ACC
4921565 CGACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:4921510 original size:19 final size:19
Alignment explanation
Indices: 4921467--4921564 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
4921457 CTGCTGGAAA
* * *
4921467 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
4921487 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
4921506 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
4921526 CCGGTTTGACCGG-TCTAAA
1 CCGGTTTGACCGGTTCT-GA
*
4921545 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
4921563 CC
1 CC
4921565 CGACCCGACC
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
18 5 0.08
19 36 0.56
20 15 0.23
21 8 0.12
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:4921528 original size:29 final size:30
Alignment explanation
Indices: 4921465--4921564 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 30
4921455 GGCTGCTGGA
*
4921465 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
4921496 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
4921524 AACCGGTTTGACCGGTCTAAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
4921553 -ACCGGTCTGACC
1 AACCGGTTTGACC
4921565 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.60
30 13 0.21
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:4921571 original size:5 final size:5
Alignment explanation
Indices: 4921561--4921644 Score: 80
Period size: 5 Copynumber: 15.8 Consensus size: 5
4921551 TGACCGGTCT
* *
4921561 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
4921610 GACCC GACCC GACCGTT GA-CC GACCC GACCC GACC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC
4921645 GTTGACCGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
4 2 0.03
5 53 0.80
6 1 0.02
7 10 0.15
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:4921587 original size:22 final size:22
Alignment explanation
Indices: 4921561--4921651 Score: 130
Period size: 27 Copynumber: 4.0 Consensus size: 22
4921551 TGACCGGTCT
4921561 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
4921583 GACCCGACCCGACCGTTGACCCGACCC
1 GACCCGACCCGACCGTT-----GACCC
4921610 GACCCGACCCGACCGTTGA-CC
1 GACCCGACCCGACCGTTGACCC
4921631 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
4921652 GTTGACCGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
21 21 0.33
22 20 0.32
27 22 0.35
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:4921653 original size:7 final size:7
Alignment explanation
Indices: 4921641--4921671 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4921631 GACCCGACCC
4921641 GACCGTT
1 GACCGTT
4921648 GACCGTT
1 GACCGTT
4921655 GACCGTT
1 GACCGTT
*
4921662 GACCATT
1 GACCGTT
4921669 GAC
1 GAC
4921672 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:4924047 original size:16 final size:15
Alignment explanation
Indices: 4924026--4924061 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
4924016 AAGGTTCTTT
*
4924026 ATTATTATAATCATTA
1 ATTATTATAAT-AGTA
4924042 ATTATTATAATAGTA
1 ATTATTATAATAGTA
4924057 ATTAT
1 ATTAT
4924062 GTGTTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTATTATAATAGTA
Found at i:4924691 original size:18 final size:18
Alignment explanation
Indices: 4924668--4924703 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4924658 AGTCTTTAAT
4924668 GTGACCTCTATTGTGGAA
1 GTGACCTCTATTGTGGAA
4924686 GTGACCTCTATTGTGGAA
1 GTGACCTCTATTGTGGAA
4924704 AACATATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (18 bp):
GTGACCTCTATTGTGGAA
Found at i:4926848 original size:11 final size:11
Alignment explanation
Indices: 4926832--4926857 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4926822 GTTTGATGCT
4926832 TTCTCTCTTGA
1 TTCTCTCTTGA
4926843 TTCTCTCTTGA
1 TTCTCTCTTGA
4926854 TTCT
1 TTCT
4926858 AGTTGCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:4935066 original size:23 final size:22
Alignment explanation
Indices: 4935024--4935106 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
4935014 TTAGTGCAGA
*
4935024 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
4935046 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* * *
4935069 GGGAACCGATTCCCCCCTGTAG
1 GGGAACCGATACCCCCTTGAAG
*
4935091 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
4935107 CTGGGGTTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
22 32 0.59
23 22 0.41
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:4938887 original size:22 final size:23
Alignment explanation
Indices: 4938807--4938876 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
4938797 CGATTCCCCT
*
4938807 AAGGAGGGAATAGGTTCCCATTCA
1 AAGG-GGGAATCGGTTCCCATTCA
*
4938831 AAGGGAGAATCGGTTCCCATTCA
1 AAGGGGGAATCGGTTCCCATTCA
*
4938854 AAGGGGGAATCGGTTCCCCTTCA
1 AAGGGGGAATCGGTTCCCATTCA
4938877 TGGGGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 38 0.90
24 4 0.10
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (23 bp):
AAGGGGGAATCGGTTCCCATTCA
Found at i:4951349 original size:20 final size:20
Alignment explanation
Indices: 4951299--4951341 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
4951289 ATCTCTTTGA
4951299 TATTGGTAATTTGGGTTGTT
1 TATTGGTAATTTGGGTTGTT
4951319 TATTGGTAATTTGGGTTGTT
1 TATTGGTAATTTGGGTTGTT
4951339 TAT
1 TAT
4951342 GTTCAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (20 bp):
TATTGGTAATTTGGGTTGTT
Found at i:4954444 original size:27 final size:28
Alignment explanation
Indices: 4954414--4954477 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
4954404 TTTGTTCGGG
4954414 TCGGGTCGGG-TTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
4954441 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
4954469 TCGGGTCGG
1 TCGGGTCGG
4954478 ATCGGGTTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.28
28 26 0.72
ACGTcount: A:0.12, C:0.09, G:0.36, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:4956635 original size:29 final size:29
Alignment explanation
Indices: 4956587--4956643 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
4956577 AGTGTTGGTC
*
4956587 GTAGGTCGCCATGTCTTCCGGGCGACCTT
1 GTAGGTCGCCATGTCCTCCGGGCGACCTT
4956616 GTAGGTCGCCATG-CACTCCGGGCGACCT
1 GTAGGTCGCCATGTC-CTCCGGGCGACCT
4956644 ACCCTTGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.12, C:0.33, G:0.32, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGTCCTCCGGGCGACCTT
Found at i:4956735 original size:29 final size:29
Alignment explanation
Indices: 4956702--4956786 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
4956692 TCCCAACACA
* * *
4956702 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCTCTCCGGACGACCTTG
4956731 TAGGTCGCCATGCTCTCCGGACGACCTTG
1 TAGGTCGCCATGCTCTCCGGACGACCTTG
4956760 TAGGTCGCCATGCTCTCCGGACGACCT
1 TAGGTCGCCATGCTCTCCGGACGACCT
4956787 ACCCTTGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.13, C:0.35, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCTCTCCGGACGACCTTG
Found at i:4956823 original size:23 final size:24
Alignment explanation
Indices: 4956797--4956849 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
4956787 ACCCTTGCTC
4956797 GCTCGCTCAGATGCCCTCGAA-TA
1 GCTCGCTCAGATGCCCTCGAAGTA
* * *
4956820 GCTCGTTCGGCTGCCCTCGAAGTA
1 GCTCGCTCAGATGCCCTCGAAGTA
*
4956844 GGTCGC
1 GCTCGC
4956850 ATAGCTCGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (24 bp):
GCTCGCTCAGATGCCCTCGAAGTA
Found at i:4959122 original size:33 final size:33
Alignment explanation
Indices: 4959080--4959146 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
4959070 ATTAGCATAG
4959080 ACATGGACATGTGCAAAAGAAGATAAGAACGTA
1 ACATGGACATGTGCAAAAGAAGATAAGAACGTA
4959113 ACATGGACATGTGCAAAAGAAGATAAGAACGTA
1 ACATGGACATGTGCAAAAGAAGATAAGAACGTA
4959146 A
1 A
4959147 GAAAACAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (33 bp):
ACATGGACATGTGCAAAAGAAGATAAGAACGTA
Found at i:4963261 original size:27 final size:29
Alignment explanation
Indices: 4963190--4963262 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 29
4963180 TTTCTAATTT
4963190 TTTAATTTATGT-TATTTTATTTTCATGTAC
1 TTTAATTTAT-TAT-TTTTATTTTCATGTAC
* *
4963220 TTT-TTTTCTTCATTTTTA-TTT-ATGTAC
1 TTTAATTTATT-ATTTTTATTTTCATGTAC
4963247 TTTAATTTATTATTTT
1 TTTAATTTATTATTTT
4963263 ATCATATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
27 14 0.39
28 9 0.25
29 9 0.25
30 4 0.11
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (29 bp):
TTTAATTTATTATTTTTATTTTCATGTAC
Found at i:4963263 original size:13 final size:14
Alignment explanation
Indices: 4963189--4963263 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
4963179 TTTTCTAATT
4963189 TTTTAATTTATGTTA
1 TTTTAATTTATG-TA
*
4963204 TTTTATTTTCATGTA
1 TTTTAATTT-ATGTA
*
4963219 CTTTT--TTTCT-TCA
1 -TTTTAATTTATGT-A
*
4963232 TTTTTATTTATGTA
1 TTTTAATTTATGTA
*
4963246 CTTTAATTTAT-TA
1 TTTTAATTTATGTA
4963259 TTTTA
1 TTTTA
4963264 TCATATAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
12 5 0.10
13 8 0.17
14 17 0.35
15 11 0.23
16 7 0.15
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (14 bp):
TTTTAATTTATGTA
Found at i:4965700 original size:31 final size:31
Alignment explanation
Indices: 4965665--4965757 Score: 100
Period size: 33 Copynumber: 2.9 Consensus size: 31
4965655 ATTATTTGTT
4965665 TGTGATTTGCAAGATGCAAGGAACAAATGTG
1 TGTGATTTGCAAGATGCAAGGAACAAATGTG
* * **
4965696 TGTGA--GGAAAGATGTCGTGGCATAACAAATGTG
1 TGTGATTTGCAAGATG-CAAGG---AACAAATGTG
4965729 TGTGATTTGCAAGATGCAAGGAACAAATG
1 TGTGATTTGCAAGATGCAAGGAACAAATG
4965758 ACAACTGTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
29 7 0.15
30 3 0.06
31 13 0.27
33 15 0.31
34 3 0.06
35 7 0.15
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (31 bp):
TGTGATTTGCAAGATGCAAGGAACAAATGTG
Found at i:4966315 original size:38 final size:38
Alignment explanation
Indices: 4966267--4966343 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
4966257 ACTCATGTAA
* *
4966267 TAAAAGATCCCCCTAGTTAATTGTAATACAGAACTATG
1 TAAAAGATCCCCCTAATTAATTGTAATAAAGAACTATG
*
4966305 TAAAAGATCCCCCTAATTAATTTTAATAAAGAACTATG
1 TAAAAGATCCCCCTAATTAATTGTAATAAAGAACTATG
4966343 T
1 T
4966344 GGGGACACAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (38 bp):
TAAAAGATCCCCCTAATTAATTGTAATAAAGAACTATG
Found at i:4977253 original size:2 final size:2
Alignment explanation
Indices: 4977188--4977235 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
4977178 TACCTAAATA
4977188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
4977229 AT AT AT A
1 AT AT AT A
4977236 CACCACATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4978806 original size:3 final size:3
Alignment explanation
Indices: 4978787--4978820 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
4978777 AGTAATGGTT
*
4978787 ATA ATA CTA ATTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
4978821 CCCCTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4980471 original size:16 final size:18
Alignment explanation
Indices: 4980440--4980480 Score: 68
Period size: 16 Copynumber: 2.4 Consensus size: 18
4980430 TTTGACTAAC
4980440 CTTTGACCTAACTATTGA
1 CTTTGACCTAACTATTGA
4980458 CTTTGACC-AA-TATTGA
1 CTTTGACCTAACTATTGA
4980474 CTTTGAC
1 CTTTGAC
4980481 TAAAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.57
17 2 0.09
18 8 0.35
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (18 bp):
CTTTGACCTAACTATTGA
Found at i:4983260 original size:2 final size:2
Alignment explanation
Indices: 4983255--4983288 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4983245 TATCCACCAT
4983255 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
4983289 AGTATTGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4985864 original size:21 final size:20
Alignment explanation
Indices: 4985838--4985935 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
4985828 ATCAGTTTCC
4985838 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
4985859 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
4985878 ACAAATTCGCATTGCGATTTTCA
1 A-AAA-TCGCAACGCGATTTT-G
* *
4985901 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
4985921 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
4985936 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 38 0.61
22 3 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:4985964 original size:20 final size:20
Alignment explanation
Indices: 4985902--4986131 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
4985892 CGATTTTCAA
* ** *
4985902 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
4985922 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
4985942 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4985962 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
4985982 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
4986002 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4986022 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4986042 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
4986062 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
4986082 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
4986102 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
4986122 AAATCACAAC
1 AAATCGCAAC
4986132 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:4986797 original size:19 final size:18
Alignment explanation
Indices: 4986751--4986804 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
4986741 TTGACCAACA
4986751 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
4986768 GAAA-G--AATCGCAACGC
1 GAAATGAAAATCGCAA-GC
4986784 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAA-GC
4986803 GA
1 GA
4986805 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 8 0.26
16 6 0.19
17 5 0.16
19 12 0.39
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (18 bp):
GAAATGAAAATCGCAAGC
Found at i:4986822 original size:19 final size:19
Alignment explanation
Indices: 4986800--4986928 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4986790 AAAATCGCAA
4986800 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4986819 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
4986833 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4986852 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
4986866 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
4986885 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
4986904 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
4986924 TGCGA
1 TGCGA
4986929 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:4986842 original size:33 final size:33
Alignment explanation
Indices: 4986800--4986891 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
4986790 AAAATCGCAA
4986800 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
4986833 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
4986866 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
4986892 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:4987092 original size:93 final size:93
Alignment explanation
Indices: 4986976--4987350 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
4986966 ATGGATTGCA
4986976 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4987040 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4987068 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4987133 TAGCAGAATTGGCAGCAACCGAACAAA-
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4987160 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4987225 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4987253 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
4987318 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4987346 TTACT
1 TTACT
4987351 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 96 0.34
93 184 0.66
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4987292 original size:185 final size:184
Alignment explanation
Indices: 4986975--4987346 Score: 726
Period size: 185 Copynumber: 2.0 Consensus size: 184
4986965 AATGGATTGC
4986975 ATTACTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 ATTACTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4987040 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
4987105 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
4987159 ATTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGT
1 ATTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGT
4987224 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
65 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
*
4987289 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAA
130 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
4987344 ATT
1 ATT
4987347 TACTAAGCAA
Statistics
Matches: 186, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
184 5 0.03
185 181 0.97
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (184 bp):
ATTACTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
Found at i:4989065 original size:14 final size:14
Alignment explanation
Indices: 4989046--4989135 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
4989036 TTGAAATGAA
4989046 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4989060 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
4989079 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4989093 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4989112 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4989126 AATCGCAACG
1 AATCGCAACG
4989136 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4989083 original size:33 final size:33
Alignment explanation
Indices: 4989038--4989152 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
4989028 TCTTTTGGTT
4989038 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
4989071 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4989104 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4989137 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
4989153 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4989084 original size:19 final size:19
Alignment explanation
Indices: 4989060--4989157 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
4989050 GCAACGAGAG
*
4989060 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
4989079 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
4989093 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4989112 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
4989126 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4989145 AATCGCAATGCGA
1 AATCGCAACGCGA
4989158 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:4989188 original size:14 final size:14
Alignment explanation
Indices: 4989169--4989225 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4989159 TTTGGTTTCG
4989169 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4989183 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4989202 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4989216 CGTTGCGATT
1 CGTTGCGATT
4989226 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4989201 original size:33 final size:33
Alignment explanation
Indices: 4989153--4989233 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
4989143 AAAATCGCAA
**
4989153 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
4989186 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
4989219 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
4989234 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:4989236 original size:21 final size:21
Alignment explanation
Indices: 4989210--4989285 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4989200 CGCGTTGCGA
4989210 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
4989231 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
4989251 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
4989272 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
4989286 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:4989266 original size:41 final size:41
Alignment explanation
Indices: 4989209--4989286 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
4989199 TCGCGTTGCG
*
4989209 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
4989250 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
4989287 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:4989407 original size:33 final size:33
Alignment explanation
Indices: 4989365--4989435 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
4989355 AATACTAACT
* *
4989365 TGAAAATCGCAACGAGATAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
4989398 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
4989431 TGAAA
1 TGAAA
4989436 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:4989668 original size:22 final size:22
Alignment explanation
Indices: 4989616--4989670 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4989606 TGGTTGTGAG
**
4989616 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
4989638 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
4989660 GGATTTCTTCG
1 GGATTTCTTCG
4989671 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:4989842 original size:20 final size:20
Alignment explanation
Indices: 4989817--4990010 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
4989807 CTTTAAATAT
4989817 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4989837 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
4989859 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4989878 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
4989898 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
4989918 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4989938 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4989958 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
4989978 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
4989998 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4990011 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:4990004 original size:60 final size:60
Alignment explanation
Indices: 4989817--4990010 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
4989807 CTTTAAATAT
**
4989817 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
4989878 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
4989938 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
4989998 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4990011 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:4990027 original size:21 final size:21
Alignment explanation
Indices: 4989997--4990079 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
4989987 ATTTTCATAT
*
4989997 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
4990018 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
4990039 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
4990060 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
4990080 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:4990070 original size:42 final size:43
Alignment explanation
Indices: 4989977--4990075 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
4989967 ATTTATGTGT
* *
4989977 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
4990018 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
4990060 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
4990076 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:4992589 original size:30 final size:30
Alignment explanation
Indices: 4992548--4992616 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
4992538 ATCCTTGCAC
*
4992548 CTCTGTCATAAATAAGACACATCCCATCAT
1 CTCTATCATAAATAAGACACATCCCATCAT
4992578 CTCTATCATAAATAAGACACATCCCATCAT
1 CTCTATCATAAATAAGACACATCCCATCAT
4992608 CTCTATCAT
1 CTCTATCAT
4992617 CAAAAACATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.29
Consensus pattern (30 bp):
CTCTATCATAAATAAGACACATCCCATCAT
Found at i:4993721 original size:13 final size:14
Alignment explanation
Indices: 4993698--4993727 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4993688 TCTCGGTTAA
4993698 GTTCGGGTTTTTCG
1 GTTCGGGTTTTTCG
4993712 GTTC-GGTTTTTCG
1 GTTCGGGTTTTTCG
4993725 GTT
1 GTT
4993728 TTTCAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.33, T:0.53
Consensus pattern (14 bp):
GTTCGGGTTTTTCG
Found at i:4996171 original size:65 final size:66
Alignment explanation
Indices: 4996096--4996239 Score: 177
Period size: 65 Copynumber: 2.2 Consensus size: 66
4996086 TACACGTGGG
* * * *
4996096 GTGCATCGGTACACTA-ATTATATTCAATGTTTCAA-AAGAGCCAGAAATACATCGATGCATGGT
1 GTGCATCGGTACACTAGAATACATTCAATGTTTCAATAAAAGCAAG-AATACATCGATGCATGGT
4996159 CT
65 CT
* * * *
4996161 GTGCATCGGTACA-TAGAATGCATTCGATGTTTCAATAAAATCAAGAATGCATCGATGCATGGTC
1 GTGCATCGGTACACTAGAATACATTCAATGTTTCAATAAAAGCAAGAATACATCGATGCATGGTC
4996225 T
66 T
*
4996226 GTGTATCGGTACAC
1 GTGCATCGGTACAC
4996240 AAAATGCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
64 2 0.03
65 59 0.88
66 6 0.09
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (66 bp):
GTGCATCGGTACACTAGAATACATTCAATGTTTCAATAAAAGCAAGAATACATCGATGCATGGTC
T
Found at i:4998388 original size:14 final size:13
Alignment explanation
Indices: 4998345--4998388 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
4998335 TCCTAATGGG
4998345 CAATGTTTGAAAA
1 CAATGTTTGAAAA
** *
4998358 TTATTTTTGAAAA
1 CAATGTTTGAAAA
4998371 CAATGTTTGAACAA
1 CAATGTTTGAA-AA
4998385 CAAT
1 CAAT
4998389 ATGTAATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:4998882 original size:20 final size:20
Alignment explanation
Indices: 4998857--4998911 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
4998847 AAACCCAAAG
4998857 AGTGTATCGATGCACTGCAT
1 AGTGTATCGATGCACTGCAT
4998877 AGTGTATCGATGCACTGCAT
1 AGTGTATCGATGCACTGCAT
*
4998897 AGTATATCGATGCAC
1 AGTGTATCGATGCAC
4998912 ATTCAAGGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGTATCGATGCACTGCAT
Found at i:4999044 original size:44 final size:44
Alignment explanation
Indices: 4998894--4999042 Score: 199
Period size: 44 Copynumber: 3.4 Consensus size: 44
4998884 CGATGCACTG
* * *
4998894 CATAGTATATCGATGCACATTCAAGGCATGCATCGCTGCTCCTT
1 CATAGTGTATCGATGCACATTCAAGGCATGCATCGGTGCACCTT
* * *
4998938 CATAGTGTACCGATACACATTCAAGGCATGCATCGGCGCACCTT
1 CATAGTGTATCGATGCACATTCAAGGCATGCATCGGTGCACCTT
* * * * *
4998982 CATAGTGTATCGATGCATATTCAAGGGATGTATCGGTACACTTT
1 CATAGTGTATCGATGCACATTCAAGGCATGCATCGGTGCACCTT
4999026 CATAGTGTATCGATGCA
1 CATAGTGTATCGATGCA
4999043 TAGTGCACAA
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGGCATGCATCGGTGCACCTT
Done.