Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 56
Found at i:4030397 original size:32 final size:32
Alignment explanation
Indices: 4030361--4030421 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
4030351 AACCAATTAC
*
4030361 TAGTCAGGTTTGTATTCAAATAATGCACAATT
1 TAGTCAGGTTTGCATTCAAATAATGCACAATT
*
4030393 TAGTCAGGTTTGCATTCATATAATGCACA
1 TAGTCAGGTTTGCATTCAAATAATGCACA
4030422 TGAGTATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (32 bp):
TAGTCAGGTTTGCATTCAAATAATGCACAATT
Found at i:4031383 original size:21 final size:22
Alignment explanation
Indices: 4031350--4031394 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4031340 CAAGAAATTT
4031350 TATTTTTATATTATT-AAAATA
1 TATTTTTATATTATTAAAAATA
4031371 TATTATTTA-ATTATTAAAAATA
1 TATT-TTTATATTATTAAAAATA
4031393 TA
1 TA
4031395 AAATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATATTATTAAAAATA
Found at i:4031404 original size:21 final size:20
Alignment explanation
Indices: 4031356--4031406 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
4031346 ATTTTATTTT
**
4031356 TATATTATTAAAATATATTA
1 TATATTATTAAAATATAAAA
*
4031376 TTTAATTATTAAAAATATAAAA
1 TAT-ATTATT-AAAATATAAAA
4031398 TATATTATT
1 TATATTATT
4031407 TAACAGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 12 0.48
22 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATTATTAAAATATAAAA
Found at i:4035711 original size:45 final size:45
Alignment explanation
Indices: 4035659--4035757 Score: 189
Period size: 45 Copynumber: 2.2 Consensus size: 45
4035649 TAAATGTATG
4035659 CGAACTAGAGATCATGCGGTTAGGTTTATTTTTCGAATAAACATA
1 CGAACTAGAGATCATGCGGTTAGGTTTATTTTTCGAATAAACATA
*
4035704 CGAACTAGAGATCATGCGGTTAGGTTTATTTTTCGAATAAACATG
1 CGAACTAGAGATCATGCGGTTAGGTTTATTTTTCGAATAAACATA
4035749 CGAACTAGA
1 CGAACTAGA
4035758 TGGCATAAGG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.31
Consensus pattern (45 bp):
CGAACTAGAGATCATGCGGTTAGGTTTATTTTTCGAATAAACATA
Found at i:4035770 original size:45 final size:45
Alignment explanation
Indices: 4035659--4035771 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
4035649 TAAATGTATG
* **
4035659 CGAACTAGAGATCATGCGGTTAGGTTTATTTTTCGAATAAACATA
1 CGAACTAGAGAGCATAAGGTTAGGTTTATTTTTCGAATAAACATA
* ** *
4035704 CGAACTAGAGATCATGCGGTTAGGTTTATTTTTCGAATAAACATG
1 CGAACTAGAGAGCATAAGGTTAGGTTTATTTTTCGAATAAACATA
4035749 CGAACTAGATG-GCATAAGGTTAG
1 CGAACTAGA-GAGCATAAGGTTAG
4035772 AATTTTCTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 62 0.98
46 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (45 bp):
CGAACTAGAGAGCATAAGGTTAGGTTTATTTTTCGAATAAACATA
Found at i:4041502 original size:18 final size:18
Alignment explanation
Indices: 4041481--4041516 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4041471 CATATTTTTC
4041481 ATTATTTATTT-ATTATAT
1 ATTA-TTATTTCATTATAT
4041499 ATTATTATTTCATTATAT
1 ATTATTATTTCATTATAT
4041517 TTTTGATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTATTATTTCATTATAT
Found at i:4044940 original size:13 final size:12
Alignment explanation
Indices: 4044918--4045055 Score: 55
Period size: 13 Copynumber: 11.0 Consensus size: 12
4044908 CTGAAGAATG
*
4044918 AAAAATGAAAGAA
1 AAAAAAGAAA-AA
4044931 AAAAAAGAAAAA
1 AAAAAAGAAAAA
*
4044943 AGAAAATGAAATAA
1 A-AAAAAGAAA-AA
** *
4044957 AGGAAAGAAACA
1 AAAAAAGAAAAA
* * *
4044969 AAGAAACAAAGA
1 AAAAAAGAAAAA
*
4044981 AACAAAGAAAATGA
1 AAAAAAGAAAA--A
* *
4044995 AATAAATG-AAAT
1 AA-AAAAGAAAAA
*
4045007 AAAAATGAGAAAA
1 AAAAAAGA-AAAA
*
4045020 TAAAAAGATAAAA
1 AAAAAAGA-AAAA
* *
4045033 GAAAAAG-AAAG
1 AAAAAAGAAAAA
4045044 AAAAAAGAAAAA
1 AAAAAAGAAAAA
4045056 GAGAACAAAT
Statistics
Matches: 94, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
11 14 0.15
12 26 0.28
13 42 0.45
14 9 0.10
15 3 0.03
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:4044973 original size:43 final size:42
Alignment explanation
Indices: 4044925--4045060 Score: 134
Period size: 43 Copynumber: 3.1 Consensus size: 42
4044915 ATGAAAAATG
4044925 AAAGAAAAAAAAGAAAAAAGAAAATGAAATAAAGGAAAGAAA
1 AAAGAAAAAAAAGAAAAAAGAAAATGAAATAAAGGAAAGAAA
* * *
4044967 CAAAG-AAACAAAGAAACAAAGAAAATGAAATAAATGAAATAAA
1 -AAAGAAAAAAAAGAAA-AAAGAAAATGAAATAAAGGAAAGAAA
* * *
4045010 AATGAGAAAATAAAAAGATAAAAGAAAAAGAAAGAAA--AAAGAAA
1 AA--AG-AAA-AAAAAGAAAAAAGAAAATGAAATAAAGGAAAGAAA
4045054 AAGAGAA
1 AA-AGAA
4045061 CAAATAAAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
42 14 0.18
43 31 0.39
44 10 0.13
46 17 0.22
47 7 0.09
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (42 bp):
AAAGAAAAAAAAGAAAAAAGAAAATGAAATAAAGGAAAGAAA
Found at i:4045038 original size:6 final size:6
Alignment explanation
Indices: 4045016--4045057 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
4045006 TAAAAATGAG
* *
4045016 AAAATA AAAAGA TAAAAGA AAAAGA AAGA-A AAAAGA AAAAGA
1 AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
4045058 GAACAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 4 0.13
6 21 0.68
7 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:4046114 original size:134 final size:134
Alignment explanation
Indices: 4045947--4046645 Score: 830
Period size: 134 Copynumber: 5.2 Consensus size: 134
4045937 CCAAATCGAA
** *
4045947 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCATATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTCA
* * * * * * *
4046012 AGAAGCAGCGGAACAAATCCATCTCTTTCAATATTTGATCTTCCCTAAGTAATAGTGGAATAAGT
66 AGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATCTTCCATGAGTAACAGTGGAACAAGT
4046077 CTAC
131 CTAC
* ** * * *
4046081 CTCGATTCAGTCTTCCCTGAAGAATGGTGGAATGAATCAACATCCCCATATTTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTCA
* * * *** * * *
4046146 AAAAGAAGCAGAACTGATATTTCGCTTTCAATATTTGATCTTCCTTGAGTAACAGTGGAACAAGT
66 AGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATCTTCCATGAGTAACAGTGGAACAAGT
4046211 CTAC
131 CTAC
* * *
4046215 CTCGATTTAATCTTCCCTGAAGAACAATGGAAT-ATGTCAACGTCCCCAGATATGATTTTCCCTC
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGA-ATCAACGTCCCCAGATATGATTTTCCCTC
* * *
4046279 AAGAAGAAGCGAAACAGATCCATCTCTTTCAAGATTTGATCTTCTATGAGTAACAGTGGAATAAG
65 AAGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATCTTCCATGAGTAACAGTGGAACAAG
*
4046344 TCTGC
130 TCTAC
* * * * * *
4046349 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATTAACATCCCCAAATCTAATTTTCCCTTA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTCA
* * * * * * * *
4046414 AGATGAAGCGGAATATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAACT
66 AGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATCTTCCATGAGTAACAGTGGAACAAGT
*
4046479 CTTC
131 CTAC
* *
4046483 CTCGATTCAATCTTCCCT-AGAGAACAGTGGAATGAATCAACG-CTCCCAGATCTAATTTTCCCT
1 CTCGATTCAATCTTCCCTGA-AGAACAGTGGAATGAATCAACGTC-CCCAGATATGATTTTCCCT
* * **
4046546 CAAGAAAAAGCGGAACATATCCCCCTCTTTCAAGATTTGATCTTCCAT-AGGTAACAGTGGAACA
64 CAAGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATCTTCCATGA-GTAACAGTGGAACA
4046610 AGTCTAC
128 AGTCTAC
* * *
4046617 CTGGATCCAATCTTCCTTGAAGAACAGTG
1 CTCGATTCAATCTTCCCTGAAGAACAGTG
4046646 AAATAAGTCA
Statistics
Matches: 480, Mismatches: 79, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
133 4 0.01
134 474 0.99
135 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTCA
AGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATCTTCCATGAGTAACAGTGGAACAAGT
CTAC
Found at i:4046833 original size:3 final size:3
Alignment explanation
Indices: 4046825--4046869 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
4046815 TTTTATCCCG
*
4046825 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
4046870 TCTGCAGGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4067049 original size:15 final size:13
Alignment explanation
Indices: 4067029--4067063 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 13
4067019 ATATATATTA
4067029 AATTTTTAATAATTT
1 AATTTTTAAT--TTT
4067044 AATTTTTAATTTT
1 AATTTTTAATTTT
4067057 AATTTTT
1 AATTTTT
4067064 TATATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
15 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
AATTTTTAATTTT
Found at i:4067059 original size:13 final size:14
Alignment explanation
Indices: 4067023--4067075 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 14
4067013 ATATATATAT
*
4067023 ATATTAAATTTTTA
1 ATATTTAATTTTTA
4067037 ATAATTTAATTTTTA
1 AT-ATTTAATTTTTA
*
4067052 AT-TTTAATTTTTT
1 ATATTTAATTTTTA
*
4067065 ATATTTTATTT
1 ATATTTAATTT
4067076 AAAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.35
14 9 0.26
15 13 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTAATTTTTA
Found at i:4067070 original size:15 final size:15
Alignment explanation
Indices: 4067029--4067072 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
4067019 ATATATATTA
* *
4067029 AATTTTTAATAATTT
1 AATTTTTTATATTTT
4067044 AA-TTTTTA-ATTTT
1 AATTTTTTATATTTT
4067057 AATTTTTTATATTTT
1 AATTTTTTATATTTT
4067072 A
1 A
4067073 TTTAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 11 0.44
15 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTTTTATATTTT
Found at i:4067111 original size:21 final size:20
Alignment explanation
Indices: 4067063--4067103 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4067053 TTTTAATTTT
*
4067063 TTATATTT-TATTTAAAATA
1 TTATATTTAGATTTAAAATA
4067082 TTATATTTAGATTTAAAATA
1 TTATATTTAGATTTAAAATA
4067102 TT
1 TT
4067104 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATATTTAGATTTAAAATA
Found at i:4069461 original size:9 final size:9
Alignment explanation
Indices: 4069447--4069527 Score: 63
Period size: 10 Copynumber: 8.4 Consensus size: 9
4069437 GGCTGCTGGA
4069447 AACCGGTTT
1 AACCGGTTT
4069456 AACCGGTTTT
1 AACCGG-TTT
4069466 CAACCGGTTCT
1 -AACCGGTT-T
* *
4069477 GACCGGTTCG
1 AACCGGTT-T
4069487 AACCGGTTT
1 AACCGGTTT
* *
4069496 GACCGGTCTG
1 AACCGGT-TT
4069506 AACCGGTTT
1 AACCGGTTT
* *
4069515 GACCGGTCT
1 AACCGGTTT
4069524 AACC
1 AACC
4069528 CGACCGATCG
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
9 23 0.40
10 27 0.47
11 7 0.12
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (9 bp):
AACCGGTTT
Found at i:4069522 original size:19 final size:19
Alignment explanation
Indices: 4069447--4069527 Score: 94
Period size: 19 Copynumber: 4.2 Consensus size: 19
4069437 GGCTGCTGGA
* * *
4069447 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
4069467 AACCGGTTCTGACCGGT-TCG
1 AACCGGTT-TGACCGGTCT-G
4069487 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
4069506 AACCGGTTTGACCGGTCT-
1 AACCGGTTTGACCGGTCTG
4069524 AACC
1 AACC
4069528 CGACCGATCG
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.07
19 28 0.50
20 18 0.32
21 6 0.11
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:4069546 original size:5 final size:5
Alignment explanation
Indices: 4069536--4069599 Score: 65
Period size: 5 Copynumber: 12.0 Consensus size: 5
4069526 CCCGACCGAT
* *
4069536 CGACC CGACC CGACC GCTGACC TGACC CGACC CGACC GTTGACC CGACC
1 CGACC CGACC CGACC -C-GACC CGACC CGACC CGACC --CGACC CGACC
*
4069585 CGACC TGACC CGACC
1 CGACC CGACC CGACC
4069600 GTTGACCGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 40 0.82
6 1 0.02
7 8 0.16
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.08
Consensus pattern (5 bp):
CGACC
Found at i:4069584 original size:27 final size:27
Alignment explanation
Indices: 4069554--4069606 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
4069544 CCCGACCGCT
*
4069554 GACCTGACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCCGACCGTTGACCC
*
4069581 GACCCGACCTGACCCGACCGTTGACC
1 GACCCGACCCGACCCGACCGTTGACC
4069607 GTTGACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.11
Consensus pattern (27 bp):
GACCCGACCCGACCCGACCGTTGACCC
Found at i:4069606 original size:22 final size:22
Alignment explanation
Indices: 4069536--4069594 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
4069526 CCCGACCGAT
4069536 CGACCCGACCCGACCGCTGACC
1 CGACCCGACCCGACCGCTGACC
* *
4069558 TGACCCGACCCGACCGTTGACC
1 CGACCCGACCCGACCGCTGACC
*
4069580 CGACCCGACCTGACC
1 CGACCCGACCCGACC
4069595 CGACCGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.19, C:0.51, G:0.22, T:0.08
Consensus pattern (22 bp):
CGACCCGACCCGACCGCTGACC
Found at i:4076820 original size:9 final size:9
Alignment explanation
Indices: 4076795--4076864 Score: 59
Period size: 10 Copynumber: 7.3 Consensus size: 9
4076785 CCGGTTTTCA
4076795 ACCGGTTCTG
1 ACCGGTT-TG
4076805 ACCGGTTTG
1 ACCGGTTTG
*
4076814 TCCGGTTTCG
1 ACCGGTTT-G
* **
4076824 ACTGGTCCG
1 ACCGGTTTG
4076833 AACCGGTTTG
1 -ACCGGTTTG
*
4076843 ACCGGTCTG
1 ACCGGTTTG
4076852 AACCGGTTTG
1 -ACCGGTTTG
4076862 ACC
1 ACC
4076865 AGTCTAATCC
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
9 21 0.45
10 26 0.55
ACGTcount: A:0.13, C:0.29, G:0.30, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:4076854 original size:19 final size:19
Alignment explanation
Indices: 4076794--4076869 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
4076784 ACCGGTTTTC
*
4076794 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
* * *
4076814 -TCCGGTTTCGACTGGTCCG
1 AACCGGTTT-GACCGGTCTG
4076833 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
4076852 AACCGGTTTGACCAGTCT
1 AACCGGTTTGACCGGTCT
4076870 AATCCGACTG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.02
19 38 0.83
20 7 0.15
ACGTcount: A:0.14, C:0.28, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:4078717 original size:11 final size:11
Alignment explanation
Indices: 4078701--4078730 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
4078691 TTAAAATATT
4078701 GTTCTTTTAGG
1 GTTCTTTTAGG
4078712 GTTCTTTTAGG
1 GTTCTTTTAGG
4078723 GTTCTTTT
1 GTTCTTTT
4078731 CTCTTGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (11 bp):
GTTCTTTTAGG
Found at i:4080178 original size:20 final size:21
Alignment explanation
Indices: 4080139--4080178 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4080129 TTAGGGTTTG
4080139 AGTATCAATACTAGGATGAAC
1 AGTATCAATACTAGGATGAAC
*
4080160 AGTATCGATACTA-GATGAA
1 AGTATCAATACTAGGATGAA
4080179 TTGGGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTATCAATACTAGGATGAAC
Found at i:4082791 original size:17 final size:17
Alignment explanation
Indices: 4082769--4082816 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
4082759 CTCTAAATAA
4082769 TTTTAATATAATTTTAT
1 TTTTAATATAATTTTAT
4082786 TTTTAATATAATTTTAT
1 TTTTAATATAATTTTAT
4082803 TTTTAATATAATTT
1 TTTTAATATAATTT
4082817 ATATATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAATATAATTTTAT
Found at i:4083044 original size:2 final size:2
Alignment explanation
Indices: 4083039--4083111 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
4083029 TATATATATA
4083039 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4083081 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4083112 AAAATAATCT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4084288 original size:17 final size:16
Alignment explanation
Indices: 4084268--4084301 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4084258 CTATTTTATG
4084268 TATTCAAAATTTTTAAA
1 TATT-AAAATTTTTAAA
*
4084285 TATTTAAATTTTTAAA
1 TATTAAAATTTTTAAA
4084301 T
1 T
4084302 CGAATCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTAAAATTTTTAAA
Found at i:4085166 original size:14 final size:14
Alignment explanation
Indices: 4085147--4085174 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4085137 TTTATAGATT
4085147 AAAGATATTGTTAA
1 AAAGATATTGTTAA
4085161 AAAGATATTGTTAA
1 AAAGATATTGTTAA
4085175 TCGATGATTA
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:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
AAAGATATTGTTAA
Found at i:4086522 original size:3 final size:3
Alignment explanation
Indices: 4086516--4086649 Score: 126
Period size: 3 Copynumber: 43.7 Consensus size: 3
4086506 TTCATTTAAA
* *
4086516 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
4086561 AAT TAA TAT TAT TAA TAT TAT TATT TAT TAT TAT AAT AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * *
4086607 TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
4086650 CAAGCCCAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
2 1 0.01
3 100 0.91
4 9 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:4088862 original size:3 final size:3
Alignment explanation
Indices: 4088846--4088918 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
4088836 TTTGGGCTTG
* * *
4088846 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
4088893 TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
4088919 TAAATTATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 55 0.92
4 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:4088873 original size:9 final size:9
Alignment explanation
Indices: 4088859--4088929 Score: 67
Period size: 9 Copynumber: 8.1 Consensus size: 9
4088849 TAATATTTAA
4088859 TAATAATAT
1 TAATAATAT
*
4088868 TAATAATAAA
1 TAATAAT-AT
4088878 TAATAATAT
1 TAATAATAT
*
4088887 TAATAATAA
1 TAATAATAT
4088896 TAAT--TA-
1 TAATAATAT
*
4088902 TAATAATAA
1 TAATAATAT
4088911 TAATAATAT
1 TAATAATAT
* *
4088920 AAATTATAT
1 TAATAATAT
4088929 T
1 T
4088930 TAAATGAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
8 2 0.04
9 35 0.69
10 8 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATAATAT
Found at i:4089285 original size:124 final size:121
Alignment explanation
Indices: 4089063--4089293 Score: 311
Period size: 124 Copynumber: 1.9 Consensus size: 121
4089053 GTTGAATAAA
* *
4089063 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGTTGACCTA
1 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAACCTA
* * * *
4089128 TTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTTATTATGAAC
66 TATCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTCTTATTATGAAC
* * *
4089184 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGTTGATGCTAA
1 TTCTTCTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGCTAA
* * *
4089248 TCTATATGCTTCTGTGATAGAATTATACAAAAGGTTGAACAAGCTC
62 CCTATATCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTC
4089294 GTTTACTCTC
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
121 13 0.14
122 33 0.35
124 48 0.51
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (121 bp):
TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAACCTA
TATCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTCTTATTATGAAC
Found at i:4091068 original size:54 final size:53
Alignment explanation
Indices: 4090939--4091145 Score: 223
Period size: 54 Copynumber: 4.0 Consensus size: 53
4090929 AGAAATCTTG
* * * *
4090939 GCAGAAACCACAGAAAAGGATGAATGTGTTGTC-AACG-CTTACGAACGTCTAA
1 GCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC-TCTGA
*
4090991 GCAGAAACCACA-AGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAACCACAGA-AAAAGATGAATGTGTTGTCAAATGTTTTACGAAC-TCTGA
* * * *
4091045 GCAGAAGCCACAGAAAAATATGAATGTGTTGTCAAGTGTTTTAC-ATCTC-GA
1 GCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTTACGAACTCTGA
* *
4091096 -CAGATAA-CACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAA-TCTG
1 GCAGA-AACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTTACGAACTCTG
4091146 CTATTCTGAT
Statistics
Matches: 133, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
50 38 0.29
51 6 0.05
52 33 0.25
53 5 0.04
54 50 0.38
55 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (53 bp):
GCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTTACGAACTCTGA
Found at i:4091517 original size:22 final size:22
Alignment explanation
Indices: 4091491--4091570 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
4091481 TACATCTACA
4091491 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
4091513 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
* * *
4091535 CTTTTTAAATATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
4091557 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
4091571 AAGTTTTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:4092026 original size:113 final size:114
Alignment explanation
Indices: 4091742--4092238 Score: 661
Period size: 116 Copynumber: 4.4 Consensus size: 114
4091732 TGATCAGATG
* * **
4091742 GAAC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGA
1 GAACGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAA
* * *
4091806 ATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
66 ATCCATCACTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAA
* * *
4091855 GAACTCGTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1 GAA--CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTC
* * *
4091920 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAA
64 AAATCCATCACTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAA
* **
4091971 GAA-ATCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGA
1 GAACGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAA
* * *
4092035 ATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
66 ATCCATCACTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAA
*
4092084 GAACTCGTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTC
1 GAA--CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTC
* * * *
4092149 AAATCCATCACTTGATAGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAA
64 AAATCCATCACTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAA
4092200 GAAC-TCATCT---GAA-GAAGAAGAAGTTCATAATGAGAAGAA
1 GAACGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
4092239 CTAATCTGAA
Statistics
Matches: 339, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
109 26 0.08
110 3 0.01
112 1 0.00
113 108 0.32
114 1 0.00
115 1 0.00
116 197 0.58
117 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (114 bp):
GAACGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAA
ATCCATCACTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAA
Found at i:4092153 original size:229 final size:229
Alignment explanation
Indices: 4091746--4092240 Score: 890
Period size: 229 Copynumber: 2.2 Consensus size: 229
4091736 CAGATGGAAC
*
4091746 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCA
*
4091811 TCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGA
66 TCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGA
*
4091876 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
131 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATAGATC
4091941 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAA
196 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAA
*
4091975 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCA
*
4092040 TCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGG
66 TCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGA
* *
4092105 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATAGATC
131 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATAGATC
*
4092170 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
196 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAA
4092204 TCATCT---GAA-GAAGAAGAAGTTCATAATGAGAAGAACT
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
4092241 AATCTGAAGA
Statistics
Matches: 257, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
225 27 0.11
226 3 0.01
229 227 0.88
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (229 bp):
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCA
TCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAGAAGA
AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATAGATC
AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAA
Found at i:4092220 original size:19 final size:18
Alignment explanation
Indices: 4092196--4092257 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
4092186 GTTCATAATG
4092196 AGAAGAACTCATCTGAAGA
1 AGAAGAACT-ATCTGAAGA
*
4092215 AGAAGAAGT-TCAT-AATG-
1 AGAAGAACTATC-TGAA-GA
4092232 AGAAGAACTAATCTGAAGA
1 AGAAGAACT-ATCTGAAGA
4092251 AGAAGAA
1 AGAAGAA
4092258 GTTCACAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
17 12 0.34
18 4 0.11
19 19 0.54
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.16
Consensus pattern (18 bp):
AGAAGAACTATCTGAAGA
Found at i:4092231 original size:36 final size:36
Alignment explanation
Indices: 4092184--4092273 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
4092174 TTTCCAGAGA
*
4092184 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAG
4092220 AAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAG
* *
4092256 AAGTTCACAATGAAAAGA
1 AAGTTCATAATGAGAAGA
4092274 GCTTGTTCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (36 bp):
AAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAG
Found at i:4092655 original size:3 final size:3
Alignment explanation
Indices: 4092649--4092754 Score: 133
Period size: 3 Copynumber: 34.7 Consensus size: 3
4092639 TTCATTTAAA
* * *
4092649 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4092694 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
4092740 TAT TAAA TAT TAT TA
1 TAT T-AT TAT TAT TA
4092755 CAAGCCCAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
2 1 0.01
3 82 0.92
4 6 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:4098772 original size:36 final size:36
Alignment explanation
Indices: 4098732--4098801 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
4098722 ATGTATCGAT
4098732 ACTTTCGC-CCTTATCGTACTTTCGCATCAATTTATC
1 ACTTTCGCTCC-TATCGTACTTTCGCATCAATTTATC
*
4098768 ACTTTCGCTCCTATCGTATTTTCGCATCAATTTA
1 ACTTTCGCTCCTATCGTACTTTCGCATCAATTTA
4098802 GCTCACAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.43
Consensus pattern (36 bp):
ACTTTCGCTCCTATCGTACTTTCGCATCAATTTATC
Found at i:4099163 original size:42 final size:42
Alignment explanation
Indices: 4099056--4099169 Score: 174
Period size: 42 Copynumber: 2.7 Consensus size: 42
4099046 CAAATTCTCG
* * * *
4099056 TGTTTGTTTCACGCAATTCGTTTCCCGAAAAATGTTTTCCCG
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
4099098 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
* *
4099140 TGTTTGTTTAACGTAATTGGTTTTCCGGAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAA
4099170 TGTAATTCAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (42 bp):
TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
Found at i:4099382 original size:20 final size:20
Alignment explanation
Indices: 4099359--4099397 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4099349 TATTTATTAT
4099359 TAATATTTATAATAATATAA
1 TAATATTTATAATAATATAA
* *
4099379 TAATATTTTTAATATTATA
1 TAATATTTATAATAATATA
4099398 TAAATAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATATTTATAATAATATAA
Found at i:4099403 original size:20 final size:20
Alignment explanation
Indices: 4099339--4099403 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
4099329 CATTTCATCA
4099339 AAATATTATTT-AT-TTATTAT
1 AAATATT-TTTAATATTA-TAT
* * *
4099359 TAATATTTATAATAATATA-
1 AAATATTTTTAATATTATAT
4099378 ATAATATTTTTAATATTATAT
1 A-AATATTTTTAATATTATAT
4099399 AAATA
1 AAATA
4099404 ATCAATTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 2 0.06
20 30 0.86
21 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTTTTAATATTATAT
Found at i:4099464 original size:21 final size:21
Alignment explanation
Indices: 4099440--4099479 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4099430 TATATTTTAT
4099440 TTTA-ATAATATATAATAAAAA
1 TTTATATAATA-ATAATAAAAA
*
4099461 TTTATATATTAATAATAAA
1 TTTATATAATAATAATAAA
4099480 TAATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTATATAATAATAATAAAAA
Found at i:4099472 original size:28 final size:28
Alignment explanation
Indices: 4099433--4099515 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
4099423 AAGATATTAT
*
4099433 ATTT-TATTTTAATAATATATAATAAAA
1 ATTTATATATTAATAATATATAATAAAA
* *
4099460 ATTTATATATTAATAATAAATAAT--AT
1 ATTTATATATTAATAATATATAATAAAA
*
4099486 ATTTATATATTTAAATAATATTTTAATAAA
1 ATTTATATA-TT-AATAATA-TATAATAAA
4099516 GATATTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
26 10 0.22
27 6 0.13
28 24 0.53
29 4 0.09
31 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTATATATTAATAATATATAATAAAA
Found at i:4099478 original size:54 final size:52
Alignment explanation
Indices: 4099369--4099515 Score: 136
Period size: 54 Copynumber: 2.7 Consensus size: 52
4099359 TAATATTTAT
* * * *
4099369 AATAATATAATAATATTTTTAATATTATATAAATAATCAATTATATTATAAAATA
1 AATAATATATTTATA-TTTTAATAATATAT-AATAA-AAATTATATTATAAAATA
*
4099424 AGATATTATATTT-TATTTTAATAATATATAATAAAAATT-TATATATTAATAATA
1 A-ATAATATATTTATATTTTAATAATATATAATAAAAATTATAT-TA-TAA-AATA
*
4099478 AATAATATATTTATATATTTAAATAATATTTTAATAAA
1 AATAATATATTTATAT-TTT-AATAATA-TATAATAAA
4099516 GATATTTAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
51 3 0.04
52 6 0.08
53 18 0.23
54 21 0.27
55 6 0.08
56 15 0.19
57 8 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (52 bp):
AATAATATATTTATATTTTAATAATATATAATAAAAATTATATTATAAAATA
Found at i:4099485 original size:18 final size:18
Alignment explanation
Indices: 4099443--4099514 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
4099433 ATTTTATTTT
4099443 AATAATATA-TAATAA-A
1 AATAATATATTAATAATA
*
4099459 AATTTATATATTAATAATA
1 AA-TAATATATTAATAATA
*
4099478 AATAATATATTTATATATTTA
1 AATAATATA-TTA-ATA-ATA
*
4099499 AATAATATTTTAATAA
1 AATAATATATTAATAA
4099515 AGATATTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 2 0.04
17 6 0.13
18 12 0.27
19 9 0.20
20 6 0.13
21 10 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAATATATTAATAATA
Found at i:4099535 original size:23 final size:23
Alignment explanation
Indices: 4099509--4099553 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4099499 AATAATATTT
4099509 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
4099532 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
4099554 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:4099921 original size:20 final size:20
Alignment explanation
Indices: 4099884--4099922 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4099874 CCGGAAAATG
**
4099884 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
4099904 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
4099923 TAGTAATTCA
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:4099946 original size:21 final size:21
Alignment explanation
Indices: 4099920--4099962 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4099910 AGAATTCAAA
**
4099920 TTCTAGTAATTCATTTTCCAG
1 TTCTAGTAATTCAAATTCCAG
4099941 TTCTAGTAATTCAAATTCCAG
1 TTCTAGTAATTCAAATTCCAG
4099962 T
1 T
4099963 AATTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (21 bp):
TTCTAGTAATTCAAATTCCAG
Found at i:4099974 original size:15 final size:15
Alignment explanation
Indices: 4099896--4099941 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4099886 TTCCAGAAAT
4099896 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
4099911 G-AATTCAAATTCTA
1 GTAATTCATTTTCCA
4099925 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
4099940 GT
1 GT
4099942 TCTAGTAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:4100328 original size:29 final size:31
Alignment explanation
Indices: 4100284--4100356 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
4100274 AAATTTTAGA
*
4100284 TAGTGACCAAAATATAAA-TTT-TAAAAGTT
1 TAGTGACCAAAATATAAACTTTGAAAAAGTT
*
4100313 TAGTGACCAAAGTATAAACTTTGAAAAAGTT
1 TAGTGACCAAAATATAAACTTTGAAAAAGTT
*
4100344 TAGGGACCAAAAT
1 TAGTGACCAAAAT
4100357 GGTAATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 17 0.45
30 3 0.08
31 18 0.47
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGTGACCAAAATATAAACTTTGAAAAAGTT
Found at i:4100344 original size:31 final size:29
Alignment explanation
Indices: 4100284--4100373 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 29
4100274 AAATTTTAGA
*
4100284 TAGTGACCAAAATATAAATTTTAAAAGTT
1 TAGTGACCAAAATATAAATTTAAAAAGTT
*
4100313 TAGTGACCAAAGTATAAACTTTGAAAAAGTT
1 TAGTGACCAAAATATAAA-TTT-AAAAAGTT
* *
4100344 TAGGGACCAAAATGGT-AATATTAAAAAGTT
1 TAGTGACCAAAAT-ATAAAT-TTAAAAAGTT
4100374 ACATTTTGGC
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 17 0.33
30 12 0.23
31 22 0.42
32 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.30
Consensus pattern (29 bp):
TAGTGACCAAAATATAAATTTAAAAAGTT
Found at i:4101392 original size:30 final size:31
Alignment explanation
Indices: 4101356--4101416 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
4101346 AGAAAATTTT
** *
4101356 GGGGACC-ATTTTTTAATTTTTCAAAAGTTA
1 GGGGACCAATTTGGTAATTTTGCAAAAGTTA
*
4101386 GGGGACCAATTTGGTAATTTTGGAAAAGTTA
1 GGGGACCAATTTGGTAATTTTGCAAAAGTTA
4101417 TGAATGGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (31 bp):
GGGGACCAATTTGGTAATTTTGCAAAAGTTA
Found at i:4101413 original size:31 final size:30
Alignment explanation
Indices: 4101347--4101416 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
4101337 ACGCACCTTA
* * ** *
4101347 GAAAATTTTGGGGACCATTTTTTAATTTTT
1 GAAAAGTTAGGGGACCATTTGGTAATTTTG
*
4101377 CAAAAGTTAGGGGACCAATTTGGTAATTTTG
1 GAAAAGTTAGGGGACC-ATTTGGTAATTTTG
4101408 GAAAAGTTA
1 GAAAAGTTA
4101417 TGAATGGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (30 bp):
GAAAAGTTAGGGGACCATTTGGTAATTTTG
Found at i:4102254 original size:21 final size:22
Alignment explanation
Indices: 4102224--4102264 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
4102214 AAACATATTT
4102224 AATATACATAT-ATATGTTTTTA
1 AATATACATATGATAT-TTTTTA
4102246 AATAT-CATATGATATTTTT
1 AATATACATATGATATTTTT
4102265 ACTTGAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
AATATACATATGATATTTTTTA
Found at i:4106374 original size:97 final size:96
Alignment explanation
Indices: 4106233--4106461 Score: 244
Period size: 97 Copynumber: 2.4 Consensus size: 96
4106223 TAAACTGGTT
* * * *
4106233 AAGTTATAAGGCTTTAACCGTTTATATTATAATAATCTACAACAAATTCGATTTTGATAGTAACA
1 AAGTTATAAGGCTTTAACCGTTTATATTATAATAACCTACAACAAATACGATTGTGAGAGTAACA
* *
4106298 CGTTAGGTTGTGCCTTGATTTTTTAATTGTTC
66 CGATAGGTTGCGCCTTG-TTTTTTAATTGTTC
** * ** * *
4106330 AAGTTATAATTCTTTAACCGTTTATATTATAGTAACCTGTAACAAATACGGTTGTGAGAGTAACG
1 AAGTTATAAGGCTTTAACCGTTTATATTATAATAACCTACAACAAATACGATTGTGAGAGTAACA
* ***
4106395 TGATAGGTTGCGCCTTGTTTTTTGAACCAATT-
66 CGATAGGTTGCGCCTTGTTTTTT-AA-TTGTTC
* * *
4106427 AAGTTATAAGACTTCAACTGTTTATATTATAATAA
1 AAGTTATAAGGCTTTAACCGTTTATATTATAATAA
4106462 ACTATTACAA
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
96 6 0.06
97 100 0.93
98 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (96 bp):
AAGTTATAAGGCTTTAACCGTTTATATTATAATAACCTACAACAAATACGATTGTGAGAGTAACA
CGATAGGTTGCGCCTTGTTTTTTAATTGTTC
Found at i:4106862 original size:41 final size:42
Alignment explanation
Indices: 4106788--4106867 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
4106778 CGATATTTCC
* * * *
4106788 ATCATAAAGTATTGAATATCATAGGATAAGTATTGATATAAA
1 ATCATAAAGTATCGAACATCATAAGATAAGTATTAATATAAA
* *
4106830 ATCA-AAAGTATCGAACATCATAATATATGTATTAATAT
1 ATCATAAAGTATCGAACATCATAAGATAAGTATTAATAT
4106868 TTTAACTATC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 28 0.88
42 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.34
Consensus pattern (42 bp):
ATCATAAAGTATCGAACATCATAAGATAAGTATTAATATAAA
Found at i:4106942 original size:73 final size:72
Alignment explanation
Indices: 4106833--4107066 Score: 237
Period size: 73 Copynumber: 3.2 Consensus size: 72
4106823 ATATAAAATC
* * * * *
4106833 AAAAGTATCGAACATCATA-ATATATGTATTAATATTTTAACTATCGATCTTATCATCAACTCTT
1 AAAAGTATCGATCATCACACATA-A-GTATCAATATTTTAACTTTCGATCTTATCTTCAACT-TT
*
4106897 TT-AGTATTT
63 TTCAATATTT
* * * ** *
4106906 AAAAGTATTGATCATCACCACATAAGTAT-AGTTATTTTATCTTTTAATCTTATCTTTAA-TTTG
1 AAAAGTATCGATCATCA-CACATAAGTATCA-ATATTTTAACTTTCGATCTTATCTTCAACTTT-
4106969 TTCAATATTT
63 TTCAATATTT
* *
4106979 AAAAGTATCGATCATCACACATAAGTATCAATA-TTTAAGTTTCGTTCTTATCTTCAACTTTTTC
1 AAAAGTATCGATCATCACACATAAGTATCAATATTTTAACTTTCGATCTTATCTTCAACTTTTTC
4107043 AATATTT
66 AATATTT
4107050 GAAAA-TATCGATCATCA
1 -AAAAGTATCGATCATCA
4107067 TATATTAAGT
Statistics
Matches: 134, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
71 42 0.31
72 24 0.18
73 63 0.47
74 2 0.01
75 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (72 bp):
AAAAGTATCGATCATCACACATAAGTATCAATATTTTAACTTTCGATCTTATCTTCAACTTTTTC
AATATTT
Found at i:4107116 original size:16 final size:17
Alignment explanation
Indices: 4107085--4107116 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4107075 GTATCGATTT
4107085 ATAACATTTTTATATTC
1 ATAACATTTTTATATTC
4107102 ATAACATTTTT-TATT
1 ATAACATTTTTATATT
4107117 TTAATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAACATTTTTATATTC
Found at i:4107508 original size:186 final size:183
Alignment explanation
Indices: 4107138--4107705 Score: 638
Period size: 186 Copynumber: 3.1 Consensus size: 183
4107128 TGTTATTGTG
* *
4107138 GTAATATTTTAGGCGCAATCAATTTTATTAAACATAAAATTAACATTCCAGATCACAACCTACTT
1 GTAACATTTTAGGCGCAATCGATTTTATTAAACATAAAATTAACATTCCAGATCACAACCTACTT
* *
4107203 TCTTAACGATCCATAACATTCTTGGGCACAACCTGATTTCTCATAGATATTCATAACA----TT-
66 TCTTAGCGATCCATAACATTCTTGGGCACAACCTGATTTCTTATAGATATTCATAACATTTTTTA
* *
4107263 TTTTAACTTA---TTTTCGTGGAAAATTCAAAAGCTCCGTCAGCTTAAACTCTA
131 TTTTAACTTATTTTTTTCGTGG-AAATTCAAAAGCTCCATCAACTTAAACTCTA
* * *
4107314 GTAACATTTTAGGCGCAATCGATTTTATCAAATATAAAAATTAACATTCAAGATCACAACCTA-T
1 GTAACATTTTAGGCGCAATCGATTTTATTAAACAT-AAAATTAACATTCCAGATCACAACCTACT
* * * ** *
4107378 TTCTTAGTGACCCCTAACATTCTTGGGCACAACCCAATTTCTTATAGATATTTATAACATTTTTT
65 TTCTTAGCGATCCATAACATTCTTGGGCACAACCTGATTTCTTATAGATATTCATAACATTTTTT
* *
4107443 ATTTTAACTTATTTTGTTATCGTGAGAAATTCAAAAAC-CCTATCAACTTAAACTTTA
130 ATTTTAACTTATTTT-TT-TCGTG-GAAATTCAAAAGCTCC-ATCAACTTAAACTCTA
* ** * * **
4107500 ATAACATTTTAGAAGCAACCGATTTCATTAAACATAAAATTAACATTCCAGATCGTAACCTACTT
1 GTAACATTTTAGGCGCAATCGATTTTATTAAACATAAAATTAACATTCCAGATCACAACCTACTT
* * * * * *
4107565 TCTTAGCGATCCATAACATTTTTAGGCGCAACATGATATCTTAT-GAATATTCATAACTTTTTTT
66 TCTTAGCGATCCATAACATTCTTGGGCACAACCTGATTTCTTATAG-ATATTCATAAC--ATTTT
* *
4107629 TTATTTAAACTTATTTTTTT-GTAATGGGAAATTCAAAAGCTCCATCAACGTAAACTCTA
128 TTATTTTAACTTATTTTTTTCG---T-GGAAATTCAAAAGCTCCATCAACTTAAACTCTA
*
4107688 GTAACATTTTAGGTGCAA
1 GTAACATTTTAGGCGCAA
4107706 CCTAACATAA
Statistics
Matches: 324, Mismatches: 46, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
176 83 0.26
177 26 0.08
180 2 0.01
181 10 0.03
184 1 0.00
185 30 0.09
186 104 0.32
187 3 0.01
188 62 0.19
189 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (183 bp):
GTAACATTTTAGGCGCAATCGATTTTATTAAACATAAAATTAACATTCCAGATCACAACCTACTT
TCTTAGCGATCCATAACATTCTTGGGCACAACCTGATTTCTTATAGATATTCATAACATTTTTTA
TTTTAACTTATTTTTTTCGTGGAAATTCAAAAGCTCCATCAACTTAAACTCTA
Found at i:4110825 original size:20 final size:20
Alignment explanation
Indices: 4110800--4110853 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
4110790 GACCAACAAA
4110800 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
4110820 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
4110840 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
4110854 ATATAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:4110907 original size:20 final size:20
Alignment explanation
Indices: 4110841--4110908 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
4110831 GTTTCCAATT
* *
4110841 TCGCAACGCGAATATATAAA
1 TCGCAACGCGAATTTTTAAA
** *
4110861 TCGCATTGC-AATTTTCCAAA
1 TCGCAACGCGAATTTT-TAAA
4110881 TTCGCAACGCGAATTTTTAAA
1 -TCGCAACGCGAATTTTTAAA
4110902 TCGCAAC
1 TCGCAAC
4110909 ACATAAGTCA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 4 0.11
20 17 0.46
21 10 0.27
22 6 0.16
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGAATTTTTAAA
Found at i:4110925 original size:20 final size:20
Alignment explanation
Indices: 4110914--4110981 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
4110904 GCAACACATA
4110914 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
4110934 AGTCAAATTCACAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
4110954 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAT
4110974 AGTCAAAT
1 AGTCAAAT
4110982 GTTTTTACGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:4110932 original size:40 final size:41
Alignment explanation
Indices: 4110877--4110981 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 41
4110867 TGCAATTTTC
** * *
4110877 CAAATTCGCAACGCGAATTTTTAAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGAATAGTCAAATTCACAACACGAT-AGT
*
4110917 CAAATTCGCAACGCG-ATAGTCAAATTCACAACGCGATAGT
1 CAAATTCGCAACGCGAATAGTCAAATTCACAACACGATAGT
4110957 CAAATTCGCAACGCGAA-AGTCAAAT
1 CAAATTCGCAACGCGAATAGTCAAAT
4110982 GTTTTTACGC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
39 6 0.11
40 48 0.84
41 3 0.05
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATAGTCAAATTCACAACACGATAGT
Found at i:4111134 original size:22 final size:22
Alignment explanation
Indices: 4111109--4111159 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
4111099 CTACGGCGAC
4111109 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
4111131 ATCCTTCCCCATTTTCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
4111153 ATTCGTC
1 ATCCGTC
4111160 TATCTCCATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.39, G:0.12, T:0.27
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:4113411 original size:4 final size:4
Alignment explanation
Indices: 4113402--4113447 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
4113392 TTTTTCGGTA
* * * *
4113402 TTAT TTAT TTAT TTAT TTAT TTAA TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
4113448 TCAGCGGCCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:4115293 original size:20 final size:20
Alignment explanation
Indices: 4115267--4115339 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
4115257 GTTGAAGGTA
4115267 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGTGAAAGT
* * * *
4115287 TAAATTCGCAAAGCGAGAGT
1 CAAATTCGCAACGTGAAAGT
4115307 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGTGAAAGT
4115327 CAAATTCGCAACG
1 CAAATTCGCAACG
4115340 CGATTTTCGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGTGAAAGT
Found at i:4115322 original size:40 final size:40
Alignment explanation
Indices: 4115267--4115342 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
4115257 GTTGAAGGTA
*
4115267 CAAATTCGCAACGTGAAAGTTAAATTCGCAAAGCGAGAGT
1 CAAATTCGCAACGTGAAAGTCAAATTCGCAAAGCGAGAGT
*
4115307 CAAATTCGCAACGTGAAAGTCAAATTCGCAACGCGA
1 CAAATTCGCAACGTGAAAGTCAAATTCGCAAAGCGA
4115343 TTTTCGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (40 bp):
CAAATTCGCAACGTGAAAGTCAAATTCGCAAAGCGAGAGT
Found at i:4115603 original size:39 final size:39
Alignment explanation
Indices: 4115549--4115635 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
4115539 TCAAGTTGTA
*
4115549 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTAGCACCATATGAGATTTG
* * *
4115588 GATTTTGTTTTCCTTTTGTTTAGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTAGCACCATATGAGATTTG
4115627 GATTTTGAT
1 GATTTTGAT
4115636 GAGCATCAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTAGCACCATATGAGATTTG
Found at i:4115968 original size:18 final size:18
Alignment explanation
Indices: 4115945--4115981 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4115935 CAAAATTTAT
4115945 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
4115963 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
4115981 A
1 A
4115982 CTCTAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:4116401 original size:25 final size:25
Alignment explanation
Indices: 4116364--4116413 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4116354 ATTATTTTTC
* *
4116364 CAAATAATTTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
4116389 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
4116414 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:4116531 original size:20 final size:20
Alignment explanation
Indices: 4116479--4116531 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4116469 TGTTGAAGGT
4116479 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
* * * *
4116499 AATTTCTCTACGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
4116519 AAATTCGCAACGC
1 AAATTCGCAACGC
4116532 TTATTTCGCG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:4116856 original size:18 final size:18
Alignment explanation
Indices: 4116833--4116868 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4116823 AATCCGGTTG
4116833 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
4116851 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
4116869 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:4119197 original size:24 final size:24
Alignment explanation
Indices: 4119146--4119197 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4119136 ATCCGAGTAT
** *
4119146 TGACCAAGATCAAATTCTGGGTAT
1 TGACCAAGATCAAATTCTGAATAC
4119170 TGACCAAGATCAAATT-TCGAATAC
1 TGACCAAGATCAAATTCT-GAATAC
4119194 TGAC
1 TGAC
4119198 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAATTCTGAATAC
Found at i:4120111 original size:19 final size:19
Alignment explanation
Indices: 4120063--4120114 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
4120053 AAACTAAAAC
4120063 CTGTTGCGAATTTGAAATT
1 CTGTTGCGAATTTGAAATT
* **
4120082 CAGTTAAGAATTTGAAATT
1 CTGTTGCGAATTTGAAATT
*
4120101 TTGTTGCGAATTTG
1 CTGTTGCGAATTTG
4120115 GAAAATCTCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (19 bp):
CTGTTGCGAATTTGAAATT
Found at i:4120130 original size:21 final size:21
Alignment explanation
Indices: 4120106--4120180 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
4120096 AAATTTTGTT
*
4120106 GCGAATTTGGAAAATCTCAAC
1 GCGAATTTGGAAAATCCCAAC
4120127 GCGAATTTGGAAAATCCCAAC
1 GCGAATTTGGAAAATCCCAAC
*
4120148 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCCCAAC
* *
4120169 ACGAAATTGGAA
1 GCGAATTTGGAA
4120181 TTCGCGTTGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCCCAAC
Found at i:4121169 original size:17 final size:17
Alignment explanation
Indices: 4121147--4121188 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
4121137 CATAACCCCT
4121147 TTCTTCCTTTTACTTTC
1 TTCTTCCTTTTACTTTC
4121164 TTCTTCCTTTTACTTTC
1 TTCTTCCTTTTACTTTC
*
4121181 TTTTTCCT
1 TTCTTCCT
4121189 CTTTCAACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTTCCTTTTACTTTC
Found at i:4125324 original size:31 final size:30
Alignment explanation
Indices: 4125284--4125349 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
4125274 TACAATATAA
4125284 TCCCCAACATTTAGTCTGTTTATAAAATGG
1 TCCCCAACATTTAGTCTGTTTATAAAATGG
* *
4125314 TCCCCTAACATTTAGTCTGTTTGTAATATGG
1 TCCCC-AACATTTAGTCTGTTTATAAAATGG
4125345 TCCCC
1 TCCCC
4125350 GACTGTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (30 bp):
TCCCCAACATTTAGTCTGTTTATAAAATGG
Found at i:4127264 original size:31 final size:31
Alignment explanation
Indices: 4127224--4127317 Score: 154
Period size: 31 Copynumber: 3.1 Consensus size: 31
4127214 TCAAACGGTC
* * *
4127224 GGGGG-CCATACTACAAATAGACTAAATGTT
1 GGGGGACCATATTGCAAACAGACTAAATGTT
4127254 GGGGGACCATATTGCAAACAGACTAAATGTT
1 GGGGGACCATATTGCAAACAGACTAAATGTT
4127285 GGGGGACCATATTGCAAACAGACTAAATGTT
1 GGGGGACCATATTGCAAACAGACTAAATGTT
4127316 GG
1 GG
4127318 AGACTGTATT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 5 0.08
31 55 0.92
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (31 bp):
GGGGGACCATATTGCAAACAGACTAAATGTT
Found at i:4131642 original size:29 final size:31
Alignment explanation
Indices: 4131605--4131662 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4131595 TTGCTAATCA
*
4131605 TTTCAACTAAC-TTGA-TTCTTTTTGTCTTG
1 TTTCAACTAACATTGATTTCCTTTTGTCTTG
*
4131634 TTTCTACTAACATTGATTTCCTTTTGTCT
1 TTTCAACTAACATTGATTTCCTTTTGTCT
4131663 GGTATTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 4 0.16
31 11 0.44
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (31 bp):
TTTCAACTAACATTGATTTCCTTTTGTCTTG
Found at i:4135808 original size:57 final size:57
Alignment explanation
Indices: 4135577--4135822 Score: 271
Period size: 55 Copynumber: 4.4 Consensus size: 57
4135567 ACTAGGTTTG
* * *
4135577 ATTTTTAGAGGTTTCTTGATATGATGTTTTC-AAACGAA-TTTGAAAGAAGCGAAGCCTG
1 ATTTTTAGGGGTTTCTTG--ATGAT-TTTTCAAAACGAATTTTGAAAGAAGCTAAGCCTA
*
4135635 AGTTTTAGGGGTTTCTTGATG--TTTTCAAAA-GAATTTTGAAAGAAGCTAAGCCTAA
1 ATTTTTAGGGGTTTCTTGATGATTTTTCAAAACGAATTTTGAAAGAAGCTAAGCCT-A
* * * *
4135690 ATTTTTAGGGGTTTCTT-AT--TGCTTTCAAAATGAGTTTTTAAA-AA-CTAAGCCTA
1 ATTTTTAGGGGTTTCTTGATGAT-TTTTCAAAACGAATTTTGAAAGAAGCTAAGCCTA
* *
4135743 ATTTTTAGGGGTTTCTTGATGATTATTTCCAAA-GAATTTTTAAAGAAGCTAAGCCTA
1 ATTTTTAGGGGTTTCTTGATGATT-TTTCAAAACGAATTTTGAAAGAAGCTAAGCCTA
4135800 ATTTTTAGGGGTTTCTTGATGAT
1 ATTTTTAGGGGTTTCTTGATGAT
4135823 AAATATAAAC
Statistics
Matches: 165, Mismatches: 11, Indels: 25
0.82 0.05 0.12
Matches are distributed among these distances:
53 26 0.16
54 33 0.20
55 36 0.22
56 22 0.13
57 32 0.19
58 16 0.10
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (57 bp):
ATTTTTAGGGGTTTCTTGATGATTTTTCAAAACGAATTTTGAAAGAAGCTAAGCCTA
Found at i:4136110 original size:59 final size:59
Alignment explanation
Indices: 4136007--4136136 Score: 181
Period size: 59 Copynumber: 2.2 Consensus size: 59
4135997 GCAGGATGTT
* * *
4136007 TTAACATTTCCTTTGCTCGATTCACAACACTTTGAATCAACAACGCCCCATTTGAGGGA
1 TTAACATTTCCTTTGCTCGATTCACAACACATCGAATCAACAACGCCCCACTTGAGGGA
* * * *
4136066 TTAACATTTACC-TTGCTTGATTCACAACACATCGAATTAGCAACGCCCCACTTGAGTGA
1 TTAACATTT-CCTTTGCTCGATTCACAACACATCGAATCAACAACGCCCCACTTGAGGGA
4136125 TTAACATTTCCT
1 TTAACATTTCCT
4136137 ATAACTCAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 2 0.03
59 58 0.94
60 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (59 bp):
TTAACATTTCCTTTGCTCGATTCACAACACATCGAATCAACAACGCCCCACTTGAGGGA
Found at i:4136274 original size:41 final size:42
Alignment explanation
Indices: 4136169--4136274 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
4136159 GAATCAGTAA
* * * * *
4136169 AAGTCCATCGAGCCAT-CAGTAAGTCTTTCGAGTATGATGCTT
1 AAGTCCTTCGGGCCATCCA-TAAGTCTTTCGAGCAAGATGCAT
* * *
4136211 AAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-AT
1 AAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAAGATGCAT
4136252 AAGTCCTTCGGGCCATCCATAAG
1 AAGTCCTTCGGGCCATCCATAAG
4136275 ACCTTCGGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
41 21 0.40
42 30 0.58
43 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAAGATGCAT
Found at i:4136425 original size:20 final size:19
Alignment explanation
Indices: 4136382--4136427 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4136372 ATTCACAATA
*
4136382 CTTCGAATCAACAAAAGTC
1 CTTCGAGTCAACAAAAGTC
*
4136401 CTTCGAGTCATCAATAAGTC
1 CTTCGAGTCAACAA-AAGTC
*
4136421 TTTCGAG
1 CTTCGAG
4136428 CACGATGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (19 bp):
CTTCGAGTCAACAAAAGTC
Found at i:4136480 original size:227 final size:227
Alignment explanation
Indices: 4136084--4136543 Score: 652
Period size: 227 Copynumber: 2.0 Consensus size: 227
4136074 TACCTTGCTT
* * *
4136084 GATTCACAACACATCGAATTAGCAACGCCCCACTTGAGTGATTAACATTTCCTATAACTCAATTC
1 GATTCACAACACATCAAATCAGCAACGCCCCACTTGAGGGATTAACATTTCCTATAACTCAATTC
** * ** * * *
4136149 ACGGCATTTCGAATCAGTAAAAGTCCATCGAGCCATCAGTAAGTCTTTCGAGTATGATGCTTAAA
66 ACAACACTTCGAATCAACAAAAGTCCATCGAGCCATCAATAAGTCTTTCGAGCACGATGCTTAAA
* *
4136214 TCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCT
131 TCCTTCAGGTCATCTATAAGTCTTCCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCT
*
4136279 TCGGGCAGGATGTTTTCACATTCCCTTTACTC
196 TCGGGCAAGATGTTTTCACATTCCCTTTACTC
* * ** *
4136311 GATTCACAACA-ATTCAAATCAGCGATGCCCCACTTGAGGGATTAACATTTCCTATTGCTCGATT
1 GATTCACAACACA-TCAAATCAGCAACGCCCCACTTGAGGGATTAACATTTCCTATAACTCAATT
* * * *
4136375 CACAATACTTCGAATCAACAAAAGTCCTTCGAGTCATCAATAAGTCTTTCGAGCACGATGTTTAA
65 CACAACACTTCGAATCAACAAAAGTCCATCGAGCCATCAATAAGTCTTTCGAGCACGATGCTTAA
*
4136440 ATCCTTCAGGTCATCTATAAGTCTTCCGAGCAATATGATAAGTCCTTCGGGCCATCCATAAGACC
130 ATCCTTCAGGTCATCTATAAGTCTTCCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACC
* ** *
4136505 TTCGGGCAAGATGTTTTCATATTTTCTTTGCTC
195 TTCGGGCAAGATGTTTTCACATTCCCTTTACTC
4136538 GATTCA
1 GATTCA
4136544 TGGCATTTAG
Statistics
Matches: 204, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
226 1 0.00
227 203 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (227 bp):
GATTCACAACACATCAAATCAGCAACGCCCCACTTGAGGGATTAACATTTCCTATAACTCAATTC
ACAACACTTCGAATCAACAAAAGTCCATCGAGCCATCAATAAGTCTTTCGAGCACGATGCTTAAA
TCCTTCAGGTCATCTATAAGTCTTCCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCT
TCGGGCAAGATGTTTTCACATTCCCTTTACTC
Found at i:4136501 original size:41 final size:42
Alignment explanation
Indices: 4136396--4136518 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 42
4136386 GAATCAACAA
* * * *
4136396 AAGTCCTTCGAGTCATCAATAAGTCTTTCGAGCACGATGTTT
1 AAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCAAGATGTAT
* * * *
4136438 AAATCCTTCAGGTCATCTATAAGTCTTCCGAGCAATATG-AT
1 AAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCAAGATGTAT
* * * *
4136479 AAGTCCTTCGGGCCATCCATAAGACCTT-CGGGCAAGATGT
1 AAGTCCTTCGGGTCATCAATAAG-TCTTCCGAGCAAGATGT
4136519 TTTCATATTT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
41 29 0.45
42 35 0.55
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (42 bp):
AAGTCCTTCGGGTCATCAATAAGTCTTCCGAGCAAGATGTAT
Found at i:4136587 original size:227 final size:226
Alignment explanation
Indices: 4136156--4136592 Score: 615
Period size: 227 Copynumber: 1.9 Consensus size: 226
4136146 TTCACGGCAT
** * * * *
4136156 TTCGAATCAGTAAAAGTCCATCGAGCCATCAGTAAGTCTTTCGAGTATGATGCTTAAATCCTTCG
1 TTCGAATCAACAAAAGTCCATCGAGCCATCAATAAGTCTTTCGAGCACGATGCTTAAATCCTTCA
*
4136221 GGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCA
66 GGTCATCTATAAGTCTTCCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCA
* *
4136286 GGATGTTTTCACATTCCCTTTACTCGATTCACAACAATTCAAATCAGCGATGCCCCACTTGAGGG
131 AGATGTTTTCACATTCCCTTTACTCGATTCACAACAATTCAAATCAGCGATGCCCCACTCGAGGG
**
4136351 ATTAACATTTCCTATTGCTCGATTCACAATAC
196 ACCAACATTT-CTATTGCTCGATTCACAATAC
* * *
4136383 TTCGAATCAACAAAAGTCCTTCGAGTCATCAATAAGTCTTTCGAGCACGATGTTTAAATCCTTCA
1 TTCGAATCAACAAAAGTCCATCGAGCCATCAATAAGTCTTTCGAGCACGATGCTTAAATCCTTCA
*
4136448 GGTCATCTATAAGTCTTCCGAGCAATATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCA
66 GGTCATCTATAAGTCTTCCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCA
* ** * *** * * * *
4136513 AGATGTTTTCATATTTTCTTTGCTCGATTCATGGC-ATTTAGAATCAGTGTTGCCTCACTCGAGG
131 AGATGTTTTCACATTCCCTTTACTCGATTCACAACAATTCA-AATCAGCGATGCCCCACTCGAGG
4136577 GACCAACATTTCTATT
195 GACCAACATTTCTATT
4136593 AGAGAATTCA
Statistics
Matches: 183, Mismatches: 26, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
226 9 0.05
227 174 0.95
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (226 bp):
TTCGAATCAACAAAAGTCCATCGAGCCATCAATAAGTCTTTCGAGCACGATGCTTAAATCCTTCA
GGTCATCTATAAGTCTTCCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCA
AGATGTTTTCACATTCCCTTTACTCGATTCACAACAATTCAAATCAGCGATGCCCCACTCGAGGG
ACCAACATTTCTATTGCTCGATTCACAATAC
Found at i:4138732 original size:3 final size:3
Alignment explanation
Indices: 4138724--4138818 Score: 142
Period size: 3 Copynumber: 32.7 Consensus size: 3
4138714 TTAATATATT
*
4138724 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4138770 TAA TAA T-A TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4138817 TA
1 TA
4138819 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
2 6 0.07
3 77 0.93
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4138747 original size:20 final size:21
Alignment explanation
Indices: 4138724--4138818 Score: 142
Period size: 20 Copynumber: 4.7 Consensus size: 21
4138714 TTAATATATT
4138724 TAATAATAA-AATAATAATAA
1 TAATAATAATAATAATAATAA
4138744 TAATAATAA-AATAATAATAA
1 TAATAATAATAATAATAATAA
*
4138764 AAATAATAATAAT-ATAATAA
1 TAATAATAATAATAATAATAA
* *
4138784 TGATAATAATAATATTAATAA
1 TAATAATAATAATAATAATAA
4138805 TAATAATAATAATA
1 TAATAATAATAATA
4138819 TGGATAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
20 46 0.68
21 22 0.32
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (21 bp):
TAATAATAATAATAATAATAA
Found at i:4139430 original size:114 final size:114
Alignment explanation
Indices: 4138954--4139601 Score: 1018
Period size: 114 Copynumber: 5.6 Consensus size: 114
4138944 ATTGAATAAA
* * * * ** *
4138954 TTCTTCTT-TTTCTCCAGATGAGTTCTTATCATTACGAACTTTCTGCTGGGGATG-AT-ATTCCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGAATGA-TCCA
* *
4139016 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 TCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
4139067 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCGTTATGAACTCTTTCTCTGGAAATG-ATGAT
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAA--CTTTCTCTGGAAAAGAATGAT
4139131 CCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
61 CCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
4139185 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGAA-GAT
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAAAGAATGAT
*
4139249 CCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
61 CCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
4139304 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
4139369 AAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 AAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
4139418 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
*
4139483 AAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 AAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
4139532 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
4139597 AAGTG
66 AAGTG
4139602 GATTTGAAAT
Statistics
Matches: 509, Mismatches: 14, Indels: 23
0.93 0.03 0.04
Matches are distributed among these distances:
113 8 0.02
114 250 0.49
115 12 0.02
116 23 0.05
117 18 0.04
118 124 0.24
119 74 0.15
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (114 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATC
AAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:4140314 original size:52 final size:52
Alignment explanation
Indices: 4140236--4140442 Score: 387
Period size: 52 Copynumber: 4.0 Consensus size: 52
4140226 CAATACTTGA
*
4140236 TTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
4140288 TTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
4140340 TTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
4140392 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
4140443 AAGCACATTC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 152 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (52 bp):
TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
Found at i:4141601 original size:15 final size:15
Alignment explanation
Indices: 4141583--4141637 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
4141573 ACCTTGACCC
4141583 TTTTCTTTTTCTATT
1 TTTTCTTTTTCTATT
4141598 TTTT-TTTCTTCTATTT
1 TTTTCTTT-TTCTA-TT
* *
4141614 TTTTTTCTTTTCTTTT
1 TTTTCT-TTTTCTATT
4141630 TTTTCTTT
1 TTTTCTTT
4141638 CTTTTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.09
15 11 0.32
16 13 0.38
17 5 0.15
18 2 0.06
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTCTATT
Found at i:4141643 original size:40 final size:41
Alignment explanation
Indices: 4141588--4141667 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
4141578 GACCCTTTTC
* * *
4141588 TTTTTCTATT-TTTTTTTCTTCTATTTTTTTTTCTTTTCTTT
1 TTTTTCTATTCTTTTTCT-TTCTATTCTTCTTTCTTTTCTTT
*
4141629 TTTTTCT-TTCTTTTTCTTTCTCTTCTTCTTTCTTTTCTT
1 TTTTTCTATTCTTTTTCTTTCTATTCTTCTTTCTTTTCTT
4141668 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 21 0.62
41 13 0.38
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (41 bp):
TTTTTCTATTCTTTTTCTTTCTATTCTTCTTTCTTTTCTTT
Found at i:4141648 original size:28 final size:29
Alignment explanation
Indices: 4141583--4141655 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
4141573 ACCTTGACCC
*
4141583 TTTTCTTTTTCTAT-TTTTTTTTCTTCTAT
1 TTTTCTTTCTCT-TCTTTTTTTTCTTCTAT
* * *
4141612 TTTTTTTTCTTTTCTTTTTTTTCTT-TCT
1 TTTTCTTTCTCTTCTTTTTTTTCTTCTAT
4141640 TTTTCTTTCTCTTCTT
1 TTTTCTTTCTCTTCTT
4141656 CTTTCTTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 17 0.46
29 20 0.54
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (29 bp):
TTTTCTTTCTCTTCTTTTTTTTCTTCTAT
Found at i:4141666 original size:12 final size:12
Alignment explanation
Indices: 4141601--4141668 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 12
4141591 TTCTATTTTT
4141601 TTTTCTTCTATT-
1 TTTTCTTCT-TTC
*
4141613 TTTTTTTCTTTTC
1 TTTTCTTC-TTTC
*
4141626 TTTTTTTTCTTTC
1 -TTTTCTTCTTTC
4141639 -TTT-TTCTTTC
1 TTTTCTTCTTTC
*
4141649 TCTTCTTCTTTC
1 TTTTCTTCTTTC
4141661 TTTTCTTC
1 TTTTCTTC
4141669 AAGCATAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
10 7 0.15
11 5 0.10
12 23 0.48
13 5 0.10
14 8 0.17
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:4141667 original size:15 final size:14
Alignment explanation
Indices: 4141583--4141668 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 14
4141573 ACCTTGACCC
4141583 TTTTC-TTT-TTCT
1 TTTTCTTTTCTTCT
*
4141595 ATTTTTTTTTCTTCT
1 -TTTTCTTTTCTTCT
*
4141610 ATTTTTTTTTCTT-T
1 -TTTTCTTTTCTTCT
*
4141624 TCTTTTTTTTCTTTCT
1 T-TTTCTTTTC-TTCT
4141640 TTTTCTTTCTCTTCT
1 TTTTCTTT-TCTTCT
4141655 TCTTTCTTTTCTTC
1 T-TTTCTTTTCTTC
4141669 AAGCATAATA
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.08
14 13 0.20
15 35 0.55
16 11 0.17
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTCTTCT
Found at i:4153888 original size:20 final size:21
Alignment explanation
Indices: 4153850--4153888 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4153840 GTTGGTATTA
**
4153850 GTTTGTTTTTTTCTTTTCTCT
1 GTTTGTTTTTTTCGGTTCTCT
4153871 GTTT-TTTTTTTCGGTTCT
1 GTTTGTTTTTTTCGGTTCT
4153889 GTTTCTGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (21 bp):
GTTTGTTTTTTTCGGTTCTCT
Found at i:4154384 original size:3 final size:3
Alignment explanation
Indices: 4154376--4154485 Score: 159
Period size: 3 Copynumber: 36.7 Consensus size: 3
4154366 TTAATATATT
* *
4154376 TAA TAA TAA -AA TAA TAA TAA TAA TAAA TAA AAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * *
4154421 TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4154469 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
4154486 TGGATAAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.02
3 90 0.95
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4156933 original size:51 final size:51
Alignment explanation
Indices: 4156764--4157056 Score: 301
Period size: 50 Copynumber: 5.9 Consensus size: 51
4156754 AATTCATACT
* * *
4156764 ACAAAAAA-AGTAGCATTTAACACATACTTACACCGATGTAAGTGAATAAA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
** * * * ** *
4156814 GTAAACAAGTGTATCACTTAACACAAACTTACACAAGTG-AAATGAATAAA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
* * *
4156864 ACAAAAAAGTGTATCACTTAACACATACTTACATCGGTGTAAATGAATAAA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
* * *
4156915 ACAAAAAAGTGTAGCACTTAACACATAC-TACATCAGTGTAAGTGAAT-TA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
* * * * * *
4156964 A-AAAAAATTATAGCACTTAACACATGCTTATAACGGTGTAAGTAAATAAA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
* * * *
4157014 ATAAAAAA-TGTATCACTTAGCACATACTTACACCGATGTAAGT
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGT
4157057 ATGCACATCT
Statistics
Matches: 201, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
48 23 0.11
49 17 0.08
50 94 0.47
51 67 0.33
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (51 bp):
ACAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAA
Found at i:4156961 original size:101 final size:98
Alignment explanation
Indices: 4156766--4157046 Score: 309
Period size: 101 Copynumber: 2.8 Consensus size: 98
4156756 TTCATACTAC
* * * * *
4156766 AAAAAAAG--TAGCATTTAACACATACTTACACCGATGTAAGTGAATAAAGTAAACAAGTGTATC
1 AAAAAAAGTATAGCACTTAACACATACTTACAACGGTGTAAGTGAATAAAATAAAAAAGTGTATC
*
4156829 ACTTAACACAAACTTACACAAGTGAAATGAATAAA
66 ACTTAACACATAC-TACACAAGTGAAATGAAT-AA
* * * * * *
4156864 ACAAAAAAGTGTATCACTTAACACATACTTACATCGGTGTAAATGAATAAAACAAAAAAGTGTAG
1 A-AAAAAAGTATAGCACTTAACACATACTTACAACGGTGTAAGTGAATAAAATAAAAAAGTGTAT
* *
4156929 CACTTAACACATACTACATC-AGTGTAAGTGAATTA
65 CACTTAACACATACTACA-CAAGTG-AAATGAATAA
* * * *
4156964 AAAAAAATTATAGCACTTAACACATGCTTATAACGGTGTAAGTAAATAAAATAAAAAA-TGTATC
1 AAAAAAAGTATAGCACTTAACACATACTTACAACGGTGTAAGTGAATAAAATAAAAAAGTGTATC
*
4157028 ACTTAGCACATACTTACAC
66 ACTTAACACATAC-TACAC
4157047 CGATGTAAGT
Statistics
Matches: 154, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
98 19 0.12
99 59 0.38
100 10 0.06
101 66 0.43
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.25
Consensus pattern (98 bp):
AAAAAAAGTATAGCACTTAACACATACTTACAACGGTGTAAGTGAATAAAATAAAAAAGTGTATC
ACTTAACACATACTACACAAGTGAAATGAATAA
Found at i:4158858 original size:12 final size:12
Alignment explanation
Indices: 4158837--4158872 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
4158827 TCACTTAAAA
4158837 ATAT-AAATAAT
1 ATATAAAATAAT
4158848 ATATAAAATAAT
1 ATATAAAATAAT
4158860 ATATAAAATAAT
1 ATATAAAATAAT
4158872 A
1 A
4158873 AAATAATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAAAATAAT
Found at i:4158875 original size:20 final size:21
Alignment explanation
Indices: 4158836--4158881 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
4158826 TTCACTTAAA
4158836 AATATAAATAATATATAAAAT
1 AATATAAATAATATATAAAAT
4158857 AATATATAA-AATA-ATAAAAT
1 AATATA-AATAATATATAAAAT
4158877 AATAT
1 AATAT
4158882 CATCAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.50
21 10 0.42
22 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATAAATAATATATAAAAT
Found at i:4159335 original size:14 final size:14
Alignment explanation
Indices: 4159328--4159387 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
4159318 AAACGAACAT
*
4159328 AAACAAACA-AATAT
1 AAACAAACATAA-AC
4159342 AAACAAACATAAAC
1 AAACAAACATAAAC
*
4159356 AAACAAATATAAAC
1 AAACAAACATAAAC
* *
4159370 GAACACA-ATAAAC
1 AAACAAACATAAAC
*
4159383 GAACA
1 AAACA
4159388 TAAATCATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
13 11 0.27
14 28 0.68
15 2 0.05
ACGTcount: A:0.68, C:0.18, G:0.03, T:0.10
Consensus pattern (14 bp):
AAACAAACATAAAC
Found at i:4159374 original size:24 final size:24
Alignment explanation
Indices: 4159287--4159374 Score: 122
Period size: 24 Copynumber: 3.6 Consensus size: 24
4159277 TCGTTCATTT
* **
4159287 AAATGATAAACGAAAATAAATGAAC
1 AAAT-ATAAACGAACATAAACAAAC
*
4159312 GAATATAAACGAACATAAACAAAC
1 AAATATAAACGAACATAAACAAAC
*
4159336 AAATATAAACAAACATAAACAAAC
1 AAATATAAACGAACATAAACAAAC
4159360 AAATATAAACGAACA
1 AAATATAAACGAACA
4159375 CAATAAACGA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
24 53 0.95
25 3 0.05
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (24 bp):
AAATATAAACGAACATAAACAAAC
Found at i:4159382 original size:13 final size:14
Alignment explanation
Indices: 4159343--4159387 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
4159333 AACAAATATA
* *
4159343 AACAAACATAAACA
1 AACAAATATAAACG
4159357 AACAAATATAAACG
1 AACAAATATAAACG
*
4159371 AACACA-ATAAACG
1 AACAAATATAAACG
4159384 AACA
1 AACA
4159388 TAAATCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.67, C:0.20, G:0.04, T:0.09
Consensus pattern (14 bp):
AACAAATATAAACG
Found at i:4160621 original size:15 final size:15
Alignment explanation
Indices: 4160603--4160633 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4160593 AAAGTGAACA
4160603 TATTTAAATAAAATT
1 TATTTAAATAAAATT
4160618 TATTTAAATAAAATT
1 TATTTAAATAAAATT
4160633 T
1 T
4160634 CATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTAAATAAAATT
Found at i:4161154 original size:27 final size:27
Alignment explanation
Indices: 4161124--4161175 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
4161114 TGTGTAAAAT
*
4161124 ATAAAAGTTTAAGGTTTTTTAAATATA
1 ATAAAAGTTTAAAGTTTTTTAAATATA
* *
4161151 ATAATATTTTAAAGTTTTTTAAATA
1 ATAAAAGTTTAAAGTTTTTTAAATA
4161176 AAAAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (27 bp):
ATAAAAGTTTAAAGTTTTTTAAATATA
Found at i:4162045 original size:29 final size:30
Alignment explanation
Indices: 4161950--4162114 Score: 176
Period size: 29 Copynumber: 5.6 Consensus size: 30
4161940 CCGAAGAGTA
* *
4161950 TCCCATGCATAATCAGGACGGGGAACGAAG
1 TCCCATGTAGAATCAGGACGGGGAACGAAG
* * *
4161980 TCCCATGCAGAATCAGGACAGGGAGCGAAG
1 TCCCATGTAGAATCAGGACGGGGAACGAAG
* * * *
4162010 TCTCATGTAGTATCA-GACGGGGAATGAAT
1 TCCCATGTAGAATCAGGACGGGGAACGAAG
* *
4162039 TCCCATGTAGAATCAGGACGGGTAA-AAAG
1 TCCCATGTAGAATCAGGACGGGGAACGAAG
*
4162068 TCCCATGTAGAATCAGGACAGGG-A-GTAAG
1 TCCCATGTAGAATCAGGACGGGGAACG-AAG
*
4162097 TCCCATGCAGAATCAGGA
1 TCCCATGTAGAATCAGGA
4162115 ATGCATCGAC
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
28 1 0.01
29 66 0.58
30 47 0.41
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (30 bp):
TCCCATGTAGAATCAGGACGGGGAACGAAG
Found at i:4162723 original size:13 final size:14
Alignment explanation
Indices: 4162705--4162742 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
4162695 AATGGGTAAA
4162705 AGTCAACGA-TCAG
1 AGTCAACGAGTCAG
4162718 AGTCAAC-AGTCAG
1 AGTCAACGAGTCAG
4162731 AGTCAACG-GTCA
1 AGTCAACGAGTCA
4162743 ATGGTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 22 0.96
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (14 bp):
AGTCAACGAGTCAG
Found at i:4168802 original size:29 final size:30
Alignment explanation
Indices: 4168764--4168919 Score: 133
Period size: 29 Copynumber: 5.3 Consensus size: 30
4168754 GATCCTATGT
* *
4168764 GAATTAGGACGGGGAATGAA-TTCCATGAA
1 GAATCAGGACGGGGAATGAAGTCCCATGAA
* * * * *
4168793 GTATCAGGACAGGGAATGGATTGCCATGCAA
1 GAATCAGGACGGGGAATGAAGTCCCATG-AA
* * *
4168824 -AATTAGGACGGGGAACGAAGTCCCATGTA
1 GAATCAGGACGGGGAATGAAGTCCCATGAA
*
4168853 GAATCAGG-CGGGGAATGAAGTCCCATGCA
1 GAATCAGGACGGGGAATGAAGTCCCATGAA
** *
4168882 GAATCAGGACAAGG-ACGAAGTCCCAT-ACA
1 GAATCAGGACGGGGAATGAAGTCCCATGA-A
4168911 GAATCAGGA
1 GAATCAGGA
4168920 ATGTATTGAT
Statistics
Matches: 102, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
29 65 0.64
30 35 0.34
31 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (30 bp):
GAATCAGGACGGGGAATGAAGTCCCATGAA
Found at i:4168867 original size:59 final size:60
Alignment explanation
Indices: 4168765--4168919 Score: 165
Period size: 59 Copynumber: 2.6 Consensus size: 60
4168755 ATCCTATGTG
* * * * * *
4168765 AATTAGGACGGGGAATGAA-TTCCATGAAGTATCAGGACAGGGAATGGATTGCCATGCAA
1 AATTAGGACGGGGAACGAAGTCCCATGAAGAATCAGGACAGGGAATGAAGTCCCATGCAA
* * *
4168824 AATTAGGACGGGGAACGAAGTCCCATGTAGAATCAGG-CGGGGAATGAAGTCCCATGCAG
1 AATTAGGACGGGGAACGAAGTCCCATGAAGAATCAGGACAGGGAATGAAGTCCCATGCAA
* **
4168883 AATCAGGACAAGG-ACGAAGTCCCAT-ACAGAATCAGGA
1 AATTAGGACGGGGAACGAAGTCCCATGA-AGAATCAGGA
4168920 ATGTATTGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
58 21 0.26
59 45 0.56
60 14 0.17
ACGTcount: A:0.36, C:0.17, G:0.30, T:0.16
Consensus pattern (60 bp):
AATTAGGACGGGGAACGAAGTCCCATGAAGAATCAGGACAGGGAATGAAGTCCCATGCAA
Found at i:4176639 original size:101 final size:101
Alignment explanation
Indices: 4176509--4176705 Score: 331
Period size: 101 Copynumber: 2.0 Consensus size: 101
4176499 GTGTTATTAT
* * *
4176509 GATCATCGTGAGTATTGTGGTTATGAAATAATCGGATGGTACTTTTACATAACTGTTGTTATTTC
1 GATCATCGTGAGTATTGTGGTTATGAAATAATCGGACGATACTTTTACATAACGGTTGTTATTTC
4176574 GATAATCGATCACAGTTTAAACCAATCCCTGGTTAA
66 GATAATCGATCACAGTTTAAACCAATCCCTGGTTAA
* * *
4176610 GATCATTGTGAGTATTTTGGTTATGAAATAATCGGACGATACTTTTACGTAACGGTTGTTATTTC
1 GATCATCGTGAGTATTGTGGTTATGAAATAATCGGACGATACTTTTACATAACGGTTGTTATTTC
*
4176675 GATAGTCGATCACAGTTTAAACCAATCCCTG
66 GATAATCGATCACAGTTTAAACCAATCCCTG
4176706 TTTATGAACA
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (101 bp):
GATCATCGTGAGTATTGTGGTTATGAAATAATCGGACGATACTTTTACATAACGGTTGTTATTTC
GATAATCGATCACAGTTTAAACCAATCCCTGGTTAA
Found at i:4185067 original size:65 final size:66
Alignment explanation
Indices: 4184996--4185131 Score: 247
Period size: 65 Copynumber: 2.1 Consensus size: 66
4184986 AGTTAGACCT
*
4184996 TTAAATTTTGATTTATTTTGATTTTGCCCCTATTTTCTATTGTTAATTATACTTTACCTCCCTG-
1 TTAAATTTTGATTTATTTTGATTTTACCCCTATTTTCTATTGTTAATTATACTTTACCTCCCTGA
4185060 A
66 A
*
4185061 TTAAATTTTGATTTATTTTGATTTTACCTCTATTTTCTATTGTTAATTATACTTTACCTCCCTGA
1 TTAAATTTTGATTTATTTTGATTTTACCCCTATTTTCTATTGTTAATTATACTTTACCTCCCTGA
4185126 A
66 A
4185127 TTAAA
1 TTAAA
4185132 ATCTTTGTTC
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 62 0.91
66 6 0.09
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (66 bp):
TTAAATTTTGATTTATTTTGATTTTACCCCTATTTTCTATTGTTAATTATACTTTACCTCCCTGA
A
Found at i:4185847 original size:2 final size:2
Alignment explanation
Indices: 4185840--4185873 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4185830 TTAAAATGTA
4185840 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
4185874 TTAGATTGTA
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):
AT
Found at i:4188073 original size:3 final size:3
Alignment explanation
Indices: 4188067--4188097 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4188057 ATTAATGCAT
4188067 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4188098 ATTTATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4204872 original size:3 final size:3
Alignment explanation
Indices: 4204866--4204909 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
4204856 TCAAAGTACA
4204866 ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT A
4204910 CTACTGCTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4207898 original size:20 final size:21
Alignment explanation
Indices: 4207843--4207935 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 21
4207833 TCAGATTGTT
4207843 CAGGGGGT-ACAGATTCCCCC
1 CAGGGGGTAACAGATTCCCCC
* *
4207863 CAGGGAG-AACAAATTCCCCC
1 CAGGGGGTAACAGATTCCCCC
*
4207883 CAGGGGGTATC-GATT--CCC
1 CAGGGGGTAACAGATTCCCCC
4207901 C---GGG-AACAGATTCCCCC
1 CAGGGGGTAACAGATTCCCCC
*
4207918 CA-GGGGTATC-GATTCCCC
1 CAGGGGGTAACAGATTCCCC
4207936 GGGTACAGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
14 2 0.03
15 7 0.12
17 4 0.07
18 4 0.07
19 11 0.19
20 28 0.48
21 2 0.03
ACGTcount: A:0.23, C:0.34, G:0.27, T:0.16
Consensus pattern (21 bp):
CAGGGGGTAACAGATTCCCCC
Found at i:4207924 original size:34 final size:35
Alignment explanation
Indices: 4207869--4207951 Score: 141
Period size: 34 Copynumber: 2.4 Consensus size: 35
4207859 CCCCCAGGGA
*
4207869 GAACAAATTCCCCCCAGGGGGTATCGATTCCCCGG
1 GAACAGATTCCCCCCAGGGGGTATCGATTCCCCGG
4207904 GAACAGATTCCCCCCA-GGGGTATCGATTCCCCGG
1 GAACAGATTCCCCCCAGGGGGTATCGATTCCCCGG
*
4207938 GTACAGATTCCCCC
1 GAACAGATTCCCCC
4207952 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 31 0.67
35 15 0.33
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (35 bp):
GAACAGATTCCCCCCAGGGGGTATCGATTCCCCGG
Found at i:4207946 original size:15 final size:15
Alignment explanation
Indices: 4207894--4207950 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
4207884 AGGGGGTATC
*
4207894 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
4207909 GATTCCCCCCAGGGGTATC-
1 GATT--CCCC--GGGTA-CA
4207928 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
4207943 GATTCCCC
1 GATTCCCC
4207951 CTGCATGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 17 0.49
17 8 0.23
19 8 0.23
20 1 0.03
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Done.