Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:413 original size:13 final size:13
Alignment explanation
Indices: 391--424 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
381 AGAGGAAGTA
*
391 ATTTTCAAAATTG
1 ATTTTCAAAAATG
404 A-TTTCAAAAATG
1 ATTTTCAAAAATG
416 ATTTTCAAA
1 ATTTTCAAA
425 GAAATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:4238 original size:31 final size:31
Alignment explanation
Indices: 4200--4354 Score: 210
Period size: 31 Copynumber: 5.0 Consensus size: 31
4190 CCCGAAGAAC
* * *
4200 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
4231 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
*
4262 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
*
4293 CAGTCAATATG-T-CCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
4323 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
4354 C
1 C
4355 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
30 29 0.26
31 83 0.73
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAA
Found at i:4338 original size:61 final size:62
Alignment explanation
Indices: 4200--4354 Score: 242
Period size: 61 Copynumber: 2.5 Consensus size: 62
4190 CCCGAAGAAC
* * * *
4200 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCAATATGTCCCGAAGAACATAGGTAAA
*
4262 CAGTCCATATATCCCGAAGAACATAGGTAAACAGTCAATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCAATATGTCCCGAAGAACATAGGTAAA
4323 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
1 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
4355 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
61 49 0.57
62 37 0.43
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (62 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCAATATGTCCCGAAGAACATAGGTAAA
Found at i:5317 original size:19 final size:19
Alignment explanation
Indices: 5293--5362 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
5283 TTTTATTTAG
5293 GGGGAATC-GATACCCCCCA
1 GGGGAATCTG-TACCCCCCA
*
5312 GGGGAATCTGT---TCCC-
1 GGGGAATCTGTACCCCCCA
5327 GGGGAATC-GATACCCCCCA
1 GGGGAATCTG-TACCCCCCA
5346 GGGGAATCTGTACCCCC
1 GGGGAATCTGTACCCCC
5363 TGGACATTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
14 1 0.02
15 9 0.21
16 3 0.07
18 3 0.07
19 24 0.57
20 2 0.05
ACGTcount: A:0.21, C:0.34, G:0.29, T:0.16
Consensus pattern (19 bp):
GGGGAATCTGTACCCCCCA
Found at i:8412 original size:31 final size:31
Alignment explanation
Indices: 8377--8532 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
8367 CCCGAAGGAC
* * *
8377 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
8408 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
8439 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
8470 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
8501 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
8532 C
1 C
8533 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:9510 original size:33 final size:34
Alignment explanation
Indices: 9468--9562 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 34
9458 TTATTTAGAG
*
9468 GGGAATCGATACCCCCTAGGGGAATCTGTTC-CC
1 GGGAATCGATACCCCCCAGGGGAATCTGTTCTCC
*
9501 GGGAATCGATACCCCCCAGGGGAATCT-TTCTCG
1 GGGAATCGATACCCCCCAGGGGAATCTGTTCTCC
9534 GGGAATCGATACCCCCCAGGGGAATCTGT
1 GGGAATCGATACCCCCCAGGGGAATCTGT
9563 ACCCCCTAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.05
33 54 0.93
34 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.20
Consensus pattern (34 bp):
GGGAATCGATACCCCCCAGGGGAATCTGTTCTCC
Found at i:39740 original size:23 final size:25
Alignment explanation
Indices: 39710--39762 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
39700 CTCCCACAAA
39710 TATTTGAACT-AA-TTTATATTATT
1 TATTTGAACTAAATTTTATATTATT
39733 TATTTGAACTAAATTTTATATTATT
1 TATTTGAACTAAATTTTATATTATT
39758 TATTT
1 TATTT
39763 TTCTTTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 10 0.36
24 2 0.07
25 16 0.57
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (25 bp):
TATTTGAACTAAATTTTATATTATT
Found at i:39860 original size:25 final size:23
Alignment explanation
Indices: 39832--39895 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
39822 TGGAGATCAT
39832 ACAATATAATATATAAAGAATAAAC
1 ACAATATAATATATAAAG--TAAAC
* *
39857 ACAAAAATAAT-TTTAAAGTAAAC
1 AC-AATATAATATATAAAGTAAAC
* *
39880 ACAATAAAATAAATAA
1 ACAATATAATATATAA
39896 TATCTAAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
22 6 0.19
23 10 0.32
25 8 0.26
26 7 0.23
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.23
Consensus pattern (23 bp):
ACAATATAATATATAAAGTAAAC
Found at i:43297 original size:29 final size:30
Alignment explanation
Indices: 43227--43299 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
43217 TTTCAAAAGT
43227 ACAAATCGGTCACTAACATTATTGATTATA
1 ACAAATCGGTCACTAACATTATTGATTATA
*
43257 ACAAATCGGTCACT-ATATTATTGATTTATA
1 ACAAATCGGTCACTAACATTATTGA-TTATA
43287 ACAAATC-GTCACT
1 ACAAATCGGTCACT
43300 CGCCGTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (30 bp):
ACAAATCGGTCACTAACATTATTGATTATA
Found at i:55642 original size:22 final size:25
Alignment explanation
Indices: 55616--55672 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
55606 GTTTCTTGTC
55616 ATATATTAAATTTTTAAACA-TAAT
1 ATATATTAAATTTTTAAACATTAAT
*
55640 ATAATATTAACTTTTTAAACATTAAAT
1 AT-ATATTAAATTTTTAAACATT-AAT
55667 ATATAT
1 ATATAT
55673 ATATCTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 2 0.07
25 17 0.59
26 5 0.17
27 5 0.17
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATATTAAATTTTTAAACATTAAT
Found at i:57459 original size:35 final size:35
Alignment explanation
Indices: 57413--57483 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
57403 GACGCATCTT
*
57413 GCACGTAAGTTCCGGCAGCAGTTGATGAAGTGTGC
1 GCACGTAAGTTCCGGCAGCAGTTGATGAAGTATGC
57448 GCACGTAAGTTCCGGCAGCAGTTGATGAAGTATGC
1 GCACGTAAGTTCCGGCAGCAGTTGATGAAGTATGC
57483 G
1 G
57484 TCCCGTGTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (35 bp):
GCACGTAAGTTCCGGCAGCAGTTGATGAAGTATGC
Found at i:63430 original size:23 final size:23
Alignment explanation
Indices: 63404--63449 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
63394 CACCACAGCT
*
63404 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
63427 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
63450 TATAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:63812 original size:2 final size:2
Alignment explanation
Indices: 63805--63832 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
63795 AGTCATATGA
63805 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
63833 CTTATGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72243 original size:17 final size:18
Alignment explanation
Indices: 72204--72243 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
72194 TCAAAATTAG
* *
72204 AATATATGCTTCAGAATA
1 AATATATGATTCAGAAAA
72222 AATATATGATTC-GAAAA
1 AATATATGATTCAGAAAA
72239 AATAT
1 AATAT
72244 TGTTATTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (18 bp):
AATATATGATTCAGAAAA
Found at i:73577 original size:40 final size:41
Alignment explanation
Indices: 73512--73661 Score: 114
Period size: 40 Copynumber: 3.7 Consensus size: 41
73502 TGCGATCGAT
* *
73512 AATTCGCAACGCGATCTCCG-GTATCGCAAAT-C-AGTTTCC
1 AATTCGCAACGCGAT-TCTGACTATCGCAAATGCGAGTTTCC
* * *
73551 AGATTCGCAACGCGATTCTGACTATCGC-ATTGCGATTTTCT
1 A-ATTCGCAACGCGATTCTGACTATCGCAAATGCGAGTTTCC
* * * * *
73592 AAATCGCAATGCGATTCTGACTATCGC-AATACTGAATTTCA
1 AATTCGCAACGCGATTCTGACTATCGCAAATGC-GAGTTTCC
* *
73633 AATTCGCAACTCGATTTCTGAAT-TCGCAA
1 AATTCGCAACGCGA-TTCTGACTATCGCAA
73662 CAGGTTTTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
39 6 0.07
40 48 0.54
41 27 0.30
42 8 0.09
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (41 bp):
AATTCGCAACGCGATTCTGACTATCGCAAATGCGAGTTTCC
Found at i:73578 original size:20 final size:20
Alignment explanation
Indices: 73555--73621 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
73545 GTTTCCAGAT
*
73555 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
73575 TCGCATTGCGATTTTCT-A-AA
1 TCGCAATGCGA--TTCTGACTA
73595 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
73615 TCGCAAT
1 TCGCAAT
73622 ACTGAATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 28 0.74
21 1 0.03
22 4 0.11
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:74515 original size:24 final size:24
Alignment explanation
Indices: 74457--74503 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
74447 AGTCAGTATT
*
74457 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
74481 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
74504 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:76928 original size:20 final size:20
Alignment explanation
Indices: 76903--76952 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
76893 ATCTTAATGT
76903 CTATCGCAACGCAGAAAT-AA
1 CTATCGCAACGC-GAAATGAA
*
76923 CTATCGCAATGCGAAATGAA
1 CTATCGCAACGCGAAATGAA
*
76943 -AATCGCAACG
1 CTATCGCAACG
76953 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAATGAA
Found at i:76947 original size:19 final size:18
Alignment explanation
Indices: 76925--77022 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
76915 AGAAATAACT
76925 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
76944 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
76958 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
76977 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
76991 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
77010 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
77023 TTTAGTTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
14 17 0.27
15 4 0.06
16 4 0.06
17 4 0.06
18 4 0.06
19 29 0.47
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:76967 original size:33 final size:33
Alignment explanation
Indices: 76925--77018 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
76915 AGAAATAACT
76925 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
76958 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
76991 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
77019 CGAATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:77040 original size:19 final size:19
Alignment explanation
Indices: 77018--77113 Score: 80
Period size: 19 Copynumber: 5.3 Consensus size: 19
77008 AAATCGCAAC
77018 GCGA-ATTTAGTTTCGCGTT
1 GCGATATTTA-TTTCGCGTT
*
77037 GCG--ATTT-TGTCG--TT
1 GCGATATTTATTTCGCGTT
*
77051 GCGATTTTTATTTCGCGTT
1 GCGATATTTATTTCGCGTT
*
77070 GCGATTTTTATTTCGCGTT
1 GCGATATTTATTTCGCGTT
**
77089 GCGAT-TTTCATTTCGAATT
1 GCGATATTT-ATTTCGCGTT
77108 GCGATA
1 GCGATA
77114 GTCATTTTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.08
16 7 0.11
17 4 0.06
18 7 0.11
19 42 0.65
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.47
Consensus pattern (19 bp):
GCGATATTTATTTCGCGTT
Found at i:77238 original size:14 final size:14
Alignment explanation
Indices: 77219--77255 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
77209 CATCAATTAA
77219 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
77233 ACAAATCATCTTTT
1 ACAAATCAACTTTT
77247 ACAAATCAA
1 ACAAATCAA
77256 TTAAACAATC
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:78666 original size:21 final size:21
Alignment explanation
Indices: 78600--78666 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
78590 GTGAATCGGG
*
78600 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
78620 CCTCTTCAACGATGATAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
78642 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
78663 CTCT
1 CTCT
78667 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:78677 original size:42 final size:41
Alignment explanation
Indices: 78600--78718 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 41
78590 GTGAATCGGG
* * *
78600 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGAT-AGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAAG-GGC
78642 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAAGGGC
* * * * *
78684 CTCTTAAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGA
78719 CAGGCGAGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
41 4 0.06
42 53 0.82
43 8 0.12
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAAGGGC
Found at i:79265 original size:19 final size:19
Alignment explanation
Indices: 79219--79342 Score: 133
Period size: 19 Copynumber: 7.0 Consensus size: 19
79209 TCTTTTGGTT
*
79219 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
79238 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
79258 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
79275 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
79291 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
79308 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAACGC
79324 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
79343 AATTATAGTT
Statistics
Matches: 88, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
14 20 0.23
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 38 0.43
20 18 0.20
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:79285 original size:14 final size:14
Alignment explanation
Indices: 79266--79320 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
79256 GCGAAATGAA
79266 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
79280 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
79299 AATCGCAACGAGAG
1 AATCGCAACGAGAG
79313 AATCGCAA
1 AATCGCAA
79321 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:79289 original size:33 final size:33
Alignment explanation
Indices: 79219--79341 Score: 183
Period size: 33 Copynumber: 3.5 Consensus size: 33
79209 TCTTTTGGTT
79219 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
79258 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
79291 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
79324 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
79342 CAATTATAGT
Statistics
Matches: 83, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
33 61 0.73
35 1 0.01
36 1 0.01
37 3 0.04
39 17 0.20
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:79375 original size:20 final size:20
Alignment explanation
Indices: 79350--79426 Score: 86
Period size: 19 Copynumber: 3.9 Consensus size: 20
79340 CGCAATTATA
*
79350 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTC
79370 GTTTCGCGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
* *
79389 ATTTCGCTTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
* *
79408 ATTCTCTCGTTGCGATTTT
1 GTT-TCGCGTTGCGATTTT
79427 CATTTCAACC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 24 0.48
20 23 0.46
21 3 0.06
ACGTcount: A:0.08, C:0.19, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTC
Found at i:79394 original size:39 final size:39
Alignment explanation
Indices: 79351--79432 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
79341 GCAATTATAG
**
79351 TTTCGCGTTGCGATTTTTGGTT-TCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTTCATTCTCGCGTTGCGATTTTCA
* *
79390 TTTCGCTTTGCGATTTTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCATTCTCGCGTTGCGATTTTCA
79429 TTTC
1 TTTC
79433 AACCAAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 6 0.16
39 32 0.84
ACGTcount: A:0.09, C:0.21, G:0.20, T:0.51
Consensus pattern (39 bp):
TTTCGCGTTGCGATTTTCATTCTCGCGTTGCGATTTTCA
Found at i:79427 original size:20 final size:19
Alignment explanation
Indices: 79351--79432 Score: 110
Period size: 20 Copynumber: 4.2 Consensus size: 19
79341 GCAATTATAG
**
79351 TTTCGCGTTGCGATTTTTGG
1 TTTCGCGTTGCGA-TTTTCA
79371 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
79390 TTTCGCTTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
79409 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
79429 TTTC
1 TTTC
79433 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
19 26 0.46
20 30 0.54
ACGTcount: A:0.09, C:0.21, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:79631 original size:94 final size:94
Alignment explanation
Indices: 79522--79901 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
79512 ATGGATTGCA
* * *
79522 TTAC-TTCAACTAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
79586 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
79615 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
79680 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
79709 TTACTTTCAACCAAAAGACAAAACAAAGACAAAAACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
79774 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
79803 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
79867 TTTAGCAGTATTGGTAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
79897 TTACT
1 TTACT
79902 AAGCAATCTA
Statistics
Matches: 274, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
93 23 0.08
94 251 0.92
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:81624 original size:20 final size:20
Alignment explanation
Indices: 81599--81692 Score: 98
Period size: 20 Copynumber: 5.2 Consensus size: 20
81589 TTTTGGTTGA
81599 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
81619 AATGAAAATCGCAACGCGAG
1 AATGAAAATCGCAACGAGAG
81639 AATG--AATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
* *
81655 -A-G--ACTCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
81670 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
81690 AAT
1 AAT
81693 CGCAACGCGA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 6 0.10
17 1 0.02
18 9 0.14
19 11 0.17
20 26 0.41
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:81685 original size:33 final size:32
Alignment explanation
Indices: 81625--81715 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 32
81615 AGAGAATGAA
81625 AATCGCAACGCGAGAATG-AATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAATCGCAACGAGAG
*
81657 ACTCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATG-AAATCGCAACGAGAG
81690 AATCGCAACGCGAAATGAAATCGCAA
1 AATCGCAACGCGAAATGAAATCGCAA
81716 TGCGATCGCG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 4 0.07
32 21 0.38
33 30 0.55
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.10
Consensus pattern (32 bp):
AATCGCAACGCGAAATGAAATCGCAACGAGAG
Found at i:81695 original size:14 final size:14
Alignment explanation
Indices: 81642--81699 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
81632 ACGCGAGAAT
81642 GAATCGCAACGAGA
1 GAATCGCAACGAGA
*
81656 GACTCGCAACGCGAAATGA
1 GAATCGCAA--CG--A-GA
*
81675 AAATCGCAACGAGA
1 GAATCGCAACGAGA
81689 GAATCGCAACG
1 GAATCGCAACG
81700 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:81714 original size:51 final size:51
Alignment explanation
Indices: 81597--81720 Score: 130
Period size: 51 Copynumber: 2.4 Consensus size: 51
81587 TCTTTTGGTT
* *
81597 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGCGAGAATGAATCGC
1 GAAATG-AAATCGCAACGCGAGAATGAAAATCGCAACGAGAGAATGAATCGC
*
81649 -AACGA-GAGACTCGCAACGCGA-AATGAAAATCGCAACGAGAGAATCGCAA-CGC
1 GAA--ATGA-AATCGCAACGCGAGAATGAAAATCGCAACGAGAGAAT-G-AATCGC
*
81701 GAAATGAAATCGCAATGCGA
1 GAAATGAAATCGCAACGCGA
81721 TCGCGTTGCG
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
51 37 0.62
52 18 0.30
53 5 0.08
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.10
Consensus pattern (51 bp):
GAAATGAAATCGCAACGCGAGAATGAAAATCGCAACGAGAGAATGAATCGC
Found at i:81758 original size:33 final size:33
Alignment explanation
Indices: 81721--81788 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
81711 CGCAATGCGA
*
81721 TCGCGTTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTATCTCGTTGCAATTTTCATT
*
81754 TCGCGTTGCGATTCTCTCGTTGCAATTTTCATT
1 TCGCGTTGCGATTATCTCGTTGCAATTTTCATT
81787 TC
1 TC
81789 TCTCGTTGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TCGCGTTGCGATTATCTCGTTGCAATTTTCATT
Found at i:81791 original size:21 final size:21
Alignment explanation
Indices: 81765--81828 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
81755 CGCGTTGCGA
*
81765 TTCTCTCGTTGCAATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
81786 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
81807 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
81827 TT
1 TT
81829 TCATGTTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:81818 original size:20 final size:20
Alignment explanation
Indices: 81793--81835 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
81783 CATTTCTCTC
*
81793 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCAT
**
81813 GTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
81833 GTT
1 GTT
81836 TAGAAACTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:82407 original size:21 final size:21
Alignment explanation
Indices: 82381--82464 Score: 159
Period size: 21 Copynumber: 4.0 Consensus size: 21
82371 CGATAGTCAG
82381 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
82402 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
82423 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
*
82444 ATTCGCATTGTGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
82465 TTTAGGATCG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTCCTA
Found at i:86280 original size:16 final size:17
Alignment explanation
Indices: 86259--86291 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
86249 TTACTATTCA
86259 CATGAATAGT-AAATTT
1 CATGAATAGTGAAATTT
86275 CATGAATAGTGAAATTT
1 CATGAATAGTGAAATTT
86292 TATCGGTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (17 bp):
CATGAATAGTGAAATTT
Found at i:93567 original size:14 final size:14
Alignment explanation
Indices: 93548--93927 Score: 265
Period size: 14 Copynumber: 27.8 Consensus size: 14
93538 TTTACTATTA
*
93548 TTAAATTATTAAAG
1 TTAAATCATTAAAG
93562 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
93576 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
93590 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
93604 TTAAATTATTAAAA
1 TTAAATCATTAAAG
93618 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
93632 TTAAATAATT--A-
1 TTAAATCATTAAAG
*
93643 TTAAATTATTAAAG
1 TTAAATCATTAAAG
*
93657 TTAAATTATTAAAG
1 TTAAATCATTAAAG
93671 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
93685 TTAAATCATTATTA-
1 TTAAATCATTA-AAG
93699 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
93713 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
93727 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * * *
93741 TTAAGTAATGATTA-
1 TTAAATCATTA-AAG
* * *
93755 TTAAATTATTTAAT
1 TTAAATCATTAAAG
93769 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
93783 TTAAATAATT--A-
1 TTAAATCATTAAAG
*
93794 TT--A-C-TAAATAG
1 TTAAATCATTAA-AG
*
93805 TTAAAT-ATTTATTAG
1 TTAAATCA-TTA-AAG
93820 -TAAATCATTAAAG
1 TTAAATCATTAAAG
* * * *
93833 TTAAGTAATGATTA-
1 TTAAATCATTA-AAG
* * *
93847 TTAAATTATTTAAT
1 TTAAATCATTAAAG
93861 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
93875 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
93889 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
93903 TTAAATCATTAAAT
1 TTAAATCATTAAAG
*
93917 TTAAATAATTA
1 TTAAATCATTA
93928 TTATTAAATA
Statistics
Matches: 285, Mismatches: 54, Indels: 54
0.73 0.14 0.14
Matches are distributed among these distances:
7 1 0.00
9 1 0.00
10 1 0.00
11 13 0.05
12 2 0.01
13 10 0.04
14 246 0.86
15 11 0.04
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:93580 original size:28 final size:27
Alignment explanation
Indices: 93548--93927 Score: 292
Period size: 28 Copynumber: 13.9 Consensus size: 27
93538 TTTACTATTA
*
93548 TTAAATTATTAAAGTTAAATCATTAAAG
1 TTAAATAATTAAA-TTAAATCATTAAAG
*
93576 TTAAATAATTATTATTAAATCATTAAAG
1 TTAAATAATTA-AATTAAATCATTAAAG
*
93604 TTAAATTATTAAAATTAAATCATTAAAG
1 TTAAATAATT-AAATTAAATCATTAAAG
*
93632 TTAAATAATT--ATTAAATTATTAAAG
1 TTAAATAATTAAATTAAATCATTAAAG
*
93657 TTAAATTATTAAAGTTAAATCATTAAAG
1 TTAAATAATTAAA-TTAAATCATTAAAG
* *
93685 TTAAATCATTATTATTAAATCATTAAAG
1 TTAAATAATTA-AATTAAATCATTAAAG
*
93713 TTAAATAATTATTATTAAATCATTAAAG
1 TTAAATAATTA-AATTAAATCATTAAAG
* * * * * *
93741 TTAAGTAATGATTATTAAATTATTTAAT
1 TTAAATAATTA-AATTAAATCATTAAAG
* * *
93769 TTAAATCATTAAAGTTAAATAATTATTA-
1 TTAAATAATTAAA-TTAAATCATTA-AAG
* * * *
93797 CTAAATAGTTAAA-T-ATTTATT--AG
1 TTAAATAATTAAATTAAATCATTAAAG
* * * * *
93820 -TAAATCATTAAAGTTAAGTAATGATTA-
1 TTAAATAATTAAA-TTAAATCATTA-AAG
* *
93847 TTAAATTATTTAATTTAAATCATTAAAG
1 TTAAA-TAATTAAATTAAATCATTAAAG
*
93875 TTAAATAATTATTATTAAATCATTAAAG
1 TTAAATAATTA-AATTAAATCATTAAAG
* *
93903 TTAAATCATTAAATTTAAATAATTA
1 TTAAATAATTAAA-TTAAATCATTA
93928 TTATTAAATA
Statistics
Matches: 286, Mismatches: 46, Indels: 40
0.77 0.12 0.11
Matches are distributed among these distances:
22 11 0.04
24 1 0.00
25 32 0.11
26 1 0.00
27 9 0.03
28 223 0.78
29 9 0.03
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (27 bp):
TTAAATAATTAAATTAAATCATTAAAG
Found at i:93591 original size:42 final size:42
Alignment explanation
Indices: 93543--93936 Score: 356
Period size: 42 Copynumber: 9.3 Consensus size: 42
93533 ATATCTTTAC
93543 TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
1 TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
* * * *
93585 TATTATTAAATCATTAAAGTTAAATTATTAAAATTAAATCAT
1 TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
* * * *
93627 TA-AAGTTAAATAATT--A-TTAAATTATTAAAGTTAAATTAT
1 TATTA-TTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
* * * *
93666 TA-AAGTTAAATCATTAAAGTTAAATCATTATTA-TTAAATCAT
1 TATTA-TTAAATTATTAAAGTTAAATCATTA-AAGTTAAATAAT
* * * *
93708 TA-AAGTTAAATAATTATTA-TTAAATCATTAAAGTTAAGTAAT
1 TATTA-TTAAATTATTA-AAGTTAAATCATTAAAGTTAAATAAT
* * *
93750 GATTATTAAATTATTTAATTTAAATCATTAAAGTTAAATAAT
1 TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
* * *
93792 TATTACTAAA-TAGTTAAATATTTATTAGTAAATCATTAAAGTTAAGTAAT
1 TATTATTAAATTA-TT--A-A---AGT--TAAATCATTAAAGTTAAATAAT
* * *
93842 GATTATTAAATTATTTAATTTAAATCATTAAAGTTAAATAAT
1 TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
* *
93884 TATTATTAAATCATTAAAGTTAAATCATTAAATTTAAATAAT
1 TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
93926 TATTATTAAAT
1 TATTATTAAAT
93937 ATATACTCGA
Statistics
Matches: 297, Mismatches: 36, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
39 35 0.12
40 1 0.00
41 6 0.02
42 211 0.71
43 3 0.01
44 3 0.01
45 1 0.00
47 1 0.00
48 3 0.01
50 31 0.10
51 2 0.01
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (42 bp):
TATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATAAT
Found at i:99947 original size:21 final size:21
Alignment explanation
Indices: 99921--100068 Score: 102
Period size: 21 Copynumber: 7.0 Consensus size: 21
99911 CCACGTAGAA
99921 ATGTCCCGAAGGACCACATAT
1 ATGTCCCGAAGGACCACATAT
* *
99942 ATGTCCCGAATGACCACATAAA
1 ATGTCCCGAAGGACCACAT-AT
**
99964 AT-TCTCTTTAAGGACCACATAT
1 ATGTC-C-CGAAGGACCACATAT
* * *
99986 ATATTCC-AATGGACCAAATAT
1 ATGTCCCGAA-GGACCACATAT
** * *
100007 ATGTTTCGAAGTACCGCATAT
1 ATGTCCCGAAGGACCACATAT
* * * **
100028 ATGTTCCAAATGATTACATAT
1 ATGTCCCGAAGGACCACATAT
100049 ATGTCCCGAAGGACCACATA
1 ATGTCCCGAAGGACCACATA
100069 GAACCCTCGA
Statistics
Matches: 95, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
20 2 0.02
21 72 0.76
22 10 0.11
23 11 0.12
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAT
Found at i:100284 original size:15 final size:15
Alignment explanation
Indices: 100264--100308 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
100254 TGATCATGTA
100264 ATCACATAACTTATT
1 ATCACATAACTTATT
* *
100279 ATCACATAGCTCA-T
1 ATCACATAACTTATT
100293 AGTCACATAACTTATT
1 A-TCACATAACTTATT
100309 TCATTTCTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 2 0.08
15 21 0.88
16 1 0.04
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (15 bp):
ATCACATAACTTATT
Found at i:102341 original size:41 final size:40
Alignment explanation
Indices: 102234--102354 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 40
102224 GCAATACAAA
*
102234 TGTTTATAGTGGTGTTTTTCAACAAACGCCACAATAGAGT
1 TGTTTATAGTGGTGTTTTTCAACAAACGCCGCAATAGAGT
* * * * *
102274 GGTAATT-TAGCGGAGTTTTT-ACACAAACGCCGCGATAGTGT
1 TGT--TTATAGTGGTGTTTTTCA-ACAAACGCCGCAATAGAGT
* *
102315 TGTTTATAGTGGTGTTTGTTCAACAAACGACGCTATAGAG
1 TGTTTATAGTGGTGTTT-TTCAACAAACGCCGCAATAGAG
102355 AAGTAATTTC
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
39 2 0.03
40 12 0.19
41 46 0.73
42 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (40 bp):
TGTTTATAGTGGTGTTTTTCAACAAACGCCGCAATAGAGT
Found at i:102416 original size:83 final size:82
Alignment explanation
Indices: 102234--102409 Score: 219
Period size: 82 Copynumber: 2.1 Consensus size: 82
102224 GCAATACAAA
* ** * *
102234 TGTTTATAGTGGTGTTT-TTCAACAAACGCCACAATAGAGTGGTAATTTAGCGGAGTTTTTACAC
1 TGTTTATAGTGGTGTTTGTTCAACAAACGACACAATAGAGAAGTAATTTAGCGGAGTTTTCAAAC
* * *
102298 AAACGCCGCGATAGTGT
66 AAACACCGCAATAGTAT
* * * *
102315 TGTTTATAGTGGTGTTTGTTCAACAAACGACGCTATAGAGAAGTAATTTCGCGGTGTTTATCAAA
1 TGTTTATAGTGGTGTTTGTTCAACAAACGACACAATAGAGAAGTAATTTAGCGGAGTTT-TCAAA
102380 CAAACACCGCAATAGTAT
65 CAAACACCGCAATAGTAT
*
102398 TTTTTATAGTGG
1 TGTTTATAGTGG
102410 CATTTGTGCG
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 17 0.21
82 34 0.43
83 29 0.36
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (82 bp):
TGTTTATAGTGGTGTTTGTTCAACAAACGACACAATAGAGAAGTAATTTAGCGGAGTTTTCAAAC
AAACACCGCAATAGTAT
Found at i:112160 original size:20 final size:21
Alignment explanation
Indices: 112132--112183 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
112122 GGGTAGACAT
* *
112132 TTTAAATTTACC-TGACTTTA
1 TTTATATTTACCATGACATTA
112152 TTTATATTTGTACCATGACATTA
1 TTTATA-TT-TACCATGACATTA
112175 TTTAT-TTTA
1 TTTATATTTA
112184 ATGATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 7 0.26
21 4 0.15
22 4 0.15
23 12 0.44
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTATATTTACCATGACATTA
Found at i:112998 original size:44 final size:43
Alignment explanation
Indices: 112878--112999 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 43
112868 CATATATTTA
* *
112878 GCGGCGTTTGTAT-C-AAAAGATGTCGCTATATACCAGACTATC
1 GCGGCGTTTGTATCCTAAAA-ACGCCGCTATATACCAGACTATC
* ** *
112920 GCGGCGTTTGTATCCTAAAAATGCCATTTTATACCAGAACTATC
1 GCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAG-ACTATC
* *
112964 GCGGCTTTTGTATCCTAAAAACGCCGCTAAATACCA
1 GCGGCGTTTGTATCCTAAAAACGCCGCTATATACCA
113000 TACCTTTAGC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 13 0.19
43 14 0.21
44 40 0.60
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
GCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACTATC
Found at i:113088 original size:43 final size:43
Alignment explanation
Indices: 113041--113125 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
113031 GCGAAATCTC
* * * *
113041 AACACTTATTGCGGCGTTTGTGATAAAAACACCGCTAAATATT
1 AACACCTATTGCGGCATTTGTAAGAAAAACACCGCTAAATATT
* * *
113084 AACACCTATTGCGGCATTTTTAAGACAAACACCGCTATATAT
1 AACACCTATTGCGGCATTTGTAAGAAAAACACCGCTAAATAT
113126 CGTTACCTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (43 bp):
AACACCTATTGCGGCATTTGTAAGAAAAACACCGCTAAATATT
Found at i:115993 original size:218 final size:220
Alignment explanation
Indices: 115611--116049 Score: 832
Period size: 218 Copynumber: 2.0 Consensus size: 220
115601 TTTTACCCTC
115611 TCATTTTATTATTTATTTTTCAATATTTACTTTTATATAATTTTTTGCTTCAATAAAATTATTTA
1 TCATTTTATTATTTATTTTTCAATATTTACTTTTATATAATTTTTTGCTTCAATAAAATTATTTA
115676 TTTTATACATGGATAATTTATTTTTTTGATATTTATATTATAGAATTATATGTTATAAATTTAAT
66 TTTTATACATGGATAATTTATTTTTTTGATATTTATATTATAGAATTATATGTTATAAATTTAAT
115741 TCTTATGTGATAAAAAATATATTATAAGGGTAAACTTATGATCAAAATGAAAAAAATAATAAACT
131 TCTTATGTGATAAAAAATATATTATAAGGGTAAACTTATGATCAAAATG-AAAAAATAATAAACT
115806 GAAACCAAAAAAGAAAACGATAATGAT
195 GAAACC-AAAAAGAAAACGATAATGAT
115833 TCATTTTATTATTTATTTTTCAATATTTAC-TTT-TATAA-TTTTTGCTTCAATAAAATTATTTA
1 TCATTTTATTATTTATTTTTCAATATTTACTTTTATATAATTTTTTGCTTCAATAAAATTATTTA
115895 -TTTATACATGGATAATTTATTTTTTTGATATTTATATTATAGAATTATATGTTATAAATTTAAT
66 TTTTATACATGGATAATTTATTTTTTTGATATTTATATTATAGAATTATATGTTATAAATTTAAT
115959 TCTTATGTGATAAAAAATATATTATAAGGGTAAACTTATGATCAAAATGAAAAAATAATAAACTG
131 TCTTATGTGATAAAAAATATATTATAAGGGTAAACTTATGATCAAAATGAAAAAATAATAAACTG
116024 AAACCAAAAAGAAAACGATAATGAT
196 AAACCAAAAAGAAAACGATAATGAT
116049 T
1 T
116050 TGATGATTAA
Statistics
Matches: 217, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
216 21 0.10
217 21 0.10
218 113 0.52
219 24 0.11
220 5 0.02
221 3 0.01
222 30 0.14
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (220 bp):
TCATTTTATTATTTATTTTTCAATATTTACTTTTATATAATTTTTTGCTTCAATAAAATTATTTA
TTTTATACATGGATAATTTATTTTTTTGATATTTATATTATAGAATTATATGTTATAAATTTAAT
TCTTATGTGATAAAAAATATATTATAAGGGTAAACTTATGATCAAAATGAAAAAATAATAAACTG
AAACCAAAAAGAAAACGATAATGAT
Found at i:119263 original size:20 final size:20
Alignment explanation
Indices: 119238--119276 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
119228 TTTTCAAGGG
119238 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
119258 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
119277 TAATTTCTTG
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:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:125161 original size:44 final size:44
Alignment explanation
Indices: 125088--125184 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
125078 TTGTGCTTAA
* * * *
125088 TGCATCGATACACTTAACAGTGCATCGATGCATC-CCTTTGATTG
1 TGCATCGATACACTCAACAGTGCACCGATGCA-CGCCCTTGAATG
*
125132 TGCATCGATACA-TCAACTGATGCACCGATGCACGCCCTTGAATG
1 TGCATCGATACACTCAACAG-TGCACCGATGCACGCCCTTGAATG
125176 TGCATCGAT
1 TGCATCGAT
125185 GCAGAAGAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 6 0.13
44 40 0.87
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTCAACAGTGCACCGATGCACGCCCTTGAATG
Found at i:127693 original size:45 final size:46
Alignment explanation
Indices: 127644--127734 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
127634 GAACATCGAA
* *
127644 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
127689 TGCATTTGATGCATCGATGCACAAGACCATGCATTGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
127735 GCTATTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:130772 original size:14 final size:14
Alignment explanation
Indices: 130753--130782 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
130743 AGGTTATATC
130753 TGAGGGTATTTGGG
1 TGAGGGTATTTGGG
130767 TGAGGGTATTTGGG
1 TGAGGGTATTTGGG
130781 TG
1 TG
130783 GATCCGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.50, T:0.37
Consensus pattern (14 bp):
TGAGGGTATTTGGG
Found at i:131252 original size:20 final size:20
Alignment explanation
Indices: 131224--131320 Score: 133
Period size: 20 Copynumber: 4.8 Consensus size: 20
131214 AATAATATTG
*
131224 TACTATATGAATAGTACTA-A
1 TACTGTATGAATAGTAC-AGA
*
131244 TACTGTATGAATAGTATAGA
1 TACTGTATGAATAGTACAGA
*
131264 TACTGTATGAATAGTACATA
1 TACTGTATGAATAGTACAGA
*
131284 TACTATATGAATAGTACAGA
1 TACTGTATGAATAGTACAGA
*
131304 TACTGTATGAACAGTAC
1 TACTGTATGAATAGTAC
131321 CGATGCTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.01
20 67 0.99
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
TACTGTATGAATAGTACAGA
Found at i:131276 original size:40 final size:40
Alignment explanation
Indices: 131210--131320 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
131200 AAAATGTTTT
* * * *
131210 TATGAATAATATTG-TACTATATGAATAGTAC-TAATACTG
1 TATGAATAGTATAGATACTGTATGAATAGTACAT-ATACTA
131249 TATGAATAGTATAGATACTGTATGAATAGTACATATACTA
1 TATGAATAGTATAGATACTGTATGAATAGTACATATACTA
* *
131289 TATGAATAGTACAGATACTGTATGAACAGTAC
1 TATGAATAGTATAGATACTGTATGAATAGTAC
131321 CGATGCTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 12 0.19
40 51 0.80
41 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (40 bp):
TATGAATAGTATAGATACTGTATGAATAGTACATATACTA
Found at i:134976 original size:20 final size:19
Alignment explanation
Indices: 134905--134976 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
134895 TAAAAGTAGG
*
134905 TTTAAAT-TTTATTTATTT
1 TTTAAATATATATTTATTT
* * *
134923 TTTAAATTTAAATTTTATAT
1 TTTAAATATATA-TTTATTT
* *
134943 TTTAACTCAAATATTTATTT
1 TTTAAAT-ATATATTTATTT
134963 TATTAAATATATAT
1 T-TTAAATATATAT
134977 ATATATATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 7 0.17
19 2 0.05
20 24 0.60
21 7 0.17
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAAATATATATTTATTT
Found at i:138289 original size:51 final size:51
Alignment explanation
Indices: 138170--138362 Score: 316
Period size: 51 Copynumber: 3.8 Consensus size: 51
138160 GATGTACGTT
138170 CTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCA
1 CTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCA
*
138221 CTTACATC-GTGTAAGTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCA
1 CTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCA
* * * *
138271 CTTACACCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTATTTTATTCA
1 CTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCA
* *
138322 CTTACATCGGTGTATGTATGTGTTAAGTGCTACATTTTTTT
1 CTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTT
138363 GTAGTATGAA
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
50 48 0.37
51 81 0.63
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (51 bp):
CTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCA
Found at i:138360 original size:101 final size:101
Alignment explanation
Indices: 138170--138364 Score: 327
Period size: 101 Copynumber: 1.9 Consensus size: 101
138160 GATGTACGTT
* * *
138170 CTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACATCGTGTAA
1 CTTACACCGGTGTAAGTATGTATTAAGTGCTACACTTGTTTATTTTATTCACTTACATCGTGTAA
138235 GTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCA
66 GTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCA
*
138271 CTTACACCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTATTTTATTCACTTACATCGGTGTA
1 CTTACACCGGTGTAAGTATGTATTAAGTGCTACACTTGTTTATTTTATTCACTTACATC-GTGTA
* *
138336 TGTATGTGTTAAGTGCTACATTTTTTTGT
65 AGTATGTGTTAAGTGCTACACTTTTTTGT
138365 AGTATGAATT
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 55 0.63
102 32 0.37
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (101 bp):
CTTACACCGGTGTAAGTATGTATTAAGTGCTACACTTGTTTATTTTATTCACTTACATCGTGTAA
GTATGTGTTAAGTGCTACACTTTTTTGTTTTATTCA
Found at i:140872 original size:2 final size:2
Alignment explanation
Indices: 140865--140911 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
140855 CCGATTACTT
140865 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
140907 TA TA T
1 TA TA T
140912 TTAATATCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:140943 original size:16 final size:17
Alignment explanation
Indices: 140924--140959 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
140914 AATATCTTTA
140924 TTATT-AAATATGTTAT
1 TTATTAAAATATGTTAT
140940 TTATTAAAATATGTTAT
1 TTATTAAAATATGTTAT
140957 TTA
1 TTA
140960 ATTATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATTAAAATATGTTAT
Found at i:140996 original size:16 final size:18
Alignment explanation
Indices: 140929--140996 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 18
140919 CTTTATTATT
* *
140929 AAATATGTTATTTATTAA
1 AAATATATTAATTATTAA
*
140947 AATATGTTATTTAATTATTAA
1 AA-AT-ATA-TTAATTATTAA
**
140968 AAATATAGAAATTA-T-A
1 AAATATATTAATTATTAA
140984 AAATATATTAATT
1 AAATATATTAATT
140997 TAACTGTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
16 12 0.31
17 1 0.03
18 7 0.18
19 4 0.10
20 3 0.08
21 12 0.31
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
AAATATATTAATTATTAA
Found at i:140998 original size:39 final size:37
Alignment explanation
Indices: 140944--141016 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
140934 TGTTATTTAT
* *
140944 TAAAATATGTTATTTAATTATTAAAAATATAGAAATTA
1 TAAAATATATTATTTAACTATTAAAAATAT-GAAATTA
* *
140982 TAAAATATATTAATTTAACTGTTTAAAATATGAAA
1 TAAAATATATT-ATTTAACTATTAAAAATATGAAA
141017 ATAATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 14 0.47
39 16 0.53
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.41
Consensus pattern (37 bp):
TAAAATATATTATTTAACTATTAAAAATATGAAATTA
Found at i:144431 original size:20 final size:21
Alignment explanation
Indices: 144402--144441 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
144392 AAATTTAGTT
*
144402 TCAAAGGAAAA-TGATGATCA
1 TCAAAAGAAAATTGATGATCA
144422 TCAAAAGAAAATTGATGATC
1 TCAAAAGAAAATTGATGATC
144442 TTAAAGCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (21 bp):
TCAAAAGAAAATTGATGATCA
Found at i:148102 original size:20 final size:19
Alignment explanation
Indices: 148077--148157 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 19
148067 TTTTGGTGCA
*
148077 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCC-T
*
148097 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC--T
**
148118 GAAGGGAACCGATTTCCCCT
1 G-AGGGAACCGATACCCCCT
*
148138 -AGGGGAATCGATACCCCCT
1 GA-GGGAACCGATACCCCCT
148157 G
1 G
148158 GGGTTCTGGA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.02
19 14 0.28
20 17 0.34
21 2 0.04
22 16 0.32
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.19
Consensus pattern (19 bp):
GAGGGAACCGATACCCCCT
Found at i:152687 original size:159 final size:159
Alignment explanation
Indices: 152490--152859 Score: 501
Period size: 160 Copynumber: 2.3 Consensus size: 159
152480 ACCCTTTTAG
* * * * **
152490 GAGCATGTAGTTTAAATTTGGTAAAAAAAAGGACTTAAAATAAAGGATGAATTG-AGGAAATAAG
1 GAGCATGTGGTTCAAATTTGGTAAAAAAACGGACTTAAAATAAATGATGAATTGAAAAAAATAAG
* * * * *
152554 GAAATTATGAAAAATTGAGGGACTAAATTTAAAAGTATAAAATTTGCTATAAAAAAGAGTAATTG
66 GAAATTATAAAAAATTGAGGGACTAAATTGAAAAGTAGAAAATTTACTATAAAAAAGAGGAATTG
* *
152619 AAATTATATATGTATTCTACAATGGTTCAA
131 AAAGTACATATGTATTCTACAAT-GTTCAA
* * *
152649 GATCATGTGGTTCAAATTTGATAAAAAAACGTACTTAAAATAAATGATGAATTGAAAAAAATAAG
1 GAGCATGTGGTTCAAATTTGGTAAAAAAACGGACTTAAAATAAATGATGAATTGAAAAAAATAAG
* * *
152714 GAAATTATAAAAAATTGAGGGACTAAATTGAAAATTAGAAAATTTATTATAAAAAATAGGAATTG
66 GAAATTATAAAAAATTGAGGGACTAAATTGAAAAGTAGAAAATTTACTATAAAAAAGAGGAATTG
* * *
152779 AAAGTACATATGTATTCTACTATGTTTAG
131 AAAGTACATATGTATTCTACAATGTTCAA
* *
152808 GAGCATTTGGTTCAAACTTGGT-AAAAAACGGACTTAAAATAAATGATGAATT
1 GAGCATGTGGTTCAAATTTGGTAAAAAAACGGACTTAAAATAAATGATGAATT
152860 TAATGAATAA
Statistics
Matches: 183, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
158 29 0.16
159 69 0.38
160 85 0.46
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (159 bp):
GAGCATGTGGTTCAAATTTGGTAAAAAAACGGACTTAAAATAAATGATGAATTGAAAAAAATAAG
GAAATTATAAAAAATTGAGGGACTAAATTGAAAAGTAGAAAATTTACTATAAAAAAGAGGAATTG
AAAGTACATATGTATTCTACAATGTTCAA
Found at i:156452 original size:2 final size:2
Alignment explanation
Indices: 156447--156479 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
156437 TTCTTAAAAC
156447 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
156480 CTTAGTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:174724 original size:53 final size:53
Alignment explanation
Indices: 174651--174751 Score: 202
Period size: 53 Copynumber: 1.9 Consensus size: 53
174641 TTAGGAACAT
174651 TCTGTCTCTATGGTTCCATCAGCGTTGCACTTTGTCTTGGACTCGAAACATTA
1 TCTGTCTCTATGGTTCCATCAGCGTTGCACTTTGTCTTGGACTCGAAACATTA
174704 TCTGTCTCTATGGTTCCATCAGCGTTGCACTTTGTCTTGGACTCGAAA
1 TCTGTCTCTATGGTTCCATCAGCGTTGCACTTTGTCTTGGACTCGAAA
174752 TCTAAGATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (53 bp):
TCTGTCTCTATGGTTCCATCAGCGTTGCACTTTGTCTTGGACTCGAAACATTA
Found at i:177026 original size:5 final size:5
Alignment explanation
Indices: 177010--177063 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
177000 AAATATTTTA
* *
177010 TATAT T-TAT TATAT TATAT TTTA- T-TAT TATTAT TATAT TATAT TTTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT
177058 TA-AT TA
1 TATAT TA
177064 ATTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
3 2 0.05
4 10 0.24
5 25 0.60
6 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:177047 original size:24 final size:24
Alignment explanation
Indices: 177002--177059 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
176992 GTCTACAAAA
177002 ATATTTTA-TATATTTATTATATT
1 ATATTTTATTATATTTATTATATT
177025 ATATTTTATTAT-TATTATTATATT
1 ATATTTTATTATAT-TTATTATATT
177049 ATATTTTATTA
1 ATATTTTATTA
177060 ATTAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 9 0.27
24 24 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
ATATTTTATTATATTTATTATATT
Found at i:177070 original size:15 final size:15
Alignment explanation
Indices: 177002--177068 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 15
176992 GTCTACAAAA
177002 ATATTTTA-TATATT
1 ATATTTTATTATATT
*
177016 -TATTATATTATATTTT
1 ATATTTTATTATA--TT
177032 ATTATTATTATTATATT
1 A-TATT-TTATTATATT
177049 ATATTTTATTA-ATT
1 ATATTTTATTATATT
177063 A-ATTTT
1 ATATTTT
177069 TTTTTTTGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
13 11 0.24
14 8 0.18
15 6 0.13
16 6 0.13
17 3 0.07
18 4 0.09
19 7 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATTTTATTATATT
Found at i:179116 original size:16 final size:16
Alignment explanation
Indices: 179087--179126 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
179077 ACCTCACTAA
179087 CTCTTTTCATTTTTATT
1 CTCTTTTCATTTTT-TT
179104 CTCTTTT-ATTTTTTT
1 CTCTTTTCATTTTTTT
179119 CATCTTTT
1 C-TCTTTT
179127 GCATCATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 12 0.55
17 7 0.32
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (16 bp):
CTCTTTTCATTTTTTT
Found at i:181128 original size:14 final size:15
Alignment explanation
Indices: 181105--181142 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
181095 AGATCAAATC
181105 AAGAAC-AAAAAGAG
1 AAGAACAAAAAAGAG
*
181119 AAGAAGAAAAAAGAG
1 AAGAACAAAAAAGAG
*
181134 AAAAACAAA
1 AAGAACAAA
181143 GAAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.00
Consensus pattern (15 bp):
AAGAACAAAAAAGAG
Found at i:181170 original size:6 final size:6
Alignment explanation
Indices: 181161--181187 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
181151 ATTAAATAAA
181161 AAAAAC AAAAAC AAAAAC AAAAAC AAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAA
181188 GGAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:183236 original size:37 final size:36
Alignment explanation
Indices: 183170--183310 Score: 126
Period size: 36 Copynumber: 3.9 Consensus size: 36
183160 ACAAGGGGTC
* *
183170 GTCTCGCTTGAGACTAATTTACTC--AAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCTTGAAACAAA-TTTT
183207 GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
* * * * * *
183243 ATCTGTCTAGAGACAGTTTCCCTTGAAACAACTTTT
1 GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
* * *
183279 TTCTCTCTCGAGACAGTTTC-CTTTGAAACAAA
1 GTCTCTCTTGAGACAATTTCTC-TTGAAACAAA
183311 ATCTTTGAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
35 4 0.04
36 65 0.73
37 20 0.22
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (36 bp):
GTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTT
Found at i:183256 original size:36 final size:36
Alignment explanation
Indices: 183195--183447 Score: 224
Period size: 36 Copynumber: 7.2 Consensus size: 36
183185 AATTTACTCA
*
183195 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
183232 AAACAAATTTTATCTGTCTAGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
183268 AAACAACTTTTTTCTCTCTCGAGACAGTTTC-CTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTC-TTG
* *
183304 AAACAAA------ATCT-TTGA-ATATGTTT-TACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-C-TTG
* * *
183333 AAACAAATTTCGTCTC-CGCTGAGATAGTTTCTCTTG
1 AAACAAATTTTGTCTCTC-TTGAGACAGTTTCTCTTG
*
183369 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
183405 AAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
183441 AAACAAA
1 AAACAAA
183448 ATCTTTGAAT
Statistics
Matches: 179, Mismatches: 21, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.01
29 14 0.08
30 6 0.03
35 5 0.03
36 140 0.78
37 12 0.07
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:183387 original size:21 final size:20
Alignment explanation
Indices: 183362--183426 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
183352 TGAGATAGTT
183362 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTT-TC
* *
183383 TCTCTTGAGAC--A-GTTTC
1 TCTCTTGAAACAAATTTTTC
183400 -C-CTTGAAACAAATTTTTTC
1 TCTCTTGAAACAAA-TTTTTC
183419 TCTCTTGA
1 TCTCTTGA
183427 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 2 0.06
19 5 0.15
20 1 0.03
21 15 0.44
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.43
Consensus pattern (20 bp):
TCTCTTGAAACAAATTTTTC
Found at i:183453 original size:137 final size:137
Alignment explanation
Indices: 183195--183585 Score: 572
Period size: 137 Copynumber: 2.8 Consensus size: 137
183185 AATTTACTCA
* * * * * *
183195 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTATCTGTCTAGAGACAGT
1 AAACAAA-TTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
* * *
183260 TTCCCTTGAAACAACTTTTTTCTCTCTCGAGACAGTTTCCTTTGAAACAAAATCTTTGAATATGT
65 TTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
183325 TTTACATT-
130 TTTAC-TTG
*
183333 AAACAAATTTCGTCTCCGC-TGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTCGTCTCC-CTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
183397 TTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
65 TTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
*
183462 TTTTCTTG
130 TTTACTTG
* * *
183470 AAACAAATTTCGTCTCCCTTGAGACAGTTTCT-TTCGGAACTAAGTTTTGTCTCTCTTGAGATAG
1 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTT-GAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
183534 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
64 TTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
183586 GTTTTGTCTC
Statistics
Matches: 231, Mismatches: 17, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
136 5 0.02
137 147 0.64
138 79 0.34
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
AAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
TCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTT
TTACTTG
Found at i:183561 original size:36 final size:36
Alignment explanation
Indices: 183460--183620 Score: 225
Period size: 37 Copynumber: 4.4 Consensus size: 36
183450 CTTTGAATAT
* * *
183460 GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
183496 GTTTCT-TTCGGAACTAAGTTTTGTCTCTCTTGAGATA
1 GTTTCTCTT-GAAAC-AAATTTTGTCTCTCTTGAGACA
183533 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
183569 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
183606 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
183621 CCAATCTTTG
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
35 2 0.02
36 45 0.41
37 61 0.55
38 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:183588 original size:73 final size:73
Alignment explanation
Indices: 183452--183620 Score: 243
Period size: 73 Copynumber: 2.3 Consensus size: 73
183442 AACAAAATCT
* * * *
183452 TTGA-ATATGTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTCGGAACTAAGTT
1 TTGAGATA-GTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTCGAAACAAAGTT
183516 TTGTCTCTC
65 TTGTCTCTC
* *
183525 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAAAGTT
1 TTGAGATAGTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTT-CCTTCGAAACAAAGTT
183589 TTGTCTCTC
65 TTGTCTCTC
*
183598 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGATAGTTTCTCTTGAAACA
183621 CCAATCTTTG
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
73 81 0.93
74 6 0.07
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.41
Consensus pattern (73 bp):
TTGAGATAGTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTCGAAACAAAGTTT
TGTCTCTC
Found at i:184070 original size:3 final size:3
Alignment explanation
Indices: 184054--184135 Score: 100
Period size: 3 Copynumber: 27.3 Consensus size: 3
184044 GTCTACAAAA
184054 TAT T-T TAT TA- TAT TATT TATT TAT TAT TAT TAT TAT TATT TATT TAT
1 TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TA-T TA-T TAT
184101 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
184136 TTTTTGCAGG
Statistics
Matches: 73, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
2 8 0.11
3 51 0.70
4 14 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:184089 original size:20 final size:19
Alignment explanation
Indices: 184058--184130 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 19
184048 ACAAAATATT
184058 TTATTA-TATTATTTATTTA
1 TTATTATTATTA-TTATTTA
184077 TTATTATTATTATTATTTA
1 TTATTATTATTATTATTTA
184096 TTTATTATTATTATTATATTA
1 -TTATTATTATTATTAT-TTA
184117 TTATTATTATTATT
1 TTATTATTATTATT
184131 TTATTTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.25
20 35 0.69
21 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTATTATTATTTA
Found at i:184135 original size:20 final size:20
Alignment explanation
Indices: 184054--184135 Score: 106
Period size: 17 Copynumber: 4.5 Consensus size: 20
184044 GTCTACAAAA
184054 TATTTTATTA-TATTA-T-T
1 TATTTTATTATTATTATTAT
184071 TA-TTTATTATTATTATTAT
1 TATTTTATTATTATTATTAT
184090 TA-TTTA-T-TTATTATTAT
1 TATTTTATTATTATTATTAT
*
184107 TATTATATTATTATTATTAT
1 TATTTTATTATTATTATTAT
184127 TATTTTATT
1 TATTTTATT
184136 TTTTTGCAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
16 7 0.12
17 19 0.33
18 5 0.09
19 8 0.14
20 18 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTATTATTATTATTAT
Found at i:185288 original size:6 final size:6
Alignment explanation
Indices: 185268--185298 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
185258 ATTCGAATTG
185268 AATTTT AAGTTTT AATTTT AATTTT AATTTT
1 AATTTT AA-TTTT AATTTT AATTTT AATTTT
185299 CGTAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:196931 original size:21 final size:19
Alignment explanation
Indices: 196893--196938 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
196883 AATTAATCCT
196893 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
196913 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
196934 A-TAAT
1 ACTAAT
196939 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:202480 original size:24 final size:24
Alignment explanation
Indices: 202448--202496 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
202438 TATCCGCTTA
202448 AGATTCATTTGACTGAGGCAATGT
1 AGATTCATTTGACTGAGGCAATGT
202472 AGATTCATTTGACTGAGGCAATGT
1 AGATTCATTTGACTGAGGCAATGT
202496 A
1 A
202497 CAGAATGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (24 bp):
AGATTCATTTGACTGAGGCAATGT
Found at i:205675 original size:28 final size:28
Alignment explanation
Indices: 205609--205698 Score: 82
Period size: 27 Copynumber: 3.3 Consensus size: 28
205599 TTGAGGGCAA
* *
205609 ATGTTACCCTTAAACTTCCTAAAAATTC
1 ATGTTACCCTTAAACTTCTTAAAAAATC
* *
205637 AATATT-GCCTT-AACTTCTTAAAAAATC
1 -ATGTTACCCTTAAACTTCTTAAAAAATC
*
205664 GATGTTACCCTTGAA---CTTAAAAAATC
1 -ATGTTACCCTTAAACTTCTTAAAAAATC
205690 ATGTTACCC
1 ATGTTACCC
205699 CTCTACATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
25 9 0.17
26 11 0.21
27 18 0.35
28 8 0.15
29 6 0.12
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (28 bp):
ATGTTACCCTTAAACTTCTTAAAAAATC
Found at i:210779 original size:17 final size:14
Alignment explanation
Indices: 210743--210770 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
210733 GTATCTTAAA
210743 GATCATCACATCTC
1 GATCATCACATCTC
210757 GATCATCACATCTC
1 GATCATCACATCTC
210771 AGTCATCATA
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:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
GATCATCACATCTC
Found at i:211264 original size:24 final size:24
Alignment explanation
Indices: 211237--211287 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
211227 TGAAATTTAG
*
211237 ATTT-ACTATTTACAATTATTATAT
1 ATTTAACTATTAACAA-TATTATAT
* *
211261 ATTTAATTATTAATAATATTATAT
1 ATTTAACTATTAACAATATTATAT
211285 ATT
1 ATT
211288 AAATTAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTAACTATTAACAATATTATAT
Found at i:211482 original size:16 final size:16
Alignment explanation
Indices: 211461--211494 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
211451 TATATGGGAT
211461 TTTTTTATATATAAAA
1 TTTTTTATATATAAAA
*
211477 TTTTTTATATATTAAA
1 TTTTTTATATATAAAA
211493 TT
1 TT
211495 AAAGTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTATATATAAAA
Found at i:211487 original size:18 final size:16
Alignment explanation
Indices: 211459--211492 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
211449 AGTATATGGG
211459 ATTTTTTTATATATAAA
1 ATTTTTTTATAT-TAAA
211476 ATTTTTTATATATTAAA
1 ATTTTTT-TATATTAAA
211493 TTAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTTTATATTAAA
Found at i:211950 original size:15 final size:14
Alignment explanation
Indices: 211930--211968 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
211920 TTTTAATATT
211930 TTTTAAATATTTTAA
1 TTTTAAATATTTT-A
211945 TTTT-AATATTTTA
1 TTTTAAATATTTTA
211958 TTTTAAGATAT
1 TTTTAA-ATAT
211969 AATGACCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.23
14 9 0.41
15 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTTAAATATTTTA
Found at i:211954 original size:14 final size:13
Alignment explanation
Indices: 211919--211963 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
211909 TTGTGTAATC
211919 ATTTTAATA-TTT
1 ATTTTAATATTTT
*
211931 -TTTAAATATTTT
1 ATTTTAATATTTT
211943 AATTTTAATATTTT
1 -ATTTTAATATTTT
211957 ATTTTAA
1 ATTTTAA
211964 GATATAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 7 0.25
12 3 0.11
13 7 0.25
14 11 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTAATATTTT
Found at i:214505 original size:114 final size:114
Alignment explanation
Indices: 214297--214519 Score: 286
Period size: 114 Copynumber: 2.0 Consensus size: 114
214287 GATATCAATT
* * * ** * *
214297 GTACTGCTTGCTGTTCCGGACAAAGATTTCGTCTCAGCTTTGTAATCATCCATCTGTTCCGTACC
1 GTACTGCTTGCTGTTCCGGACAAAAAATTAGTCTCAGCTTCATAATCATCCACCTGTTCCGTACA
* * *
214362 CTTTTCCCAGTCAACATCAGTCTTGTTGCCTGATTCAGAATCAAGAATG
66 CTTTTCCCAATCAACATCAATCTTATTGCCTGATTCAGAATCAAGAATG
* * *
214411 GTACTGCTTGCTGTTTCC-GATAAAAAATTATTCTCAGCTTCATATTCATCCACCTGTTCCGTAC
1 GTACTGCTTGCTG-TTCCGGACAAAAAATTAGTCTCAGCTTCATAATCATCCACCTGTTCCGTAC
* * *
214475 ACTTTTCCGAATCAGCATCAATCTTATTGCCTGATTCGGAATCAA
65 ACTTTTCCCAATCAACATCAATCTTATTGCCTGATTCAGAATCAA
214520 TATCGTTTCT
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
114 88 0.96
115 4 0.04
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (114 bp):
GTACTGCTTGCTGTTCCGGACAAAAAATTAGTCTCAGCTTCATAATCATCCACCTGTTCCGTACA
CTTTTCCCAATCAACATCAATCTTATTGCCTGATTCAGAATCAAGAATG
Found at i:222174 original size:23 final size:23
Alignment explanation
Indices: 222130--222174 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
222120 TAATATATAG
**
222130 GTAGCGCTTATATAATGTAATAA
1 GTAGCGCTTATATAATAAAATAA
222153 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
222175 GGCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAA
Found at i:222676 original size:199 final size:197
Alignment explanation
Indices: 222253--222966 Score: 752
Period size: 199 Copynumber: 3.6 Consensus size: 197
222243 GCGTTTATAT
* * * * * * *
222253 TGACCTATTTTATAAGTAAACCGATATATTTATACCGCTAACATTGCAAATTTACCTATTACATT
1 TGACCTATTTTCTCA-TAAAACGGTATATTTATACCGATTACATTGTAAATTTACCTATTACATT
* * * * *
222318 ATAATTATCGGTTTCGATATTTTTTGGATCGATACAATTT--GAAATGTATCGACACTTTATGCG
65 ATAATTATCTGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCG
* * *
222381 TACACCTCGTTGGGAATTCATTCTA-A-AAAAGTATCGATACAAACTTAAAAAGTGTCGATACAT
129 TACACCTCGTTTGGCATTCATTCTAGACAAAAGTATCGACACAAA-TTAAAAAGTGTCGATACAT
*
222444 TATTC
193 TATGC
* * * ** *
222449 AGACCTATTTTCTCATAAAACTGGTATATTTCTATCGGGTACATTGTAAATTTACCTATCACATT
1 TGACCTATTTTCTCATAAAAC-GGTATATTTATACCGATTACATTGTAAATTTACCTATTACATT
* *
222514 GTAATGATCTGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
65 ATAATTATCTGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
* * * *
222579 ACACC-CGTTTGGCATTCATTATAGACAAAATGTACCGACACAAATTTAATAAGTGTCGATACTT
130 ACACCTCGTTTGGCATTCATTCTAGACAAAA-GTATCGACACAAA-TTAAAAAGTGTCGATACAT
222643 TATGC
193 TATGC
* *
222648 TGACCTATTTTCTCATAAAATCGGTATATTTATACCGATTACATTGTAAATTTACATATTATA-T
1 TGACCTATTTTCTCATAAAA-CGGTATATTTATACCGATTACATTGTAAATTTACCTATTACATT
* ** * *
222712 ACAAATTTAAAAT-TATCGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACGCTTTATG
65 A-TAA-TT-ATCTGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATG
* * * *
222775 CATGCACCTCGTTTGGGCATTCATTCTAGACAATAAGTATCGACACAAATTACACAAGGGTCGAT
127 CGTACACCTCGTTT-GGCATTCATTCTAGACAA-AAGTATCGACACAAATTA-AAAAGTGTCGAT
* *
222840 ACATTGTGT
189 ACATTATGC
* * * * * * * *
222849 TGACTTGTTTTCTAATTAACCGGTATTTTTATACCGTTTACATTGTTAATTTA--TATTACATTA
1 TGACCTATTTTCTCATAAAACGGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTA
222912 TAATTAT-TAGTTTCGATGTTTTTTGGG-TCGATACTTTTAGA-AAATGTATCGACAC
66 TAATTATCT-GTTTCGATG-TTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
222967 ATATTTAGGT
Statistics
Matches: 433, Mismatches: 65, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
195 9 0.02
196 93 0.21
197 37 0.09
198 38 0.09
199 146 0.34
200 46 0.11
201 62 0.14
202 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (197 bp):
TGACCTATTTTCTCATAAAACGGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTA
TAATTATCTGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTA
CACCTCGTTTGGCATTCATTCTAGACAAAAGTATCGACACAAATTAAAAAGTGTCGATACATTAT
GC
Found at i:224913 original size:200 final size:201
Alignment explanation
Indices: 224547--225110 Score: 624
Period size: 200 Copynumber: 2.8 Consensus size: 201
224537 CTAGACGAAG
* * * *
224547 TATCGACACAAATTCTAGAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAATA-CGGTAT
1 TATCAACAAAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAA-ACCGGTAT
* * * * * * *
224611 AGTTATGCTGTTTACATTGTAAATTTATCTATTACATTGTAATTATGGGTTTTGATGTTTATGGG
65 ATTTATACTGATTATATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGG
* *
224676 ATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCAT-TTTGGGCATTCATTCTGGA
130 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATGTTTGGGCATTCATTCTGGA
*
224740 CAAAAAG
195 CAAAAAA
*
224747 TAT-AGACAAAAAATT-CA-AACGTGTCGACACATTATGTAGACCTATTCTCAT-ATAAAACCGG
1 TATCA-AC-AAAAATTCCACAA-GTGTCGATACATTATGTAGACCTATTCTC-TCATAAAACCGG
** * * * *
224808 TATATTTATACTGATTATATTACAAAATTACCTATTATATTATAATTATGGGTTTCGATATTTTT
62 TATATTTATACTGATTATATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTT
* * ** * *
224873 GGGATCAATACTTTTTAAAAATGTATCGATA-TTGTATGCGTGCACCATGTTTTTGTATTCATTT
127 GGGATCGATACTTTTTAAAAATGTATCGACACTT-TATGCGTGCACCATGTTTGGGCATTCATTC
224937 TGGACAAAAAA
191 TGGACAAAAAA
* * * * * * * *
224948 TATCAACACAAATTCCACAAATGTCAATACATTATATATATCTATTTTCTCA-AAAACCTAGTAT
1 TATCAACAAAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC-GGTAT
* * * *
225012 ATTTATA-TCGGTTATATTGTAAATTTACCTATTACATTACAATTTTCGGTTTTGATGTTTTTGG
65 ATTTATACT-GATTATATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGG
* *
225076 GATCGATACTTTTTAAACATGTATCAACACTTTAT
129 GATCGATACTTTTTAAAAATGTATCGACACTTTAT
225111 AGGAAACTAT
Statistics
Matches: 301, Mismatches: 49, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
199 5 0.02
200 149 0.50
201 142 0.47
202 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (201 bp):
TATCAACAAAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
TTTATACTGATTATATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGA
TCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATGTTTGGGCATTCATTCTGGAC
AAAAAA
Found at i:228403 original size:199 final size:199
Alignment explanation
Indices: 228053--229203 Score: 1306
Period size: 199 Copynumber: 5.8 Consensus size: 199
228043 TTTTAAAATG
* * * * * *
228053 GTATCGACACAAATT-TAACAATTGTCGATACTTTATGCT-GACCTATTTTCTCATAAAACTGGT
1 GTATCGACACAAATTCCAA-AAGTGTCGATACATTATG-TAGACCTATTCTCACATAAAACCGGT
* * * * ** * * *
228116 ATATTTATATCGGTTACATTGGAAATTTATCTATTACATTATAATTACCGATTTTGATGTTTTTG
64 ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTG
* * * * *
228181 GGATCGACACTTTTTAAAAATGTATCGACACTTAATGGGTGCACCCTTTTGGCATTCATTCTGGA
129 GGATCGACACTTTTTATAAATGTATCGACACTTTATGTGTGCACCATTTTGGCATTCATTATGGA
228246 CAAAAA
194 CAAAAA
* * * * * **
228252 GTATCAAAACAAATTCCAGAAGTGTCGATACATTTTCTAGACCTATTCTCGTATAAAACCGGTAT
1 GTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * *
228317 ATTTATACCGGTTACATTGAAAAATTACATATTACATTACAA-TATTGGGTTTCGATATTTCTGG
66 ATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTA-TGGGTTTCGATGTTTCTGG
* * *
228381 GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTGGGCATTTATTATG
130 GATCGACACTTTTTATAAATGTATCGACACTTTATGTGTGCACCA--TTTT-GGCATTCATTATG
* *
228446 GACAAGAT
192 GACAAAAA
* *
228454 GTATCGACACATAATT-AAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAACCGGTA
1 GTATCGACACA-AATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
* *
228518 TATTTATACCGGTTACATTGCAAAATTACCTATTACA-TATAATTATGGG-TTCGATGTCTCTGG
65 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * * * * * * *
228581 AATTGACACTTTTTA-AAATGTATCGACACTTTATGTGTTCATCATGCTAGGCATTCATTTTAGA
130 GATCGACACTTTTTATAAATGTATCGACACTTTATGTGTGCACCAT-TTTGGCATTCATTATGGA
228645 CAAAAA
194 CAAAAA
* * * * * * *
228651 GTATCGACACCAATTTCAAATGTGTTGATACATTATGTAGACTTATTTTCACATAAAACTGGTAT
1 GTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * **
228716 ATTTATACCAGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTAA
66 ATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * * * * * * *
228780 GATTGACACTTTTGAAAAATGTATCGATAC-TTATTTGTGCACCCTTTTGGGCATTCCTTCTGGA
130 GATCGACACTTTTTATAAATGTATCGACACTTTATGTGTGCACCATTTT-GGCATTCATTATGGA
228844 -AAAACA
194 CAAAA-A
* * * * * *
228850 GTATCGACACAAATTCCATAAGTGTTGATACATTATATAGACCTATTCTCTCATAAAATCAGTAT
1 GTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* *
228915 AGTTATACCGGTTACATTGAAAAATTACATATTACATTATAATTATGGGTTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * * *
228980 ATCGATA-GTTTTATAAATATATCGACACTTTAT-TGTTCACCATTTTGGGATTCATTATGGACA
131 ATCGACACTTTTTATAAATGTATCGACACTTTATGTGTGCACCATTTTGGCATTCATTATGGACA
229043 AAAA
196 AAAA
* * * *
229047 GTATCGACACCAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTTACATAAAACTGGTAT
1 GTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* *
229112 ATTTATACCGGTTATATT-ACAAAATTACCTATTACATTAT-ATTATGGGTTTCGATATTT-TGG
66 ATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* *
229174 GATCGATACTTTTTATAAATGTATCAACAC
130 GATCGACACTTTTTATAAATGTATCGACAC
229204 ATCTGCTTAC
Statistics
Matches: 802, Mismatches: 129, Indels: 45
0.82 0.13 0.05
Matches are distributed among these distances:
195 11 0.01
196 41 0.05
197 206 0.26
198 52 0.06
199 333 0.42
200 39 0.05
201 12 0.01
202 104 0.13
203 4 0.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (199 bp):
GTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
ATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
ATCGACACTTTTTATAAATGTATCGACACTTTATGTGTGCACCATTTTGGCATTCATTATGGACA
AAAA
Found at i:229578 original size:19 final size:19
Alignment explanation
Indices: 229554--229602 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
229544 TTACATTCAC
229554 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
229573 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
229592 ATACAAAATTA
1 ATACAAAATTA
229603 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:231154 original size:17 final size:18
Alignment explanation
Indices: 231127--231160 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
231117 TCCTCCTCAT
231127 TTCCTTCATCTTTTCTTC
1 TTCCTTCATCTTTTCTTC
231145 TTCC-TCATCTTTTCTT
1 TTCCTTCATCTTTTCTT
231161 TTTCATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCCTTCATCTTTTCTTC
Found at i:231359 original size:18 final size:18
Alignment explanation
Indices: 231332--231366 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
231322 TCCTCCTCAT
*
231332 TTCCTTCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
231350 TTCCTCCATCTTTTCTT
1 TTCCTCCATCTTTTCTT
231367 TTTCATATTT
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:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:231571 original size:21 final size:21
Alignment explanation
Indices: 231532--231572 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
231522 CCATCAATTT
* *
231532 TTCACCCATCACCATCTCAAG
1 TTCACCCATCAACACCTCAAG
*
231553 TTCACCCCTCAACACCTCAA
1 TTCACCCATCAACACCTCAA
231573 CTTCTTTCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.46, G:0.02, T:0.22
Consensus pattern (21 bp):
TTCACCCATCAACACCTCAAG
Found at i:231597 original size:33 final size:33
Alignment explanation
Indices: 231553--231617 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
231543 CCATCTCAAG
231553 TTCACCCCTCAACACCTCAACTTCTTTCACCAA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAA
*
231586 TTCACCGCTCAACACCTCAACTTCTTTCACCA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCA
231618 CTCCATCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.45, G:0.02, T:0.28
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAA
Found at i:231778 original size:15 final size:15
Alignment explanation
Indices: 231758--231791 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
231748 TACTCTGTTT
231758 CCCCTCACCGTCATC
1 CCCCTCACCGTCATC
* *
231773 CCCCTCAGCGTTATC
1 CCCCTCACCGTCATC
231788 CCCC
1 CCCC
231792 AATACAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.59, G:0.09, T:0.21
Consensus pattern (15 bp):
CCCCTCACCGTCATC
Found at i:232098 original size:22 final size:23
Alignment explanation
Indices: 232070--232124 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
232060 AACATGTATT
232070 TATAATAAAATT-TATAATTTTA
1 TATAATAAAATTCTATAATTTTA
* *
232092 TATAATAACTATTCTATCATTTTA
1 TATAATAA-AATTCTATAATTTTA
232116 TAT-ATAAAA
1 TATAATAAAA
232125 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 7 0.25
24 12 0.43
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
TATAATAAAATTCTATAATTTTA
Found at i:234650 original size:182 final size:182
Alignment explanation
Indices: 234090--234967 Score: 988
Period size: 183 Copynumber: 4.7 Consensus size: 182
234080 TACGCGTACT
* * *
234090 TATTAAAGTATTGACACTTTCAATATA-TCTGGTAACGCT-T-TACCGGTTTTGTCATTTCGAGA
1 TATTAAAGTATCGACACTTTCAATATATTC-GGT--CGCTCTATACCGGTTTTGTCCTTTAGAGA
* * *
234152 CCGGTTTTGTCATATTTTTTACATGTTATATCGTTGTGGATCGATACATTGGTATAAAGTATCGA
63 CCGGTTTTGTCATA-TTTTTACATGTTATATTGTTGTGGATCGATACATTGTTATAAAGTATAGA
* *
234217 TACTTTATAGGCGCTAAAATTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
127 CACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
*
234273 TATTAAAGTATCAACACTTTCAATATA-TCTGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACC
1 TATTAAAGTATCGACACTTTCAATATATTC-GGTCGCTCTATACCGGTTTTGTCCTTTAGAGACC
* * * *
234337 GGTTTTGTCATATTTTTACCTGTTATATTTTTTTTGGATCGATACATTGTTATAAAGTATCGACA
65 GGTTTTGTCATATTTTTACATGTTATA-TTGTTGTGGATCGATACATTGTTATAAAGTATAGACA
* * * * * *
234402 CTTTATGGGCACTAAAATTGCTTCTCTTTTAAATTTACAAAGTGTCGATACTTA
129 CTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
* * *
234456 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATATCGATTTTATCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* * *
234521 GTTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTGTTATAAAATATAGACACT
66 GTTTTGTCATATTTTTACATGTTATATTGTTGTGGATCGATACATTGTTATAAAGTATAGACACT
* *
234586 TTATAGGCGCTAAAACTGATTCTCTTTTAAATTTACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
234638 TATTAAAGTATCGACACTTTCAATATATAT-GGTCGCTCTATACCGGTTTTGTCCTTTAGAGACC
1 TATTAAAGTATCGACACTTTCAATATAT-TCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACC
* * * * * * * *
234702 GATTTTGTCCTTTAGAGACCGGTTTTGTCATATTTTTACCTATTATATCTTTG-TGGAT-CGATA
65 GGTTTTGT-C-----ATA----TTTT-T-ACA-TGTTA--TATTGT-T-GTGGATCGATAC-AT-
* * *
234765 TATTGTTATAAAGTATCA-ACACTTTATAGGCTCTAAAGCTGCTTCTCTTTTAAATTCACAAAGT
111 T---GTTATAAAGTAT-AGACACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGT
234829 GTCAATACTTA
172 GTCAATACTTA
* * * *
234840 TATTAAAGTATCGACACTTTCAATATATCCGGTACCGCT-T-TACCGATTTTGTCTTTTCGAGAC
1 TATTAAAGTATCGACACTTTCAATATATTCGGT--CGCTCTATACCGGTTTTGTCCTTTAGAGAC
234903 CGGTTTTGTCATATTTTTACATGTTATATTGATT-TGGATCGATACAGTT-TTATAAAGTATAGA
64 CGGTTTTGTCATATTTTTACATGTTATATTG-TTGTGGATCGATACA-TTGTTATAAAGTATAGA
234966 CA
127 CA
234968 TAAACCGTCA
Statistics
Matches: 600, Mismatches: 59, Indels: 73
0.82 0.08 0.10
Matches are distributed among these distances:
181 5 0.01
182 177 0.29
183 231 0.38
184 2 0.00
185 2 0.00
186 6 0.01
187 7 0.01
188 3 0.00
189 4 0.01
190 2 0.00
191 1 0.00
192 8 0.01
193 1 0.00
194 1 0.00
195 4 0.01
196 2 0.00
197 5 0.01
198 7 0.01
199 3 0.00
201 1 0.00
202 122 0.20
203 2 0.00
204 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
GTTTTGTCATATTTTTACATGTTATATTGTTGTGGATCGATACATTGTTATAAAGTATAGACACT
TTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCAATACTTA
Found at i:234707 original size:20 final size:20
Alignment explanation
Indices: 234679--234730 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
234669 GTCGCTCTAT
234679 ACCGGTTTTGTCCTTTAGAG
1 ACCGGTTTTGTCCTTTAGAG
*
234699 ACCGATTTTGTCCTTTAGAG
1 ACCGGTTTTGTCCTTTAGAG
234719 ACCGGTTTTGTC
1 ACCGGTTTTGTC
234731 ATATTTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
ACCGGTTTTGTCCTTTAGAG
Found at i:234845 original size:202 final size:201
Alignment explanation
Indices: 234499--234912 Score: 625
Period size: 202 Copynumber: 2.0 Consensus size: 201
234489 CGCTCTATAT
* * *
234499 CGATTTTATCCTTTAGAGACCGGTTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATAC
1 CGATTTTGTCCTTTAGAGACCGGTTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATAC
*
234564 ATTGTTATAAAATATAGACACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTTACAAAGTGT
66 ATTGTTATAAAATATAGACACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGT
* * *
234629 CGATACTTATATTAAAGTATCGACACTTTCAATATATATGGT-CGCTCTATACCGGTTTTGTCCT
131 CAATACTTATATTAAAGTATCGACACTTTCAATATATACGGTACGCT-T-TACCGATTTTGTCCT
234693 TTAGAGAC
194 TTAGAGAC
* *
234701 CGATTTTGTCCTTTAGAGACCGGTTTTGTCATATTTTTACCTATTATATCTTTGTGGATCGATAT
1 CGATTTTGTCCTTTAGAGACCGGTTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATAC
* * * *
234766 ATTGTTATAAAGTATCA-ACACTTTATAGGCTCTAAAGCTGCTTCTCTTTTAAATTCACAAAGTG
66 ATTGTTATAAAATAT-AGACACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTG
* *
234830 TCAATACTTATATTAAAGTATCGACACTTTCAATATATCCGGTACCGCTTTACCGATTTTGTCTT
130 TCAATACTTATATTAAAGTATCGACACTTTCAATATATACGGTA-CGCTTTACCGATTTTGTCCT
*
234895 TTCGAGAC
194 TTAGAGAC
*
234903 CGGTTTTGTC
1 CGATTTTGTC
234913 ATATTTTTAC
Statistics
Matches: 192, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
202 186 0.97
203 2 0.01
204 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (201 bp):
CGATTTTGTCCTTTAGAGACCGGTTTTGTCATATTTTTACCTATTATATCGTTGTGGATCGATAC
ATTGTTATAAAATATAGACACTTTATAGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGT
CAATACTTATATTAAAGTATCGACACTTTCAATATATACGGTACGCTTTACCGATTTTGTCCTTT
AGAGAC
Found at i:236357 original size:19 final size:20
Alignment explanation
Indices: 236313--236362 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
236303 TTTTTAAAAG
236313 ATTAAA-TTATATTTTAGTA
1 ATTAAATTTATATTTTAGTA
236332 ATT-AATTTATATTTTA-TA
1 ATTAAATTTATATTTTAGTA
*
236350 TTTAAATTT-TATT
1 ATTAAATTTATATT
236363 GTTGAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTAAATTTATATTTTAGTA
Found at i:237893 original size:11 final size:10
Alignment explanation
Indices: 237855--237891 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
237845 TAAATAAATC
237855 AAAAAATTAA
1 AAAAAATTAA
*
237865 AAAAAATGTAG
1 AAAAAAT-TAA
237876 AAAAAATTAA
1 AAAAAATTAA
237886 AAAAAA
1 AAAAAA
237892 ATCAGAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:238432 original size:2 final size:2
Alignment explanation
Indices: 238425--238494 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
238415 TTTTAGTGAG
238425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238467 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
238495 GTAATGATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:240083 original size:18 final size:18
Alignment explanation
Indices: 240056--240096 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
240046 ACATTCTCAT
*
240056 TAATCTTATTCCTACTGA
1 TAATCATATTCCTACTGA
240074 TAATCATATTCCTACTGA
1 TAATCATATTCCTACTGA
240092 TAATC
1 TAATC
240097 TTATATTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (18 bp):
TAATCATATTCCTACTGA
Found at i:241970 original size:30 final size:30
Alignment explanation
Indices: 241932--241999 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
241922 GTAAAGAACT
* *
241932 GGTA-GAACCAGCTGAGAACCGGTAAAACC
1 GGTATGAACCAGCTGAAAACCGGCAAAACC
* *
241961 GGTGTGAACCAGCTGAAAACCGGCAAAATC
1 GGTATGAACCAGCTGAAAACCGGCAAAACC
241991 GGTATGAAC
1 GGTATGAAC
242000 TGCCAGTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.37, C:0.22, G:0.28, T:0.13
Consensus pattern (30 bp):
GGTATGAACCAGCTGAAAACCGGCAAAACC
Found at i:243336 original size:42 final size:42
Alignment explanation
Indices: 243283--243647 Score: 590
Period size: 42 Copynumber: 8.7 Consensus size: 42
243273 ACTATCGCAA
*
243283 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * *
243323 TGTGATTTATTCCAAGTTCATTGCGATAGTCGAAGTTCCCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* *
243365 TGCAATTTATTACAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
243407 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * * *
243449 TGCGATTTATTCTAAATTTGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
243491 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* *
243533 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
243575 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
**
243617 TGCGATTTATTTTAAGTTCGTTGCGATAGTC
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTC
243648 CAAAATCGCA
Statistics
Matches: 298, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
40 4 0.01
41 2 0.01
42 292 0.98
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:243386 original size:21 final size:20
Alignment explanation
Indices: 243320--243643 Score: 163
Period size: 21 Copynumber: 15.4 Consensus size: 20
243310 TCGAAGTTCG
*
243320 CGTTGTGATTTATTCCAAGTT
1 CGTTGCGATTTATT-CAAGTT
* *
243341 CATTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTC-AAGTT
*
243360 CCCGTTGCAATTTATTACAAGTT
1 --CGTTGCGATTTATT-CAAGTT
*
243383 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTC-AAGTT
243402 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATT-CAAGTT
*
243425 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTC-AAGTT
*
243444 CGCGTTGCGATTTATTCTAAATT
1 --CGTTGCGATTTATTC-AAGTT
* *
243467 TGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTA-TTCAAGTT
243486 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATT-CAAGTT
*
243509 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTC-AAGTT
*
243528 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATT-CAAGTT
*
243551 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTA-TTCAAGTT
243570 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATT-CAAGTT
*
243593 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTC-AAGTT
*
243612 CGCGTTGCGATTTATTTTAAGTT
1 --CGTTGCGATTTA-TTCAAGTT
243635 CGTTGCGAT
1 CGTTGCGAT
243644 AGTCCAAAAT
Statistics
Matches: 235, Mismatches: 27, Indels: 82
0.68 0.08 0.24
Matches are distributed among these distances:
18 5 0.02
19 53 0.23
20 3 0.01
21 114 0.49
22 2 0.01
23 54 0.23
24 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTATTCAAGTT
Found at i:244533 original size:21 final size:21
Alignment explanation
Indices: 244508--244787 Score: 229
Period size: 21 Copynumber: 13.2 Consensus size: 21
244498 TGGACTATCA
244508 CAACGAACTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
* * *
244529 CAACGCGAACTTCGACT--ATCT
1 CAA--CGAACTTGGAATAAATCG
244550 CAACGAACTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
* *
244571 CAACGCGAACTTCGACT--ATCG
1 CAA--CGAACTTGGAATAAATCG
*
244592 CAACGAATTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
*
244613 CAACGCGAACTTGGACT--ATCG
1 CAA--CGAACTTGGAATAAATCG
*
244634 CAACGAATTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
*
244655 CAACGCGAACTTGGACT--ATCG
1 CAA--CGAACTTGGAATAAATCG
* *
244676 CAACGAATTTGAAATAAATCG
1 CAACGAACTTGGAATAAATCG
244697 CAACGCGAACTTGGAATAAATCG
1 CAA--CGAACTTGGAATAAATCG
*
244720 CAACGAATTTGGAATAAATCG
1 CAACGAACTTGGAATAAATCG
* *
244741 CAACGCGAACTTCGACT--ATCG
1 CAA--CGAACTTGGAATAAATCG
* *
244762 CAACGAATTTGTAATAAATCG
1 CAACGAACTTGGAATAAATCG
*
244783 TAACG
1 CAACG
244788 CAAACTTCGA
Statistics
Matches: 206, Mismatches: 31, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
19 46 0.22
21 92 0.45
23 68 0.33
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACGAACTTGGAATAAATCG
Found at i:244558 original size:19 final size:19
Alignment explanation
Indices: 244500--244868 Score: 100
Period size: 21 Copynumber: 17.6 Consensus size: 19
244490 TGCAATTTTG
* *
244500 GACTATCACAACGAACTTG
1 GACTATCGCAACGAACTTC
*
244519 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
* *
244542 GACTATCTCAACGAACTTG
1 GACTATCGCAACGAACTTC
*
244561 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
* *
244584 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAACTTC
* *
244603 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAA--CGAACTTC
* *
244626 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAACTTC
* *
244645 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAA--CGAACTTC
*
244668 GACTATCGCAACGAA-TTT
1 GACTATCGCAACGAACTTC
* *
244686 GAAATAAATCGCAACGCGAACTTG
1 G-ACT--ATCGCAA--CGAACTTC
* * *
244710 GAATAAATCGCAACGAATTTG
1 GACT--ATCGCAACGAACTTC
*
244731 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
*
244754 GACTATCGCAACGAA-TTT
1 GACTATCGCAACGAACTTC
* *
244772 GTAATAAATCGTAACGCAAACTTC
1 G-ACT--ATCGCAACG--AACTTC
**
244796 GACTATCGCAAATC-AGTTTCC
1 GACTATCGC-AA-CGAACTT-C
244817 AGA-T-TCGCAACGCGAACTTC
1 -GACTATCGCAA--CGAACTTC
*
244837 GACTATCGCAACGCGAACTTG
1 GACTATCGCAA--CGAACTTC
244858 GACTATCGCAA
1 GACTATCGCAA
244869 TGCAAATATG
Statistics
Matches: 274, Mismatches: 38, Indels: 74
0.71 0.10 0.19
Matches are distributed among these distances:
18 6 0.02
19 48 0.18
20 10 0.04
21 130 0.47
22 4 0.01
23 70 0.26
24 6 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (19 bp):
GACTATCGCAACGAACTTC
Found at i:244559 original size:42 final size:42
Alignment explanation
Indices: 244500--244849 Score: 492
Period size: 42 Copynumber: 8.3 Consensus size: 42
244490 TGCAATTTTG
* *
244500 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
244542 GACTATCTCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
244584 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
244626 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
244668 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
244710 GAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
244754 GACTATCGCAACGAATTTGTAATAAATCGTAACGCAAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* **
244796 GACTATCGCAAATC-AGTTTCCAGAT---TCGCAACGCGAACTTC
1 GACTATCGC-AA-CGAATTTGGA-ATAAATCGCAACGCGAACTTC
244837 GACTATCGCAACG
1 GACTATCGCAACG
244850 CGAACTTGGA
Statistics
Matches: 285, Mismatches: 17, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 23 0.08
42 210 0.74
43 7 0.02
44 42 0.15
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:245350 original size:20 final size:20
Alignment explanation
Indices: 245325--245417 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
245315 TTTTCCCAAT
245325 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
245345 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
245365 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
245386 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
245407 TCGCAATGCGA
1 TCGCAATGCGA
245418 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Done.