Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 110 of 126
Found at i:32964362 original size:258 final size:262
Alignment explanation
Indices: 32964076--32964615 Score: 935
Period size: 258 Copynumber: 2.1 Consensus size: 262
32964066 CTAAAGTAAA
* * *
32964076 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAAGTA
1 TAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
32964141 AATGATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAG
66 AATGATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAG
32964206 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
131 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
**
32964271 AAAGATTTAATC-ATTTAATTATACTAAAGTAAATAATTA-T-ATTAAATTAAA-TATTTAATTA
196 AAAGATTTAATCAATTTAATTATACTAAAGTAAATAATTATTAATTAAATTAAAGTAACTAATTA
32964332 TT
261 TT
32964334 TAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
1 TAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
*
32964399 AATGATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACATTATCGATTAG
66 AATGATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAG
32964464 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
131 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
* * * *
32964529 AAAGATTTAATCATAATTTATTTATATTAAAGTAACTAATTATTTAATTATATTAAAGTAACTAA
196 AAAGATTTAATC--AATTTAATTATACTAAAGTAAATAATTA-TTAATTAAATTAAAGTAACTAA
32964594 TTATT
258 TTATT
32964599 TAATTATATTAAAGTAA
1 TAATTATATTAAAGTAA
32964616 CCATAATTTA
Statistics
Matches: 265, Mismatches: 10, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
258 203 0.77
261 24 0.09
263 1 0.00
264 10 0.04
265 27 0.10
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (262 bp):
TAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
AATGATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAG
TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
AAAGATTTAATCAATTTAATTATACTAAAGTAAATAATTATTAATTAAATTAAAGTAACTAATTA
TT
Found at i:32964530 original size:18 final size:18
Alignment explanation
Indices: 32964497--32964535 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
32964487 TAATTATTTA
*
32964497 ATTATATTAAAGTAAATG
1 ATTATATTAAAGTAAAAG
32964515 ATTATATT-AAGTTAAAAG
1 ATTATATTAAAG-TAAAAG
32964533 ATT
1 ATT
32964536 TAATCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (18 bp):
ATTATATTAAAGTAAAAG
Found at i:32964616 original size:26 final size:26
Alignment explanation
Indices: 32964487--32964616 Score: 142
Period size: 26 Copynumber: 5.0 Consensus size: 26
32964477 TTAAAAGATT
*
32964487 TAATTATTTAATTATATTAAAGTAAA
1 TAATTATTTAATTATATTAAAGTAAC
* *
32964513 TGATTATATTAAGTTA-A--AAGATTTAA-
1 TAATTAT-TTAA-TTATATTAA-A-GTAAC
* * *
32964539 TCATAATTTATTTATATTAAAGTAAC
1 TAATTATTTAATTATATTAAAGTAAC
32964565 TAATTATTTAATTATATTAAAGTAAC
1 TAATTATTTAATTATATTAAAGTAAC
32964591 TAATTATTTAATTATATTAAAGTAAC
1 TAATTATTTAATTATATTAAAGTAAC
32964617 CATAATTTAT
Statistics
Matches: 87, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
24 3 0.03
25 9 0.10
26 62 0.71
27 10 0.11
28 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (26 bp):
TAATTATTTAATTATATTAAAGTAAC
Found at i:32970129 original size:66 final size:66
Alignment explanation
Indices: 32970023--32970179 Score: 199
Period size: 66 Copynumber: 2.4 Consensus size: 66
32970013 CAAATTGCTC
* *
32970023 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTACAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
32970087 AA
65 AA
* ** * *
32970089 AACTTAAAGAGGAGGTTACAGTGAGGGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTACAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
32970154 C
66 A
* * *
32970155 AACTTAAAGTGGAGGCAACAGCGAG
1 AACTTAAAGAGGAGGCTACAACGAG
32970180 GCAAGCGGAG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 1 0.01
66 77 0.99
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTACAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:32970191 original size:21 final size:21
Alignment explanation
Indices: 32970165--32970207 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
32970155 AACTTAAAGT
32970165 GGAGGCAACAGCGAGGCAAGC
1 GGAGGCAACAGCGAGGCAAGC
*
32970186 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAACAGCGAGGCAAGC
32970207 G
1 G
32970208 AAGGAAGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.47, T:0.00
Consensus pattern (21 bp):
GGAGGCAACAGCGAGGCAAGC
Found at i:32970216 original size:21 final size:21
Alignment explanation
Indices: 32970173--32970217 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
32970163 GTGGAGGCAA
* *
32970173 CAGCGAGGCAAGCGGAGGCAG
1 CAGCGAGGCAAGCGAAGGAAG
32970194 CAGCGAGGCAAGCGAAGGAAG
1 CAGCGAGGCAAGCGAAGGAAG
32970215 CAG
1 CAG
32970218 AGGCTACAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.44, T:0.00
Consensus pattern (21 bp):
CAGCGAGGCAAGCGAAGGAAG
Found at i:32970566 original size:43 final size:43
Alignment explanation
Indices: 32970518--32970848 Score: 450
Period size: 43 Copynumber: 7.7 Consensus size: 43
32970508 CTGTTATATT
*
32970518 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
* *
32970561 AGCGGCGCTTCTGGAGAAAGCGCCGCTAAAGGACATGGCCTTC
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
* * * *
32970604 AGCGGCGCTTGTGGAAAAAACGCCGCTGAAGGACATGGCCTTC
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
* * *
32970647 AACGGCGCTTTTGGATG-AAGCGCCGCTGAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGA-GAAAGCGCCGCTAAAGAACATGGCCTTC
*
32970690 AGCGGCGCTTCTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
* ** ****
32970733 AGCGACGCTTGTTAATCCTGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
32970776 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
* * *
32970819 AACGGCGCTTATGG-GTAAGCGCCGCTAAAG
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAG
32970849 GTCATGTTCT
Statistics
Matches: 253, Mismatches: 33, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
42 16 0.06
43 237 0.94
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.18
Consensus pattern (43 bp):
AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTC
Found at i:32970886 original size:129 final size:130
Alignment explanation
Indices: 32970518--32970889 Score: 479
Period size: 129 Copynumber: 2.9 Consensus size: 130
32970508 CTGTTATATT
*
32970518 AGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTCTGGAGAAAGCG
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTCTGGAGAAAGCG
* * * * * *
32970583 CCGCTAAAGGACATGGCCTTCAGCGGCGC-TTGTGGAAAAAACGCCGCTGAAGGACATGGCCTTC
66 CCGCTAAAGGACATGGCCTTCAGCGGCGCTTTTTCGCATAAACGCCGCTAAAGAACATGGCCTTC
* * *
32970647 AACGGCGCTTTTGGATG-AAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTCTGGAGAAAGC
1 AGCGGCGCTTGTGGA-GAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTCTGGAGAAAGC
* * *
32970711 GCCGCTAAAGAACATGGCCTTCAGCGACGCTTGTTAATC-C-T--GCGCCGCTAAAGAACATGGC
65 GCCGCTAAAGGACATGGCCTTCAGCGGCGCTT-TT--TCGCATAAACGCCGCTAAAGAACATGGC
32970772 CTTC
127 CTTC
* * *
32970776 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTCAACGGCGCTTATGG-GTAAGCG
1 AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTCTGGAGAAAGCG
* ** *
32970840 CCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCGCATAAACGCCGCTA
66 CCGCTAAAGGACATGGCCTTCAGCGGCGCTTTTTCGCATAAACGCCGCTA
32970890 TTTTTTGCGG
Statistics
Matches: 207, Mismatches: 26, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
125 2 0.01
126 1 0.00
127 3 0.01
128 32 0.15
129 166 0.80
130 1 0.00
131 1 0.00
133 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.20
Consensus pattern (130 bp):
AGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTCTGGAGAAAGCG
CCGCTAAAGGACATGGCCTTCAGCGGCGCTTTTTCGCATAAACGCCGCTAAAGAACATGGCCTTC
Found at i:32971369 original size:22 final size:22
Alignment explanation
Indices: 32971330--32971384 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
32971320 TGTATATTGA
*
32971330 ATAT-TTTAAAAATGTTTTAATT
1 ATATATTTGAAAATGTTTT-ATT
*
32971352 AT-TATTTGAAAATTTTTTATT
1 ATATATTTGAAAATGTTTTATT
32971373 ATAATATTTGAA
1 AT-ATATTTGAA
32971385 TTGTTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.21
22 14 0.50
23 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATATATTTGAAAATGTTTTATT
Found at i:32971373 original size:21 final size:23
Alignment explanation
Indices: 32971330--32971384 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
32971320 TGTATATTGA
*
32971330 ATAT-TTTAAAAATGTTTTAATT
1 ATATATTTGAAAATGTTTTAATT
*
32971352 AT-TATTTGAAAAT-TTTTTATT
1 ATATATTTGAAAATGTTTTAATT
32971373 ATAATATTTGAA
1 AT-ATATTTGAA
32971385 TTGTTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 10 0.36
22 10 0.36
23 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
ATATATTTGAAAATGTTTTAATT
Found at i:32971380 original size:23 final size:24
Alignment explanation
Indices: 32971329--32971384 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
32971319 TTGTATATTG
*
32971329 AATATTTTAAAAATGTTTTAATTAT
1 AATA-TTTGAAAATGTTTTAATTAT
*
32971354 --TATTTGAAAAT-TTTTTATTAT
1 AATATTTGAAAATGTTTTAATTAT
32971375 AATATTTGAA
1 AATATTTGAA
32971385 TTGTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 9 0.33
22 8 0.30
23 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (24 bp):
AATATTTGAAAATGTTTTAATTAT
Found at i:32974385 original size:10 final size:9
Alignment explanation
Indices: 32974328--32974387 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
32974318 AAAAACTAAT
32974328 AAATTATTAA
1 AAATTATT-A
32974338 AAATTA-TA
1 AAATTATTA
*
32974346 AAATTAATA
1 AAATTATTA
*
32974355 AAATATATTT
1 AAAT-TATTA
*
32974365 AAA-TATAA
1 AAATTATTA
32974373 AAATGTATTA
1 AAAT-TATTA
32974383 AAATT
1 AAATT
32974388 CTAATAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 13 0.32
9 8 0.20
10 20 0.49
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
AAATTATTA
Found at i:32974865 original size:9 final size:9
Alignment explanation
Indices: 32974853--32974903 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
32974843 TTTTATGATT
32974853 TTTTTATAA
1 TTTTTATAA
32974862 TTTTTATAA
1 TTTTTATAA
* *
32974871 GCTTATATTAA
1 -TTTTTA-TAA
*
32974882 TTTTAAT-A
1 TTTTTATAA
32974890 TTTTTATAA
1 TTTTTATAA
32974899 TTTTT
1 TTTTT
32974904 TACAATTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
8 7 0.21
9 16 0.48
10 7 0.21
11 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:32974992 original size:27 final size:28
Alignment explanation
Indices: 32974931--32974993 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
32974921 TTTTAATACG
32974931 TTTTTAA-TTTAAATATTTTAAATAAGCT
1 TTTTTAATTTTAAATATTTT-AATAAGCT
* *
32974959 TTATTAATTTTATAATA-TTT-ATAAGTT
1 TTTTTAATTTTA-AATATTTTAATAAGCT
32974986 TTTTTAAT
1 TTTTTAAT
32974994 AATTTTAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 13 0.43
28 6 0.20
29 7 0.23
30 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTTAATTTTAAATATTTTAATAAGCT
Found at i:32978606 original size:23 final size:22
Alignment explanation
Indices: 32978580--32978626 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
32978570 TTTTAATGCA
* *
32978580 TATTTTAGTTTCTATTATTTTTT
1 TATTTTAATTTCTAAT-TTTTTT
*
32978603 TATTTTAATTTTTAATTTTTTT
1 TATTTTAATTTCTAATTTTTTT
32978625 TA
1 TA
32978627 CCTCAACCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TATTTTAATTTCTAATTTTTTT
Found at i:32979216 original size:15 final size:16
Alignment explanation
Indices: 32979169--32979216 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
32979159 ATTGTTTCTC
32979169 AAAAATATTTTTGAAAT
1 AAAAATATTTTT-AAAT
* *
32979186 AAAAATATTATAAAAT
1 AAAAATATTTTTAAAT
*
32979202 -AAAATGTTTTTAAAT
1 AAAAATATTTTTAAAT
32979217 TTTTTAAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 4 0.15
17 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (16 bp):
AAAAATATTTTTAAAT
Found at i:32980040 original size:47 final size:46
Alignment explanation
Indices: 32979969--32980063 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 46
32979959 ATTGTTTTAG
* * * * *
32979969 AAAATTTTTAAACTTTTAATTTTTTATATATTTTTTAGAATTTTAAA
1 AAAATTTATAAACTTTTAAATTTTTATAAATATTTT-GAAATTTAAA
32980016 AAAATTTATAAA-TTTTGAAATTTTTATAAATATTTTGAAATTTAAA
1 AAAATTTATAAACTTTT-AAATTTTTATAAATATTTTGAAATTTAAA
32980062 AA
1 AA
32980064 TTATTTTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 15 0.36
47 27 0.64
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (46 bp):
AAAATTTATAAACTTTTAAATTTTTATAAATATTTTGAAATTTAAA
Found at i:32980041 original size:18 final size:20
Alignment explanation
Indices: 32980027--32980078 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
32980017 AAATTTATAA
32980027 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTTATAAAT
*
32980047 ATTTTGAAA--TTTAAAAATT
1 ATTTTGAAATTTTTATAAA-T
32980066 ATTTTG-AATTTTT
1 ATTTTGAAATTTTT
32980079 TTTTGTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
ATTTTGAAATTTTTATAAAT
Found at i:32980052 original size:20 final size:21
Alignment explanation
Indices: 32980027--32980079 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
32980017 AAATTTATAA
*
32980027 ATTTTGAAATTTTTATAAA-T
1 ATTTTGAAATTTTTAAAAATT
32980047 ATTTTGAAA--TTTAAAAATT
1 ATTTTGAAATTTTTAAAAATT
*
32980066 ATTTTGAATTTTTT
1 ATTTTGAAATTTTT
32980080 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 7 0.25
19 9 0.32
20 9 0.32
21 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
ATTTTGAAATTTTTAAAAATT
Found at i:32990036 original size:43 final size:42
Alignment explanation
Indices: 32989987--32990080 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
32989977 CCTGATGTTA
**
32989987 GCAAAAAATTTATCCAACTGAATGTGCTTTCCTGATAACTAT
1 GCAAAAAATTTATCCAACTGAATGAACTTTCCTGATAACTAT
* * *
32990029 GCAAAAAATTTATCCAACTGGATGAATTTTCCTGATAACTGT
1 GCAAAAAATTTATCCAACTGAATGAACTTTCCTGATAACTAT
32990071 GCAAAAAATT
1 GCAAAAAATT
32990081 CACCGAGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (42 bp):
GCAAAAAATTTATCCAACTGAATGAACTTTCCTGATAACTAT
Found at i:33000931 original size:8 final size:8
Alignment explanation
Indices: 33000918--33000946 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
33000908 GATCTTCTCA
33000918 TTCTTTTG
1 TTCTTTTG
33000926 TTCTTTTG
1 TTCTTTTG
33000934 TTCTTTTG
1 TTCTTTTG
33000942 TTCTT
1 TTCTT
33000947 CTTCTAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (8 bp):
TTCTTTTG
Found at i:33002732 original size:3 final size:3
Alignment explanation
Indices: 33002724--33002755 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33002714 GAATACTACA
33002724 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
33002756 GTAATTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:33014137 original size:23 final size:22
Alignment explanation
Indices: 33014088--33014137 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
33014078 TTTATATGTT
* *
33014088 TTTGTAGCATGTTTTTTCTCTG
1 TTTGTAGCACGTTTTTCCTCTG
*
33014110 TTTGTAGTACGTTTTTCCTCTG
1 TTTGTAGCACGTTTTTCCTCTG
33014132 TCTTGT
1 T-TTGT
33014138 GGAATGCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.08, C:0.16, G:0.18, T:0.58
Consensus pattern (22 bp):
TTTGTAGCACGTTTTTCCTCTG
Found at i:33021705 original size:57 final size:57
Alignment explanation
Indices: 33021617--33021731 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
33021607 TTGATCCTAC
33021617 CAAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTCGCAATG
1 CAAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTCGCAATG
*
33021674 CAAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCTGTGAGCCCCTCGCAATG
1 CAAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTCGCAATG
33021731 C
1 C
33021732 CAATCTCCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (57 bp):
CAAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTCGCAATG
Found at i:33032943 original size:4 final size:4
Alignment explanation
Indices: 33032928--33032970 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
33032918 TTTCTTTCGT
* * *
33032928 TGTA TGTT TGTA TGTA TGTT TGTA TGTA TGTA TGCA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
33032971 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.53
Consensus pattern (4 bp):
TGTA
Found at i:33032945 original size:12 final size:12
Alignment explanation
Indices: 33032928--33032970 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
33032918 TTTCTTTCGT
33032928 TGTATGTTTGTA
1 TGTATGTTTGTA
33032940 TGTATGTTTGTA
1 TGTATGTTTGTA
* *
33032952 TGTATGTATGCA
1 TGTATGTTTGTA
33032964 TGTATGT
1 TGTATGT
33032971 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.53
Consensus pattern (12 bp):
TGTATGTTTGTA
Found at i:33032975 original size:2 final size:2
Alignment explanation
Indices: 33032968--33032999 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33032958 TATGCATGTA
33032968 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
33033000 GGTTTTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:33038407 original size:59 final size:60
Alignment explanation
Indices: 33038326--33038536 Score: 214
Period size: 59 Copynumber: 3.5 Consensus size: 60
33038316 TTAATCTGAT
* * * **
33038326 AAAAAATTTAAAGTTTTGGGTGTTGGCCATGCAATGGTTGACACCCTTTTTTTTCAGAT-
1 AAAAAATTAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCTTTTTTTTCAGATA
* * * * * * *
33038385 AAAAAATTTAATTTTTTTGGTGTTGGCCATACCATGGCCGACATCCC-TATTTATCTGATA
1 AAAAAATTAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCTTTTTTTTCAGATA
* * * *
33038445 AAAAAA-TCAAATTTTTCT-GTGTTGGTCATGCAATGGCCGACACACTCTTTTTTCAGATAA
1 AAAAAATTAAAATTTTT-TGGTGTTGGCCATGCAATGGCCGACACCCTTTTTTTTCAGAT-A
33038505 AAAAAATTCAAAATTTTTTGGTGTTGGCCATG
1 AAAAAATT-AAAATTTTTTGGTGTTGGCCATG
33038537 TTTATCTGAA
Statistics
Matches: 122, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.02
59 82 0.67
60 17 0.14
61 2 0.02
62 19 0.16
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (60 bp):
AAAAAATTAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCTTTTTTTTCAGATA
Found at i:33038625 original size:103 final size:103
Alignment explanation
Indices: 33038434--33038638 Score: 290
Period size: 103 Copynumber: 2.0 Consensus size: 103
33038424 GACATCCCTA
* *
33038434 TTTATCTGATAAAAAAATCAAATTTTTCTGTGTTGGTCATGCAATGGCCGACACACTCTTTTTTC
1 TTTATCTGATAAAAAAATCAAATTTTTCGGTGTTGGTCATGCAATGACCGACACACTCTTTTTTC
33038499 AGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATG
66 AGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATG
* * * *
33038537 TTTATCTGA-ATAAAAAATTAAATTTTTGGGTGTTGGTCATGCCATGACCGACACCCTCTTTTTA
1 TTTATCTGATA-AAAAAATCAAATTTTTCGGTGTTGGTCATGCAATGACCGACACACTCTTTTT-
* * *
33038601 TCA-A-ATAAAAAATTTAAATTTTTTTGGTGTTGGCCATG
64 TCAGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATG
33038639 CCATGGCCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
102 32 0.35
103 56 0.62
104 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (103 bp):
TTTATCTGATAAAAAAATCAAATTTTTCGGTGTTGGTCATGCAATGACCGACACACTCTTTTTTC
AGATAAAAAAAATTCAAAATTTTTTGGTGTTGGCCATG
Found at i:33038642 original size:61 final size:60
Alignment explanation
Indices: 33038545--33038776 Score: 226
Period size: 57 Copynumber: 3.9 Consensus size: 60
33038535 TGTTTATCTG
* *
33038545 AATAAAAAATTAAATTTTTGGGTGTTGGTCATGCCATGACCGACAC-CCTCTTTTTATCA
1 AATAAAAAATTAAATTTTTTGGTGTTGGCCATGCCATGACCGACACGCCTCTTTTTATCA
* *
33038604 AATAAAAAATTTAAATTTTTTTGGTGTTGGCCATGCCATGGCCGACACGCCT-TTTTTATCT
1 AATAAAAAA-TTAAA-TTTTTTGGTGTTGGCCATGCCATGACCGACACGCCTCTTTTTATCA
** * * * * * *
33038665 GGTAAAAAA-T-CATTTTTTTGTGTTGGCCATGCAATGACCGACACTCC-CTTTTTGTTA
1 AATAAAAAATTAAATTTTTTGGTGTTGGCCATGCCATGACCGACACGCCTCTTTTTATCA
* * ** * *
33038722 GATAAAAAATTTGAA-TTTTTGGTGTTGGCCATTACATGGCCGACAC-CCCCTTTTT
1 AATAAAAAA-TTAAATTTTTTGGTGTTGGCCATGCCATGACCGACACGCCTCTTTTT
33038777 TATCTGGTAA
Statistics
Matches: 144, Mismatches: 21, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
57 45 0.31
58 3 0.02
59 43 0.30
60 6 0.04
61 44 0.31
62 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (60 bp):
AATAAAAAATTAAATTTTTTGGTGTTGGCCATGCCATGACCGACACGCCTCTTTTTATCA
Found at i:33038708 original size:221 final size:218
Alignment explanation
Indices: 33038299--33038753 Score: 589
Period size: 221 Copynumber: 2.1 Consensus size: 218
33038289 GAAAAAAAAA
* * **
33038299 TTTGGTGTCGGCCATTTTTAATCTGATAAAAAATTTAAAGTTTTGGGTGTTGGCCATGCAATGGT
1 TTTGGTGTTGGCCATGTTTAATCTGATAAAAAATTTAAAGTTTTGGGTGTTGGCCATGCAATGAC
* * *
33038364 TGACACCCTTTTTTTTCAGATAAAAAATTTAATTTTTTTGGTGTTGGCCATACCATGGCCGACAT
66 CGACACCCTTTTTTATCAAATAAAAAATTTAATTTTTTTGGTGTTGGCCATACCATGGCCGACAT
* * *
33038429 CCCTATTTATCTGATAAAAAAATCAAATTTTTCTGTGTTGGTCATGCAATGGCCGACACACTCTT
131 CCCTATTTATCTGATAAAAAAATC-AATTTTTCTGTGTTGGCCATGCAATGACCGACACACCCTT
33038494 TTT-TCAGATAAAAAAAATTCAAAATTT
195 TTTGTCAGAT--AAAAAATT-AAAA-TT
* * *
33038521 TTTGGTGTTGGCCATGTTT-ATCTGAATAAAAAA-TTAAATTTTTGGGTGTTGGTCATGCCATGA
1 TTTGGTGTTGGCCATGTTTAATCTG-ATAAAAAATTTAAAGTTTTGGGTGTTGGCCATGCAATGA
*
33038584 CCGACACCCTCTTTTTATCAAATAAAAAATTTAAATTTTTTTGGTGTTGGCCATGCCATGGCCGA
65 CCGACACCCT-TTTTTATCAAATAAAAAATTT-AATTTTTTTGGTGTTGGCCATACCATGGCCGA
* * * *
33038649 CA-CGCCTTTTTTATCTGGT-AAAAAATC-ATTTTTTTGTGTTGGCCATGCAATGACCGACACTC
128 CATC-CC-TATTTATCTGATAAAAAAATCAATTTTTCTGTGTTGGCCATGCAATGACCGACACAC
* **
33038711 CCTTTTTGTTAGATAAAAAATTTGAATT
191 CCTTTTTGTCAGATAAAAAATTAAAATT
33038739 TTTGGTGTTGGCCAT
1 TTTGGTGTTGGCCAT
33038754 TACATGGCCG
Statistics
Matches: 206, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
218 17 0.08
219 2 0.01
220 8 0.04
221 76 0.37
222 50 0.24
223 43 0.21
224 10 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (218 bp):
TTTGGTGTTGGCCATGTTTAATCTGATAAAAAATTTAAAGTTTTGGGTGTTGGCCATGCAATGAC
CGACACCCTTTTTTATCAAATAAAAAATTTAATTTTTTTGGTGTTGGCCATACCATGGCCGACAT
CCCTATTTATCTGATAAAAAAATCAATTTTTCTGTGTTGGCCATGCAATGACCGACACACCCTTT
TTGTCAGATAAAAAATTAAAATT
Found at i:33038777 original size:118 final size:117
Alignment explanation
Indices: 33038566--33038793 Score: 334
Period size: 118 Copynumber: 1.9 Consensus size: 117
33038556 AAATTTTTGG
* *
33038566 GTGTTGGTCATGCCATGACCGACACCCTCTTTTTATCAAATAAAAAATTTAAATTTTTTTGGTGT
1 GTGTTGGCCATGCAATGACCGACACCCTCTTTTTATCAAATAAAAAATTTAAA-TTTTTTGGTGT
* *
33038631 TGGCCATGCCATGGCCGACACGCCTTTTTTATCTGGTAAAAAATCATTTTTTT
65 TGGCCATGACATGGCCGACACCCCTTTTTTATCTGGTAAAAAATCATTTTTTT
* * * *
33038684 GTGTTGGCCATGCAATGACCGACACTCC-CTTTTTGTTAGATAAAAAATTTGAA-TTTTTGGTGT
1 GTGTTGGCCATGCAATGACCGACAC-CCTCTTTTTATCAAATAAAAAATTTAAATTTTTTGGTGT
*
33038747 TGGCCATTACATGGCCGACACCCCCTTTTTTATCTGGTAAAAAATCA
65 TGGCCATGACATGGCCGACA-CCCCTTTTTTATCTGGTAAAAAATCA
33038794 ATTATAAAAT
Statistics
Matches: 99, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
116 28 0.28
117 25 0.25
118 44 0.44
119 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (117 bp):
GTGTTGGCCATGCAATGACCGACACCCTCTTTTTATCAAATAAAAAATTTAAATTTTTTGGTGTT
GGCCATGACATGGCCGACACCCCTTTTTTATCTGGTAAAAAATCATTTTTTT
Found at i:33038789 original size:59 final size:59
Alignment explanation
Indices: 33038537--33038789 Score: 228
Period size: 59 Copynumber: 4.3 Consensus size: 59
33038527 GTTGGCCATG
* * *
33038537 TTTATCTGAATAAAAAATTAAATTTTTGGGTGTTGGTCATGCCATGACCGACACCCTC-TT
1 TTTATCTG-ATAAAAATTTAAATTTTT-GGTGTTGGCCATGCCATGACCGACACCCCCTTT
** * *
33038597 TTTATCAAATAAAAAATTTAAATTTTTTTGGTGTTGGCCATGCCATGGCCGACA-CGCCTTT
1 TTTATCTGAT-AAAAATTTAAA--TTTTTGGTGTTGGCCATGCCATGACCGACACCCCCTTT
* * * * * * *
33038658 TTTATCTGGTAAAAA-ATCATTTTTTTGTGTTGGCCATGCAATGACCGACACTCCCTTT
1 TTTATCTGATAAAAATTTAAATTTTTGGTGTTGGCCATGCCATGACCGACACCCCCTTT
* * ** *
33038716 TTGT-T-AGATAAAAAATTTGAATTTTTGGTGTTGGCCATTACATGGCCGACACCCCCTTT
1 TT-TATCTGAT-AAAAATTTAAATTTTTGGTGTTGGCCATGCCATGACCGACACCCCCTTT
*
33038775 TTTATCTGGTAAAAA
1 TTTATCTGATAAAAA
33038790 ATCAATTATA
Statistics
Matches: 152, Mismatches: 31, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
57 29 0.19
58 14 0.09
59 47 0.31
60 25 0.16
61 32 0.21
62 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (59 bp):
TTTATCTGATAAAAATTTAAATTTTTGGTGTTGGCCATGCCATGACCGACACCCCCTTT
Found at i:33039632 original size:30 final size:30
Alignment explanation
Indices: 33039598--33039689 Score: 130
Period size: 30 Copynumber: 3.1 Consensus size: 30
33039588 TCTGTTTACT
* * * *
33039598 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
*
33039628 TTTTAAATTTAATTTTTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
*
33039658 TTTTAATTTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
33039688 TT
1 TT
33039690 CTAATTATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTGTATA
Found at i:33039661 original size:17 final size:17
Alignment explanation
Indices: 33039641--33039695 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
33039631 TAAATTTAAT
33039641 TTTTAATTTCCTGTATA
1 TTTTAATTTCCTGTATA
33039658 TTTTAA-TT--T-TA-A
1 TTTTAATTTCCTGTATA
33039670 TTTCTAATTTCCTGTATA
1 TTT-TAATTTCCTGTATA
*
33039688 TTCTAATT
1 TTTTAATT
33039696 ATTATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
12 4 0.13
13 5 0.16
14 3 0.10
16 3 0.10
17 13 0.42
18 3 0.10
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (17 bp):
TTTTAATTTCCTGTATA
Found at i:33040591 original size:59 final size:59
Alignment explanation
Indices: 33040503--33041185 Score: 475
Period size: 59 Copynumber: 11.5 Consensus size: 59
33040493 AGAGAAAGTT
* * * * * *
33040503 GGTGTCGGCGATTG-CATGACTAATACCAAAAAATTTGATTTTTTTATCAAATAAATAGG
1 GGTGTCGGCCA-TGACATGACCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAGG
* * * * * *
33040562 GGTGTCGCCCATGGCATTACCAACACCAAAAAAATTGAATTTTTTATCTGA-CAAAAGG
1 GGTGTCGGCCATGACATGACCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAGG
** *
33040620 GAGTGTCAACCATGACATGACCAATATCC-AAAAATTTG-ATTTTTTATTCAGATAAAAAGG
1 G-GTGTCGGCCATGACATGACCAACA-CCAAAAAATTTGAATTTTTTA-TCAGATAAAAAGG
* * * * *
33040680 GGTGTCGGCCATGAAATGGCCAACA-CAAAAAAATTAAATTTTTTTACCAGATAAAAAAGG
1 GGTGTCGGCCATGACATGACCAACACCAAAAAATTTGAA-TTTTTTATCAGAT-AAAAAGG
** *
33040740 GGTGTCGGCCATGGA-ATGACCAACACC-AAAAATTTGAATTTTTTATTTGACAAAAAGG
1 GGTGTCGGCCAT-GACATGACCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAGG
* * * * *
33040798 GAGTGTCGGCCATGAAATGGCCAACACAAAAAAAAATT-AATTTTTTGTCAGATAAAAAAGG
1 G-GTGTCGGCCATGACATGACCAACAC-CAAAAAATTTGAATTTTTTATCAGAT-AAAAAGG
* * * *
33040859 GGTGTCGGCCATGACATGACCAACA-AAAAAAATTCGAAATTTTTATCTA-ACAAAAAGG
1 GGTGTCGGCCATGACATGACCAACACCAAAAAATTTGAATTTTTTATC-AGATAAAAAGG
* * * * * * *
33040917 GAATGTCAGTCATGGCATGACCAACACC-CAAAATTTTAATTTTTTATTCAAATAAAAAGGG
1 G-GTGTCGGCCATGACATGACCAACACCAAAAAATTTGAATTTTTTA-TCAGATAAAAA-GG
* * * * * * *
33040978 GGTGTTGGCCATG-CAATGGCTAAGACCAAAAAAATTTTAAATTTTTTTATCTGA-AAAAAGA
1 GGTGTCGGCCATGAC-ATGACCAACACC-AAAAAA-TTTGAA-TTTTTTATCAGATAAAAAGG
* * * ** * * *
33041039 GGTGTTGACCATTG-CACGGTCAACA-TAAAAAGTTTGATTTTTTTATCAGATAAAAAGG
1 GGTGTCGGCCA-TGACATGACCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAGG
* * * * * * * *
33041097 GATGTCAGTCATTG-CATGGCAAACACCCAAAAATTT-AATTTTTTATCATATTAAAAGGG
1 GGTGTCGGCCA-TGACATGACCAACACCAAAAAATTTGAATTTTTTATCAGA-TAAAAAGG
*
33041156 GGTGTCGGCCATG-CAATGGCCAACACCAAA
1 GGTGTCGGCCATGAC-ATGACCAACACCAAA
33041186 TTTTTTTTCC
Statistics
Matches: 491, Mismatches: 100, Indels: 66
0.75 0.15 0.10
Matches are distributed among these distances:
57 12 0.02
58 91 0.19
59 211 0.43
60 112 0.23
61 38 0.08
62 12 0.02
63 8 0.02
64 7 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (59 bp):
GGTGTCGGCCATGACATGACCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAGG
Found at i:33040809 original size:119 final size:117
Alignment explanation
Indices: 33040503--33041181 Score: 473
Period size: 119 Copynumber: 5.7 Consensus size: 117
33040493 AGAGAAAGTT
* * * * * ** * *
33040503 GGTGTCGGCGATTGCATGACTAATACCAAAAAATTTGATTTTTTTATCAAATAAATAGGGGTGTC
1 GGTGTCGGCCA-TGAATGACCAACACC-AAAAATTTGAATTTTTTATCTGACAAAAAGGGGTGTC
* ** ** * * *
33040568 GCCCATGGCATTACCAACACCAAAAAAATTGAA-TTTTTTATCTG--ACAAAAGG
64 GGCCATGAAATGGCCAACA-CAAAAAAATTTAATTTTTTTATCAGATAAAAAAGG
** * * *
33040620 GAGTGTCAACCATGACATGACCAATATCCAAAAATTTG-ATTTTTTATTCAGATAAAAAGGGGTG
1 G-GTGTCGGCCATGA-ATGACCAACA-CCAAAAATTTGAATTTTTTA-TCTGACAAAAAGGGGTG
* *
33040684 TCGGCCATGAAATGGCCAACACAAAAAAATTAAATTTTTTTACCAGATAAAAAAGG
62 TCGGCCATGAAATGGCCAACACAAAAAAATTTAATTTTTTTATCAGATAAAAAAGG
*
33040740 GGTGTCGGCCATGGAATGACCAACACCAAAAATTTGAATTTTTTATTTGACAAAAAGGGAGTGTC
1 GGTGTCGGCCAT-GAATGACCAACACCAAAAATTTGAATTTTTTATCTGACAAAAAGGG-GTGTC
* *
33040805 GGCCATGAAATGGCCAACACAAAAAAAAATTAA-TTTTTTGTCAGATAAAAAAGG
64 GGCCATGAAATGGCCAACAC-AAAAAAATTTAATTTTTTTATCAGATAAAAAAGG
** * * * *
33040859 GGTGTCGGCCATGACATGACCAACAAAAAAAATTCGAAATTTTTATCTAACAAAAAGGGAATGTC
1 GGTGTCGGCCATGA-ATGACCAACACCAAAAATTTGAATTTTTTATCTGACAAAAAGGG-GTGTC
* * ** * ** * * *
33040924 AGTCATGGCATGACCAACACCCAAAATTTTAA-TTTTTTATTCAAATAAAAAGGG
64 GGCCATGAAATGGCCAACACAAAAAAATTTAATTTTTTTA-TCAGATAAAAAAGG
* * * * * *
33040978 GGTGTTGGCCATGCAATGGCTAAGACCAAAAAAATTTTAAATTTTTTTATCTGA-AAAAAGAGGT
1 GGTGTCGGCCATG-AATGACCAACACC--AAAAA-TTTGAA-TTTTTTATCTGACAAAAAGGGGT
* * * * * * * *
33041042 GTTGACCATTG-CACGGTCAACA-TAAAAAGTTTGATTTTTTTATCAGAT-AAAAAGG
61 GTCGGCCA-TGAAATGGCCAACACAAAAAAATTTAATTTTTTTATCAGATAAAAAAGG
* * * * * * * *
33041097 GATGTCAGTCATTGCATGGCAAACACCCAAAAATTT-AATTTTTTATCAT-ATTAAAAGGGGGTG
1 GGTGTCGGCCA-TGAATGACCAACA-CCAAAAATTTGAATTTTTTATC-TGA-CAAAAAGGGGTG
*
33041160 TCGGCCATGCAATGGCCAACAC
62 TCGGCCATGAAATGGCCAACAC
33041182 CAAATTTTTT
Statistics
Matches: 450, Mismatches: 85, Indels: 53
0.77 0.14 0.09
Matches are distributed among these distances:
115 10 0.02
116 5 0.01
117 47 0.10
118 108 0.24
119 194 0.43
120 38 0.08
121 25 0.06
122 13 0.03
123 10 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (117 bp):
GGTGTCGGCCATGAATGACCAACACCAAAAATTTGAATTTTTTATCTGACAAAAAGGGGTGTCGG
CCATGAAATGGCCAACACAAAAAAATTTAATTTTTTTATCAGATAAAAAAGG
Found at i:33040854 original size:178 final size:177
Alignment explanation
Indices: 33040530--33041185 Score: 571
Period size: 178 Copynumber: 3.7 Consensus size: 177
33040520 GACTAATACC
** * * * * *
33040530 AAAAAATTTGATTTTTTTATCAAATAAATAGGGGTGTC-GCCCATGGCATTACCAACACCAAAAA
1 AAAAAATTAAATTTTTTTACCAGATAAAAAGGGATGTCAG-CCATGGCATGACCAACACC-AAAA
* * ** * * *
33040594 AATTGAATTTTTTATCTGAC-AAAAGGGAGTGTCAACCATGACATGACCAATATCC---AAAAAT
64 ATTTGAATTTTTTATTTGACAAAAAGGGAGTGTCGGCCATGAAATGGCCAACA-CCAAAAAAAAT
* *
33040655 TTGATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGAAATGGCCAACACA
128 TTAATTTTTTA-TCAGATAAAAAGGGGTGTCGGCCATGACATGGCCAACA-A
* * *
33040707 AAAAAATTAAATTTTTTTACCAGATAAAAAAGGGGTGTCGGCCATGGAATGACCAACACCAAAAA
1 AAAAAATTAAATTTTTTTACCAGAT-AAAAAGGGATGTCAGCCATGGCATGACCAACACCAAAAA
*
33040772 TTTGAATTTTTTATTTGACAAAAAGGGAGTGTCGGCCATGAAATGGCCAACA-CAAAAAAAAATT
65 TTTGAATTTTTTATTTGACAAAAAGGGAGTGTCGGCCATGAAATGGCCAACACCAAAAAAAATTT
* *
33040836 AATTTTTTGTCAGATAAAAAAGGGGTGTCGGCCATGACATGACCAACAA
130 AATTTTTTATCAGAT-AAAAAGGGGTGTCGGCCATGACATGGCCAACAA
* * * * *
33040885 AAAAAATTCGAAATTTTTAT-CTA-ACAAAAAGGGAATGTCAGTCATGGCATGACCAACACCCAA
1 AAAAAATT--AAATTTTTTTACCAGATAAAAAGGG-ATGTCAGCCATGGCATGACCAACACCAAA
* ** * * * * * * *
33040948 AATTTTAATTTTTTATTCAAATAAAAAGGGGGTGTTGGCCATGCAATGGCTAAGACCAAAAAAAT
63 AATTTGAATTTTTTATT-TGACAAAAAGGGAGTGTCGGCCATGAAATGGCCAACACCAAAAAAAA
* * * * * * *
33041013 TTTAAATTTTTTTATCTGA-AAAAAGAGGTGTTGACCATTG-CACGGTCAACAT
127 TTT-AA-TTTTTTATCAGATAAAAAGGGGTGTCGGCCA-TGACATGGCCAACAA
* ** * * * * *
33041065 AAAAAGTTTGATTTTTTTATCAGATAAAAAGGGATGTCAGTCATTGCATGGCAAACACCCAAAAA
1 AAAAAATTAAATTTTTTTACCAGATAAAAAGGGATGTCAGCCATGGCATGACCAACA-CCAAAAA
* ** * *
33041130 TTT-AATTTTTTATCAT-ATTAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAAA
65 TTTGAATTTTTTAT-TTGACAAAAAGGGAGTGTCGGCCATGAAATGGCCAACACCAAA
33041186 TTTTTTTTCC
Statistics
Matches: 396, Mismatches: 64, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
176 1 0.00
177 51 0.13
178 155 0.39
179 108 0.27
180 67 0.17
181 4 0.01
182 10 0.03
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (177 bp):
AAAAAATTAAATTTTTTTACCAGATAAAAAGGGATGTCAGCCATGGCATGACCAACACCAAAAAT
TTGAATTTTTTATTTGACAAAAAGGGAGTGTCGGCCATGAAATGGCCAACACCAAAAAAAATTTA
ATTTTTTATCAGATAAAAAGGGGTGTCGGCCATGACATGGCCAACAA
Found at i:33041011 original size:179 final size:176
Alignment explanation
Indices: 33040649--33041185 Score: 539
Period size: 179 Copynumber: 3.0 Consensus size: 176
33040639 ACCAATATCC
* *
33040649 AAAAATTTGATTTTTTATTCAGAT-AAAAAGGGGTGTCGGCCATGAAATGGCCAACACAAAAAAA
1 AAAAATTT-AATTTTT-TTCAGATAAAAAAGGGGTGTCGGCCATGACATGGCCAACA-AAAAAAA
* * * * * * *
33040713 TT-AAATTTTTTTACCAGATAAAAAAGGGGTGTCGGCCATGGAATGACCAACACCAAAAATTTGA
63 TTGAAA--TTTTTATCAGA-AAAAAAGGGATGTCAGTCATGGCATGACCAACACCCAAAATTTTA
** * * * *
33040777 ATTTTTTATT-TGACAAAAAGGGAGTGTCGGCCATGAAATGGCCAACACAAA
125 ATTTTTTATTCAAATAAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAA
* *
33040828 AAAAAATTAATTTTTTGTCAGATAAAAAAGGGGTGTCGGCCATGACATGACCAACAAAAAAAATT
1 AAAAATTTAATTTTTT-TCAGATAAAAAAGGGGTGTCGGCCATGACATGGCCAACAAAAAAAATT
*
33040893 CGAAATTTTTATCTA-ACAAAAAGGGAATGTCAGTCATGGCATGACCAACACCCAAAATTTTAAT
65 -GAAATTTTTATC-AGAAAAAAAGGG-ATGTCAGTCATGGCATGACCAACACCCAAAATTTTAAT
* * *
33040957 TTTTTATTCAAATAAAAAGGGGGTGTTGGCCATGCAATGGCTAAGACCAA
127 TTTTTATTCAAATAAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAA
** * * * * *
33041007 AAAAATTTTAAATTTTTTT-ATCTGAAAAAAGAGGTGTTGACCATTG-CACGGTCAACATAAAAA
1 AAAAA-TTT-AATTTTTTTCAGAT-AAAAAAGGGGTGTCGGCCA-TGACATGGCCAACA-AAAAA
** ** * * * * *
33041070 GTTTGATTTTTTTATCAGATAAAAAGGGATGTCAGTCATTGCATGGCAAACACCCAAAAATTTAA
61 AATTGAAATTTTTATCAGAAAAAAAGGGATGTCAGTCATGGCATGACCAACACCCAAAATTTTAA
* *
33041135 TTTTTTA-TCATATTAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAA
126 TTTTTTATTCAAATAAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAA
33041185 A
1 A
33041186 TTTTTTTTCC
Statistics
Matches: 301, Mismatches: 44, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
177 9 0.03
178 108 0.36
179 118 0.39
180 49 0.16
181 17 0.06
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (176 bp):
AAAAATTTAATTTTTTTCAGATAAAAAAGGGGTGTCGGCCATGACATGGCCAACAAAAAAAATTG
AAATTTTTATCAGAAAAAAAGGGATGTCAGTCATGGCATGACCAACACCCAAAATTTTAATTTTT
TATTCAAATAAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCAA
Found at i:33059276 original size:71 final size:70
Alignment explanation
Indices: 33059160--33059305 Score: 265
Period size: 71 Copynumber: 2.1 Consensus size: 70
33059150 CTAGACGATC
*
33059160 AAAGAGACATATAGTAGACACGGAAAGTGCTAATAAACCAAACAGTTTTTACTGTGCATCAAATT
1 AAAGAGACATATAGTAGACACAGAAAGTGCTAATAAACCAAACAG-TTTTACTGTGCATCAAATT
33059225 AAATAT
65 AAATAT
*
33059231 AAAGAGACATATAGTAGACACAGAAAGTGCTAATAAACCAAACAGTTTTAGTGTGCATCAAATTA
1 AAAGAGACATATAGTAGACACAGAAAGTGCTAATAAACCAAACAGTTTTACTGTGCATCAAATTA
33059296 AATAT
66 AATAT
33059301 AAAGA
1 AAAGA
33059306 AGTAGTTAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 29 0.40
71 44 0.60
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (70 bp):
AAAGAGACATATAGTAGACACAGAAAGTGCTAATAAACCAAACAGTTTTACTGTGCATCAAATTA
AATAT
Found at i:33073764 original size:13 final size:13
Alignment explanation
Indices: 33073746--33073854 Score: 119
Period size: 13 Copynumber: 8.2 Consensus size: 13
33073736 TTTTTTGAAA
33073746 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
33073759 AAAGTCAACGGTT
1 AAAGTCAACGGTC
**
33073772 AGTGGTCAACGGTC
1 A-AAGTCAACGGTC
*
33073786 AAAGTCAACGGCC
1 AAAGTCAACGGTC
** *
33073799 AGTGGTCAACAGTC
1 A-AAGTCAACGGTC
*
33073813 AAAGTCAACGTTC
1 AAAGTCAACGGTC
33073826 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
33073839 AAAGTCAACGATC
1 AAAGTCAACGGTC
33073852 AAA
1 AAA
33073855 CAACACCGAT
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
13 58 0.75
14 19 0.25
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:33073787 original size:27 final size:27
Alignment explanation
Indices: 33073749--33073848 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
33073739 TTTGAAAAAA
33073749 GTCAACGGTCAAAGTCAACGGTTAGTG
1 GTCAACGGTCAAAGTCAACGGTTAGTG
**
33073776 GTCAACGGTCAAAGTCAACGGCCAGTG
1 GTCAACGGTCAAAGTCAACGGTTAGTG
* **
33073803 GTCAACAGTCAAAGTCAAC-GTTCA-AA
1 GTCAACGGTCAAAGTCAACGGTT-AGTG
33073829 GTCAACGGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
33073849 ATCAAACAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 19 0.30
27 44 0.70
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
GTCAACGGTCAAAGTCAACGGTTAGTG
Found at i:33073879 original size:21 final size:20
Alignment explanation
Indices: 33073855--33073898 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
33073845 AACGATCAAA
*
33073855 CAACACCGATCAACGGTCGGT
1 CAACACCGATCAAC-ATCGGT
* *
33073876 CAACGCCGGTCAACATCGGT
1 CAACACCGATCAACATCGGT
33073896 CAA
1 CAA
33073899 TGGTTTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.30, C:0.34, G:0.23, T:0.14
Consensus pattern (20 bp):
CAACACCGATCAACATCGGT
Found at i:33073975 original size:21 final size:22
Alignment explanation
Indices: 33073949--33073994 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
33073939 TGGTTCAAAA
33073949 GGGTTTGGTTTAAAT-GAATTT
1 GGGTTTGGTTTAAATAGAATTT
*
33073970 GGGTTTGGTTTAAATAGGATTT
1 GGGTTTGGTTTAAATAGAATTT
33073992 GGG
1 GGG
33073995 CTTAATGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (22 bp):
GGGTTTGGTTTAAATAGAATTT
Found at i:33074478 original size:10 final size:10
Alignment explanation
Indices: 33074463--33074497 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
33074453 TAAGGCAATG
33074463 GAAAAAGAAA
1 GAAAAAGAAA
33074473 GAAAAAG-AA
1 GAAAAAGAAA
33074482 -AAAAAGAAA
1 GAAAAAGAAA
33074491 GAAAAAG
1 GAAAAAG
33074498 GTTTGGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.26
9 4 0.17
10 13 0.57
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:33079939 original size:3 final size:3
Alignment explanation
Indices: 33079931--33079972 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
33079921 TACATCCCAA
33079931 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
33079973 GAATAGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:33081049 original size:20 final size:20
Alignment explanation
Indices: 33081024--33081104 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
33081014 TGAAAAAGTA
*
33081024 AACGGTCAAAGTCAATGGTC
1 AACGGTCAAAGTCAACGGTC
*
33081044 AACGGTCAAAGTCAACGGCC
1 AACGGTCAAAGTCAACGGTC
** *
33081064 AGTGGTCAACAGTCAA-AGTC
1 AACGGTCAA-AGTCAACGGTC
**
33081084 AACATTCAAAGTCAACGGTC
1 AACGGTCAAAGTCAACGGTC
33081104 A
1 A
33081105 GACAACACCG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
19 6 0.12
20 36 0.75
21 6 0.12
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
AACGGTCAAAGTCAACGGTC
Found at i:33081057 original size:13 final size:13
Alignment explanation
Indices: 33081041--33081104 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
33081031 AAAGTCAATG
33081041 GTCAACGGTCAAA
1 GTCAACGGTCAAA
* **
33081054 GTCAACGGCCAGTG
1 GTCAACGGTCA-AA
*
33081068 GTCAACAGTCAAA
1 GTCAACGGTCAAA
**
33081081 GTCAACATTCAAA
1 GTCAACGGTCAAA
33081094 GTCAACGGTCA
1 GTCAACGGTCA
33081105 GACAACACCG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
13 31 0.77
14 9 0.22
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:33081119 original size:21 final size:21
Alignment explanation
Indices: 33081094--33081142 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
33081084 AACATTCAAA
33081094 GTCAACGGTCAGACAACACCG
1 GTCAACGGTCAGACAACACCG
* * **
33081115 GTCAACGGTCGGTCAACGTCG
1 GTCAACGGTCAGACAACACCG
33081136 GTCAACG
1 GTCAACG
33081143 CCGGTCAACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.14
Consensus pattern (21 bp):
GTCAACGGTCAGACAACACCG
Found at i:33081135 original size:10 final size:10
Alignment explanation
Indices: 33081113--33081160 Score: 78
Period size: 10 Copynumber: 4.7 Consensus size: 10
33081103 CAGACAACAC
33081113 CGGTCAACGGT
1 CGGTCAAC-GT
33081124 CGGTCAACGT
1 CGGTCAACGT
*
33081134 CGGTCAACGC
1 CGGTCAACGT
33081144 CGGTCAACGT
1 CGGTCAACGT
33081154 CGGTCAA
1 CGGTCAA
33081161 TGGTTTGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 27 0.77
11 8 0.23
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:33081748 original size:9 final size:10
Alignment explanation
Indices: 33081725--33081760 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
33081715 TAAGGCAAGG
33081725 GAAAAAGAAA
1 GAAAAAGAAA
33081735 GAAAAAGAAA
1 GAAAAAGAAA
33081745 -AAAAAGAAA
1 GAAAAAGAAA
33081754 GAAAAAG
1 GAAAAAG
33081761 GTTTGGGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:33082465 original size:34 final size:34
Alignment explanation
Indices: 33082404--33082485 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
33082394 TTTGGATTGT
* * * *
33082404 TTTTAAAATTTTAATTTATTTTAAGTTTAATTTTA
1 TTTT-AAATTTAAACTTACTTTAAGTTTAAATTTA
*
33082439 TTTTAAATTTAAACTTACTTTGAGTTTAAATTTA
1 TTTTAAATTTAAACTTACTTTAAGTTTAAATTTA
*
33082473 TTTTAAAATTAAA
1 TTTTAAATTTAAA
33082486 ATTTAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 37 0.90
35 4 0.10
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTTAAATTTAAACTTACTTTAAGTTTAAATTTA
Found at i:33082484 original size:17 final size:17
Alignment explanation
Indices: 33082404--33082490 Score: 84
Period size: 17 Copynumber: 5.0 Consensus size: 17
33082394 TTTGGATTGT
*
33082404 TTTTAAAATTTTAATTTA
1 TTTT-AAATTTAAATTTA
* *
33082422 TTTTAAGTTTAATTTTA
1 TTTTAAATTTAAATTTA
*
33082439 TTTTAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
* * *
33082456 CTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
33082473 TTTTAAAATTAAAATTTA
1 TTTT-AAATTTAAATTTA
33082491 ATTAAAAGTG
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
17 40 0.74
18 14 0.26
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:33084446 original size:30 final size:30
Alignment explanation
Indices: 33084369--33084478 Score: 84
Period size: 30 Copynumber: 3.7 Consensus size: 30
33084359 CCCAGGAGGT
* *
33084369 CCCT-AAACTATC-TAAAAATCATATTTTGA
1 CCCTCAAACT-TCATAAAAATTATATTTTAA
* * *
33084398 CCC-CTTAAGTTCACAAAAATTATATTTTAA
1 CCCTC-AAACTTCATAAAAATTATATTTTAA
* * **
33084428 CCCTCGAACTTCATAAAAATTACATTTTTG
1 CCCTCAAACTTCATAAAAATTATATTTTAA
*
33084458 CCCTTAAACTTC-TAAAAATTA
1 CCCTCAAACTTCATAAAAATTA
33084479 CCATTTTACC
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
29 14 0.22
30 49 0.77
31 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTCATAAAAATTATATTTTAA
Found at i:33084475 original size:59 final size:58
Alignment explanation
Indices: 33084412--33084578 Score: 178
Period size: 59 Copynumber: 2.8 Consensus size: 58
33084402 TTAAGTTCAC
*
33084412 AAAAATTA-TATTTTAACCCTCGAACT-TCATAAAAATTACATTTTTGCCCTTAAACTTCT
1 AAAAATTACTATTTT-ACCCTCGAA-TGTC-TAAAAATTACATTTTTGCCCTGAAACTTCT
* * * * * * *
33084471 AAAAATTACCATTTTACCCCCGGATGTTTGAAAATTCCATTTTTGACTCC-GAAATTTCT
1 AAAAATTACTATTTTACCCTCGAATGTCTAAAAATTACATTTTTG-C-CCTGAAACTTCT
* *
33084530 AAAAATTACTATTTTACCCTCGAATGTCCAAAAATTACATTTCTGCCCT
1 AAAAATTACTATTTTACCCTCGAATGTCTAAAAATTACATTTTTGCCCT
33084579 CGAGTGTCCA
Statistics
Matches: 87, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
57 2 0.02
58 17 0.20
59 61 0.70
60 7 0.08
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (58 bp):
AAAAATTACTATTTTACCCTCGAATGTCTAAAAATTACATTTTTGCCCTGAAACTTCT
Found at i:33084564 original size:29 final size:29
Alignment explanation
Indices: 33084530--33084638 Score: 123
Period size: 29 Copynumber: 3.8 Consensus size: 29
33084520 CGAAATTTCT
33084530 AAAAATTACTATTTTACCCTCGAATGTCC
1 AAAAATTACTATTTTACCCTCGAATGTCC
* *
33084559 AAAAATTAC-ATTTCTGCCCTCGAGTGTCC
1 AAAAATTACTATTT-TACCCTCGAATGTCC
* * *
33084588 AAAAATTACTATTTTGCCATTGAAGTGTCC
1 AAAAATTACTATTTTACCCTCGAA-TGTCC
**
33084618 -AAAATTACCGTTTTACCCTCG
1 AAAAATTACTATTTTACCCTCG
33084639 GGCATCCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.06
29 54 0.81
30 9 0.13
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (29 bp):
AAAAATTACTATTTTACCCTCGAATGTCC
Found at i:33084617 original size:30 final size:30
Alignment explanation
Indices: 33084530--33084625 Score: 128
Period size: 29 Copynumber: 3.3 Consensus size: 30
33084520 CGAAATTTCT
*
33084530 AAAAATTACTATTTTACCCTCGAA-TGTCC
1 AAAAATTACTATTTTGCCCTCGAAGTGTCC
33084559 AAAAATTAC-ATTTCTGCCCTCG-AGTGTCC
1 AAAAATTACTATTT-TGCCCTCGAAGTGTCC
* *
33084588 AAAAATTACTATTTTGCCATTGAAGTGTCC
1 AAAAATTACTATTTTGCCCTCGAAGTGTCC
33084618 -AAAATTAC
1 AAAAATTAC
33084626 CGTTTTACCC
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
28 5 0.08
29 44 0.73
30 11 0.18
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (30 bp):
AAAAATTACTATTTTGCCCTCGAAGTGTCC
Found at i:33084647 original size:58 final size:58
Alignment explanation
Indices: 33084530--33084651 Score: 140
Period size: 58 Copynumber: 2.1 Consensus size: 58
33084520 CGAAATTTCT
* * **
33084530 AAAAATTACTATTTTACCCTCGAATGTCCAAAAATTACATTTCTGCCCTCGAGTGTCC
1 AAAAATTACTATTTTACCATCGAATGTCCAAAAATTACATTTCTACCCTCGAGCATCC
* * * *
33084588 AAAAATTACTATTTTGCCATTGAAGTGTCC-AAAATTACCGTTT-TACCCTCGGGCATCC
1 AAAAATTACTATTTTACCATCGAA-TGTCCAAAAATTA-CATTTCTACCCTCGAGCATCC
33084646 AAAAAT
1 AAAAAT
33084652 CGCATTTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 45 0.83
59 9 0.17
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (58 bp):
AAAAATTACTATTTTACCATCGAATGTCCAAAAATTACATTTCTACCCTCGAGCATCC
Found at i:33089275 original size:23 final size:23
Alignment explanation
Indices: 33089249--33089294 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
33089239 ACCGAGTATG
33089249 ATCTAAAAAATACATTTCATTGT
1 ATCTAAAAAATACATTTCATTGT
33089272 ATCTAAAAAATACATTTCATTGT
1 ATCTAAAAAATACATTTCATTGT
33089295 TTGAAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (23 bp):
ATCTAAAAAATACATTTCATTGT
Found at i:33093760 original size:124 final size:124
Alignment explanation
Indices: 33093591--33093840 Score: 500
Period size: 124 Copynumber: 2.0 Consensus size: 124
33093581 AAACTTGAAG
33093591 CTTATTAAGAACTCTATCCTTTATAAAACTCATAGCCATCTTTTTGTTTTACCTCAGACAAAAGG
1 CTTATTAAGAACTCTATCCTTTATAAAACTCATAGCCATCTTTTTGTTTTACCTCAGACAAAAGG
33093656 AATCCCCAAATAAGTACTCGGATTATCAGCCTTAGAAATTTGCAACATGTCTGCCAGTT
66 AATCCCCAAATAAGTACTCGGATTATCAGCCTTAGAAATTTGCAACATGTCTGCCAGTT
33093715 CTTATTAAGAACTCTATCCTTTATAAAACTCATAGCCATCTTTTTGTTTTACCTCAGACAAAAGG
1 CTTATTAAGAACTCTATCCTTTATAAAACTCATAGCCATCTTTTTGTTTTACCTCAGACAAAAGG
33093780 AATCCCCAAATAAGTACTCGGATTATCAGCCTTAGAAATTTGCAACATGTCTGCCAGTT
66 AATCCCCAAATAAGTACTCGGATTATCAGCCTTAGAAATTTGCAACATGTCTGCCAGTT
33093839 CT
1 CT
33093841 CTCCTCTTCT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 126 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (124 bp):
CTTATTAAGAACTCTATCCTTTATAAAACTCATAGCCATCTTTTTGTTTTACCTCAGACAAAAGG
AATCCCCAAATAAGTACTCGGATTATCAGCCTTAGAAATTTGCAACATGTCTGCCAGTT
Found at i:33095131 original size:13 final size:14
Alignment explanation
Indices: 33095115--33095147 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
33095105 CCCCACATTT
33095115 ATTTT-CCCCCAAA
1 ATTTTACCCCCAAA
33095128 ATTTTACCCCCAAA
1 ATTTTACCCCCAAA
33095142 ACTTTT
1 A-TTTT
33095148 TATTTCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 9 0.50
15 4 0.22
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTTTACCCCCAAA
Found at i:33097768 original size:16 final size:16
Alignment explanation
Indices: 33097735--33097771 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
33097725 TTAGTTTTGA
33097735 TAAAAAATATTAATTG
1 TAAAAAATATTAATTG
33097751 TAAATAAATATTAA-TG
1 TAAA-AAATATTAATTG
33097767 TAAAA
1 TAAAA
33097772 CTCAAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 10 0.50
17 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
TAAAAAATATTAATTG
Found at i:33098090 original size:12 final size:12
Alignment explanation
Indices: 33098073--33098121 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
33098063 TTAGTATTGT
33098073 TTTTGAAAAATA
1 TTTTGAAAAATA
33098085 TTTTGAAAAAGTGA
1 TTTTGAAAAA-T-A
*
33098099 TTTTGAAAAGTA
1 TTTTGAAAAATA
*
33098111 TTTTTAAAAAT
1 TTTTGAAAAAT
33098122 TTTGGTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 20 0.62
13 2 0.06
14 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (12 bp):
TTTTGAAAAATA
Found at i:33104309 original size:34 final size:34
Alignment explanation
Indices: 33104266--33104333 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
33104256 GATAACATTG
33104266 TCATTGATCACCACAAAGAAAGATTGATCAATTA
1 TCATTGATCACCACAAAGAAAGATTGATCAATTA
33104300 TCATTGATCACCACAAAGAAAGATTGATCAATTA
1 TCATTGATCACCACAAAGAAAGATTGATCAATTA
33104334 GATCAATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (34 bp):
TCATTGATCACCACAAAGAAAGATTGATCAATTA
Found at i:33106836 original size:73 final size:74
Alignment explanation
Indices: 33106699--33106842 Score: 245
Period size: 73 Copynumber: 1.9 Consensus size: 74
33106689 GGAAAAAAAG
*
33106699 AGAACTTTATCAGTAACATGTGATAGATAATGTTGTTCTAATTGAAGGCTTCTCAGCAAAACAAG
1 AGAACTTTATCAGTAACATGTGATAG--AATGATGTTCTAATTGAAGGCTTCTCAGCAAAACAAG
33106764 AGTATGGTAAA
64 AGTATGGTAAA
*
33106775 AGAACTTTATGAGTAACATGTGATAG-ATGATGTTCTAATTGAAGGCTTCTCAGCAAAACAAGAG
1 AGAACTTTATCAGTAACATGTGATAGAATGATGTTCTAATTGAAGGCTTCTCAGCAAAACAAGAG
33106839 TATG
66 TATG
33106843 ATAGGAGGAT
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
73 41 0.62
76 25 0.38
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (74 bp):
AGAACTTTATCAGTAACATGTGATAGAATGATGTTCTAATTGAAGGCTTCTCAGCAAAACAAGAG
TATGGTAAA
Found at i:33121014 original size:85 final size:83
Alignment explanation
Indices: 33120759--33121051 Score: 293
Period size: 85 Copynumber: 3.5 Consensus size: 83
33120749 TTTTTATTAC
** * * *
33120759 TATTTATTTGTATATTTGTTACTTAATTAGTATAAATAAACTAATTAAATACTGAAATGACATAT
1 TATTTATTTGTATGCTTATTACTTAATTAGTATAAAAAAACTAATTAAATACTGAAATGGCATAT
* * * * *
33120824 TTGAGATATTATTATTAT
66 TTGATATTTTTTTGTAAT
* * * * *
33120842 TATTTATTTGTATGCTTCTTAC--AATTAGTATGAAAAAAACTAATTAAGTACTGAAATAGTATG
1 TATTTATTTGTATGCTTATTACTTAATTAGTAT-AAAAAAACTAATTAAATACTGAAATGGCATA
*
33120905 TTTGAGATTTTTTTGTATTAT
65 TTTGATATTTTTTTGTA--AT
* * * * *
33120926 TATTTATTTGTATGCTTATCACTTAATTAGTATCAAGAAATTAATTAAATACTGGAATGGCATAT
1 TATTTATTTGTATGCTTATTACTTAATTAGTATAAAAAAACTAATTAAATACTGAAATGGCATAT
*
33120991 TTGATTTTTTTTTTGTAAAT
66 TTGA-TATTTTTTTGT-AAT
* * *
33121011 TATTTATTTGTATGCTTCTTATTTATTTAGTATGAAAAAAA
1 TATTTATTTGTATGCTTATTACTTAATTAGTAT-AAAAAAA
33121052 AATAGTGAAA
Statistics
Matches: 171, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
81 9 0.05
82 38 0.22
83 19 0.11
84 22 0.13
85 59 0.35
86 23 0.13
87 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (83 bp):
TATTTATTTGTATGCTTATTACTTAATTAGTATAAAAAAACTAATTAAATACTGAAATGGCATAT
TTGATATTTTTTTGTAAT
Found at i:33122093 original size:176 final size:178
Alignment explanation
Indices: 33121814--33122237 Score: 486
Period size: 176 Copynumber: 2.4 Consensus size: 178
33121804 GACAAAATTT
* * * * *
33121814 TTTTTTTAGTGTTGA-CCATTGCATGGTTGAAACCTCCTTTTAATCTG-ATAAAAAAATAAAAAT
1 TTTTTTTAGTGTTGAGCCATTGCATGGCTGACACC-CCTTTT-ATTTGAAT-AAAAAATTAAATT
* * *
33121877 TTTGGGTGTTGGTCATGCAATGATCGACGCCCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTA
63 TTTGGGCGTTGGTCATGCAATGAGCGACACCCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTA
* *
33121942 ATGTTGGTCATGTCATGGCCGGCACT-CC-TATTATCTGATAAAAAATTAA
128 ATGTTGGTCATGCCATGGCCGACACTCCCTTATTATCTGATAAAAAATTAA
*
33121991 TTTTTTTGGTG-TGAGCCATTGCATGGCTGACACCCCTTCTTATTTGAATAAAAAATTAAATTTT
1 TTTTTTTAGTGTTGAGCCATTGCATGGCTGACACCCCTT-TTATTTGAATAAAAAATTAAATTTT
* * ** * *
33122055 TGGGCGTTGGTCATGCCATGGGCGACACCCTTTTTTTGTCAGATAAAAAATTTATTTTTTTTAGT
65 TGGGCGTTGGTCATGCAATGAGCGACACCCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTAAT
* * *
33122120 TTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCTGGTAAAAAATTAA
130 GTTGGTCATGCCATGGCCGACACTCCC-TTATTATCTGATAAAAAATTAA
* * ** *
33122170 TTTTTTTTGTGTTG-GCCA-TGCAATGGCCGACATTCCTTTT-TTGTCAAATAAAAAATTCAAAT
1 TTTTTTTAGTGTTGAGCCATTGC-ATGGCTGACACCCCTTTTATT-T-GAATAAAAAATT-AAAT
33122232 TTTTGG
62 TTTTGG
33122238 TGTCGACCAT
Statistics
Matches: 211, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
176 101 0.48
177 35 0.17
178 6 0.03
179 57 0.27
180 12 0.06
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (178 bp):
TTTTTTTAGTGTTGAGCCATTGCATGGCTGACACCCCTTTTATTTGAATAAAAAATTAAATTTTT
GGGCGTTGGTCATGCAATGAGCGACACCCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTAATG
TTGGTCATGCCATGGCCGACACTCCCTTATTATCTGATAAAAAATTAA
Found at i:33122167 original size:61 final size:60
Alignment explanation
Indices: 33121882--33122235 Score: 271
Period size: 60 Copynumber: 6.0 Consensus size: 60
33121872 AAAATTTTGG
* ** * * * *
33121882 GTGTTGGTCATGCAATGATCGACGC-CCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTA
1 GTGTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCAGATAAAAAA-TTAATTTTTTTT
* * * * * *
33121942 ATGTTGGTCATGTCATGGCCGGCACT-CC--TATTATCTGATAAAAAATTAATTTTTTTG
1 GTGTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCAGATAAAAAATTAATTTTTTTT
* * * * **
33121999 GTG-TGAGCCATTG-CATGGCTGACAC-CCCTTCTTATT-TGA-ATAAAAAATTAAATTTTTGG
1 GTGTTG-GTCA-TGCCATGGCCGACACTCCCTT-TT-TTATCAGATAAAAAATTAATTTTTTTT
* * * * *
33122058 GCGTTGGTCATGCCATGGGCGACAC-CCTTTTTTTGTCAGATAAAAAATTTATTTTTTTT
1 GTGTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCAGATAAAAAATTAATTTTTTTT
* * *
33122117 AGTTTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCTGGTAAAAAATTAATTTTTTTT
1 -GTGTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCAGATAAAAAATTAATTTTTTTT
* * * * * *
33122178 GTGTTGGCCATGCAATGGCCGACA-TTCCTTTTTTGTCAAATAAAAAATTCAAATTTTT
1 GTGTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCAGATAAAAAATT-AATTTTTT
33122236 GGTGTCGACC
Statistics
Matches: 232, Mismatches: 47, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
56 2 0.01
57 30 0.13
58 22 0.09
59 73 0.31
60 74 0.32
61 31 0.13
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (60 bp):
GTGTTGGTCATGCCATGGCCGACACTCCCTTTTTTATCAGATAAAAAATTAATTTTTTTT
Found at i:33125664 original size:21 final size:21
Alignment explanation
Indices: 33125623--33125666 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33125613 ATGACAAATA
*
33125623 TTTCAACTTTCTTTTCTCCAT
1 TTTCAACTTTCTTTTCGCCAT
*
33125644 TTTCATCTTTCCTTTT-GCCAT
1 TTTCAACTTT-CTTTTCGCCAT
33125665 TT
1 TT
33125667 CCTTGTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.11, C:0.27, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTCAACTTTCTTTTCGCCAT
Found at i:33130070 original size:31 final size:31
Alignment explanation
Indices: 33130029--33130088 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
33130019 AATATAATTT
33130029 TATACATAAAATTTTAATTATGATTTAAATG
1 TATACATAAAATTTTAATTATGATTTAAATG
* *
33130060 TATACGTAAAATTTTAATTTTGATTTAAA
1 TATACATAAAATTTTAATTATGATTTAAA
33130089 CATAGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (31 bp):
TATACATAAAATTTTAATTATGATTTAAATG
Found at i:33130464 original size:19 final size:18
Alignment explanation
Indices: 33130424--33130471 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
33130414 AAAATTTTAA
*
33130424 AATTTAAATTATCGATATTT
1 AATTTAAA--ATCGATAATT
33130444 AATTTAAAATCAGATAATT
1 AATTTAAAATC-GATAATT
33130463 AA-TTAAAAT
1 AATTTAAAAT
33130472 TAATAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 8 0.31
20 8 0.31
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATTTAAAATCGATAATT
Found at i:33133221 original size:23 final size:23
Alignment explanation
Indices: 33133180--33133227 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
33133170 GTGGAAGAAG
*
33133180 ATTTTTTTTTTTTCCCATTTTATA
1 ATTTTTTTTTTTT-CCATTTCATA
33133204 ATTTTTTCTTTTTT-CATTTCATA
1 ATTTTTT-TTTTTTCCATTTCATA
33133227 A
1 A
33133228 ATTAGTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 7 0.32
25 6 0.27
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTTTTTTTTTCCATTTCATA
Found at i:33137124 original size:41 final size:41
Alignment explanation
Indices: 33137041--33137125 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
33137031 TACCGGAAGT
33137041 AACCACATGATGACATTATCAGCACTGATTGATAACAGAGA
1 AACCACATGATGACATTATCAGCACTGATTGATAACAGAGA
* *
33137082 AACCCCATGATGACATTTATCAGCAGC-GATTGAT-ACATAGA
1 AACCACATGATGACA-TTATCAGCA-CTGATTGATAACAGAGA
33137123 AAC
1 AAC
33137126 ACTGCCTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 23 0.57
42 16 0.40
43 1 0.03
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (41 bp):
AACCACATGATGACATTATCAGCACTGATTGATAACAGAGA
Found at i:33142615 original size:7 final size:7
Alignment explanation
Indices: 33142603--33142642 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
33142593 TTCAGAAAAA
33142603 GTCAACG
1 GTCAACG
*
33142610 GTCAACA
1 GTCAACG
*
33142617 GTCAACA
1 GTCAACG
33142624 GTCAACG
1 GTCAACG
33142631 GTCAACG
1 GTCAACG
33142638 GTCAA
1 GTCAA
33142643 AATCAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:33142628 original size:21 final size:21
Alignment explanation
Indices: 33142602--33142642 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
33142592 TTTCAGAAAA
33142602 AGTCAACGGTCAACAGTCAAC
1 AGTCAACGGTCAACAGTCAAC
*
33142623 AGTCAACGGTCAACGGTCAA
1 AGTCAACGGTCAACAGTCAA
33142643 AATCAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.15
Consensus pattern (21 bp):
AGTCAACGGTCAACAGTCAAC
Found at i:33149839 original size:7 final size:7
Alignment explanation
Indices: 33149816--33149875 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
33149806 TTTGGAAAAA
33149816 GTCAACG
1 GTCAACG
* *
33149823 ATCAA-A
1 GTCAACG
33149829 GTCAACG
1 GTCAACG
33149836 GTCAACG
1 GTCAACG
* *
33149843 ATCAATG
1 GTCAACG
33149850 GTCAACG
1 GTCAACG
*
33149857 GTCAATG
1 GTCAACG
*
33149864 GTCAATG
1 GTCAACG
33149871 GTCAA
1 GTCAA
33149876 TGGTTGGTCA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
6 4 0.09
7 39 0.91
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (7 bp):
GTCAACG
Found at i:33149852 original size:14 final size:14
Alignment explanation
Indices: 33149829--33149879 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
33149819 AACGATCAAA
*
33149829 GTCAACGGTCAACG
1 GTCAATGGTCAACG
*
33149843 ATCAATGGTCAACG
1 GTCAATGGTCAACG
*
33149857 GTCAATGGTCAATG
1 GTCAATGGTCAACG
33149871 GTCAATGGT
1 GTCAATGGT
33149880 TGGTCAACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (14 bp):
GTCAATGGTCAACG
Found at i:33149855 original size:21 final size:21
Alignment explanation
Indices: 33149816--33149875 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
33149806 TTTGGAAAAA
*
33149816 GTCAACGATCAA-AGTCAACG
1 GTCAACGATCAATGGTCAACG
33149836 GTCAACGATCAATGGTCAACG
1 GTCAACGATCAATGGTCAACG
* *
33149857 GTCAATGGTCAATGGTCAA
1 GTCAACGATCAATGGTCAA
33149876 TGGTTGGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 12 0.33
21 24 0.67
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (21 bp):
GTCAACGATCAATGGTCAACG
Found at i:33149876 original size:7 final size:7
Alignment explanation
Indices: 33149829--33149879 Score: 66
Period size: 7 Copynumber: 7.3 Consensus size: 7
33149819 AACGATCAAA
*
33149829 GTCAACG
1 GTCAATG
*
33149836 GTCAACG
1 GTCAATG
*
33149843 ATCAATG
1 GTCAATG
*
33149850 GTCAACG
1 GTCAATG
33149857 GTCAATG
1 GTCAATG
33149864 GTCAATG
1 GTCAATG
33149871 GTCAATG
1 GTCAATG
33149878 GT
1 GT
33149880 TGGTCAACGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (7 bp):
GTCAATG
Found at i:33151024 original size:18 final size:18
Alignment explanation
Indices: 33151001--33151038 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
33150991 ATTACCATGT
33151001 AATCACACCAGTATATTA
1 AATCACACCAGTATATTA
*
33151019 AATCACACTAGTATATTA
1 AATCACACCAGTATATTA
33151037 AA
1 AA
33151039 AAAAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (18 bp):
AATCACACCAGTATATTA
Found at i:33165831 original size:41 final size:41
Alignment explanation
Indices: 33165776--33165869 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
33165766 GTTCGTAGAA
* *
33165776 AATTCTTGTCAAGGT-GTAGATTGTTAGAATTGGGTGACTAG
1 AATTCTTGTTAAGGTAG-AGATTGTTAGAATCGGGTGACTAG
33165817 AATTCTTGTTAAGGTAGAGATTGTTAGAATCGGGTGACTAG
1 AATTCTTGTTAAGGTAGAGATTGTTAGAATCGGGTGACTAG
33165858 AATTCTTGTTAA
1 AATTCTTGTTAA
33165870 AATAAAATTC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 49 0.98
42 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (41 bp):
AATTCTTGTTAAGGTAGAGATTGTTAGAATCGGGTGACTAG
Found at i:33168112 original size:31 final size:30
Alignment explanation
Indices: 33168077--33168169 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 30
33168067 ATTTTAGAAT
*
33168077 TGTGTACAA-TTGAATCAAAATCAAAGTTTTA
1 TGTGTA-AAGTTGAA-CAAAATCAAAGTTTCA
* * *
33168108 TGTGTAAAGTTGAACCAAGTTAAAGTTTCA
1 TGTGTAAAGTTGAACAAAATCAAAGTTTCA
* * * * *
33168138 TGTGTATATTTGCACTAAATCAATG-TTCA
1 TGTGTAAAGTTGAACAAAATCAAAGTTTCA
33168167 TGT
1 TGT
33168170 ATCAAATTGC
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 7 0.14
30 32 0.64
31 11 0.22
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (30 bp):
TGTGTAAAGTTGAACAAAATCAAAGTTTCA
Found at i:33171384 original size:2 final size:2
Alignment explanation
Indices: 33171377--33171402 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33171367 GTTTTGCAAC
33171377 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
33171403 AATAAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33171564 original size:17 final size:17
Alignment explanation
Indices: 33171544--33171578 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
33171534 ACATGAATTT
33171544 TTTTTAAATAAAACTTA
1 TTTTTAAATAAAACTTA
*
33171561 TTTTTAAATAAAATTTA
1 TTTTTAAATAAAACTTA
33171578 T
1 T
33171579 ACATGAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTTAAATAAAACTTA
Found at i:33176839 original size:41 final size:41
Alignment explanation
Indices: 33176763--33177184 Score: 314
Period size: 41 Copynumber: 10.3 Consensus size: 41
33176753 GTTTGGACAC
* * *
33176763 AAAGCGCCGCAAAAGGT-GAAG-CATTAGCGGCGCTTTTCCT
1 AAAGCGCCGCTAAAGGTCG-GGTCATTAGCGGCGCTTTACCT
* * *
33176803 AATGCGCCGCTAAAGGTCGGGTCTTTAGCGGCGCTTTACCC
1 AAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTACCT
** *
33176844 ACAAGCGCCGCTAAAGGTCGATTCATTAGCGGCGC-TTAGAC-
1 A-AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTA-CCT
* * * *
33176885 ACAAGTGCCACTAAAAGTCGGGTCATTAGCGGCGC-TTAGAC-
1 A-AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTA-CCT
* *
33176926 ACAAGCGCCGCTAAAGGTCGAGTCATTAGCGGCGCTTTA-CA
1 A-AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTACCT
* * *
33176967 AAAGCGCCGCTAAAAGTCGGGTTATTAGCGGCGC-TTAGAC-
1 AAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTA-CCT
* * ** *
33177007 ACAAGCGCCACTAAAAGTCGGGTCATTAGCAACGC-TTAGCT
1 A-AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTACCT
* * * **
33177048 ACAAGCACCGCTAATGGTCTGGTCATTAGCGGCGCTTATATAT
1 A-AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTT-TACCT
* * * *
33177091 AAAGCGCCGGTAAAGGTCAGGTTATTAGCGGCGCTTT-TCT
1 AAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTACCT
* * *
33177131 AATAAGCGCCGCTAAAGGT-GTGT-ATTAGCGGCACTTT-TCT
1 -A-AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTACCT
33177171 ATAAGCGCCGCTAA
1 A-AAGCGCCGCTAA
33177185 TTTATTTAAA
Statistics
Matches: 321, Mismatches: 47, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
39 17 0.05
40 67 0.21
41 154 0.48
42 79 0.25
43 4 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTACCT
Found at i:33177025 original size:122 final size:120
Alignment explanation
Indices: 33176806--33177126 Score: 437
Period size: 122 Copynumber: 2.6 Consensus size: 120
33176796 TTTTCCTAAT
* * *
33176806 GCGCCGCTAAAGGTCGGGTCTTTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGATTCATT
1 GCGCCGCTAAAGGTC-GGTCATTAGCGGCGCTTTA--CAAAAGCGCCGCTAAAGGTCGGTT-ATT
* **
33176871 AGCGGCGCTTAGACACAAGTGCCACTAAAAGTCGGGTCATTAGCGGCGCTTAGAC-ACAA
62 AGCGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCAACGCTTAG-CTACAA
*
33176930 GCGCCGCTAAAGGTCGAGTCATTAGCGGCGCTTTACAAAAGCGCCGCTAAAAGTCGGGTTATTAG
1 GCGCCGCTAAAGGTCG-GTCATTAGCGGCGCTTTACAAAAGCGCCGCTAAAGGTC-GGTTATTAG
33176995 CGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCAACGCTTAGCTACAA
64 CGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCAACGCTTAGCTACAA
* * * *
33177052 GCACCGCTAATGGTCTGGTCATTAGCGGCGCTTATATATAAAGCGCCGGTAAAGGTCAGGTTATT
1 GCGCCGCTAAAGGTC-GGTCATTAGCGGCGCTT-TACA-AAAGCGCCGCTAAAGGTC-GGTTATT
33177117 AGCGGCGCTT
62 AGCGGCGCTT
33177127 TTCTAATAAG
Statistics
Matches: 178, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
121 1 0.01
122 104 0.58
123 8 0.04
124 65 0.37
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.21
Consensus pattern (120 bp):
GCGCCGCTAAAGGTCGGTCATTAGCGGCGCTTTACAAAAGCGCCGCTAAAGGTCGGTTATTAGCG
GCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCAACGCTTAGCTACAA
Found at i:33177179 original size:164 final size:163
Alignment explanation
Indices: 33176758--33177184 Score: 449
Period size: 164 Copynumber: 2.6 Consensus size: 163
33176748 GTGACGTTTG
*
33176758 GACACAAAGCGCCGCAAAAGGT-GAAG-CATTAGCGGCGCTTTTCCTAAT--GCGCCGCTAAAGG
1 GACA-AAAGCGCCGCTAAAGGTCG-AGTCATTAGCGGCGCTTTT-CTAATAAGCGCCGCTAAAGG
* * * **
33176819 TCGGGTCTTTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGATTCATTAGCGGCGCTTAGA
63 TCGGGT-ATTAGCGGCGCTTTA--CACAAGCGCCGCTAAAAGTCGAGTCATTAGCAACGCTTAGA
**
33176884 CACAAGTGCCACTAAAAGTCGGGTCATTAGCGGCGCTTA
125 CACAAGCACCACTAAAAGTCGGGTCATTAGCGGCGCTTA
* * *
33176923 GACACAAGCGCCGCTAAAGGTCGAGTCATTAGCGGCGCTTTAC-AA-AAGCGCCGCTAAAAGTCG
1 GACAAAAGCGCCGCTAAAGGTCGAGTCATTAGCGGCGCTTTTCTAATAAGCGCCGCTAAAGGTCG
* * *
33176986 GGTTATTAGCGGCGCTTAGACACAAGCGCCACTAAAAGTCGGGTCATTAGCAACGCTTAG-CTAC
66 GG-TATTAGCGGCGCTT-TACACAAGCGCCGCTAAAAGTCGAGTCATTAGCAACGCTTAGAC-AC
* ** *
33177050 AAGCACCGCTAATGGTCTGGTCATTAGCGGCGCTTA
128 AAGCACCACTAAAAGTCGGGTCATTAGCGGCGCTTA
* * * *
33177086 TATATAAAGCGCCGGTAAAGGTC-AGGTTATTAGCGGCGCTTTTCTAATAAGCGCCGCTAAAGGT
1 GACA-AAAGCGCCGCTAAAGGTCGA-GTCATTAGCGGCGCTTTTCTAATAAGCGCCGCTAAAGGT
* * * *
33177150 -GTGTATTAGCGGCACTTTTCTATAAGCGCCGCTAA
64 CGGGTATTAGCGGCGCTTTAC-ACAAGCGCCGCTAA
33177185 TTTATTTAAA
Statistics
Matches: 219, Mismatches: 31, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
162 1 0.00
163 72 0.33
164 105 0.48
165 26 0.12
166 15 0.07
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22
Consensus pattern (163 bp):
GACAAAAGCGCCGCTAAAGGTCGAGTCATTAGCGGCGCTTTTCTAATAAGCGCCGCTAAAGGTCG
GGTATTAGCGGCGCTTTACACAAGCGCCGCTAAAAGTCGAGTCATTAGCAACGCTTAGACACAAG
CACCACTAAAAGTCGGGTCATTAGCGGCGCTTA
Found at i:33177361 original size:44 final size:44
Alignment explanation
Indices: 33177310--33177455 Score: 186
Period size: 44 Copynumber: 3.3 Consensus size: 44
33177300 CTCCAGACCA
* * * **
33177310 CAGAACCCTCTGCTGTTTCCCTCACTCCGTTGCCTCTTCACCTG
1 CAGAACCCGCTTCTGTTCCCCTCACTCCGTTGCCTCTTCACCCC
*
33177354 CAGAACCCGCTTCTGTTCCCCTCAC-CTCGTTCCCTCTTCACCCC
1 CAGAACCCGCTTCTGTTCCCCTCACTC-CGTTGCCTCTTCACCCC
* * *
33177398 CAAAACCCGCTTCTCTTCCCCTCACTCCATTGCCTCTTCACCCC
1 CAGAACCCGCTTCTGTTCCCCTCACTCCGTTGCCTCTTCACCCC
*
33177442 TAGAACCCGCTTCT
1 CAGAACCCGCTTCT
33177456 TGAGCCGATC
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
43 1 0.01
44 86 0.98
45 1 0.01
ACGTcount: A:0.14, C:0.48, G:0.10, T:0.29
Consensus pattern (44 bp):
CAGAACCCGCTTCTGTTCCCCTCACTCCGTTGCCTCTTCACCCC
Found at i:33179650 original size:23 final size:23
Alignment explanation
Indices: 33179577--33179750 Score: 158
Period size: 23 Copynumber: 7.5 Consensus size: 23
33179567 TATACGGAAC
* *
33179577 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
33179599 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
33179620 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
33179646 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
33179669 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
33179692 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
33179715 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
33179740 AAACAGAGAGC
1 AAACAGAGAGC
33179751 GCGCTAGTGT
Statistics
Matches: 126, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
21 17 0.13
23 71 0.56
24 2 0.02
25 29 0.23
26 7 0.06
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:33179699 original size:69 final size:67
Alignment explanation
Indices: 33179577--33179726 Score: 205
Period size: 69 Copynumber: 2.1 Consensus size: 67
33179567 TATACGGAAC
*
33179577 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAG
33179642 TGCT-
63 TGCTA
33179646 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACA
33179710 GTGCTA
62 GTGCTA
33179716 ATAACAGAGAG
1 A-AACAGAGAG
33179727 CACGAGACGT
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
68 2 0.03
69 33 0.45
70 12 0.16
71 20 0.27
72 7 0.09
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGC
TA
Found at i:33182653 original size:112 final size:109
Alignment explanation
Indices: 33182502--33183979 Score: 1087
Period size: 112 Copynumber: 13.9 Consensus size: 109
33182492 AATAATTAAA
* * *
33182502 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA-TTAAAAGATTTAATTAT
*
33182567 TTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCATGTT
65 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAA--ATGTT
33182614 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAATTATAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAATTA-AAAGATTTAATTAT
*
33182679 TTAATTATATTAAAGTAAATAATTATATTAAGTTA---AAA-GATT
65 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAAATG-TT
* *
33182721 T-A--AT-TATTTAATTAT-ATTAA-A-CTAAATAATT--ATA-TTAATTTAAAAGATTTAATTA
1 TAATTATGTATTTAATTATAAATAATATC-AATTAATTAAATATTTAA-TTAAAAGATTTAATTA
* *
33182776 TTTAATTATATTAAACTAAATAATTATATTAAATTTTTTAATCATGTT
64 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAA--ATGTT
* * *
33182824 TAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA-TTAAAAGATTTAATTAT
33182889 TTAATTATATTAAAGTAAATAATTATATT-AA--A-TTAAA-GATT
65 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAAATG-TT
* * * *
33182930 TAATTATTTAATTATATTA-AAGTAA-AT-AATTATATT--A-A----GTTAAAAGATTTAATTA
1 TAATTATGTATTTA-ATTATAAATAATATCAATTA-ATTAAATATTTAATTAAAAGATTTAATTA
*
33182985 TTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTT
64 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAA--ATGTT
*
33183033 TAATTATGTATTTAATTATAAA-AACTATCGATTAATTAAATATTTAAATTAAAAGATTTAATTA
1 TAATTATGTATTTAATTATAAATAA-TATCAATTAATTAAATATTT-AATTAAAAGATTTAATTA
* **
33183097 TTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AAAAATT
64 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAAATGTT
* * * *
33183140 TAATTATTTA-TTATATTA-AACTAA-AT-AATTATATTAAATTATTTAA-T-CATG-TTTAATT
1 TAATTATGTATTTA-ATTATAAATAATATCAATTA-ATTAAA-TATTTAATTAAAAGATTTAATT
* * ** * *
33183198 ATGTATTTA-ATTATAAACACTATCGATTA-ATTAAA-TATTT-AA-G-T
63 ATTTAATTATATTA-AAGTA-AAT-AATTATATTAAATTATTTAAATGTT
* * * * * * *
33183242 TAA--AAG-ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTTAAT
1 TAATTATGTATTTAATTA-TAAATAATA-TCAATTAATTAA--ATATTTAATTAAAAGATTTAAT
* **
33183304 TATTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AAAAATT
62 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAAATGTT
* * * * *
33183349 TAATTATTTA-TTATATTA-AACTAA-AT-AATTATATTAAATTTTTAA-T-CATG-TTTAATTA
1 TAATTATGTATTTA-ATTATAAATAATATCAATTA-ATTAAATATTTAATTAAAAGATTTAATTA
* * ** * *
33183407 TGTATTTA-ATTATAAACACTATCGATTA-ATTAAATT-TTT-AA-G-T
64 TTTAATTATATTA-AAGTA-AAT-AATTATATTAAATTATTTAAATGTT
* * * * * * *
33183450 TAA--AAG-ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAAT
1 TAATTATGTATTTAATTA-TAAATAATA-TCAATTAATTAAATAT-TTAA-TTAAAAGATTTAAT
* *
33183512 TATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATATT
62 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAA--ATGTT
* *
33183562 TAATTATGTATTTAATTATAAA-AACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATCA
1 TAATTATGTATTTAATTATAAATAA-TATCAATTAATTAAATATTTAA-TTAAAAGATTTAATTA
* *
33183626 TTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AAATATT
64 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAAATGTT
* * * * *
33183669 TAATTATTTAATTATATTA-AACTAA-AT-AATTATATTAAATTATTTAA-T--CATATTTAATT
1 TAATTATGTATTTA-ATTATAAATAATATCAATTA-ATTAAA-TATTTAATTAAAAGATTTAATT
* * ** * *
33183728 ATGTATTTA-ATTATAAACACTATCGATTA-ATTAAATT-TTT-AA-G-T
63 ATTTAATTATATTA-AAGTA-AAT-AATTATATTAAATTATTTAAATGTT
* * * * * * *
33183772 TAA--AAG-ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAAT
1 TAATTATGTATTTAATTA-TAAATAATA-TCAATTAATTAAATAT-TTAA-TTAAAAGATTTAAT
*
33183834 TATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTT
62 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAA--ATGTT
* * *
33183884 TAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA-TTAAAAGATTTAATTAT
33183949 TTAATTATATTAAAGTAAATAATTATATTAA
65 TTAATTATATTAAAGTAAATAATTATATTAA
33183980 GTTAAAAGAT
Statistics
Matches: 1075, Mismatches: 157, Indels: 268
0.72 0.10 0.18
Matches are distributed among these distances:
97 45 0.04
98 57 0.05
99 19 0.02
100 17 0.02
101 47 0.04
102 61 0.06
103 93 0.09
104 54 0.05
105 53 0.05
106 77 0.07
107 130 0.12
108 29 0.03
109 17 0.02
110 8 0.01
111 9 0.01
112 304 0.28
113 23 0.02
114 14 0.01
115 18 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (109 bp):
TAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAATTAAAAGATTTAATTATT
TAATTATATTAAAGTAAATAATTATATTAAATTATTTAAATGTT
Found at i:33182689 original size:32 final size:34
Alignment explanation
Indices: 33182612--33182689 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 34
33182602 TTTAATCATG
33182612 TTTAATTATGTATTTAATTATAAATAATATCAATTA
1 TTTAATTA--TATTTAATTATAAATAATATCAATTA
* * *
33182648 ATTAA--ATATTTAATTATAAA-GAT-TTAATTA
1 TTTAATTATATTTAATTATAAATAATATCAATTA
33182678 TTTAATTATATT
1 TTTAATTATATT
33182690 AAAGTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
30 10 0.28
31 2 0.06
32 19 0.53
34 1 0.03
36 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTAATTATATTTAATTATAAATAATATCAATTA
Found at i:33182725 original size:161 final size:161
Alignment explanation
Indices: 33182545--33184027 Score: 1582
Period size: 161 Copynumber: 9.3 Consensus size: 161
33182535 AATTAAATAT
* *
33182545 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
33182610 TGTTTAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAA-TTATAAAGATTTA
66 TGTTTAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTA-AAAGATTTA
33182674 ATTATTTAATTATATTAAAGTAAATAATTATA
130 ATTATTTAATTATATTAAAGTAAATAATTATA
33182706 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATT--A--ATTTAA--A
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
* * * * *
33182765 AGATTTAATTATTTAATTATATTA-AACTAA-AT-AATTATATTAAAT-TTT---TTAATCATG-
66 TG-TTTAATTATGTATTTA-ATTATAAATAATATCAATTA-ATTAAATATTTAAGTTAA--AAGA
* * * * *
33182822 TTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATA
126 TTTAATTATTTAATT-A-TATTAA-AGTA---AATAATT--ATA
* *
33182866 TTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTA---AA-G
1 -TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATC
* *
33182927 A--TTT-A--AT-TATTTAATTAT-ATTAA-AGT-AAATAATT--ATA-TTAAGTTAAAAGATTT
65 ATGTTTAATTATGTATTTAATTATAAATAATA-TCAATTAATTAAATATTTAAGTTAAAAGATTT
*
33182980 AATTATTTAATTATATTAAACTAAATAATTATA
129 AATTATTTAATTATATTAAAGTAAATAATTATA
* * *
33183013 TTAAATTATTTAATCATG-TTTAATTATGTATTTAATTATA-AAAACT--ATCGATTA-ATTAAA
1 TTAAGTTA---AA--A-GATTT-A--AT-TATTTAATTATATTAAACTAAAT-AATTATATTAAA
* * * * * * *
33183073 -TATTTAA--A---TTAA--AAG-ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAA
55 TTATTTAATCATGTTTAATTATGTATTTAATTA-TAAATAATA-TCAATTAATTAAATAT-TTAA
* *
33183129 GTTAAAAAATTTAATTATTT-ATTATATTAAACTAAATAATTATA
117 GTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * * * *
33183173 TTAAATTATTTAATCATG-TTTAATTATGTATTTA-ATTATAAAC-ACTATCGATTA-ATTAAA-
1 TTAAGTTA---AA--A-GATTTAATTATTTAATTATA-T-TAAACTA-AAT-AATTATATTAAAT
* * * * * * * *
33183233 TATTT-A--A-G-TTAA--AAG-ATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAA
56 TATTTAATCATGTTTAATTATGTATTTAATTA-TAAATAATA-TCAATTAATTAAATAT-TTAAG
33183290 TTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
118 TTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
*
33183334 TTAAGTTAAAAAATTTAATTATTT-ATTATATTAAACTAAATAATTATATTAAATT-TTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
* * * *
33183397 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATTTTTAAGTTAAAAGATTTAA
66 TGTTTAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAA
33183462 TTATTTAATTATATTAAAGTAAATAATTATA
131 TTATTTAATTATATTAAAGTAAATAATTATA
33183493 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
* *
33183558 TATTTAATTATGTATTTAATTATAAA-AACTATCGATTAATTAAATATTTAAGTTAAAAGATTTA
66 TGTTTAATTATGTATTTAATTATAAATAA-TATCAATTAATTAAATATTTAAGTTAAAAGATTTA
*
33183622 ATCATTTAATTATATTAAAGTAAATAATTATA
130 ATTATTTAATTATATTAAAGTAAATAATTATA
*
33183654 TTAAGTTAAAATATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
* * * * *
33183719 TATTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATTTTTAAGTTAAAAGATTTAA
66 TGTTTAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAA
33183784 TTATTTAATTATATTAAAGTAAATAATTATA
131 TTATTTAATTATATTAAAGTAAATAATTATA
33183815 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
* * *
33183880 TGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAA
66 TGTTTAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAA
33183945 TTATTTAATTATATTAAAGTAAATAATTATA
131 TTATTTAATTATATTAAAGTAAATAATTATA
*
33183976 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGT--ATAATTATATTAAA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAA
33184028 GTAAATAATT
Statistics
Matches: 1177, Mismatches: 70, Indels: 152
0.84 0.05 0.11
Matches are distributed among these distances:
146 7 0.01
147 3 0.00
149 8 0.01
151 7 0.01
152 32 0.03
153 32 0.03
154 41 0.03
155 62 0.05
156 55 0.05
157 21 0.02
158 13 0.01
159 96 0.08
160 178 0.15
161 607 0.52
162 12 0.01
163 2 0.00
165 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (161 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCA
TGTTTAATTATGTATTTAATTATAAATAATATCAATTAATTAAATATTTAAGTTAAAAGATTTAA
TTATTTAATTATATTAAAGTAAATAATTATA
Found at i:33182817 original size:18 final size:18
Alignment explanation
Indices: 33182561--33184096 Score: 364
Period size: 18 Copynumber: 87.3 Consensus size: 18
33182551 TAAAAGATTT
33182561 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* ** *
33182579 AAGTAAATAATTACATTA
1 AATTATTTAATTATATTA
* * *
33182597 AATTATTTAATCATGTTT
1 AATTATTTAATTATATTA
* *
33182615 AATTATGTATTTA-ATTATA
1 AATTATTTAATTATA-T-TA
* *
33182634 AATAATATCAATTA-ATTA
1 AATTAT-TTAATTATATTA
*
33182652 AA-TATTTAATTATAAAGATTT
1 AATTATTTAATTAT----ATTA
33182673 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33182691 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33182709 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
33182722 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33182740 AACTAAATAATTATATT-
1 AATTATTTAATTATATTA
* * *
33182757 -A--ATTTAA-AAGATTT
1 AATTATTTAATTATATTA
33182771 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33182789 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33182807 AATTTTTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
33182826 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
33182845 ACACTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
33182862 AA-TATTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
33182883 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33182901 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
33182919 AATTA---AA-GAT-TT-
1 AATTATTTAATTATATTA
33182931 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33182949 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33182967 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
33182980 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33182998 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
33183016 AATTATTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
*
33183035 ATTATGTATTTAATTATA-AA
1 A--AT-TATTTAATTATATTA
* **
33183055 AACTA-TCGATTA-ATTA
1 AATTATTTAATTATATTA
* *
33183071 AA-TATTTAAATTAAAAGATTT
1 AATTATTT-AATT---ATATTA
33183092 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183110 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33183128 AGTTA---AA--AAATTT
1 AATTATTTAATTATATTA
33183141 AATTATTT-ATTATATTA
1 AATTATTTAATTATATTA
* **
33183158 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
33183176 AATTATTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
33183195 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
33183214 ACACTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
33183231 AA-TATTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
33183252 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183270 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
33183288 AATTA---AA--AGATTT
1 AATTATTTAATTATATTA
33183301 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183319 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33183337 AGTTA---AA--AAATTT
1 AATTATTTAATTATATTA
33183350 AATTATTT-ATTATATTA
1 AATTATTTAATTATATTA
* **
33183367 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
33183385 AATT-TTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
33183403 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
33183422 ACACTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
33183439 AATT-TTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
33183460 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183478 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33183496 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
33183509 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183527 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
33183545 AATTATTTAATCATATTTA
1 AATTATTTAATTATA-TTA
*
33183564 ATTATGTATTTAATTATA-AA
1 A--AT-TATTTAATTATATTA
* **
33183584 AACTA-TCGATTA-ATTA
1 AATTATTTAATTATATTA
* *
33183600 AA-TATTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
*
33183621 AATCATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183639 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
33183657 AGTTA---AA--ATATTT
1 AATTATTTAATTATATTA
33183670 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183688 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
33183706 AATTATTTAATCATATTTA
1 AATTATTTAATTATA-TTA
33183725 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
33183744 ACACTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
33183761 AATT-TTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
33183782 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183800 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33183818 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
33183831 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183849 AACTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
33183867 AATTATTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
33183886 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
33183905 ACACTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
33183922 AA-TATTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
33183943 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
33183961 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
33183979 AGTTA---AA--AGATTT
1 AATTATTTAATTATATTA
33183992 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
*
33184010 AAGTA--TAATTATATTA
1 AATTATTTAATTATATTA
* **
33184026 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
33184044 AATTA---AA-TAT-TT-
1 AATTATTTAATTATATTA
33184056 AATTATTTAATTATATTAA
1 AATTATTTAATTATATT-A
*
33184075 AATT-TTTAATTATATTT
1 AATTATTTAATTATATTA
33184092 AATTA
1 AATTA
33184097 ACTATTTAAC
Statistics
Matches: 1085, Mismatches: 266, Indels: 334
0.64 0.16 0.20
Matches are distributed among these distances:
12 10 0.01
13 82 0.08
14 9 0.01
15 46 0.04
16 103 0.09
17 79 0.07
18 498 0.46
19 45 0.04
20 18 0.02
21 73 0.07
22 122 0.11
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (18 bp):
AATTATTTAATTATATTA
Found at i:33182933 original size:48 final size:48
Alignment explanation
Indices: 33182875--33183020 Score: 265
Period size: 48 Copynumber: 3.0 Consensus size: 48
33182865 ATTTAAGTTA
33182875 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
*
33182923 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
*
33182971 AAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATT
1 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
33183020 A
1 A
33183021 TTTAATCATG
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
48 48 0.51
49 46 0.49
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (48 bp):
AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
Found at i:33183082 original size:160 final size:161
Alignment explanation
Indices: 33182916--33183337 Score: 785
Period size: 160 Copynumber: 2.6 Consensus size: 161
33182906 AATAATTATA
33182916 TTAAATT-AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
33182980 AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
66 AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
33183045 TAATTATAAAAACTATCGATTAATTAAATAT
131 TAATTATAAAAACTATCGATTAATTAAATAT
*
33183076 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAAATTT
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
33183141 AATTATTT-ATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
66 AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
*
33183205 TAATTATAAACACTATCGATTAATTAAATAT
131 TAATTATAAAAACTATCGATTAATTAAATAT
* *
33183236 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTT
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
*
33183301 AATTATTTAATTATATTAAAGTAAATAATTATATTAA
66 AATTATTTAATTATATTAAACTAAATAATTATATTAA
33183338 GTTAAAAAAT
Statistics
Matches: 254, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
160 163 0.64
161 91 0.36
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (161 bp):
TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
TAATTATAAAAACTATCGATTAATTAAATAT
Found at i:33183240 original size:369 final size:371
Alignment explanation
Indices: 33182545--33183706 Score: 1859
Period size: 369 Copynumber: 3.1 Consensus size: 371
33182535 AATTAAATAT
* * *
33182545 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTACATTAAATTATTTAATCA
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA---AA--A
* * * * **** *
33182610 TG-TTTAATTATGTATTTA-ATTATAAATAATATCAATTA-ATTAAA-TATTTAATTATAAAGAT
61 -GATTTAATTATTTAATTATATTA-AACTAA-AT-AATTATATTAAATTATTTAATCATGTTTAA
* * *
33182671 TTAAT-TATTTAATTATATTAAAGTA---AATAATT--ATA-TTAAGTTAAAAGATTTAATTATT
122 TT-ATGTATTTAATTATA-AAAACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATT
* *
33182729 TAATTATATTAAACTAAATAATTATATTAATTTAAAAGATTTAATTATTTAATTATATTAAACTA
185 TAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTA
*
33182794 AATAATTATATTAAATTTTTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
250 AATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
33182859 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
315 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
33182916 TTAAATT-AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
33182980 AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
66 AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
*
33183045 TAATTATAAAAACTATCGATTAATTAAATATTTAAATTAAAAGATTTAATTATTTAATTATATTA
131 TAATTATAAAAACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTA
*
33183110 AAGTAAATAATTATATTAAGTTAAAAAATTTAATTATTT-ATTATATTAAACTAAATAATTATAT
196 AAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATAT
33183174 TAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTA
261 TAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTA
33183239 AGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
326 AGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
*
33183285 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAAATTT
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
33183350 AATTATTT-ATTATATTAAACTAAATAATTATATTAAATT-TTTAATCATGTTTAATTATGTATT
66 AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
* *
33183413 TAATTATAAACACTATCGATTAATTAAATTTTTAAGTTAAAAGATTTAATTATTTAATTATATTA
131 TAATTATAAAAACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTA
33183478 AAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATAT
196 AAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATAT
* *
33183543 TAAATTATTTAATCATATTTAATTATGTATTTAATTATAAAAACTATCGATTAATTAAATATTTA
261 TAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTA
*
33183608 AGTTAAAAGATTTAATCATTTAATTATATTAAAGTAAATAATTATA
326 AGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
33183654 TTAAGTTAAAATATTTAATTATTTAATTATATTAAACTAAATAATTATATTAA
1 TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAA
33183707 ATTATTTAAT
Statistics
Matches: 747, Mismatches: 31, Indels: 28
0.93 0.04 0.03
Matches are distributed among these distances:
363 5 0.01
364 16 0.02
365 45 0.06
366 4 0.01
367 8 0.01
368 124 0.17
369 359 0.48
370 180 0.24
371 6 0.01
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (371 bp):
TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATT
TAATTATAAAAACTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTA
AAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATAT
TAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATTAAATATTTA
AGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:33183358 original size:49 final size:49
Alignment explanation
Indices: 33182653--33183020 Score: 461
Period size: 49 Copynumber: 7.2 Consensus size: 49
33182643 AATTAATTAA
* *
33182653 ATATTTAATTATAAAGATTTAATTATTTAATTATATTAAAGTAAATAATT
1 ATATTAAATTA-AAAGATTTAATTATTTAATTATATTAAACTAAATAATT
*
33182703 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
1 ATATTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
*
33182752 ATATTAATTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
1 ATATTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
* * * * *
33182801 ATATTAAATTTTTTAATCATG-TTTAATTATGTATTTAATTATAAACACTATCGATTAATT
1 ATATTAAA----TTAA--AAGATTTAATTATTTAATT-A-TATTAA-ACTA---AATAATT
* *
33182861 AAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATT
1 --ATA-TTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
*
33182913 ATATTAAATT-AAAGATTTAATTATTTAATTATATTAAAGTAAATAATT
1 ATATTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
*
33182961 ATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
1 ATATTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
33183010 ATATTAAATTA
1 ATATTAAATTA
33183021 TTTAATCATG
Statistics
Matches: 280, Mismatches: 21, Indels: 35
0.83 0.06 0.10
Matches are distributed among these distances:
48 47 0.17
49 145 0.52
50 12 0.04
52 6 0.02
53 4 0.01
54 13 0.05
55 6 0.02
56 10 0.04
57 7 0.03
58 13 0.05
59 4 0.01
60 6 0.02
62 3 0.01
63 4 0.01
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (49 bp):
ATATTAAATTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATT
Found at i:33183502 original size:49 final size:49
Alignment explanation
Indices: 33183444--33184026 Score: 260
Period size: 49 Copynumber: 11.1 Consensus size: 49
33183434 AATTAAATTT
33183444 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
*
33183493 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * * * *
33183542 TTAAATT-----ATTTAATCATATTTAATTATGTATTTAATTATAAAAACTATCGA
1 TTAAGTTAAAAGATTTAAT--TATTTAATTA--TATTAAAGTA-AATAATTAT--A
*
33183593 TTAA-TT-AAATATTTAAGTTAAAAGATTTAATCATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAA-TT-----ATTT-A--A-TT----ATATTAAAGTAAATAATTATA
* *
33183654 TTAAGTTAAAATATTTAATTATTTAATTATATTAAACTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * * * ** * *
33183703 TTAAATTATTTAATCATATTTAATTATGTATTTA-ATTATAAACACTATCGATTA-A
1 TTAAGTTA---AA--AGATTTAATTATTTAATTATATTA-AAGTA-AAT-AATTATA
* * * * *
33183758 TTAAATTTTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TT-AA--GTTAA---AAGA-TTTAATT-ATTTAATTATATTAAAGTAAATAATTATA
*
33183815 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAACTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * * ** * *
33183864 TTAAATTATTTAATCATG-TTTAATTATGTATTTA-ATTATAAACACTATCGATTA-A
1 TTAAGTTA---AA--A-GATTTAATTATTTAATTATATTA-AAGTA-AAT-AATTATA
* ** *
33183919 TTAAATATTTAAG-TTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGT-TAAAAGATT--TA-A-TT-ATT---TAATTATATTAAAGTAAATAATTATA
33183976 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGT--ATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
33184023 TTAA
1 TTAA
33184027 AGTAAATAAT
Statistics
Matches: 413, Mismatches: 55, Indels: 134
0.69 0.09 0.22
Matches are distributed among these distances:
44 7 0.02
46 10 0.02
47 13 0.03
48 8 0.02
49 138 0.33
50 9 0.02
51 9 0.02
52 8 0.02
53 15 0.04
54 52 0.13
55 20 0.05
56 28 0.07
57 23 0.06
58 26 0.06
59 9 0.02
61 6 0.01
62 6 0.01
63 17 0.04
64 8 0.02
66 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:33183550 original size:10 final size:9
Alignment explanation
Indices: 33183458--33183729 Score: 59
Period size: 8 Copynumber: 30.9 Consensus size: 9
33183448 GTTAAAAGAT
33183458 TTAATTAT-
1 TTAATTATA
33183466 TTAATTATA
1 TTAATTATA
*
33183475 TTAAAGTA-A
1 TT-AATTATA
*
33183484 ATAATTATA
1 TTAATTATA
33183493 TTAAGTTA-A
1 TTAA-TTATA
*
33183502 --AA-GAT-
1 TTAATTATA
33183507 TTAATTAT-
1 TTAATTATA
33183515 TTAATTATA
1 TTAATTATA
*
33183524 TTAAACTA-A
1 TT-AATTATA
*
33183533 ATAATTATA
1 TTAATTATA
33183542 TTAAATTAT-
1 TT-AATTATA
*
33183551 TTAATCATA
1 TTAATTATA
33183560 TTTAATTATGTA
1 -TTAATTA--TA
33183572 TTTAATTATA
1 -TTAATTATA
** *
33183582 AAAACTATCGA
1 TTAATTAT--A
33183593 TTAATTA-A
1 TTAATTATA
* *
33183601 ATATTTA-A
1 TTAATTATA
* *
33183609 GTTAA-AAGA
1 -TTAATTATA
*
33183618 TTTAATCAT-
1 -TTAATTATA
33183627 TTAATTATA
1 TTAATTATA
*
33183636 TTAAAGTA-A
1 TT-AATTATA
*
33183645 ATAATTATA
1 TTAATTATA
33183654 TTAAGTTA-A
1 TTAA-TTATA
33183663 --AA-TAT-
1 TTAATTATA
33183668 TTAATTAT-
1 TTAATTATA
33183676 TTAATTATA
1 TTAATTATA
*
33183685 TTAAACTA-A
1 TT-AATTATA
*
33183694 ATAATTATA
1 TTAATTATA
33183703 TTAAATTAT-
1 TT-AATTATA
*
33183712 TTAATCATA
1 TTAATTATA
33183721 TTTAATTAT
1 -TTAATTAT
33183730 GTATTTAATT
Statistics
Matches: 192, Mismatches: 37, Indels: 68
0.65 0.12 0.23
Matches are distributed among these distances:
5 3 0.02
7 8 0.04
8 70 0.36
9 46 0.24
10 50 0.26
11 5 0.03
12 10 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (9 bp):
TTAATTATA
Found at i:33184022 original size:65 final size:64
Alignment explanation
Indices: 33183950--33184075 Score: 225
Period size: 65 Copynumber: 2.0 Consensus size: 64
33183940 TTTAATTATT
*
33183950 TAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTA
1 TAATTATATTAAAGTAAATAATTATATTAAATT-AAAGATTTAATTATTTAATTATATTAAAGTA
*
33184015 TAATTATATTAAAGTAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAA
1 TAATTATATTAAAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAA
33184076 ATTTTTAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 27 0.46
65 32 0.54
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (64 bp):
TAATTATATTAAAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAAGTA
Found at i:33184161 original size:8 final size:8
Alignment explanation
Indices: 33184125--33184218 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
33184115 TGGTCGTAAA
33184125 TAATTATAT
1 TAATTAT-T
33184134 ATAATTATT
1 -TAATTATT
33184143 TAAGCTTATT
1 TAA--TTATT
33184153 TAATTATT
1 TAATTATT
33184161 TAATTGA--
1 TAATT-ATT
**
33184168 -AAAGATT
1 TAATTATT
33184175 TAATTATT
1 TAATTATT
33184183 TAATTATAT
1 TAATTAT-T
33184192 TAA--A-T
1 TAATTATT
*
33184197 TAAATATT
1 TAATTATT
33184205 TAATTATT
1 TAATTATT
33184213 TAATTA
1 TAATTA
33184219 ATAAAAACAG
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
5 5 0.07
6 2 0.03
7 2 0.03
8 39 0.57
9 6 0.09
10 15 0.22
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (8 bp):
TAATTATT
Found at i:33184184 original size:30 final size:30
Alignment explanation
Indices: 33184148--33184218 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
33184138 TTATTTAAGC
33184148 TTATTTAATTAT-TT-AATTGAAAAGATTTAA
1 TTATTTAATTATATTAAATT--AAAGATTTAA
*
33184178 TTATTTAATTATATTAAATTAAATATTTAA
1 TTATTTAATTATATTAAATTAAAGATTTAA
33184208 TTATTTAATTA
1 TTATTTAATTA
33184219 ATAAAAACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 32 0.84
31 2 0.05
32 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TTATTTAATTATATTAAATTAAAGATTTAA
Found at i:33189830 original size:64 final size:64
Alignment explanation
Indices: 33189724--33189846 Score: 210
Period size: 64 Copynumber: 1.9 Consensus size: 64
33189714 CAAATTGCTC
* *
33189724 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATGATGAACTCCATCTAA
1 AACTGAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATGAAGAACTCCATCTAA
* *
33189788 AACTGAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAATGAAGAACTCCA
1 AACTGAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATGAAGAACTCCA
33189847 CGTACAACTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.45, C:0.16, G:0.26, T:0.13
Consensus pattern (64 bp):
AACTGAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATGAAGAACTCCATCTAA
Found at i:33189894 original size:21 final size:21
Alignment explanation
Indices: 33189864--33189904 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
33189854 CTTAAAGTGA
*
33189864 AGGCAGCAGCGAGGCAAGCGG
1 AGGCAACAGCGAGGCAAGCGG
33189885 AGGCAACAGCGAGGCAAGCG
1 AGGCAACAGCGAGGCAAGCG
33189905 AAGGAAGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.44, T:0.00
Consensus pattern (21 bp):
AGGCAACAGCGAGGCAAGCGG
Found at i:33190262 original size:43 final size:43
Alignment explanation
Indices: 33190200--33190306 Score: 169
Period size: 43 Copynumber: 2.5 Consensus size: 43
33190190 AGGCCTGTCG
* * *
33190200 AAAGCGCCGCTAAAGAACATGGCTTTTCGCGGCGCTTGTGGTA
1 AAAGCGCCGCTAAAGAACATGGCCTTTCACGGCGCTTGTGGAA
*
33190243 AAAGCGCCGCTAAAAAACATGGCCTTTCACGGCGCTTGTGGAA
1 AAAGCGCCGCTAAAGAACATGGCCTTTCACGGCGCTTGTGGAA
*
33190286 AAAGCGTCGCTAAAGAACATG
1 AAAGCGCCGCTAAAGAACATG
33190307 TTCTTTAGCG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGAACATGGCCTTTCACGGCGCTTGTGGAA
Found at i:33190319 original size:43 final size:42
Alignment explanation
Indices: 33190200--33190322 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 42
33190190 AGGCCTGTCG
* * *
33190200 AAAGCGCCGCTAAAGAACATGGCTTTTCGCGGCGCTTGTGGTA
1 AAAGCGCCGCTAAAGAACAT-GCCTTTAGCGGCGCTTGTGGAA
*
33190243 AAAGCGCCGCTAAAAAACATGGCCTTTCA-CGGCGCTTGTGGAA
1 AAAGCGCCGCTAAAGAACAT-GCCTTT-AGCGGCGCTTGTGGAA
* *
33190286 AAAGCGTCGCTAAAGAACATGTTCTTTAGCGGCGCTT
1 AAAGCGCCGCTAAAGAACATG-CCTTTAGCGGCGCTT
33190323 TTTCGCATAA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
42 2 0.03
43 68 0.97
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGAACATGCCTTTAGCGGCGCTTGTGGAA
Found at i:33193620 original size:31 final size:31
Alignment explanation
Indices: 33193585--33193660 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
33193575 CAATTTGATG
* * *
33193585 AATTTTAATTTTTATATTCTTTAAATTAAT-C
1 AATTTTAATTTTTATAAT-TTTAAAATAATAA
*
33193616 AATTTTAATCTTTATAATTTTAAAATAATAA
1 AATTTTAATTTTTATAATTTTAAAATAATAA
33193647 AATTTTAATTTTTA
1 AATTTTAATTTTTA
33193661 CCCAAGGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 10 0.26
31 29 0.74
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (31 bp):
AATTTTAATTTTTATAATTTTAAAATAATAA
Found at i:33194697 original size:2 final size:2
Alignment explanation
Indices: 33194686--33194725 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
33194676 TATTCCCACC
33194686 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
33194726 AATCTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33200961 original size:42 final size:42
Alignment explanation
Indices: 33200902--33200986 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
33200892 AGATGATGTT
*
33200902 AATTAGGGATCATTGAGACACTCATATAGTCATATGGTCATA
1 AATTAGGGATCATTGAGACACTCATATAGTCATATGCTCATA
*
33200944 AATTATGGATCATTGAGACACTCATATAGTCATATGCTCATA
1 AATTAGGGATCATTGAGACACTCATATAGTCATATGCTCATA
33200986 A
1 A
33200987 CCCTTATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (42 bp):
AATTAGGGATCATTGAGACACTCATATAGTCATATGCTCATA
Found at i:33204868 original size:28 final size:29
Alignment explanation
Indices: 33204804--33204868 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
33204794 TAATTTATAA
33204804 TTTTAAAAATTCAAAAAAATATAAAAATG
1 TTTTAAAAATTCAAAAAAATATAAAAATG
* * *
33204833 -TTTAAAAATTTAAAAACAT-TAAAATTG
1 TTTTAAAAATTCAAAAAAATATAAAAATG
*
33204860 TTTTTAAAA
1 TTTTAAAAA
33204869 GTGTAGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTAAAAATTCAAAAAAATATAAAAATG
Found at i:33206496 original size:16 final size:18
Alignment explanation
Indices: 33206475--33206508 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33206465 AAATTAAAAA
33206475 AATCG-ATT-TTCGAGTT
1 AATCGAATTATTCGAGTT
33206491 AATCGAATTATTCGAGTT
1 AATCGAATTATTCGAGTT
33206509 TTGAGTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (18 bp):
AATCGAATTATTCGAGTT
Found at i:33206700 original size:18 final size:19
Alignment explanation
Indices: 33206664--33206702 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33206654 ATCAAAAAAA
33206664 ATTAAAAATTAAAATATTT
1 ATTAAAAATTAAAATATTT
* *
33206683 ATTAAAATTTTAAA-ATTT
1 ATTAAAAATTAAAATATTT
33206701 AT
1 AT
33206703 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAAAAATTAAAATATTT
Found at i:33206725 original size:17 final size:17
Alignment explanation
Indices: 33206705--33206775 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
33206695 AAATTTATAT
*
33206705 TTTAAAAAAATAAAAAA
1 TTTAAAAAAATATAAAA
* * *
33206722 TTTAAATATATATATAA
1 TTTAAAAAAATATAAAA
*
33206739 TATAAACAAAAT-TAAAA
1 TTTAAA-AAAATATAAAA
33206756 TTATAAAAAAATTATAAAA
1 TT-TAAAAAAA-TATAAAA
33206775 T
1 T
33206776 AATAATTTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 27 0.66
18 8 0.20
19 6 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTAAAAAAATATAAAA
Found at i:33207588 original size:20 final size:19
Alignment explanation
Indices: 33207550--33207599 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
33207540 ATTGCAAAAT
33207550 AATTCAAAATAACTTTAAA
1 AATTCAAAATAACTTTAAA
*
33207569 ACATTCAAAAT-ATTTATAAA
1 A-ATTCAAAATAACTT-TAAA
33207589 AACTTCAAAAT
1 AA-TTCAAAAT
33207600 TTATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTCAAAATAACTTTAAA
Found at i:33207625 original size:27 final size:26
Alignment explanation
Indices: 33207578--33207633 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
33207568 AACATTCAAA
* *
33207578 ATATTTATAAAAACTTCAAAATTTAT
1 ATATTTATAAAAAATTCAAAATGTAT
* *
33207604 ATATTTTTAAAAAATTATAAAATGTAT
1 ATATTTATAAAAAATT-CAAAATGTAT
33207631 ATA
1 ATA
33207634 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
ATATTTATAAAAAATTCAAAATGTAT
Found at i:33225273 original size:36 final size:31
Alignment explanation
Indices: 33225248--33225314 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
33225238 ATTACTTAAA
33225248 ATAAAAATAAAATATAAATAAATGATATTTT
1 ATAAAAATAAAATATAAATAAATGATATTTT
* **
33225279 TTAAATGTAAAATATAAATAAATGATATTTT
1 ATAAAAATAAAATATAAATAAATGATATTTT
*
33225310 TTAAA
1 ATAAA
33225315 TGTATTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (31 bp):
ATAAAAATAAAATATAAATAAATGATATTTT
Found at i:33225290 original size:31 final size:31
Alignment explanation
Indices: 33225255--33225318 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
33225245 AAAATAAAAA
33225255 TAAAATATAAATAAATGATATTTTTTAAATG
1 TAAAATATAAATAAATGATATTTTTTAAATG
33225286 TAAAATATAAATAAATGATATTTTTTAAATG
1 TAAAATATAAATAAATGATATTTTTTAAATG
33225317 TA
1 TA
33225319 TTTATAAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (31 bp):
TAAAATATAAATAAATGATATTTTTTAAATG
Found at i:33225626 original size:25 final size:23
Alignment explanation
Indices: 33225592--33225644 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 23
33225582 TACTAAATTA
33225592 ATATATTATTAATACATAAAATAAT
1 ATATATTATTAATA-ATAAAAT-AT
*
33225617 ATATATTATTAATAATATAATAT
1 ATATATTATTAATAATAAAATAT
33225640 ATATA
1 ATATA
33225645 ACTATTGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.26
24 6 0.22
25 14 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATTATTAATAATAAAATAT
Found at i:33225631 original size:21 final size:22
Alignment explanation
Indices: 33225581--33225643 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
33225571 CTTAAATCAT
*
33225581 ATAC-TAAATTAATATATTATTA
1 ATACATAAAATAATATA-TATTA
33225603 ATACATAAAATAATATATATTA
1 ATACATAAAATAATATATATTA
* *
33225625 TTA-ATAATATAATATATAT
1 ATACATAAAATAATATATAT
33225644 AACTATTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.41
22 11 0.30
23 11 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
ATACATAAAATAATATATATTA
Done.