Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold309
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: 1359455
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 63696 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:260397 original size:79 final size:77
Alignment explanation
Indices: 259781--260988 Score: 1127
Period size: 74 Copynumber: 15.7 Consensus size: 77
259771 TGTGTGCCTA
* * * *
259781 AGGCTCAACTCACC-CATAGCAATATGAGTTGATTTTTTTTAACAAC-GGAA-TTAAA-AAATAC
1 AGGCTCAACTCACCTC-TCGCAATATGAGTTGA-TTTTTGTAAAAACAGAAATTTAAAGAAATAC
* * *
259842 TTCAGCGTACGACCCG
64 CTC-G-GCATGACCCG
* *
259858 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA-TTGAA-AAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGT-AAAAACAGAAATTTAAAGAAATACC
** * * *
259921 TCATCTTAACCTG
65 TCGGCATGACCCG
* *
259934 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTG-AAAAGCAGAAA-TT--GGAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGTAAAAACAGAAATTTAAAGAAATACC
* *
259995 TCAGCGTGACCCG
65 TCGGCATGACCCG
* *
260008 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTG-AAAAGCAGAAA-TT--GGAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGTAAAAACAGAAATTTAAAGAAATACC
* * *
260069 TCAGCGTGGCCCG
65 TCGGCATGACCCG
* * * *
260082 CGGCTCAACTCACCTCTCCCAATATGAGTTGATTCTTTG-AAAAGCAGAAA-TT--GGAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGTAAAAACAGAAATTTAAAGAAATACC
* * *
260143 TCAGCGTGGCCCG
65 TCGGCATGACCCG
* * * *
260156 CGGCTCAACTCACCTCTCCCAATATGAGTTGATTCTTTG-AAAAGCAGAAA-TT--GGAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGTAAAAACAGAAATTTAAAGAAATACC
* * *
260217 TCAGCGTGGCCCG
65 TCGGCATGACCCG
* * * *
260230 CGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAAACAAAAATTGT--A-AA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGT-AAAAACAGAAATT-TAAAGAA
*
260292 ATACTTCAGG-ATGACCCG
60 ATACCTC-GGCATGACCCG
* * *
260310 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAAAACGGAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-TAAAAACAGAAATTT-AAAGAAATAC
260375 CTCGGCATGACCCG
64 CTCGGCATGACCCG
* * *
260389 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTATTG-AAAAAC-GAAAATTTGAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGTAAAAACAG-AAATTT-AAAGAAATAC
260451 CTCGGCATGACCCG
64 CTCGGCATGACCCG
* * *
260465 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGT-AAAAACAGAAATTT-AAAGAAATAC
* **
260529 CTCGACATGGTCCG
64 CTCGGCATGACCCG
* *
260543 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGT-AAAAACAGAAATTT-AAAGAAATAC
* *
260608 CTCGACATGGTCCCG
64 CTCGGCAT-GACCCG
* * *
260623 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGT-AAAAACAGAAATTT-AAAGAAATAC
* **
260687 CTCGACATGGTCCG
64 CTCGGCATGACCCG
* * *
260701 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAACATAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGT-AAAAACAGAAATTT-AAAGAAATAC
**
260766 CTCGGCATGGTCCG
64 CTCGGCATGACCCG
*
260780 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-TGAGAAACAGAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGT-AAAAACAGAAATTT-AAAGAAATAC
*
260844 CTCGGTATGTGACCCG
64 CTCGGCA--TGACCCG
* ** * *
260860 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTGAGA-AAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGTAAAAACAGAAATTTAAAGAAATACCT
*
260924 CGGCATGTGCCCCG
66 CGGCA--TGACCCG
* * *
260938 AGGCTCAACTCACCTC-CAGCATTATGAGTTGATTTTT-AAAAAACAAAAATT
1 AGGCTCAACTCACCTCTC-GCAATATGAGTTGATTTTTGTAAAAACAGAAATT
260989 GAAAAATATT
Statistics
Matches: 1024, Mismatches: 76, Indels: 62
0.88 0.07 0.05
Matches are distributed among these distances:
74 265 0.26
75 14 0.01
76 132 0.13
77 54 0.05
78 192 0.19
79 247 0.24
80 118 0.12
81 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (77 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGTAAAAACAGAAATTTAAAGAAATACCT
CGGCATGACCCG
Found at i:260663 original size:158 final size:156
Alignment explanation
Indices: 259781--260974 Score: 1185
Period size: 158 Copynumber: 7.7 Consensus size: 156
259771 TGTGTGCCTA
* * * * * *
259781 AGGCTCAACTCACC-CATAGCAATATGAGTTGATTTTTTTTAACAAC-GGAA-TTAAAAAATACT
1 AGGCTCAACTCACCTC-TCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTTAAGAAATACC
* *
259843 TC-AGCGTACGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGA
64 TCGA-CAT-GGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGA
* * ** *
259907 AA-TT-GAA-AAATACCTC-ATCTTAACCTG
127 AATTTAAAAGAAATACCTCGA-CATGGCCCG
* * *
259934 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTGAAAAGCAGAAA-TT-GGAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAGAAATACCTC
* * *
259997 -AGCGT-GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTCTTTGAAAAGCAGAAA-
66 GA-CATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT
* *
260058 TT---GGAAATACCTC-AGCGTGGCCCG
130 TTAAAAGAAATACCTCGA-CATGGCCCG
* * * * *
260082 CGGCTCAACTCACCTCTCCCAATATGAGTTGATTCTTTGAAAAGCAGAAA-TT-GGAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAGAAATACCTC
* * * * *
260145 -AGCGTGG-CCCGCGGCTCAACTCACCTCTCCCAATATGAGTTGA-TTCTTTGAAAAGCAGAAA-
66 GA-CATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT
* *
260206 TT---GGAAATACCTC-AGCGTGGCCCG
130 TTAAAAGAAATACCTCGA-CATGGCCCG
* * *
260230 CGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAAACAAAAATTGT-A-AAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAAACAGAAATT-TAAGAAA
* * * ***
260293 TACTTC-AGGAT-GACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAAAAC
60 TACCTCGA-CATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAC
* * *
260356 GGAAATTTAAAAGAAATACCTCGGCATGACCCG
124 AGAAATTTAAAAGAAATACCTCGACATGGCCCG
* * *
260389 AGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTATTGAAAAAC-GAAAATTTGAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAG-AAATTT--AAGAAATAC
* * *
260451 CTCGGCAT-GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTGAAAAACAGAA
63 CTCGACATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAA
*
260514 ATTTAAAAGAAATACCTCGACATGGTCCG
128 ATTTAAAAGAAATACCTCGACATGGCCCG
*
260543 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTT--AAGAAATAC
* * *
260608 CTCGACATGGTCCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTGAAAAACAGAA
63 CTCGACATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAA
*
260672 ATTTAAAAGAAATACCTCGACATGGTCCG
128 ATTTAAAAGAAATACCTCGACATGGCCCG
* *
260701 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAACATAAATTTAAAAGAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTT--AAGAAATAC
* * *
260766 CTCGGCATGG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAGAAACAGAA
63 CTCGACATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAA
**
260829 ATTTAAAAGAAATACCTCGGTATGTGACCCG
128 ATTTAAAAGAAATACCTCGACATG-G-CCCG
* ** *
260860 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAA-TTGAGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAG-AAATACCT
* * *
260924 CGGCATGTGCCCCGAGGCTCAACTCACCTC-CAGCATTATGAGTTGATTTTT
65 CGACATG-GACCCGAGGCTCAACTCACCTCTC-GCAATATGAGTTGATTTTT
260975 AAAAAACAAA
Statistics
Matches: 921, Mismatches: 83, Indels: 68
0.86 0.08 0.06
Matches are distributed among these distances:
148 187 0.20
149 19 0.02
150 38 0.04
151 1 0.00
152 38 0.04
153 50 0.05
154 116 0.13
155 61 0.07
156 17 0.02
157 96 0.10
158 228 0.25
159 70 0.08
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (156 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAGAAATACCTC
GACATGGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT
TAAAAGAAATACCTCGACATGGCCCG
Found at i:261870 original size:28 final size:27
Alignment explanation
Indices: 261850--261950 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 27
261840 TTCATCTTGA
*
261850 TTTTTTATTTTTTGTTGTTTCTTTCTG
1 TTTTTTATTTTTTGTTGTTTCTCTCTG
*
261877 TTTTTTATTTTTTGTT-TCTT-T-TTTG
1 TTTTTTATTTTTTGTTGT-TTCTCTCTG
* * * *
261902 TTTTTTGTTTTTT-TTGTTTTTTTTTG
1 TTTTTTATTTTTTGTTGTTTCTCTCTG
* *
261928 TTTTTTTTTGTTTTTTTGTTTCT
1 TTTTTTATT-TTTTGTTGTTTCT
261951 TTTTTGTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.06
25 17 0.27
26 14 0.22
27 22 0.34
28 7 0.11
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (27 bp):
TTTTTTATTTTTTGTTGTTTCTCTCTG
Found at i:261880 original size:20 final size:20
Alignment explanation
Indices: 261857--261982 Score: 89
Period size: 20 Copynumber: 6.3 Consensus size: 20
261847 TGATTTTTTA
261857 TTTTTTGTTGTTTCTTTCTG
1 TTTTTTGTTGTTTCTTTCTG
* * * *
261877 TTTTTTATTTTTTGTTTCTTT
1 TTTTTTGTTGTTTCTTTC-TG
* *
261898 TTTGTTTTTTGTTT-TTTTTG
1 TTT-TTTGTTGTTTCTTTCTG
* * *
261918 TTTTTTTTTGTTTTTTTTTG
1 TTTTTTGTTGTTTCTTTCTG
*
261938 -TTTTT-TTGTTTCTTTTTTG
1 TTTTTTGTTGTTTC-TTTCTG
*
261957 TTTTTTTGTT-TTTTTTTCTG
1 -TTTTTTGTTGTTTCTTTCTG
261977 TTTTTT
1 TTTTTT
261983 AGGCATAACA
Statistics
Matches: 88, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
18 6 0.07
19 27 0.31
20 30 0.34
21 15 0.17
22 10 0.11
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.85
Consensus pattern (20 bp):
TTTTTTGTTGTTTCTTTCTG
Found at i:261880 original size:27 final size:26
Alignment explanation
Indices: 261850--261983 Score: 145
Period size: 25 Copynumber: 5.3 Consensus size: 26
261840 TTCATCTTGA
*
261850 TTTTTTATTTTTTGTTGTTTCTTTCTG
1 TTTTTTATTTTTTGTT-TTTTTTTCTG
*
261877 TTTTTTATTTTTTGTTTCTTTTT-TG
1 TTTTTTATTTTTTGTTTTTTTTTCTG
* *
261902 TTTTTTGTTTTTT-TTGTTTTTTTTTG
1 TTTTTTATTTTTTGTT-TTTTTTTCTG
* *
261928 TTTTTT-TTTGTT-TTTTTGTTTCT-
1 TTTTTTATTTTTTGTTTTTTTTTCTG
261951 TTTTTGT-TTTTTTGTTTTTTTTTCTG
1 TTTTT-TATTTTTTGTTTTTTTTTCTG
261977 TTTTTTA
1 TTTTTTA
261984 GGCATAACAT
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.05
24 15 0.16
25 38 0.41
26 18 0.20
27 16 0.17
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (26 bp):
TTTTTTATTTTTTGTTTTTTTTTCTG
Found at i:261899 original size:19 final size:17
Alignment explanation
Indices: 261877--261973 Score: 122
Period size: 18 Copynumber: 5.4 Consensus size: 17
261867 TTTCTTTCTG
*
261877 TTTTTTATTTTTTGTTT
1 TTTTTTTTTTTTTGTTT
*
261894 CTTTTTTGTTTTTTGTTTT
1 -TTTTTTTTTTTTTG-TTT
261913 TTTTGTTTTTTTTTGTTT
1 TTTT-TTTTTTTTTGTTT
261931 TTTTTTGTTTTTTTGTTT
1 TTTTTT-TTTTTTTGTTT
261949 CTTTTTTGTTTTTTTGTTT
1 -TTTTTT-TTTTTTTGTTT
261968 TTTTTT
1 TTTTTT
261974 CTGTTTTTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
17 2 0.03
18 41 0.56
19 30 0.41
ACGTcount: A:0.01, C:0.02, G:0.09, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTTGTTT
Found at i:261980 original size:19 final size:18
Alignment explanation
Indices: 261852--261982 Score: 138
Period size: 19 Copynumber: 6.9 Consensus size: 18
261842 CATCTTGATT
* *
261852 TTTTATTTTTTGTTGTTTC
1 TTTT-TTTTTTGTTTTTTG
*
261871 TTTCTGTTTTTTATTTTTTG
1 TTT-T-TTTTTTGTTTTTTG
*
261891 TTTCTTTTTTGTTTTTTG
1 TTTTTTTTTTGTTTTTTG
*
261909 TTTTTTTTGTTTTTTTTTG
1 TTTTTTTT-TTGTTTTTTG
261928 -TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTTG-TTTTTTG
*
261946 TTTCTTTTTTGTTTTTTTG
1 TTTTTTTTTTG-TTTTTTG
261965 TTTTTTTTTCTGTTTTTT
1 TTTTTTTTT-TGTTTTTT
261983 AGGCATAACA
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.02
18 34 0.35
19 43 0.45
20 17 0.18
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTGTTTTTTG
Found at i:261982 original size:1 final size:1
Alignment explanation
Indices: 261877--261973 Score: 86
Period size: 1 Copynumber: 97.0 Consensus size: 1
261867 TTTCTTTCTG
* * * * * * * *
261877 TTTTTTATTTTTTGTTTCTTTTTTGTTTTTTGTTTTTTTTGTTTTTTTTTGTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
261942 TTTGTTTCTTTTTTGTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
261974 CTGTTTTTTA
Statistics
Matches: 72, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.01, C:0.02, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:268471 original size:17 final size:17
Alignment explanation
Indices: 268444--268547 Score: 88
Period size: 16 Copynumber: 6.2 Consensus size: 17
268434 ACGAAAATAT
268444 TTTTA-AAACACGAGAA
1 TTTTAGAAACACGAGAA
* *
268460 TTTTAGAGACACGAAAA
1 TTTTAGAAACACGAGAA
* *
268477 TTCTTAAAAACACGAAAA
1 TT-TTAGAAACACGAGAA
* * *
268495 TTTTTGAAAACACAACAA
1 TTTTAG-AAACACGAGAA
*
268513 TTTT-GAAACATGAGAA
1 TTTTAGAAACACGAGAA
*
268529 ATTTA-AAACACGAGAA
1 TTTTAGAAACACGAGAA
268545 TTT
1 TTT
268548 GTTTTGAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
16 28 0.40
17 14 0.20
18 28 0.40
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (17 bp):
TTTTAGAAACACGAGAA
Found at i:268491 original size:18 final size:18
Alignment explanation
Indices: 268431--268516 Score: 86
Period size: 18 Copynumber: 4.8 Consensus size: 18
268421 TATTTTTGCG
*
268431 AACACGAAAATATTTTTAA
1 AACACGAAAAT-TTTTAAA
* *
268450 AACACGAGAA-TTTTAGA
1 AACACGAAAATTTTTAAA
* *
268467 GACACGAAAATTCTTAAA
1 AACACGAAAATTTTTAAA
*
268485 AACACGAAAATTTTTGAA
1 AACACGAAAATTTTTAAA
268503 AACAC-AACAATTTT
1 AACACGAA-AATTTT
268517 GAAACATGAG
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
17 15 0.27
18 31 0.56
19 9 0.16
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (18 bp):
AACACGAAAATTTTTAAA
Found at i:268559 original size:21 final size:21
Alignment explanation
Indices: 268533--268606 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
268523 TGAGAAATTT
268533 AAAACACGAGAATTTGTTTTG
1 AAAACACGAGAATTTGTTTTG
* * **
268554 AAAACATGAAACATGAGAATTTT-
1 AAAACACGAGA-ATTTG--TTTTG
*
268577 AAAACACGAGAATTTTTTTTG
1 AAAACACGAGAATTTGTTTTG
268598 AAAACACGA
1 AAAACACGA
268607 TTTTTTTGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 4 0.10
21 18 0.45
22 5 0.12
23 9 0.22
24 4 0.10
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAACACGAGAATTTGTTTTG
Found at i:268579 original size:44 final size:44
Alignment explanation
Indices: 268516--268603 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
268506 ACAACAATTT
268516 TGAAACATGAGAAATTTAAAACACGAGAATTTGTTTTGAAAACA
1 TGAAACATGAGAAATTTAAAACACGAGAATTTGTTTTGAAAACA
* *
268560 TGAAACATGAGAATTTTAAAACACGAGAATTTTTTTTGAAAACA
1 TGAAACATGAGAAATTTAAAACACGAGAATTTGTTTTGAAAACA
268604 CGATTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.30
Consensus pattern (44 bp):
TGAAACATGAGAAATTTAAAACACGAGAATTTGTTTTGAAAACA
Found at i:268587 original size:16 final size:16
Alignment explanation
Indices: 268562--268592 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
268552 TGAAAACATG
*
268562 AAACATGAGAATTTTA
1 AAACACGAGAATTTTA
268578 AAACACGAGAATTTT
1 AAACACGAGAATTTT
268593 TTTTGAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (16 bp):
AAACACGAGAATTTTA
Found at i:268819 original size:20 final size:21
Alignment explanation
Indices: 268791--268830 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
268781 ATCGGGATTC
*
268791 TATTAAAACGCGAG-AATTTT
1 TATTAAAACACGAGTAATTTT
*
268811 TATTTAAACACGAGTAATTT
1 TATTAAAACACGAGTAATTT
268831 CGAACATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
TATTAAAACACGAGTAATTTT
Found at i:269148 original size:19 final size:20
Alignment explanation
Indices: 269124--269165 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
269114 TTGTGGGCCC
269124 TTTTCTT-T-TTTCCCTTTTT
1 TTTTCTTCTCTTT-CCTTTTT
269143 TTTTCTTCTCTTTCCTTTTT
1 TTTTCTTCTCTTTCCTTTTT
269163 TTT
1 TTT
269166 CTGCTGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTCTCTTTCCTTTTT
Found at i:269155 original size:15 final size:14
Alignment explanation
Indices: 269121--269163 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
269111 AAGTTGTGGG
269121 CCCTTTTCTTTTTT
1 CCCTTTTCTTTTTT
*
269135 CCCTTTTTTTTTCTT
1 CCCTTTTCTTTT-TT
* *
269150 CTCTTTCCTTTTTT
1 CCCTTTTCTTTTTT
269164 TTCTGCTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
CCCTTTTCTTTTTT
Found at i:269495 original size:9 final size:10
Alignment explanation
Indices: 269481--269572 Score: 50
Period size: 9 Copynumber: 9.3 Consensus size: 10
269471 CGACTGTTAA
269481 TTTATTT-TT
1 TTTATTTCTT
269490 TTTATTTC-T
1 TTTATTTCTT
* *
269499 TTTCTTTCCT
1 TTTATTTCTT
*
269509 TTT-TTTCTC
1 TTTATTTCTT
269518 TTT-TTTCTT
1 TTTATTTCTT
269527 TCTT-TTTCTT
1 T-TTATTTCTT
* *
269537 CTTTCTTTTTT
1 -TTTATTTCTT
*
269548 CTTTCTTTCTT
1 -TTTATTTCTT
*
269559 TCTTCTTTCTT
1 T-TTATTTCTT
269570 TTT
1 TTT
269573 TCTTCCTTCT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
9 28 0.39
10 17 0.24
11 26 0.37
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTCTT
Found at i:269512 original size:11 final size:11
Alignment explanation
Indices: 269498--269576 Score: 83
Period size: 11 Copynumber: 7.0 Consensus size: 11
269488 TTTTTATTTC
269498 TTTTCTTTCCTT
1 TTTTCTTT-CTT
*
269510 TTTT-TCTCTT
1 TTTTCTTTCTT
269520 TTTTCTTTCTTT
1 TTTTCTTTC-TT
269532 TTCTTCTTTCTT
1 TT-TTCTTTCTT
269544 TTTTCTTTCTT
1 TTTTCTTTCTT
269555 TCTTTC-TTCTT
1 T-TTTCTTTCTT
269566 TCTTT-TTTCTT
1 T-TTTCTTTCTT
269577 CCTTCTCCGT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
10 7 0.12
11 30 0.50
12 16 0.27
13 7 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:269514 original size:22 final size:21
Alignment explanation
Indices: 269486--269573 Score: 96
Period size: 22 Copynumber: 4.3 Consensus size: 21
269476 GTTAATTTAT
*
269486 TTTTTTTATTTCTTTTCTTTCC
1 TTTTTTTCTTTCTTTTCTTT-C
269508 TTTTTTTCTCTT-TTTTCTTTC
1 TTTTTTTCT-TTCTTTTCTTTC
269529 TTTTTCTTCTTTC-TTT-TTTC
1 TTTTT-TTCTTTCTTTTCTTTC
*
269549 TTTCTTTCTTTC--TTCTTTC
1 TTTTTTTCTTTCTTTTCTTTC
269568 TTTTTT
1 TTTTTT
269574 CTTCCTTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.03
19 16 0.27
20 8 0.14
21 11 0.19
22 20 0.34
23 2 0.03
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTCTTTCTTTTCTTTC
Found at i:269528 original size:26 final size:24
Alignment explanation
Indices: 269485--269576 Score: 98
Period size: 26 Copynumber: 3.7 Consensus size: 24
269475 TGTTAATTTA
*
269485 TTTTTT-TTATTTCTTTTCTTTCCTT
1 TTTTTTCTTTTTTC-TTTCTTT-CTT
269510 TTTTTCTCTTTTTTCTTTCTTT-TT
1 TTTTT-TCTTTTTTCTTTCTTTCTT
*
269534 CTTCTTTCTTTTTTCTTTCTTTCTT
1 -TTTTTTCTTTTTTCTTTCTTTCTT
269559 TCTTCTTTCTTTTTTCTT
1 T-TT-TTTCTTTTTTCTT
269577 CCTTCTCCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
24 19 0.33
25 12 0.21
26 21 0.36
27 6 0.10
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTTCTTTTTTCTTTCTTTCTT
Found at i:269552 original size:4 final size:4
Alignment explanation
Indices: 269494--269576 Score: 82
Period size: 4 Copynumber: 20.5 Consensus size: 4
269484 ATTTTTTTTA
* * *
269494 TTTC TTTTC TTTCC TTTT TTTC TCTTT TTTC TTTC TTTT TCTTC TTTC
1 TTTC -TTTC TTT-C TTTC TTTC T-TTC TTTC TTTC TTTC T-TTC TTTC
269542 TTT- TTTC TTTC TTTC TTTC -TTC TTTC TTT- TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
269577 CCTTCTCCGT
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
3 9 0.14
4 43 0.65
5 14 0.21
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:269567 original size:7 final size:7
Alignment explanation
Indices: 269512--269582 Score: 71
Period size: 7 Copynumber: 10.7 Consensus size: 7
269502 CTTTCCTTTT
269512 TTTC-TC
1 TTTCTTC
*
269518 TTTTTTC
1 TTTCTTC
269525 TTTCTT-
1 TTTCTTC
269531 TTTCTTC
1 TTTCTTC
269538 TTTC-T-
1 TTTCTTC
269543 TTT-TTC
1 TTTCTTC
269549 TTTCTTTC
1 TTTC-TTC
269557 TTTCTTC
1 TTTCTTC
*
269564 TTTCTTT
1 TTTCTTC
269571 TTTCTTC
1 TTTCTTC
*
269578 CTTCT
1 TTTCT
269583 CCGTTCAGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
5 4 0.07
6 13 0.24
7 30 0.56
8 7 0.13
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTC
Found at i:269706 original size:22 final size:24
Alignment explanation
Indices: 269681--269736 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
269671 CCCCCTTTTC
269681 CTTTTTCTTTTTCT-TCTTTGC-T-
1 CTTTTTCTTTTTCTCT-TTTGCTTG
*
269703 CTTTCTCTTTTTCTCTTTTGCTTG
1 CTTTTTCTTTTTCTCTTTTGCTTG
269727 CTTTTTCTTT
1 CTTTTTCTTT
269737 GTTTTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 18 0.62
23 2 0.07
24 9 0.31
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.71
Consensus pattern (24 bp):
CTTTTTCTTTTTCTCTTTTGCTTG
Found at i:270201 original size:29 final size:29
Alignment explanation
Indices: 270103--270217 Score: 115
Period size: 30 Copynumber: 3.9 Consensus size: 29
270093 TAATTTTGAG
*
270103 AAAA-TTTAGGGGTCAAAATATAATTTCA
1 AAAAGTTTAGGGGTCAAAATGTAATTTCA
* * * * *
270131 AGAAGTTGATGGGCCAAAATGTAATTTTA
1 AAAAGTTTAGGGGTCAAAATGTAATTTCA
* * *
270160 GGAAAGTTTAGGGGTGAAAATGCAATTTCA
1 -AAAAGTTTAGGGGTCAAAATGTAATTTCA
*
270190 AAAAGTTTAGGGGGTCAAAATATAATTT
1 AAAAGTTTA-GGGGTCAAAATGTAATTT
270218 TTTATTTTTG
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
28 3 0.05
29 27 0.41
30 36 0.55
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.30
Consensus pattern (29 bp):
AAAAGTTTAGGGGTCAAAATGTAATTTCA
Found at i:270451 original size:17 final size:17
Alignment explanation
Indices: 270424--270582 Score: 92
Period size: 17 Copynumber: 9.2 Consensus size: 17
270414 ACGAAAATAT
270424 TTTTA-AAACACGAGAA
1 TTTTAGAAACACGAGAA
* *
270440 TTTTAGAGACACGAAAA
1 TTTTAGAAACACGAGAA
* *
270457 TTATTAAAAACACGAAAA
1 TT-TTAGAAACACGAGAA
* * *
270475 TTTTTGAAAACACAACAA
1 TTTTAG-AAACACGAGAA
* *
270493 TTTT-GAAGCATGAGAA
1 TTTTAGAAACACGAGAA
270509 TTTTA-AAACACGAGAA
1 TTTTAGAAACACGAGAA
* *
270525 TTTTTTTTGCAAACACGA-AT
1 ---TTTTAG-AAACACGAGAA
* * *
270545 TTTTTGAAACTCGAAAA
1 TTTTAGAAACACGAGAA
* *
270562 TTTGAGAAATACGAGAA
1 TTTTAGAAACACGAGAA
270579 TTTT
1 TTTT
270583 GAAGAATTGA
Statistics
Matches: 109, Mismatches: 24, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
16 32 0.29
17 36 0.33
18 28 0.26
19 4 0.04
20 1 0.01
21 8 0.07
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTAGAAACACGAGAA
Found at i:270471 original size:18 final size:18
Alignment explanation
Indices: 270411--270496 Score: 86
Period size: 18 Copynumber: 4.8 Consensus size: 18
270401 TATTTTTGCG
*
270411 AACACGAAAATATTTTTAA
1 AACACGAAAAT-TTTTAAA
* *
270430 AACACGAGAA-TTTTAGA
1 AACACGAAAATTTTTAAA
* *
270447 GACACGAAAATTATTAAA
1 AACACGAAAATTTTTAAA
*
270465 AACACGAAAATTTTTGAA
1 AACACGAAAATTTTTAAA
270483 AACAC-AACAATTTT
1 AACACGAA-AATTTT
270497 GAAGCATGAG
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
17 15 0.27
18 31 0.56
19 9 0.16
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (18 bp):
AACACGAAAATTTTTAAA
Found at i:270512 original size:16 final size:16
Alignment explanation
Indices: 270424--270528 Score: 93
Period size: 16 Copynumber: 6.2 Consensus size: 16
270414 ACGAAAATAT
270424 TTTTAAAACACGAGAA
1 TTTTAAAACACGAGAA
* *
270440 TTTTAGAGACACGAAAA
1 TTTTA-AAACACGAGAA
*
270457 TTATTAAAAACACGAAAA
1 TT-TT-AAAACACGAGAA
* *
270475 TTTTTGAAAACACAACAA
1 -TTTT-AAAACACGAGAA
* * *
270493 TTTTGAAGCATGAGAA
1 TTTTAAAACACGAGAA
270509 TTTTAAAACACGAGAA
1 TTTTAAAACACGAGAA
270525 TTTT
1 TTTT
270529 TTTTGCAAAC
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
16 29 0.41
17 15 0.21
18 24 0.34
19 3 0.04
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (16 bp):
TTTTAAAACACGAGAA
Found at i:270554 original size:16 final size:17
Alignment explanation
Indices: 270527--270559 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
270517 CACGAGAATT
270527 TTTTTTGCAAACACGAA
1 TTTTTTGCAAACACGAA
*
270544 TTTTTTG-AAACTCGAA
1 TTTTTTGCAAACACGAA
270560 AATTTGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (17 bp):
TTTTTTGCAAACACGAA
Found at i:270959 original size:15 final size:16
Alignment explanation
Indices: 270933--270962 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
270923 ACCATACTAA
270933 TATTTCTAAAAAAAAC
1 TATTTCTAAAAAAAAC
270949 TATTT-TAAAAAAAA
1 TATTTCTAAAAAAAA
270963 TGCTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
TATTTCTAAAAAAAAC
Found at i:271081 original size:19 final size:20
Alignment explanation
Indices: 271057--271098 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
271047 TTGTTGGCCC
271057 TTTTCTT-T-TTTCCCTTTTT
1 TTTTCTTCTCTTT-CCTTTTT
271076 TTTTCTTCTCTTTCCTTTTT
1 TTTTCTTCTCTTTCCTTTTT
271096 TTT
1 TTT
271099 CTGCTGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTCTCTTTCCTTTTT
Found at i:271088 original size:15 final size:14
Alignment explanation
Indices: 271054--271096 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
271044 AAGTTGTTGG
271054 CCCTTTTCTTTTTT
1 CCCTTTTCTTTTTT
*
271068 CCCTTTTTTTTTCTT
1 CCCTTTTCTTTT-TT
* *
271083 CTCTTTCCTTTTTT
1 CCCTTTTCTTTTTT
271097 TTCTGCTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
CCCTTTTCTTTTTT
Found at i:271444 original size:21 final size:19
Alignment explanation
Indices: 271418--271482 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 19
271408 GTTAATTTAT
271418 TTTTTTATTTCTTTTCTTTCC
1 TTTTTT-TTTCTTTTCTTT-C
*
271439 TTTTTTTTTTCTCTTTTTTTC
1 -TTTTTTTTTCT-TTTCTTTC
*
271460 TTTCTTTTTC--TTCTTTC
1 TTTTTTTTTCTTTTCTTTC
271477 TTTTTT
1 TTTTTT
271483 CTTCCTTCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.29
20 9 0.24
21 6 0.16
22 12 0.32
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTCTTTTCTTTC
Found at i:271454 original size:13 final size:12
Alignment explanation
Indices: 271417--271482 Score: 75
Period size: 13 Copynumber: 5.5 Consensus size: 12
271407 TGTTAATTTA
*
271417 TTTTTTTATTTC
1 TTTTTTTCTTTC
271429 TTTTCTTTCCTTT-
1 TTTT-TTT-CTTTC
271442 TTTTTTTC--TC
1 TTTTTTTCTTTC
271452 TTTTTTTCTTTC
1 TTTTTTTCTTTC
271464 TTTTTCTTCTTTC
1 TTTTT-TTCTTTC
271477 TTTTTT
1 TTTTTT
271483 CTTCCTTCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
9 1 0.02
10 8 0.17
11 1 0.02
12 15 0.32
13 19 0.40
14 3 0.06
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:271464 original size:35 final size:34
Alignment explanation
Indices: 271417--271484 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
271407 TGTTAATTTA
*
271417 TTTTTTTATTTC-TTTTCTTTCCTTTTTTTTTTCTC
1 TTTTTTTATTTCTTTTTC-TT-CTTTCTTTTTTCTC
*
271452 TTTTTTTCTTTCTTTTTCTTCTTTCTTTTTTCT
1 TTTTTTTATTTCTTTTTCTTCTTTCTTTTTTCT
271485 TCCTTCTCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 12 0.40
35 13 0.43
36 5 0.17
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (34 bp):
TTTTTTTATTTCTTTTTCTTCTTTCTTTTTTCTC
Found at i:271469 original size:20 final size:20
Alignment explanation
Indices: 271418--271485 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
271408 GTTAATTTAT
*
271418 TTTTTTATTTCTT-TTCTTTC
1 TTTTTTCTTT-TTCTTCTTTC
* *
271438 CTTTTT-TTTTTC-TCTTTT
1 TTTTTTCTTTTTCTTCTTTC
271456 TTTCTTTCTTTTTCTTCTTTC
1 TTT-TTTCTTTTTCTTCTTTC
271477 TTTTTTCTT
1 TTTTTTCTT
271486 CCTTCTCCGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 9 0.22
19 6 0.15
20 17 0.43
21 8 0.20
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTCTTTTTCTTCTTTC
Found at i:271478 original size:25 final size:26
Alignment explanation
Indices: 271429--271489 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
271419 TTTTTATTTC
*
271429 TTTTCTTTCCTTTTTTTTTTCTCTTT
1 TTTTCTTTCCTTTTTTTCTTCTCTTT
271455 TTTTCTTT-CTTTTTCTTCTT-TC-TT
1 TTTTCTTTCCTTTTT-TTCTTCTCTTT
271479 TTTTC-TTCCTT
1 TTTTCTTTCCTT
271490 CTCCGTTCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.06
24 10 0.31
25 8 0.25
26 12 0.38
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTCTTTCCTTTTTTTCTTCTCTTT
Found at i:271491 original size:14 final size:14
Alignment explanation
Indices: 271429--271491 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
271419 TTTTTATTTC
271429 TTTTCTTTCCTT-TT
1 TTTTC-TTCCTTCTT
271443 TTTT-TT-C-TC-T
1 TTTTCTTCCTTCTT
*
271453 TTTT-TTCTTTC-T
1 TTTTCTTCCTTCTT
*
271465 TTTTCTTCTTTCTT
1 TTTTCTTCCTTCTT
271479 TTTTCTTCCTTCT
1 TTTTCTTCCTTCT
271492 CCGTTCAGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
10 8 0.19
11 1 0.02
12 9 0.21
13 7 0.17
14 17 0.40
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTCCTTCTT
Found at i:272030 original size:30 final size:30
Alignment explanation
Indices: 271997--272124 Score: 116
Period size: 30 Copynumber: 4.2 Consensus size: 30
271987 GGGCCAAGCA
* * *
271997 TAATTTTGAGAAAATTTAGGGGTCAAAATA
1 TAATTTTAAGAAAATTGAGGGGTCAAAATG
* * * *
272027 TAATTTCAAG-AAGTTGATGGGCCAAAATG
1 TAATTTTAAGAAAATTGAGGGGTCAAAATG
* * *
272056 TAATTTTAAGAAAGTTTAGGGGTGAAAATG
1 TAATTTTAAGAAAATTGAGGGGTCAAAATG
*
272086 TAATTTTTTAA-AAAAGTTGAGGGGTTAAAATG
1 TAA--TTTTAAGAAAA-TTGAGGGGTCAAAATG
272118 TAATTTT
1 TAATTTT
272125 TGTTTTTGTT
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
29 23 0.29
30 30 0.38
31 3 0.04
32 23 0.29
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (30 bp):
TAATTTTAAGAAAATTGAGGGGTCAAAATG
Found at i:272059 original size:29 final size:30
Alignment explanation
Indices: 272005--272123 Score: 96
Period size: 32 Copynumber: 3.9 Consensus size: 30
271995 CATAATTTTG
* * * *
272005 AGAAAATTTAGGGGTCAAAATATAATTTCA
1 AGAAAGTTGAGGGGCCAAAATGTAATTTCA
* *
272035 AG-AAGTTGATGGGCCAAAATGTAATTTTA
1 AGAAAGTTGAGGGGCCAAAATGTAATTTCA
* ** *
272064 AGAAAGTTTAGGGGTGAAAATGTAATTTTTTA
1 AGAAAGTTGAGGGGCCAAAATGTAA--TTTCA
* **
272096 AAAAAGTTGAGGGGTTAAAATGTAATTT
1 AGAAAGTTGAGGGGCCAAAATGTAATTT
272124 TTGTTTTTGT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 23 0.32
30 23 0.32
32 27 0.37
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
AGAAAGTTGAGGGGCCAAAATGTAATTTCA
Found at i:272102 original size:32 final size:32
Alignment explanation
Indices: 272050--272125 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
272040 TTGATGGGCC
* *
272050 AAAATGTAA--TTTTAAGAAAGTTTAGGGGTG
1 AAAATGTAATTTTTTAAAAAAGTTGAGGGGTG
*
272080 AAAATGTAATTTTTTAAAAAAGTTGAGGGGTT
1 AAAATGTAATTTTTTAAAAAAGTTGAGGGGTG
272112 AAAATGTAATTTTT
1 AAAATGTAATTTTT
272126 GTTTTTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.22
32 32 0.78
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (32 bp):
AAAATGTAATTTTTTAAAAAAGTTGAGGGGTG
Found at i:273533 original size:18 final size:18
Alignment explanation
Indices: 273506--273542 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
273496 CTGGTGCATT
*
273506 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
273524 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
273542 T
1 T
273543 TCTTTTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:274001 original size:24 final size:25
Alignment explanation
Indices: 273974--274020 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
273964 TATTTTGATA
273974 TTATTTGATGTAAT-AAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
273998 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
274021 ATTTTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:274141 original size:45 final size:46
Alignment explanation
Indices: 274063--274153 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
274053 CTACTAACAA
* *
274063 TTAATACCCTTAACTTAAAAACCCTAACATAATTTAATTAAAAACC
1 TTAATACCCCTAACTTAAAAACCCTAACATAATTAAATTAAAAACC
* *
274109 TTAA-ACCCCTAACTTAAAAATCCTAACCTAATTAAATTAAAAACC
1 TTAATACCCCTAACTTAAAAACCCTAACATAATTAAATTAAAAACC
274154 CTAACCTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 37 0.90
46 4 0.10
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (46 bp):
TTAATACCCCTAACTTAAAAACCCTAACATAATTAAATTAAAAACC
Found at i:274176 original size:22 final size:23
Alignment explanation
Indices: 274072--274223 Score: 127
Period size: 23 Copynumber: 6.8 Consensus size: 23
274062 ATTAATACCC
* *
274072 TTAACTTAAAAACCCTAACATAA
1 TTAAATTAAAAACCCTAACCTAA
* * *
274095 TTTAATTAAAAACCTTAAACC--C
1 TTAAATTAAAAACCCT-AACCTAA
* * *
274117 CTAACTTAAAAATCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
274140 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
274163 TTAAATT-AAAACCCTAATCC---
1 TTAAATTAAAAACCCTAA-CCTAA
* *
274183 TTAACTTAAAAACCCTAACCAAA
1 TTAAATTAAAAACCCTAACCTAA
** *
274206 TTTTATTAAAAACTCTAA
1 TTAAATTAAAAACCCTAA
274224 ACCCTAAACT
Statistics
Matches: 102, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
20 8 0.08
21 14 0.14
22 21 0.21
23 56 0.55
24 3 0.03
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAACCTAA
Found at i:274179 original size:45 final size:44
Alignment explanation
Indices: 274080--274204 Score: 114
Period size: 45 Copynumber: 2.8 Consensus size: 44
274070 CCTTAACTTA
* * * ** *
274080 AAAACCCTAACATAATTTAATTAAAAACCTTAAACC-CCTAACTT
1 AAAACCCTAACCTAATTAAATTAAAAACCCT-AACCAATTAAATT
*
274124 AAAAATCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT
1 -AAAACCCTAACCTAATTAAATTAAAAACCCTAACC-AATTAAATT
*
274170 AAAACCCTAATCC---TTAACTTAAAAACCCTAACCAA
1 AAAACCCTAA-CCTAATTAAATTAAAAACCCTAACCAA
274205 ATTTTATTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 19 0.28
44 4 0.06
45 36 0.53
46 7 0.10
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.26
Consensus pattern (44 bp):
AAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTAAATT
Found at i:274218 original size:66 final size:68
Alignment explanation
Indices: 274072--274486 Score: 241
Period size: 66 Copynumber: 6.3 Consensus size: 68
274062 ATTAATACCC
* * * *
274072 TTAACTTAAAAACCCTAACATAATTTAATTAAAAACCTTAAACCCCTAACTTAAAAATCCTAACC
1 TTAAATTAAAAACCCTAACATAATTAAATTAAAAACCCTAAACCCCTAACTTAAAAACCCTAACC
*
274137 TAA
66 AAA
* * *
274140 TTAAATTAAAAACCCTAACCTAATTAAATT-AAAACCCT-AATCCTTAACTTAAAAACCCTAACC
1 TTAAATTAAAAACCCTAACATAATTAAATTAAAAACCCTAAACCCCTAACTTAAAAACCCTAACC
274203 AAA
66 AAA
** * *** * * *
274206 TTTTATTAAAAACTCTAA-A-CCCTAAACTTAAAAA-CCTTAACCCGTTACTTAAAAACCCTAAC
1 TTAAATTAAAAACCCTAACATAATTAAA-TTAAAAACCCTAAACCCCTAACTTAAAAACCCTAAC
*
274268 C--C
65 CAAA
* * *** * * * *
274270 TTAACTTAAAAACACTAA-ACCCTTAACTTAAAAACACTAAACCCTTAACTTAAAAACACTAAAC
1 TTAAATTAAAAACCCTAACATAATTAAATTAAAAACCCTAAACCCCTAACTTAAAAACCCT-AAC
*
274334 C--C
65 CAAA
* * *** * * * *
274336 TTAACTTAAAAACACTAA-ACCCTTAACTTAAAAACACTAAACCCTTAACTTAAAAACACTAAAC
1 TTAAATTAAAAACCCTAACATAATTAAATTAAAAACCCTAAACCCCTAACTTAAAAACCCT-AAC
*
274400 C--C
65 CAAA
* * *** * * * *
274402 TTAACTTAAAAACACTAA-ACCCTTAACTTAAAAACACTAAACCCTTAACTTAAAAACACTAAAC
1 TTAAATTAAAAACCCTAACATAATTAAATTAAAAACCCTAAACCCCTAACTTAAAAACCCT-AAC
*
274466 C--C
65 CAAA
*
274468 TTAACTTAAAAACCCTAAC
1 TTAAATTAAAAACCCTAAC
274487 CCTTAACTTA
Statistics
Matches: 309, Mismatches: 31, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
64 26 0.08
65 30 0.10
66 219 0.71
67 7 0.02
68 27 0.09
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.25
Consensus pattern (68 bp):
TTAAATTAAAAACCCTAACATAATTAAATTAAAAACCCTAAACCCCTAACTTAAAAACCCTAACC
AAA
Found at i:274236 original size:22 final size:22
Alignment explanation
Indices: 274211--274506 Score: 501
Period size: 22 Copynumber: 13.6 Consensus size: 22
274201 CCAAATTTTA
* *
274211 TTAAAAACTCTAAACCCTAAAC
1 TTAAAAACACTAAACCCTTAAC
*
274233 TTAAAAAC-CTTAACCCGTT-AC
1 TTAAAAACACTAAACCC-TTAAC
*
274254 TTAAAAACCCT-AACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274275 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274297 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274319 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274341 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274363 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274385 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274407 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274429 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
274451 TTAAAAACACTAAACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
*
274473 TTAAAAACCCT-AACCCTTAAC
1 TTAAAAACACTAAACCCTTAAC
*
274494 TTAAAAACCCTAA
1 TTAAAAACACTAA
274507 CCTAATTAAN
Statistics
Matches: 265, Mismatches: 4, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
20 2 0.01
21 55 0.21
22 208 0.78
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.23
Consensus pattern (22 bp):
TTAAAAACACTAAACCCTTAAC
Found at i:277780 original size:124 final size:125
Alignment explanation
Indices: 277453--277826 Score: 606
Period size: 125 Copynumber: 3.0 Consensus size: 125
277443 AACATGCTAT
* *
277453 TGTAGCAAAAGCGCATTCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTCCTAG
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
277518 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
* ** * * *
277578 TGTAGCAAAAGCACATCCACGAGGGCGTAATTTTCACAAATTCTTCTCAAATGGTATCCTGCTAA
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
277643 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
* *
277703 TGTAGCAAAAGCGCGTCCACTAGGGCGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
* ** *
277767 AAGCGATTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCTA
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGACCTA
277827 AAAATCCTAA
Statistics
Matches: 228, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
124 64 0.28
125 164 0.72
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (125 bp):
TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
Found at i:279950 original size:29 final size:27
Alignment explanation
Indices: 279903--279973 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 27
279893 AAAAATTATA
*
279903 AAAAATAAAAAAATATTAAACTTTAAT
1 AAAAATAAAAAAATATTAAAATTTAAT
*
279930 AAAAATATAAAAAATATTTAAAATTTAGT
1 AAAAATA-AAAAAATA-TTAAAATTTAAT
279959 AAAAATTAGAAAAAA
1 AAAAA-TA-AAAAAA
279974 AAATTGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.18
28 8 0.21
29 15 0.39
30 8 0.21
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATAAAAAAATATTAAAATTTAAT
Found at i:280011 original size:19 final size:19
Alignment explanation
Indices: 279996--280033 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
279986 TTGTAAAATT
279996 TTATGAAAAT-CATAAAAAA
1 TTAT-AAAATGCATAAAAAA
280015 TTATAAAATGCATAAAAAA
1 TTATAAAATGCATAAAAAA
280034 AGGTCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
TTATAAAATGCATAAAAAA
Found at i:280290 original size:10 final size:10
Alignment explanation
Indices: 280276--280333 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
280266 AATTTATAAA
280276 ATTTTATATAT
1 ATTTT-TATAT
* *
280287 TTTTTTCTAT
1 ATTTTTATAT
*
280297 ATTTCTATAT
1 ATTTTTATAT
280307 A-TTTTATA-
1 ATTTTTATAT
280315 ATTTTTA-AT
1 ATTTTTATAT
280324 GATTTTTATA
1 -ATTTTTATA
280334 ATCTTTTTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 2 0.05
9 11 0.30
10 19 0.51
11 5 0.14
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:288005 original size:22 final size:23
Alignment explanation
Indices: 287970--288016 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
287960 ACATATACAT
**
287970 TGATTCTATGATGTAA-AAAAAA
1 TGATTCTACAATGTAAGAAAAAA
*
287992 TGATTCTACAATGTAAGAAAGAA
1 TGATTCTACAATGTAAGAAAAAA
288015 TG
1 TG
288017 GAGTGATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (23 bp):
TGATTCTACAATGTAAGAAAAAA
Found at i:296986 original size:105 final size:106
Alignment explanation
Indices: 296833--297024 Score: 246
Period size: 105 Copynumber: 1.8 Consensus size: 106
296823 ACTCAAAAAT
* * *
296833 AGCAGCTAATTTTAAATATTAATAGAAATTCAGCTTCTACAATCAAAAACAAAATAATC-AATGA
1 AGCAGCTAATTTTAAATATTAATAGAAACTCAGCTTCTAAAATAAAAAACAAAAT-ATCTAATGA
* * *
296897 AAATTAACGATCCTTATACCAATAATATTGCAATCACTAGAC
65 AAATTAACAATCCTCACACCAATAATATTGCAATCACTAGAC
* * * * *
296939 AGCAGCTAATTTTAGA-CTTATTAGAAACTCAGCATT-TAAAATAAAAAACCAACTATCTAATGA
1 AGCAGCTAATTTTAAATATTAATAGAAACTCAGC-TTCTAAAATAAAAAACAAAATATCTAATGA
297002 AAATTAACAATCCTCACACCAAT
65 AAATTAACAATCCTCACACCAAT
297025 TAAAATTTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
104 3 0.04
105 53 0.73
106 17 0.23
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (106 bp):
AGCAGCTAATTTTAAATATTAATAGAAACTCAGCTTCTAAAATAAAAAACAAAATATCTAATGAA
AATTAACAATCCTCACACCAATAATATTGCAATCACTAGAC
Found at i:298316 original size:236 final size:235
Alignment explanation
Indices: 297889--298329 Score: 686
Period size: 236 Copynumber: 1.9 Consensus size: 235
297879 GAGGGCTGAA
* *
297889 TTCAAACAGAAATCAATGATAGACTGGATACAAAGGGCAACTTAACACAAAATTGGTTCATATGA
1 TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
* * * * *
297954 TGGTCAAACGCAAGCACTGTAGGGCCACTATAAGGATATTAACTGATTTGGTGGGGAATAAATTG
66 TGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
* *
298019 GAAACTTCGCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAGTTGTTGCCTACTGCAGA
131 GAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGCCTACTGCAGA
*
298084 TGGCCAGATTCAAAGAGTTGAGCTGGCCGAGGAATGTTTC
196 CGGCCAGATTCAAAGAGTTGAGCTGGCCGAGGAATGTTTC
*
298124 TTCAAACAGAAATCAATAATAGACTGGATACAAATGGGCAACTCAACACAAAATTGTTTCATATG
1 TTCAAACAGAAATCAATAATAGACTGGATACAAA-GGGCAACTCAACACAAAATTGGTTCATATG
* * * *
298189 ATGGTCAAAAGCAAGCACTTTAGGGACACTATAA-CATTTTTATCTGATTTGGAGGTAAATAAAT
65 ATGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCA-TATTAACTGATTTGGAGGGAAATAAAT
** * *
298253 TGGAAACTTCCCAGCAGATTTTAAGGGAAGTCACAATGTTCTTCAAGTAATTGTTGGCTACTGCA
129 TGGAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGCCTACTGCA
298318 GACGGCCAGATT
194 GACGGCCAGATT
298330 ACAGGATGCA
Statistics
Matches: 185, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
235 34 0.18
236 151 0.82
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (235 bp):
TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
TGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
GAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGCCTACTGCAGA
CGGCCAGATTCAAAGAGTTGAGCTGGCCGAGGAATGTTTC
Found at i:301312 original size:107 final size:108
Alignment explanation
Indices: 301137--301339 Score: 304
Period size: 107 Copynumber: 1.9 Consensus size: 108
301127 ACCAATAACA
*
301137 TTAAATACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
1 TTAAACACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
*
301202 TCCTCA-GACCAAT-GATATTCCAATCAGTAAACAGCAGCTAATT
66 TCCT-AGGACCAATAAAT-TTCCAATCAGTAAACAGCAGCTAATT
* * * *
301245 TTAAACACTACTAGAAACTTAGCATTTACAATAAA-AAAACTAAATAATCCATTAAAATTAACAA
1 TTAAACACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
*
301309 TCCTAGGACCAATAAATTTCCATTCAGTAAA
66 TCCTAGGACCAATAAATTTCCAATCAGTAAA
301340 TTTATAAACC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
106 1 0.01
107 50 0.58
108 35 0.41
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.26
Consensus pattern (108 bp):
TTAAACACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
TCCTAGGACCAATAAATTTCCAATCAGTAAACAGCAGCTAATT
Found at i:303287 original size:27 final size:27
Alignment explanation
Indices: 303257--303311 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
303247 AGTAGCAGAA
*
303257 CAAACATTATATGCAATCTCTCAGTTT
1 CAAACATTATATGCAATCGCTCAGTTT
*
303284 CAAACATTATATGCAATCGCTCGGTTT
1 CAAACATTATATGCAATCGCTCAGTTT
303311 C
1 C
303312 TCTTATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (27 bp):
CAAACATTATATGCAATCGCTCAGTTT
Found at i:326129 original size:16 final size:16
Alignment explanation
Indices: 326109--326147 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
326099 TGGAATATGA
326109 CTGTAATAGAATAAAG
1 CTGTAATAGAATAAAG
* * *
326125 TTGTAATGGAATGAAG
1 CTGTAATAGAATAAAG
326141 CTGTAAT
1 CTGTAAT
326148 TAGTAATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (16 bp):
CTGTAATAGAATAAAG
Found at i:326218 original size:44 final size:46
Alignment explanation
Indices: 326129--326221 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
326119 ATAAAGTTGT
* *
326129 AATGGAATGAAGCTGTAATTAGTAATTCATTTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATTAGTAATTCATTTGTTTGGTTGAATGG
*
326175 AATGGAATAAAACTGTAA-TA-TCATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATTAGTAATTCATT-TGTTTGGTTGAATGG
326219 AAT
1 AAT
326222 AAATGTTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 23 0.53
45 2 0.05
46 16 0.37
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (46 bp):
AATGGAATAAAACTGTAATTAGTAATTCATTTGTTTGGTTGAATGG
Found at i:329359 original size:17 final size:18
Alignment explanation
Indices: 329333--329367 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
329323 AGGCCAATCT
*
329333 GGGCGTGTGGG-CCACAC
1 GGGCGCGTGGGCCCACAC
329350 GGGCGCGTGGGCCCACAC
1 GGGCGCGTGGGCCCACAC
329368 AGGCATGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.34, G:0.46, T:0.09
Consensus pattern (18 bp):
GGGCGCGTGGGCCCACAC
Found at i:329618 original size:13 final size:13
Alignment explanation
Indices: 329586--329621 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
329576 AAGCATGTTA
329586 TATT-TATATCTG
1 TATTCTATATCTG
329598 TA-TCTATATCTG
1 TATTCTATATCTG
329610 TATTCTATATCT
1 TATTCTATATCT
329622 ATTTTTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 12 0.55
13 9 0.41
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.56
Consensus pattern (13 bp):
TATTCTATATCTG
Found at i:329834 original size:13 final size:13
Alignment explanation
Indices: 329818--329855 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
329808 GGGGGTAGGA
329818 ATCTGTATATCTG
1 ATCTGTATATCTG
*
329831 ATCTGCATATCTG
1 ATCTGTATATCTG
329844 ATCTGTATATCT
1 ATCTGTATATCT
329856 ATAACTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (13 bp):
ATCTGTATATCTG
Found at i:333762 original size:26 final size:26
Alignment explanation
Indices: 333683--333763 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
333673 ATGGGGAAGT
* *
333683 ATACTA-TATTGGCAGCTTTGCCATA-T
1 ATACTATTACTGGCAGCTTTG-C-TACG
* *** *
333709 ATACTGTTACTGGCAGCTTCATTGCG
1 ATACTATTACTGGCAGCTTTGCTACG
333735 ATACTATTACTGGCAGCTTTGCTACG
1 ATACTATTACTGGCAGCTTTGCTACG
333761 ATA
1 ATA
333764 TTGGTGTGTT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
25 1 0.02
26 29 0.71
27 11 0.27
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTACG
Found at i:335693 original size:13 final size:13
Alignment explanation
Indices: 335675--335702 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
335665 GTTCTTCTAA
335675 AAGGCCTAAAAAG
1 AAGGCCTAAAAAG
335688 AAGGCCTAAAAAG
1 AAGGCCTAAAAAG
335701 AA
1 AA
335703 TGTCATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.21, T:0.07
Consensus pattern (13 bp):
AAGGCCTAAAAAG
Found at i:336950 original size:26 final size:26
Alignment explanation
Indices: 336914--336963 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
336904 AAGTATACTG
336914 TACTGGCAGCTTTGCTGCAATATTAA
1 TACTGGCAGCTTTGCTGCAATATTAA
*
336940 TACTGGCAGCTTTGCTGCGATATT
1 TACTGGCAGCTTTGCTGCAATATT
336964 GGTATGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCAATATTAA
Found at i:337100 original size:33 final size:33
Alignment explanation
Indices: 337058--337122 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
337048 TGCATTATTG
337058 CACTGTACTGATACTGTATT-GGGCTAAGGCCCA
1 CACTGTACTGATACTG-ATTAGGGCTAAGGCCCA
* *
337091 CACTGTACTGTTACTGATTAGGGCTCAGGCCC
1 CACTGTACTGATACTGATTAGGGCTAAGGCCC
337123 GGACTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (33 bp):
CACTGTACTGATACTGATTAGGGCTAAGGCCCA
Found at i:341365 original size:31 final size:31
Alignment explanation
Indices: 341330--341428 Score: 119
Period size: 31 Copynumber: 3.1 Consensus size: 31
341320 TTCATGTATC
341330 ATTATATTAAATTATTTAAATATTATTCGTT
1 ATTATATTAAATTATTTAAATATTATTCGTT
* **
341361 ATTATATTAAATTATTTAAATCTTATTTATT
1 ATTATATTAAATTATTTAAATATTATTCGTT
* *
341392 ATTATATTTAATT-TTTAAAATAGTTTATGCGTT
1 ATTATATTAAATTATTT-AAATA--TTATTCGTT
341425 ATTA
1 ATTA
341429 ATTTTACAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
30 3 0.05
31 44 0.77
33 10 0.18
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATTATTCGTT
Found at i:342536 original size:43 final size:43
Alignment explanation
Indices: 342475--342560 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
342465 TATTATATTT
342475 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
1 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
*
342518 CTATTACCATAATTTAAATGACCTAAATTGATAAGTGCTAAAA
1 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
342561 GAAACATGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (43 bp):
CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
Found at i:343861 original size:20 final size:20
Alignment explanation
Indices: 343827--343875 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
343817 TTTATATCTA
*
343827 TTAATTTAGCCATTTTTATTT
1 TTAATTTAG-TATTTTTATTT
* *
343848 TTATTTTAGTATTTTTGTTT
1 TTAATTTAGTATTTTTATTT
343868 TTAATTTA
1 TTAATTTA
343876 ATTTTTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.67
Consensus pattern (20 bp):
TTAATTTAGTATTTTTATTT
Found at i:345954 original size:28 final size:29
Alignment explanation
Indices: 345914--345968 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
345904 GTATGATCAA
* *
345914 GAAATGAGTAGATCAGTTG-TTAATCGTGG
1 GAAATGAGAAGATC-GTTGAGTAATCGTGG
345943 GAAA-GAGAAGATCGTTGAGTAATCGT
1 GAAATGAGAAGATCGTTGAGTAATCGT
345969 CTTCGATCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 15 0.65
29 4 0.17
ACGTcount: A:0.35, C:0.07, G:0.31, T:0.27
Consensus pattern (29 bp):
GAAATGAGAAGATCGTTGAGTAATCGTGG
Found at i:356019 original size:12 final size:12
Alignment explanation
Indices: 356002--356049 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
355992 ACCGTGTGTC
356002 ACACATGGTCCA
1 ACACATGGTCCA
**
356014 ACACATGGTCTGTT
1 ACACATGGTC--CA
356028 ACACATGGTCCA
1 ACACATGGTCCA
356040 ACACATGGTC
1 ACACATGGTC
356050 TGTCACACGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 20 0.67
14 10 0.33
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (12 bp):
ACACATGGTCCA
Found at i:356038 original size:26 final size:26
Alignment explanation
Indices: 355998--356057 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
355988 CCAGACCGTG
355998 TGTCACACATGGTCCAACACATGGTC
1 TGTCACACATGGTCCAACACATGGTC
*
356024 TGTTACACATGGTCCAACACATGGTC
1 TGTCACACATGGTCCAACACATGGTC
356050 TGTCACAC
1 TGTCACAC
356058 GGCCTACCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (26 bp):
TGTCACACATGGTCCAACACATGGTC
Found at i:363741 original size:6 final size:5
Alignment explanation
Indices: 363714--363761 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
363704 ATGGTAACCA
* * *
363714 AAAAT AAAAT AAAAT AAAAT AAAGAT AATAT AAACT AAAAC AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AA
363762 TACAATTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:367076 original size:20 final size:20
Alignment explanation
Indices: 367051--367098 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
367041 GAGCATTTGA
367051 GAGCAAAATGAGCGAAAAAC
1 GAGCAAAATGAGCGAAAAAC
* *
367071 GAGCAAAATGAGCGCAAAAT
1 GAGCAAAATGAGCGAAAAAC
367091 GAGCAAAA
1 GAGCAAAA
367099 ACCAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.15, G:0.25, T:0.06
Consensus pattern (20 bp):
GAGCAAAATGAGCGAAAAAC
Found at i:367078 original size:9 final size:9
Alignment explanation
Indices: 367051--367098 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 9
367041 GAGCATTTGA
367051 GAGCAAAAT
1 GAGCAAAAT
*
367060 GAGCGAAAAAC
1 GAGC--AAAAT
367071 GAGCAAAAT
1 GAGCAAAAT
367080 GAGCGCAAAAT
1 GA--GCAAAAT
367091 GAGCAAAA
1 GAGCAAAA
367099 ACCAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 16 0.48
11 17 0.52
ACGTcount: A:0.54, C:0.15, G:0.25, T:0.06
Consensus pattern (9 bp):
GAGCAAAAT
Found at i:367228 original size:17 final size:17
Alignment explanation
Indices: 367206--367243 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
367196 GCTTGACCAT
*
367206 ACGGTCGTGTGAGCCAC
1 ACGGTCATGTGAGCCAC
367223 ACGGTCATGTGAGCCAC
1 ACGGTCATGTGAGCCAC
367240 ACGG
1 ACGG
367244 GCTACCACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (17 bp):
ACGGTCATGTGAGCCAC
Found at i:368997 original size:22 final size:20
Alignment explanation
Indices: 368946--368990 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
368936 TTTAGTAAAG
368946 AACTTAAAGTTCTATGAAAA
1 AACTTAAAGTTCTATGAAAA
*
368966 AACTTAAAGTTTTATGAAAA
1 AACTTAAAGTTCTATGAAAA
368986 AACTT
1 AACTT
368991 GAGAAGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
AACTTAAAGTTCTATGAAAA
Found at i:370853 original size:2 final size:2
Alignment explanation
Indices: 370846--370873 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
370836 TGTAAGGTAA
370846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
370874 GGATATGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:392258 original size:17 final size:17
Alignment explanation
Indices: 392236--392270 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
392226 GCGTTTTTAG
*
392236 GAGAGAGAAATGAAAAC
1 GAGAGAAAAATGAAAAC
392253 GAGAGAAAAATGAAAAC
1 GAGAGAAAAATGAAAAC
392270 G
1 G
392271 CGTCCTGAAG
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:0.60, C:0.06, G:0.29, T:0.06
Consensus pattern (17 bp):
GAGAGAAAAATGAAAAC
Found at i:392265 original size:58 final size:58
Alignment explanation
Indices: 392195--392311 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 58
392185 GTTGTTTTTG
* * *
392195 GAGAGAGAAATGAAAACGCATCATGTAGGACGCGTTTTTAGGAGAGAGAAATGAAAAC
1 GAGAGAAAAATGAAAACGCATCATGAAGGACGCGTTTTTAGGAGAGAAAAATGAAAAC
* * *
392253 GAGAGAAAAATGAAAACGCGTCCTGAAGGACGTGTTTTTAGGAGAGAAAAATGAAAAC
1 GAGAGAAAAATGAAAACGCATCATGAAGGACGCGTTTTTAGGAGAGAAAAATGAAAAC
392311 G
1 G
392312 CGTCCTGCAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (58 bp):
GAGAGAAAAATGAAAACGCATCATGAAGGACGCGTTTTTAGGAGAGAAAAATGAAAAC
Found at i:395925 original size:15 final size:17
Alignment explanation
Indices: 395907--395939 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
395897 AAAATAGAAT
395907 TTTA-AAAAAATT-ATA
1 TTTATAAAAAATTGATA
395922 TTTATAAAAAATTGATA
1 TTTATAAAAAATTGATA
395939 T
1 T
395940 AAATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTATAAAAAATTGATA
Found at i:405030 original size:36 final size:38
Alignment explanation
Indices: 404989--405063 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
404979 TGAATCAAAG
404989 TTAATTGGTTCATGTAA-C-AAAAAAAAAAAGAATTAA
1 TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAATTAA
*
405025 TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAGTTAA
1 TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAATTAA
405063 T
1 T
405064 GGTTTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 17 0.47
37 1 0.03
38 18 0.50
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (38 bp):
TTAATTGGTTCATGTAACCAAAAAAAAAAAAGAATTAA
Found at i:419682 original size:96 final size:96
Alignment explanation
Indices: 419518--419715 Score: 371
Period size: 96 Copynumber: 2.1 Consensus size: 96
419508 TACATTCCAT
* *
419518 GTGTAGACTTCACAGATGTGTTTTCTCCAGTTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
1 GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
419583 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
66 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
419614 GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
1 GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
419679 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
66 TTGTTGCCACGTATGATTTGGAGCTTGAGCA
419710 GT-TAGA
1 GTGTAGA
419716 TGTAAGAACA
Statistics
Matches: 100, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
95 4 0.04
96 96 0.96
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (96 bp):
GTGTAGACTTCACAGATGTGTTCTCTCCAATTATGAAGCATAGTTCGATTCGAGCCTACTTGGTA
TTGTTGCCACGTATGATTTGGAGCTTGAGCA
Found at i:421477 original size:18 final size:18
Alignment explanation
Indices: 421456--421516 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
421446 AAAATAAATA
*
421456 AAATGAAAAAAAAGATAG
1 AAATGAAAAAAAAGAAAG
** *
421474 AAATGACGAAGAAGAAAG
1 AAATGAAAAAAAAGAAAG
* *
421492 AAATAAAAAAATAAAAAAG
1 AAATGAAAAAA-AAGAAAG
421511 -AATGAA
1 AAATGAA
421517 CTATCGTTAA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.10
Consensus pattern (18 bp):
AAATGAAAAAAAAGAAAG
Found at i:427773 original size:24 final size:25
Alignment explanation
Indices: 427722--427779 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
427712 TGGCTTTCAC
* * *
427722 GAGCTTCCCGTTATATGGTTCTTGT
1 GAGCTTCCCGTTATATAGCTCTTAT
*
427747 GAGCTTTCCGTTA-ATAGCTCTTAT
1 GAGCTTCCCGTTATATAGCTCTTAT
*
427771 GAGCATCCC
1 GAGCTTCCC
427780 AATTTGGTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTAT
Found at i:427870 original size:25 final size:26
Alignment explanation
Indices: 427842--427899 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
427832 CCCGATATAT
427842 GGCTCTTC-GGAGCTTCCCAATTAAA
1 GGCTCTTCAGGAGCTTCCCAATTAAA
* * *
427867 GGCTCTTTCATGAGCTTCCTAATTAAT
1 GGCTC-TTCAGGAGCTTCCCAATTAAA
427894 GGCTCT
1 GGCTCT
427900 CTAGAGCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.18
26 4 0.14
27 19 0.68
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (26 bp):
GGCTCTTCAGGAGCTTCCCAATTAAA
Found at i:432857 original size:19 final size:19
Alignment explanation
Indices: 432833--432869 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
432823 ATTTTGATGT
432833 TGTGGTATG-ATAGTTTAAA
1 TGTGGTATGTAT-GTTTAAA
432852 TGTGGTATGTATGTTTAA
1 TGTGGTATGTATGTTTAA
432870 TTCCATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (19 bp):
TGTGGTATGTATGTTTAAA
Found at i:437136 original size:20 final size:19
Alignment explanation
Indices: 437112--437158 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
437102 AAAGGAGAGT
**
437112 GAAAAAAATGAGAAAA-GAA
1 GAAAAAAAAAAGAAAATG-A
437131 GAAAAAGAAAAAGAAAATGA
1 GAAAAA-AAAAAGAAAATGA
437151 GAAAAAAA
1 GAAAAAAA
437159 GTTTGAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (19 bp):
GAAAAAAAAAAGAAAATGA
Found at i:444624 original size:3 final size:3
Alignment explanation
Indices: 444616--444644 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
444606 GAAAAAGGAA
444616 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
444645 AGAGATGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:445313 original size:13 final size:12
Alignment explanation
Indices: 445295--445353 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
445285 TGGGAAAGAA
445295 AAAGATATGAGAG
1 AAAGATA-GAGAG
445308 AAAGATAGAG-G
1 AAAGATAGAGAG
* *
445319 AACGAGAGAGA-
1 AAAGATAGAGAG
*
445330 AAGAGATATGGGAG
1 AA-AGATA-GAGAG
445344 AAAGATAGAG
1 AAAGATAGAG
445354 GGTTAAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 11 0.31
12 8 0.22
13 15 0.42
14 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.36, T:0.10
Consensus pattern (12 bp):
AAAGATAGAGAG
Found at i:445353 original size:19 final size:19
Alignment explanation
Indices: 445297--445353 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
445287 GGAAAGAAAA
445297 AGATATGAGAGAAAGATAG
1 AGATATGAGAGAAAGATAG
* *
445316 AGGA-ACGAGAG--AGAAAG
1 A-GATATGAGAGAAAGATAG
*
445333 AGATATGGGAGAAAGATAG
1 AGATATGAGAGAAAGATAG
445352 AG
1 AG
445354 GGTTAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.07
17 11 0.38
19 14 0.48
20 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.37, T:0.11
Consensus pattern (19 bp):
AGATATGAGAGAAAGATAG
Found at i:446266 original size:35 final size:35
Alignment explanation
Indices: 446220--446290 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
446210 AAAAAATTCA
*
446220 AGCCAATATTTTAATAATAATAAAGTATTTAAACT
1 AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
* * *
446255 AGCCAATATTTTAATAAGATTACATTATTTAAACT
1 AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
446290 A
1 A
446291 ACTAATGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (35 bp):
AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
Found at i:448264 original size:34 final size:34
Alignment explanation
Indices: 448226--448303 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
448216 GCAATATGAC
** * *
448226 ATGCTTATAACAGA-TCAATGTGGTAGCAATTTAT
1 ATGCTTATAACA-ATTCAATACGGTAGCAAATAAT
* *
448260 ATGCTAATAACAATTCGATACGGTAGCAAATAAT
1 ATGCTTATAACAATTCAATACGGTAGCAAATAAT
448294 ATGCTTATAA
1 ATGCTTATAA
448304 TGGACCAACA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 1 0.03
34 35 0.97
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (34 bp):
ATGCTTATAACAATTCAATACGGTAGCAAATAAT
Found at i:463168 original size:45 final size:47
Alignment explanation
Indices: 463079--463171 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 47
463069 TATAAAAAAA
*
463079 TATTTATATTTATGTAAAAATACCAGATTTAAATGAAAAATTAAATAAT
1 TATTTATATTTATGTAAAAACACCAGATTT--ATGAAAAATTAAATAAT
*
463128 TATTTGTATTTATGT-AAAACACCAGA-TT-TGAAACAATTAAATAA
1 TATTTATATTTATGTAAAAACACCAGATTTATGAAA-AATTAAATAA
463172 ACAAGGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 5 0.12
45 10 0.24
47 2 0.05
48 10 0.24
49 14 0.34
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (47 bp):
TATTTATATTTATGTAAAAACACCAGATTTATGAAAAATTAAATAAT
Found at i:466777 original size:12 final size:12
Alignment explanation
Indices: 466760--466790 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
466750 ACATTACATT
466760 AAATTATAAAAA
1 AAATTATAAAAA
466772 AAATTAT-AAAA
1 AAATTATAAAAA
466783 AAATTATA
1 AAATTATA
466791 TAGATATCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATTATAAAAA
Found at i:466872 original size:14 final size:14
Alignment explanation
Indices: 466853--466880 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
466843 TTTAATTTAC
466853 ATTAAAAAATAAAA
1 ATTAAAAAATAAAA
466867 ATTAAAAAATAAAA
1 ATTAAAAAATAAAA
466881 GAATACATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
ATTAAAAAATAAAA
Found at i:471828 original size:26 final size:26
Alignment explanation
Indices: 471798--471851 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
471788 TCTGTAAAAA
471798 AAATCCAGTGTTTACTTCAAATAAAT
1 AAATCCAGTGTTTACTTCAAATAAAT
*
471824 AAATCCGGTGTTTACTTCAAATAAAT
1 AAATCCAGTGTTTACTTCAAATAAAT
471850 AA
1 AA
471852 GGAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (26 bp):
AAATCCAGTGTTTACTTCAAATAAAT
Found at i:472162 original size:40 final size:40
Alignment explanation
Indices: 472090--472165 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
472080 ATTGTTCATG
*
472090 CCACGTCAGCAAATCGCGTCCTAGGGGGCGCGATTTGTGT
1 CCACGTCAGCAAATCGCGTCCTAGGGGACGCGATTTGTGT
* *
472130 CCACGTCAGCAAATCGCG-CTTACGTGGACGCGATTT
1 CCACGTCAGCAAATCGCGTCCTA-GGGGACGCGATTT
472166 CCTGGCGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 3 0.09
40 29 0.91
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (40 bp):
CCACGTCAGCAAATCGCGTCCTAGGGGACGCGATTTGTGT
Found at i:474013 original size:17 final size:17
Alignment explanation
Indices: 473969--474016 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
473959 TAGAGAGTTT
*
473969 TTTTAAATAATTATAAA
1 TTTTAAATAATTTTAAA
** **
473986 AATTATTTAATTTTAAA
1 TTTTAAATAATTTTAAA
474003 TTTTAAATAATTTT
1 TTTTAAATAATTTT
474017 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAATAATTTTAAA
Found at i:475753 original size:40 final size:40
Alignment explanation
Indices: 475700--475810 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
475690 GTTTGGATAA
* *
475700 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTACA-T
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTT-CAGG
* *
475740 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGATTTCAGG
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGG
* **
475780 GAAGTGCCGCTAAAAA-TGAGCATTAGCGGCG
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCG
475811 TTTGTTGGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 16 0.26
40 45 0.74
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGG
Found at i:475834 original size:39 final size:39
Alignment explanation
Indices: 475699--475835 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 39
475689 CGTTTGGATA
* **
475699 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCG-CTTTAC
1 AAAAACGCCGCTAAAAA-TGAGCATTAGCGGCGTTTTTGG
* **
475738 ATAAAACGCCGCTAAAGATCGAGCATTAGCGGCGATTTCAGG
1 A-AAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-TTTTTGG
* **
475780 -GAAGTGCCGCTAAAAATGAGCATTAGCGGCGTTTGTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTT-TTGG
*
475819 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
475836 CTAAGCCCAA
Statistics
Matches: 76, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
38 3 0.04
39 18 0.24
40 54 0.71
42 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTGG
Found at i:475937 original size:41 final size:41
Alignment explanation
Indices: 475892--476145 Score: 291
Period size: 41 Copynumber: 6.2 Consensus size: 41
475882 GCTTCTTGAA
*
475892 AAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAG
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* *
475933 AAGCGCCACTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAG
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* *
475974 AAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTGAAG
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* * * * * *
476015 AAGCGCCACTAATGTTCGGGGTTTTAGCGGCGTTTTTTAAA-
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCG-TTTTTAAAG
* *
476056 AAGCGCCGC-AACTGCTCAGAGCTTTAGCACCGTTTTTAAGG
1 AAGCGCCGCTAA-TGCTCAGAGCTTTAGCAGCGTTTTTAAAG
* * * * *
476097 AAGTGCCACTAATGCTC-GGGATTTAGCGGCGTTTTTGAAA-
1 AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTT-AAAG
476137 AAGCGCCGC
1 AAGCGCCGC
476146 AAAAACATTT
Statistics
Matches: 180, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
40 31 0.17
41 140 0.78
42 9 0.05
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAG
Found at i:476008 original size:82 final size:80
Alignment explanation
Indices: 475873--476145 Score: 350
Period size: 82 Copynumber: 3.3 Consensus size: 80
475863 CTTTCGGGGC
* * *
475873 TTTAGCGGCGCTTCTTGAAAAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCG
1 TTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCG
* * *
475938 CCACTAGTGCTCAGAGC
65 CCACTAATGCTC-GGGA
* * *
475955 TTTAGCAGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTGAAGAAGCG
1 TTTAGCGGCGTTTTTAAA-AAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCG
* *
476020 CCACTAATGTTCGGGGT
65 CCACTAATGCTC-GGGA
* * *
476037 TTTAGCGGCGTTTTTTAAAAAGCGCCGC-AACTGCTCAGAGCTTTAGCACCGTTTTTAAGGAAGT
1 TTTAGCGGCG-TTTTTAAAAAGCGCCGCTAA-TGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGC
476101 GCCACTAATGCTCGGGA
64 GCCACTAATGCTCGGGA
476118 TTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 TTTAGCGGCGTTTTT-AAAAAGCGCCGC
476146 AAAAACATTT
Statistics
Matches: 168, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
80 5 0.03
81 33 0.20
82 122 0.73
83 8 0.05
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (80 bp):
TTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCGC
CACTAATGCTCGGGA
Found at i:476090 original size:123 final size:121
Alignment explanation
Indices: 475871--476143 Score: 341
Period size: 123 Copynumber: 2.2 Consensus size: 121
475861 ACCTTTCGGG
* * *
475871 GCTTTAGCGGCGCTTCTTGAAAAGCGCCGCTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAG
1 GCTTTAGCGGCG-TTTTTGAAAAGCGCCACTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAG
* * * *
475936 CGCCACTAGTGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGA
65 CGCCACAACTGCTCAGAGCTTTAGCACCGTTTTTAAAGAAGCGCCACTAATGCTC-GA
* * * * *
475994 GCTTTAGCGGCGTTTTTGAAGAAGCGCCACTAATGTTCGGGGTTTTAGCGGCGTTTTTTAAA-AA
1 GCTTTAGCGGCGTTTTTGAA-AAGCGCCACTAATGCTCAGAGCTTTAGCAGCG-TTTTTAAAGAA
* * * *
476058 GCGCCGCAACTGCTCAGAGCTTTAGCACCGTTTTTAAGGAAGTGCCACTAATGCTCGG
64 GCGCCACAACTGCTCAGAGCTTTAGCACCGTTTTTAAAGAAGCGCCACTAATGCTCGA
*
476116 GATTTAGCGGCGTTTTTGAAAAAGCGCC
1 GCTTTAGCGGCGTTTTTG-AAAAGCGCC
476144 GCAAAAACAT
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
122 32 0.25
123 90 0.69
124 8 0.06
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (121 bp):
GCTTTAGCGGCGTTTTTGAAAAGCGCCACTAATGCTCAGAGCTTTAGCAGCGTTTTTAAAGAAGC
GCCACAACTGCTCAGAGCTTTAGCACCGTTTTTAAAGAAGCGCCACTAATGCTCGA
Found at i:476636 original size:21 final size:21
Alignment explanation
Indices: 476592--476636 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
476582 AATTTAAGGT
* * *
476592 TTATGGGTTAGGGGCTAGGGG
1 TTATGGGTTAGAGGCTAAGAG
*
476613 TTATGGGTTAGAGGTTAAGAG
1 TTATGGGTTAGAGGCTAAGAG
476634 TTA
1 TTA
476637 GGGATTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.42, T:0.33
Consensus pattern (21 bp):
TTATGGGTTAGAGGCTAAGAG
Found at i:476735 original size:14 final size:14
Alignment explanation
Indices: 476712--476787 Score: 84
Period size: 14 Copynumber: 5.5 Consensus size: 14
476702 ATATATTAAA
* *
476712 TAAGGTTTAGGAGT
1 TAAGGGTTAGGGGT
476726 TAAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
*
476740 TGAA--GTTAGTGGT
1 T-AAGGGTTAGGGGT
*
476753 TAGGGGTTAGGGGT
1 TAAGGGTTAGGGGT
*
476767 TTAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
476781 TAAGGGT
1 TAAGGGT
476788 CGAGTTAGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
12 1 0.02
13 9 0.18
14 39 0.76
15 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (14 bp):
TAAGGGTTAGGGGT
Found at i:476739 original size:7 final size:7
Alignment explanation
Indices: 476718--476787 Score: 63
Period size: 7 Copynumber: 10.1 Consensus size: 7
476708 TAAATAAGGT
*
476718 TTAGGAG
1 TTAGGGG
*
476725 TTAAGGG
1 TTAGGGG
476732 TTAGGGG
1 TTAGGGG
**
476739 TT-GAAG
1 TTAGGGG
*
476745 TTAGTGG
1 TTAGGGG
476752 TTAGGGG
1 TTAGGGG
476759 TTAGGGG
1 TTAGGGG
476766 TTTA-GGG
1 -TTAGGGG
476773 TTAGGGG
1 TTAGGGG
*
476780 TTAAGGG
1 TTAGGGG
476787 T
1 T
476788 CGAGTTAGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 7 0.14
7 41 0.80
8 3 0.06
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:476883 original size:18 final size:18
Alignment explanation
Indices: 476850--476884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
476840 TAAATAAGGT
*
476850 TTAGGGGTTAGTGGTTAA
1 TTAGGGGTTAGGGGTTAA
*
476868 TTAGGGGTTTGGGGTTA
1 TTAGGGGTTAGGGGTTA
476885 GAGATTAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (18 bp):
TTAGGGGTTAGGGGTTAA
Found at i:476905 original size:21 final size:20
Alignment explanation
Indices: 476867--476923 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
476857 TTAGTGGTTA
* *
476867 ATTAGGGGTTTGGGGTTAGAG
1 ATTA-GGGTTTAGAGTTAGAG
*
476888 ATTAGAGGTTTAGAGTTAGTG
1 ATTAG-GGTTTAGAGTTAGAG
476909 ATTTAGGGTTTAGAG
1 A-TTAGGGTTTAGAG
476924 ATTTGGGGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 26 0.84
22 4 0.13
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.37
Consensus pattern (20 bp):
ATTAGGGTTTAGAGTTAGAG
Found at i:476917 original size:130 final size:128
Alignment explanation
Indices: 476681--476917 Score: 271
Period size: 130 Copynumber: 1.8 Consensus size: 128
476671 AGGGTTTAGA
*
476681 TTAATTAGAGTGTTTTAATTTATATATTAAATAAGGTTTAGGAGTTAAGGGTTAGGGGTTGAAGT
1 TTAATTAGAGTGTTTTAATTTATATATTAAATAAGGTTTAGGAGTTAAGGGTTA--GATTGAAGT
* * * * * *
476746 TAGTGGTTAGGGGTTAGGGGTTTAGGGTTAGGGGTTAAGGGTCGAGTTAGAGTATAGTATTTTAT
64 TAGGGGTTAGAGATTAGAGGTTTAGAGTTAGGGATTAAGGGTCGAGTTAGAGTATAGTATTTTAT
* * * **
476811 TTAATTAGTGTTTTTTAATTTATATATATTAAATAAGGTTTAGGGGTT-AGTGGTTA-ATTAGGG
1 TTAATTAGAGTGTTTTAA-TT-TATATATTAAATAAGGTTTAGGAGTTAAG-GGTTAGATT-GAA
* * *
476874 GTTTGGGGTTAGAGATTAGAGGTTTAGAGTTAGTGATTTAGGGT
62 GTTAGGGGTTAGAGATTAGAGGTTTAGAGTTAGGGATTAAGGGT
476918 TTAGAGATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
129 2 0.02
130 52 0.59
131 4 0.05
132 30 0.34
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.41
Consensus pattern (128 bp):
TTAATTAGAGTGTTTTAATTTATATATTAAATAAGGTTTAGGAGTTAAGGGTTAGATTGAAGTTA
GGGGTTAGAGATTAGAGGTTTAGAGTTAGGGATTAAGGGTCGAGTTAGAGTATAGTATTTTAT
Found at i:480848 original size:7 final size:7
Alignment explanation
Indices: 480836--480877 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
480826 ATGTGAATTT
480836 GATATTA
1 GATATTA
480843 GATATTA
1 GATATTA
*
480850 GATATTT
1 GATATTA
*
480857 GGTATT-
1 GATATTA
480863 GATATTA
1 GATATTA
480870 GATATTA
1 GATATTA
480877 G
1 G
480878 GCTGTGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (7 bp):
GATATTA
Found at i:480868 original size:20 final size:21
Alignment explanation
Indices: 480832--480875 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
480822 TTTGATGTGA
480832 ATTTGATATTAGATATTAGAT
1 ATTTGATATTAGATATTAGAT
*
480853 ATTTGGTATT-GATATTAGAT
1 ATTTGATATTAGATATTAGAT
480873 ATT
1 ATT
480876 AGGCTGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (21 bp):
ATTTGATATTAGATATTAGAT
Found at i:481045 original size:13 final size:13
Alignment explanation
Indices: 481027--481054 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
481017 GCATTTTCAG
481027 AGTTGTTAAATTT
1 AGTTGTTAAATTT
481040 AGTTGTTAAATTT
1 AGTTGTTAAATTT
481053 AG
1 AG
481055 GCTACTGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (13 bp):
AGTTGTTAAATTT
Found at i:481232 original size:7 final size:7
Alignment explanation
Indices: 481220--481261 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
481210 ATGTGAATTT
481220 GATATTA
1 GATATTA
481227 GATATTA
1 GATATTA
*
481234 GATATTT
1 GATATTA
*
481241 GGTATTA
1 GATATTA
481248 -ATATTA
1 GATATTA
481254 GATATTA
1 GATATTA
481261 G
1 G
481262 GGTTTAGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (7 bp):
GATATTA
Found at i:481253 original size:20 final size:21
Alignment explanation
Indices: 481216--481259 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
481206 TTTGATGTGA
481216 ATTTGATATTAGATATTAGAT
1 ATTTGATATTAGATATTAGAT
*
481237 ATTTGGTATTA-ATATTAGAT
1 ATTTGATATTAGATATTAGAT
481257 ATT
1 ATT
481260 AGGGTTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
ATTTGATATTAGATATTAGAT
Found at i:481561 original size:25 final size:25
Alignment explanation
Indices: 481522--481940 Score: 306
Period size: 25 Copynumber: 16.9 Consensus size: 25
481512 AACTTATTAA
* *
481522 TACATAACCTACATAAGACATAACT
1 TACATAACTTACATAATACATAACT
* * * *
481547 TCCATAACTTCCATAATACAAAATT
1 TACATAACTTACATAATACATAACT
* * *
481572 TATATAACTTATATAAGAC--AACT
1 TACATAACTTACATAATACATAACT
* *
481595 TACATAATTTACTTAATACATAACT
1 TACATAACTTACATAATACATAACT
*** *
481620 TACATGTTTTACATAATATATAACT
1 TACATAACTTACATAATACATAACT
* *
481645 TACATAACCTACATAAGACATAACT
1 TACATAACTTACATAATACATAACT
* * *
481670 TCCATAACTTTCATAATACACAACT
1 TACATAACTTACATAATACATAACT
* *
481695 TACACAACTTAAATAACTTACATAAC-
1 TACATAACTTACATAA--TACATAACT
*
481721 T-CACAACTTACATAACTTACATAACT
1 TACATAACTTACATAA--TACATAACT
* *
481747 TACATAACTCACA-ACTTACAT-A--
1 TACATAACTTACATA-ATACATAACT
* * *
481769 T-CTTAA-TTACATTATACACAACT
1 TACATAACTTACATAATACATAACT
* ** *
481792 TACATAGCTTACATTCTACACAACT
1 TACATAACTTACATAATACATAACT
*
481817 TACATAACATACATAACTTACATAA--
1 TACATAACTTACATAA--TACATAACT
*
481842 TACATAACTTA-ATTTAATACACAACT
1 TACATAACTTACA--TAATACATAACT
*
481868 TACATAGCTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
*
481893 TACATAACTTATATAATACATAACT
1 TACATAACTTACATAATACATAACT
* * * *
481918 TATATGATTTACTTAATACATAA
1 TACATAACTTACATAATACATAA
481941 ATATATATCA
Statistics
Matches: 309, Mismatches: 65, Indels: 40
0.75 0.16 0.10
Matches are distributed among these distances:
20 8 0.03
21 5 0.02
22 1 0.00
23 18 0.06
24 11 0.04
25 227 0.73
26 16 0.05
27 23 0.07
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.33
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:481651 original size:9 final size:9
Alignment explanation
Indices: 481522--481919 Score: 221
Period size: 9 Copynumber: 47.2 Consensus size: 9
481512 AACTTATTAA
*
481522 TACATAACC
1 TACATAACT
481531 TACATAA--
1 TACATAACT
*
481538 GACATAACT
1 TACATAACT
*
481547 TCCATAACT
1 TACATAACT
*
481556 TCCATAA--
1 TACATAACT
* *
481563 TACAAAATT
1 TACATAACT
*
481572 TATATAACT
1 TACATAACT
*
481581 TATATAA--
1 TACATAACT
*
481588 GAC--AACT
1 TACATAACT
*
481595 TACATAATT
1 TACATAACT
*
481604 TACTTAA--
1 TACATAACT
481611 TACATAACT
1 TACATAACT
***
481620 TACATGTTT
1 TACATAACT
481629 TACATAA--
1 TACATAACT
*
481636 TATATAACT
1 TACATAACT
*
481645 TACATAACC
1 TACATAACT
481654 TACATAA--
1 TACATAACT
*
481661 GACATAACT
1 TACATAACT
*
481670 TCCATAACT
1 TACATAACT
*
481679 TTCATAA--
1 TACATAACT
*
481686 TACACAACT
1 TACATAACT
*
481695 TACACAACT
1 TACATAACT
*
481704 TAAATAACT
1 TACATAACT
481713 TACATAAC-
1 TACATAACT
*
481721 T-CACAACT
1 TACATAACT
481729 TACATAACT
1 TACATAACT
481738 TACATAACT
1 TACATAACT
481747 TACATAAC-
1 TACATAACT
*
481755 T-CACAACT
1 TACATAACT
*
481763 TACATATCT
1 TACATAACT
*
481772 TA-ATTACATT
1 TACA-TA-ACT
*
481782 ATACACAACT
1 -TACATAACT
*
481792 TACATAGCT
1 TACATAACT
*
481801 TACAT-TC-
1 TACATAACT
*
481808 TACACAACT
1 TACATAACT
*
481817 TACATAACA
1 TACATAACT
481826 TACATAACT
1 TACATAACT
481835 TACATAA--
1 TACATAACT
481842 TACATAACT
1 TACATAACT
481851 TA-ATTTAA--
1 TACA--TAACT
*
481859 TACACAACT
1 TACATAACT
*
481868 TACATAGCT
1 TACATAACT
481877 TACATAA--
1 TACATAACT
481884 TACATAACT
1 TACATAACT
481893 TACATAACT
1 TACATAACT
*
481902 TATATAA--
1 TACATAACT
481909 TACATAACT
1 TACATAACT
481918 TA
1 TA
481920 TATGATTTAC
Statistics
Matches: 298, Mismatches: 54, Indels: 74
0.70 0.13 0.17
Matches are distributed among these distances:
5 2 0.01
7 73 0.24
8 10 0.03
9 203 0.68
10 6 0.02
11 3 0.01
12 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:481677 original size:34 final size:32
Alignment explanation
Indices: 481639--481917 Score: 118
Period size: 34 Copynumber: 8.5 Consensus size: 32
481629 TACATAATAT
* *
481639 ATAACTTACATAACCTACATAAGACATAACTTCC
1 ATAACTTACATAA-CTACA-AATACATAACTTAC
* * *
481673 ATAACTTTCATAA-TACACAACTTACACAACTTAA
1 ATAACTTACATAACTACA-AA--TACATAACTTAC
*
481707 ATAACTTACATAACTCACAACTTACATAACTTAC
1 ATAACTTACATAACT-ACAA-ATACATAACTTAC
* *
481741 ATAACTTACATAACTCACAACTTACATATCTTA-
1 ATAACTTACATAACT-ACAA-ATACATAACTTAC
* * *
481774 ATTACATT--AT-AC-ACAACTTACATAGCTTAC
1 ATAAC-TTACATAACTACAA-ATACATAACTTAC
* *
481804 AT-TC-TACACAACTTACATAACATACATAACTTAC
1 ATAACTTACATAAC-TAC--AA-ATACATAACTTAC
*
481838 ATAA--TACATAACTTA-ATTTAATACACAACTTAC
1 ATAACTTACATAAC-TACA---AATACATAACTTAC
* *
481871 ATAGCTTACATAA-TACATAACTTACATAACTTAT
1 ATAACTTACATAACTACA-AA--TACATAACTTAC
481905 ATAA--TACATAACT
1 ATAACTTACATAACT
481918 TATATGATTT
Statistics
Matches: 197, Mismatches: 24, Indels: 49
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.01
29 18 0.09
30 4 0.02
31 3 0.02
32 20 0.10
33 22 0.11
34 117 0.59
35 9 0.05
36 3 0.02
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (32 bp):
ATAACTTACATAACTACAAATACATAACTTAC
Found at i:481922 original size:16 final size:16
Alignment explanation
Indices: 481504--481919 Score: 142
Period size: 16 Copynumber: 24.9 Consensus size: 16
481494 TTTAAATTTT
*
481504 TAATACATAACTTA-T
1 TAATACATAACTTACA
*
481519 TAATACATAACCTACA
1 TAATACATAACTTACA
* *
481535 TAAGACATAACTTCCA
1 TAATACATAACTTACA
*
481551 TAACTTCCATAA--TACA
1 TAA--TACATAACTTACA
* * *
481567 AAATTTATATAACTTATA
1 TAA--TACATAACTTACA
*
481585 TAAGAC--AACTTACA
1 TAATACATAACTTACA
*
481599 TAATTTACTTAA--TACA
1 TAA--TACATAACTTACA
***
481615 TAACTTACATGTTTTACA
1 TAA--TACATAACTTACA
*
481633 TAATATATAACTTACA
1 TAATACATAACTTACA
*
481649 TAACCTACATAA--GACA
1 TAA--TACATAACTTACA
* *
481665 TAACTTCCATAACTTTCA
1 TAA--TACATAACTTACA
*
481683 TAATACACAACTTACA
1 TAATACATAACTTACA
* *
481699 CAACTTAAATAACTTACA
1 TAA--TACATAACTTACA
*
481717 TAACT-CACAACTTACA
1 TAA-TACATAACTTACA
481733 TAACTTACATAACTTACA
1 TAA--TACATAACTTACA
*
481751 TAACT-CACAACTTACA
1 TAA-TACATAACTTACA
* *
481767 TATCTTA-ATTACATTATACA
1 TA--ATACA-TA-ACT-TACA
* *
481787 CAACTTACATAGCTTACA
1 TAA--TACATAACTTACA
** *
481805 TTCTACACAACTTACA
1 TAATACATAACTTACA
481821 TAACATACATAACTTACA
1 T-A-ATACATAACTTACA
481839 TAATACATAACTTA-A
1 TAATACATAACTTACA
*
481854 TTTAATACACAACTTACA
1 --TAATACATAACTTACA
*
481872 TAGCTTACATAA--TACA
1 TA--ATACATAACTTACA
*
481888 TAACTTACATAACTTATA
1 TAA--TACATAACTTACA
481906 TAATACATAACTTA
1 TAATACATAACTTA
481920 TATGATTTAC
Statistics
Matches: 296, Mismatches: 66, Indels: 77
0.67 0.15 0.18
Matches are distributed among these distances:
14 10 0.03
15 14 0.05
16 153 0.52
17 19 0.06
18 87 0.29
19 3 0.01
20 9 0.03
21 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (16 bp):
TAATACATAACTTACA
Found at i:483764 original size:43 final size:43
Alignment explanation
Indices: 483717--483825 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
483707 AGTTTATAGA
* * * **
483717 AAAAGTGCCGCTAAAAGTCATGTTCTTTAGTGGCGTTTGGGGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCAGCGTTTGGGGG
* *
483760 AAAAGCGCCGCTAAAAGTTATGATCTATAGCAGCGTTTGTGGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCAGCGTTTGGGGG
* *
483803 AAAAGCGCCACTAAAGGTCATGA
1 AAAAGCGCCGCTAAAAGTCATGA
483826 CCTTTAGAGG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAAGTCATGATCTATAGCAGCGTTTGGGGG
Found at i:485678 original size:35 final size:35
Alignment explanation
Indices: 485632--485727 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
485622 TACTCTCTGT
*
485632 TTGGTGTGTTTCGGAGGGATTAGCTCTTTTAAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATAAGCA
** * *
485667 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATAAGCA
* * *
485702 ATGGTGTGTTTTGGAGGGATTGGCTC
1 TTGGTGTGTTTCGGAGGGATTAGCTC
485728 GTGTGAGCAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.15, C:0.11, G:0.34, T:0.40
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATAAGCA
Done.