Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 22 of 125
Found at i:6695131 original size:6 final size:6
Alignment explanation
Indices: 6695122--6695230 Score: 75
Period size: 6 Copynumber: 18.3 Consensus size: 6
6695112 TAATTTTATG
* * * * **
6695122 TTTAAA TTTAGTA TTTTAA TTTTAA TTTTAA TTTAAA TTT-AA GGTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
6695170 TTTAAA TAATTAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --CAAA
1 TTTAAA T--TTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
*
6695217 TTTAAA TTCAAA TT
1 TTTAAA TTTAAA TT
6695231 AAAACAAGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.05
5 6 0.07
6 62 0.75
7 5 0.06
8 6 0.07
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:6695149 original size:12 final size:12
Alignment explanation
Indices: 6695109--6695161 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
6695099 CTTTATGGAC
6695109 TTTTAATTTT-A
1 TTTTAATTTTAA
*
6695120 TGTTTAAATTTAGTA
1 T-TTTAATTTTA--A
6695135 TTTTAATTTTAA
1 TTTTAATTTTAA
*
6695147 TTTTAATTTAAA
1 TTTTAATTTTAA
6695159 TTT
1 TTT
6695162 AAGGTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 1 0.03
12 23 0.66
14 9 0.26
15 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (12 bp):
TTTTAATTTTAA
Found at i:6695162 original size:11 final size:11
Alignment explanation
Indices: 6695136--6695212 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
6695126 AATTTAGTAT
*
6695136 TTTAATTTTAAT
1 TTTAA-TTTAAA
6695148 TTTAATTTAAA
1 TTTAATTTAAA
**
6695159 TTTAAGGTAAA
1 TTTAATTTAAA
*
6695170 TTTAA-AT-AA
1 TTTAATTTAAA
*
6695179 TTAAATTTAAA
1 TTTAATTTAAA
**
6695190 TTTAAGATAAA
1 TTTAATTTAAA
6695201 TTTAAATTTAAA
1 TTT-AATTTAAA
6695213 CAAATTTAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 32 0.63
12 11 0.22
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:6695162 original size:17 final size:17
Alignment explanation
Indices: 6695136--6695224 Score: 87
Period size: 17 Copynumber: 5.5 Consensus size: 17
6695126 AATTTAGTAT
* * *
6695136 TTTAATTTTAATTTTAA
1 TTTAAATTTAAGTTAAA
*
6695153 TTTAAATTTAAGGTAAA
1 TTTAAATTTAAGTTAAA
6695170 TTTAAA--TAA-TTAAA
1 TTTAAATTTAAGTTAAA
*
6695184 TTTAAATTTAAGATAAA
1 TTTAAATTTAAGTTAAA
**
6695201 TTTAAATTTAA-ACAAA
1 TTTAAATTTAAGTTAAA
6695217 TTTAAATT
1 TTTAAATT
6695225 CAAATTAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 15 0.24
17 34 0.55
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAGTTAAA
Found at i:6695700 original size:76 final size:75
Alignment explanation
Indices: 6695572--6696320 Score: 916
Period size: 76 Copynumber: 10.0 Consensus size: 75
6695562 CTTTGTCTAA
* ** *
6695572 CTCTTATTTCAATTTCGGAGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAGAGGATA
1 CTCTTACTTCAATTTC--AGAGATAAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGAGGATA
6695637 GGAAATGATGTTG
63 GGAAATGATGTTG
** *
6695650 CTCTTACTTTGATTTCAGAGATAAAGACGCGTTTATCCACTCTACTTCAATTTCAAGCGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCG-TTATCCACTCTACTTCAATTTCAAGAGGATAGG
*
6695715 AAATGACGTTG
65 AAATGATGTTG
6695726 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAA-ACGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAAGA-GGATAGG
* *
6695790 AAAAGATCTTG
65 AAATGATGTTG
** * *
6695801 CTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCA-CTCTACTTCAATTTCAAGAGGATAGG
6695866 AAATGAT-TCTG
65 AAATGATGT-TG
** ** * * *
6695877 CTCTTACTTCAA-GAC-TTGAT--A-TC-C---A---GCTTTACTTCAATTTCAAGAGGATAGGA
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAAGAGGATAGGA
* *
6695930 AATGGTCTTG
66 AATGATGTTG
**
6695940 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGG
*
6696005 AAATGATGTAG
65 AAATGATGTTG
* * *
6696016 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTTATCCACTCTACTTAAATATCAAGCGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCG-TTATCCACTCTACTTCAATTTCAAGAGGATAGG
*
6696081 AAATGACGTTG
65 AAATGATGTTG
6696092 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAA-ACGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAAGA-GGATAGG
* *
6696156 AAAAGATCTTG
65 AAATGATGTTG
* * *
6696167 CTCTTACTTCAATTTCAGAGATAAAGACTCGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCA-CTCTACTTCAATTTCAAGAGGATAGG
*
6696232 AAATGATCTTG
65 AAATGATGTTG
***
6696243 CTCTTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGG
* *
6696308 GAATGATCTTG
65 AAATGATGTTG
6696319 CT
1 CT
6696321 GTGGTCTGAT
Statistics
Matches: 587, Mismatches: 60, Indels: 50
0.84 0.09 0.07
Matches are distributed among these distances:
63 46 0.08
64 2 0.00
65 3 0.01
67 2 0.00
68 1 0.00
71 1 0.00
72 2 0.00
74 3 0.01
75 149 0.25
76 351 0.60
77 14 0.02
78 13 0.02
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (75 bp):
CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAAGAGGATAGGA
AATGATGTTG
Found at i:6695703 original size:38 final size:37
Alignment explanation
Indices: 6695661--6695779 Score: 120
Period size: 38 Copynumber: 3.2 Consensus size: 37
6695651 TCTTACTTTG
6695661 ATTTCAGAGATAAAGACGCGTTTATCCACTCTACTTCA
1 ATTTCAGAGATAAAGACGCG-TTATCCACTCTACTTCA
* * * *
6695699 ATTTCAAGCGGATAGGAA-ATGACG-T-TGCTCT-TACTTCA
1 ATTTC-AG-AGATA--AAGACG-CGTTATCCACTCTACTTCA
6695737 ATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCA
1 ATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCA
6695774 ATTTCA
1 ATTTCA
6695780 AACGGATAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
34 4 0.06
35 3 0.05
36 8 0.12
37 15 0.23
38 17 0.27
39 6 0.09
40 5 0.08
41 2 0.03
42 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (37 bp):
ATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCA
Found at i:6695886 original size:151 final size:149
Alignment explanation
Indices: 6695572--6696320 Score: 954
Period size: 151 Copynumber: 5.0 Consensus size: 149
6695562 CTTTGTCTAA
* ** *
6695572 CTCTTATTTCAATTTCGGAGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCAAGAGGATA
1 CTCTTACTTCAATTTC--AGAGATAAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGAGGATA
* ** **
6695637 GGAAATGATGTTGCTCTTACTTTGATTTCAGAGATAAAGACGCGTTTATCCACTCTACTTCAATT
63 GGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTG-TTATCCACTCTACTTCAATT
* *
6695702 TCAAGCGGATAGGAAATGACGTTG
127 TCAAGAGGATAGGAAATGA-TTTG
6695726 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAA-ACGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAAGA-GGATAGG
* * *
6695790 AAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTC
65 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCA-CTCTACTTCAATTTC
6695855 AAGAGGATAGGAAATGATTCTG
129 AAGAGGATAGGAAATGATT-TG
* * *
6695877 CTCTTACTTC-A----AGA-CT--TGA-----TATCCAGCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCA-CTCTACTTCAATTTCAAGAGGATAGG
*
6695929 AAATGGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC
65 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTC
*
6695994 AAGAGGATAGGAAATGATGTAG
129 AAGAGGATAGGAAATGAT-TTG
* * *
6696016 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTTATCCACTCTACTTAAATATCAAGCGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCG-TTATCCACTCTACTTCAATTTCAAGAGGATAGG
**
6696081 AAATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTC
65 AAATGATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTC
*
6696145 AA-ACGGATAGGAAAAGATCTTG
129 AAGA-GGATAGGAAATGAT-TTG
* * *
6696167 CTCTTACTTCAATTTCAGAGATAAAGACTCGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCA-CTCTACTTCAATTTCAAGAGGATAGG
*
6696232 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTC
65 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTC
*
6696297 AAGAGGATAGGGAATGATCTTG
129 AAGAGGATAGGAAATGAT-TTG
6696319 CT
1 CT
6696321 GTGGTCTGAT
Statistics
Matches: 523, Mismatches: 45, Indels: 56
0.84 0.07 0.09
Matches are distributed among these distances:
138 6 0.01
139 111 0.21
140 4 0.01
143 2 0.00
144 3 0.01
145 2 0.00
146 3 0.01
147 2 0.00
150 16 0.03
151 232 0.44
152 120 0.23
153 7 0.01
154 15 0.03
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (149 bp):
CTCTTACTTCAATTTCAGAGATAAAGACGCGTTATCCACTCTACTTCAATTTCAAGAGGATAGGA
AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAA
GAGGATAGGAAATGATTTG
Found at i:6695923 original size:63 final size:63
Alignment explanation
Indices: 6695824--6695951 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
6695814 TTCAGAGATA
*
6695824 AAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGAT-TCTGCTCTTACTTC
1 AAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGGTCT-TGCTCTTACTTC
6695887 AAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGGTCTTGCTCTTACTTC
1 AAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGGTCTTGCTCTTACTTC
6695950 AA
1 AA
6695952 TTTCAGAGAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 62 0.98
64 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (63 bp):
AAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGGTCTTGCTCTTACTTC
Found at i:6696307 original size:227 final size:227
Alignment explanation
Indices: 6695896--6696313 Score: 653
Period size: 227 Copynumber: 1.8 Consensus size: 227
6695886 CAAGACTTGA
* * *
6695896 TATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGGTCTTGCTCTTACTTCAATTTCAGAGA
1 TATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGA
* * *
6695961 TAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATGTAGCTCTTACTTC
66 TAAAGACTCGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTAGCTCTTACTTC
*
6696026 AATTTCAGAGATAAAGACGCGTTTATCCACTCTACTTAAATATCAAGCGGATAGGAAATGACGTT
131 AATTTCAGAGATAAAGAC-CGTTTATCCACTCTACTTAAATATCAAGAGGATAGGAAATGACGTT
6696091 GCTCTTACTTCAATTTCAGAGATAAAGACGCGT
195 GCTCTTACTTCAATTTCAGAGATAAAGACGCGT
6696124 TATCCA-CTCTACTTCAATTTCAA-ACGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAG
1 TATCCAGCTCTACTTCAATTTCAAGA-GGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAG
* * *
6696187 ATAAAGACTCGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTT
65 ATAAAGACTCGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTAGCTCTTACTT
* * * *
6696252 CAATTTCAGAGATAAAGA-CTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGGAATGA
130 CAATTTCAGAGATAAAGACCGT-TTATCC-ACTCTACTTAAATATCAAGAGGATAGGAAATGA
6696314 TCTTGCTGTG
Statistics
Matches: 173, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
225 2 0.01
226 7 0.04
227 158 0.91
228 6 0.03
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (227 bp):
TATCCAGCTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGA
TAAAGACTCGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTAGCTCTTACTTC
AATTTCAGAGATAAAGACCGTTTATCCACTCTACTTAAATATCAAGAGGATAGGAAATGACGTTG
CTCTTACTTCAATTTCAGAGATAAAGACGCGT
Found at i:6696910 original size:17 final size:18
Alignment explanation
Indices: 6696884--6696917 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6696874 CTATGATATC
*
6696884 AAATATTTACA-AAGAAT
1 AAATAATTACAGAAGAAT
6696901 AAATAATTACAGAAGAA
1 AAATAATTACAGAAGAA
6696918 CGGTATTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.24
Consensus pattern (18 bp):
AAATAATTACAGAAGAAT
Found at i:6708255 original size:59 final size:59
Alignment explanation
Indices: 6708164--6708648 Score: 665
Period size: 59 Copynumber: 8.3 Consensus size: 59
6708154 ACCCGAGGGC
* ** *
6708164 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGC
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*
6708222 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAGAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * * *
6708280 AAAATGGTAATTTTTGGTAAAATCGAGATTAAAAATGAAATTTTAGAGAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * * * *
6708339 AAAATGGTAATTTTTTGTAAAATAGGGGTTAAAAATAGAATTTTGGAGAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * *
6708398 AAAAATGGTAATTTTTGGTGAAATAGAGGTTAAAAATTGAATTTTTGAGAGTTTAGGGGT
1 -AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * *
6708458 -AAATGGTAATTTTTGGTGAAAT-TAGGGTTAAAGATGGAATTTT-TAAGAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAA-AGTTTAGGGGT
* *
6708516 AAAATGGTAATTTTTGGTGAAACCGAGGTTAAAAATTGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
6708575 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
6708634 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
6708649 CTGAAATTTT
Statistics
Matches: 384, Mismatches: 35, Indels: 15
0.88 0.08 0.03
Matches are distributed among these distances:
57 2 0.01
58 111 0.29
59 214 0.56
60 57 0.15
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:6710384 original size:6 final size:6
Alignment explanation
Indices: 6710375--6710465 Score: 80
Period size: 6 Copynumber: 15.0 Consensus size: 6
6710365 TAATTTTATG
* * * **
6710375 TTTAAA TTTAGTA TTTTAA TTTTAA TTTAAA TTTAAA TTT-AA GGTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
6710423 TTTAAA TAATTAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA
1 TTTAAA T--TTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
6710466 CAAATTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 1 0.01
5 6 0.09
6 52 0.74
7 5 0.07
8 6 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:6710409 original size:11 final size:11
Alignment explanation
Indices: 6710389--6710465 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
6710379 AATTTAGTAT
*
6710389 TTTAATTTTAA
1 TTTAATTTAAA
6710400 TTTAAATTTAAA
1 TTT-AATTTAAA
**
6710412 TTTAAGGTAAA
1 TTTAATTTAAA
*
6710423 TTTAA-AT-AA
1 TTTAATTTAAA
*
6710432 TTAAATTTAAA
1 TTTAATTTAAA
**
6710443 TTTAAGATAAA
1 TTTAATTTAAA
6710454 TTTAAATTTAAA
1 TTT-AATTTAAA
6710466 CAAATTTAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 27 0.53
12 16 0.31
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:6710415 original size:17 final size:17
Alignment explanation
Indices: 6710389--6710464 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
6710379 AATTTAGTAT
* *
6710389 TTTAATTTTAATTTAAA
1 TTTAAATTTAAGTTAAA
*
6710406 TTTAAATTTAAGGTAAA
1 TTTAAATTTAAGTTAAA
6710423 TTTAAA--TAA-TTAAA
1 TTTAAATTTAAGTTAAA
*
6710437 TTTAAATTTAAGATAAA
1 TTTAAATTTAAGTTAAA
6710454 TTTAAATTTAA
1 TTTAAATTTAA
6710465 ACAAATTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 3 0.06
17 35 0.69
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAGTTAAA
Found at i:6710436 original size:31 final size:31
Alignment explanation
Indices: 6710401--6710460 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
6710391 TAATTTTAAT
*
6710401 TTAAATTTAAATTTAAGGTAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATTTAAATAA
6710432 TTAAATTTAAATTTAAGATAAATTTAAAT
1 TTAAATTTAAATTTAAGATAAATTTAAAT
6710461 TTAAACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (31 bp):
TTAAATTTAAATTTAAGATAAATTTAAATAA
Found at i:6710477 original size:17 final size:17
Alignment explanation
Indices: 6710403--6710475 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
6710393 ATTTTAATTT
**
6710403 AAATTTAAATTTAAGGT
1 AAATTTAAATTTAAGAC
**
6710420 AAATTTAAA--TAA-TT
1 AAATTTAAATTTAAGAC
*
6710434 AAATTTAAATTTAAGAT
1 AAATTTAAATTTAAGAC
6710451 AAATTTAAATTTAA-AC
1 AAATTTAAATTTAAGAC
6710467 AAATTTAAA
1 AAATTTAAA
6710476 ATCAAATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 13 0.26
17 24 0.48
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (17 bp):
AAATTTAAATTTAAGAC
Found at i:6718521 original size:26 final size:27
Alignment explanation
Indices: 6718477--6718541 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
6718467 TGGATGTCAA
6718477 ATAT-TATAATTTTGAATATTATTAAAC
1 ATATATATAATTTT-AATATTATTAAAC
* **
6718504 ATATATATAATTTT-ATATTTTTAATT
1 ATATATATAATTTTAATATTATTAAAC
6718530 ATATA-ATAATTT
1 ATATATATAATTT
6718542 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.21
26 14 0.41
27 4 0.12
28 9 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
ATATATATAATTTTAATATTATTAAAC
Found at i:6718645 original size:24 final size:22
Alignment explanation
Indices: 6718623--6718665 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
6718613 TTGGTAATAA
6718623 ATTTT-TAATATAATATATGAAT
1 ATTTTATAATATAA-ATATGAAT
6718645 ATTTTAATAATATAAATATGA
1 ATTTT-ATAATATAAATATGA
6718666 GTTCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTTTATAATATAAATATGAAT
Found at i:6718809 original size:17 final size:18
Alignment explanation
Indices: 6718787--6718827 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
6718777 AAGTTTATAC
*
6718787 AAAATATTAA-TTATTAT
1 AAAATATGAATTTATTAT
6718804 AAAATATGAATTTATTAT
1 AAAATATGAATTTATTAT
6718822 AAAATA
1 AAAATA
6718828 AATTTCGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AAAATATGAATTTATTAT
Found at i:6720061 original size:390 final size:390
Alignment explanation
Indices: 6719336--6720123 Score: 1432
Period size: 390 Copynumber: 2.0 Consensus size: 390
6719326 ATGGTGTCAG
* * * *
6719336 CAGCTTCACCATCTTATTGCAATTGCATGAAAAAGGCTTGGAAATTTCATTTCAAGTAGTGATGG
1 CAGCTCCACCATCTTACTACAATTGCATGAAAAAGACTTGGAAATTTCATTTCAAGTAGTGATGG
* *
6719401 ATCAATATCAACAATTTGTCACCTAACAACGTCGTCACACTCAATGAATGAAAAATATAAATGGA
66 ATCAATATCAACAATTTGGCACCTAACAACGTCGTCACAATCAATGAATGAAAAATATAAATGGA
*
6719466 TAATAATAATGCACAGTTGAGAACCTAACTCTTCCATAATATCAACAAACCATCCCTCATTCACT
131 TAATAATAATGCACAATTGAGAACCTAACTCTTCCATAATATCAACAAACCATCCCTCATTCACT
*
6719531 TCGTCATCCTTGTTATTATTATCTTTAATATTCTTAGTTGCCTCACAATAAACAAAGCAAGAAGT
196 TCGTCATCCCTGTTATTATTATCTTTAATATTCTTAGTTGCCTCACAATAAACAAAGCAAGAAGT
* *
6719596 TTATGAATGAACATAGTATAAATTGAAATATCAACAACTGTGGGATATATACCAAAATCCCCTCC
261 TTATGAATGAACATAGTATAAATTGAAATAGCAACAACTGTGGCATATATACCAAAATCCCCTCC
6719661 TTTTCGATGCATAGTGACCAACACAAAAGATAAATGAAAAAGGTCGGAATTCCAATATTATTTCT
326 TTTTCGATGCATAGTGACCAACACAAAAGATAAATGAAAAAGGTCGGAATTCCAATATTATTTCT
*
6719726 CAGCTCCACCATCTTACTACAATTGCATGAAAAAGACTTGGAAATTTCGTTTCAAGTAGTGATGG
1 CAGCTCCACCATCTTACTACAATTGCATGAAAAAGACTTGGAAATTTCATTTCAAGTAGTGATGG
6719791 ATCAATATCAACAATTTGGCACCTAACAACGTCGTCACAATCAATGAATGAAAAATATAAATGGA
66 ATCAATATCAACAATTTGGCACCTAACAACGTCGTCACAATCAATGAATGAAAAATATAAATGGA
*
6719856 TAATAATAATGCACAATTGAGAACCTAACTCTTCCATAATATCAACAAACCATCCCTCATTCATT
131 TAATAATAATGCACAATTGAGAACCTAACTCTTCCATAATATCAACAAACCATCCCTCATTCACT
6719921 TCGTCATCCCTGTTATTATTATCTTTAATATTCTTAGTTGCCTCACAATAAACAAAGCAAGAAGT
196 TCGTCATCCCTGTTATTATTATCTTTAATATTCTTAGTTGCCTCACAATAAACAAAGCAAGAAGT
* * *
6719986 TTATGAATGAACATAGTATAAATTGAAATAGCAACAATTGTGGCATATATACCAAAATCCCTTTC
261 TTATGAATGAACATAGTATAAATTGAAATAGCAACAACTGTGGCATATATACCAAAATCCCCTCC
*
6720051 TTTTCGATGCATAGTGACCAACACAAAAGATAAATGAAAAAGGTCGGAATTCCAATATTGTTTCT
326 TTTTCGATGCATAGTGACCAACACAAAAGATAAATGAAAAAGGTCGGAATTCCAATATTATTTCT
6720116 CAGCTCCA
1 CAGCTCCA
6720124 TGTTCTTGGT
Statistics
Matches: 382, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
390 382 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (390 bp):
CAGCTCCACCATCTTACTACAATTGCATGAAAAAGACTTGGAAATTTCATTTCAAGTAGTGATGG
ATCAATATCAACAATTTGGCACCTAACAACGTCGTCACAATCAATGAATGAAAAATATAAATGGA
TAATAATAATGCACAATTGAGAACCTAACTCTTCCATAATATCAACAAACCATCCCTCATTCACT
TCGTCATCCCTGTTATTATTATCTTTAATATTCTTAGTTGCCTCACAATAAACAAAGCAAGAAGT
TTATGAATGAACATAGTATAAATTGAAATAGCAACAACTGTGGCATATATACCAAAATCCCCTCC
TTTTCGATGCATAGTGACCAACACAAAAGATAAATGAAAAAGGTCGGAATTCCAATATTATTTCT
Found at i:6720391 original size:6 final size:6
Alignment explanation
Indices: 6720380--6720414 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
6720370 GGGAAAACAA
* *
6720380 GCATAG GCATAG GCATAA GCATAA GCATAG GCATA
1 GCATAG GCATAG GCATAG GCATAG GCATAG GCATA
6720415 AGGAGATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (6 bp):
GCATAG
Found at i:6720401 original size:12 final size:12
Alignment explanation
Indices: 6720378--6720416 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
6720368 AGGGGAAAAC
6720378 AAGCATAGGCAT
1 AAGCATAGGCAT
* *
6720390 AGGCATAAGCAT
1 AAGCATAGGCAT
6720402 AAGCATAGGCAT
1 AAGCATAGGCAT
6720414 AAG
1 AAG
6720417 GAGATGACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (12 bp):
AAGCATAGGCAT
Found at i:6720401 original size:18 final size:18
Alignment explanation
Indices: 6720378--6720416 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
6720368 AGGGGAAAAC
*
6720378 AAGCATAGGCATAGGCAT
1 AAGCATAAGCATAGGCAT
6720396 AAGCATAAGCATAGGCAT
1 AAGCATAAGCATAGGCAT
6720414 AAG
1 AAG
6720417 GAGATGACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (18 bp):
AAGCATAAGCATAGGCAT
Found at i:6723898 original size:4 final size:4
Alignment explanation
Indices: 6723886--6723920 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
6723876 TGCATGCATG
*
6723886 AGGC A-GC AGGC AGGC AGGC AGGC AGGC GGGC AGGC
1 AGGC AGGC AGGC AGGC AGGC AGGC AGGC AGGC AGGC
6723921 GTGTGCTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.23, C:0.26, G:0.51, T:0.00
Consensus pattern (4 bp):
AGGC
Found at i:6727834 original size:27 final size:27
Alignment explanation
Indices: 6727804--6727879 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
6727794 TAAAATCTCG
*
6727804 AACCCAAACCCCAAACTTTAAACACTA
1 AACCCAAACCCCAAACTCTAAACACTA
* ** * *
6727831 AACCTAAACATCAAACTCTAAGCATTA
1 AACCCAAACCCCAAACTCTAAACACTA
* **
6727858 TACCCAAACCTTAAACTCTAAA
1 AACCCAAACCCCAAACTCTAAA
6727880 TCCGAATCCT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (27 bp):
AACCCAAACCCCAAACTCTAAACACTA
Found at i:6730746 original size:18 final size:17
Alignment explanation
Indices: 6730711--6730751 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
6730701 TATATAATTT
* *
6730711 TTAAATATATAAATACA
1 TTAAAAATATAAAAACA
6730728 TTAAAAATACTAAAAACA
1 TTAAAAATA-TAAAAACA
6730746 TTAAAA
1 TTAAAA
6730752 TAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAATATAAAAACA
Found at i:6730876 original size:30 final size:30
Alignment explanation
Indices: 6730830--6730894 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
6730820 CAACTTAACA
* *
6730830 AACAAATGCCTCTAAAATAGTAACAAAATT
1 AACAAACGCCTCTAAAATAATAACAAAATT
* *
6730860 AACAAACGCCTTTAAAATAATAATAAAATT
1 AACAAACGCCTCTAAAATAATAACAAAATT
6730890 AACAA
1 AACAA
6730895 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (30 bp):
AACAAACGCCTCTAAAATAATAACAAAATT
Found at i:6731007 original size:20 final size:22
Alignment explanation
Indices: 6730971--6731010 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
6730961 AAATAGGGAG
6730971 AAAACAACAAGAAAATAGCATT
1 AAAACAACAAGAAAATAGCATT
6730993 AAAA-AACAA-AAAATAGCA
1 AAAACAACAAGAAAATAGCA
6731011 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.10
Consensus pattern (22 bp):
AAAACAACAAGAAAATAGCATT
Found at i:6731485 original size:32 final size:31
Alignment explanation
Indices: 6731449--6731516 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 31
6731439 GGCAAGGATG
*
6731449 ATAGGATGGAGGGCCATCCTGAAGGGTGTGAA
1 ATAGGA-GGAGGGCCATCATGAAGGGTGTGAA
**
6731481 AT---AGGAGGGCCATCATGACTGGTGTGAA
1 ATAGGAGGAGGGCCATCATGAAGGGTGTGAA
6731509 ATAGGAGG
1 ATAGGAGG
6731517 CCACCCGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
28 24 0.80
29 1 0.03
31 3 0.10
32 2 0.07
ACGTcount: A:0.29, C:0.12, G:0.40, T:0.19
Consensus pattern (31 bp):
ATAGGAGGAGGGCCATCATGAAGGGTGTGAA
Found at i:6731488 original size:28 final size:28
Alignment explanation
Indices: 6731456--6731516 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
6731446 ATGATAGGAT
*
6731456 GGAGGGCCATCCTGAAGGGTGTGAAATA
1 GGAGGGCCATCATGAAGGGTGTGAAATA
**
6731484 GGAGGGCCATCATGACTGGTGTGAAATA
1 GGAGGGCCATCATGAAGGGTGTGAAATA
6731512 GGAGG
1 GGAGG
6731517 CCACCCGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.41, T:0.18
Consensus pattern (28 bp):
GGAGGGCCATCATGAAGGGTGTGAAATA
Found at i:6733945 original size:52 final size:52
Alignment explanation
Indices: 6733867--6734106 Score: 365
Period size: 52 Copynumber: 4.6 Consensus size: 52
6733857 ATAAATGAAA
*
6733867 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTAT
*
6733919 AAGGTCCGATGACTATGTTTCATCGTGAGTATACGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTAT
* *
6733971 GAGGTCCGATGACTATGTTTCATCGTGAGTATACGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTAT
* * * *
6734023 GAGGTCTGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTA-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTAT
* **
6734074 AGAGGTCCTATGACTATGTGTCATAATGAGTAT
1 A-AGGTCCGATGACTATGTGTCATCGTGAGTAT
6734107 TAAATGAAAT
Statistics
Matches: 175, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
52 175 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTAT
Found at i:6734853 original size:21 final size:21
Alignment explanation
Indices: 6734813--6734882 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
6734803 GAGTTTTTAA
6734813 TATCGGTAGAAGTAA-T-ACTTG
1 TATCGGTAGAA--AAGTCACTTG
*
6734834 TTTCGGTAGAAAAGTCACTTG
1 TATCGGTAGAAAAGTCACTTG
***
6734855 TATCGGTAGACCTGTCACTTG
1 TATCGGTAGAAAAGTCACTTG
6734876 TATCGGT
1 TATCGGT
6734883 GGAAGTATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 1 0.02
21 39 0.93
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (21 bp):
TATCGGTAGAAAAGTCACTTG
Found at i:6740427 original size:5 final size:5
Alignment explanation
Indices: 6740419--6740454 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
6740409 CCCCCCTCCC
6740419 CCTCT CCTCT CCTCT CCTCT CCTCT CCTCCT CCTCT
1 CCTCT CCTCT CCTCT CCTCT CCTCT CCT-CT CCTCT
6740455 TTCGATCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CCTCT
Found at i:6740439 original size:15 final size:16
Alignment explanation
Indices: 6740413--6740454 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
6740403 CACTTCCCCC
*
6740413 CCTCCCCCTCTCCTCT
1 CCTCCTCCTCTCCTCT
6740429 CCT-CTCCTCTCCTCT
1 CCTCCTCCTCTCCTCT
6740444 CCTCCTCCTCT
1 CCTCCTCCTCT
6740455 TTCGATCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (16 bp):
CCTCCTCCTCTCCTCT
Found at i:6745186 original size:58 final size:58
Alignment explanation
Indices: 6745120--6745237 Score: 193
Period size: 58 Copynumber: 2.0 Consensus size: 58
6745110 ACCCATCAAC
*
6745120 AAATTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCAT
1 AAATTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTCAT
* *
6745178 AAATTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAATTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
6745236 AA
1 AA
6745238 GCAACTCCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 3 0.05
58 53 0.95
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (58 bp):
AAATTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:6751496 original size:58 final size:59
Alignment explanation
Indices: 6751420--6751870 Score: 198
Period size: 59 Copynumber: 7.7 Consensus size: 59
6751410 GAAGAAACGA
* *
6751420 TGAAATCAGGGG-TGAAAATGGGACTTTTGGATA-CCCGGGGGCAAAATGG-AAATTTTGG
1 TGAAATC-GGGGTTAAAAAT-GGACTTTTGGAGAGCCCGGGGGCAAAATGGTAAATTTTGG
* * ** * *
6751478 TGAAATCGGGGTTAAAAATGGAGTTTTTGAGAGTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGACTTTTGGAGAGCCCGGGGGCAAAATGGTAAATTTTGG
* * * ** *** * * **
6751537 TAAAATTGGGGTT-AAAATGGAATTTTTAAGAGTTTGAGGGGTAAATTGGTAGTTTTTGG
1 TGAAATCGGGGTTAAAAATGGACTTTTGGAGAGCCCG-GGGGCAAAATGGTAAATTTTGG
* * * * * * * * *
6751596 TGAAA-CTGGGTTAAAAATGGAATTTTAGAAAGTTCAGGGGGTAAGATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGACTTTTGGAGAG-CCCGGGGGCAAAATGGTAAATTTTGG
* * * ***** * * * *
6751655 TGAAATCGAGGTTTAAAATGGTA-TTTTGGAAAATTTAGGGGTAAAACGATAATTTTTGG
1 TGAAATCGGGGTTAAAAATGG-ACTTTTGGAGAGCCCGGGGGCAAAATGGTAAATTTTGG
** * * * * **** * * *
6751714 TCG-AATTAGGGTTAAAAATAGAGTTTTTGAAAGTTTAGGGGTAAAATGGTAATTTTTAG
1 T-GAAATCGGGGTTAAAAATGGACTTTTGGAGAGCCCGGGGGCAAAATGGTAAATTTTGG
* * * * ** * *
6751773 TGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCGGGGG-TAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGACTTTTGGAGAGCCCGGGGGCAAAATGGTAAATTTTGG
* * * *
6751831 TGAAATCGGGATTAAAAATGGAATTTTGGAAAGCTCGGGG
1 TGAAATCGGGGTTAAAAATGGACTTTTGGAGAGCCCGGGG
6751871 ATAAAACGGT
Statistics
Matches: 322, Mismatches: 60, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
57 14 0.04
58 104 0.32
59 180 0.56
60 23 0.07
61 1 0.00
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (59 bp):
TGAAATCGGGGTTAAAAATGGACTTTTGGAGAGCCCGGGGGCAAAATGGTAAATTTTGG
Found at i:6751498 original size:30 final size:29
Alignment explanation
Indices: 6751462--6751857 Score: 126
Period size: 29 Copynumber: 13.4 Consensus size: 29
6751452 ACCCGGGGGC
*
6751462 AAAATGGAAATTTTGGTGAAATCGGGGTT
1 AAAATGGAATTTTTGGTGAAATCGGGGTT
* * ** *
6751491 AAAAATGGAGTTTTT-GAGAGTTCGGGGGT
1 -AAAATGGAATTTTTGGTGAAATCGGGGTT
* *
6751520 AAAATGGTAATTTTTGGTAAAATTGGGGTT
1 AAAATGG-AATTTTTGGTGAAATCGGGGTT
** ** * *
6751550 AAAATGGAATTTTT-AAGAGTTTGAGGGGT
1 AAAATGGAATTTTTGGTGAAATCG-GGGTT
* * *
6751579 AAATTGGTAGTTTTTGGTGAAA-CTGGGTT
1 AAAATGG-AATTTTTGGTGAAATCGGGGTT
* *
6751608 AAAAATGGAA-TTTT--AGAAAGTTCAGGGGGT
1 -AAAATGGAATTTTTGGTGAAA--TC-GGGGTT
* *
6751638 AAGATGGTAATTTTTGGTGAAATCGAGGTTT
1 AAAATGG-AATTTTTGGTGAAATCG-GGGTT
* * *
6751669 AAAATGGTA-TTTTGG-AAAATTTAGGGG-T
1 AAAATGGAATTTTTGGTGAAA--TCGGGGTT
* * **
6751697 AAAACGATAATTTTTGGTCG-AATTAGGGTT
1 AAAATG-GAATTTTTGGT-GAAATCGGGGTT
* * *
6751727 AAAAATAG-AGTTTT--TGAAAGTTTAGGGG-T
1 -AAAATGGAATTTTTGGTGAAA---TCGGGGTT
* *
6751756 AAAATGGTAATTTTTAGTGAAATCGAGGTT
1 AAAATGG-AATTTTTGGTGAAATCGGGGTT
* *
6751786 AAAAATAGAA-TTTT-G-GAAAGTTCGGGGGT
1 -AAAATGGAATTTTTGGTGAAA--TCGGGGTT
*
6751815 -AAATGGTAATTTTTGGTGAAATCGGGATT
1 AAAATGG-AATTTTTGGTGAAATCGGGGTT
6751844 AAAAATGGAATTTT
1 -AAAATGGAATTTT
6751858 GGAAAGCTCG
Statistics
Matches: 261, Mismatches: 64, Indels: 82
0.64 0.16 0.20
Matches are distributed among these distances:
26 5 0.02
27 12 0.05
28 33 0.13
29 88 0.34
30 75 0.29
31 39 0.15
32 5 0.02
33 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGTGAAATCGGGGTT
Found at i:6751504 original size:29 final size:29
Alignment explanation
Indices: 6751462--6751563 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 29
6751452 ACCCGGGGGC
6751462 AAAATGGAAATTTTGGTGAAATCGGGGTT
1 AAAATGGAAATTTTGGTGAAATCGGGGTT
* * * ** *
6751491 AAAAATGG-AGTTTTTGAGAGTTCGGGGGT
1 -AAAATGGAAATTTTGGTGAAATCGGGGTT
* * *
6751520 AAAATGGTAATTTTTGGTAAAATTGGGGTT
1 AAAATGG-AAATTTTGGTGAAATCGGGGTT
*
6751550 AAAATGGAATTTTT
1 AAAATGGAAATTTT
6751564 AAGAGTTTGA
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
28 7 0.12
29 22 0.39
30 27 0.48
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.35
Consensus pattern (29 bp):
AAAATGGAAATTTTGGTGAAATCGGGGTT
Found at i:6751578 original size:59 final size:59
Alignment explanation
Indices: 6751457--6751857 Score: 390
Period size: 59 Copynumber: 6.8 Consensus size: 59
6751447 TGGATACCCG
* * * * *
6751457 GGGGCAAAATGG-AAATTTTGGTGAAATCGGGGTTAAAAATGGAGTTTTTGAGAGTTCG-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTT-AAAGTTTGA
* *
6751515 GGGGTAAAATGGTAATTTTTGGTAAAATTGGGGTT-AAAATGGAATTTTTAAGAGTTTGA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTAA-AGTTTGA
* * * * *
6751574 GGGGTAAATTGGTAGTTTTTGGTGAAA-CTGGGTTAAAAATGGAATTTTAGAAAG-TTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-TAAAGTTTGA
* * * * * *
6751632 GGGGGTAAGATGGTAATTTTTGGTGAAATCGAGGTTTAAAATGGTATTTTGGAAAATTT-A
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-TAAAGTTTGA
* * ** * *
6751692 GGGGTAAAACGATAATTTTTGGTCG-AATTAGGGTTAAAAATAGAGTTTTTGAAAGTTT-A
1 GGGGTAAAATGGTAATTTTTGGT-GAAATCGGGGTTAAAAATGGAATTTTT-AAAGTTTGA
* * * * *
6751751 GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCG-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-TAAAGTTTGA
*
6751810 GGGGT-AAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT
6751858 GGAAAGCTCG
Statistics
Matches: 282, Mismatches: 48, Indels: 26
0.79 0.13 0.07
Matches are distributed among these distances:
57 1 0.00
58 77 0.27
59 177 0.63
60 25 0.09
61 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTAAAGTTTGA
Found at i:6751581 original size:29 final size:28
Alignment explanation
Indices: 6751492--6751581 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 28
6751482 ATCGGGGTTA
* * *
6751492 AAAATGGAGTTTTTGAGAGTTCGGGGGT
1 AAAATGGAATTTTTAAGAGTTTGGGGGT
* *
6751520 AAAATGGTAATTTTTGGTAA-A-ATTGGGGTT
1 AAAATGG-AA-TTTT--TAAGAGTTTGGGGGT
6751550 AAAATGGAATTTTTAAGAGTTTGAGGGGT
1 AAAATGGAATTTTTAAGAGTTTG-GGGGT
6751579 AAA
1 AAA
6751582 TTGGTAGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 14 0.29
29 10 0.21
30 17 0.35
31 1 0.02
32 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTAAGAGTTTGGGGGT
Found at i:6751639 original size:118 final size:117
Alignment explanation
Indices: 6751463--6751886 Score: 450
Period size: 118 Copynumber: 3.6 Consensus size: 117
6751453 CCCGGGGGCA
* * * *
6751463 AAATGG-AAATTTTGGTGAAA-TCGGGGTTAAAAATGGAGTTTTTGAGAGTTCGGGGGTAAAATG
1 AAATGGTAATTTTTGGTGAAACT-AGGGTTAAAAATGGAATTTTTGAAAGTTCGGGGGTAAAATG
* * *
6751526 GTAATTTTTGGTAAAATTGGGGTTAAAATGGAATTTT-TAAGAGTTTGAGGGGT
65 GTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAA-AGTTTGAGGGGT
* * *
6751579 AAATTGGTAGTTTTTGGTGAAACT-GGGTTAAAAATGGAATTTTAGAAAGTTCAGGGGGTAAGAT
1 AAA-TGGTAATTTTTGGTGAAACTAGGGTTAAAAATGGAATTTTTGAAAGTTC-GGGGGTAAAAT
* * *
6751643 GGTAATTTTTGGTGAAATCGAGGTTTAAAATGGTATTTTGGAAAATTT-AGGGGT
64 GGTAATTTTTGGTGAAATCG-GGGTTAAAATGGAATTTTGGAAAGTTTGAGGGGT
* * * * * **
6751697 AAAACGATAATTTTTGGTCG-AATTAGGGTTAAAAATAGAGTTTTTGAAAGTTTAGGGGTAAAAT
1 -AAATGGTAATTTTTGGT-GAAACTAGGGTTAAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAT
* * * *
6751761 GGTAATTTTTAGTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCG-GGGGT
64 GGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTTGAGGGGT
* * * * *
6751815 AAATGGTAATTTTTGGTGAAA-TCGGGATTAAAAATGGAATTTTGGAAAGCTCGGGGATAAAACG
1 AAATGGTAATTTTTGGTGAAACTAGGG-TTAAAAATGGAATTTTTGAAAGTTCGGGGGTAAAATG
6751879 GTAATTTT
65 GTAATTTT
6751887 CGAAAGTTTC
Statistics
Matches: 255, Mismatches: 40, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
116 8 0.03
117 85 0.33
118 111 0.44
119 49 0.19
120 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (117 bp):
AAATGGTAATTTTTGGTGAAACTAGGGTTAAAAATGGAATTTTTGAAAGTTCGGGGGTAAAATGG
TAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTGAGGGGT
Found at i:6751817 original size:29 final size:28
Alignment explanation
Indices: 6751785--6751915 Score: 76
Period size: 29 Copynumber: 4.5 Consensus size: 28
6751775 AAATCGAGGT
* *
6751785 TAAAAATAGAATTTTGGAAAGTTCGGGGG
1 TAAAAATGGAATTTTGGAAAG-TCGGGGA
6751814 T--AAATGGTAATTTTTGGTGAAA-TC-GGGA
1 TAAAAATGG-AA-TTTT-G-GAAAGTCGGGGA
6751842 TTAAAAATGGAATTTTGGAAAGCTCGGGGA
1 -TAAAAATGGAATTTTGGAAAG-TCGGGGA
* *
6751872 T-AAAACGGTAATTTTCGAAAGTTTCGGGG-
1 TAAAAATGG-AATTTTGGAAAG--TCGGGGA
* *
6751901 TCAAAATGTAATTTT
1 TAAAAATGGAATTTT
6751916 TTGAAATTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
27 9 0.11
28 12 0.15
29 33 0.40
30 18 0.22
31 10 0.12
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (28 bp):
TAAAAATGGAATTTTGGAAAGTCGGGGA
Found at i:6753851 original size:12 final size:12
Alignment explanation
Indices: 6753834--6753889 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
6753824 ATAATAATTT
6753834 TAAATTTAAAAA
1 TAAATTTAAAAA
*
6753846 TAAATTT-AAAC
1 TAAATTTAAAAA
*
6753857 TCAAA-TTAAAAT
1 T-AAATTTAAAAA
6753869 TAAATTTAAAAA
1 TAAATTTAAAAA
*
6753881 CAAATTTAA
1 TAAATTTAA
6753890 TCTTAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:6753852 original size:35 final size:33
Alignment explanation
Indices: 6753813--6753907 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 33
6753803 TGGACTTTTG
* *
6753813 AATTTAGATTTATAATAATTTTAAATTTAAAAATA
1 AATTTA-ATTTA-AATAAATTTAAATTTAAAAACA
* * *
6753848 AATTTAAACTCAAATTAAAATTAAATTTAAAAACA
1 AATTT-AATTTAAA-TAAATTTAAATTTAAAAACA
6753883 AATTTAATCTTAAAATAAATTTAAA
1 AATTTAAT-TT-AAATAAATTTAAA
6753908 ATGGGTTTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
34 4 0.08
35 40 0.83
36 4 0.08
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (33 bp):
AATTTAATTTAAATAAATTTAAATTTAAAAACA
Found at i:6753884 original size:23 final size:23
Alignment explanation
Indices: 6753839--6753886 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6753829 AATTTTAAAT
**
6753839 TTAAAAATAAATTTAAACTCAAA
1 TTAAAAATAAATTTAAAAACAAA
*
6753862 TTAAAATTAAATTTAAAAACAAA
1 TTAAAAATAAATTTAAAAACAAA
6753885 TT
1 TT
6753887 TAATCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAAAAATAAATTTAAAAACAAA
Found at i:6753902 original size:17 final size:17
Alignment explanation
Indices: 6753842--6753906 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
6753832 TTTAAATTTA
* *
6753842 AAAATAAATTTAAACTC
1 AAAATAAATTTAATCTT
* *
6753859 AAATTAAAATTAAAT-TT
1 AAAAT-AAATTTAATCTT
*
6753876 AAAAACAAATTTAATCTT
1 -AAAATAAATTTAATCTT
6753894 AAAATAAATTTAA
1 AAAATAAATTTAA
6753907 AATGGGTTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
17 25 0.68
18 12 0.32
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATAAATTTAATCTT
Found at i:6754344 original size:38 final size:37
Alignment explanation
Indices: 6754293--6754648 Score: 140
Period size: 38 Copynumber: 9.4 Consensus size: 37
6754283 TTATCCACTC
6754293 TACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCT
1 TACTTCAATTTCAAG-GGATAGGAAAAGATCTTGCTCT
* * * ** * **
6754331 TACTTCAACTTCAAAGAGATAAGACTTGATATCCAGCT-T
1 TACTTCAATTTC-AAGGGATAGGA--AAAGATCTTGCTCT
*
6754370 TACTTCAATTTCAAGAGGATGGGAAATA-ATCTTGCTCT
1 TACTTCAATTTCAAG-GGATAGGAAA-AGATCTTGCTCT
* * * * *
6754408 TACTTCAATTT-TAGAGATA--AAGACG-TGTTGTCCACT
1 TACTTCAATTTCAAGGGATAGGAA-AAGATCTTG--CTCT
*
6754444 CTACTTCAATTTCAAACGGATAGGAAAAGATCTTGCTCT
1 -TACTTCAATTTC-AAGGGATAGGAAAAGATCTTGCTCT
* * ** * **
6754483 TACTTCAATTTCAGAGAGATAAGACTTGATATCCAGCT-T
1 TACTTCAATTTCA-AGGGATAGGA--AAAGATCTTGCTCT
* * *
6754522 TACTTCAATTTCAAGAGGATGGGAAACA-ATCTTACTTT
1 TACTTCAATTTCAAG-GGATAGGAAA-AGATCTTGCTCT
* * *** ***
6754560 TACTTCAATTTC-AGAGATAAAGACTTGTTATCCAACTC-
1 TACTTCAATTTCAAGGGAT-AGGAAAAG--ATCTTGCTCT
*
6754598 TACTTCAATTTCAAGAGGAT-GTGAAATGATCTTGCTCT
1 TACTTCAATTTCAAG-GGATAG-GAAAAGATCTTGCTCT
6754636 TACTTCAATTTCA
1 TACTTCAATTTCA
6754649 GAGATAAAGA
Statistics
Matches: 228, Mismatches: 60, Indels: 60
0.66 0.17 0.17
Matches are distributed among these distances:
34 6 0.03
35 1 0.00
36 9 0.04
37 35 0.15
38 93 0.41
39 59 0.26
40 19 0.08
41 6 0.03
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (37 bp):
TACTTCAATTTCAAGGGATAGGAAAAGATCTTGCTCT
Found at i:6754612 original size:76 final size:76
Alignment explanation
Indices: 6754170--6755229 Score: 1504
Period size: 76 Copynumber: 14.1 Consensus size: 76
6754160 TTAGGCTTCG
*
6754170 TCTTGCTCTTACTTCAATTTCAGAGATAACGACCTT-TTATCCAACTCTACTTCAAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGA-CTTGTTATCCAACTCTACTTC-AATTTCAAGA
* * *
6754234 GTATAGGCAATGA
64 GGATGGGAAATGA
* * *
6754247 TGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
* *
6754311 ATAGGAAAAGA
66 ATGGGAAATGA
* * * *
6754322 TCTTGCTCTTACTTCAACTTCAAAGAGAT-AAGACTTGATATCCAGCTTTACTTCAATTTCAAGA
1 TCTTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
*
6754386 GGATGGGAAATAA
64 GGATGGGAAATGA
* * *
6754399 TCTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTGTCC-ACTCTACTTCAATTTCAA-ACG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA-G
* *
6754462 GATAGGAAAAGA
65 GATGGGAAATGA
* * * *
6754474 TCTTGCTCTTACTTCAATTTCAGAGAGATAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 TCTTGCTCTTACTTCAATTTCAGAGATA-AAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
**
6754539 GATGGGAAACAA
65 GATGGGAAATGA
* *
6754551 TCTTACTTTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6754616 ATGTGAAATGA
66 ATGGGAAATGA
6754627 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6754692 ATGGGAAACGA
66 ATGGGAAATGA
* *
6754703 TCTTACTTTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6754768 ATGTGAAATGA
66 ATGGGAAATGA
*
6754779 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCGAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6754844 ATGTGAAATGA
66 ATGGGAAATGA
6754855 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAA--CT-C-T--A---C-AGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6754910 ATGTGAAATGA
66 ATGGGAAATGA
6754921 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
* *
6754986 ATAGGAAATAA
66 ATGGGAAATGA
*
6754997 TCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6755062 ATGTGAAATGA
66 ATGGGAAATGA
* * * *
6755073 TCTTGCTCTTACTTCAATTTCAGAGATAAAGGCTTGATATCCAGCTTTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6755138 AAT-GGAAACGA
66 -ATGGGAAATGA
* * * *
6755149 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
*
6755214 ATAGGAAATGA
66 ATGGGAAATGA
6755225 TCTTG
1 TCTTG
6755230 GTGCGGTCTG
Statistics
Matches: 888, Mismatches: 74, Indels: 43
0.88 0.07 0.04
Matches are distributed among these distances:
66 60 0.07
67 1 0.00
68 2 0.00
69 1 0.00
70 2 0.00
72 2 0.00
73 1 0.00
74 3 0.00
75 99 0.11
76 575 0.65
77 141 0.16
78 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (76 bp):
TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
ATGGGAAATGA
Found at i:6767215 original size:59 final size:59
Alignment explanation
Indices: 6767128--6767494 Score: 467
Period size: 59 Copynumber: 6.3 Consensus size: 59
6767118 ACCCGAGGGC
* * *
6767128 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGAGAGTTCGGGAGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGAGT
* * * *
6767186 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATTGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGAGT
* * * * *
6767245 AAGATGGTAATTCTTGGTGAAATCGAGGTTTAAAATGGTATTTTAGAAAGTTTAGGG-GT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAG-TTCGGGAGT
* * * *
6767304 AAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAGTTTTGGAAAGTTCAGGGA-T
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTC-GGGAGT
* * *
6767363 AAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGG-GT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCG-GGAGT
* *
6767422 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAAATTCAGGGA-T
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTC-GGGAGT
6767480 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
6767495 AGAAGTTTCG
Statistics
Matches: 268, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
58 51 0.19
59 212 0.79
60 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGAGT
Found at i:6767281 original size:118 final size:116
Alignment explanation
Indices: 6767128--6767493 Score: 518
Period size: 118 Copynumber: 3.1 Consensus size: 116
6767118 ACCCGAGGGC
* *
6767128 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGAGAGTTCGGGAGTAAAATGG
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGG-GTAAAATGG
* * * ** *
6767193 TAATTTTTGGTGAAATCGGGGTTAAAAATTGAATTTTAGAAAGTTTGGGGGT
65 TAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCAGGGAT
* * * * *
6767245 AAGATGGTAATTCTTGGTGAAATCGAGGTTTAAAATGGTATTTTAGAAAGTTTAGGGGTAAAATG
1 AAAATGGTAATT-TTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAG-TTCGGGGTAAAATG
* *
6767310 GTAATTTTTGGTAAAATCGAGGTTAAAAATAGAGTTTTGGAAAGTTCAGGGAT
64 GTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCAGGGAT
*
6767363 AAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATG
1 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCG-GGGTAAAATG
* *
6767428 GTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAAATTCAGGGAT
64 GTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCAGGGAT
6767480 AAAATGGTAATTTT
1 AAAATGGTAATTTT
6767494 TAGAAGTTTC
Statistics
Matches: 220, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
117 55 0.25
118 160 0.73
119 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (116 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGTAAAATGGT
AATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCAGGGAT
Found at i:6767441 original size:177 final size:176
Alignment explanation
Indices: 6767128--6767494 Score: 540
Period size: 177 Copynumber: 2.1 Consensus size: 176
6767118 ACCCGAGGGC
* * * * *
6767128 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGAGAGTTCGGGAGTAAAATG
1 AAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCGGGAGTAAAATG
* * * * * *
6767192 GTAATTTTTGGTGAAATCGGGGTTAAAAATTGAATTTTAGAAAGTTTGGGGGTAAGATGGTAATT
66 GTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATGGTAATT
* * * *
6767257 CTTGGTGAAATCGAGGTTTAAAATGGTATTTTAGAAAGTTTAGGGGT
131 CTTGGTGAAATCGAGG-TTAAAATGGAATTTTAGAAAATTCAGGGAT
*
6767304 AAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAGTTTTGGAAAGTTCAGGGA-TAAAAT
1 AAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTC-GGGAGTAAAAT
6767368 GGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATGGTAAT
65 GGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATGGTAAT
* *
6767433 TTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAAAATTCAGGGAT
130 TCTTGGTGAAATCGAGGTTAAAATGGAATTTTAGAAAATTCAGGGAT
6767480 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
6767495 AGAAGTTTCG
Statistics
Matches: 171, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
176 50 0.29
177 117 0.68
178 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (176 bp):
AAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCGGGAGTAAAATG
GTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATGGTAATT
CTTGGTGAAATCGAGGTTAAAATGGAATTTTAGAAAATTCAGGGAT
Found at i:6767518 original size:29 final size:28
Alignment explanation
Indices: 6767128--6767550 Score: 119
Period size: 29 Copynumber: 14.4 Consensus size: 28
6767118 ACCCGAGGGC
6767128 AAAATGGTAATTTTGGT-GAAA-TCGGGGTT
1 AAAAT-GTAATTTT--TAGAAATTCGGGGTT
* *
6767157 AAAAATGGAATTTTT-GAGAGTTCGGGAG-T
1 -AAAATGTAATTTTTAGA-AATTCGGG-GTT
*
6767186 AAAATGGTAATTTTTGGTGAAA-TCGGGGTT
1 AAAAT-GTAATTTTT--AGAAATTCGGGGTT
* *
6767216 AAAAAT-TGAA-TTTTAGAAAGTTTGGGGGT
1 -AAAATGT-AATTTTTAGAAA-TTCGGGGTT
* *
6767245 AAGATGGTAATTCTTGGT-GAAA-TCGAGGTTT
1 AAAAT-GTAATT-TT--TAGAAATTCG-GGGTT
*
6767276 AAAATGGT-A-TTTTAGAAAGTTTAGGGG-T
1 AAAAT-GTAATTTTTAGAAA--TTCGGGGTT
* * *
6767304 AAAATGGTAATTTTTGGTAAAATCGAGGTT
1 AAAAT-GTAATTTTTAG-AAATTCGGGGTT
* * * * *
6767334 AAAA-ATAGAGTTTTGGAAAGTTCAGGGAT
1 AAAATGTA-ATTTTTAGAAA-TTCGGGGTT
*
6767363 AAAATGGTAATTTTCGATGAAA-TCGGGGTT
1 AAAAT-GTAATTTT-TA-GAAATTCGGGGTT
*
6767393 AAAAATGGAA-TTTTAGAAAGTTCGAGGG-T
1 -AAAATGTAATTTTTAGAAA-TTCG-GGGTT
* *
6767422 AAAATGGTAATTTTTGGTGAAA-TCGAGGTT
1 AAAAT-GTAATTTTT--AGAAATTCGGGGTT
* * * *
6767452 AAAATGGAA-TTTTGGAAAATTCAGGGAT
1 AAAATGTAATTTTTAG-AAATTCGGGGTT
*
6767480 AAAATGGTAATTTTTAGAAGTTTCGGGGTT
1 AAAAT-GTAATTTTTAGAA-ATTCGGGGTT
* *
6767510 AAAATGTAATTTTTTA-AAATTTTGGGGTC
1 AAAATGTAA-TTTTTAGAAA-TTCGGGGTT
*
6767539 AAAATGCAATTT
1 AAAATGTAATTT
6767551 CTAGGCTGTT
Statistics
Matches: 295, Mismatches: 49, Indels: 100
0.66 0.11 0.23
Matches are distributed among these distances:
26 2 0.01
27 18 0.06
28 49 0.17
29 100 0.34
30 83 0.28
31 28 0.09
32 14 0.05
33 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTTAGAAATTCGGGGTT
Found at i:6767983 original size:2 final size:2
Alignment explanation
Indices: 6767976--6768006 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6767966 AAACGGGTCC
6767976 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6768007 TATTTTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6769452 original size:17 final size:16
Alignment explanation
Indices: 6769425--6769534 Score: 98
Period size: 17 Copynumber: 6.5 Consensus size: 16
6769415 TGAACTTTTG
*
6769425 AATTTAGATTTATAATA
1 AATTTAAATTTA-AATA
*
6769442 ATTTTAAATTTGAAAATA
1 AATTTAAATTT--AAATA
*
6769460 AATTTAAATTCAAATTA
1 AATTTAAATTTAAA-TA
6769477 AATTTAAATTTAAAAATA
1 AATTTAAATTT--AAATA
6769495 AATTT-AATCTTAAAATA
1 AATTTAAAT-TT-AAATA
*
6769512 AATTT-AATTAAAATA
1 AATTTAAATTTAAATA
6769527 AATTTAAA
1 AATTTAAA
6769535 ATGGGTTTGG
Statistics
Matches: 80, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.12
16 6 0.08
17 38 0.47
18 22 0.28
19 4 0.05
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:6769469 original size:6 final size:6
Alignment explanation
Indices: 6769444--6769534 Score: 61
Period size: 6 Copynumber: 16.0 Consensus size: 6
6769434 TTATAATAAT
* *
6769444 TTTAAA TTTGAAA -ATAAA TTTAAA TTCAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
6769491 AATAAA TTT-AA TCTTAAA -ATAAA TTT-AA -TTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
6769535 ATGGGTTTGG
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
4 2 0.03
5 22 0.34
6 36 0.55
7 5 0.08
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:6769483 original size:35 final size:35
Alignment explanation
Indices: 6769438--6769534 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 35
6769428 TTAGATTTAT
*
6769438 AATAATTTTAAATTTGAAAATAAATTTAAAT-TCAA
1 AATAAATTTAAATTT-AAAATAAATTTAAATCTCAA
* *
6769473 ATTAAATTTAAATTTAAAAATAAATTT-AATCTTAA
1 AATAAATTTAAATTT-AAAATAAATTTAAATCTCAA
6769508 AATAAATTT-AA-TTAAAATAAATTTAAA
1 AATAAATTTAAATTTAAAATAAATTTAAA
6769535 ATGGGTTTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
32 11 0.20
33 4 0.07
34 5 0.09
35 35 0.64
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (35 bp):
AATAAATTTAAATTTAAAATAAATTTAAATCTCAA
Found at i:6770031 original size:2 final size:2
Alignment explanation
Indices: 6769969--6770017 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
6769959 TAACTTTTCG
6769969 AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6770009 AT AT AT AT A
1 AT AT AT AT A
6770018 ATTAGCATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6782192 original size:18 final size:18
Alignment explanation
Indices: 6782145--6782192 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
6782135 ACTTAAAGAT
6782145 GTATGAAATTTATA-ATA
1 GTATGAAATTTATATATA
* *
6782162 -TAT--ACTTTTTATATA
1 GTATGAAATTTATATATA
6782177 GTATGAAATTTATATA
1 GTATGAAATTTATATA
6782193 AAATTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 7
0.68 0.12 0.21
Matches are distributed among these distances:
14 6 0.26
15 3 0.13
16 6 0.26
18 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (18 bp):
GTATGAAATTTATATATA
Found at i:6784440 original size:15 final size:15
Alignment explanation
Indices: 6784403--6784452 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
6784393 AAAACAATTT
6784403 ATTTTAAAAAAT-AA
1 ATTTTAAAAAATAAA
6784417 A--TTACAAAAA-AAA
1 ATTTTA-AAAAATAAA
*
6784430 CTTTTAAAAAATAAA
1 ATTTTAAAAAATAAA
6784445 ATTTTAAA
1 ATTTTAAA
6784453 GTTACAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
12 3 0.10
13 7 0.24
14 6 0.21
15 13 0.45
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTTTAAAAAATAAA
Found at i:6785794 original size:24 final size:24
Alignment explanation
Indices: 6785767--6785820 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
6785757 GAAAAGAGAT
6785767 CCATTATCCAATGCTAAATATAAC
1 CCATTATCCAATGCTAAATATAAC
*
6785791 CCATTATCCAATGCTAAGTATAAC
1 CCATTATCCAATGCTAAATATAAC
6785815 CCATTA
1 CCATTA
6785821 CCTTTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
CCATTATCCAATGCTAAATATAAC
Found at i:6788427 original size:17 final size:18
Alignment explanation
Indices: 6788358--6788432 Score: 50
Period size: 18 Copynumber: 4.2 Consensus size: 18
6788348 CAAATCAGAA
6788358 AAAATTATAAA-A-TAT-
1 AAAATTATAAATATTATC
* *
6788373 AAAAGTTATTAAATATTTTG
1 AAAA-TTA-TAAATATTATC
* * *
6788393 AAAAATAAAAATTGTTAT-
1 AAAATTATAAA-TATTATC
6788411 AAAATTATAAATATTATC
1 AAAATTATAAATATTATC
6788429 AAAA
1 AAAA
6788433 AATATATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
15 4 0.09
16 3 0.07
17 9 0.20
18 17 0.38
19 8 0.18
20 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (18 bp):
AAAATTATAAATATTATC
Found at i:6788512 original size:19 final size:18
Alignment explanation
Indices: 6788450--6788513 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
6788440 ATAAAAAATC
* *
6788450 TAATAAACTATAAGAAAAA
1 TAATAAAAT-TAATAAAAA
6788469 T-ATAAAATTAATAAAACA
1 TAATAAAATTAATAAAA-A
* *
6788487 TATTAAAATTCTATAAAAA
1 TAATAAAATT-AATAAAAA
6788506 TAATAAAA
1 TAATAAAA
6788514 AATTATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 7 0.19
18 8 0.22
19 16 0.43
20 6 0.16
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (18 bp):
TAATAAAATTAATAAAAA
Found at i:6789115 original size:33 final size:34
Alignment explanation
Indices: 6789078--6789144 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
6789068 AAAAAATAGT
* *
6789078 TTTTAATATTAAACTAAAAAATTGA-AATTAATG
1 TTTTAACATTAAACTAAAAAATTAATAATTAATG
* * *
6789111 TTTTAGCATTAAATTTAAAAATTAATAATTAATG
1 TTTTAACATTAAACTAAAAAATTAATAATTAATG
6789145 AATCCACTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 20 0.71
34 8 0.29
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (34 bp):
TTTTAACATTAAACTAAAAAATTAATAATTAATG
Found at i:6805796 original size:18 final size:18
Alignment explanation
Indices: 6805754--6805796 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
6805744 AAAAAAATAT
* *
6805754 GTATATTTAAATATTTTTA
1 GTAT-TTTAAAGATTCTTA
6805773 -TATTTTAAAGATTCTTA
1 GTATTTTAAAGATTCTTA
6805790 GTATTTT
1 GTATTTT
6805797 TTAATACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (18 bp):
GTATTTTAAAGATTCTTA
Found at i:6810691 original size:28 final size:28
Alignment explanation
Indices: 6810637--6810692 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
6810627 AAAAAATGCC
* * ***
6810637 AAGTTTAGGTACCAAATTGGGTCAAAAA
1 AAGTTTAGCTACCAAATTAGAAAAAAAA
6810665 AAGTTTAGCTACCAAATTAGAAAAAAAA
1 AAGTTTAGCTACCAAATTAGAAAAAAAA
6810693 GTATCAAGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (28 bp):
AAGTTTAGCTACCAAATTAGAAAAAAAA
Found at i:6811106 original size:20 final size:20
Alignment explanation
Indices: 6811078--6811123 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
6811068 TACTCCCCCA
6811078 TTTACTTTCCCT-CAAAACT
1 TTTACTTTCCCTCCAAAACT
* *
6811097 CTTTATTTTCTCTCCAAAACT
1 -TTTACTTTCCCTCCAAAACT
6811118 TTTACT
1 TTTACT
6811124 CTCTCTCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTACTTTCCCTCCAAAACT
Found at i:6811128 original size:20 final size:21
Alignment explanation
Indices: 6811090--6811130 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6811080 TACTTTCCCT
* *
6811090 CAAAACTCTTTATTTTCTCTC
1 CAAAACTCTTTACTCTCTCTC
6811111 CAAAACT-TTTACTCTCTCTC
1 CAAAACTCTTTACTCTCTCTC
6811131 ACTTTCCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (21 bp):
CAAAACTCTTTACTCTCTCTC
Found at i:6813752 original size:12 final size:12
Alignment explanation
Indices: 6813737--6813762 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6813727 CTCTTGCATT
6813737 TTTTCTTTATAA
1 TTTTCTTTATAA
6813749 TTTTCTTTATAA
1 TTTTCTTTATAA
6813761 TT
1 TT
6813763 CTAATCTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCTTTATAA
Found at i:6826455 original size:57 final size:57
Alignment explanation
Indices: 6826367--6826482 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
6826357 TTTAATTAAA
6826367 AAACAAAATAAAAGAATTATAAGAAATTAAAACAACAAAAGCTTATTGAAATTTTTC
1 AAACAAAATAAAAGAATTATAAGAAATTAAAACAACAAAAGCTTATTGAAATTTTTC
*
6826424 AAACACAATAAAAGAATTATAAGAAATTAAAACAACAAAAGCTTATTGAAATTTTTC
1 AAACAAAATAAAAGAATTATAAGAAATTAAAACAACAAAAGCTTATTGAAATTTTTC
6826481 AA
1 AA
6826483 GCATATATCT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (57 bp):
AAACAAAATAAAAGAATTATAAGAAATTAAAACAACAAAAGCTTATTGAAATTTTTC
Found at i:6834944 original size:37 final size:38
Alignment explanation
Indices: 6834885--6834963 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
6834875 TTCGAAGCAA
** **
6834885 TAAAGTGACACCCAGTGTCTCATC-GGTCTAGCCGAAG
1 TAAAGTGACACCCAGTACCTCATCAAATCTAGCCGAAG
** *
6834922 TAAAGTGGTACCCAGTACCTCATCAAATCTATCCGAAG
1 TAAAGTGACACCCAGTACCTCATCAAATCTAGCCGAAG
6834960 TAAA
1 TAAA
6834964 ATAATGACAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (38 bp):
TAAAGTGACACCCAGTACCTCATCAAATCTAGCCGAAG
Found at i:6835110 original size:6 final size:6
Alignment explanation
Indices: 6835091--6835129 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
6835081 ACAATTCATA
*
6835091 TCACTT TCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
6835130 ATTTTGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:6835306 original size:22 final size:22
Alignment explanation
Indices: 6835280--6835325 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
6835270 TAAACATATA
6835280 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
6835302 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
6835324 AT
1 AT
6835326 CACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:6835330 original size:18 final size:20
Alignment explanation
Indices: 6835284--6835333 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
6835274 CATATAATAT
6835284 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
6835305 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
6835325 -TCACATATA
1 TTCACATATA
6835334 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:6839457 original size:19 final size:20
Alignment explanation
Indices: 6839435--6839479 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
6839425 TTAAAATATA
*
6839435 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
*
6839454 AA-TTTCAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
6839473 AATTTTT
1 AATTTTT
6839480 TTTTTTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.33
19 11 0.52
20 3 0.14
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:6840334 original size:30 final size:30
Alignment explanation
Indices: 6840277--6840335 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
6840267 CCTCTCTTTG
*
6840277 TTATTTTATTTTATTTTTTATGGAATTATT
1 TTATTTTATTTTATTTTTTATGAAATTATT
*
6840307 TTATTTTATTTTATATTTT-TGTAAATTAT
1 TTATTTTATTTTATTTTTTATG-AAATTAT
6840336 AAAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (30 bp):
TTATTTTATTTTATTTTTTATGAAATTATT
Found at i:6849824 original size:18 final size:18
Alignment explanation
Indices: 6849801--6849835 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6849791 GATATTGTGT
6849801 AATTAACCGAA-TTAATGG
1 AATTAA-CGAACTTAATGG
6849819 AATTAACGAACTTAATG
1 AATTAACGAACTTAATG
6849836 ATTAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
AATTAACGAACTTAATGG
Found at i:6852626 original size:13 final size:14
Alignment explanation
Indices: 6852604--6852632 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6852594 CTGTGTCTTT
6852604 TTTTTAAATATTTA
1 TTTTTAAATATTTA
6852618 TTTTT-AATATTTA
1 TTTTTAAATATTTA
6852631 TT
1 TT
6852633 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTAAATATTTA
Found at i:6864036 original size:204 final size:204
Alignment explanation
Indices: 6863686--6864071 Score: 673
Period size: 204 Copynumber: 1.9 Consensus size: 204
6863676 CTTCCATGAA
* *
6863686 TTCTTCTCTTTGCAGCCTTAAAGCTAATGCCGCATCTTCATCTTGGCTCGGTGTCCCTCTCCTCC
1 TTCTTCTCTCTGCAGCCTTAAAGCTAATGCAGCATCTTCATCTTGGCTCGGTGTCCCTCTCCTCC
6863751 TCCCGGCACGTACTAACCGTGAAAGTTCATTGTCTCGTTGCAGCCTTGCTGATGCTGCATTGTTA
66 TCCCGGCACGTACTAACCGTGAAAGTTCATTGTCTCGTTGCAGCCTTGCTGATGCTGCATTGTTA
* ** *
6863816 TCTTGGTTCGGGTTCCCTTGCCTTCTCATCATGTTCGTATCTGTGTTTACTATTCGGGTTCCCTC
131 TCTTGGTTCGGGTTCCCTCGCCTTCTCATCATGTTCACATCCGTGTTTACTATTCGGGTTCCCTC
6863881 TATGAATTC
196 TATGAATTC
*
6863890 TTCTTCTCTCTGCAGCCTTAAAGCTAATGCAGCATCTTCATCTTGGCTTGGTGTCCCTCTCCTCC
1 TTCTTCTCTCTGCAGCCTTAAAGCTAATGCAGCATCTTCATCTTGGCTCGGTGTCCCTCTCCTCC
* * *
6863955 TCCCGGCACGTACTAACCGTGAGAGTTCATTGTCTCGTTGCGGTCTTGCTGATGCTGCATTGTTA
66 TCCCGGCACGTACTAACCGTGAAAGTTCATTGTCTCGTTGCAGCCTTGCTGATGCTGCATTGTTA
*
6864020 TCTTGGTTTGGGTTCCCTCGCCTTCTCATCATGTTCACATCCGTGTTTACTA
131 TCTTGGTTCGGGTTCCCTCGCCTTCTCATCATGTTCACATCCGTGTTTACTA
6864072 GTCGCGAAAG
Statistics
Matches: 171, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
204 171 1.00
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (204 bp):
TTCTTCTCTCTGCAGCCTTAAAGCTAATGCAGCATCTTCATCTTGGCTCGGTGTCCCTCTCCTCC
TCCCGGCACGTACTAACCGTGAAAGTTCATTGTCTCGTTGCAGCCTTGCTGATGCTGCATTGTTA
TCTTGGTTCGGGTTCCCTCGCCTTCTCATCATGTTCACATCCGTGTTTACTATTCGGGTTCCCTC
TATGAATTC
Found at i:6865028 original size:17 final size:17
Alignment explanation
Indices: 6865006--6865039 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6864996 ATTTAAATTC
*
6865006 TTTAGATTCATGAATGG
1 TTTAGATTCACGAATGG
6865023 TTTAGATTCACGAATGG
1 TTTAGATTCACGAATGG
6865040 AAATTGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (17 bp):
TTTAGATTCACGAATGG
Found at i:6869726 original size:17 final size:17
Alignment explanation
Indices: 6869704--6869739 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
6869694 AAGACAATTA
6869704 GATAGATTTTCTAATGG
1 GATAGATTTTCTAATGG
6869721 GATAGATTTTCTAATGG
1 GATAGATTTTCTAATGG
6869738 GA
1 GA
6869740 AATGACTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.39
Consensus pattern (17 bp):
GATAGATTTTCTAATGG
Found at i:6871851 original size:279 final size:279
Alignment explanation
Indices: 6871331--6872156 Score: 1480
Period size: 279 Copynumber: 3.0 Consensus size: 279
6871321 TGTAGGCAGT
*
6871331 AAACATTTCTACTAAAGCTTGAAATATGGCAGGAATAATCCCCCAAATTTTGCTTC--A-AACA-
1 AAACATTTCTACTGAAGCTTGAAATATGGCAGGAATAATCCCCCAAATTTTGCTTCAGACAACAC
* * *
6871392 -AC-ACTGCAAATTCAAACGGAAAAAGCAAAAAAAGGGAAGAGAGAGCCTGTCAGACAACTGCGT
66 TGCAACTGCAAATTCAAATGGAAAAAGCAAAAAAAGGGAAGAGAGAGTCTGTCAGACAACTGCGT
6871455 GAGCGTAACCTTCCCAGCCGCACAAGGC-AAGCTGAGAACGATCCTCTGCGGTCGAAGAAAGCCA
131 GAGCGTAACCTTCCCAGCCGCACAAGGCAAAGCTGAGAACGATCCTCTGCGGTCGAAGAAAGCCA
*
6871519 GCATGGGCATCAACCAGACCAGTAATCACGCTCAGATCACACAGTCGTAGTTCATCAACCAGACT
196 GCATGGGCATCCACCAGACCAGTAATCACGCTCAGATCACACAGTCGTAGTTCATCAACCAGACT
6871584 TGGAATCCTGTCTCCTTTG
261 TGGAATCCTGTCTCCTTTG
6871603 AAACATTTCTACTGAAGCTTGAAATATGGCAGGAATAATCCCCCAAATTTTGCTTCAGACAACAC
1 AAACATTTCTACTGAAGCTTGAAATATGGCAGGAATAATCCCCCAAATTTTGCTTCAGACAACAC
6871668 TGCAACTGCAAATTCAAATGGAAAAAGCAAAAAAAGGGAAGAGAGAGTCTGTCAGACAACTGCGT
66 TGCAACTGCAAATTCAAATGGAAAAAGCAAAAAAAGGGAAGAGAGAGTCTGTCAGACAACTGCGT
6871733 GAGCGTAACCTTCCCAGCCGCACAAGGCAAAGCTGAGAACGATCCTCTGCGGTCGAAGAAAGCCA
131 GAGCGTAACCTTCCCAGCCGCACAAGGCAAAGCTGAGAACGATCCTCTGCGGTCGAAGAAAGCCA
6871798 GCATGGGCATCCACCAGACCAGTAATCACGCTCAGATCACACAGTCGTAGTTCATCAACCAGACT
196 GCATGGGCATCCACCAGACCAGTAATCACGCTCAGATCACACAGTCGTAGTTCATCAACCAGACT
6871863 TGGAATCCTGTCTCCTTTG
261 TGGAATCCTGTCTCCTTTG
6871882 AAACATTTCTACTGAAGCTTGAAATATGGCAGGAATAATCCCCCAAATTTTGCTTCAGACAACAC
1 AAACATTTCTACTGAAGCTTGAAATATGGCAGGAATAATCCCCCAAATTTTGCTTCAGACAACAC
6871947 TGCAACTGCAAATTCAAATGGAAAAAGCAAAAAAAGGGAAGAGAGAGTCTGTCAGACAACTGCGT
66 TGCAACTGCAAATTCAAATGGAAAAAGCAAAAAAAGGGAAGAGAGAGTCTGTCAGACAACTGCGT
* * *
6872012 ----G--ACCTTCCCAGCCGCACAAGGCAAAGCTGAGAACGATCCTCTGCAGTCGAGGAGAGCCA
131 GAGCGTAACCTTCCCAGCCGCACAAGGCAAAGCTGAGAACGATCCTCTGCGGTCGAAGAAAGCCA
6872071 GCATGGGCATCCACCAGACCAGTAATCACGCTCAGATCACACAGTCGTAGTTCATCAACCAGACT
196 GCATGGGCATCCACCAGACCAGTAATCACGCTCAGATCACACAGTCGTAGTTCATCAACCAGACT
*
6872136 TGGAATCCTGTCTCCTATG
261 TGGAATCCTGTCTCCTTTG
6872155 AA
1 AA
6872157 CTTAAGGACA
Statistics
Matches: 538, Mismatches: 9, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
272 55 0.10
273 140 0.26
274 1 0.00
275 5 0.01
277 1 0.00
278 87 0.16
279 249 0.46
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (279 bp):
AAACATTTCTACTGAAGCTTGAAATATGGCAGGAATAATCCCCCAAATTTTGCTTCAGACAACAC
TGCAACTGCAAATTCAAATGGAAAAAGCAAAAAAAGGGAAGAGAGAGTCTGTCAGACAACTGCGT
GAGCGTAACCTTCCCAGCCGCACAAGGCAAAGCTGAGAACGATCCTCTGCGGTCGAAGAAAGCCA
GCATGGGCATCCACCAGACCAGTAATCACGCTCAGATCACACAGTCGTAGTTCATCAACCAGACT
TGGAATCCTGTCTCCTTTG
Found at i:6874106 original size:27 final size:28
Alignment explanation
Indices: 6874035--6874111 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
6874025 GATTTTGTTT
* *
6874035 TCAATTAAAATAATAATT-TTAAATATTA
1 TCAATCAAAAT-ATTATTATTAAATATTA
6874063 TCAATCAAAATATTATTATTAAATATT-
1 TCAATCAAAATATTATTATTAAATATTA
6874090 T-AATCCAAAGATA-TATTATTAA
1 TCAAT-CAAA-ATATTATTATTAA
6874112 GAAAGTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 3 0.07
27 19 0.43
28 22 0.50
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (28 bp):
TCAATCAAAATATTATTATTAAATATTA
Found at i:6879237 original size:223 final size:223
Alignment explanation
Indices: 6878849--6879299 Score: 893
Period size: 223 Copynumber: 2.0 Consensus size: 223
6878839 TGCCTTCTAA
6878849 AATCCCCCAAATTTTGCTTCAAAATGCACCGCCAAGGAGAACCGCAAATTCAAATGGAAAAAACA
1 AATCCCCCAAATTTTGCTTCAAAATGCACCGCCAAGGAGAACCGCAAATTCAAATGGAAAAAACA
6878914 AAAAAGGATGGGGAGTCTGTCAGACAACTGCGTGACCTTCTCAGCCGCACAAGGCAAGCTGAGAA
66 AAAAAGGATGGGGAGTCTGTCAGACAACTGCGTGACCTTCTCAGCCGCACAAGGCAAGCTGAGAA
6878979 CGATCCTCTGCGGTCAAGGTGAACCAGCAAGGGCATCACCAGACCAGTAATCACGCTCAGATCAC
131 CGATCCTCTGCGGTCAAGGTGAACCAGCAAGGGCATCACCAGACCAGTAATCACGCTCAGATCAC
*
6879044 ACAGTCGTAGTTCATCAACCAGACTTGG
196 ACAGTCGTACTTCATCAACCAGACTTGG
6879072 AATCCCCCAAATTTTGCTTCAAAATGCACCGCCAAGGAGAACCGCAAATTCAAATGGAAAAAACA
1 AATCCCCCAAATTTTGCTTCAAAATGCACCGCCAAGGAGAACCGCAAATTCAAATGGAAAAAACA
6879137 AAAAAGGATGGGGAGTCTGTCAGACAACTGCGTGACCTTCTCAGCCGCACAAGGCAAGCTGAGAA
66 AAAAAGGATGGGGAGTCTGTCAGACAACTGCGTGACCTTCTCAGCCGCACAAGGCAAGCTGAGAA
6879202 CGATCCTCTGCGGTCAAGGTGAACCAGCAAGGGCATCACCAGACCAGTAATCACGCTCAGATCAC
131 CGATCCTCTGCGGTCAAGGTGAACCAGCAAGGGCATCACCAGACCAGTAATCACGCTCAGATCAC
6879267 ACAGTCGTACTTCATCAACCAGACTTGG
196 ACAGTCGTACTTCATCAACCAGACTTGG
6879295 AATCC
1 AATCC
6879300 TGTCTCCTTT
Statistics
Matches: 227, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
223 227 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (223 bp):
AATCCCCCAAATTTTGCTTCAAAATGCACCGCCAAGGAGAACCGCAAATTCAAATGGAAAAAACA
AAAAAGGATGGGGAGTCTGTCAGACAACTGCGTGACCTTCTCAGCCGCACAAGGCAAGCTGAGAA
CGATCCTCTGCGGTCAAGGTGAACCAGCAAGGGCATCACCAGACCAGTAATCACGCTCAGATCAC
ACAGTCGTACTTCATCAACCAGACTTGG
Found at i:6886244 original size:22 final size:23
Alignment explanation
Indices: 6886219--6886277 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
6886209 TATAAATATT
6886219 AATAAAATAATTT-TGAAAATTA
1 AATAAAATAATTTATGAAAATTA
* *
6886241 AATAGAATAATTATTATTAAAATTA
1 AATAAAATAA-T-TTATGAAAATTA
*
6886266 AATATAATAATT
1 AATAAAATAATT
6886278 ACTAATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 9 0.29
23 2 0.06
24 3 0.10
25 17 0.55
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (23 bp):
AATAAAATAATTTATGAAAATTA
Found at i:6886266 original size:25 final size:25
Alignment explanation
Indices: 6886234--6886294 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
6886224 AATAATTTTG
* *
6886234 AAAATTAAATAGAATAATTATTATT
1 AAAATTAAATAGAATAATTACTAAT
*
6886259 AAAATTAAATATAATAATTACTAAT
1 AAAATTAAATAGAATAATTACTAAT
*
6886284 AAATTTAAATA
1 AAAATTAAATA
6886295 CATTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATTAAATAGAATAATTACTAAT
Found at i:6886278 original size:22 final size:22
Alignment explanation
Indices: 6886211--6886278 Score: 59
Period size: 25 Copynumber: 3.0 Consensus size: 22
6886201 AAATAGTGTA
*
6886211 TAAATATT-AATAAAATAATT-T
1 TAAA-ATTAAATATAATAATTAT
*
6886232 TGAAAATTAAATAGAATAATTATTAT
1 T-AAAATTAAAT---ATAATAATTAT
6886258 TAAAATTAAATATAATAATTA
1 TAAAATTAAATATAATAATTA
6886279 CTAATAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
21 4 0.11
22 15 0.39
25 17 0.45
26 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAAATTAAATATAATAATTAT
Found at i:6886675 original size:16 final size:16
Alignment explanation
Indices: 6886656--6886705 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
6886646 ATATCTAATC
6886656 ATATAATAAATTATTA
1 ATATAATAAATTATTA
6886672 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
6886685 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
6886702 ATAT
1 ATAT
6886706 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:6893114 original size:2 final size:2
Alignment explanation
Indices: 6893107--6893141 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6893097 ATACTTTGTT
6893107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6893142 GTATGTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6906984 original size:58 final size:58
Alignment explanation
Indices: 6906914--6907033 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
6906904 ATTCATCAAC
6906914 AAACTAAACCCAAATATTTTAAAACCCAAATATAATTTCATTCTTCAAA-AACACTTAT
1 AAACTAAACCCAAATATTTTAAAACCCAAATATAATTTCATTCTT-AAATAACACTTAT
* * * *
6906972 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCTTAAATAATACTTAT
1 AAACTAAACCCAAATATTTTAAAACCCAAATATAATTTCATTCTTAAATAACACTTAT
6907030 AAAC
1 AAAC
6907034 AACTCTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
57 3 0.05
58 54 0.95
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTAAAACCCAAATATAATTTCATTCTTAAATAACACTTAT
Found at i:6907712 original size:16 final size:16
Alignment explanation
Indices: 6907675--6907727 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
6907665 TTTCTTGAAT
6907675 TTAAT-TTATAATTAA
1 TTAATATTATAATTAA
6907690 TTAATATTATAATATAA
1 TTAATATTATAAT-TAA
* *
6907707 TT-ATATAAATAATTAT
1 TTAATAT-TATAATTAA
6907723 TTAAT
1 TTAAT
6907728 TAGTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.16
16 15 0.47
17 12 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATATTATAATTAA
Found at i:6908489 original size:6 final size:6
Alignment explanation
Indices: 6908480--6908509 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6908470 TATATTTAAT
*
6908480 AAGTGA AAGTGA AAGTGA AATTGA AAGTGA
1 AAGTGA AAGTGA AAGTGA AAGTGA AAGTGA
6908510 TATGAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (6 bp):
AAGTGA
Found at i:6914834 original size:14 final size:14
Alignment explanation
Indices: 6914817--6914850 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6914807 TATATAAATA
6914817 ATTATTTAATTAGT
1 ATTATTTAATTAGT
* *
6914831 ATTATTTTATTATT
1 ATTATTTAATTAGT
6914845 ATTATT
1 ATTATT
6914851 AACTAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
ATTATTTAATTAGT
Found at i:6915591 original size:12 final size:12
Alignment explanation
Indices: 6915574--6915615 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
6915564 TATATTTAAT
*
6915574 AAGTGAAAGTGA
1 AAGTGAAATTGA
6915586 AAGTGAAATTGA
1 AAGTGAAATTGA
* *
6915598 AATTAAAATTGA
1 AAGTGAAATTGA
6915610 AAGTGA
1 AAGTGA
6915616 TATGAATTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAGTGAAATTGA
Found at i:6915628 original size:24 final size:23
Alignment explanation
Indices: 6915583--6915634 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
6915573 TAAGTGAAAG
6915583 TGAAAGTGAAATTGAAATTAAAAT
1 TGAAAGTGAAATTGAAATT-AAAT
* *
6915607 TGAAAGTGATA-TGAATTGTAAAT
1 TGAAAGTGAAATTGAAAT-TAAAT
6915630 TGAAA
1 TGAAA
6915635 ATCCCTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (23 bp):
TGAAAGTGAAATTGAAATTAAAT
Found at i:6917817 original size:21 final size:21
Alignment explanation
Indices: 6917791--6917841 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
6917781 CCTACTATTT
*
6917791 CTACCGATACAAGCATGTGAA
1 CTACCGATAAAAGCATGTGAA
*
6917812 CTACCGAAAAAAGCATGTGAA
1 CTACCGATAAAAGCATGTGAA
6917833 CTACCGATA
1 CTACCGATA
6917842 TTTCTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (21 bp):
CTACCGATAAAAGCATGTGAA
Found at i:6918464 original size:24 final size:24
Alignment explanation
Indices: 6918433--6918507 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
6918423 ATAGATAACT
* *
6918433 TTAGCTCTCACAAGCCCAGAATAG
1 TTAGCTCTTACGAGCCCAGAATAG
* *
6918457 TTAGCTCTTACGAGTCCAAAATAG
1 TTAGCTCTTACGAGCCCAGAATAG
* *
6918481 TTAACTCTTACGAGCCTAGAATAG
1 TTAGCTCTTACGAGCCCAGAATAG
6918505 TTA
1 TTA
6918508 ACCAGTATAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATAG
Found at i:6919286 original size:18 final size:18
Alignment explanation
Indices: 6919263--6919300 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
6919253 TAATATAGTT
6919263 TTATTC-AGTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
6919281 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
6919299 TT
1 TT
6919301 CGAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:6920803 original size:14 final size:15
Alignment explanation
Indices: 6920784--6920818 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
6920774 ACTAACAATT
*
6920784 AATTCACTAATT-AA
1 AATTCACAAATTCAA
6920798 AATTCACAAATTCAA
1 AATTCACAAATTCAA
6920813 AATTCA
1 AATTCA
6920819 ATATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTCACAAATTCAA
Found at i:6922462 original size:20 final size:20
Alignment explanation
Indices: 6922421--6922475 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
6922411 AAAAGCATAC
** *
6922421 TTGTATCGGTAGAATTGTAG
1 TTGTATCGGTAGAAGAGGAG
6922441 TTGTATCGGTAGAAGAGGAG
1 TTGTATCGGTAGAAGAGGAG
* *
6922461 TTCTACCGGTAGAAG
1 TTGTATCGGTAGAAG
6922476 TCCCAGGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.31
Consensus pattern (20 bp):
TTGTATCGGTAGAAGAGGAG
Found at i:6923763 original size:21 final size:21
Alignment explanation
Indices: 6923739--6923790 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
6923729 TGAGACAATA
6923739 CTACCGATACAAGT-ATAACTT
1 CTACCGATACAAGTAAT-ACTT
* * *
6923760 CTACCGAAACATGTAATGCTT
1 CTACCGATACAAGTAATACTT
6923781 CTACCGATAC
1 CTACCGATAC
6923791 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTAATACTT
Found at i:6924969 original size:201 final size:195
Alignment explanation
Indices: 6924543--6924996 Score: 517
Period size: 201 Copynumber: 2.3 Consensus size: 195
6924533 TATCAGTACT
* **
6924543 CGATGCTGCTCACACGAGCTGTCGAGGACTCATAATGTATGCGGTACC-CTAGCCATC-AGTACG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTC-AGCCATCGAGTACG
* * * * *
6924606 GTGCCTGTCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAGTATGCA
65 ATACCTG-CTGCACTATAAACTGTTCCCTAACGATGATGCTCACACGAGCTGTCGAGAATATGCA
* ** * * *
6924671 ATAAGTATTGTCTCAGCCATCGTAGGGTCTGTAATCCATTTAGGATCCATATCTCTTTCTCGAGT
129 ATAAGCATAATCTCAACCATCGTAGGGTCTGTAATCCATTTAGGATCCATATCTCTTTCCCGACT
6924736 CA
194 CA
* * *
6924738 CGATGCTGCTCACACGAGCTGTCAAGGACTCGTAACATATGCGGCACCTCAACCATCGA-TACGA
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGAGTACGA
* * * *
6924802 TATCTG-TGCA-TAT-AACTGTTCCCTAACGATGATGCTCATACGAGTTGTCGAGAATATGCACT
66 TACCTGCTGCACTATAAACTGTTCCCTAACGATGATGCTCACACGAGCTGTCGAGAATATGCA-A
* *
6924864 TATGCATAAATCTCAACCATCGTAGGG-CTTGTAATCCATTTAGGATCCAAATTTCTTTTCTCAT
130 TAAGCAT-AATCTCAACCATCGTAGGGTC-TGTAATCCATTTAGGATCC--A-----TATCTC-T
6924928 TTCCCGACTCA
185 TTCCCGACTCA
* *
6924939 CGATGCTGCTCGCACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCG
6924997 CGTCGATTTT
Statistics
Matches: 218, Mismatches: 28, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
191 43 0.20
192 9 0.04
193 38 0.17
195 58 0.27
196 2 0.01
200 5 0.02
201 63 0.29
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (195 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAGCCATCGAGTACGA
TACCTGCTGCACTATAAACTGTTCCCTAACGATGATGCTCACACGAGCTGTCGAGAATATGCAAT
AAGCATAATCTCAACCATCGTAGGGTCTGTAATCCATTTAGGATCCATATCTCTTTCCCGACTCA
Found at i:6926054 original size:3 final size:3
Alignment explanation
Indices: 6926046--6926096 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
6926036 TACATCCCAA
6926046 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6926093 AAT A
1 AAT A
6926097 GAATAGAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6927158 original size:7 final size:7
Alignment explanation
Indices: 6927146--6927202 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
6927136 TTTCGAAAAA
6927146 GTCAACG
1 GTCAACG
6927153 GTCAACG
1 GTCAACG
*
6927160 GTCAA-A
1 GTCAACG
6927166 GTCAACG
1 GTCAACG
*
6927173 ATCAACG
1 GTCAACG
* *
6927180 ATCAA-A
1 GTCAACG
6927186 GTCAACG
1 GTCAACG
*
6927193 GTCAGCG
1 GTCAACG
6927200 GTC
1 GTC
6927203 GGTCAACGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
6 9 0.22
7 32 0.78
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:6927168 original size:20 final size:20
Alignment explanation
Indices: 6927143--6927202 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
6927133 TTTTTTCGAA
6927143 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
* *
6927163 AAAGTCAACGATCAACGATC
1 AAAGTCAACGGTCAACGGTC
*
6927183 AAAGTCAACGGTCAGCGGTC
1 AAAGTCAACGGTCAACGGTC
6927203 GGTCAACGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGGTC
Found at i:6927227 original size:21 final size:20
Alignment explanation
Indices: 6927201--6927270 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
6927191 CGGTCAGCGG
*
6927201 TCGGTCAACGATCAATCAACA
1 TCGGTCAACG-TCAGTCAACA
* *
6927222 TCGGTCAACGGTCGGTTAACA
1 TCGGTCAAC-GTCAGTCAACA
* *
6927243 TCGGTCAACGCCAGTCAACG
1 TCGGTCAACGTCAGTCAACA
6927263 TCGGTCAA
1 TCGGTCAA
6927271 TGGTTTGACT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 15 0.37
21 25 0.61
22 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (20 bp):
TCGGTCAACGTCAGTCAACA
Found at i:6927236 original size:11 final size:10
Alignment explanation
Indices: 6927200--6927270 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
6927190 ACGGTCAGCG
6927200 GTCGGTCAAC
1 GTCGGTCAAC
**
6927210 GATCAATCAAC
1 G-TCGGTCAAC
*
6927221 ATCGGTCAAC
1 GTCGGTCAAC
*
6927231 GGTCGGTTAAC
1 -GTCGGTCAAC
*
6927242 ATCGGTCAAC
1 GTCGGTCAAC
* *
6927252 GCCAGTCAAC
1 GTCGGTCAAC
6927262 GTCGGTCAA
1 GTCGGTCAA
6927271 TGGTTTGACT
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
10 30 0.67
11 15 0.33
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (10 bp):
GTCGGTCAAC
Found at i:6927327 original size:15 final size:15
Alignment explanation
Indices: 6927307--6927336 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6927297 TGGTTCATTT
6927307 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
6927322 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
6927337 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:6927346 original size:21 final size:21
Alignment explanation
Indices: 6927320--6927387 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
6927310 TTGGTTCAAA
6927320 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
6927341 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
*
6927362 TGGGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTTAAAT-GAATT
6927384 TGGG
1 TGGG
6927388 CTTAATGCGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:6927798 original size:18 final size:17
Alignment explanation
Indices: 6927775--6927820 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
6927765 AAGAAAATAG
6927775 AAAAGAAAAGAATGAGA
1 AAAAGAAAAGAATGAGA
*
6927792 AATAAGAAATGAATGAGA
1 AA-AAGAAAAGAATGAGA
6927810 AAAAGAAAAGA
1 AAAAGAAAAGA
6927821 GAAAGGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAGAATGAGA
Found at i:6933227 original size:3 final size:3
Alignment explanation
Indices: 6933219--6933251 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
6933209 TACATCCCAA
6933219 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6933252 GAATAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:6934323 original size:20 final size:20
Alignment explanation
Indices: 6934298--6934379 Score: 137
Period size: 20 Copynumber: 4.1 Consensus size: 20
6934288 GTTTTTCGAA
6934298 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
6934318 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
* *
6934338 AAAGTCAACGATCAACGATC
1 AAAGTCAACGGTCAACGGTC
*
6934358 AAAGTCAACGGTCAGCGGTC
1 AAAGTCAACGGTCAACGGTC
6934378 AA
1 AA
6934380 CGATCAATCA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGGTC
Found at i:6934326 original size:13 final size:13
Alignment explanation
Indices: 6934308--6934371 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
6934298 AAAGTCAACG
6934308 GTCAACGGTCAAA
1 GTCAACGGTCAAA
*
6934321 GTCAACGGTCAACG
1 GTCAACGGTCAA-A
* *
6934335 GTCAA-AGTCAAC
1 GTCAACGGTCAAA
*
6934347 GATCAACGATCAAA
1 G-TCAACGGTCAAA
6934361 GTCAACGGTCA
1 GTCAACGGTCA
6934372 GCGGTCAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 1 0.02
13 30 0.73
14 10 0.24
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:6934405 original size:7 final size:7
Alignment explanation
Indices: 6934301--6934386 Score: 88
Period size: 7 Copynumber: 12.7 Consensus size: 7
6934291 TTTCGAAAAA
6934301 GTCAACG
1 GTCAACG
6934308 GTCAACG
1 GTCAACG
*
6934315 GTCAA-A
1 GTCAACG
6934321 GTCAACG
1 GTCAACG
6934328 GTCAACG
1 GTCAACG
*
6934335 GTCAA-A
1 GTCAACG
6934341 GTCAACG
1 GTCAACG
*
6934348 ATCAACG
1 GTCAACG
* *
6934355 ATCAA-A
1 GTCAACG
6934361 GTCAACG
1 GTCAACG
*
6934368 GTCAGCG
1 GTCAACG
6934375 GTCAACG
1 GTCAACG
*
6934382 ATCAA
1 GTCAA
6934387 TCAACACCGG
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
6 14 0.22
7 51 0.78
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:6934416 original size:10 final size:10
Alignment explanation
Indices: 6934394--6934441 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
6934384 CAATCAACAC
6934394 CGGTCAACGGT
1 CGGTCAAC-GT
*
6934405 CGGTCAATGT
1 CGGTCAACGT
*
6934415 CGGTCAACGC
1 CGGTCAACGT
*
6934425 CAGTCAACGT
1 CGGTCAACGT
6934435 CGGTCAA
1 CGGTCAA
6934442 TGGTTTGACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
10 24 0.77
11 7 0.23
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.19
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:6934498 original size:15 final size:15
Alignment explanation
Indices: 6934478--6934507 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6934468 TGGTTCATTT
6934478 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
6934493 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
6934508 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:6934517 original size:21 final size:21
Alignment explanation
Indices: 6934491--6934558 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
6934481 TTGGTTCAAA
6934491 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
*
6934512 TGGGTTTGGTTTAAATGAATG
1 TGGGTTTGGTTTAAATGAATT
*
6934533 TGGGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTTAAAT-GAATT
6934555 TGGG
1 TGGG
6934559 CTTAATGCGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:6934969 original size:18 final size:18
Alignment explanation
Indices: 6934948--6935009 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
6934938 GAAAATAGAA
6934948 AAGAAAAGAATGAGAAAT
1 AAGAAAAGAATGAGAAAT
*
6934966 AAGAAATGAATGAGAAAT
1 AAGAAAAGAATGAGAAAT
*
6934984 AAGAAATGAATGAGAAA-
1 AAGAAAAGAATGAGAAAT
*
6935001 AAAAAAAGA
1 AAGAAAAGA
6935010 GAAAGGAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 7 0.17
18 34 0.83
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (18 bp):
AAGAAAAGAATGAGAAAT
Found at i:6935019 original size:36 final size:36
Alignment explanation
Indices: 6934948--6935020 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
6934938 GAAAATAGAA
* * * *
6934948 AAGAAAAGAATGAGAAATAAGAAATGAATGAGAAAT
1 AAGAAAAGAATGAGAAAAAAAAAAAGAAAGAGAAAT
*
6934984 AAGAAATGAATGAGAAAAAAAAAAGAGAAAG-GAAAT
1 AAGAAAAGAATGAGAAAAAAAAAA-AGAAAGAGAAAT
6935020 A
1 A
6935021 TGAGAGGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (36 bp):
AAGAAAAGAATGAGAAAAAAAAAAAGAAAGAGAAAT
Found at i:6937054 original size:24 final size:23
Alignment explanation
Indices: 6937027--6937071 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
6937017 TTTTGGAAAT
6937027 TTTTTGATTTTTT-AATTATTTTTA
1 TTTTT-ATTTTTTGAATT-TTTTTA
6937051 TTTTTATTTTTTGAATTTTTT
1 TTTTTATTTTTTGAATTTTTT
6937072 ATGAATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTTATTTTTTGAATTTTTTTA
Found at i:6937070 original size:16 final size:15
Alignment explanation
Indices: 6937025--6937073 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
6937015 TTTTTTGGAA
6937025 ATTTTTTGATTTTTT
1 ATTTTTTGATTTTTT
*
6937040 AATTATTTTTA-TTTTT
1 -ATT-TTTTGATTTTTT
6937056 ATTTTTTGAATTTTTT
1 ATTTTTTG-ATTTTTT
6937072 AT
1 AT
6937074 GAATGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 15 0.54
17 5 0.18
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (15 bp):
ATTTTTTGATTTTTT
Done.